# HG changeset patch # User pfrommolt # Date 1321881139 18000 # Node ID 89ad0a9cca528078ea2d320274c4fee2548f3458 Uploaded diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/.classpath --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/.classpath Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,6 @@ + + + + + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/.project --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/.project Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,17 @@ + + + NGSrich_0.5.5 + + + + + + org.eclipse.jdt.core.javabuilder + + + + + + org.eclipse.jdt.core.javanature + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/.settings/org.eclipse.jdt.core.prefs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/.settings/org.eclipse.jdt.core.prefs Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,12 @@ +#Tue Sep 13 11:09:23 CEST 2011 +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 +org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve +org.eclipse.jdt.core.compiler.compliance=1.6 +org.eclipse.jdt.core.compiler.debug.lineNumber=generate +org.eclipse.jdt.core.compiler.debug.localVariable=generate +org.eclipse.jdt.core.compiler.debug.sourceFile=generate +org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.compiler.problem.enumIdentifier=error +org.eclipse.jdt.core.compiler.source=1.6 diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/R/eval_details.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/R/eval_details.R Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,163 @@ +#!/usr/bin/Rscript + + +##Input parameters######################################################################################################################## +xml=as.character(commandArgs()[6]) +bed=as.character(commandArgs()[7]) +cov=as.character(commandArgs()[8]) +chrinfo=as.character(commandArgs()[9]) +outdir=as.character(commandArgs()[10]) +genome=as.character(commandArgs()[11]) +########################################################################################################################################## + + + +##Read data############################################################################################################################### +bedfile<-read.table(bed,header=FALSE,stringsAsFactors=FALSE) +wunknown<-which(bedfile$V4=="unknown") +bedfile$V4[wunknown]<-paste("unknown",seq(1,length(wunknown),1),sep="") +bedfile$V4<-gsub("/","-",bedfile$V4) +covdata<-readLines(cov,warn=FALSE) + +xmldata<-readLines(xml,warn=FALSE) +nbrline<-xmldata[grep("",xmldata)] +rlenline<-xmldata[grep("",xmldata)] +nbreads<-as.numeric(strsplit(strsplit(nbrline,">")[[1]][2],"<")[[1]][1]) +rlength<-as.numeric(strsplit(strsplit(rlenline,">")[[1]][2],"<")[[1]][1]) + +expect<-0 +allchr<-levels(as.factor(bedfile$V1)) +if(chrinfo!="none"){ + cinfo<-read.table(chrinfo,header=FALSE,stringsAsFactors=FALSE) + gsize<-sum(as.numeric(cinfo[,2])) + expect=(rlength*nbreads)/gsize +} + +dir.create(paste(outdir,"/chromosomes",sep=""),showWarnings=FALSE) +for(chr in allchr){dir.create(paste(outdir,"/chromosomes/",chr,sep=""),showWarnings=FALSE)} + +tcov<-list() +tstarts<-numeric(0) +tcov0<-character(0) +firstt=1 +for(i in 1:length(covdata)){ + if(i%%10000==0){cat(i,"/",length(covdata),"\n")} + if(nchar(covdata[i])>10){ + if(firstt==0){ + tcov[[tname]]<-as.numeric(tcov0) + tcov0<-character(0) + } + firstt=0 + nameel<-strsplit(covdata[i],"\t") + tname<-paste(nameel[[1]][1],":",nameel[[1]][2],"-",nameel[[1]][3],sep="") + } + else{tcov0<-c(tcov0,covdata[i])} +} +########################################################################################################################################## + + +sortchr<-function(x){ + if(sum(substr(x,1,3)=="chr")==length(x)){ + x0<-strsplit(x,"chr") + xspl<-character(0) + for(i in 1:length(x0)){xspl<-c(xspl,x0[[i]][2])} + xnum<-xspl[!is.na(as.numeric(xspl))] + xchar<-setdiff(xspl,xnum) + xsorted<-paste("chr",c(sort(as.numeric(xnum)),sort(xchar)),sep="") + return(xsorted) + } + else{return(x)} +} + + +##Create gene index####################################################################################################################### +allchr<-sortchr(levels(as.factor(bedfile$V1))) +outfile=paste(outdir,"/chromosomes/chromosomes.html",sep="") +cat(file=outfile,paste( + "\n\nIndex of Target Regions\n", + "\n", + "\n\n", + "\n\n", + "\n

Show Details on Genewise Coverage

",sep="")) + +for(chr in allchr){ + cat(file=outfile,paste("",chr,"\n",sep=""),append=TRUE) +} +cat(file=outfile,"

\n\n",append=TRUE) + +for(chr in allchr){ + + thischr<-bedfile[bedfile$V1==chr,] + thischr<-thischr[order(thischr$V2),] + allgenes<-intersect(thischr$V4,thischr$V4) + cat(file=outfile,paste("
\n\n",sep=""),append=TRUE) + for(gene in allgenes){ + genebed<-thischr[thischr$V4==gene,] + firststart=genebed$V2[1] + lastend<-genebed$V3[nrow(genebed)] + tname=paste(chr,":",firststart,"-",lastend,sep="") + if(substr(gene,1,7)=="unknown"){genelab="unknown"} + else{genelab=gene} + cat(file=outfile,paste("\n",sep=""),append=TRUE) + } + cat(file=outfile,"
GeneRegionLink
",genelab,"",tname,"Show Details
\n
\n",append=TRUE) + +} +cat(file=outfile,"\n",append=TRUE) +########################################################################################################################################## + + + +##Create genewise reports################################################################################################################# +firstgene=1 +partest<-cv<-goftest<-numeric(0) +genebed<-split(bedfile,bedfile$V4) + +for(gene in names(genebed)){ + + thisbed<-genebed[[gene]] + chr=thisbed$V1[1] + + if(substr(gene,1,7)=="unknown"){genelab="unknown"} + else{genelab=gene} + + ##Write HTML header + outfile=paste(outdir,"/chromosomes/",chr,"/",gene,"/index.html",sep="") + dir.create(paste(outdir,"/chromosomes/",chr,"/",gene,sep=""),showWarnings=FALSE) + cat(file=outfile,paste("\n\nEnrichment Details\n\n\n\n\n

Enrichment Details for ",genelab,"

\n\n\n",sep="")) + + for(i in 1:nrow(thisbed)){ + + start=thisbed$V2[i] + end=thisbed$V3[i] + region=seq(start,end,1) + tname=paste(chr,":",start,"-",end,sep="") + + if(is.element(tname,names(tcov))){ + basecov=tcov[[tname]] + if(expect!=0){enrratio<-round(mean(basecov)/expect,1)} + else{enrratio<-"unknown"} + stddev=round(sd(basecov),2) + + ##Create plots + png(file=paste(outdir,"/chromosomes/",chr,"/",gene,"/h_",tname,".png",sep="")) + plot(region,basecov,pch=".",xlab=paste("Physical Position [",chr,"]",sep=""),ylab="Coverage",col="tomato3") + edgesx<-c(region,end,start) + edgesy<-c(basecov,0,0) + polygon(edgesx,edgesy,col="tomato3",border=NA) + lines(c(start,start),c(-1000,1000000)) + lines(c(end,end),c(-1000,1000000)) + lines(c(start,end),c(mean(basecov),mean(basecov)),col="darkblue") + lines(c(start,end),c(mean(basecov)-stddev,mean(basecov)-stddev),lty="dashed",col="darkblue") + lines(c(start,end),c(mean(basecov)+stddev,mean(basecov)+stddev),lty="dashed",col="darkblue") + dev.off() + + ##Write HTML table + ucsclink<-paste("http://www.genome.ucsc.edu/cgi-bin/hgTracks?&db=",genome,"&position=",chr,"%3A",start,"-",end,"&hgt.suggest=&pix=800&Submit=submit&hgsid=183341879",sep="") + cat(file=outfile,paste("\n",sep=""),append=TRUE) + } + } + cat(file=outfile,"
Target RegionCoveragePercentageEnrichment
Factor		Target HistogramExternal Link
",tname,"
(",end-start+1," bp)
Mean:",thisbed[i,5],"
Std Dev:",stddev,"
1x:",thisbed[i,6],"%
5x:",thisbed[i,7],"%
10x:",thisbed[i,8],"%
20x:",thisbed[i,9],"%
30x:",thisbed[i,10],"%
",enrratio,"Show in Genome Browser
\n\n",append=TRUE) + +} +########################################################################################################################################## diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/R/eval_enrichment.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/R/eval_enrichment.R Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,401 @@ +#!/usr/bin/Rscript + +xmlfile=as.character(commandArgs()[6]) +bedfile=as.character(commandArgs()[7]) +outdir=as.character(commandArgs()[8]) +genome=as.character(commandArgs()[9]) +poor=as.numeric(commandArgs()[10]) +high=as.numeric(commandArgs()[11]) +samplename=as.character(commandArgs()[12]) +targetfile=as.character(commandArgs()[13]) +details=as.numeric(commandArgs()[14]) +cutoff=0 +sdetails="" +#samplename0=strsplit(strsplit(xmlfile,"_")[[1]][1],"/")[[1]] +#samplename<-samplename0[length(samplename0)] +outfile=paste(outdir,"/",samplename,"_enrichment.html",sep="") + +##Read XML summary +cat("Reading XML file ... ") +xmltag<-function(line){ + return(strsplit(strsplit(line,">")[[1]][2],"0)){ + readlength<-as.numeric(xmltag(line)) + } + if(length(grep("NumberReads",line)>0)){ + numreads<-c(numreads,as.numeric(xmltag(line))) + } + if(length(grep("AvTargetCoverage",line)>0)){ + averagecov=as.numeric(xmltag(line)) + } + if(details==1){ + sdetails="[Show Details]
" + } + if(length(grep("SDTargetCoverage",line)>0)){ + stddevcov=as.numeric(xmltag(line)) + } + if(length(grep("TargetSize",line)>0)){ + targetsize=as.numeric(xmltag(line)) + } + if(length(grep("",line)>0)){nextfold=1} + else{ + if((nextfold==1) && length(grep("PercBases",line))>0){ + sample1<-as.numeric(xmltag(line)) + nextfold=0 + } + } + if(length(grep("",line)>0)){nextfold=5} + else{ + if((nextfold==5) && length(grep("PercBases",line))>0){ + sample5<-as.numeric(xmltag(line)) + nextfold=0 + } + } + if(length(grep("",line)>0)){nextfold=10} + else{ + if((nextfold==10) && length(grep("PercBases",line))>0){ + sample10<-as.numeric(xmltag(line)) + nextfold=0 + } + } + if(length(grep("",line)>0)){nextfold=20} + else{ + if((nextfold==20) && length(grep("PercBases",line))>0){ + sample20<-as.numeric(xmltag(line)) + nextfold=0 + } + } + if(length(grep("",line)>0)){nextfold=30} + else{ + if((nextfold==30) && length(grep("PercBases",line))>0){ + + sample30<-as.numeric(xmltag(line)) + nextfold=0 + } + } +} + +numreads_total<-numreads[1] +numreads_target<-numreads[3] +tpkm=round(numreads_target/((targetsize/1000)*(numreads_total/1000000)),2) + +cat("ready.\n") + + +##Read BED enrichment file and summarize output +cat("Reading BED file ... ") +bed<-read.table(bedfile,stringsAsFactors=FALSE) +area0_2<-sum(bed$V5<2) +area2_10<-sum((bed$V5>=2) & (bed$V5<10)) +area10_20<-sum((bed$V5>=10) & (bed$V5<20)) +area20_30<-sum((bed$V5>=20) & (bed$V5<30)) +area30_50<-sum((bed$V5>=30) & (bed$V5<50)) +area50_100<-sum((bed$V5>=50) & (bed$V5<100)) +areagr100<-sum(bed$V5>100) +cat("ready.\n") + + +##Create pieplot +cat("Creating coverage pieplot ... ") +png(file=paste(outdir,"/plots/",samplename,"_pieplot.png",sep=""),width=580) +par(mar=c(1,7,1,7)) +pie(c(area0_2,area2_10,area10_20,area20_30,area30_50,area50_100,areagr100), + labels=c(paste("0x to 2x (",area0_2,")",sep=""), + paste("2x to 10x (",area2_10,")",sep=""), + paste("10x to 20x (",area10_20,")",sep=""), + paste("20x to 30x (",area20_30,")",sep=""), + paste("30x to 50x (",area30_50,")",sep=""), + paste("50x to 100x (",area50_100,")",sep=""), + paste("above 100x (",areagr100,")",sep="")), + col=c("gray30","gray40","gray50","gray60","gray70","gray80","gray90"),main="") ##Mean Coverage of Target Regions") +garbage<-dev.off() +cat("ready.\n") + + +cat("Preparing coverage barplots ... ") +maxgenemean=0 +genes<-levels(as.factor(bed$V4)) +genes<-genes[genes!="unknown"] +ngenes<-length(genes) + +for(i in 1:ngenes){ + genemean<-mean(bed[bed$V4==genes[i],5]) + if(maxgenemean0) && (maxgenemean>cutoff)){ + maxgenemean=cutoff +} +cat("ready.\n") + +fwidth<-function(genes){ + fwidth0=10*length(genes) + if(length(genes)<=100){fwidth0=10*length(genes)} + if(length(genes)<=70){fwidth0=10*length(genes)} + if(length(genes)<=40){fwidth0=25*length(genes)} + if(length(genes)<=20){fwidth0=30*length(genes)} + if(length(genes)<=10){fwidth0=35*length(genes)} + if(length(genes)<=5){fwidth0=50*length(genes)} + return(fwidth0) +} + + +chromosomes<-levels(as.factor(bed$V1)) +if(length(genes)>=2000){ + cat("Creating coverage barplots ... ") + for(chr in chromosomes){ + + chrbed<-bed[bed$V1==chr,] + genemean<-numeric(0) + genes<-levels(as.factor(chrbed$V4)) + genes<-genes[genes!="unknown"] + + for(i in 1:length(genes)){ + if(cutoff>0){genemean[i]<-min(mean(chrbed[chrbed$V4==genes[i],5]),cutoff)} + else{genemean[i]<-mean(chrbed[chrbed$V4==genes[i],5])} + } + + png(file=paste(outdir,"/plots/",samplename,"_target_coverage_",chr,".png",sep=""),width=fwidth(genes),height=450) + par(mar=c(7,5,1,2)) + barplot(as.numeric(genemean),names.arg=genes,las=2, + ylab=paste("Average Coverage at Gene Locus (",chr,")",sep=""),col="tomato3",xlim=c(0.043*length(genemean),1.2*length(genes)-0.043*length(genemean)),ylim=c(0,maxgenemean)) + lineh=0 + while(lineh0){genemean[i]<-min(mean(bed[bed$V4==genes[i],5]),cutoff)} + else{genemean[i]<-mean(bed[bed$V4==genes[i],5])} + } + + + png(file=paste(outdir,"/plots/",samplename,"_target_coverage.png",sep=""),width=fwidth(genes),height=450) + par(mar=c(7,5,1,2)) + barplot(as.numeric(genemean),names.arg=genes,las=2, + ylab="Average Coverage at Gene Locus",col="tomato3",xlim=c(0,1.2*ngenes),ylim=c(0,maxgenemean)) + lineh=0 + while(lineh",high,"x) covered genes ... ",sep="") +genes<-levels(as.factor(bed$V4)) +chr<-start<-end<-gene1<-ave<-stddev<-gr1x<-gr5x<-gr10x<-gr20x<-gr30x<-numeric(0) +for(gene in genes){ + + bed0<-bed[bed$V4==gene,] + len<-bed0[,3]-bed0[,2] + fold1<-fold5<-fold10<-fold20<-fold30<-numeric(0) + for(i in 1:nrow(bed0)){fold1<-c(fold1,as.numeric(bed0$V6[i]))} + for(i in 1:nrow(bed0)){fold5<-c(fold5,as.numeric(bed0$V7[i]))} + for(i in 1:nrow(bed0)){fold10<-c(fold10,as.numeric(bed0$V8[i]))} + for(i in 1:nrow(bed0)){fold20<-c(fold20,as.numeric(bed0$V9[i]))} + + for(i in 1:nrow(bed0)){fold30<-c(fold30,as.numeric(bed0$V10[i]))} + fold1_gene<-paste(round(sum(fold1*len)/sum(len),2),"%",sep="") + fold5_gene<-paste(round(sum(fold5*len)/sum(len),2),"%",sep="") + fold10_gene<-paste(round(sum(fold10*len)/sum(len),2),"%",sep="") + fold20_gene<-paste(round(sum(fold20*len)/sum(len),2),"%",sep="") + fold30_gene<-paste(round(sum(fold30*len)/sum(len),2),"%",sep="") + + chr<-c(chr,bed0[1,1]) + start<-c(start,min(bed0[,2])) + end<-c(end,max(bed0[,3])) + gene1<-c(gene1,gene) + ave<-c(ave,round(mean(bed0[,5]),2)) + if(is.na(sd(bed0[,5]))){ + stddev<-c(stddev,0) + } + else{ + stddev<-c(stddev,round(sd(bed0[,5]),2)) + } + + gr1x<-c(gr1x,fold1_gene) + gr5x<-c(gr5x,fold5_gene) + gr10x<-c(gr10x,fold10_gene) + gr20x<-c(gr20x,fold20_gene) + gr30x<-c(gr30x,fold30_gene) + +} + +bed_gene<-data.frame(chr,start,end,gene1,ave,stddev,gr1x,gr5x,gr10x,gr20x,gr30x) + +poorly_covered<-bed_gene[bed_gene$avehigh,] +highly_covered<-highly_covered[order(highly_covered[,5],decreasing=TRUE),] + +linkpoor<-paste("http://www.genome.ucsc.edu/cgi-bin/hgTracks?&db=",genome,"&position=", + poorly_covered$chr,"%3A",poorly_covered$start,"-", + poorly_covered$end,"&hgt.suggest=&pix=800&Submit=submit&hgsid=183341879",sep="") +linkhigh<-paste("http://www.genome.ucsc.edu/cgi-bin/hgTracks?&db=",genome,"&position=", + highly_covered$chr,"%3A",highly_covered$start,"-", + highly_covered$end,"&hgt.suggest=&pix=800&Submit=submit&hgsid=183341879",sep="") +cat("ready.\n",sep="") + + +##Output HTML document +cat("Writing HTML output ... "); + +cat(file=outfile,paste( + "\n", + "\n", + "Enrichment Performance\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "", + "

Enrichment Performance of Sample ",samplename,"

\n", + "\n", + "\n", + "\n", + "", + "\n", + "\n", + "
\n", + "

Summary Statistics

\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
# Reads",numreads_total,"
# On Target ± 100 bp",numreads_target,"
Target Size (bp)",targetsize,"
# Target Regions",nrow(bed),"
Coverage Mean",averagecov,"
Coverage Std Dev",stddevcov,"
Covered 1x",sample1,"
Covered 5x",sample5,"
Covered 10x",sample10,"
Covered 20x",sample20,"
Covered 30x",sample30,"
TPKM",tpkm,"
\n", + "		\n", + "\n", + "
\n", + "
\n", + "

Genewise Target Coverage

",sdetails,"
\n",sep="")) + + +if(ngenes>=2000){ +for(chromosome in chromosomes){ + cat(file=outfile,paste("",chromosome,"\n",sep=""),append=TRUE) +} +for(chromosome in chromosomes){ + cat(file=outfile,paste("
\n",sep=""),append=TRUE) +} +} else{ + cat(file=outfile,paste("
\n",sep=""),append=TRUE) +} + +cat(file=outfile,paste("

\n", + "

Poorly Covered Genes (Cutoff: ",poor,"x)

\n",sep=""),append=TRUE) +if(nrow(poorly_covered)==0){ + cat(file=outfile,"

Nothing found for this cutoff.

",append=TRUE) +} else{ +cat(file=outfile,paste( + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n",sep=""),append=TRUE) + +for(i in 1:nrow(poorly_covered)){ +cat(file=outfile,paste( + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n",sep=""),append=TRUE) +} + +cat(file=outfile,"
RegionGeneCoverage MeanCovered 1xCovered 5xCovered 10xCovered 20xCovered 30xExternal Link
",poorly_covered[i,1],":",poorly_covered[i,2],"-",poorly_covered[i,3],"",poorly_covered[i,4],"",poorly_covered[i,5],"",poorly_covered[i,7],"",poorly_covered[i,8],"",poorly_covered[i,9],"",poorly_covered[i,10],"",poorly_covered[i,11],"Show in Genome Browser

\n",append=TRUE) +} + +cat(file=outfile,paste("

Highly Covered Genes (Cutoff: ",high,"x)

\n",sep=""),append=TRUE) +if(nrow(highly_covered)==0){ + cat(file=outfile,"

Nothing found for this cutoff.

",append=TRUE) +} else{ +cat(file=outfile,paste( + "\n", + " \n", + " ", + " ", + " \n", + " \n",sep=""),append=TRUE) +for(i in 1:nrow(highly_covered)){ +cat(file=outfile,paste(" \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " ",sep=""),append=TRUE) +} + +cat(file=outfile,"
TargetGeneCoverage MeanCovered 1xCovered 5xCovered 10xCovered 20xCovered 30xExternal Link
",highly_covered[i,1],":",highly_covered[i,2],"-",highly_covered[i,3],"",highly_covered[i,4],"",highly_covered[i,5],"",highly_covered[i,7],"",highly_covered[i,8],"",highly_covered[i,9],"",highly_covered[i,10],"",highly_covered[i,11],"Show in Genome Browser
\n",append=TRUE) +} +cat(file=outfile,"
BED file used for specification of target regions:
",targetfile,append=TRUE) +cat(file=outfile,"\n\n",append=TRUE) + +cat("ready.\n") diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/R/summarize_enrichment.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/R/summarize_enrichment.R Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,223 @@ +#!/usr/bin/Rscript + +infile=as.character(commandArgs()[6]) +outdir=as.character(commandArgs()[7]) +poor=as.numeric(commandArgs()[8]) +high=as.numeric(commandArgs()[9]) + + +outfile=paste(outdir,"/summary.html",sep="") +cutoff=c(poor,high) + +xmlfiles<-bedfiles<-character(0) +indirs<-as.character(readLines(infile)) +for(thisdir in indirs){ + thisdir=paste(thisdir,"/data",sep="") + xmlfiles=c(xmlfiles,list.files(thisdir,pattern=".xml",full.names=TRUE)) + bedfiles=c(bedfiles,list.files(thisdir,pattern=".bed",full.names=TRUE)) +} +nsamples<-length(indirs) + +samplenames<-character(0) +diffs<-matrix(nrow=5,ncol=nsamples) +averagecov<-stddevcov<-targetsize<-numreads_total<-numreads_target<-numeric(0) +sample1<-sample5<-sample10<-sample20<-sample30<-numeric(0) + + +##Read XML input files +xmltag<-function(line){ + return(strsplit(strsplit(line,">")[[1]][2],"0)){samplenames<-c(samplenames,xmltag(line))} + if(length(grep("NumberReads",line)>0)){numreads<-c(numreads,as.numeric(xmltag(line)))} + if(length(grep("AvTargetCoverage",line)>0)){averagecov=c(averagecov,as.numeric(xmltag(line)))} + if(length(grep("SDTargetCoverage",line)>0)){stddevcov=c(stddevcov,as.numeric(xmltag(line)))} + if(length(grep("TargetSize",line)>0)){targetsize=as.numeric(xmltag(line))} + if(length(grep("",line)>0)){nextfold=1} + else{ + if((nextfold==1) && length(grep("PercBases",line))>0){ + sample1<-c(sample1,as.numeric(xmltag(line))) + nextfold=0 + } + } + if(length(grep("",line)>0)){nextfold=5} + else{ + if((nextfold==5) && length(grep("PercBases",line))>0){ + sample5<-c(sample5,as.numeric(xmltag(line))) + nextfold=0 + } + } + if(length(grep("",line)>0)){nextfold=10} + else{ + if((nextfold==10) && length(grep("PercBases",line))>0){ + sample10<-c(sample10,as.numeric(xmltag(line))) + nextfold=0 + } + } + if(length(grep("",line)>0)){nextfold=20} + else{ + if((nextfold==20) && length(grep("PercBases",line))>0){ + sample20<-c(sample20,as.numeric(xmltag(line))) + nextfold=0 + } + } + if(length(grep("",line)>0)){nextfold=30} + else{ + if((nextfold==30) && length(grep("PercBases",line))>0){ + sample30<-c(sample30,as.numeric(xmltag(line))) + nextfold=0 + } + } + } + numreads_total<-c(numreads_total,numreads[1]) + numreads_target<-c(numreads_target,numreads[2]) + diffs[,i]<-c(sample30[i],sample20[i]-sample30[i],sample10[i]-sample20[i],sample5[i]-sample10[i],sample1[i]-sample5[i]) + i=i+1 +} + + +##Create barplot +rownames(diffs)<-c("Covered 30x","Covered 20x","Covered 10x","Covered 5x","Covered 1x") +plot_samplenames<-samplenames +s=0 +for(sname in plot_samplenames){ + s=s+1 + if(nchar(sname)>10){plot_samplenames[s]<-paste("Sample ",s,"\n(table above)",sep="")} +} +colnames(diffs)<-plot_samplenames +png(file=paste(outdir,"/summary_plot.png",sep=""),width=66*(4+nsamples),height=400) +par(oma=c(1,0,0,1)) +barplot(diffs, + legend=TRUE, + col=c("darkblue","steelblue1","tomato1","tomato3","tomato4"), + xlim=c(0,4+nsamples),ylim=c(0,100), + ylab="Percentage",las=2 ) #, +# args.legend=list(x=nsamples+4,y=80)) +dev.off() + + + +##Read BED files +sametarget=TRUE +thisbed<-read.table(bedfiles[1],stringsAsFactors=FALSE) +genes<-levels(as.factor(thisbed$V4)) +meancov<-matrix(nrow=length(genes),ncol=length(bedfiles)) +chr<-start<-end<-character(0) + +i=1 +for(file in bedfiles){ + thisbed<-read.table(file,stringsAsFactors=FALSE) + genes_thissample<-levels(as.factor(thisbed$V4)) + if(length(genes_thissample)!=length(genes)){sametarget=FALSE} + for(j in 1:length(genes)){ + thisgene<-thisbed[thisbed$V4==genes[j],] + chr[j]<-thisgene[1,1] + start[j]<-thisgene[1,2] + end[j]<-thisgene[1,3] + meancov[j,i]<-as.numeric(mean(thisgene[,5])) + } + i=i+1 +} + +meancov<-data.frame(chr,start,end,genes,meancov) +for(i in 1:nrow(meancov)){ + print(i) + meancov$ave[i]<-round(mean(as.numeric(meancov[i,4+(1:nsamples)])),4) + meancov$stddev[i]<-round(sd(as.numeric(meancov[i,4+(1:nsamples)])),4) + meancov$mini[i]<-round(min(as.numeric(meancov[i,4+(1:nsamples)])),4) + meancov$maxi[i]<-round(max(as.numeric(meancov[i,4+(1:nsamples)])),4) +} +meancov_sorted<-meancov[order(meancov$ave),] +poorly_all<-meancov_sorted[meancov_sorted$max\n", + "\n", + "Enrichment Performance\n", + "\n", + "\n", + "\n", + "

Target Enrichment Performance


\n", + "\n", + " \n", + " \n", + "\n",sep="")) +for(i in 1:nsamples){ + cat(file=outfile,paste( + "", + "", + "", + "", + "\n", + sep=""),append=TRUE) +} +cat(file=outfile,paste( + "
Sample# Reads# On TargetCoverage MeanCoverage Std DevCovered 1xCovered 5xCovered 10xCovered 20xCovered 30xDetails
",samplenames[i],"",numreads_total[i],"",numreads_target[i],"",averagecov[i],"",stddevcov[i],"",sample1[i],"",sample5[i],"",sample10[i],"",sample20[i],"",sample30[i],"Show
\n", + "

\n", + "

Target Base Percentage Covered

\n", + "\n",sep=""),append=TRUE) +if(!sametarget){ + warning("Target regions are not the same for all samples.") +} else{ +cat(file=outfile,paste( + "

Poorly Covered in All Samples (Cutoff: ",cutoff[1],"x)

\n",sep=""),append=TRUE) +if(nrow(poorly_all)==0){ +cat(file=outfile,"

Nothing found for this cutoff.

",append=TRUE) +} else{ +cat(file=outfile,paste( + "\n", + "\n", + "\n",sep=""),append=TRUE) +for(i in 1:nrow(poorly_all)){ + cat(file=outfile,paste( + "\n", + "\n", + "\n", + "\n", + "\n", + "\n",sep=""),append=TRUE) +} +cat(file=outfile,"
Target RegionGeneMean Across SamplesStd Dev Across Samples
",poorly_all$chr[i],":",poorly_all$start[i],"-",poorly_all$end[i],"",poorly_all$genes[i],"",poorly_all$ave[i],"",poorly_all$stddev[i],"
\n",append=TRUE) +} + +meancov_sorted<-meancov[order(meancov$ave,decreasing=TRUE),] ##Highly Covered +highly_all<-meancov_sorted[meancov_sorted$min>cutoff[2],] +cat(file=outfile,paste( + "

Highly Covered in All Samples (Cutoff: ",cutoff[2],"x)

\n",sep=""),append=TRUE) +if(nrow(highly_all)==0){ +cat(file=outfile,"

Nothing found for this cutoff.

",append=TRUE) +} else{ + cat(file=outfile,paste("\n", + "\n", + "\n",sep=""),append=TRUE) +for(i in 1:nrow(highly_all)){ + cat(file=outfile,paste( + "\n", + "\n", + "\n", + "\n", + "\n", + "\n",sep=""),append=TRUE) +} +cat(file=outfile,"
Target RegionGeneMean Across SampleStd Dev Across Samples
",highly_all$chr[i],":",highly_all$start[i],"-",highly_all$end[i],"",highly_all$genes[i],"",highly_all$ave[i],"",highly_all$stddev[i],"
\n",append=TRUE) +} + +} + +cat(file=outfile,"\n\n",append=TRUE) diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/README Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,89 @@ +NGSrich - Version 0.5.4 +Target enrichment performance for next-generation sequencing. + + +Description: +NGSrich is a tool for researchers concerned with target enrichment issues in next-generation sequencing. +It evaluates the target enrichment performance of target regions given in BED format and outputs +summary statistics, visualizations, and some additional files giving details on the analysis. + + +--------------------------------------------------------------------------------------------------------- + + +Usage: +java NGSrich evaluate -r -u -t + [(-a|-g) ] [ -s ] [-T ] [ -o ] [-p -h ][--no-details] + + +The program should be started from the bin directory of the software. +Required arguments: + : Path to the read alignment file in SAM or BAM alignment format + (http://samtools.sourceforge.net/SAM-1.3.pdf) + : UCSC genome version name (e.g. 'hg19'). + : Path to the target file in BED annotation format + (http://genome.ucsc.edu/FAQ/FAQformat.html#format1, 3 columns required) +Optional arguments: + : the local path of the annotation of the genome + [default: genome annotation is downloaded from the site of the ucsc genome + browser and placed into the temporary directory of the sample.] + : Name of the sample being processed - defaults to prefix of . + : Temporary directory - defaults to '/tmp'. + : Output directory - defaults to '/enrichment'. + : Coverage cutoff to define poorly covered genes - defaults to 2. + : Coverage cutoff to define highly covered genes - defaults to 200. + --no-details: Represses the computation of the evaluation details. + + +Output: +1. The HTML file contains a report of the target enrichment results including + tables of poorly and highly covered genes (defined by cutoffs and . + For vizualisation, plots are embedded in this document. The contents of this report + are actually based on an evaluation of the XML and BED files. +2. The XML file contains the summary statistics for the enrichment performance. +3. The BED file contains detailed coverage information for each single region specified in + the input target file. +4. The WIG files (http://genome.ucsc.edu/goldenPath/help/wiggle.html) contain a per-base + description of the coverage on the target regions, one for the target regions specified in + the input target file and one for the whole genome (gaps are skipped). These files can be + used for visualization in a Genome Browser, e.g. at http://genome.ucsc.edu/cgi-bin/hgGateway. + + +--------------------------------------------------------------------------------------------------------- + + +Several enrichment performance reports can be summarized by the command NGSrich-summarize. +This should also be started from the bin directory of the software. + +Usage: java NGSrich summarize -r -o [ -p -h ] + +Required arguments: + : Text file with each line containing the output directory of + the report for one of the samples to be summarized. + : Output directory. + +Optional arguments: + : Coverage cutoff to define poorly covered genes - defaults to 2. + : Coverage cutoff to define highly covered genes - defaults to 200. + + +Output: +The HTML file contains a summary report and summarizing performance statistics for several +target enrichment experiments. For each sample, the detailed performance report can be +accessed by a hyperlink. + + +--------------------------------------------------------------------------------------------------------- + + +Requirements: +The NGSrich software runs only on 64-bit Linux. It requires an installation of R and the Java +Runtime Environment (JRE), which are preinstalled on most Linux distributions. If not, +please visit the official sites for detailed installation instructions. + + +Contact: +You can send an e-mail to the NGSrich mailing list at . +Please tell us your experiences with the software itself and the documentation. We particularly welcome new +bug reports and suggestions for new or enhanced features. + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/DEFAULT.properties --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/DEFAULT.properties Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,10 @@ +! Path of the temporary directory. +tmpDir: /tmp +! Path of the father directory of the output directory. When empty the output directory is placed in the directory containing the reads alignment file. +outDirPath: +! Name of the output directory (not the path). +outDir: enrichment +! Define poorly covered genes. +poor: 2 +! Defines highly covered genes. +high: 200 diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/NGSrich.class Binary file NGSrich_0.5.5/bin/NGSrich.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/_main/Enrichment.class Binary file NGSrich_0.5.5/bin/_main/Enrichment.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/_main/EnrichmentStatsComputer.class Binary file NGSrich_0.5.5/bin/_main/EnrichmentStatsComputer.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/_main/NGSrichEvaluate.class Binary file NGSrich_0.5.5/bin/_main/NGSrichEvaluate.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/_main/NGSrichSummarize.class Binary file NGSrich_0.5.5/bin/_main/NGSrichSummarize.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/converters/Read2Wig.class Binary file NGSrich_0.5.5/bin/converters/Read2Wig.class has changed diff -r 000000000000 -r 89ad0a9cca52 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NGSrich_0.5.5/bin/exceptions/ChromosomeException.class Binary file NGSrich_0.5.5/bin/exceptions/ChromosomeException.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/exceptions/ChromosomeFormatException.class Binary file NGSrich_0.5.5/bin/exceptions/ChromosomeFormatException.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/exceptions/ChromosomeMismatchException.class Binary file NGSrich_0.5.5/bin/exceptions/ChromosomeMismatchException.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/exceptions/ChromosomeNotFoundException.class Binary file NGSrich_0.5.5/bin/exceptions/ChromosomeNotFoundException.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/exceptions/FileFormatException.class Binary file NGSrich_0.5.5/bin/exceptions/FileFormatException.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/exceptions/GenomeAnnotationException.class Binary file 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file NGSrich_0.5.5/bin/org/jdom/adapters/XML4JDOMAdapter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/adapters/XercesDOMAdapter.class Binary file NGSrich_0.5.5/bin/org/jdom/adapters/XercesDOMAdapter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/adapters/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/org/jdom/adapters/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,7 @@ + + +Classes to interface with various DOM implementations. Not generally +needed except in truly advanced situations. JAXPDOMAdapter is most commonly +used. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/AbstractFilter.class Binary file NGSrich_0.5.5/bin/org/jdom/filter/AbstractFilter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/AndFilter.class Binary file NGSrich_0.5.5/bin/org/jdom/filter/AndFilter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/ContentFilter.class Binary file NGSrich_0.5.5/bin/org/jdom/filter/ContentFilter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/ElementFilter.class Binary file NGSrich_0.5.5/bin/org/jdom/filter/ElementFilter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/Filter.class Binary file NGSrich_0.5.5/bin/org/jdom/filter/Filter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/NegateFilter.class Binary file NGSrich_0.5.5/bin/org/jdom/filter/NegateFilter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/OrFilter.class Binary file NGSrich_0.5.5/bin/org/jdom/filter/OrFilter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/org/jdom/filter/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,9 @@ + + +Classes to programmatically filter nodes of a document based on type, name, +value, or other aspects and to boolean and/or/negate these rules. Filters can +be used in methods like getContent(Filter) and getDescendants(Filter). A +sampling of generally useful filters are provided here. Alternate filters can +be user defined. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/BuilderErrorHandler.class Binary file NGSrich_0.5.5/bin/org/jdom/input/BuilderErrorHandler.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/DOMBuilder.class Binary file NGSrich_0.5.5/bin/org/jdom/input/DOMBuilder.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/JAXPParserFactory.class Binary file NGSrich_0.5.5/bin/org/jdom/input/JAXPParserFactory.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/JDOMParseException.class Binary file NGSrich_0.5.5/bin/org/jdom/input/JDOMParseException.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/SAXBuilder.class Binary file NGSrich_0.5.5/bin/org/jdom/input/SAXBuilder.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/SAXHandler.class Binary file NGSrich_0.5.5/bin/org/jdom/input/SAXHandler.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/TextBuffer.class Binary file NGSrich_0.5.5/bin/org/jdom/input/TextBuffer.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/org/jdom/input/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,10 @@ + + +Classes to build JDOM documents from various sources. The most common builder +class is SAXBuilder which constructs a JDOM document using a SAX parser and +can pull content from files, streams, sockets, readers, and so on. It can use +any underlying SAX parser to handle the parsing chores. SAXHandler provides +support for SAXBuilder. DOMBuilder lets you build from a pre-existing DOM +tree. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/DOMOutputter.class Binary file NGSrich_0.5.5/bin/org/jdom/output/DOMOutputter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/EscapeStrategy.class Binary file NGSrich_0.5.5/bin/org/jdom/output/EscapeStrategy.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/Format$DefaultEscapeStrategy.class Binary file NGSrich_0.5.5/bin/org/jdom/output/Format$DefaultEscapeStrategy.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/Format$TextMode.class Binary file NGSrich_0.5.5/bin/org/jdom/output/Format$TextMode.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/Format.class Binary file NGSrich_0.5.5/bin/org/jdom/output/Format.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/JDOMLocator.class Binary file NGSrich_0.5.5/bin/org/jdom/output/JDOMLocator.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/NamespaceStack.class Binary file NGSrich_0.5.5/bin/org/jdom/output/NamespaceStack.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/SAXOutputter.class Binary file NGSrich_0.5.5/bin/org/jdom/output/SAXOutputter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/XMLOutputter$NamespaceStack.class Binary file NGSrich_0.5.5/bin/org/jdom/output/XMLOutputter$NamespaceStack.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/XMLOutputter.class Binary file NGSrich_0.5.5/bin/org/jdom/output/XMLOutputter.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/org/jdom/output/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,15 @@ + + +Classes to output JDOM documents to various destinations. The most common +outputter class is XMLOutputter which outputs a document (or part of a +document) as a stream of bytes. Format and EscapeStrategy support the +XMLOutputter in letting you choose how the output should be formatted and how +special characters should be escaped. + +SAXOutputter lets you output as a stream of SAX events (handy especially in +transformations). JDOMLocator supports SAXOutputter and helps you observe the +SAX output process. + +DOMOutputter lets you output a JDOM document as a DOM tree. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/org/jdom/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,13 @@ + + +Classes to represent the components of an XML document. The Verifier is a +special class useful in ensuring well-formedness of documents. The Parent +interface is implemented by Document and Element exposing their commonality. +The Content abstract class is extended by all the node types of a document +except Document itself. + +The JDOMFactory interface and DefaultJDOMFactory standard implementation +provide advanced users with the ability to create subtypes of the org.jdom +classes. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/JDOMResult$DocumentBuilder.class Binary file NGSrich_0.5.5/bin/org/jdom/transform/JDOMResult$DocumentBuilder.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/JDOMResult$FragmentHandler.class Binary file NGSrich_0.5.5/bin/org/jdom/transform/JDOMResult$FragmentHandler.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/JDOMResult.class Binary file NGSrich_0.5.5/bin/org/jdom/transform/JDOMResult.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/JDOMSource$DocumentReader.class Binary file NGSrich_0.5.5/bin/org/jdom/transform/JDOMSource$DocumentReader.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/JDOMSource$JDOMInputSource.class Binary file NGSrich_0.5.5/bin/org/jdom/transform/JDOMSource$JDOMInputSource.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/JDOMSource.class Binary file NGSrich_0.5.5/bin/org/jdom/transform/JDOMSource.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/XSLTransformException.class Binary file NGSrich_0.5.5/bin/org/jdom/transform/XSLTransformException.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/XSLTransformer.class Binary file NGSrich_0.5.5/bin/org/jdom/transform/XSLTransformer.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/org/jdom/transform/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,8 @@ + + +Classes to help with transformations, based on the JAXP TrAX classes. +JDOMTransformer supports simple transformations with one line of code. +Advanced features are available with the JDOMSource and JDOMResult classes +that interface with TrAX. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/xpath/XPath$XPathString.class Binary file NGSrich_0.5.5/bin/org/jdom/xpath/XPath$XPathString.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/xpath/XPath.class Binary file NGSrich_0.5.5/bin/org/jdom/xpath/XPath.class has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/xpath/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/org/jdom/xpath/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,6 @@ + + +Support for XPath from within JDOM. XPath provides a common interface with a +pluggable back-end. The default back end is Jaxen. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/xmlFilePattern.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/bin/xmlFilePattern.xml Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,62 @@ + + + 1 + + name + 0 + 0 + 0 + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + + \ No newline at end of file diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/DEFAULT.properties --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/DEFAULT.properties Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,10 @@ +! Path of the temporary directory. +tmpDir: /tmp +! Path of the father directory of the output directory. When empty the output directory is placed in the directory containing the reads alignment file. +outDirPath: +! Name of the output directory (not the path). +outDir: enrichment +! Define poorly covered genes. +poor: 2 +! Defines highly covered genes. +high: 200 diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/NGSrich.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/NGSrich.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,58 @@ +import java.io.IOException; + +import _main.NGSrichEvaluate; +import _main.NGSrichSummarize; +import exceptions.FileFormatException; + +/** + * This is the main class. + * + * @author Peter Frommolt + * @author Ali Abdallah + */ + +public class NGSrich { + + /** + * Self Explanatory. + * + * @param args an Array of argument. The first argument is command and the + * other arguments are its options. + * + * @throws FileFormatException if the used files have formally a bad format. + * @throws IOException + * @throws InterruptedException + */ + public static void main(String[] args) throws FileFormatException, + IOException, InterruptedException { + + String usagestr = + "\nThis is NGSrich, version 0.5.4.\n\n" + + "Usage: java NGSrich [command] [options]\n\n" + + "\tCommands:\n" + + "\tevaluate" + + "\tEvaluate target enrichment for a single sample.\n" + + "\tsummarize" + + "\tCreate a summary report for several evaluations.\n"; + + int alen = args.length; + if (alen == 0) { + System.out.println(usagestr); + System.exit(0); + } else { + String[] cparams = new String[alen - 1]; + for (int i = 0; i < alen - 1; i = i + 1) { + cparams[i] = args[i + 1]; + } + String eval = "evaluate", summ = "summarize"; + if (eval.equals(args[0])) { + // Geändert von AA 27.07.2011. + new NGSrichEvaluate(cparams).evaluate(); + } + if (summ.equals(args[0])) { + // Geändert von AA 27.07.2011. + new NGSrichSummarize(cparams).summarize(); + } + } + } +} \ No newline at end of file diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/_main/Enrichment.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/_main/Enrichment.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,490 @@ +package _main; + +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.sql.Time; +import java.util.Scanner; + +import middlewares.Misc; +import converters.Read2Wig; +import converters.ReadOnTarget2Wig; +import exceptions.ChromosomeFormatException; +import exceptions.ChromosomeMismatchException; +import exceptions.ChromosomeNotFoundException; +import exceptions.FileFormatException; +import exceptions.GenomeAnnotationException; +import exceptions.NullOrNegativeRangeException; +import exceptions.RangeFormatException; +import exceptions.RangeLimitNotFoundException; +import filters.Filter; +import filters.GenomeFilter; +import filters.ReadFilter; +import filters.TargetFilter; + +/** + * This is a scheduler for the phases of the evaluation. + * + * @author Ali Abdallah + * @version 19.03.2011 + * @since jdk 1.6 + */ + +public class Enrichment { + + String + /** + * The name of the read alignment file. + */ + readFileName, + /** + * the name of the genome annotation file. + */ + genomeFName, + /** + * the ucsc-name of the genome (e.g. hg19). + */ + genomeName, + /** + * the name of the file of the targeted regions. + */ + targetFName, + /** + * the temporary directory. + */ + tmpDir, + /** + * the output directory. + */ + outDir, + /** + * the xml summary file containing various overall statistics. + */ + xmlSummaryFile, + /** + * the name of the detailed coverage data file. + */ + detailsFileName, + /** + * the .bed file containing target-level coverage statistics data. + */ + beddetailsFileName, + /** + * the process number used for unique naming. + */ + proc, + /** + * the name of the read alignment file without extension. + */ + prefix, + /** + * the extension of the read alignment file. + */ + suffix, + /** + * The name of the read alignment file after the reduction. + */ + areadFileName, + /** + * The name of the genome annotation file after the reduction. + */ + aGenomeFName, + /** + * the name of the file of the targeted regions after the reduction. + */ + aTargetFName; + int + /** + * Cutoff for poor coverage [default: 2]. + * + */ + poor, + /** + * Cutoff for high coverage [default: 200]. + */ + high, + details; + + /** + * Construcs an enrichment object and initializes the evaluation parameters. + * @param args the list of all evaluation parameters. + */ + public Enrichment(String... args) { + readFileName = args[0]; + genomeName = args[8]; + targetFName = args[2]; + if (!targetFName.endsWith("bed")) { + System.out.println("WARNING: Target file: " + targetFName + " must be in the bed format."); + } + if (args.length > 3) { + Time time = new Time(System.currentTimeMillis()); + String nano = ""+System.nanoTime(); + + tmpDir = args[3] + Misc.slash(args[3]) +"Sample_From_"+ + time.getHours()+"_"+ + time.getMinutes()+"_"+ + time.getSeconds()+"_"+nano+ "/"; + new File(tmpDir).mkdir(); + new File(tmpDir).setReadable(true); + new File(tmpDir).setWritable(true); + outDir = args[4] + Misc.slash(args[4]); + + if (!(new File(tmpDir).isDirectory()) && new File(tmpDir).exists()) { + System.out.println("File " + tmpDir + + " is not a directory.\nProgram stopped."); + System.exit(0); + } else if (!(new File(tmpDir).exists())) { + System.out.println("File " + tmpDir + + " not found.\nProgram stopped."); + System.exit(0); + } + } + if (args.length > 5) { + try { + poor = Integer.parseInt(args[5]); + high = Integer.parseInt(args[6]); + } catch (NumberFormatException nfe) { + System.out + .println("Warning: poor or high must be integers.\n and are set to the standard values."); + poor = 2; + high = 200; + } + } else { + poor = 2; + high = 200; + } + + genomeFName = (args[1].equals("none"))?downloadGenomeAnnotation():args[1]; + + prefix = Misc.prefix(readFileName); + if (args[7] != "none") { + prefix = args[7]; + } + details = Integer.parseInt(args[9]); + + suffix = Misc.suffix(readFileName); + proc = Misc.getHostName(); + areadFileName = tmpDir + "NGSrich_" + prefix + "_" + proc + ".txt"; + aGenomeFName = tmpDir + "NGSrich_genome_" + proc + ".txt"; + aTargetFName = tmpDir + "NGSrich_target_" + proc + ".bed"; + detailsFileName = tmpDir + "coverage_" + proc + ".txt"; + xmlSummaryFile = outDir + "data/" + prefix + "_enrichment.xml"; + beddetailsFileName = outDir + "data/" + prefix + "_enrichment.bed"; + } + + public static final String[] GENOME_NAMES = { + "anoGam1", "bosTau4", "cb3", "ce4", "ce6", + "danRer5", "danRer6", "danRer7", "dm2", "dm3", + "galGal2", "galGal3", "hg19", "hg18", "mm8", + "mm9", "panTro3", "rn3", "rn4", "susScr2" + }; + + public int genomeID(String gname){ + for(int i = 0; i < GENOME_NAMES.length; i++) + if(GENOME_NAMES[i].equals(gname)) + return i; + return -1; + } + + /** + * Downloads the specified genome annotation, if internet connection + * exists. + * + * @param genome the ucsc-name of the genome. (e.g. hg18, hg19) + * @return the very same name of the genome. + * @throws GenomeAnnotationException + */ + + public String getGenomeAnnotation() throws GenomeAnnotationException{ + try{ + return downloadGenomeAnnotation(); + }catch(Exception e){ + if(genomeID(genomeName)!=-1) + return Misc.scriptDir()+"thirdparty/annotations/"+genomeName+".txt"; + else if(new File(genomeName).exists()) + return genomeName; + else + throw new GenomeAnnotationException(); + } + } + + public String getChromInfo(){ + //genomeName + return Misc.scriptDir()+"thirdparty/chromInfo/"+genomeName+".txt"; + } + + public String downloadGenomeAnnotation() { + if (genomeName.indexOf("/") == -1) { + String tmpGenomeDir = tmpDir + genomeName; + try { + if (!new File(tmpGenomeDir).exists()) { + new File(tmpGenomeDir).mkdir(); + } + File getGenomeScript = new File(tmpGenomeDir + Misc.slash(tmpGenomeDir) + "getGenome.sh"); + if (!getGenomeScript.exists()) { + getGenomeScript.createNewFile(); + } + FileWriter fw = new FileWriter(getGenomeScript); + + getGenomeScript.setReadable(true); + getGenomeScript.setWritable(true); + getGenomeScript.setExecutable(true); + getGenomeScript.setExecutable(true); + String tmpGenomeFile = tmpGenomeDir + Misc.slash(tmpGenomeDir) + + "refGene.txt.gz"; + fw.write("#!/bin/bash\n" + "cd " + tmpGenomeDir + "\n" + + "wget http://hgdownload.cse.ucsc.edu/goldenPath/" + genomeName + + "/database/refGene.txt.gz " + "-O " + tmpGenomeFile + + "\n" + "gunzip " + tmpGenomeFile + "\n"); + fw.close(); + Runtime.getRuntime().exec("sh " + getGenomeScript); + try { + Thread.sleep(10000); + } catch (InterruptedException e) { + e.printStackTrace(); + } + + } catch (IOException e) { + e.printStackTrace(); + } + return tmpGenomeDir + Misc.slash(tmpGenomeDir) + "refGene.txt"; + } else { + return genomeName; + } + } + + /** + * A bridge method which converts a bam file to a sam file for further + * processing. This method assures therefore the compatibility of the + * software with the bam format. + * + * @return the name of the generated sam file. + * @throws IOException + */ + public String bam2sam() throws IOException { + + String[] bampath = readFileName.split("/"); + String bamfile = bampath[bampath.length - 1]; + String samfile = tmpDir + bamfile.split(".bam")[0] + ".sam"; + + File getBam2SamScript = new File(tmpDir + "bam2sam.sh"); + if (!getBam2SamScript.exists()) { + getBam2SamScript.createNewFile(); + } + FileWriter fw = new FileWriter(getBam2SamScript); + fw.write("#!/bin/bash\n" + Misc.binDir() + + "/../thirdparty/samtools/0.1.16/samtools view " + + readFileName + " > " + samfile); + fw.close(); + + Process p = Runtime.getRuntime().exec("sh " + getBam2SamScript); + // try { + // @SuppressWarnings("unused") + // "exitstate" variable unused + //int exitstate = p.waitFor(); + // } catch (InterruptedException e) { + //e.printStackTrace(); + // } + + Scanner stderr=new Scanner(p.getErrorStream()); + while(stderr.hasNextLine()){System.out.println(stderr.nextLine());} + stderr.close(); + + return (samfile); + + } + + /** + * First phase of the evaluation. In this phase input files are being + * simplified for further processing. + * + * @throws FileFormatException + * @throws ChromosomeMismatchException + */ + public void reduceFiles() throws FileFormatException, ChromosomeMismatchException { + String aReadFileName = tmpDir+"NGSrich_"+prefix+"_"+ proc + ".txt"; + String aGenomeFName = tmpDir+"NGSrich_genome_" + proc + ".txt"; + String aTargetFName = tmpDir+"NGSrich_target_"+ proc+".txt"; + + + Filter[] filters = {new ReadFilter(readFileName, aReadFileName), + new GenomeFilter(genomeFName, aGenomeFName), + new TargetFilter(targetFName, aTargetFName)}; + + for(Filter f: filters) f.filter(); + + if(!Misc.areChromosomeCompatible(new File(aReadFileName), + new File(aTargetFName))) + throw new ChromosomeMismatchException(); + + System.out.println("\nSTEP 1 successfully completed"); + } + + /** + * Second phase of the evaluation. An EnrichmentStatsComputer object is + * called with the right parameters and computation is checked for formal + * correctness. + */ + public void computeTargetCoverageFiles() { + + File data = new File(outDir + "/data"); + data.mkdir(); + File plots = new File(outDir + "/plots"); + plots.mkdir(); + + EnrichmentStatsComputer esc = + new EnrichmentStatsComputer(prefix, proc,tmpDir, outDir); + + try { + esc.compute(); + } catch (RangeFormatException e) { + e.printStackTrace(); + } catch (ChromosomeFormatException e) { + e.printStackTrace(); + } catch (ChromosomeNotFoundException e) { + e.printStackTrace(); + } catch (RangeLimitNotFoundException e) { + e.printStackTrace(); + } catch (NullOrNegativeRangeException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + + if (new File(detailsFileName).exists()) { + System.out.println("\nSTEP 2 successfully completed"); + } else { + System.out.println("STEP 2 incomplete."); + } + + } + + /** + * Third phase of the evaluation. Based on the results from phase 2, the + * evaluation is further developed and evaluation data are visualized by + * calling "eval_enrichment.R" Script. + */ + public void evaluate() { + Runtime rt = Runtime.getRuntime(); + try { + String script = Misc.scriptDir() + Misc.slash(Misc.scriptDir())+"R/eval_enrichment.R"; + int lastSlash = outDir.lastIndexOf("/"); + String outDirR = (lastSlash == outDir.length() - 1) ? outDir + .substring(0, lastSlash) : outDir; + + String call = "Rscript " + script + " "+ xmlSummaryFile + " " + beddetailsFileName + " " + + outDirR + " " + genomeName + " " + poor + " " + high + " " + prefix + " " + + targetFName+" "+details; + + Process p=rt.exec(call); + + Scanner stdout = new Scanner(p.getInputStream()); + Scanner stderr=new Scanner(p.getErrorStream()); + while (stdout.hasNextLine()){System.out.println(stdout.nextLine());} + while (stderr.hasNextLine()){System.out.println(stderr.nextLine());} + stdout.close(); stderr.close(); + + if(details == 1){ + String chrInfoPath = getChromInfo(); + + //System.out.println("chrInfoPath\t"+chrInfoPath); + script = Misc.scriptDir() + Misc.slash(Misc.scriptDir())+"R/eval_details.R"; + outDirR = (lastSlash == outDir.length() - 1) ? outDir.substring(0, lastSlash) : outDir; + + String call2 = "Rscript "+ script + " " + xmlSummaryFile + " " + beddetailsFileName + + " " + detailsFileName + " " + chrInfoPath + " " + outDirR + " " + + genomeName; + Process p2 = rt.exec(call2); + stdout=new Scanner(p2.getInputStream()); + stderr=new Scanner(p2.getErrorStream()); + + while(stdout.hasNextLine()){System.out.println(stdout.nextLine());} + while(stderr.hasNextLine()){System.out.println(stderr.nextLine());} + stdout.close(); stderr.close(); + } + + String path = outDir+prefix+"_enrichment.html"; + System.out.println("Created plots and HTML summary report"); + if (new File(path).exists()) { + System.out.println("\nSTEP 3 successfully completed"); + } else { + System.out.println("HTML FILE " + path + " not found"); + System.out.println("\nSTEP 3 unsuccessful"); + } + } + catch (IOException e) { + e.printStackTrace(); + } + } + + /** + * This is the fourth phase. In this phase the detailed datta from phase 2 + * are converted to the wiggle format. The method uses a ReadOnTarget2Wig + * object to accomplish this task. + * + */ + public void computeWiggleFile() { + try { + System.out.println("Computing wiggle file for on-target reads"); + if (!new File(detailsFileName).exists()) + detailsFileName = tmpDir + new File(detailsFileName).getName(); + + new ReadOnTarget2Wig(detailsFileName, prefix, outDir + "data", + Misc.prefix(readFileName)+ "\nonTarget"); + System.out.println("Wiggle file for on-target reads created"); + System.out.println("Output written to " + outDir + "data/" + prefix + "_onTarget.wig"); + File[] outputFiles = new File(outDir + "data/") + .listFiles(); + for (int i = 0; i < outputFiles.length; i++) { + if (outputFiles[i].getName().endsWith("wig") + && outputFiles[i].getName().startsWith( + detailsFileName.substring( + detailsFileName.lastIndexOf("/") + 1, + detailsFileName.lastIndexOf(".")))) { + File f = new File(outDir + "data" + + "/" + Misc.prefix(readFileName) + "_onTarget.wig"); + outputFiles[i].renameTo(f); + break; + } + } + if (new File(outDir+"data/"+prefix+"_onTarget.wig").exists()){ + System.out.println("\nSTEP 4 successfully completed."); + } else { + System.out.println(outDir+"data/"+ prefix + + "_onTarget.wig not found!\n\nSTEP 4 unsuccessful"); + } + } catch (IOException e) { + System.err.println("Target conversion in Wig unsuccessful"); + e.printStackTrace(); + } + } + + /** + * This is the fifth and last phase of the evaluation process. In contrast + * to the fourth phase, this method uses a Read2Wig object to convert the + * detailed data for all reads (and not only for reads on targets) to the + * wiggle format. + * + */ + void computeOverallWiggleFile() { + try { + System.out.println("Computing wiggle file for all reads"); + new Read2Wig(areadFileName, prefix, outDir + "data", + genomeFName, tmpDir); + String overallWiggleFileName = prefix + ".wig"; + System.out.println("Wiggle file for all reads created"); + System.out.println("Output written to " + outDir + "data/" + + overallWiggleFileName); + if (new File(outDir + "data/" + overallWiggleFileName).exists()) { + System.out.println("\nSTEP 5 successfully completed."); + } else { + System.out.println(outDir + "data/" + overallWiggleFileName + + "not found\n\nSTEP 5 unsuccessful"); + } + } catch (IOException e) { + System.err + .println("Creating wiggle file for all reads was unsuccessful"); + e.printStackTrace(); + } + } +} \ No newline at end of file diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/_main/EnrichmentStatsComputer.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/_main/EnrichmentStatsComputer.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,595 @@ +package _main; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileWriter; +import java.io.IOException; +import java.util.Scanner; + +import org.jdom.Element; + +import datastructures.ReducedReadLine; +import datastructures.TargetLine; +import exceptions.ChromosomeFormatException; +import exceptions.ChromosomeNotFoundException; +import exceptions.NullOrNegativeRangeException; +import exceptions.RangeFormatException; +import exceptions.RangeLimitNotFoundException; + +import middlewares.GeneExtractor; +import middlewares.HitsCounter; +import middlewares.Misc; +import middlewares.ReadCounter; +import middlewares.XMLSummaryFileBuilder; + +/** + * This class is for computation of the coverage, BED coverage and statistics + * output files. + * + * @author Ali Abdallah + * @version 02.02.2011 + * @since jdk 1.6.0 + */ + +public class EnrichmentStatsComputer { + + /* *********************************************************************** + * FIELDS OF THE CLASS + * ***********************************************************************/ + private String + /** + * 4-column alignment file sorted by alignment subject and position. + */ + align, + /** + * 3-column target file sorted by subject and target starting position. + */ + target, + /** + * Annotation file. + */ + genome, + /** + * Statistics file in the xml-format. + */ + summary, + /** + * Coverage file. + */ + details, + /** + * Coverage BED file. + */ + targetCS, + /** + * The absolute name of the read alignment file without the extension. + */ + prefix, + + /** + * The directory under which temporary data are saved (temporary directory). + */ + tmpDir, + /** + * The directory of the computed results (output directory). + */ + outDir; + + + private Scanner + /** + * Scanner of the read alignment file (sam format). + */ + rScanner, + /** + * Scanner of the genome annotation file. + */ + gScanner, + /** + * Scanner of the file of targets. + */ + tScanner; + + private FileWriter + /** + * Writer used to write the computed statistics into the statistics file. + */ + summaryWriter, + /** + * Writer used to write coverage data at base-level into the coverage file. + */ + detailsWriter, + /** + * Writer used to write the summarized coverage data at target level into + * the coverage BED file. + */ + targetCSWriter; + + /** + * Counter used to counts the coverage frequencies at different levels. + */ + private HitsCounter hc; + /** + * Counter used to count both: Reads exactly on the targets or overlapping + * the targets and Reads doing this in a scope of 100 resp. 200 bases from + * both end. + */ + private ReadCounter rc; + + /** + * A Gene Extractor used to extract the genes overlapping the specified + * targets. + */ + private GeneExtractor ge; + + /** + * Counter for the reads. + */ + private int numReads = 0, + /** + * Counter for all target bases. + */ + targetBases = 0, + /** + * Counter for the bases in a specific target. + */ + currTargetBases = 0; + + /** + * The average Coverage of the targets. + */ + private double avCov = 0; + /** + * The average Coverage of the current observed target. + */ + private double curAvCov = 0; + /** + * Flag indicating the end of the read file. + */ + private boolean endReads = false; + /** + * Flag indicates if the coverage line was written or not. + */ + private boolean covWritten = false; + + /** + * Contains always the current observers read line from the sam file. + */ + private ReducedReadLine rLine; + + + private int rlength; + + /** + * ID's of the leaf-tags in the XML summary file. + */ + private static final int + from30xPERC = 28, from30xBASES = 27,from20xPERC = 26, from20xBASES = 25, + from10xPERC = 24, from10xBASES = 23,from5xPERC = 22, from5xBASES = 21, + from1xPERC = 20, from1xBASES = 19, OV200P = 18, OV_200 = 17, + OV100P = 16, OV_100 = 15, OV_PERC = 14, OV = 13, ON200P = 12, + ON_200 = 11, ON100P = 10, ON_100 = 9, ON_PERC = 8, ON = 7, + STANDARD_ERROR = 6, AVERAGE_COVERAGE = 5, TARGET_BASES = 4, + NUMBER_OF_READS = 3, READ_LENGTH = 2, SAMPLE_NAME = 1, SAMPLE_NUMBER = 0; + + /** + * Constructs a EnrichmentStatsComputer object. + * + * @param prefix the name of the sam file without its extension. + * @param proc the number of the process running the software. + * @param tmpDir the temporary directory + * @param outDir the output directory. + */ + public EnrichmentStatsComputer(String prefix, String proc, String tmpDir, + String outDir) { + super(); + + this.prefix = prefix; + + // Setting the paths. + this.tmpDir = tmpDir + Misc.slash(tmpDir); + this.outDir = outDir + Misc.slash(outDir); + this.align = this.tmpDir + "NGSrich_" + prefix + "_" + proc+ ".txt"; + this.target = this.tmpDir + "NGSrich_target_" + proc + ".txt"; + this.genome = this.tmpDir + "NGSrich_genome_" + proc + ".txt"; + this.details = this.tmpDir + "coverage_" + proc + ".txt"; + this.summary = this.outDir + "data/" + prefix + "_enrichment.xml"; + this.targetCS = this.outDir + "data/" + prefix + "_enrichment.bed"; + + // Constructing and initializing various objects. + try { + init(); + } catch (ChromosomeFormatException e) { + e.printStackTrace(); + } catch (ChromosomeNotFoundException e) { + e.printStackTrace(); + } catch (RangeFormatException e) { + e.printStackTrace(); + } catch (RangeLimitNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + } + + public void init() throws IOException, ChromosomeFormatException, + ChromosomeNotFoundException, RangeFormatException, + RangeLimitNotFoundException { + hc = new HitsCounter(); + rc = new ReadCounter(); + rScanner = new Scanner(new File(align)); + tScanner = new Scanner(new File(target)); + gScanner = new Scanner(new File(genome)); + File sum = new File(summary); + if (!sum.exists()) { + sum.createNewFile(); + } + summaryWriter = new FileWriter(sum); + detailsWriter = new FileWriter(new File(details)); + targetCSWriter = new FileWriter(new File(targetCS)); + rLine = new ReducedReadLine(rScanner.nextLine()); + rlength = (rLine.isForwardRead())?rLine.end()-rLine.start()+1 + :rLine.start()-rLine.end()+1; + numReads++; + ge = new GeneExtractor(genome); + } + + private void finit() throws IOException { + summaryWriter.close(); + rScanner.close(); + tScanner.close(); + gScanner.close(); + detailsWriter.close(); + } + + /* *********************************************************************** + * MAIN COMPUTATION + * ***********************************************************************/ + /** + * The main computation method. + * + * @throws IOException if the coverage file or the summary file can't be + * written. + * @throws NullOrNegativeRangeException + * @throws RangeLimitNotFoundException + * @throws ChromosomeNotFoundException + * @throws ChromosomeFormatException + * @throws RangeFormatException + */ + public void compute() throws IOException, + RangeFormatException, + ChromosomeFormatException, + ChromosomeNotFoundException, + RangeLimitNotFoundException, + NullOrNegativeRangeException { + // run over all targets. + while (tScanner.hasNextLine()) { + // Set a flag indicating if the target file and the read file are + // at the same chromosome level. (Standard value: false) + boolean chromAlreadyReached = false; + // Read the next target. + TargetLine tLine = new TargetLine(tScanner.nextLine()); + // Save the number of target bases. + currTargetBases = tLine.end() - tLine.start() + 1; + // Initialize the array of the number if hits on each base of the + // target. + int[] bases = new int[currTargetBases]; + // Update the current total number of observed target bases. + targetBases += currTargetBases; + // Initialize the average coverage of the current target. + curAvCov = 0; + // Set a flag indicating if the coverage data for the current target + // are already written or not. + covWritten = false; + // Find the gene overlapping the current target by using the + // logarithmic time gene extractor. + String currTargetGene = ge.extractGene(tLine); + + // Stop if end of the alignment file is reached. + while (!endReads) { + // Otherwise. + // Check if the alignment file and the target file are at the + // same chromosome level. + if (rLine.chrom().equals(tLine.chrom())) { + chromAlreadyReached = true; + // Target not exceeded yet. + if (!readExceededTarget(rLine, tLine)) { + // Increment "on target" and "overlapping" values. + incOnTargetValues(rLine, tLine); + incOverlapsValues(rLine, tLine, bases); + } else { + // Compute the average coverage of the current target + // and update the target hits values at the 5 different + // levels. + curAvCov = updateTargetHitsValues(bases); + // Write the coverage data for the current target. + writeCoverageLines(currTargetBases, curAvCov, tLine + + "", bases, currTargetGene); + // Break the while-loop, since all next reads belong + // to next targets. + break; + } + } + // otherwise + else { + // alignment took already place beforehand. + if (!covWritten && chromAlreadyReached) { + curAvCov = updateTargetHitsValues(bases); + writeCoverageLines(currTargetBases, curAvCov, tLine + + "", bases, currTargetGene); + break; + } + } + // If exists, get the next read for the next target and + // increment the number of reads by one. + if (rScanner.hasNextLine()) { + rLine = new ReducedReadLine(rScanner.nextLine()); + numReads++; + } + // otherwise (no reads anymore). + else { + endReads = true; + } + } + // Reads completely processed but last coverage line not written. + if (endReads && covWritten == false) { + curAvCov = updateTargetHitsValues(bases); + writeCoverageLines(currTargetBases, curAvCov, tLine + "", + bases, currTargetGene); + } + } + // Count the remaining reads. + while (rScanner.hasNextLine()) { + rScanner.nextLine(); + numReads++; + } + targetCSWriter.close(); + System.out.println("Target BED coverage file created ("+targetCS+")"); + System.out.println("Per-base coverage file created ("+details+")"); + + // Self explanatory. + double sd = Math.sqrt(var(targetBases, avCov)); + writeSummary(numReads, targetBases, avCov, sd); + + System.out.println("Summary statistics file created ("+summary+")"); + finit(); + } + + /* *********************************************************************** + * AUXILIARY METHODS + * ***********************************************************************/ + /** + * Updates the hits values at 5 different levels (1x, 5x, 10x, 20x, 30x) and + * the average target coverage. + * + * @param bases the hits on the bases of the current target. + * @return the average coverage of the current target. + */ + private double updateTargetHitsValues(int[] bases) { + double curAvCov = 0; + for(int i = 0; i < bases.length; i++) { + curAvCov += bases[i]; + hc.updateCurrentHits(bases[i]); + } + hc.updateHits(); + avCov += curAvCov; + return curAvCov; + } + + /** + * Writes the summary file containing overall statistics for the observed + * sample. + * + * @param numReads the total number of reads. + * @param targetBases the total number of target bases. + * @param avCov the average target coverage. + * @param sd the standard deviation of the target coverage. + * + */ + private void writeSummary(int numReads, int targetBases, double avCov, + double sd){ + + int x1 = hc.getNextLevelHits(); + int x5 = hc.getNextLevelHits(); + int x10 = hc.getNextLevelHits(); + int x20 = hc.getNextLevelHits(); + int x30 = hc.getNextLevelHits(); + + XMLSummaryFileBuilder xbf = + new XMLSummaryFileBuilder(summary, prefix); + Element[] tags = xbf.getLeafs(); + tags[SAMPLE_NUMBER].setText("1"); + tags[SAMPLE_NAME].setText(prefix); + tags[READ_LENGTH].setText(rlength+""); + tags[NUMBER_OF_READS].setText(numReads+""); + tags[TARGET_BASES].setText(targetBases+""); + int d = 2; + tags[AVERAGE_COVERAGE].setText(dfloor(avCov / targetBases, d)+""); + tags[STANDARD_ERROR].setText(dfloor(sd, d)+""); + + tags[ON].setText(rc.on()+""); + tags[ON_PERC].setText(dfloor((rc.on()/(double)numReads)*100, d)+""); + tags[ON_100].setText(rc.on100()+""); + tags[ON100P].setText(dfloor((rc.on100()/(double)numReads)*100, d)+""); + tags[ON_200].setText(rc.on200()+""); + tags[ON200P].setText(dfloor((rc.on200()/(double)numReads)*100, d)+""); + + tags[OV].setText(rc.over()+""); + tags[OV_PERC].setText(dfloor((rc.over()/(double)numReads)*100, d)+""); + tags[OV_100].setText(rc.over100()+""); + tags[OV100P].setText(dfloor((rc.over100()/(double)numReads)*100, d)+""); + tags[OV_200].setText(rc.over200()+""); + tags[OV200P].setText(dfloor((rc.over200()/(double)numReads)*100, d)+""); + + tags[from1xBASES].setText(x1+""); + tags[from1xPERC].setText(dfloor((x1/(double)targetBases)*100, d)+""); + tags[from5xBASES].setText(x5+""); + tags[from5xPERC].setText(dfloor((x5/(double)targetBases)*100, d)+""); + tags[from10xBASES].setText(x10+""); + tags[from10xPERC].setText(dfloor((x10/(double)targetBases)*100, d)+""); + tags[from20xBASES].setText(x20+""); + tags[from20xPERC].setText(dfloor((x20/(double)targetBases)*100, d)+""); + tags[from30xBASES].setText(x30+""); + tags[from30xPERC].setText(dfloor((x30/(double)targetBases)*100, d)+""); + + xbf.writeXMLFile(summary); + } + + /** + * Computes the variance of the target coverage. + * + * @param targetBases the total number of target bases. + * @param avCov the average target coverage. + * @return The variance of the target coverage. + * @throws FileNotFoundException if the coverage BED file can't be found. + */ + private double var(int targetBases, double avCov) + throws FileNotFoundException { + + Scanner mdScanner = new Scanner(new File(targetCS)); + int n = 0; + double X = avCov / targetBases; + double sum = 0; + + while (mdScanner.hasNextLine()) { + String mdLine = mdScanner.nextLine(); + String[] mdFields = mdLine.split("\t"); + double X_i = Double.parseDouble(mdFields[4]); + sum += (X_i - X) * (X_i - X); + n += 1; + } + + sum /= n - 1; + return sum; + } + + /** + * Writes detailed coverage data to the coverage file and a coverage line + * to the coverage BED file. + * + * @param currTargetBases number of bases of the current target. + * @param curAvCov the average coverage on the specified target tLine. + * @param tLine the target line. + * @param bases the hits on the bases of the target tLine. + * @param currTargetGene the gene overlapping the current target. + * @throws IOException if the writer fails to write to coverage line. + */ + private void writeCoverageLines(int currTargetBases, double curAvCov, + String tLine, int[] bases, String currTargetGene) + throws IOException { + detailsWriter.write(tLine + "\r\n"); + for(int i = 0; i < bases.length; i++) + detailsWriter.write(bases[i] + "\n"); + targetCSWriter.write(tLine + "\t" + currTargetGene + "\t" + + dfloor((curAvCov / (double)currTargetBases), 2) + "\t" + + dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2) + + "\t" + + dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2) + + "\t" + + dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2) + + "\t" + + dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2) + + "\t" + + dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2) + + "\r\n"); + covWritten = true; + hc.resetCurrentHits(); + } + + /** + * Cut decimal places greater than the specified one. + * @param number the number to be cut. + * @param decimalPlace the decimalPlace after which the cut-operation + * take place. + * @return the cut number. + */ + public static double dfloor(double number, int decimalPlace) { + return Math.floor(number * Math.pow(10, decimalPlace)) + / Math.pow(10, decimalPlace); + } + + /** + * Checks if the read exceeded the target. + * @param rl read line. + * @param tl target line. + * @return true if the read starts right to the end position of the target + * and false otherwise. + */ + public static boolean readExceededTarget(ReducedReadLine rl, TargetLine tl) { + return !(rl.start() <= tl.end() || rl.end() <= tl.end()); + } + + /** + * 
 
+	 * 1. Increments the number of Reads, overlapping targets within a scope of 
+	 * 	  0, 100 and 200 bases from both ends, by one.
+	 * 2. Increments the number of hits on the hitted bases by one.   
+	 *
+ * @param rl the read line. + * @param tl the target line. + * @param bases the base hits array of the target. + */ + private void incOverlapsValues(ReducedReadLine rl, TargetLine tl, int[] bases) { + // Forward reads. + if (rl.isForwardRead()) { + if (rl.end() >= tl.start() && rl.start() <= tl.end()) { + // incrementing the number of his on the hitted bases by one. + int start = Math.max(0, rl.start() - tl.start()); + int stop = Math.min(bases.length - 1, rl.end() - tl.start()); + for (int i = start; i <= stop; i++) + bases[i]++; + // incrementing the number of Reads overlapping targets by one. + rc.incOver(); + } + if (tl.start() - 100 <= rl.end() && rl.start() <= tl.end() + 100) + // incrementing the number of Reads overlapping targets(+/-100) + // by one. + rc.incOver100(); + if (tl.start() - 100 <= rl.end() && rl.start() <= tl.end() + 100) + // incrementing the number of Reads overlapping targets(+/-200) + // by one. + rc.incOver200(); + } + // Reverse reads. + else { + if (rl.start() >= tl.start() && rl.end() <= tl.end()) { + int start = Math.max(0, rl.end() - tl.start()); + int stop = Math.min(bases.length - 1, rl.start() - tl.start()); + for (int i = start; i <= stop; i++) bases[i]++; + rc.incOver(); + } + if (rl.start() >= tl.start() - 100 && rl.end() <= tl.end() + 100) + rc.incOver100(); + if (rl.start() >= tl.start() - 100 && rl.end() <= tl.end() + 100) + rc.incOver200(); + } + } + + /** + * Increments the number of Reads on targets within a scope of 0, 100 and + * 200 bases from both ends, by one. + * @param rl the read line. + * @param tl the target line. + */ + private void incOnTargetValues(ReducedReadLine rl, TargetLine tl) { + // Forward read. + if (rl.isForwardRead()) { + if ((tl.start() <= rl.start()) && (rl.end() <= tl.end())) + rc.incOn(); + if ((tl.start()-100 <= rl.start()) && (rl.end() <= tl.end()+100)) + rc.incOn100(); + if ((tl.start()-200 <= rl.start()) && (rl.end() <= tl.end()+200)) + rc.incOn200(); + } + // Reverse read. + else { + if (tl.start() <= rl.end() && rl.start() <= tl.end()) + rc.incOn(); + if (tl.start()-100 <= rl.end() && rl.start()<= tl.end()+100) + rc.incOn100(); + if (tl.start()-200 <= rl.end() && rl.start() <= tl.end()+200) + rc.incOn200(); + } + } + +} \ No newline at end of file diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/_main/NGSrichEvaluate.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/_main/NGSrichEvaluate.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,227 @@ +package _main; + +import java.io.BufferedInputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileWriter; +import java.io.IOException; +import java.sql.Time; +import java.util.Properties; +import middlewares.Misc; +import exceptions.ChromosomeMismatchException; +import exceptions.FileFormatException; + +/** + * This is the Main-class of the evaluation part of the software. This class + * uses the Enrichment-class to process the phases (the parts) of the pipeline. + * + * @author Ali Abdallah + */ + +public class NGSrichEvaluate { + + /** + * An array of arguments containing the following option elements in the + * following order: + * -r (-a|-g) -t [-s ] + * [-T ][-o ][-p -h ][-no_details] + * + * Required: + * Path to read alignment file in SAM or BAM format. + * UCSC genome version name. + * Path to target file in BED format. + * + * Optional: + * Sample name [default: prefix of ]. + * Temporary directory [default: '/tmp']. + * Output directory [default: '/enrichment']. + * Cutoff for poor coverage [default: 2]. + * Cutoff for high coverage [default: 200]. + */ + String[] args; + + public NGSrichEvaluate(String[] args) { + this.args = args; + } + + public void evaluate() throws IOException, FileFormatException, + InterruptedException { + /** + * Ordered List of Parameter (left/right): readFName genomeFName + * targetFName tmpDir outDir + * + */ + + int alen = args.length; + String[] params = new String[10]; + + String usagestr = + "\nUsage: java NGSrich evaluate -r " + + "-u -t [(-a|-g) " + + "] [-s ] [-T ] " + + "[-o ] [-p -h ][--no-details>]\n\n\tRequired:\n\t" + + "\tPath to read alignment file in SAM or BAM format." + + "\n\t\tUCSC genome version name.\n\t\tPath " + + "to target file in BED format.\n\n\tOptional:\n\t\t\t" + + "Sample name [default: prefix of ].\n\t\t\t" + + "path of the annotation file [default: the genome is " + + "downloaded based on the genome version name].\n\t\t" + + "Temporary directory [default: '/tmp'].\n\t\tOutput " + + "directory [default: '/enrichment'].\n\t" + + "\t\tCutoff for poor coverage [default: 2].\n\t" + + "\t\tCutoff for high coverage [default: 200]. \n\t--no-details\tto repress the computation of the" + + " evaluation details\n"; + + if (alen == 0) { + System.out.println(usagestr); + System.exit(0); + } + + boolean t = false, o = false, h = false, po = false, sname = false, u = false, r = false, g = false, + a = false, T = false; + params[9] = "1"; + for (int i = 0; i < alen; i = i + 2) { + if ((args[i].length() == 2 && args[i].charAt(0) == '-') || args[i].equals("--no-details")) { + char flag = (args[i].length()==2)?args[i].charAt(1):args[i].charAt(2); + switch (flag) { + case 'r': params[0] = args[i + 1];r = true;break; + case 'g': params[1] = args[i + 1];g = true;break; + case 'a': params[1] = args[i + 1];a = true;break; + case 't': params[2] = args[i + 1];t = true;break; + case 'T': params[3] = args[i + 1];T = true;break; + case 'o': params[4] = args[i + 1];o = true;break; + case 'p': params[5] = args[i + 1];po = true;break; + case 'h': params[6] = args[i + 1];h = true;break; + // Added by PF 2011-07-12 + case 's': params[7] = args[i + 1];sname = true;break; + case 'u': params[8] = args[i+1]; u = true;break; + case 'n': params[9]="0";break; + } + } else { + System.out.println(usagestr); + System.exit(0); + } + } + + boolean required = r && t && u; + + if(!required){ + System.out.println("Some required arguments are missing.\n"); + System.out.println(usagestr); + System.exit(0); + } + + String default_properties_file = createDefaultPropertiesFile(); + Properties p = new Properties(); + BufferedInputStream stream = + new BufferedInputStream( + new FileInputStream(default_properties_file)); + + p.load(stream); + stream.close(); + if (!T)params[3] = p.getProperty("tmpDir"); + if (!o) { + String oPath = p.getProperty("outDirPath"); + if (oPath.equals(""))oPath = Misc.path(params[0]); + params[4] = oPath + Misc.slash(oPath) + p.getProperty("outDir"); + new File(params[4]).mkdir(); + } + if (!po)params[5] = p.getProperty("poor"); + if (!h)params[6] = p.getProperty("high"); + if (!sname)params[7] = "none"; + if (!(a||g))params[1] = "none"; + + Enrichment ngs = new Enrichment(params); + // Convert BAM to SAM if necessary. + String infile = params[0]; + if (infile.endsWith(".bam")) { + System.out.println("======================0======================"); + System.out.println("\n>>> Found BAM file: converting to SAM\n"); + infile = ngs.bam2sam(); + } + ngs.readFileName = infile; + + // File timeReport = + // new File(params[3] + Misc.slash(params[3])+"TimeReport.txt"); + // FileWriter trWriter = new FileWriter(timeReport); + + // Reduce the files. + System.out.println("======================1======================"); + System.out.println(">>> STEP 1: reducing files\n"); + try { + long start = System.currentTimeMillis(); + ngs.reduceFiles(); + long rtime = System.currentTimeMillis() - start; + Time time = new Time(rtime); + //trWriter.write("Reducing files took: " + time + "\n"); + + } catch (ChromosomeMismatchException e) { + e.printStackTrace(); + } + + // Compute the target coverage files. + System.out.println("\n======================2======================"); + System.out.println(">>> STEP 2: computing target coverage data\n"); + long start = System.currentTimeMillis(); + ngs.computeTargetCoverageFiles(); + long rtime = System.currentTimeMillis() - start; + Time time = new Time(rtime); + // trWriter.write("Computing target coverage data took: " + time + "\n"); + + // Evaluate enrichment. + System.out.println("\n======================3======================"); + System.out.println(">>> STEP 3: evaluating enrichment files\n"); + start = System.currentTimeMillis(); + ngs.evaluate(); + rtime = System.currentTimeMillis() - start; + time = new Time(rtime); + //trWriter.write("Evaluating enrichment files took: " + time + "\n"); + Thread.sleep(10000); + + // Compute the target wiggle files. + System.out.println("\n======================4======================"); + System.out.println(">>> STEP 4: computing targets wiggle data\n"); + start = System.currentTimeMillis(); + ngs.computeWiggleFile(); + rtime = System.currentTimeMillis() - start; + time = new Time(rtime); + //trWriter.write("Computing targets wiggle data took: " + time + "\n"); + + // Compute the overall wiggle files. + System.out.println("\n======================5======================"); + System.out.println(">>> STEP 5: computing overall wiggle data\n"); + ngs.computeOverallWiggleFile(); + start = System.currentTimeMillis(); + ngs.computeOverallWiggleFile(); + rtime = System.currentTimeMillis() - start; + time = new Time(rtime); + //trWriter.write("Computing targets wiggle data took: " + time + "\n"); + System.out.println("\n============================================="); + //trWriter.close(); + } + + private String createDefaultPropertiesFile() throws IOException { + String default_properties_file = + Misc.binDir()+Misc.slash(Misc.binDir())+"DEFAULT.properties"; + if(!new File(default_properties_file).exists()){ + String default_str = + "! Path of the temporary directory.\n" + + "tmpDir: /tmp\n" + + "! Path of the father directory of the output directory. " + + "When empty the output directory is placed in the directory " + + "containing the reads alignment file.\n" + + "outDirPath:\n" + + "! Name of the output directory (not the path).\n" + + "outDir: enrichment\n" + + "! Define poorly covered genes.\n" + + "poor: 2\n" + + "! Defines highly covered genes.\n" + + "high: 200"; + FileWriter properties_writer = + new FileWriter(default_properties_file); + properties_writer.write(default_str); + properties_writer.close(); + } + return default_properties_file; + } +} \ No newline at end of file diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/_main/NGSrichSummarize.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/_main/NGSrichSummarize.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,106 @@ +package _main; +import java.io.FileInputStream; +import java.io.IOException; +import java.util.Properties; +import java.util.Scanner; + +import middlewares.Misc; +import exceptions.FileFormatException; + +/** + * This is the Main-class of the summarization part of the software. This class + * is a wrapper class. It calls the r-script "summarize_enrichment.R" which + * summarizes the evaluations of multiple samples. + * + * @author Peter Frommolt + */ + +public class NGSrichSummarize { + + /** + * An array of arguments containing the following option elements in the + * very same order: -i -o [-p -h ] + * + * Required: + * File with evaluation directories to be summarized, one per + * line. + * Output directory. + * + * Optional: + * Cutoff for poorly covered genes [default: 2]. + * Cutoff for highly covered genes [default: 200]. + * + */ + String[] args; + + public NGSrichSummarize(String[] args){ + this.args = args; + } + + public void summarize() throws FileFormatException, + IOException, + InterruptedException{ + int alen = args.length; + String[] params = new String[4]; + + String usagestr="\nUsage: NGSrich summarize -i -o " + + "[-p -h ]\n\n\tRequired:\n\t\tFile " + + "with evaluation directories to be summarized, one per line." + + "\n\t\tOutput directory.\n\n\tOptional:\n\t\t\t" + + "Cutoff for poorly covered genes [default: 2].\n\t\t\t" + + "Cutoff for highly covered genes [default: 200].\n"; + + if(alen==0){ + System.out.println(usagestr); + System.exit(0); + } + + boolean i=false, o=false, h=false, po=false; + for(int k = 0; k < alen; k=k+2){ + if(args[k].length() == 2 && args[k].charAt(0)=='-'){ + char flag = args[k].charAt(1); + switch(flag){ + case 'i': params[0]=args[k+1]; i=true; break; + case 'o': params[1]=args[k+1]; o=true; break; + case 'p': params[2]=args[k+1]; po=true; break; + case 'h': params[3]=args[k+1]; h=true; break; + } + } + else{ + System.out.println(usagestr); + System.exit(0); + } + } + + Properties p = new Properties(); + FileInputStream stream=new FileInputStream(Misc.binDir()+Misc.slash(Misc.binDir())+"DEFAULT.properties"); + p.load(stream); stream.close(); + + String infile, outdir, poor, high; + + if(!i){System.out.println("Error: Argument -i is mandatory"); System.exit(1);} + if(!o){System.out.println("Error: Argument -o is mandatory"); System.exit(1);} + infile=params[0]; outdir=params[1]; + + if(!po){poor=p.getProperty("poor");} + else{poor=params[2];} + + if(!h){high=p.getProperty("high");} + else{high=params[3];} + + Runtime rt=Runtime.getRuntime(); + String rScriptAbsolutePathName=Misc.binDir()+Misc.slash(Misc.binDir())+"../R/summarize_enrichment.R"; + Process proc = rt.exec(rScriptAbsolutePathName+" "+infile+" "+outdir+" "+poor+" "+high); + + /*Scanner sc=new Scanner(proc.getInputStream()); String erg = ""; + while(sc.hasNextLine()){erg += (sc.nextLine());} + sc.close();*/ + + Scanner stdout = new Scanner(proc.getInputStream()); + Scanner stderr=new Scanner(proc.getErrorStream()); + while (stdout.hasNextLine()){System.out.println(stdout.nextLine());} + while(stderr.hasNextLine()){System.out.println(stderr.nextLine());} + stdout.close(); stderr.close(); + + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/converters/Read2Wig.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/converters/Read2Wig.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,267 @@ +package converters; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileWriter; +import java.io.IOException; +import java.util.Scanner; + +import datastructures.GenomeFrame; +import datastructures.ReadFrame; +import datastructures.ReducedReadLine; +import exceptions.ChromosomeFormatException; +import exceptions.ChromosomeNotFoundException; +import exceptions.RangeFormatException; +import exceptions.RangeLimitNotFoundException; + +import middlewares.Misc; + +/** + *

This is a converter class, wich convert a reduced alignment file with the + * following format:

+ * + * + * + * + * + * + * + * + *
read-namechromosom-namestart-positionend-position
+ *

to the wiggle-format. The wiggle format (WIG) allows the display of continuous- + * valued data in a track format and it is used to visualize the read enrichment + * with the ucsc genome browser. Click on the following link: + * + * http://genome.ucsc.edu/goldenPath/help/wiggle.html for more information.

+ * + * @author Ali Abdallah + * @version 06.01.2011 + * @since jdk 1.6.0 + */ + +public class Read2Wig { + + private static final int LENGTH = 1024; + private File alignFile; + private File outputFile; + private String outputDir; + private int gMin = Integer.MAX_VALUE; + private int gMax = Integer.MIN_VALUE; + private FileWriter tmpWigWriter; + + /** + * Constructs and initialzes a new Read2Wig object. + * Converts the read alignment file to a overall covrage wig file. + * + * @param alignFileName the name of the alignment file. + * @throws IOException + */ + public Read2Wig(String alignFileName,String outPrefix,String outputDir,String genome,String tmpDir) throws IOException{ + // Das File-Objekt zur Behandlung der Alignment-Datei erzeugen. + this.alignFile = new File(alignFileName); + this.outputDir = outputDir+Misc.slash(outputDir); + tmpWigWriter = new FileWriter(tmpDir+Misc.slash(tmpDir)+"tmpWig.wig"); + convert(alignFileName,this.outputDir,outPrefix); + try{ + wigToBigWig("hg19",tmpDir); + } + catch(Exception e){ + System.err.println("Converting wig file to a bigwig file failed. " + + "Check whether you have a 64-bit linux system!"); + } + } + + private void convert(String alignFileName, String outputDir,String outPrefix) throws FileNotFoundException, IOException { + Scanner s = new Scanner(this.alignFile); + computeExtremas(s); s.close(); + Scanner readScanner = new Scanner(this.alignFile); + alignFileName = Misc.prefix(alignFileName); + Scanner as = new Scanner(alignFileName); + as.useDelimiter("_"); + as.next(); + outputFile = new File(outputDir+outPrefix+".wig"); + FileWriter fw = new FileWriter(outputFile); + + annotationHeader(fw); + + ReadFrame readF = computeNextRead(readScanner); //Current read frame + GenomeFrame frame = new GenomeFrame(readF.start(), LENGTH); //Current base frame + String chrom = readF.chrom(); //Current chromosome + if(frame.contains(readF)){frame.updateHits(readF);} //Sum up all hits of curr read + writeHeader(fw, frame, readF); //Write header line + + while(true){ + while(readScanner.hasNextLine() && chrom.equals(readF.chrom()) && frame.contains(readF)){ + frame.updateHits(readF); readF = computeNextRead(readScanner); + } + while(readScanner.hasNextLine() && chrom.equals(readF.chrom()) && frame.overlaps(readF) && !frame.limitExceeded(readF)){ + frame.updateFrameFromRightEnd(readF); frame.updateHits(readF); readF = computeNextRead(readScanner); + } + if(!readScanner.hasNextLine()){break;} + else if(!chrom.equals(readF.chrom())){ + frame = new GenomeFrame(readF.start(), LENGTH); + writeHeader(fw, frame, readF); + chrom = readF.chrom(); + } + else if(!frame.overlaps(readF)){ + GenomeFrame last = frame; writeFrame(fw, last); + frame = new GenomeFrame(readF.start(), LENGTH); + writeFrameLeak(fw, last, frame, readF); + } + else if(frame.limitExceeded(readF)){ + writeFramePortion(fw, frame, readF.start()); frame.updateFrameFromBothEnds(readF, LENGTH); + } + } + fw.close(); + tmpWigWriter.close(); + readScanner.close(); + } + + private void wigToBigWig(String genome,String tmpDir){ + String scriptDir = Misc.binDir()+Misc.slash(Misc.binDir()); + String wig2bw = scriptDir + "../thirdparty/wigToBigWig"; + String fetchChromSizes = scriptDir + "fetchChromSizes"; + + try { + Process p = Runtime.getRuntime().exec("sh "+fetchChromSizes+" "+genome); + FileWriter fw = new FileWriter(outputDir+Misc.slash(outputDir)+genome+".chrom.sizes"); + Scanner s = new Scanner(p.getInputStream()); + while(s.hasNextLine()) + fw.write(s.nextLine()+"\r\n"); + fw.close(); + + Runtime.getRuntime().exec(wig2bw+" "+outputFile.getAbsolutePath() + +" "+outputDir+Misc.slash(outputDir)+genome+".chrom.sizes "+ + outputDir+Misc.slash(outputDir)+ + Misc.prefix(outputFile.getAbsolutePath())+".bw"); + new File(outputDir+Misc.slash(outputDir)+genome+".chrom.sizes").delete(); + new File(tmpDir+Misc.slash(tmpDir)+"tmpWig.wig").delete(); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + + private void computeExtremas(Scanner s){ + String chrom = "Datei falsch formatiert."; + String oldChrom = null; + int start = -1; + int end = -1; + String line = s.nextLine(); + + oldChrom = chrom(line); start = start(line); end = end(line); + + while(s.hasNextLine()){ + line = s.nextLine(); + if(isHeader(line)){ + chrom = chrom(line); start = start(line); end = end(line); + if(gMin > start && chrom.equals(oldChrom)) + gMin = start; + + if(gMax < end && chrom.equals(oldChrom)) + gMax = end; + } + } + } + + private boolean isHeader(String line){ + return line.indexOf("chr")!=-1; + } + + private int start(String line){ + Scanner s = new Scanner(line); + s.next();s.next(); + return s.nextInt(); + } + + private int end(String line){ + Scanner s = new Scanner(line); + s.next();s.next();s.next(); + return s.nextInt(); + } + + private String chrom(String line){ + Scanner s = new Scanner(line); + s.next(); + return s.next(); + } + + private void writeFramePortion(FileWriter fw, GenomeFrame frame, int start2) throws IOException { + for(int base = frame.start(); base < start2; base++){ + fw.write(frame.getHit(base)+"\r\n"); + tmpWigWriter.write(frame.getHit(base)+"\r\n"); + } + } + + private void writeFrameLeak(FileWriter fw, + GenomeFrame last, GenomeFrame frame, ReadFrame read) + throws IOException { + if(frame.start()-last.end() > 50){ + writeHeader(fw, frame, read); + } + else{ + for(int i = 0; i < frame.start()-last.end()-1; i++){ + fw.write(0+"\r\n"); + tmpWigWriter.write(0+"\r\n"); + } + } + } + + private void annotationHeader(FileWriter fw) throws IOException{ + String browserLines = "browser position chr1:"+gMin+"-"+gMax+"\r\n"+ + "browser hide all"+"\r\n"+ + "browser pack refGene encodeRegions"+"\r\n"+ + "browser full altGraph"; + Scanner as = new Scanner(alignFile.getName()); + as.useDelimiter("_");as.next(); + String trackLine = "track type=wiggle_0 name=\""+as.next()+"\" " + + "description=\"Base read coverage\" visibility=full " + + "color=0,0,0 altColor=255,0,0 priority=20 " + + "autoScale=on"; + fw.write(browserLines+"\r\n"+trackLine+"\r\n"); + } + + private void writeHeader(FileWriter fw, GenomeFrame frame, ReadFrame read) + throws IOException { + fw.write("fixedStep chrom="+read.chrom() + +" start="+frame.start() + + " step=1\r\n"); + tmpWigWriter.write("fixedStep chrom="+read.chrom() + +" start="+frame.start() + + " step=1\r\n"); + } + + private void writeFrame(FileWriter fw, GenomeFrame frame) throws IOException { + // TODO Auto-generated method stub + for(int base = frame.start(); base <= frame.end(); base++){ + fw.write(frame.getHit(base)+"\r\n"); + tmpWigWriter.write(frame.getHit(base)+"\r\n"); + } + } + + private ReadFrame computeNextRead(Scanner afScanner) { + ReducedReadLine rl = null; + try { + rl = new ReducedReadLine(afScanner.nextLine()); + } catch (ChromosomeFormatException e) { + e.printStackTrace(); + } catch (ChromosomeNotFoundException e) { + e.printStackTrace(); + } catch (RangeFormatException e) { + e.printStackTrace(); + } catch (RangeLimitNotFoundException e) { + e.printStackTrace(); + } + return new ReadFrame(rl.name(), rl.chrom(), rl.start(), rl.end()); + } + +} + + + + + + + + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/converters/ReadOnTarget2Wig.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/converters/ReadOnTarget2Wig.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,187 @@ +package converters; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.util.Scanner; +import middlewares.Misc; + +/** + * Converts the detailed coverage data to the wig format. Used for the + * visualization of the coverage data in the ucsc-browser. + * + * @author Ali Abdallah + * @version 20.07.2011 + * @since Java 1.6 + */ +public class ReadOnTarget2Wig { + + private int + /** + * The maximal number of hits on a base. + */ + max, + /** + * The minimal number of hits on a base. + */ + min, + /** + * The minimal position on chr1. + */ + gMin, + /** + * the maximal position on chr1. + */ + gMax; + + private String + /** + * The name of the file of detailed coverage data. + */ + filename, + /** + * The title of the track. + */ + title; + + /** + * Constructs an new ReadOnTarget2Wig object, initializes the parameters + * and call the conversion method. + * + * @param filename + * @param prefix + * @param outDir + * @param title + * @throws IOException + */ + public ReadOnTarget2Wig(String filename, String prefix, String outDir, String title) throws IOException{ + this.filename = filename; + max = Integer.MIN_VALUE; gMax = Integer.MIN_VALUE; + min = Integer.MAX_VALUE; gMin = Integer.MAX_VALUE; + this.title = title; + File f=new File(this.filename); + FileWriter fw=new FileWriter(outDir+Misc.slash(outDir) + +prefix+"_onTarget.wig"); + Scanner scanForMinMax=new Scanner(f); + computeExtremas(scanForMinMax); + scanForMinMax.close(); + + Scanner s = new Scanner(f); + annotationHeader(fw); + toWiggleFormat(fw,s); + fw.close(); + } + + /** + * Writes the annotation header to the wig file. + * + * @param fw FileWriter + * @throws IOException if write operation is not possible. + */ + private void annotationHeader(FileWriter fw) throws IOException{ + String browserLines = "browser position chr1:"+gMin+"-"+gMax+"\r\n"+ + "browser hide all"+"\r\n"+ + "browser pack refGene encodeRegions"+"\r\n"+ + "browser full altGraph"; + String trackLine = "track type=wiggle_0 name=\""+title+"\" " + + "description=\"Base read coverage\" visibility=full " + +"color=0,0,0 altColor=255,0,0 priority=20 " + + "autoScale=off graphType=bar " + + "viewLimits="+min+":"+max; + fw.write(browserLines+"\r\n"+trackLine+"\r\n"); + } + + /** + * Computes the hit and position minimas and maxima. + * + * @param s the reader of the file of detailed coverage data. + */ + private void computeExtremas(Scanner s){ + String chrom = "Datei falsch formatiert."; + int start = -1; int end = -1; + while(s.hasNextLine()){ + String line = s.nextLine(); + if(isHeader(line)){ + chrom = chrom(line); start = start(line); end = end(line); + if(gMin > start && chrom.equals("chr1")){gMin = start;} + if(gMax < end && chrom.equals("chr1")){gMax = end;} + } + else{ + if(min > Integer.parseInt(line.trim())){ + min = Integer.parseInt(line.trim()); + } + if(max < Integer.parseInt(line.trim())){ + max = Integer.parseInt(line.trim()); + } + } + } + } + + /** + * The main computation: conversion to wiggle format. + * + * @param fw FileWriter into the wig-file. + * @param s the reader of the file of detailed coverage data. + * @throws IOException if i/o fails. + */ + private void toWiggleFormat(FileWriter fw, Scanner s) throws IOException { + String chrom = "Datei falsch formatiert."; + int start = -1; + while(s.hasNextLine()){ + String line = s.nextLine(); + if(isHeader(line)){ + chrom = chrom(line); start = start(line); + fw.write(declarationLine(chrom, start)); + } + else fw.write(line+"\r\n"); + } + } + + /** + * @param chrom + * @param start + * @return a String representing the declaration line corresponding to the + * specified parameters. + */ + private String declarationLine(String chrom, int start) { + return "fixedStep chrom="+chrom+" start="+start+" step=1\r\n"; + } + + /** + * Check if the specified line is a header line. + * + * @param line the current observerd line in the file of detailed coverage + * data. + * @return true if line is a header and false otherwise. + */ + private boolean isHeader(String line){ + return line.indexOf("chr")!=-1; + } + + /** + * @param line + * @return the start position of the current frame (header). + */ + private int start(String line){ + Scanner s = new Scanner(line); + s.next(); return s.nextInt(); + } + + /** + * @param line + * @return the end position of the current frame. + */ + private int end(String line){ + Scanner s = new Scanner(line); + s.next(); s.next(); + return s.nextInt(); + } + + /** + * @param line + * @return the chromosome corresponding to the current frame. + */ + private String chrom(String line){ + Scanner s = new Scanner(line); + return s.next(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/dataGenerators/AnnotationDataGenerator.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/dataGenerators/AnnotationDataGenerator.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,5 @@ +package dataGenerators; + +public class AnnotationDataGenerator { + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/dataGenerators/ReadAlginmentDataGenerator.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/dataGenerators/ReadAlginmentDataGenerator.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,30 @@ +package dataGenerators; + +import java.util.Random; + +public class ReadAlginmentDataGenerator { + + String[] chrs = {"chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12", + "chr13","chr14", "chr15","chr16","chr17","chr18","chr19","chr20","chr21","chrX","chrY"}; + + String qname = "dummy"; + String flag = "0"; + String chr; + int start; + String mapq = "0"; + String cigar = "dummy"; + String mrnm = "*"; + String mpos = "0"; + String isize = "0"; + String seq = "CAACCCTAACCCTAACCCAAACCCCAACCCTAACCCTACCCCTACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC"; + String qua = "#################################################FCCGGGFGGD=GDDIHIGHIJIGHGDJJIHGIHHHGFIHHBHFFFFFFBCB"; + String tvv = "dummy"; + + public String generateReadLine(int pos, int length){ + Random r = new Random(); + return null; + + + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/dataGenerators/TargetDataGenerator.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/dataGenerators/TargetDataGenerator.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,5 @@ +package dataGenerators; + +public class TargetDataGenerator { + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/dataGenerators/TestDataGenerator.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/dataGenerators/TestDataGenerator.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,7 @@ +package dataGenerators; + +public class TestDataGenerator { + + + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/AVLNode.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/AVLNode.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,32 @@ +package datastructures; + + +// Basic node stored in AVL trees +// Note that this class is not accessible outside +// of package DataStructures + +class AVLNode +{ + // Constructors + @SuppressWarnings("unchecked") + AVLNode( Comparable theElement ) + { + this( theElement, null, null ); + } + + @SuppressWarnings("unchecked") + AVLNode( Comparable theElement, AVLNode lt, AVLNode rt ) + { + element = theElement; + left = lt; + right = rt; + height = 0; + } + + // Friendly data; accessible by other package routines + @SuppressWarnings("unchecked") + Comparable element; // The data in the node + AVLNode left; // Left child + AVLNode right; // Right child + int height; // Height +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/AVLTree.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/AVLTree.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,294 @@ +package datastructures; + +// BinarySearchTree class +// +// CONSTRUCTION: with no initializer +// +// ******************PUBLIC OPERATIONS********************* +// void insert( x ) --> Insert x +// void remove( x ) --> Remove x (unimplemented) +// Comparable find( x ) --> Return item that matches x +// Comparable findMin( ) --> Return smallest item +// Comparable findMax( ) --> Return largest item +// boolean isEmpty( ) --> Return true if empty; else false +// void makeEmpty( ) --> Remove all items +// void printTree( ) --> Print tree in sorted order + +/** + * Implements an AVL tree. + * Note that all "matching" is based on the compareTo method. + * @author Mark Allen Weiss + */ +public class AVLTree +{ + /** + * Construct the tree. + */ + public AVLTree( ) + { + root = null; + } + + /** + * Insert into the tree; duplicates are ignored. + * @param x the item to insert. + */ + @SuppressWarnings("unchecked") + public void insert(Comparable x ) + { + root = insert( x, root ); + } + + /** + * Remove from the tree. Nothing is done if x is not found. + * @param x the item to remove. + */ + @SuppressWarnings("unchecked") + public void remove( Comparable x ) + { + System.out.println( "Sorry, remove unimplemented" ); + } + + /** + * Find the smallest item in the tree. + * @return smallest item or null if empty. + */ + @SuppressWarnings("unchecked") + public Comparable findMin( ) + { + return elementAt( findMin( root ) ); + } + + /** + * Find the largest item in the tree. + * @return the largest item of null if empty. + */ + @SuppressWarnings("unchecked") + public Comparable findMax( ) + { + return elementAt( findMax( root ) ); + } + + /** + * Find an item in the tree. + * @param x the item to search for. + * @return the matching item or null if not found. + */ + @SuppressWarnings("unchecked") + public Comparable find( Comparable x ) + { + return elementAt( find( x, root ) ); + } + + /** + * Make the tree logically empty. + */ + public void makeEmpty( ) + { + root = null; + } + + /** + * Test if the tree is logically empty. + * @return true if empty, false otherwise. + */ + public boolean isEmpty( ) + { + return root == null; + } + + /** + * Print the tree contents in sorted order. + */ + public void printTree( ) + { + if( isEmpty( ) ) + System.out.println( "Empty tree" ); + else + printTree( root ); + } + + /** + * Internal method to get element field. + * @param t the node. + * @return the element field or null if t is null. + */ + @SuppressWarnings("unchecked") + private Comparable elementAt( AVLNode t ) + { + return t == null ? null : t.element; + } + + /** + * Internal method to insert into a subtree. + * @param x the item to insert. + * @param t the node that roots the tree. + * @return the new root. + */ + @SuppressWarnings("unchecked") + private AVLNode insert( Comparable x, AVLNode t ) + { + if( t == null ) + t = new AVLNode( x, null, null ); + else if( x.compareTo( t.element ) < 0 ) + { + t.left = insert( x, t.left ); + if( height( t.left ) - height( t.right ) == 2 ) + if( x.compareTo( t.left.element ) < 0 ) + t = rotateWithLeftChild( t ); + else + t = doubleWithLeftChild( t ); + } + else if( x.compareTo( t.element ) > 0 ) + { + t.right = insert( x, t.right ); + if( height( t.right ) - height( t.left ) == 2 ) + if( x.compareTo( t.right.element ) > 0 ) + t = rotateWithRightChild( t ); + else + t = doubleWithRightChild( t ); + } + else + ; // Duplicate; do nothing + t.height = max( height( t.left ), height( t.right ) ) + 1; + return t; + } + + /** + * Internal method to find the smallest item in a subtree. + * @param t the node that roots the tree. + * @return node containing the smallest item. + */ + private AVLNode findMin( AVLNode t ) + { + if( t == null ) + return t; + + while( t.left != null ) + t = t.left; + return t; + } + + /** + * Internal method to find the largest item in a subtree. + * @param t the node that roots the tree. + * @return node containing the largest item. + */ + private AVLNode findMax( AVLNode t ) + { + if( t == null ) + return t; + + while( t.right != null ) + t = t.right; + return t; + } + + /** + * Internal method to find an item in a subtree. + * @param x is item to search for. + * @param t the node that roots the tree. + * @return node containing the matched item. + */ + @SuppressWarnings("unchecked") + private AVLNode find( Comparable x, AVLNode t ) + { + while( t != null ) + if( x.compareTo( t.element ) < 0 ) + t = t.left; + else if( x.compareTo( t.element ) > 0 ) + t = t.right; + else + return t; // Match + + return null; // No match + } + + /** + * Internal method to print a subtree in sorted order. + * @param t the node that roots the tree. + */ + private void printTree( AVLNode t ) + { + if( t != null ) + { + printTree( t.left ); + System.out.println( t.element ); + printTree( t.right ); + } + } + + /** + * Return the height of node t, or -1, if null. + */ + private static int height( AVLNode t ) + { + return t == null ? -1 : t.height; + } + + /** + * Return maximum of lhs and rhs. + */ + private static int max( int lhs, int rhs ) + { + return lhs > rhs ? lhs : rhs; + } + + /** + * Rotate binary tree node with left child. + * For AVL trees, this is a single rotation for case 1. + * Update heights, then return new root. + */ + private static AVLNode rotateWithLeftChild( AVLNode k2 ) + { + AVLNode k1 = k2.left; + k2.left = k1.right; + k1.right = k2; + k2.height = max( height( k2.left ), height( k2.right ) ) + 1; + k1.height = max( height( k1.left ), k2.height ) + 1; + return k1; + } + + /** + * Rotate binary tree node with right child. + * For AVL trees, this is a single rotation for case 4. + * Update heights, then return new root. + */ + private static AVLNode rotateWithRightChild( AVLNode k1 ) + { + AVLNode k2 = k1.right; + k1.right = k2.left; + k2.left = k1; + k1.height = max( height( k1.left ), height( k1.right ) ) + 1; + k2.height = max( height( k2.right ), k1.height ) + 1; + return k2; + } + + /** + * Double rotate binary tree node: first left child + * with its right child; then node k3 with new left child. + * For AVL trees, this is a double rotation for case 2. + * Update heights, then return new root. + */ + private static AVLNode doubleWithLeftChild( AVLNode k3 ) + { + k3.left = rotateWithRightChild( k3.left ); + return rotateWithLeftChild( k3 ); + } + + /** + * Double rotate binary tree node: first right child + * with its left child; then node k1 with new right child. + * For AVL trees, this is a double rotation for case 3. + * Update heights, then return new root. + */ + private static AVLNode doubleWithRightChild( AVLNode k1 ) + { + k1.right = rotateWithLeftChild( k1.right ); + return rotateWithRightChild( k1 ); + } + + /** The tree root. */ + private AVLNode root; + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/AnnotationLine.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/AnnotationLine.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,99 @@ +package datastructures; + +import java.util.Scanner; + +public class AnnotationLine implements Comparable{ + + String seqName, chrom, gene; + int start, end; + + public AnnotationLine(String seqName, String chrom, String gene, + int start, int end){ + this.seqName = seqName; + this.chrom = chrom; + this.gene = gene; + this.start = start; + this.end = end; + } + + public AnnotationLine(String line){ + Scanner s = new Scanner(line); + seqName = s.next(); + this.chrom = s.next(); + this.start = s.nextInt(); + this.end = s.nextInt(); + this.gene = s.next(); + } + + public String seqName() { + return seqName; + } + + public String chrom() { + return chrom; + } + + public String gene() { + return gene; + } + + public int start() { + return start; + } + + public int end() { + return end; + } + + public static AnnotationLine targetLine(String chrom, int tstart, int tend){ + return new AnnotationLine("000\t"+chrom+"\t"+tstart+"\t"+tend+"\tdummy"); + } + + public int compareTo(Object otherLine) { + AnnotationLine other = (AnnotationLine)otherLine; + + if(chrom.compareTo(other.chrom()) < 0 + && !other.gene.equals("dummy")) + return -1; + else if(chrom.compareTo(other.chrom()) > 0 + && !other.chrom().equals("dummy")) + return 1; + else{ + /* + * 1. Eine Region überlappt mit einem Gen, wenn einer der folgenden + * 3 Fälle eintritt: + * a) Targetanfang kleiner als Genanfang und Targetende größer als + * Genende. (Gen ganz im Target enthalten) + * b) Targetanfang liegt zwischen Genanfang und Genende. + * c) Targetende liegt zwischen Genanfang und Genende. + */ + + // Für Targetsuche + if(this.gene().equals("dummy") && + this.chrom().equals(other.chrom()) && ( + (this.start() <= other.start() && this.end() >= other.end()) || + (this.start() >= other.start() && this.start() <= other.end()) || + (this.end() >= other.start() && this.end() <= other.end()) + ) + ) + return 0; + // Für Gensuche zu Insertzwecken. + else if(start < other.start()) + return -1; + else if(start > other.start()) + return 1; + else{ + if(end < other.end()) + return -1; + else if(end > other.end()) + return 1; + else return 0; + } + } + } + + public String toString(){ + return seqName +"\t" + chrom + "\t" + start + "\t" + end + "\t" + gene; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/Format.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/Format.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,32 @@ +package datastructures; + +public enum Format{ + type("type"), + sam("sam"), + maq("maq"), + megablast("megablast"), + eland("eland"), + roche("roche"), + genome("genome"), + target("target"), + invalid("invalid"); + + private String f; + + Format(String format){ + this.f = format; + } + + public Format compile(String f){ + this.f = f; + try{ + return Format.valueOf(this.f); + }catch(IllegalArgumentException iae){ + return invalid; + } + } + + public boolean equals(Format other){ + return this.f.equals(other.f); + } +}; diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/Frame.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/Frame.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,94 @@ +package datastructures; + +/** + * Used for various purposes. + * + * @author Ali Abdallah + * @version 01.2011 + * @since jdk 1.6.0 + */ +public class Frame { + + // Self explanatory. + protected int start; + protected int end; + protected int length; + + /** + * Constructs a frame with start position "start", length "length" and + * end position "start+length-1". + * @param start the start position of the frame. + * @param length the length of the frame. + */ + public Frame(int start, int length) { + this.start = start; end = start+length-1; + this.length = length; + } + + /** + * Verify if this frame overlaps the frame specified in the parameter. + * @param f the frame which potentially overlaps the calling frame. + * @return true if the two frames overlap each other and false otherwise. + */ + public boolean overlaps(Frame f){ + return (end >= f.start() && start < f.end()); + } + + /** + * Computes the size of the overlap area. + * @param f the frame overlapping the calling frame. + * @return the size of the overlap if an overlap exists and -1 otherwise. + */ + public int overlapSize(Frame f){ + if(this.overlaps(f)){ + int s = Math.max(start, f.start()); + int e = Math.min(end, f.end()); + return e-s+1; + } + return -1; + } + + /** + * Unify the calling frame with the frame specified in the parameter. + * @param f the frame to be unified with the calling frame. + * @return the union of the calling frame and f. + */ + public Frame unify(Frame f){ + return + new Frame(Math.min(this.start, f.start), + Math.max(this.end,f.end)-Math.min(this.start, f.start)+1); + } + + /** + * self explanatory + * @return start of the frame. + */ + public int start(){ + return start; + } + + /** + * self explanatory + * @return end of the frame. + */ + public int end(){ + return end; + } + + /** + * self explanatory + * @return length of the frame. + */ + public int length(){ + return length; + } + + /** + * Make a string representation of the frame. + * @return a string representation of the string. + */ + public String toString(){ + return start+":"+end; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/GenomeFrame.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/GenomeFrame.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,87 @@ +package datastructures; + +import java.util.Vector; + +/** + * @author Ali Abdallah + * @version 01.2011 + * @since jdk 1.6.0 + */ + +public class GenomeFrame extends Frame{ + + int limit; + Vector hits; + + public GenomeFrame(int start, int length) { + super(start, length); + limit = end; + hits = new Vector(length); + hits.setSize(length); + for(int i = 0; i < length; i++){ + hits.set(i, 0); + } + } + + public int getHit(int base){ + if(base-start < hits.size()) + return hits.get(base-start); + else + return -1; + } + + public void setHit(int base, int bhits){ + if(base-start < hits.size()){ + hits.set(base-start, bhits); + } + } + + public boolean contains(ReadFrame r){ + return (start <= r.start() && end >= r.end()); + } + + public boolean overlaps(ReadFrame r){ + return (end >= r.start() && end < r.end()); + } + + + + public void addBases(int nr){ + for(int i = 0; i < nr; i++){ + hits.add(1); + } + } + + public String toString(){ + return start+":"+end+" ("+limit+")"; + } + + + public void updateHits(ReadFrame read) { + for(int base = read.start(); base <= read.end(); base++){ + setHit(base, getHit(base)+1); + } + } + + public void updateFrameFromRightEnd(ReadFrame readF) { + // TODO Auto-generated method stub + for(int i = end+1; i <= readF.end(); i++) + hits.add(0); + end = readF.end(); + } + + public boolean limitExceeded(ReadFrame readF) { + return readF.start() > limit; + } + + public void updateFrameFromBothEnds(ReadFrame readF, int length) { + for(int i = end-readF.start()+1; i < length; i++ ) + hits.add(0); + for(int i = 0; i < readF.start()-start; i++) + hits.remove(0); + start = readF.start(); + end = start+length-1; + limit = end; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/GenomeLine.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/GenomeLine.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,57 @@ +package datastructures; + +import java.util.Scanner; + +public class GenomeLine implements Line { + + boolean misformat = false; + String seqName, chrom, gene; + int start, end; + + //fw.write(field(1)+"\t"+field(3)+"\t" + // +field(5)+"\t"+field(6)+"\t"+field(13)+"\r\n"); + + public GenomeLine(String line){ + Scanner s = new Scanner(line); + if(line.startsWith("#")) misformat = true; + else + try{ + seqName = s.next();s.next(); + chrom = s.next();s.next(); + start = s.nextInt(); + end = s.nextInt();s.next();s.next();s.next();s.next();s.next();s.next(); + gene = s.next();} + catch(Exception e){ + misformat = true; + } + } + + public boolean valid(){ + return misformat == false; + } + + public String chrom() { + return chrom; + } + + public int end() { + return end; + } + + public int start() { + return start; + } + + public String gene(){ + return gene; + } + + public String seqName(){ + return seqName; + } + + public String toString(){ + return seqName + "\t" + chrom + "\t" + start + "\t" + end + "\t" + gene; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/Line.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/Line.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,9 @@ +package datastructures; + +public interface Line { + + public String chrom(); + public int start(); + public int end(); + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/Read.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/Read.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,96 @@ +package datastructures; + +import java.io.File; +import java.io.IOException; +import java.lang.InterruptedException; +import java.util.Scanner; +import java.util.Vector; + +public class Read implements Comparable { + + String query; + int flag; + String rname; + int pos; + int mapq; + String cigar; + String rnext; + int pnext; + int tlen; + String seq; + String qual; + Vector optional; + + public Read(String line) { + Scanner s = new Scanner(line); + query = s.next(); + flag = s.nextInt(); + rname = s.next(); + pos = s.nextInt(); + mapq = s.nextInt(); + cigar = s.next(); + rnext = s.next(); + pnext = s.nextInt(); + tlen = s.nextInt(); + seq = s.next(); + qual = s.next(); + if (s.hasNext()) { + optional = new Vector(); + while (s.hasNext()) { + optional.add(s.next()); + } + } + } + + public String getRname() { + return rname; + } + + public int getPos() { + return pos; + } + + @Override + public int compareTo(Object o) { + return 0; + } + + public static void sort(File input) { + Runtime rt = Runtime.getRuntime(); + try { + String rawOutput = input.getAbsolutePath(), + tmpD = input.getParentFile().getAbsolutePath(), + outputName = input.getName(), + pathname = input.getParentFile().getAbsolutePath() + "/" + + outputName + "Sorted"; + + input = new File(pathname); + + if (!input.exists()) + input.createNewFile(); + + String command = "sort -k3,3 -k4n,4 -T " + tmpD + " " + rawOutput+" > "+pathname; + Process p = rt.exec(command); + try{p.waitFor();} + catch(InterruptedException e){e.printStackTrace();} + System.out.println("Fertig"); + /* Scanner ps = new Scanner(p.getInputStream()); + FileWriter fw = new FileWriter(input); + + while (ps.hasNextLine()) { + String nextLine = ps.nextLine(); + fw.write(nextLine + "\r\n"); + } + + fw.close(); */ + + new File(rawOutput).delete(); + new File(pathname).renameTo(new File(rawOutput)); + System.out.println("File " + new File(rawOutput).getAbsolutePath() + + " sorted\n"); + + } catch (IOException e1) { + e1.printStackTrace(); + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/ReadFrame.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/ReadFrame.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,23 @@ +package datastructures; + +public class ReadFrame extends Frame{ + + private String chrom, name; + + public ReadFrame(String name,String chrom, int start, int end) { + super(start, end-start+1); + this.chrom = chrom; this.name = name; + } + + public String chrom(){ + return chrom; + } + + public String name(){ + return name; + } + + public int size(){ + return end-start+1; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/ReadLine.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/ReadLine.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,73 @@ +package datastructures; + +import java.util.Scanner; + +/** + * Represents a read line from the read alignment file. + * + * @author Ali Abdallah + * @version 03.08.2011 + * @since Java 1.6 + */ + +public class ReadLine implements Line { + + String + /** + * Query (pair) name. + */ + name, + /** + * Reference sequence name. + */ + chrom; + /** + * Start position of the read. + */ + int start, + /** + * End Position of the read. + */ + end, + /** + * Length of the read. + */ + length; + + public ReadLine(String line){ + // line format: + // qname flag rname pos mapq cigar mrnm mpos isize seq qual tag + Scanner s = new Scanner(line); + name = s.next(); + s.next(); + chrom = s.next(); + start = s.nextInt(); + s.next(); s.next();s.next();s.next();s.next(); + length = s.next().length(); + end = start+length-1; + } + + public String name(){ + return name; + } + + public String chrom() { + return chrom; + } + + public int end() { + return end; + } + + public int start() { + return start; + } + + public int length(){ + return length; + } + + public String toString(){ + return name+"\t"+chrom+"\t"+start+"\t"+end; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/ReducedReadLine.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/ReducedReadLine.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,89 @@ +package datastructures; + +import java.util.Scanner; +import exceptions.ChromosomeFormatException; +import exceptions.ChromosomeNotFoundException; +import exceptions.RangeFormatException; +import exceptions.RangeLimitNotFoundException; + +/** + * Represents a read Line from the read alignment file. + * + * @author Ali Abdallah + * @version 22.07.2011 + * @since Java 1.6 + */ +public class ReducedReadLine implements Line{ + + String line; + String rName; + String chrom; + int start, end; + + public ReducedReadLine(String line) throws ChromosomeFormatException, + ChromosomeNotFoundException, + RangeFormatException, + RangeLimitNotFoundException{ + this.line = line; + Scanner s = new Scanner(line); + if(s.hasNext()) + rName = s.next(); + if(s.hasNext()){ + chrom = s.next(); + if(!(chrom.toLowerCase().startsWith("chr") || chrom.equals("*"))) + throw new ChromosomeFormatException(chrom); + } + else + throw new ChromosomeNotFoundException(); + + if(s.hasNextInt()){ + start = s.nextInt(); + if(start < 0){ + throw new RangeFormatException("Start position must be a positive integer."); + } + } + else if(!s.hasNext()) + throw new RangeLimitNotFoundException("No range start found!"); + else + throw new RangeFormatException("Found: "+start+". Start position ist not an integer. " + + "It must be a positive integer."); + + if(s.hasNextInt()){ + end = s.nextInt(); + if(end < 0){ + throw new RangeFormatException("End position must be a positive integer."); + } + } + else if(!s.hasNext()) + throw new RangeLimitNotFoundException("No range end found!"); + else + throw new RangeFormatException("Found: "+end+". End position ist not an integer. " + + "It must be a positive integer."); + } + + public String chrom(){ + return chrom; + } + + public int start(){ + return start; + } + + public int end(){ + return end; + } + + public String toString(){ + return line; + } + + public boolean isForwardRead(){ + return start <= end; + } + + public String name() { + // TODO Auto-generated method stub + return rName; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/TargetLine.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/datastructures/TargetLine.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,87 @@ +package datastructures; + +import java.util.Scanner; + +import exceptions.ChromosomeFormatException; +import exceptions.ChromosomeNotFoundException; +import exceptions.NullOrNegativeRangeException; +import exceptions.RangeFormatException; +import exceptions.RangeLimitNotFoundException; + +/** + * Represents a target Line from the target file. + * + * @author Ali Abdallah + * @version 19.07.2011 + * @since Java 1.6 + */ + +public class TargetLine { + + String line; + String chrom; + int start, end; + + public TargetLine(String line) throws RangeFormatException, + ChromosomeFormatException, + ChromosomeNotFoundException, + RangeLimitNotFoundException, + NullOrNegativeRangeException { + this.line = line; + Scanner s = new Scanner(line); + if(s.hasNext()){ + chrom = s.next(); + if(!(chrom.toLowerCase().startsWith("chr") || chrom.equals("*"))) + throw new ChromosomeFormatException(chrom); + } + else + throw new ChromosomeNotFoundException(); + + if(s.hasNextInt()){ + start = s.nextInt(); + if(start < 0){ + throw new RangeFormatException("Start position of the target must be a " + + "positive integer."); + } + } + else if(!s.hasNext()) + throw new RangeLimitNotFoundException("No target range start found!"); + else + throw new RangeFormatException("Target start position" + + " is not an integer. It must be a positive" + + " integer."+ " Found: "+start); + + if(s.hasNextInt()){ + end = s.nextInt(); + if(end < 0){ + throw new RangeFormatException("Target end position must be a positive " + + "integer."+ " Found: "+end); + } + } + else if(!s.hasNext()) + throw new RangeLimitNotFoundException("No range end found!"); + else + throw new RangeFormatException("Found: "+end+". End position ist not an integer. " + + "It must be a positive integer."); + + if(start >= end) + throw new NullOrNegativeRangeException("Target line \""+line+"\""); + } + + public String chrom(){ + return chrom; + } + + public int start(){ + return start; + } + + public int end(){ + return end; + } + + public String toString(){ + return line; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/ChromosomeException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/ChromosomeException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,16 @@ +package exceptions; + +public class ChromosomeException extends Exception { + + private static final long serialVersionUID = -2075266777182180011L; + + public ChromosomeException(String curr){ + super(curr); + } + + public ChromosomeException(){ + super(); + System.out.println(this.getMessage()); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/ChromosomeFormatException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/ChromosomeFormatException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,12 @@ +package exceptions; + +public class ChromosomeFormatException extends ChromosomeException { + + private static final long serialVersionUID = 2920204775834301041L; + + public ChromosomeFormatException(String curr){ + super("The format of the chromosome name is invalid\n" + + "Found chromosome name is: "+curr); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/ChromosomeMismatchException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/ChromosomeMismatchException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,12 @@ +package exceptions; + +public class ChromosomeMismatchException extends ChromosomeException { + + private static final long serialVersionUID = -2902763382812748929L; + + public ChromosomeMismatchException(){ + super("The chromosome names in target and alignment are different. " + + "The naming must be consistent."); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/ChromosomeNotFoundException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/ChromosomeNotFoundException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,11 @@ +package exceptions; + +public class ChromosomeNotFoundException extends ChromosomeException { + + private static final long serialVersionUID = 1L; + + public ChromosomeNotFoundException(){ + super("No chromosomes found."); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/FileFormatException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/FileFormatException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,11 @@ +package exceptions; + +public class FileFormatException extends Exception { + + private static final long serialVersionUID = -9091546054856311514L; + + public FileFormatException(String s) { + super("Datei Format \""+s+"\" wird nicht unterstützt"); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/GenomeAnnotationException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/GenomeAnnotationException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,11 @@ +package exceptions; + +public class GenomeAnnotationException extends Throwable { + + private static final long serialVersionUID = -9050133395128460361L; + + public GenomeAnnotationException(){ + super("The specified genome annotation is invalid\n"); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/NullOrNegativeRangeException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/NullOrNegativeRangeException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,16 @@ +package exceptions; + +public class NullOrNegativeRangeException extends RangeException { + + private static final long serialVersionUID = 1L; + + public NullOrNegativeRangeException(){ + super("The start position is bigger than or equal to the end position."); + } + + public NullOrNegativeRangeException(String message){ + super( message + "\n" + + "The start position is bigger than or equal to the end position."); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/RangeException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/RangeException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,15 @@ +package exceptions; + +public class RangeException extends Exception { + + private static final long serialVersionUID = -8250851930700369771L; + + public RangeException(){ + super(); + } + + public RangeException(String s){ + super(s); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/RangeFormatException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/RangeFormatException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,15 @@ +package exceptions; + +public class RangeFormatException extends RangeException { + + private static final long serialVersionUID = -7603714654119196278L; + + public RangeFormatException(){ + super("The range limits are misformatted."); + } + + public RangeFormatException(String message){ + super( message + "\n" + + "The range limits are misformatted."); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/RangeLimitNotFoundException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/exceptions/RangeLimitNotFoundException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,12 @@ +package exceptions; + + +public class RangeLimitNotFoundException extends RangeException { + + private static final long serialVersionUID = -4135602280097231477L; + + public RangeLimitNotFoundException(String string) { + super(string); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/filters/Filter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/filters/Filter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,45 @@ +package filters; + +/** + * This abstract class is a framework for classes. It filters versatile formats + * into a single reduced format compatible with converter classes, such as the + * Read2Wig class. + * + * @author Ali Abdallah + * @version 01.08.2011 + * @since jdk 1.6 + */ +public abstract class Filter { + + private String + /** + * The path of the input file. + */ + input, + /** + * The path of the output file. + */ + output; + + public Filter(String input, String output){ + this.input = input; + this.output = output; + } + + public abstract void filter(); + + public abstract void sort(); + + + public String getInputPath() { + return input; + } + + public String getOutputPath() { + return output; + } + + public void setInputPath(String input){ + this.input = input; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/filters/GenomeFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/filters/GenomeFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,91 @@ +package filters; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileWriter; +import java.io.IOException; +import java.util.Scanner; +import datastructures.GenomeLine; + +public class GenomeFilter extends Filter{ + + private File input, output; + + + public GenomeFilter(String inputFileName, String outputFileName) { + super(inputFileName, outputFileName); + input = new File(getInputPath()); + output = new File(getOutputPath()); + } + + public void filter() { + + Scanner s = null; + try { + s = new Scanner(input); + + FileWriter fw = null; + fw = new FileWriter(getOutputPath()); + + while(s.hasNextLine()){ + try { + GenomeLine gl = new GenomeLine(s.nextLine()); +// if(gl.chrom().equals("chr10")) System.out.println(gl); + if(gl.valid()) fw.write(gl+"\n"); + } catch (IOException e) { + e.printStackTrace(); + } + } + fw.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + + System.out.println("GENOME ANNOTATION FILE:"); + System.out.println(getInputPath() + " reduced to " + getOutputPath()); + sort(); + } + + public static void main(String[] args){ + GenomeFilter gf = + new GenomeFilter("/home/abdallah/Desktop/input/refGene.txt", + "/home/abdallah/Desktop/output/refGeneReduced.txt"); + gf.filter(); + } + + public void sort() { + Runtime rt = Runtime.getRuntime(); + try { + String rawOutput = getOutputPath(); + String outputName = output.getName(); + String tmpD= output.getParentFile().getAbsolutePath(); + String pathname = output.getParentFile().getAbsolutePath()+"/"+outputName+"Sorted"; + output = new File(pathname); + if(!output.exists()) output.createNewFile(); + String command = "sort -k2,2 -k3n,3 -k5,5 -T "+tmpD+" "+rawOutput; + Process p = rt.exec(command); + Scanner ps = new Scanner(p.getInputStream()); + FileWriter fw = new FileWriter(output); + while(ps.hasNextLine()){ + String nextLine = ps.nextLine(); + fw.write(nextLine+"\n"); + } + fw.close(); + + new File(rawOutput).delete(); + new File(pathname).renameTo(new File(rawOutput)); + System.out.println("Reduced file "+new File(rawOutput).getAbsolutePath()+" sorted\n"); + + } catch (IOException e1) { + e1.printStackTrace(); + } + } + + public String toString(){ + return "GenomeFilter"; + } + + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/filters/ReadFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/filters/ReadFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,177 @@ +package filters; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileWriter; +import java.io.IOException; +import java.util.Scanner; +import datastructures.ReadLine; + +public class ReadFilter extends Filter{ + + File input, output; + + /** + * Constructs a SamAdapter object. The output of an adaption is written to the + * given file outputFileName. + * + * @param inputFileName the name of the read alignment input file. + * @param outputFileName the name of the output file containing the reduced + * format of the read alignment file. It must ends with ".red". + */ + public ReadFilter(String inputFileName, String outputFileName) { + super(inputFileName, outputFileName); + input = new File(inputFileName); + output = new File(outputFileName); + } + + /** + *

+ * Uses ReadLine zu reduce each line of the read alignment file to following format:
+ * <name> <chrom> <start> <end> (tab delimited). + *

+ * In the following we list the 12 fields of the sam-alignment-file. We mark the fields we are + * interessted in with (!!): + * 
+	 * 1. <QNAME>	: Query pair NAME if paired; or Query NAME if unpaired 	(Ex: 6:105:18438:14421)	(!!)
+	 * 2. <FLAG>	: bitwise FLAG a₀a₁a₂a₃a₄a₅a₆a₇a₈a₉a₁₀		(Ex: 0 forward, 16 reverse strand)
+	 *		  a₀ : 	the read is paired in sequencing, (no matter whether it is mapped in a pair)
+	 *		  a₁ : 	the read is mapped in a proper pair	
+	 *		  a₂ : 	the query sequence itself is unmapped
+	 *		  a₃ : 	the mate is unmapped
+	 *		  a₄ : 	strand of the query (0 for forward; 1 for reverse strand)
+	 *		  a₅ : 	strand of the mate
+	 *		  a₆ : 	the read is the first read in a pair
+	 *		  a₇ : 	the read is the second read in a pair
+	 *		  a₈ : 	the alignment is not primary
+	 *		  a₉ : 	the read fails platform/vendor quality checks
+	 *  		  a₁₀: 	the read is either a PCR duplicate or an optical duplicate
+	 * 3. <RNAME>	: Reference sequence NAME					(Ex: chr10)			(!!)
+	 * 4. <POS>		: 1-based leftmost POSition/coordinate of the clipped sequence 	(Ex: 60041)			(!!)
+	 * 5. <MAPQ>	: MAPping Quality 						(Ex: 0)
+	 *		 			  (phred-scaled posterior probability that the mapping position of this read is incorrect)
+	 * 6. <CIGAR>	: extended CIGAR string						(Ex: 150M)
+	 * 7. <MRNM>	: Mate Reference sequence NaMe; “=” if the same as <RNAME>	(Ex:*)
+	 * 8. <MPOS>	: 1-based leftmost Mate POSition of the clipped sequence	(Ex: 0)
+	 * 9. <ISIZE>	: inferred Insert SIZE						(Ex: 0)
+	 * 10. <SEQ>	: query SEQuence; “=” for a match to the reference; n/N/. for ambiguity; cases are not maintained (!!)
+	 *					(Ex:	TGTTGTTGTTATTTCTGAATGACATTTACTTTGCTGCTCTTTATTTTGCG
+	 *							TATTTAAAACTATTAGATCGTGTGATTATATTTGACAGGTCTTAATTGAC
+	 *							GCGCTGTTCAGCCCTTTGAGTTCGGTTGAGTTTTGTGTTGGAGAATTTTC)
+	 * 11. <QUAL>	: query QUALity; ASCII-33 gives the Phred base quality
+	 *					(Ex: 	/.8349-7:95@=8999;1:=;===AABD:=@A;>AD:E:9@==69<;@B3CBC@B8B;B89=8=3;@@@.:->>B?
+	 *							C4CBB8EDGDD8GDEEDEEE8EBA9B???=B;,8:+5;;A??>?#############################)
+	 * 12. [<TAG>:<VTYPE>:<VALUE> [...]]: TAG/Value TYPE/match  (space allowed)
+	 * 			(Ex:	XT:A:R	NM:i:2	X0:i:2	X1:i:0)
+	 *
+ */ + public void filter() { + FileWriter fw = null; + Scanner s = null; + + try { + s= new Scanner(input); + } catch (FileNotFoundException e) { + System.err.println("sam file not found"); + e.printStackTrace(); + } + + try { + if(output == null){ + output = new File(input.getName(). + substring(0,input.getName().lastIndexOf("."))+".rsam"); + } + + fw = new FileWriter(output); + + } catch (IOException e) { + System.err.println("Error generating rsam file"); + e.printStackTrace(); + } + + String rawline; + ReadLine line = null; + + do{ + rawline = s.nextLine(); + }while(rawline.startsWith("@")); + + do{ + try { + line = new ReadLine(rawline); + fw.write(line+"\r\n"); + } catch (IOException e) { + System.err.println("Error writing reduced form of:\n"+rawline); + e.printStackTrace(); + } + if(s.hasNextLine()) + rawline = s.nextLine(); + }while(s.hasNextLine()); + + + try { + fw.write(line +"\r\n"); + } catch (IOException e) { + System.err.println("Error writing reduced form of:\n"+line); + e.printStackTrace(); + } + + try { + fw.close(); + } catch (IOException e) { + System.err.println("Error closing file"); + e.printStackTrace(); + } + s.close(); + + System.out.println("READS FILE:"); + System.out.println(input.getAbsolutePath()+" reduced to "+ + output.getAbsolutePath()); + sort(); + } + + + public void sort() { + Runtime rt = Runtime.getRuntime(); + try { + String rawOutput = output.getAbsolutePath(); + String outputName = output.getName(); + String pathname = output.getParentFile().getAbsolutePath()+"/"+outputName+"Sorted"; + + output = new File(pathname); + String tmpD=output.getParentFile().getAbsolutePath(); + + if(!output.exists())output.createNewFile(); + String command = "sort -k2,2 -k3n,3 -T "+tmpD+" "+rawOutput; + Process p = rt.exec(command); + Scanner ps = new Scanner(p.getInputStream()); + + FileWriter fw = new FileWriter(output); + while(ps.hasNextLine()){ + String nextLine = ps.nextLine(); + fw.write(nextLine+"\n"); + } + fw.close(); + + Scanner psStdErr=new Scanner(p.getErrorStream()); + while(psStdErr.hasNextLine()){ + String errLine=psStdErr.nextLine(); + System.out.println(errLine); + } + + new File(rawOutput).delete(); + new File(pathname).renameTo(new File(rawOutput)); + System.out.println("Reduced file "+new File(rawOutput).getAbsolutePath()+" sorted\n"); + + } catch (IOException e1) { + e1.printStackTrace(); + } + } + + + public String toString(){ + return "ReadFilter"; + } + + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/filters/TargetFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/filters/TargetFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,195 @@ +package filters; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileWriter; +import java.io.IOException; +import java.util.Scanner; +import middlewares.Misc; +import datastructures.Frame; +import datastructures.TargetLine; +import exceptions.ChromosomeFormatException; +import exceptions.ChromosomeNotFoundException; +import exceptions.NullOrNegativeRangeException; +import exceptions.RangeFormatException; +import exceptions.RangeLimitNotFoundException; + +public class TargetFilter extends Filter { + + // variables used for test purposes. + public int target_size, target_regions; + + public TargetFilter(String input, String output) { + super(input, output); + target_size = 0; + target_regions = 0; + } + + public void filter() { + try { + + Scanner s = new Scanner(new File(getInputPath())); + FileWriter fw; + System.out.println("TARGET REGIONS FILE:"); + /* + * 1. STEP: + * a. Remove all but the first track. + * b. Remove browser and track header lines of the first track + * c. Save the output in the output directory and return the path of the output file. + */ + String finput = filterTracks(s); + setInputPath(finput); + + /* + * 2. STEP: + * a. Sort the target region file lexicographically by chromomose-name. + * b. If chr-names are identical then numerically by the start position. + * c. If start positions are identical then numerically by the end position. + */ + sort(); + + /* + * 3. STEP: + * Unify all overlapping target regions. + */ + s = new Scanner(new File(getInputPath())); + fw = new FileWriter(getOutputPath()); + // for all target regions do the following: + if (s.hasNextLine()) { + try { + // parse the current target region. + TargetLine tl = new TargetLine(s.nextLine()); + // create a new frame representing the current target region. + Frame union = new Frame(tl.start(), tl.end() - tl.start() + 1); + String chrom = tl.chrom(); + while (s.hasNextLine()) { + // parse the next target region. + tl = new TargetLine(s.nextLine()); + // create the corresponding frame. + Frame nextTarget = new Frame(tl.start(), tl.end() - tl.start() + 1); + String nextChrom = tl.chrom(); + // if current and next overlap each other. + if (union.overlaps(nextTarget) && chrom.equals(nextChrom)) { + // unify regions. + union = union.unify(nextTarget); + // go to the next iteration. + continue; + } + // else + // write the computed overlap-free target region. + target_size += union.end()-union.start()+1; + target_regions++; + fw.write(chrom +"\t"+ union.start() +"\t"+ union.end() +"\n"); + // refresh the union and chrom variables for the next computation. + union = nextTarget; + chrom = nextChrom; + } + + try { + target_size += union.end()-union.start()+1; + target_regions++; + fw.write(chrom+"\t"+union.start()+"\t"+union.end()+"\n"); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + fw.close(); + } catch (RangeFormatException e) { + e.printStackTrace(); + } catch (ChromosomeFormatException e) { + e.printStackTrace(); + } catch (ChromosomeNotFoundException e) { + e.printStackTrace(); + } catch (RangeLimitNotFoundException e) { + e.printStackTrace(); + } catch (NullOrNegativeRangeException e) { + e.printStackTrace(); + } + } + } catch (FileNotFoundException fnfe) { + fnfe.printStackTrace(); + } catch (IOException ioe) { + ioe.printStackTrace(); + } + System.out.println(getInputPath()+" reduced to "+getOutputPath()); + } + + /** + * 1. Removes all but the first track. + * 2. Removes browser and track header lines of the first track + * 3. Saves the output in the output directory and return the path of the output file. + * + * @param s the scanner reading the raw file. + * @return the path of the output file. + * @throws IOException if writing fails. + */ + private String filterTracks(Scanner s) throws IOException { + + String finput = Misc.path(getOutputPath())+ Misc.prefix(getInputPath()) + ".bed"; + FileWriter fw = new FileWriter(finput); + // Counters for browser header lines and track header lines. + int browserRead = 0; + int trackRead = 0; + while (s.hasNextLine()) { + String line = s.nextLine(); + // Count browser lines. + if (line.startsWith("browser")) { + browserRead++; + // Count header lines. + } else if (line.startsWith("track")) { + trackRead++; + } else { + // Write lines as long as they corresponds to the first track. + if (trackRead <= 1 && browserRead <= 1) + fw.write(line + "\n"); + else + // Otherwise cancel the computation. + break; + } + } + fw.close(); + return finput; + } + + /** + * 1. Sort the target region file lexicographically by chromomose-name. + * 2. If chr-names are identical then numerically by the start position. + * 3. If start positions are identical then numerically by the end position. + */ + public void sort() { + Runtime rt = Runtime.getRuntime(); + try { + String unsorted = getInputPath(); + String tmpD = new File(getOutputPath()).getParentFile().getAbsolutePath(); + String sorted = tmpD+Misc.slash(tmpD)+Misc.prefix(unsorted)+"Sorted"; + setInputPath(sorted); + + if(!new File(getInputPath()).exists()) + new File(getInputPath()).createNewFile(); + + String command = "sort -k1,1 -k2n,2 -k3n,3 -T "+tmpD+" "+unsorted; + Process p = rt.exec(command); + Scanner ps = new Scanner(p.getInputStream()); + FileWriter fw = new FileWriter(getInputPath()); + while(ps.hasNextLine()){ + String nextLine = ps.nextLine(); + fw.write(nextLine+"\n"); + } + fw.close(); + new File(sorted).renameTo(new File(unsorted)); + setInputPath(unsorted); + System.out.println("Target file "+new File(unsorted).getAbsolutePath()+" sorted"); + + } catch (IOException e1) { + e1.printStackTrace(); + } + } + + public static void main(String[] args){ + new TargetFilter("/home/abdallah/Desktop/input/Agilent_SureSelect_50Mb.bed", + "/home/abdallah/Desktop/output/Agilent_SureSelect_50Mb_Output.bed") + .filter(); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/GeneExtractor.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/middlewares/GeneExtractor.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,68 @@ +package middlewares; +import java.io.File; +import java.io.FileNotFoundException; +import java.util.Scanner; + +import datastructures.AVLTree; +import datastructures.AnnotationLine; +import datastructures.TargetLine; + +/** + * + * Generate a AVL-Tree for fast extraction of genes (logarithmic time). + * + * @author Ali Abdallah + * @version 0.4.5, 14.07.2011 + * @since jdk 1.6.0 + * + */ + +public class GeneExtractor { + + /** + * The path of the genome annotation file. + */ + String genomeAnnotation; + + /** + * The avl tree representing the genome annotation file. + */ + AVLTree genesTree; + + /** + * The scanner scanning the genome file. + */ + Scanner s; + + /** + * Constructs the avl-tree based on the genome annotation file. + * @param genomeAnnotation the genome annotation file. + */ + public GeneExtractor(String genomeAnnotation) { + genesTree = new AVLTree(); + this.genomeAnnotation = genomeAnnotation; + try { + s = new Scanner(new File(genomeAnnotation)); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } + while (s.hasNextLine()) { + genesTree.insert(new AnnotationLine(s.nextLine())); + } + s.close(); + } + + /** + * Search the tree for a gene overlapping the specified target. + * + * @param tl the target line of the current target. + * @return the gene overlapping the specified target, if it exists and + * "unknown" otherwise. + */ + public String extractGene(TargetLine tl) { + AnnotationLine a = + (AnnotationLine) genesTree.find(new AnnotationLine + ("*", tl.chrom(), "dummy", tl.start(), tl.end())); + return ((a != null) ? a.gene() : "unknown"); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/HitsCounter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/middlewares/HitsCounter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,105 @@ +package middlewares; +import java.util.Vector; + +/** + * Counts the number of bases hit at least 1, 5, 10, 20 or 30 times. + * + * @author Ali Abdallah + * @version 22.07.2011 + * @since Java 1.6 + */ +public class HitsCounter { + + /** + * The hits vector with the number of bases hit at different levels. + */ + private Vector hits; + + /** + * The number of bases hit at the five different levels for a specific + * target. + */ + private Vector currentHits; + + /** + * The levels at which the number of bases is counted. + */ + private int[] levels = { 1, 5, 10, 20, 30 }; + + /** + * Creates and initializes a hit counter. + */ + public HitsCounter() { + hits = new Vector(); + currentHits = new Vector(); + for (int i = 0; i < levels.length; i++) { + hits.add(0); + currentHits.add(0); + } + } + + /** + * Update the number of bases hit at the specified different levels. + */ + public void updateHits() { + for (int i = 0; i < hits.size(); i++) { + hits.set(i, hits.get(i) + currentHits.get(i)); + } + } + + /** + * Reset the number of bases hit at the specified different leverls for + * a specific target for user for the next target. + */ + public void resetCurrentHits() { + currentHits = new Vector(); + for (int i = 0; i < levels.length; i++) { + currentHits.add(0); + } + } + + /** + * Increments the number of bases hit at some levels by one, if the number + * of hits on this base reach or exceed this level. + * + * @param hitsOnBase + */ + public void updateCurrentHits(int hitsOnBase) { + for (int i = 0; i < currentHits.size(); i++) { + if (hitsOnBase >= levels[i]) { + currentHits.set(i, currentHits.get(i) + 1); + } + } + } + + // Index of the bases level of the current target. + int currHit = 0; + + /** + * @return the number of bases hit at the next higher level in the current + * target. + */ + public int getNextLevelCurrentHits() { + if (currHit < currentHits.size()) + return currentHits.get(currHit++); + else { + currHit = 1; + return currentHits.get(0); + } + } + + // Index of the bases level of the target. + int hit = -1; + + /** + * @return the number of bases hit at the next higher level. + */ + public int getNextLevelHits() { + if (++hit < hits.size()) { + return hits.get(hit); + } else { + return (hit = -1); + } + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/Misc.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/middlewares/Misc.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,206 @@ +package middlewares; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileWriter; +import java.io.IOException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Scanner; + +import datastructures.ReducedReadLine; +import datastructures.TargetLine; +import exceptions.ChromosomeFormatException; +import exceptions.ChromosomeNotFoundException; +import exceptions.NullOrNegativeRangeException; +import exceptions.RangeFormatException; +import exceptions.RangeLimitNotFoundException; + +/** + * Miscellaneous methods for different uses. + * + * @author Ali Abdallah + * @version 01.2011 + * @since jdk 1.6.0 + */ +public class Misc { + + /** + * Make the first letter big, if possible. nGSrich -> NGSrich. + * + * @param s the string + * @return the same string with the first letter big. + */ + public static String bigFirst(String s) { + return s.substring(0, 1).toUpperCase() + s.substring(1); + } + + /** + * Creates a shortcut for the file with a different file extension. + * + * @param fName the original file name. + * @param newExt the new extension of the file. + * @param dir the directory of the mad link. + * @return a link to the file fName with a different extension. + */ + public static File rename(String fName, String newExt, String dir) { + + String inDirShortCut = dir + Misc.slash(dir); + String fShortcutName = inDirShortCut + Misc.prefix(fName) + "." + + newExt; + Runtime r = Runtime.getRuntime(); + try { + r.exec("ln -s " + fName + " " + fShortcutName); + } catch (IOException e) { + e.printStackTrace(); + } + try { + Thread.sleep(100); + } catch (InterruptedException e) { + e.printStackTrace(); + } + return new File(fShortcutName); + } + + /** + * @return the path of the bin directory of this software. + */ + public static String binDir() { + URL url = new Misc().getClass().getResource("Misc.class"); + String path = url.toString().substring(url.toString().indexOf(":") + 1); + path = path.substring(0, path.lastIndexOf("/")); + + return path.substring(0, path.lastIndexOf("/")); + + } + + /** + * @return the path of this software. + */ + public static String scriptDir() { + URL url = new Misc().getClass().getResource("../NGSrich.class"); + String path = url.toString().substring(url.toString().indexOf(":") + 1); + path = path.substring(0, path.lastIndexOf("/")); + return path.substring(0, path.lastIndexOf("/")+1); + + } + + public static void main(String[] args) { + System.out.println(scriptDir()); + } + + /** + * @param path + * @return extends the path by a slash at the end, in the case it don't + * exists. + */ + public static String slash(String path) { + return (path.endsWith("/") ? "" : "/"); + } + + /** + * @return the name of the host. + */ + public static String getHostName() { + Runtime rt = Runtime.getRuntime(); + String erg = ""; + try { + File f = new File("hostname.sh"); + FileWriter fw = new FileWriter(f); + + fw.write("#!/bin/bash\r\nproc=$(hostname -s).$$\r\necho $proc"); + fw.close(); + Process p = rt.exec("chmod 700 " + f.getAbsolutePath()); + p = rt.exec("sh " + f.getAbsolutePath()); + + Scanner s = new Scanner(p.getInputStream()); + + while (s.hasNextLine()) { + erg += (s.nextLine()); + } + s.close(); + + f.delete(); + } catch (IOException e) { + e.printStackTrace(); + } + return erg; + } + + /** + * @param fileName + * @return the extension of the file. + */ + public static String suffix(String fileName) { + return fileName.substring(fileName.lastIndexOf(".") + 1); + } + + /** + * @param fileName + * @return the name of the file without the extension. + */ + public static String prefix(String fileName) { + return fileName.substring(fileName.lastIndexOf("/") + 1, + fileName.lastIndexOf(".")); + } + + /** + * @param fileName + * @return the directory of the specified file. + */ + public static String path(String fileName) { + String absolutePath = + new File(fileName).getParentFile().getAbsolutePath(); + return absolutePath+slash(absolutePath); + } + + /** + * Check if the chromosome names in the target file are a subset of the + * chromosome name in the alignment file. + * + * @param alignment the alignment file. + * @param target the target file. + * @return true if target chromosomes are a subset of alignment chromosome + * and false otherwise. + */ + public static boolean areChromosomeCompatible(File alignment, File target){ + Scanner aScan = null, tScan = null; + try { + aScan = new Scanner(alignment); + tScan = new Scanner(target); + + ArrayList alist = new ArrayList(); + ArrayList tlist = new ArrayList(); + while(aScan.hasNextLine()){ + ReducedReadLine rl = new ReducedReadLine(aScan.nextLine()); + if(alist.indexOf(rl.chrom())==-1) + alist.add(rl.chrom()); + } + while(tScan.hasNextLine()){ + TargetLine tl = new TargetLine(tScan.nextLine()); + if(tlist.indexOf(tl.chrom())==-1) + tlist.add(tl.chrom()); + } + for(int i = 0; i < tlist.size(); i++){ + if(alist.indexOf(tlist.get(i))!=-1) + return true; + } + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (ChromosomeFormatException e) { + e.printStackTrace(); + } catch (ChromosomeNotFoundException e) { + e.printStackTrace(); + } catch (RangeFormatException e) { + e.printStackTrace(); + } catch (RangeLimitNotFoundException e) { + e.printStackTrace(); + } catch (NullOrNegativeRangeException e) { + e.printStackTrace(); + } + + + return false; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/ReadCounter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/middlewares/ReadCounter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,33 @@ +package middlewares; +/** + * Counter for the reads on targets (+/- 0/100/200) and the reads overlapping + * targets (+/- 0/100/200). + * + * @author Ali Abdallah + * @version 14.07.2011 + * @since jdk 1.6.0 + */ +public class ReadCounter { + + // Self explanatory. + private int on, on100, on200, over, over100, over200; + + public ReadCounter(){on=0; on100=0; on200=0; over=0; over100=0; over200=0;} + + public void incOn(){on++;} + public void incOn100(){on100++;} + public void incOn200(){on200++;} + + public void incOver(){over++;} + public void incOver100(){over100++;} + public void incOver200(){over200++;} + + public int on(){return on;} + public int on100(){return on100;} + public int on200(){return on200;} + + public int over(){return over;} + public int over100(){return over100;} + public int over200(){return over200;} + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/XMLSummaryFileBuilder.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/middlewares/XMLSummaryFileBuilder.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,136 @@ +package middlewares; + +import java.util.*; +import java.io.*; +import org.jdom.*; +import org.jdom.input.*; +import org.jdom.output.*; + +/** + * Used to construct the summary file based on the computation of an + * EnrichmentStatsComputer object. It uses a file pattern to generate this file + * dynamically. + * + * @author Ali Abdallah + * @version 20.07.2011 + * @since Java 1.6 + */ + +public class XMLSummaryFileBuilder { + + /** + * The pattern file containing the structure of the summary without real + * data. + */ + static String xmlPatternFile; + + /** + * The summary file containing the computed data. + */ + static String xmlOutputFile; + + /** + * An object with an abstract representation on an xml-file. + */ + static Document doc; + + /** + * The leaf-tags containing data as text. + */ + List leafs; + + /** + * The name of the current sample. + */ + static String currSample; + + /** + * Creates and initializes a XMLSummaryFileBuilder object. + * + * @param xmlPatternFile the pattern file. + * @param xmlOutputFile the output file. + * @param currSample the current read alignment sample name without + * the extension. + */ + public XMLSummaryFileBuilder(String xmlPatternFile, String xmlOutputFile, + String currSample) { + + leafs = new ArrayList(); + XMLSummaryFileBuilder.xmlPatternFile = xmlPatternFile; + XMLSummaryFileBuilder.xmlOutputFile = xmlOutputFile; + XMLSummaryFileBuilder.currSample = currSample; + SAXBuilder builder = new SAXBuilder(); + try { + doc = builder.build(xmlPatternFile); + } catch (JDOMException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + } + + /** + * Same as the constructor above but the pattern file is internally + * specified. + * + * @param xmlOutputFile the output file. + * @param currSample the current read alignment sample name without + * the extension. + */ + public XMLSummaryFileBuilder(String xmlOutputFile, + String currSample) { + this(Misc.binDir()+"/xmlFilePattern.xml", xmlOutputFile, currSample); + } + + /** + * Computes all the leafs of the subtree with root e. + * + * @param e an Element. + * @return all the leafs of the subtree with root e. + */ + public Element[] getLeafs(Element e){ + @SuppressWarnings("unchecked") + List children = e.getChildren(); + for(int i = 0; i < children.size(); i++){ + Element child = children.get(i); + if(child.getChildren().size() == 0) + leafs.add(child); + else + getLeafs(child); + } + + Object[] oleafs = leafs.toArray(); + Element[] eleafs = new Element[oleafs.length]; + for(int i = 0; i < eleafs.length; i++) + eleafs[i] = (Element)oleafs[i]; + + return eleafs; + } + + /** + * Same as the above method but the element is internally specified as the + * root of the document. + * + * @return an array with all leaf elements of the document. + */ + public Element[] getLeafs(){ + return getLeafs(doc.getRootElement()); + } + + /** + * Write the summary file created. + * @param name the name of the file. + */ + public void writeXMLFile(String name) { + XMLOutputter outp = new XMLOutputter(); + outp.setFormat(Format.getPrettyFormat()); + try { + outp.output(doc, new FileOutputStream(name)); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Attribute.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Attribute.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,717 @@ +/*-- + + $Id: Attribute.java,v 1.56 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.io.*; + +/** + * An XML attribute. Methods allow the user to obtain the value of the attribute + * as well as namespace and type information. + * + * @version $Revision: 1.56 $, $Date: 2007/11/10 05:28:58 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Elliotte Rusty Harold + * @author Wesley Biggs + * @author Victor Toni + */ +public class Attribute implements Serializable, Cloneable { + + private static final String CVS_ID = + "@(#) $RCSfile: Attribute.java,v $ $Revision: 1.56 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + /** + * Attribute type: the attribute has not been declared or type + * is unknown. + * + * @see #getAttributeType + */ + public final static int UNDECLARED_TYPE = 0; + + /** + * Attribute type: the attribute value is a string. + * + * @see #getAttributeType + */ + public final static int CDATA_TYPE = 1; + + /** + * Attribute type: the attribute value is a unique identifier. + * + * @see #getAttributeType + */ + public final static int ID_TYPE = 2; + + /** + * Attribute type: the attribute value is a reference to a + * unique identifier. + * + * @see #getAttributeType + */ + public final static int IDREF_TYPE = 3; + + /** + * Attribute type: the attribute value is a list of references to + * unique identifiers. + * + * @see #getAttributeType + */ + public final static int IDREFS_TYPE = 4; + + /** + * Attribute type: the attribute value is the name of an entity. + * + * @see #getAttributeType + */ + public final static int ENTITY_TYPE = 5; + + /** + *

+ * Attribute type: the attribute value is a list of entity names. + *

+ * + * @see #getAttributeType + */ + public final static int ENTITIES_TYPE = 6; + + /** + * Attribute type: the attribute value is a name token. + *

+ * According to SAX 2.0 specification, attributes of enumerated + * types should be reported as "NMTOKEN" by SAX parsers. But the + * major parsers (Xerces and Crimson) provide specific values + * that permit to recognize them as {@link #ENUMERATED_TYPE}. + * + * @see #getAttributeType + */ + public final static int NMTOKEN_TYPE = 7; + + /** + * Attribute type: the attribute value is a list of name tokens. + * + * @see #getAttributeType + */ + public final static int NMTOKENS_TYPE = 8; + + /** + * Attribute type: the attribute value is the name of a notation. + * + * @see #getAttributeType + */ + public final static int NOTATION_TYPE = 9; + + /** + * Attribute type: the attribute value is a name token from an + * enumeration. + * + * @see #getAttributeType + */ + public final static int ENUMERATED_TYPE = 10; + + // Keep the old constant names for one beta cycle to help migration + + + + /** The local name of the Attribute */ + protected String name; + + /** The {@link Namespace} of the Attribute */ + protected transient Namespace namespace; + + /** The value of the Attribute */ + protected String value; + + /** The type of the Attribute */ + protected int type = UNDECLARED_TYPE; + + /** Parent element, or null if none */ + protected Element parent; + + /** + * Default, no-args constructor for implementations to use if needed. + */ + protected Attribute() {} + + /** + * This will create a new Attribute with the + * specified (local) name and value, and in the provided + * {@link Namespace}. + * + * @param name String name of Attribute. + * @param value String value for new attribute. + * @param namespace Namespace namespace for new attribute. + * @throws IllegalNameException if the given name is illegal as an + * attribute name or if if the new namespace is the default + * namespace. Attributes cannot be in a default namespace. + * @throws IllegalDataException if the given attribute value is + * illegal character data (as determined by + * {@link org.jdom.Verifier#checkCharacterData}). + */ + public Attribute(final String name, final String value, final Namespace namespace) { + this(name, value, UNDECLARED_TYPE, namespace); + } + + /** + * This will create a new Attribute with the + * specified (local) name, value, and type, and in the provided + * {@link Namespace}. + * + * @param name String name of Attribute. + * @param value String value for new attribute. + * @param type int type for new attribute. + * @param namespace Namespace namespace for new attribute. + * @throws IllegalNameException if the given name is illegal as an + * attribute name or if if the new namespace is the default + * namespace. Attributes cannot be in a default namespace. + * @throws IllegalDataException if the given attribute value is + * illegal character data (as determined by + * {@link org.jdom.Verifier#checkCharacterData}) or + * if the given attribute type is not one of the + * supported types. + */ + public Attribute(final String name, final String value, final int type, final Namespace namespace) { + setName(name); + setValue(value); + setAttributeType(type); + setNamespace(namespace); + } + + /** + * This will create a new Attribute with the + * specified (local) name and value, and does not place + * the attribute in a {@link Namespace}. + *

+ * Note: This actually explicitly puts the + * Attribute in the "empty" Namespace + * ({@link Namespace#NO_NAMESPACE}). + * + * @param name String name of Attribute. + * @param value String value for new attribute. + * @throws IllegalNameException if the given name is illegal as an + * attribute name. + * @throws IllegalDataException if the given attribute value is + * illegal character data (as determined by + * {@link org.jdom.Verifier#checkCharacterData}). + */ + public Attribute(final String name, final String value) { + this(name, value, UNDECLARED_TYPE, Namespace.NO_NAMESPACE); + } + + /** + * This will create a new Attribute with the + * specified (local) name, value and type, and does not place + * the attribute in a {@link Namespace}. + *

+ * Note: This actually explicitly puts the + * Attribute in the "empty" Namespace + * ({@link Namespace#NO_NAMESPACE}). + * + * @param name String name of Attribute. + * @param value String value for new attribute. + * @param type int type for new attribute. + * @throws IllegalNameException if the given name is illegal as an + * attribute name. + * @throws IllegalDataException if the given attribute value is + * illegal character data (as determined by + * {@link org.jdom.Verifier#checkCharacterData}) or + * if the given attribute type is not one of the + * supported types. + */ + public Attribute(final String name, final String value, final int type) { + this(name, value, type, Namespace.NO_NAMESPACE); + } + + /** + * This will return the parent of this Attribute. + * If there is no parent, then this returns null. + * + * @return parent of this Attribute + */ + public Element getParent() { + return parent; + } + + /** + * This retrieves the owning {@link Document} for + * this Attribute, or null if not a currently a member of a + * {@link Document}. + * + * @return Document owning this Attribute, or null. + */ + public Document getDocument() { + final Element parentElement = getParent(); + if (parentElement != null) { + return parentElement.getDocument(); + } + + return null; + } + + /** + * This will set the parent of this Attribute. + * + * @param parent Element to be new parent. + * @return this Attribute modified. + */ + protected Attribute setParent(final Element parent) { + this.parent = parent; + return this; + } + + /** + * This detaches the Attribute from its parent, or does + * nothing if the Attribute has no parent. + * + * @return Attribute - this Attribute modified. + */ + public Attribute detach() { + final Element parentElement = getParent(); + if (parentElement != null) { + parentElement.removeAttribute(getName(),getNamespace()); + } + + return this; + } + + /** + * This will retrieve the local name of the + * Attribute. For any XML attribute + * which appears as + * [namespacePrefix]:[attributeName], + * the local name of the attribute would be + * [attributeName]. When the attribute + * has no namespace, the local name is simply the attribute + * name. + *

+ * To obtain the namespace prefix for this + * attribute, the + * {@link #getNamespacePrefix()} + * method should be used. + * + * @return String - name of this attribute, + * without any namespace prefix. + */ + public String getName() { + return name; + } + + /** + * This sets the local name of the Attribute. + * + * @param name the new local name to set + * @return Attribute - the attribute modified. + * @throws IllegalNameException if the given name is illegal as an + * attribute name. + */ + public Attribute setName(final String name) { + final String reason = Verifier.checkAttributeName(name); + if (reason != null) { + throw new IllegalNameException(name, "attribute", reason); + } + this.name = name; + return this; + } + + /** + * This will retrieve the qualified name of the Attribute. + * For any XML attribute whose name is + * [namespacePrefix]:[elementName], + * the qualified name of the attribute would be + * everything (both namespace prefix and + * element name). When the attribute has no + * namespace, the qualified name is simply the attribute's + * local name. + *

+ * To obtain the local name of the attribute, the + * {@link #getName()} method should be used. + *

+ * To obtain the namespace prefix for this attribute, + * the {@link #getNamespacePrefix()} + * method should be used. + * + * @return String - full name for this element. + */ + public String getQualifiedName() { + // Note: Any changes here should be reflected in + // XMLOutputter.printQualifiedName() + final String prefix = namespace.getPrefix(); + + // no prefix found + if ((prefix == null) || ("".equals(prefix))) { + return getName(); + } else { + return new StringBuffer(prefix) + .append(':') + .append(getName()) + .toString(); + } + } + + /** + * This will retrieve the namespace prefix of the + * Attribute. For any XML attribute + * which appears as + * [namespacePrefix]:[attributeName], + * the namespace prefix of the attribute would be + * [namespacePrefix]. When the attribute + * has no namespace, an empty String is returned. + * + * @return String - namespace prefix of this + * attribute. + */ + public String getNamespacePrefix() { + return namespace.getPrefix(); + } + + /** + * This returns the URI mapped to this Attribute's + * prefix. If no mapping is found, an empty String is + * returned. + * + * @return String - namespace URI for this Attribute. + */ + public String getNamespaceURI() { + return namespace.getURI(); + } + + /** + * This will return this Attribute's + * {@link Namespace}. + * + * @return Namespace - Namespace object for this Attribute + */ + public Namespace getNamespace() { + return namespace; + } + + /** + * This sets this Attribute's {@link Namespace}. + * If the provided namespace is null, the attribute will have no namespace. + * The namespace must have a prefix. + * + * @param namespace the new namespace + * @return Element - the element modified. + * @throws IllegalNameException if the new namespace is the default + * namespace. Attributes cannot be in a default namespace. + */ + public Attribute setNamespace(Namespace namespace) { + if (namespace == null) { + namespace = Namespace.NO_NAMESPACE; + } + + // Verify the attribute isn't trying to be in a default namespace + // Attributes can't be in a default namespace + if (namespace != Namespace.NO_NAMESPACE && + "".equals(namespace.getPrefix())) { + throw new IllegalNameException("", "attribute namespace", + "An attribute namespace without a prefix can only be the " + + "NO_NAMESPACE namespace"); + } + this.namespace = namespace; + return this; + } + + /** + * This will return the actual textual value of this + * Attribute. This will include all text + * within the quotation marks. + * + * @return String - value for this attribute. + */ + public String getValue() { + return value; + } + + /** + * This will set the value of the Attribute. + * + * @param value String value for the attribute. + * @return Attribute - this Attribute modified. + * @throws IllegalDataException if the given attribute value is + * illegal character data (as determined by + * {@link org.jdom.Verifier#checkCharacterData}). + */ + public Attribute setValue(final String value) { + final String reason = Verifier.checkCharacterData(value); + if (reason != null) { + throw new IllegalDataException(value, "attribute", reason); + } + this.value = value; + return this; + } + + /** + * This will return the actual declared type of this + * Attribute. + * + * @return int - type for this attribute. + */ + public int getAttributeType() { + return type; + } + + /** + * This will set the type of the Attribute. + * + * @param type int type for the attribute. + * @return Attribute - this Attribute modified. + * @throws IllegalDataException if the given attribute type is + * not one of the supported types. + */ + public Attribute setAttributeType(final int type) { + if ((type < UNDECLARED_TYPE) || (type > ENUMERATED_TYPE)) { + throw new IllegalDataException(String.valueOf(type), + "attribute", "Illegal attribute type"); + } + this.type = type; + return this; + } + + /** + * This returns a String representation of the + * Attribute, suitable for debugging. + * + * @return String - information about the + * Attribute + */ + public String toString() { + return new StringBuffer() + .append("[Attribute: ") + .append(getQualifiedName()) + .append("=\"") + .append(value) + .append("\"") + .append("]") + .toString(); + } + + /** + * This tests for equality of this Attribute to the supplied + * Object. + * + * @param ob Object to compare to. + * @return boolean - whether the Attribute is + * equal to the supplied Object. + */ + public final boolean equals(final Object ob) { + return (ob == this); + } + + /** + * This returns the hash code for this Attribute. + * + * @return int - hash code. + */ + public final int hashCode() { + return super.hashCode(); + } + + /** + * This will return a clone of this Attribute. + * + * @return Object - clone of this Attribute. + */ + public Object clone() { + Attribute attribute = null; + try { + attribute = (Attribute) super.clone(); + } + catch (final CloneNotSupportedException ignore) { + // Won't happen + } + + // Name, namespace, and value are references to imutable objects + // and are copied by super.clone() (aka Object.clone()) + + // super.clone() copies reference to set parent to null + attribute.parent = null; + return attribute; + } + + ///////////////////////////////////////////////////////////////// + // Convenience Methods below here + ///////////////////////////////////////////////////////////////// + + /** + * This gets the value of the attribute, in + * int form, and if no conversion + * can occur, throws a + * {@link DataConversionException} + * + * @return int value of attribute. + * @throws DataConversionException when conversion fails. + */ + public int getIntValue() throws DataConversionException { + try { + return Integer.parseInt(value.trim()); + } catch (final NumberFormatException e) { + throw new DataConversionException(name, "int"); + } + } + + /** + * This gets the value of the attribute, in + * long form, and if no conversion + * can occur, throws a + * {@link DataConversionException} + * + * @return long value of attribute. + * @throws DataConversionException when conversion fails. + */ + public long getLongValue() throws DataConversionException { + try { + return Long.parseLong(value.trim()); + } catch (final NumberFormatException e) { + throw new DataConversionException(name, "long"); + } + } + + /** + * This gets the value of the attribute, in + * float form, and if no conversion + * can occur, throws a + * {@link DataConversionException} + * + * @return float value of attribute. + * @throws DataConversionException when conversion fails. + */ + public float getFloatValue() throws DataConversionException { + try { + // Avoid Float.parseFloat() to support JDK 1.1 + return Float.valueOf(value.trim()).floatValue(); + } catch (final NumberFormatException e) { + throw new DataConversionException(name, "float"); + } + } + + /** + * This gets the value of the attribute, in + * double form, and if no conversion + * can occur, throws a + * {@link DataConversionException} + * + * @return double value of attribute. + * @throws DataConversionException when conversion fails. + */ + public double getDoubleValue() throws DataConversionException { + try { + // Avoid Double.parseDouble() to support JDK 1.1 + return Double.valueOf(value.trim()).doubleValue(); + } catch (final NumberFormatException e) { + // Specially handle INF and -INF that Double.valueOf doesn't do + String v = value.trim(); + if ("INF".equals(v)) { + return Double.POSITIVE_INFINITY; + } + if ("-INF".equals(v)) { + return Double.NEGATIVE_INFINITY; + } + throw new DataConversionException(name, "double"); + } + } + + /** + * This gets the effective boolean value of the attribute, or throws a + * {@link DataConversionException} if a conversion can't be + * performed. True values are: "true", "on", "1", and "yes". False + * values are: "false", "off", "0", and "no". Values are trimmed before + * comparison. Values other than those listed here throw the exception. + * + * @return boolean value of attribute. + * @throws DataConversionException when conversion fails. + */ + public boolean getBooleanValue() throws DataConversionException { + final String valueTrim = value.trim(); + if ( + (valueTrim.equalsIgnoreCase("true")) || + (valueTrim.equalsIgnoreCase("on")) || + (valueTrim.equalsIgnoreCase("1")) || + (valueTrim.equalsIgnoreCase("yes"))) { + return true; + } else if ( + (valueTrim.equalsIgnoreCase("false")) || + (valueTrim.equalsIgnoreCase("off")) || + (valueTrim.equalsIgnoreCase("0")) || + (valueTrim.equalsIgnoreCase("no")) + ) { + return false; + } else { + throw new DataConversionException(name, "boolean"); + } + } + + // Support a custom Namespace serialization so no two namespace + // object instances may exist for the same prefix/uri pair + private void writeObject(final ObjectOutputStream out) throws IOException { + + out.defaultWriteObject(); + + // We use writeObject() and not writeUTF() to minimize space + // This allows for writing pointers to already written strings + out.writeObject(namespace.getPrefix()); + out.writeObject(namespace.getURI()); + } + + private void readObject(final ObjectInputStream in) + throws IOException, ClassNotFoundException { + + in.defaultReadObject(); + + namespace = Namespace.getNamespace( + (String) in.readObject(), (String) in.readObject()); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/AttributeList.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/AttributeList.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,518 @@ +/*-- + + $Id: AttributeList.java,v 1.24 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +/** + * AttributeList represents legal JDOM Attribute + * content. This class is NOT PUBLIC; users should see it as a simple List + * implementation. + * + * @author Alex Rosen + * @author Philippe Riand + * @author Bradley S. Huffman + * @version $Revision: 1.24 $, $Date: 2007/11/10 05:28:58 $ + * @see CDATA + * @see Comment + * @see Element + * @see EntityRef + * @see ProcessingInstruction + * @see Text + */ +class AttributeList extends AbstractList + implements List, java.io.Serializable { + + private static final String CVS_ID = + "@(#) $RCSfile: AttributeList.java,v $ $Revision: 1.24 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + private static final int INITIAL_ARRAY_SIZE = 5; + + /** The backing list */ + private Attribute elementData[]; + private int size; + + /** The parent Element */ + private Element parent; + + /** Force an Element parent */ + private AttributeList() {} + + /** + * Create a new instance of the AttributeList representing + * Element content + * + * @param parent element whose attributes are to be held + */ + AttributeList(Element parent) { + this.parent = parent; + } + + /** + * Package internal method to support building from sources that are + * 100% trusted. + * + * @param a attribute to add without any checks + */ + final void uncheckedAddAttribute(Attribute a) { + a.parent = parent; + ensureCapacity(size + 1); + elementData[size++] = a; + modCount++; + } + + /** + * Add a attribute to the end of the list or replace a existing + * attribute with the same name and Namespace. + * + * @param obj The object to insert into the list. + * @return true (as per the general contract of Collection.add). + * @throws IndexOutOfBoundsException if index < 0 || index > size() + */ + public boolean add(Object obj) { + if (obj instanceof Attribute) { + Attribute attribute = (Attribute) obj; + int duplicate = indexOfDuplicate(attribute); + if (duplicate < 0) { + add(size(), attribute); + } + else { + set(duplicate, attribute); + } + } + else if (obj == null) { + throw new IllegalAddException("Cannot add null attribute"); + } + else { + throw new IllegalAddException("Class " + + obj.getClass().getName() + + " is not an attribute"); + } + return true; + } + + /** + * Inserts the specified attribute at the specified position in this list. + * Shifts the attribute currently at that position (if any) and any + * subsequent attributes to the right (adds one to their indices). + * + * @param index The location to set the value to. + * @param obj The object to insert into the list. + * throws IndexOutOfBoundsException if index < 0 || index > size() + */ + public void add(int index, Object obj) { + if (obj instanceof Attribute) { + Attribute attribute = (Attribute) obj; + int duplicate = indexOfDuplicate(attribute); + if (duplicate >= 0) { + throw new IllegalAddException("Cannot add duplicate attribute"); + } + add(index, attribute); + } + else if (obj == null) { + throw new IllegalAddException("Cannot add null attribute"); + } + else { + throw new IllegalAddException("Class " + + obj.getClass().getName() + + " is not an attribute"); + } + modCount++; + } + + /** + * Check and add the Attribute to this list at + * the given index. Note: does not check for duplicate + * attributes. + * + * @param index index where to add Attribute + * @param attribute Attribute to add + */ + void add(int index, Attribute attribute) { + if (attribute.getParent() != null) { + throw new IllegalAddException( + "The attribute already has an existing parent \"" + + attribute.getParent().getQualifiedName() + "\""); + } + + String reason = Verifier.checkNamespaceCollision(attribute, parent); + if (reason != null) { + throw new IllegalAddException(parent, attribute, reason); + } + + if (index<0 || index>size) { + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + } + + attribute.setParent(parent); + + ensureCapacity(size+1); + if( index==size ) { + elementData[size++] = attribute; + } else { + System.arraycopy(elementData, index, elementData, index + 1, size - index); + elementData[index] = attribute; + size++; + } + modCount++; + } + + /** + * Add all the objects in the specified collection. + * + * @param collection The collection containing all the objects to add. + * @return true if the list was modified as a result of + * the add. + */ + public boolean addAll(Collection collection) { + return addAll(size(), collection); + } + + /** + * Inserts the specified collecton at the specified position in this list. + * Shifts the attribute currently at that position (if any) and any + * subsequent attributes to the right (adds one to their indices). + * + * @param index The offset to start adding the data in the collection + * @param collection The collection to insert into the list. + * @return true if the list was modified as a result of + * the add. + * throws IndexOutOfBoundsException if index < 0 || index > size() + */ + public boolean addAll(int index, Collection collection) { + if (index<0 || index>size) { + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + } + + if ((collection == null) || (collection.size() == 0)) { + return false; + } + ensureCapacity(size() + collection.size()); + + int count = 0; + + try { + Iterator i = collection.iterator(); + while (i.hasNext()) { + Object obj = i.next(); + add(index + count, obj); + count++; + } + } + catch (RuntimeException exception) { + for (int i = 0; i < count; i++) { + remove(index); + } + throw exception; + } + + return true; + } + + /** + * Clear the current list. + */ + public void clear() { + if (elementData != null) { + for (int i = 0; i < size; i++) { + Attribute attribute = elementData[i]; + attribute.setParent(null); + } + elementData = null; + size = 0; + } + modCount++; + } + + /** + * Clear the current list and set it to the contents + * of the Collection. + * object. + * + * @param collection The collection to use. + */ + void clearAndSet(Collection collection) { + Attribute[] old = elementData; + int oldSize = size; + + elementData = null; + size = 0; + + if ((collection != null) && (collection.size() != 0)) { + ensureCapacity(collection.size()); + try { + addAll(0, collection); + } + catch (RuntimeException exception) { + elementData = old; + size = oldSize; + throw exception; + } + } + + if (old != null) { + for (int i = 0; i < oldSize; i++) { + Attribute attribute = old[i]; + attribute.setParent(null); + } + } + modCount++; + } + + /** + * Increases the capacity of this AttributeList instance, + * if necessary, to ensure that it can hold at least the number of + * items specified by the minimum capacity argument. + * + * @param minCapacity the desired minimum capacity. + */ + private void ensureCapacity(int minCapacity) { + if (elementData == null) { + elementData = new Attribute[Math.max(minCapacity, INITIAL_ARRAY_SIZE)]; + } + else { + int oldCapacity = elementData.length; + if (minCapacity > oldCapacity) { + Attribute oldData[] = elementData; + int newCapacity = (oldCapacity * 3)/2 + 1; + if (newCapacity < minCapacity) + newCapacity = minCapacity; + elementData = new Attribute[newCapacity]; + System.arraycopy(oldData, 0, elementData, 0, size); + } + } + } + + /** + * Return the object at the specified offset. + * + * @param index The offset of the object. + * @return The Object which was returned. + */ + public Object get(int index) { + if (index<0 || index>=size) { + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + } + + return elementData[index]; + } + + /** + * Return the Attribute with the + * given name and Namespace. + * + * @param name name of attribute to return + * @param namespace Namespace to match + * @return the Attribute, or null if one doesn't exist. + */ + Object get(String name, Namespace namespace) { + int index = indexOf(name, namespace); + if (index < 0) { + return null; + } + return elementData[index]; + } + + /** + * Return index of the Attribute with the + * given name and uri. + */ + int indexOf(String name, Namespace namespace) { + String uri = namespace.getURI(); + if (elementData != null) { + for (int i = 0; i < size; i++) { + Attribute old = elementData[i]; + String oldURI = old.getNamespaceURI(); + String oldName = old.getName(); + if (oldURI.equals(uri) && oldName.equals(name)) { + return i; + } + } + } + return -1; + } + + /** + * Remove the object at the specified offset. + * + * @param index The offset of the object. + * @return The Object which was removed. + */ + public Object remove(int index) { + if (index<0 || index>=size) + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + + Attribute old = elementData[index]; + old.setParent(null); + int numMoved = size - index - 1; + if (numMoved > 0) + System.arraycopy(elementData, index+1, elementData, index,numMoved); + elementData[--size] = null; // Let gc do its work + modCount++; + return old; + } + + /** + * Remove the Attribute with the + * given name and Namespace. + * + * @param namespace Namespace to match + * @return the true if attribute was removed, + * false otherwise + */ + boolean remove(String name, Namespace namespace) { + int index = indexOf(name, namespace); + if (index < 0) { + return false; + } + remove(index); + return true; + } + + /** + * Set the object at the specified location to the supplied + * object. + * + * @param index The location to set the value to. + * @param obj The location to set the value to. + * @return The object which was replaced. + * throws IndexOutOfBoundsException if index < 0 || index >= size() + */ + public Object set(int index, Object obj) { + if (obj instanceof Attribute) { + Attribute attribute = (Attribute) obj; + int duplicate = indexOfDuplicate(attribute); + if ((duplicate >= 0) && (duplicate != index)) { + throw new IllegalAddException("Cannot set duplicate attribute"); + } + return set(index, attribute); + } + else if (obj == null) { + throw new IllegalAddException("Cannot add null attribute"); + } + else { + throw new IllegalAddException("Class " + + obj.getClass().getName() + + " is not an attribute"); + } + } + + /** + * Set the object at the specified location to the supplied + * object. Note: does not check for duplicate attributes. + * + * @param index The location to set the value to. + * @param attribute The attribute to set. + * @return The object which was replaced. + * throws IndexOutOfBoundsException if index < 0 || index >= size() + */ + Object set(int index, Attribute attribute) { + if (index < 0 || index >= size) + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + + if (attribute.getParent() != null) { + throw new IllegalAddException( + "The attribute already has an existing parent \"" + + attribute.getParent().getQualifiedName() + "\""); + } + + String reason = Verifier.checkNamespaceCollision(attribute, parent); + if (reason != null) { + throw new IllegalAddException(parent, attribute, reason); + } + + Attribute old = (Attribute) elementData[index]; + old.setParent(null); + + elementData[index] = attribute; + attribute.setParent(parent); + return old; + } + + /** + * Return index of attribute with same name and Namespace, or + * -1 if one doesn't exist + */ + private int indexOfDuplicate(Attribute attribute) { + int duplicate = -1; + String name = attribute.getName(); + Namespace namespace = attribute.getNamespace(); + duplicate = indexOf(name, namespace); + return duplicate; + } + + /** + * Return the number of items in this list + * + * @return The number of items in this list. + */ + public int size() { + return size; + } + + /** + * Return this list as a String + */ + public String toString() { + return super.toString(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/CDATA.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/CDATA.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,205 @@ +/*-- + + $Id: CDATA.java,v 1.32 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * An XML CDATA section. Represents character-based content within an XML + * document that should be output within special CDATA tags. Semantically it's + * identical to a simple {@link Text} object, but output behavior is different. + * CDATA makes no guarantees about the underlying textual representation of + * character data, but does expose that data as a Java String. + * + * @version $Revision: 1.32 $, $Date: 2007/11/10 05:28:58 $ + * @author Dan Schaffer + * @author Brett McLaughlin + * @author Jason Hunter + * @author Bradley S. Huffman + * @author Victor Toni + */ +public class CDATA extends Text { + + private static final String CVS_ID = + "@(#) $RCSfile: CDATA.java,v $ $Revision: 1.32 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + /** + * This is the protected, no-args constructor standard in all JDOM + * classes. It allows subclassers to get a raw instance with no + * initialization. + */ + protected CDATA() { } + + /** + * This constructor creates a new CDATA node, with the + * supplied string value as it's character content. + * + * @param string the node's character content. + * @throws IllegalDataException if str contains an + * illegal character such as a vertical tab (as determined + * by {@link org.jdom.Verifier#checkCharacterData}) + * or the CDATA end delimiter ]]>. + */ + public CDATA(final String string) { + setText(string); + } + + /** + * This will set the value of this CDATA node. + * + * @param str value for node's content. + * @return the object on which the method was invoked + * @throws IllegalDataException if str contains an + * illegal character such as a vertical tab (as determined + * by {@link org.jdom.Verifier#checkCharacterData}) + * or the CDATA end delimiter ]]>. + */ + public Text setText(final String str) { + // Overrides Text.setText() because this needs to check that CDATA rules + // are enforced. We could have a separate Verifier check for CDATA + // beyond Text and call that alone before super.setText(). + + if (str == null || "".equals(str)) { + value = EMPTY_STRING; + return this; + } + + final String reason = Verifier.checkCDATASection(str); + if (reason != null) { + throw new IllegalDataException(str, "CDATA section", reason); + } + + value = str; + + return this; + } + + /** + * This will append character content to whatever content already + * exists within this CDATA node. + * + * @param str character content to append. + * @throws IllegalDataException if str contains an + * illegal character such as a vertical tab (as determined + * by {@link org.jdom.Verifier#checkCharacterData}) + * or the CDATA end delimiter ]]>. + */ + public void append(final String str) { + // Overrides Text.append(String) because this needs to check that CDATA + // rules are enforced. We could have a separate Verifier check for CDATA + // beyond Text and call that alone before super.setText(). + + if (str == null || "".equals(str)) { + return; + } + + // we need a temp value to ensure that the value is changed _after_ + // validation + final String tmpValue; + if (value == EMPTY_STRING) { + tmpValue = str; + } else { + tmpValue = value + str; + } + + // we have to do late checking since the end of a CDATA section could + // have been created by concating both strings: + // "]" + "]>" + // or + // "]]" + ">" + // TODO: maybe this could be optimized for this two cases + final String reason = Verifier.checkCDATASection(tmpValue); + if (reason != null) { + throw new IllegalDataException(str, "CDATA section", reason); + } + + value = tmpValue; + } + + /** + * This will append the content of another Text node + * to this node. + * + * @param text Text node to append. + */ + public void append(final Text text) { + // Overrides Text.append(Text) because this needs to check that CDATA + // rules are enforced. We could have a separate Verifier check for CDATA + // beyond Text and call that alone before super.setText(). + + if (text == null) { + return; + } + append(text.getText()); + } + + /** + * This returns a String representation of the + * CDATA node, suitable for debugging. If the XML + * representation of the CDATA node is desired, + * either {@link #getText} or + * {@link org.jdom.output.XMLOutputter#output(CDATA, java.io.Writer)} + * should be used. + * + * @return String - information about this node. + */ + public String toString() { + return new StringBuffer(64) + .append("[CDATA: ") + .append(getText()) + .append("]") + .toString(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Comment.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Comment.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,145 @@ +/*-- + + $Id: Comment.java,v 1.33 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * An XML comment. Methods allow the user to get and set the text of the + * comment. + * + * @version $Revision: 1.33 $, $Date: 2007/11/10 05:28:58 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public class Comment extends Content { + + private static final String CVS_ID = + "@(#) $RCSfile: Comment.java,v $ $Revision: 1.33 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + /** Text of the Comment */ + protected String text; + + /** + * Default, no-args constructor for implementations to use if needed. + */ + protected Comment() {} + + /** + * This creates the comment with the supplied text. + * + * @param text String content of comment. + */ + public Comment(String text) { + setText(text); + } + + + /** + * Returns the XPath 1.0 string value of this element, which is the + * text of this comment. + * + * @return the text of this comment + */ + public String getValue() { + return text; + } + + /** + * This returns the textual data within the Comment. + * + * @return String - text of comment. + */ + public String getText() { + return text; + } + + /** + * This will set the value of the Comment. + * + * @param text String text for comment. + * @return Comment - this Comment modified. + * @throws IllegalDataException if the given text is illegal for a + * Comment. + */ + public Comment setText(String text) { + String reason; + if ((reason = Verifier.checkCommentData(text)) != null) { + throw new IllegalDataException(text, "comment", reason); + } + + this.text = text; + return this; + } + + /** + * This returns a String representation of the + * Comment, suitable for debugging. If the XML + * representation of the Comment is desired, + * {@link org.jdom.output.XMLOutputter#outputString(Comment)} + * should be used. + * + * @return String - information about the + * Attribute + */ + public String toString() { + return new StringBuffer() + .append("[Comment: ") + .append(new org.jdom.output.XMLOutputter().outputString(this)) + .append("]") + .toString(); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Content.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Content.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,192 @@ +/*-- + + $Id: Content.java,v 1.6 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.io.*; + +/** + * Superclass for JDOM objects which can be legal child content + * of {@link org.jdom.Parent} nodes. + * + * @see org.jdom.Comment + * @see org.jdom.DocType + * @see org.jdom.Element + * @see org.jdom.EntityRef + * @see org.jdom.Parent + * @see org.jdom.ProcessingInstruction + * @see org.jdom.Text + * + * @author Bradley S. Huffman + * @author Jason Hunter + * @version $Revision: 1.6 $, $Date: 2007/11/10 05:28:58 $ + */ +public abstract class Content implements Cloneable, Serializable { + + protected Parent parent = null; + + protected Content() {} + + /** + * Detaches this child from its parent or does nothing if the child + * has no parent. + * + * @return this child detached + */ + public Content detach() { + if (parent != null) { + parent.removeContent(this); + } + return this; + } + + /** + * Return this child's parent, or null if this child is currently + * not attached. The parent can be either an {@link Element} + * or a {@link Document}. + * + * @return this child's parent or null if none + */ + public Parent getParent() { + return parent; + } + + /** + * A convenience method that returns any parent element for this element, + * or null if the element is unattached or is a root element. This was the + * original behavior of getParent() in JDOM Beta 9 which began returning + * Parent in Beta 10. This method provides a convenient upgrade path for + * JDOM Beta 10 and 1.0 users. + * + * @return the containing Element or null if unattached or a root element + */ + public Element getParentElement() { + Parent parent = getParent(); + return (Element) ((parent instanceof Element) ? parent : null); + } + + /** + * Sets the parent of this Content. The caller is responsible for removing + * any pre-existing parentage. + * + * @param parent new parent element + * @return the target element + */ + protected Content setParent(Parent parent) { + this.parent = parent; + return this; + } + + /** + * Return this child's owning document or null if the branch containing + * this child is currently not attached to a document. + * + * @return this child's owning document or null if none + */ + public Document getDocument() { + if (parent == null) return null; + return parent.getDocument(); + } + + + /** + * Returns the XPath 1.0 string value of this child. + * + * @return xpath string value of this child. + */ + public abstract String getValue(); + + /** + * Returns a deep, unattached copy of this child and its descendants + * detached from any parent or document. + * + * @return a detached deep copy of this child and descendants + */ + public Object clone() { + try { + Content c = (Content)super.clone(); + c.parent = null; + return c; + } catch (CloneNotSupportedException e) { + //Can not happen .... + //e.printStackTrace(); + return null; + } + } + + /** + * This tests for equality of this Content object to the supplied object. + * Content items are considered equal only if they are referentially equal + * (i.e. the same object). User code may choose to compare objects + * based on their properties instead. + * + * @param ob Object to compare to. + * @return boolean - whether the Content is + * equal to the supplied Object. + */ + public final boolean equals(Object ob) { + return (ob == this); + } + + /** + * This returns the hash code for this Content item. + * + * @return int - hash code. + */ + public final int hashCode() { + return super.hashCode(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/ContentList.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/ContentList.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,944 @@ +/*-- + + $Id: ContentList.java,v 1.42 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +import org.jdom.filter.*; + +/** + * A non-public list implementation holding only legal JDOM content, including + * content for Document or Element nodes. Users see this class as a simple List + * implementation. + * + * @see CDATA + * @see Comment + * @see Element + * @see EntityRef + * @see ProcessingInstruction + * @see Text + * + * @version $Revision: 1.42 $, $Date: 2007/11/10 05:28:58 $ + * @author Alex Rosen + * @author Philippe Riand + * @author Bradley S. Huffman + */ +final class ContentList extends AbstractList implements java.io.Serializable { + + private static final String CVS_ID = + "@(#) $RCSfile: ContentList.java,v $ $Revision: 1.42 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + private static final long serialVersionUID = 1L; + + private static final int INITIAL_ARRAY_SIZE = 5; + + /** Our backing list */ + private Content elementData[]; + private int size; + + /** Document or Element this list belongs to */ + private Parent parent; + + /** Force either a Document or Element parent */ + ContentList(Parent parent) { + this.parent = parent; + } + + /** + * Package internal method to support building from sources that are + * 100% trusted. + * + * @param c content to add without any checks + */ + final void uncheckedAddContent(Content c) { + c.parent = parent; + ensureCapacity(size + 1); + elementData[size++] = c; + modCount++; + } + + /** + * Inserts the specified object at the specified position in this list. + * Shifts the object currently at that position (if any) and any + * subsequent objects to the right (adds one to their indices). + * + * @param index The location to set the value to. + * @param obj The object to insert into the list. + * throws IndexOutOfBoundsException if index < 0 || index > size() + */ + public void add(int index, Object obj) { + if (obj == null) { + throw new IllegalAddException("Cannot add null object"); + } + if (obj instanceof String) { // String is OK to add as special case + obj = new Text(obj.toString()); // wrap it as a Content + } + if ((obj instanceof Content)) { + add(index, (Content) obj); + } else { + throw new IllegalAddException("Class " + + obj.getClass().getName() + + " is of unrecognized type and cannot be added"); + } + } + + /** + * @see org.jdom.ContentList#add(int, org.jdom.Content) + */ + private void documentCanContain(int index, Content child) throws IllegalAddException { + if (child instanceof Element) { + if (indexOfFirstElement() >= 0) { + throw new IllegalAddException( + "Cannot add a second root element, only one is allowed"); + } + if (indexOfDocType() > index) { + throw new IllegalAddException( + "A root element cannot be added before the DocType"); + } + } + if (child instanceof DocType) { + if (indexOfDocType() >= 0) { + throw new IllegalAddException( + "Cannot add a second doctype, only one is allowed"); + } + int firstElt = indexOfFirstElement(); + if (firstElt != -1 && firstElt < index) { + throw new IllegalAddException( + "A DocType cannot be added after the root element"); + } + } + if (child instanceof CDATA) { + throw new IllegalAddException("A CDATA is not allowed at the document root"); + } + + if (child instanceof Text) { + throw new IllegalAddException("A Text is not allowed at the document root"); + } + + if (child instanceof EntityRef) { + throw new IllegalAddException("An EntityRef is not allowed at the document root"); + } + } + + private static void elementCanContain(int index, Content child) throws IllegalAddException { + if (child instanceof DocType) { + throw new IllegalAddException( + "A DocType is not allowed except at the document level"); + } + } + + /** + * Check and add the Element to this list at + * the given index. + * + * @param index index where to add Element + * @param child Element to add + */ + void add(int index, Content child) { + if (child == null) { + throw new IllegalAddException("Cannot add null object"); + } + if (parent instanceof Document) { + documentCanContain(index, child); + } + else { + elementCanContain(index, child); + } + + if (child.getParent() != null) { + Parent p = child.getParent(); + if (p instanceof Document) { + throw new IllegalAddException((Element)child, + "The Content already has an existing parent document"); + } + else { + throw new IllegalAddException( + "The Content already has an existing parent \"" + + ((Element)p).getQualifiedName() + "\""); + } + } + + if (child == parent) { + throw new IllegalAddException( + "The Element cannot be added to itself"); + } + + // Detect if we have and c.add(a) + if ((parent instanceof Element && child instanceof Element) && + ((Element) child).isAncestor((Element)parent)) { + throw new IllegalAddException( + "The Element cannot be added as a descendent of itself"); + } + + if (index<0 || index>size) { + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + } + + child.setParent(parent); + + ensureCapacity(size+1); + if( index==size ) { + elementData[size++] = child; + } else { + System.arraycopy(elementData, index, elementData, index + 1, size - index); + elementData[index] = child; + size++; + } + modCount++; + } + + /** + * Add the specified collecton to the end of this list. + * + * @param collection The collection to add to the list. + * @return true if the list was modified as a result of + * the add. + */ + public boolean addAll(Collection collection) { + return addAll(size(), collection); + } + + /** + * Inserts the specified collecton at the specified position in this list. + * Shifts the object currently at that position (if any) and any + * subsequent objects to the right (adds one to their indices). + * + * @param index The offset to start adding the data in the collection + * @param collection The collection to insert into the list. + * @return true if the list was modified as a result of + * the add. + * throws IndexOutOfBoundsException if index < 0 || index > size() + */ + public boolean addAll(int index, Collection collection) { + if (index<0 || index>size) { + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + } + + if ((collection == null) || (collection.size() == 0)) { + return false; + } + ensureCapacity(size() + collection.size()); + + int count = 0; + try { + Iterator i = collection.iterator(); + while (i.hasNext()) { + Object obj = i.next(); + add(index + count, obj); + count++; + } + } + catch (RuntimeException exception) { + for (int i = 0; i < count; i++) { + remove(index); + } + throw exception; + } + + return true; + } + + /** + * Clear the current list. + */ + public void clear() { + if (elementData != null) { + for (int i = 0; i < size; i++) { + Content obj = elementData[i]; + removeParent(obj); + } + elementData = null; + size = 0; + } + modCount++; + } + + /** + * Clear the current list and set it to the contents + * of the Collection. + * object. + * + * @param collection The collection to use. + */ + void clearAndSet(Collection collection) { + Content[] old = elementData; + int oldSize = size; + + elementData = null; + size = 0; + + if ((collection != null) && (collection.size() != 0)) { + ensureCapacity(collection.size()); + try { + addAll(0, collection); + } + catch (RuntimeException exception) { + elementData = old; + size = oldSize; + throw exception; + } + } + + if (old != null) { + for (int i = 0; i < oldSize; i++) { + removeParent(old[i]); + } + } + modCount++; + } + + /** + * Increases the capacity of this ContentList instance, + * if necessary, to ensure that it can hold at least the number of + * items specified by the minimum capacity argument. + * + * @param minCapacity the desired minimum capacity. + */ + void ensureCapacity(int minCapacity) { + if( elementData==null ) { + elementData = new Content[Math.max(minCapacity, INITIAL_ARRAY_SIZE)]; + } else { + int oldCapacity = elementData.length; + if (minCapacity > oldCapacity) { + Object oldData[] = elementData; + int newCapacity = (oldCapacity * 3)/2 + 1; + if (newCapacity < minCapacity) + newCapacity = minCapacity; + elementData = new Content[newCapacity]; + System.arraycopy(oldData, 0, elementData, 0, size); + } + } + } + + /** + * Return the object at the specified offset. + * + * @param index The offset of the object. + * @return The Object which was returned. + */ + public Object get(int index) { + if (index<0 || index>=size) { + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + } + return elementData[index]; + } + + /** + * Return a view of this list based on the given filter. + * + * @param filter Filter for this view. + * @return a list representing the rules of the Filter. + */ + List getView(Filter filter) { + return new FilterList(filter); + } + + /** + * Return the index of the first Element in the list. If the parent + * is a Document then the element is the root element. + * If the list contains no Elements, it returns -1. + * + * @return index of first element, or -1 if one doesn't exist + */ + int indexOfFirstElement() { + if( elementData!=null ) { + for (int i = 0; i < size; i++) { + if (elementData[i] instanceof Element) { + return i; + } + } + } + return -1; + } + + /** + * Return the index of the DocType element in the list. If the list contains + * no DocType, it returns -1. + * + * @return index of the DocType, or -1 if it doesn't + * exist + */ + int indexOfDocType() { + if (elementData != null) { + for (int i = 0; i < size; i++) { + if (elementData[i] instanceof DocType) { + return i; + } + } + } + return -1; + } + + /** + * Remove the object at the specified offset. + * + * @param index The offset of the object. + * @return The Object which was removed. + */ + public Object remove(int index) { + if (index<0 || index>=size) + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + + Content old = elementData[index]; + removeParent(old); + int numMoved = size - index - 1; + if (numMoved > 0) + System.arraycopy(elementData, index+1, elementData, index,numMoved); + elementData[--size] = null; // Let gc do its work + modCount++; + return old; + } + + + /** Remove the parent of a Object */ + private static void removeParent(Content c) { + c.setParent(null); + } + + /** + * Set the object at the specified location to the supplied + * object. + * + * @param index The location to set the value to. + * @param obj The location to set the value to. + * @return The object which was replaced. + * throws IndexOutOfBoundsException if index < 0 || index >= size() + */ + public Object set(int index, Object obj) { + if (index<0 || index>=size) + throw new IndexOutOfBoundsException("Index: " + index + + " Size: " + size()); + + if ((obj instanceof Element) && (parent instanceof Document)) { + int root = indexOfFirstElement(); + if ((root >= 0) && (root != index)) { + throw new IllegalAddException( + "Cannot add a second root element, only one is allowed"); + } + } + + if ((obj instanceof DocType) && (parent instanceof Document)) { + int docTypeIndex = indexOfDocType(); + if ((docTypeIndex >= 0) && (docTypeIndex != index)) { + throw new IllegalAddException( + "Cannot add a second doctype, only one is allowed"); + } + } + + Object old = remove(index); + try { + add(index, obj); + } + catch (RuntimeException exception) { + add(index, old); + throw exception; + } + return old; + } + + /** + * Return the number of items in this list + * + * @return The number of items in this list. + */ + public int size() { + return size; + } + + /** + * Return this list as a String + * + * @return The number of items in this list. + */ + public String toString() { + return super.toString(); + } + + /** Give access of ContentList.modCount to FilterList */ + private int getModCount() { + return modCount; + } + + /* * * * * * * * * * * * * FilterList * * * * * * * * * * * * * * * */ + /* * * * * * * * * * * * * FilterList * * * * * * * * * * * * * * * */ + + /** + * FilterList represents legal JDOM content, including content + * for Documents or Elements. + */ + + class FilterList extends AbstractList implements java.io.Serializable { + + /** The Filter */ + Filter filter; + + /** Current number of items in this view */ + int count = 0; + + /** Expected modCount in our backing list */ + int expected = -1; + + // Implementation Note: Directly after size() is called, expected + // is sync'd with ContentList.modCount and count provides + // the true size of this view. Before the first call to + // size() or if the backing list is modified outside this + // FilterList, both might contain bogus values and should + // not be used without first calling size(); + + /** + * Create a new instance of the FilterList with the specified Filter. + */ + FilterList(Filter filter) { + this.filter = filter; + } + + /** + * Inserts the specified object at the specified position in this list. + * Shifts the object currently at that position (if any) and any + * subsequent objects to the right (adds one to their indices). + * + * @param index The location to set the value to. + * @param obj The object to insert into the list. + * throws IndexOutOfBoundsException if index < 0 || index > size() + */ + public void add(int index, Object obj) { + if (filter.matches(obj)) { + int adjusted = getAdjustedIndex(index); + ContentList.this.add(adjusted, obj); + expected++; + count++; + } + else throw new IllegalAddException("Filter won't allow the " + + obj.getClass().getName() + + " '" + obj + "' to be added to the list"); + } + + /** + * Return the object at the specified offset. + * + * @param index The offset of the object. + * @return The Object which was returned. + */ + public Object get(int index) { + int adjusted = getAdjustedIndex(index); + return ContentList.this.get(adjusted); + } + + public Iterator iterator() { + return new FilterListIterator(filter, 0); + } + + public ListIterator listIterator() { + return new FilterListIterator(filter, 0); + } + + public ListIterator listIterator(int index) { + return new FilterListIterator(filter, index); + } + + /** + * Remove the object at the specified offset. + * + * @param index The offset of the object. + * @return The Object which was removed. + */ + public Object remove(int index) { + int adjusted = getAdjustedIndex(index); + Object old = ContentList.this.get(adjusted); + if (filter.matches(old)) { + old = ContentList.this.remove(adjusted); + expected++; + count--; + } + else { + throw new IllegalAddException("Filter won't allow the " + + (old.getClass()).getName() + + " '" + old + "' (index " + index + + ") to be removed"); + } + return old; + } + + /** + * Set the object at the specified location to the supplied + * object. + * + * @param index The location to set the value to. + * @param obj The location to set the value to. + * @return The object which was replaced. + * throws IndexOutOfBoundsException if index < 0 || index >= size() + */ + public Object set(int index, Object obj) { + Object old = null; + if (filter.matches(obj)) { + int adjusted = getAdjustedIndex(index); + old = ContentList.this.get(adjusted); + if (!filter.matches(old)) { + throw new IllegalAddException("Filter won't allow the " + + (old.getClass()).getName() + + " '" + old + "' (index " + index + + ") to be removed"); + } + old = ContentList.this.set(adjusted, obj); + expected += 2; + } + else { + throw new IllegalAddException("Filter won't allow index " + + index + " to be set to " + + (obj.getClass()).getName()); + } + return old; + } + + /** + * Return the number of items in this list + * + * @return The number of items in this list. + */ + public int size() { + // Implementation Note: Directly after size() is called, expected + // is sync'd with ContentList.modCount and count provides + // the true size of this view. Before the first call to + // size() or if the backing list is modified outside this + // FilterList, both might contain bogus values and should + // not be used without first calling size(); + + if (expected == ContentList.this.getModCount()) { + return count; + } + + count = 0; + for (int i = 0; i < ContentList.this.size(); i++) { + Object obj = ContentList.this.elementData[i]; + if (filter.matches(obj)) { + count++; + } + } + expected = ContentList.this.getModCount(); + return count; + } + + /** + * Return the adjusted index + * + * @param index Index of in this view. + * @return True index in backing list + */ + final private int getAdjustedIndex(int index) { + int adjusted = 0; + for (int i = 0; i < ContentList.this.size; i++) { + Object obj = ContentList.this.elementData[i]; + if (filter.matches(obj)) { + if (index == adjusted) { + return i; + } + adjusted++; + } + } + + if (index == adjusted) { + return ContentList.this.size; + } + + return ContentList.this.size + 1; + } + } + + /* * * * * * * * * * * * * FilterListIterator * * * * * * * * * * * */ + /* * * * * * * * * * * * * FilterListIterator * * * * * * * * * * * */ + + class FilterListIterator implements ListIterator { + + /** The Filter that applies */ + Filter filter; + + /** Whether this iterator is in forward or reverse. */ + private boolean forward = false; + /** Whether a call to remove() is valid */ + private boolean canremove = false; + /** Whether a call to set() is valid */ + private boolean canset = false; + + /** Index in backing list of next object */ + private int cursor = -1; + /** the backing index to use if we actually DO move */ + private int tmpcursor = -1; + /** Index in ListIterator */ + private int index = -1; + + /** Expected modCount in our backing list */ + private int expected = -1; + + /** Number of elements matching the filter. */ + private int fsize = 0; + + /** + * Default constructor + */ + FilterListIterator(Filter filter, int start) { + this.filter = filter; + expected = ContentList.this.getModCount(); + // always start list iterators in backward mode .... + // it makes sense... really. + forward = false; + + if (start < 0) { + throw new IndexOutOfBoundsException("Index: " + start); + } + + // the number of matching elements.... + fsize = 0; + + // go through the list, count the matching elements... + for (int i = 0; i < ContentList.this.size(); i++) { + if (filter.matches(ContentList.this.get(i))) { + if (start == fsize) { + // set the back-end cursor to the matching element.... + cursor = i; + // set the front-end cursor too. + index = fsize; + } + fsize++; + } + } + + if (start > fsize) { + throw new IndexOutOfBoundsException("Index: " + start + " Size: " + fsize); + } + if (cursor == -1) { + // implies that start == fsize (i.e. after the last element + // put the insertion point at the end of the Underlying + // content list .... + // i.e. an add() at this point may potentially end up with + // filtered content between previous() and next() + // the alternative is to put the cursor on the Content after + // the last Content that the filter passed + // The implications are ambiguous. + cursor = ContentList.this.size(); + index = fsize; + } + + } + + /** + * Returns true if this list iterator has a next element. + */ + public boolean hasNext() { + return nextIndex() < fsize; + } + + /** + * Returns the next element in the list. + */ + public Object next() { + if (!hasNext()) + throw new NoSuchElementException("next() is beyond the end of the Iterator"); + index = nextIndex(); + cursor = tmpcursor; + forward = true; + canremove = true; + canset = true; + return ContentList.this.get(cursor); + } + + /** + * Returns true if this list iterator has more elements + * when traversing the list in the reverse direction. + */ + public boolean hasPrevious() { + return previousIndex() >= 0; + } + + /** + * Returns the previous element in the list. + */ + public Object previous() { + if (!hasPrevious()) + throw new NoSuchElementException("previous() is before the start of the Iterator"); + index = previousIndex(); + cursor = tmpcursor; + forward = false; + canremove = true; + canset = true; + return ContentList.this.get(cursor); + } + + /** + * Returns the index of the element that would be returned by a + * subsequent call to next. + */ + public int nextIndex() { + checkConcurrentModification(); + if (forward) { + // Starting with next possibility .... + for (int i = cursor + 1; i < ContentList.this.size(); i++) { + if (filter.matches(ContentList.this.get(i))) { + tmpcursor = i; + return index + 1; + } + } + // Never found another match.... put the insertion point at + // the end of the list.... + tmpcursor = ContentList.this.size(); + return index + 1; + } + + // We've been going back... so nextIndex() returns the same + // element. + tmpcursor = cursor; + return index; + } + + /** + * Returns the index of the element that would be returned by a + * subsequent call to previous. (Returns -1 if the + * list iterator is at the beginning of the list.) + */ + public int previousIndex() { + checkConcurrentModification(); + if (!forward) { + // starting with next possibility .... + for (int i = cursor - 1; i >= 0; i--) { + if (filter.matches(ContentList.this.get(i))) { + tmpcursor = i; + return index - 1; + } + } + // Never found another match.... put the insertion point at + // the start of the list.... + tmpcursor = -1; + return index - 1; + } + + // We've been going forwards... so previousIndex() returns same + // element. + tmpcursor = cursor; + return index; + } + + /** + * Inserts the specified element into the list. + */ + public void add(Object obj) { + // Call to nextIndex() will check concurrent. + nextIndex(); + // tmpcursor is the backing cursor of the next element + // Remember that List.add(index,obj) is really an insert.... + ContentList.this.add(tmpcursor, obj); + forward = true; + expected = ContentList.this.getModCount(); + canremove = canset = false; + index = nextIndex(); + cursor = tmpcursor; + fsize++; + } + + /** + * Removes from the list the last element that was returned by + * the last call to next or previous. + */ + public void remove() { + if (!canremove) + throw new IllegalStateException("Can not remove an " + + "element unless either next() or previous() has been called " + + "since the last remove()"); + nextIndex(); // to get out cursor ... + ContentList.this.remove(cursor); + cursor = tmpcursor - 1; + expected = ContentList.this.getModCount(); + + forward = false; + canremove = false; + canset = false; + fsize--; + } + + /** + * Replaces the last element returned by next or + * previous with the specified element. + */ + public void set(Object obj) { + if (!canset) + throw new IllegalStateException("Can not set an element " + + "unless either next() or previous() has been called since the " + + "last remove() or set()"); + checkConcurrentModification(); + + if (!filter.matches(obj)) { + throw new IllegalAddException("Filter won't allow index " + index + " to be set to " + + (obj.getClass()).getName()); + } + + ContentList.this.set(cursor, obj); + expected = ContentList.this.getModCount(); + + } + + /** + * Check if are backing list is being modified by someone else. + */ + private void checkConcurrentModification() { + if (expected != ContentList.this.getModCount()) { + throw new ConcurrentModificationException(); + } + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/DataConversionException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/DataConversionException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,87 @@ +/*-- + + $Id: DataConversionException.java,v 1.14 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * Thrown when a data conversion from a string to value type fails, such as + * can happen with the {@link Attribute} convenience getter functions. + * + * @version $Revision: 1.14 $, $Date: 2007/11/10 05:28:58 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public class DataConversionException extends JDOMException { + + private static final String CVS_ID = + "@(#) $RCSfile: DataConversionException.java,v $ $Revision: 1.14 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + /** + * Constructs an exception where the named construct couldn't be converted + * to the named data type. + * + * @param name name of the construct whose value failed conversion + * @param dataType type the conversion was attempting to create + */ + public DataConversionException(String name, String dataType) { + super(new StringBuffer() + .append("The XML construct ") + .append(name) + .append(" could not be converted to a ") + .append(dataType) + .toString()); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/DefaultJDOMFactory.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/DefaultJDOMFactory.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,191 @@ +/*-- + + $Id: DefaultJDOMFactory.java,v 1.7 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +/** + * Creates the standard top-level JDOM classes (Element, Document, Comment, + * etc). A subclass of this factory might construct custom classes. + * + * @version $Revision: 1.7 $, $Date: 2007/11/10 05:28:58 $ + * @author Ken Rune Holland + * @author Phil Nelson + * @author Bradley S. Huffman + */ +public class DefaultJDOMFactory implements JDOMFactory { + + private static final String CVS_ID = + "@(#) $RCSfile: DefaultJDOMFactory.java,v $ $Revision: 1.7 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + public DefaultJDOMFactory() { } + + // Allow Javadocs to inherit from JDOMFactory + + public Attribute attribute(String name, String value, Namespace namespace) { + return new Attribute(name, value, namespace); + } + + public Attribute attribute(String name, String value, + int type, Namespace namespace) { + return new Attribute(name, value, type, namespace); + } + + public Attribute attribute(String name, String value) { + return new Attribute(name, value); + } + + public Attribute attribute(String name, String value, int type) { + return new Attribute(name, value, type); + } + + public CDATA cdata(String text) { + return new CDATA(text); + } + + public Text text(String text) { + return new Text(text); + } + + public Comment comment(String text) { + return new Comment(text); + } + + public DocType docType(String elementName, + String publicID, String systemID) { + return new DocType(elementName, publicID, systemID); + } + + public DocType docType(String elementName, String systemID) { + return new DocType(elementName, systemID); + } + + public DocType docType(String elementName) { + return new DocType(elementName); + } + + public Document document(Element rootElement, DocType docType) { + return new Document(rootElement, docType); + } + + public Document document(Element rootElement, DocType docType, String baseURI) { + return new Document(rootElement, docType, baseURI); + } + + public Document document(Element rootElement) { + return new Document(rootElement); + } + + public Element element(String name, Namespace namespace) { + return new Element(name, namespace); + } + + public Element element(String name) { + return new Element(name); + } + + public Element element(String name, String uri) { + return new Element(name, uri); + } + + public Element element(String name, String prefix, String uri) { + return new Element(name, prefix, uri); + } + + public ProcessingInstruction processingInstruction(String target, + Map data) { + return new ProcessingInstruction(target, data); + } + + public ProcessingInstruction processingInstruction(String target, + String data) { + return new ProcessingInstruction(target, data); + } + + public EntityRef entityRef(String name) { + return new EntityRef(name); + } + + public EntityRef entityRef(String name, String publicID, String systemID) { + return new EntityRef(name, publicID, systemID); + } + + public EntityRef entityRef(String name, String systemID) { + return new EntityRef(name, systemID); + } + + // ===================================================================== + // List manipulation + // ===================================================================== + + public void addContent(Parent parent, Content child) { + if (parent instanceof Document) { + ((Document) parent).addContent(child); + } + else { + ((Element) parent).addContent(child); + } + } + + public void setAttribute(Element parent, Attribute a) { + parent.setAttribute(a); + } + + public void addNamespaceDeclaration(Element parent, Namespace additional) { + parent.addNamespaceDeclaration(additional); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/DescendantIterator.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/DescendantIterator.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,173 @@ +/*-- + + $Id: DescendantIterator.java,v 1.6 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; +import org.jdom.Content; +import org.jdom.Element; +import org.jdom.Parent; + +/** + * Traverse all a parent's descendants (all children at any level below + * the parent). + * + * @author Bradley S. Huffman + * @author Jason Hunter + * @version $Revision: 1.6 $, $Date: 2007/11/10 05:28:58 $ + */ +class DescendantIterator implements Iterator { + + private Iterator iterator; + private Iterator nextIterator; + private List stack = new ArrayList(); + + private static final String CVS_ID = + "@(#) $RCSfile: DescendantIterator.java,v $ $Revision: 1.6 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + /** + * Iterator for the descendants of the supplied object. + * + * @param parent document or element whose descendants will be iterated + */ + DescendantIterator(Parent parent) { + if (parent == null) { + throw new IllegalArgumentException("parent parameter was null"); + } + this.iterator = parent.getContent().iterator(); + } + + /** + * Returns true> if the iteration has more {@link Content} descendants. + * + * @return true is the iterator has more descendants + */ + public boolean hasNext() { + if (iterator != null && iterator.hasNext()) return true; + if (nextIterator != null && nextIterator.hasNext()) return true; + if (stackHasAnyNext()) return true; + return false; + } + + /** + * Returns the next {@link Content} descendant. + * + * @return the next descendant + */ + public Object next() { + if (!hasNext()) { + throw new NoSuchElementException(); + } + + // If we need to descend, go for it and record where we are. + // We do the shuffle here on the next next() call so remove() is easy + // to code up. + if (nextIterator != null) { + push(iterator); + iterator = nextIterator; + nextIterator = null; + } + + // If this iterator is finished, try moving up the stack + while (!iterator.hasNext()) { + if (stack.size() > 0) { + iterator = pop(); + } + else { + throw new NoSuchElementException("Somehow we lost our iterator"); + } + } + + Content child = (Content) iterator.next(); + if (child instanceof Element) { + nextIterator = ((Element)child).getContent().iterator(); + } + return child; + } + + /** + * Detaches the last {@link org.jdom.Content} returned by the last call to + * next from it's parent. Note: this does not affect + * iteration and all children, siblings, and any node following the + * removed node (in document order) will be visited. + */ + public void remove() { + iterator.remove(); + } + + private Iterator pop() { + int stackSize = stack.size(); + if (stackSize == 0) { + throw new NoSuchElementException("empty stack"); + } + return (Iterator) stack.remove(stackSize - 1); + } + + private void push(Iterator itr) { + stack.add(itr); + } + + private boolean stackHasAnyNext() { + int size = stack.size(); + for (int i = 0; i < size; i++) { + Iterator itr = (Iterator) stack.get(i); + if (itr.hasNext()) { + return true; + } + } + return false; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/DocType.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/DocType.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,280 @@ +/*-- + + $Id: DocType.java,v 1.32 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * An XML DOCTYPE declaration. Method allow the user to get and set the + * root element name, public id, and system id. + * + * @author Brett McLaughlin + * @author Jason Hunter + * @version $Revision: 1.32 $, $Date: 2007/11/10 05:28:58 $ + */ +public class DocType extends Content { + + private static final String CVS_ID = + "@(#) $RCSfile: DocType.java,v $ $Revision: 1.32 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + /** The element being constrained */ + protected String elementName; + + /** The public ID of the DOCTYPE */ + protected String publicID; + + /** The system ID of the DOCTYPE */ + protected String systemID; + + /** The internal subset of the DOCTYPE */ + protected String internalSubset; + + /** + * Default, no-args constructor for implementations to use if needed. + */ + protected DocType() {} + + /* + * XXX: + * We need to take care of entities and notations here. + */ + + /** + * This will create the DocType with + * the specified element name and a reference to an + * external DTD. + * + * @param elementName String name of + * element being constrained. + * @param publicID String public ID of + * referenced DTD + * @param systemID String system ID of + * referenced DTD + * @throws IllegalDataException if the given system ID is not a legal + * system literal or the public ID is not a legal public ID. + * @throws IllegalNameException if the given root element name is not a + * legal XML element name. + */ + public DocType(String elementName, String publicID, String systemID) { + setElementName(elementName); + setPublicID(publicID); + setSystemID(systemID); + } + + /** + * This will create the DocType with + * the specified element name and reference to an + * external DTD. + * + * @param elementName String name of + * element being constrained. + * @param systemID String system ID of + * referenced DTD + * @throws IllegalDataException if the given system ID is not a legal + * system literal. + * @throws IllegalNameException if the given root element name is not a + * legal XML element name. + */ + public DocType(String elementName, String systemID) { + this(elementName, null, systemID); + } + + /** + * This will create the DocType with + * the specified element name + * + * @param elementName String name of + * element being constrained. + * @throws IllegalNameException if the given root element name is not a + * legal XML element name. + */ + public DocType(String elementName) { + this(elementName, null, null); + } + + /** + * This will retrieve the element name being constrained. + * + * @return String - element name for DOCTYPE + */ + public String getElementName() { + return elementName; + } + + /** + * This will set the root element name declared by this + * DOCTYPE declaration. + * + * @return DocType DocType this DocType object + * @param elementName String name of + * root element being constrained. + * @throws IllegalNameException if the given root element name is not a + * legal XML element name. + */ + public DocType setElementName(String elementName) { + // This can contain a colon so we use checkXMLName() + // instead of checkElementName() + String reason = Verifier.checkXMLName(elementName); + if (reason != null) { + throw new IllegalNameException(elementName, "DocType", reason); + } + this.elementName = elementName; + return this; + } + + /** + * This will retrieve the public ID of an externally + * referenced DTD, or an empty String if + * none is referenced. + * + * @return String - public ID of referenced DTD. + */ + public String getPublicID() { + return publicID; + } + + /** + * This will set the public ID of an externally + * referenced DTD. + * + * @param publicID id to set + * @return DocType DocType this DocType object + * @throws IllegalDataException if the given public ID is not a legal + * public ID. + */ + public DocType setPublicID(String publicID) { + String reason = Verifier.checkPublicID(publicID); + if (reason != null) { + throw new IllegalDataException(publicID, "DocType", reason); + } + this.publicID = publicID; + + return this; + } + + /** + * This will retrieve the system ID of an externally + * referenced DTD, or an empty String if + * none is referenced. + * + * @return String - system ID of referenced DTD. + */ + public String getSystemID() { + return systemID; + } + + /** + * This will set the system ID of an externally + * referenced DTD. + * + * @param systemID id to set + * @return systemID String system ID of + * referenced DTD. + * @throws IllegalDataException if the given system ID is not a legal + * system literal. + */ + public DocType setSystemID(String systemID) { + String reason = Verifier.checkSystemLiteral(systemID); + if (reason != null) { + throw new IllegalDataException(systemID, "DocType", reason); + } + this.systemID = systemID; + + return this; + } + + /** + * Returns the empty string since doctypes don't have an XPath + * 1.0 string value. + * @return the empty string + */ + public String getValue() { + return ""; // doctypes don't have an XPath string value + } + + /** + * This sets the data for the internal subset. + * + * @param newData data for the internal subset, as a + * String. + */ + public void setInternalSubset(String newData) { + internalSubset = newData; + } + + /** + * This returns the data for the internal subset. + * + * @return String - the internal subset + */ + public String getInternalSubset() { + return internalSubset; + } + + /** + * This returns a String representation of the + * DocType, suitable for debugging. + * + * @return String - information about the + * DocType + */ + public String toString() { + return new StringBuffer() + .append("[DocType: ") + .append(new org.jdom.output.XMLOutputter().outputString(this)) + .append("]") + .toString(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Document.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Document.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,767 @@ +/*-- + + $Id: Document.java,v 1.85 2007/11/10 05:28:58 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; +import org.jdom.filter.*; + +/** + * An XML document. Methods allow access to the root element as well as the + * {@link DocType} and other document-level information. + * + * @version $Revision: 1.85 $, $Date: 2007/11/10 05:28:58 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Jools Enticknap + * @author Bradley S. Huffman + */ +public class Document implements Parent { + + private static final String CVS_ID = + "@(#) $RCSfile: Document.java,v $ $Revision: 1.85 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $"; + + /** + * This document's content including comments, PIs, a possible + * DocType, and a root element. + * Subclassers have to track content using their own + * mechanism. + */ + ContentList content = new ContentList(this); + + /** + * See http://www.w3.org/TR/2003/WD-DOM-Level-3-Core-20030226/core.html#baseURIs-Considerations + */ + protected String baseURI = null; + + // Supports the setProperty/getProperty calls + private HashMap propertyMap = null; + + /** + * Creates a new empty document. A document must have a root element, + * so this document will not be well-formed and accessor methods will + * throw an IllegalStateException if this document is accessed before a + * root element is added. This method is most useful for build tools. + */ + public Document() {} + + /** + * This will create a new Document, + * with the supplied {@link Element} + * as the root element, the supplied + * {@link DocType} declaration, and the specified + * base URI. + * + * @param rootElement Element for document root. + * @param docType DocType declaration. + * @param baseURI the URI from which this doucment was loaded. + * @throws IllegalAddException if the given docType object + * is already attached to a document or the given + * rootElement already has a parent + */ + public Document(Element rootElement, DocType docType, String baseURI) { + if (rootElement != null) { + setRootElement(rootElement); + } + if (docType != null) { + setDocType(docType); + } + if (baseURI != null) { + setBaseURI(baseURI); + } + } + + /** + * This will create a new Document, + * with the supplied {@link Element} + * as the root element and the supplied + * {@link DocType} declaration. + * + * @param rootElement Element for document root. + * @param docType DocType declaration. + * @throws IllegalAddException if the given DocType object + * is already attached to a document or the given + * rootElement already has a parent + */ + public Document(Element rootElement, DocType docType) { + this(rootElement, docType, null); + } + + /** + * This will create a new Document, + * with the supplied {@link Element} + * as the root element, and no {@link DocType} + * declaration. + * + * @param rootElement Element for document root + * @throws IllegalAddException if the given rootElement already has + * a parent. + */ + public Document(Element rootElement) { + this(rootElement, null, null); + } + + /** + * This will create a new Document, + * with the supplied list of content, and a + * {@link DocType} declaration only if the content + * contains a DocType instance. A null list is treated the + * same as the no-arg constructor. + * + * @param content List of starter content + * @throws IllegalAddException if the List contains more than + * one Element or objects of illegal types. + */ + public Document(List content) { + setContent(content); + } + + public int getContentSize() { + return content.size(); + } + + public int indexOf(Content child) { + return content.indexOf(child); + } + +// /** +// * Starting at the given index (inclusive), return the index of +// * the first child matching the supplied filter, or -1 +// * if none is found. +// * +// * @return index of child, or -1 if none found. +// */ +// private int indexOf(int start, Filter filter) { +// int size = getContentSize(); +// for (int i = start; i < size; i++) { +// if (filter.matches(getContent(i))) { +// return i; +// } +// } +// return -1; +// } + + /** + * This will return true if this document has a + * root element, false otherwise. + * + * @return true if this document has a root element, + * false otherwise. + */ + public boolean hasRootElement() { + return (content.indexOfFirstElement() < 0) ? false : true; + } + + /** + * This will return the root Element + * for this Document + * + * @return Element - the document's root element + * @throws IllegalStateException if the root element hasn't been set + */ + public Element getRootElement() { + int index = content.indexOfFirstElement(); + if (index < 0) { + throw new IllegalStateException("Root element not set"); + } + return (Element) content.get(index); + } + + /** + * This sets the root {@link Element} for the + * Document. If the document already has a root + * element, it is replaced. + * + * @param rootElement Element to be new root. + * @return Document - modified Document. + * @throws IllegalAddException if the given rootElement already has + * a parent. + */ + public Document setRootElement(Element rootElement) { + int index = content.indexOfFirstElement(); + if (index < 0) { + content.add(rootElement); + } + else { + content.set(index, rootElement); + } + return this; + } + + /** + * Detach the root {@link Element} from this document. + * + * @return removed root Element + */ + public Element detachRootElement() { + int index = content.indexOfFirstElement(); + if (index < 0) + return null; + return (Element) removeContent(index); + } + + /** + * This will return the {@link DocType} + * declaration for this Document, or + * null if none exists. + * + * @return DocType - the DOCTYPE declaration. + */ + public DocType getDocType() { + int index = content.indexOfDocType(); + if (index < 0) { + return null; + } + else { + return (DocType) content.get(index); + } + } + + /** + * This will set the {@link DocType} + * declaration for this Document. Note + * that a DocType can only be attached to one Document. + * Attempting to set the DocType to a DocType object + * that already belongs to a Document will result in an + * IllegalAddException being thrown. + * + * @param docType DocType declaration. + * @return object on which the method was invoked + * @throws IllegalAddException if the given docType is + * already attached to a Document. + */ + public Document setDocType(DocType docType) { + if (docType == null) { + // Remove any existing doctype + int docTypeIndex = content.indexOfDocType(); + if (docTypeIndex >= 0) content.remove(docTypeIndex); + return this; + } + + if (docType.getParent() != null) { + throw new IllegalAddException(docType, + "The DocType already is attached to a document"); + } + + // Add DocType to head if new, replace old otherwise + int docTypeIndex = content.indexOfDocType(); + if (docTypeIndex < 0) { + content.add(0, docType); + } + else { + content.set(docTypeIndex, docType); + } + + return this; + } + + /** + * Appends the child to the end of the content list. + * + * @param child child to append to end of content list + * @return the document on which the method was called + * @throws IllegalAddException if the given child already has a parent. + */ + public Document addContent(Content child) { + content.add(child); + return this; + } + + /** + * Appends all children in the given collection to the end of + * the content list. In event of an exception during add the + * original content will be unchanged and the objects in the supplied + * collection will be unaltered. + * + * @param c collection to append + * @return the document on which the method was called + * @throws IllegalAddException if any item in the collection + * already has a parent or is of an illegal type. + */ + public Document addContent(Collection c) { + content.addAll(c); + return this; + } + + /** + * Inserts the child into the content list at the given index. + * + * @param index location for adding the collection + * @param child child to insert + * @return the parent on which the method was called + * @throws IndexOutOfBoundsException if index is negative or beyond + * the current number of children + * @throws IllegalAddException if the given child already has a parent. + */ + public Document addContent(int index, Content child) { + content.add(index, child); + return this; + } + + /** + * Inserts the content in a collection into the content list + * at the given index. In event of an exception the original content + * will be unchanged and the objects in the supplied collection will be + * unaltered. + * + * @param index location for adding the collection + * @param c collection to insert + * @return the parent on which the method was called + * @throws IndexOutOfBoundsException if index is negative or beyond + * the current number of children + * @throws IllegalAddException if any item in the collection + * already has a parent or is of an illegal type. + */ + public Document addContent(int index, Collection c) { + content.addAll(index, c); + return this; + } + + public List cloneContent() { + int size = getContentSize(); + List list = new ArrayList(size); + for (int i = 0; i < size; i++) { + Content child = getContent(i); + list.add(child.clone()); + } + return list; + } + + public Content getContent(int index) { + return (Content) content.get(index); + } + +// public Content getChild(Filter filter) { +// int i = indexOf(0, filter); +// return (i < 0) ? null : getContent(i); +// } + + /** + * This will return all content for the Document. + * The returned list is "live" in document order and changes to it + * affect the document's actual content. + * + *

+ * Sequential traversal through the List is best done with a Iterator + * since the underlying implement of List.size() may require walking the + * entire list. + *

+ * + * @return List - all Document content + * @throws IllegalStateException if the root element hasn't been set + */ + public List getContent() { + if (!hasRootElement()) + throw new IllegalStateException("Root element not set"); + return content; + } + + /** + * Return a filtered view of this Document's content. + * + *

+ * Sequential traversal through the List is best done with a Iterator + * since the underlying implement of List.size() may require walking the + * entire list. + *

+ * + * @param filter Filter to apply + * @return List - filtered Document content + * @throws IllegalStateException if the root element hasn't been set + */ + public List getContent(Filter filter) { + if (!hasRootElement()) + throw new IllegalStateException("Root element not set"); + return content.getView(filter); + } + + /** + * Removes all child content from this parent. + * + * @return list of the old children detached from this parent + */ + public List removeContent() { + List old = new ArrayList(content); + content.clear(); + return old; + } + + /** + * Remove all child content from this parent matching the supplied filter. + * + * @param filter filter to select which content to remove + * @return list of the old children detached from this parent + */ + public List removeContent(Filter filter) { + List old = new ArrayList(); + Iterator itr = content.getView(filter).iterator(); + while (itr.hasNext()) { + Content child = (Content) itr.next(); + old.add(child); + itr.remove(); + } + return old; + } + + /** + * This sets the content of the Document. The supplied + * List should contain only objects of type Element, + * Comment, and ProcessingInstruction. + * + *

+ * When all objects in the supplied List are legal and before the new + * content is added, all objects in the old content will have their + * parentage set to null (no parent) and the old content list will be + * cleared. This has the effect that any active list (previously obtained + * with a call to {@link #getContent}) will also + * change to reflect the new content. In addition, all objects in the + * supplied List will have their parentage set to this document, but the + * List itself will not be "live" and further removals and additions will + * have no effect on this document content. If the user wants to continue + * working with a "live" list, then a call to setContent should be + * followed by a call to {@link #getContent} to + * obtain a "live" version of the content. + *

+ * + *

+ * Passing a null or empty List clears the existing content. + *

+ * + *

+ * In event of an exception the original content will be unchanged and + * the objects in the supplied content will be unaltered. + *

+ * + * @param newContent List of content to set + * @return this document modified + * @throws IllegalAddException if the List contains objects of + * illegal types or with existing parentage. + */ + public Document setContent(Collection newContent) { + content.clearAndSet(newContent); + return this; + } + + /** + * + *

+ * Sets the effective URI from which this document was loaded, + * and against which relative URLs in this document will be resolved. + *

+ * + * @param uri the base URI of this document + */ + public final void setBaseURI(String uri) { + this.baseURI = uri; // XXX We don't check the URI + } + + /** + *

+ * Returns the URI from which this document was loaded, + * or null if this is not known. + *

+ * + * @return the base URI of this document + */ + public final String getBaseURI() { + return baseURI; + } + + /* + * Replace the current child the given index with the supplied child. + *

+ * In event of an exception the original content will be unchanged and + * the supplied child will be unaltered. + *

+ * + * @param index - index of child to replace. + * @param child - child to add. + * @throws IllegalAddException if the supplied child is already attached + * or not legal content for this parent. + * @throws IndexOutOfBoundsException if index is negative or greater + * than the current number of children. + */ + public Document setContent(int index, Content child) { + content.set(index, child); + return this; + } + + /** + * Replace the child at the given index whith the supplied + * collection. + *

+ * In event of an exception the original content will be unchanged and + * the content in the supplied collection will be unaltered. + *

+ * + * @param index - index of child to replace. + * @param collection - collection of content to add. + * @return object on which the method was invoked + * @throws IllegalAddException if the collection contains objects of + * illegal types. + * @throws IndexOutOfBoundsException if index is negative or greater + * than the current number of children. + */ + public Document setContent(int index, Collection collection) { + content.remove(index); + content.addAll(index, collection); + return this; + } + + public boolean removeContent(Content child) { + return content.remove(child); + } + + public Content removeContent(int index) { + return (Content) content.remove(index); + } + + /** + * Set this document's content to be the supplied child. + *

+ * If the supplied child is legal content for a Document and before + * it is added, all content in the current content list will + * be cleared and all current children will have their parentage set to + * null. + *

+ * This has the effect that any active list (previously obtained with + * a call to one of the {@link #getContent} methods will also change + * to reflect the new content. In addition, all content in the supplied + * collection will have their parentage set to this Document. If the user + * wants to continue working with a "live" list of this Document's + * child, then a call to setContent should be followed by a call to one + * of the {@link #getContent} methods to obtain a "live" + * version of the children. + *

+ * Passing a null child clears the existing content. + *

+ * In event of an exception the original content will be unchanged and + * the supplied child will be unaltered. + * + * @param child new content to replace existing content + * @return the parent on which the method was called + * @throws IllegalAddException if the supplied child is already attached + * or not legal content for this parent + */ + public Document setContent(Content child) { + content.clear(); + content.add(child); + return this; + } + + /** + * This returns a String representation of the + * Document, suitable for debugging. If the XML + * representation of the Document is desired, + * {@link org.jdom.output.XMLOutputter#outputString(Document)} + * should be used. + * + * @return String - information about the + * Document + */ + public String toString() { + StringBuffer stringForm = new StringBuffer() + .append("[Document: "); + + DocType docType = getDocType(); + if (docType != null) { + stringForm.append(docType.toString()) + .append(", "); + } else { + stringForm.append(" No DOCTYPE declaration, "); + } + + Element rootElement = getRootElement(); + if (rootElement != null) { + stringForm.append("Root is ") + .append(rootElement.toString()); + } else { + stringForm.append(" No root element"); // shouldn't happen + } + + stringForm.append("]"); + + return stringForm.toString(); + } + + /** + * This tests for equality of this Document to the supplied + * Object. + * + * @param ob Object to compare to + * @return boolean whether the Document is + * equal to the supplied Object + */ + public final boolean equals(Object ob) { + return (ob == this); + } + + /** + * This returns the hash code for this Document. + * + * @return int hash code + */ + public final int hashCode() { + return super.hashCode(); + } + + /** + * This will return a deep clone of this Document. + * + * @return Object clone of this Document + */ + public Object clone() { + Document doc = null; + + try { + doc = (Document) super.clone(); + } catch (CloneNotSupportedException ce) { + // Can't happen + } + + // The clone has a reference to this object's content list, so + // owerwrite with a empty list + doc.content = new ContentList(doc); + + // Add the cloned content to clone + + for (int i = 0; i < content.size(); i++) { + Object obj = content.get(i); + if (obj instanceof Element) { + Element element = (Element)((Element)obj).clone(); + doc.content.add(element); + } + else if (obj instanceof Comment) { + Comment comment = (Comment)((Comment)obj).clone(); + doc.content.add(comment); + } + else if (obj instanceof ProcessingInstruction) { + ProcessingInstruction pi = (ProcessingInstruction) + ((ProcessingInstruction)obj).clone(); + doc.content.add(pi); + } + else if (obj instanceof DocType) { + DocType dt = (DocType) ((DocType)obj).clone(); + doc.content.add(dt); + } + } + + return doc; + } + + /** + * Returns an iterator that walks over all descendants in document order. + * + * @return an iterator to walk descendants + */ + public Iterator getDescendants() { + return new DescendantIterator(this); + } + + /** + * Returns an iterator that walks over all descendants in document order + * applying the Filter to return only elements that match the filter rule. + * With filters you can match only Elements, only Comments, Elements or + * Comments, only Elements with a given name and/or prefix, and so on. + * + * @param filter filter to select which descendants to see + * @return an iterator to walk descendants within a filter + */ + public Iterator getDescendants(Filter filter) { + return new FilterIterator(new DescendantIterator(this), filter); + } + + public Parent getParent() { + return null; // documents never have parents + } + + + + /** + * @see org.jdom.Parent#getDocument() + */ + public Document getDocument() { + return this; + } + + /** + * Assigns an arbitrary object to be associated with this document under + * the given "id" string. Null values are permitted. Strings beginning + * with "http://www.jdom.org/ are reserved for JDOM use. + * + * @param id the id of the stored object + * @param value the object to store + */ + public void setProperty(String id, Object value) { + if (propertyMap == null) { + propertyMap = new HashMap(); + } + propertyMap.put(id, value); + } + + /** + * Returns the object associated with this document under the given "id" + * string, or null if there is no binding or if the binding explicitly + * stored a null value. + * + * @param id the id of the stored object to return + * @return the object associated with the given id + */ + public Object getProperty(String id) { + if (propertyMap == null) return null; + return propertyMap.get(id); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Element.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Element.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,1564 @@ +/*-- + + $Id: Element.java,v 1.159 2007/11/14 05:02:08 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.io.*; +import java.util.*; + +import org.jdom.filter.*; + +/** + * An XML element. Methods allow the user to get and manipulate its child + * elements and content, directly access the element's textual content, + * manipulate its attributes, and manage namespaces. + * + * @version $Revision: 1.159 $, $Date: 2007/11/14 05:02:08 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Lucas Gonze + * @author Kevin Regan + * @author Dan Schaffer + * @author Yusuf Goolamabbas + * @author Kent C. Johnson + * @author Jools Enticknap + * @author Alex Rosen + * @author Bradley S. Huffman + * @author Victor Toni + */ +public class Element extends Content implements Parent { + + private static final String CVS_ID = + "@(#) $RCSfile: Element.java,v $ $Revision: 1.159 $ $Date: 2007/11/14 05:02:08 $ $Name: jdom_1_1_1 $"; + + private static final int INITIAL_ARRAY_SIZE = 5; + + /** The local name of the element */ + protected String name; + + /** The namespace of the element */ + protected transient Namespace namespace; + + /** Additional namespace declarations to store on this element; useful + * during output */ + protected transient List additionalNamespaces; + + // See http://lists.denveronline.net/lists/jdom-interest/2000-September/003030.html + // for a possible memory optimization here (using a RootElement subclass) + + /** + * The attributes of the element. Subclassers have to + * track attributes using their own mechanism. + */ + AttributeList attributes = new AttributeList(this); + + /** + * The content of the element. Subclassers have to + * track content using their own mechanism. + */ + ContentList content = new ContentList(this); + + /** + * This protected constructor is provided in order to support an Element + * subclass that wants full control over variable initialization. It + * intentionally leaves all instance variables null, allowing a lightweight + * subclass implementation. The subclass is responsible for ensuring all the + * get and set methods on Element behave as documented. + *

+ * When implementing an Element subclass which doesn't require full control + * over variable initialization, be aware that simply calling super() (or + * letting the compiler add the implicit super() call) will not initialize + * the instance variables which will cause many of the methods to throw a + * NullPointerException. Therefore, the constructor for these subclasses + * should call one of the public constructors so variable initialization is + * handled automatically. + */ + protected Element() { } + + /** + * Creates a new element with the supplied (local) name and namespace. If + * the provided namespace is null, the element will have no namespace. + * + * @param name local name of the element + * @param namespace namespace for the element + * @throws IllegalNameException if the given name is illegal as an element + * name + */ + public Element(final String name, final Namespace namespace) { + setName(name); + setNamespace(namespace); + } + + /** + * Create a new element with the supplied (local) name and no namespace. + * + * @param name local name of the element + * @throws IllegalNameException if the given name is illegal as an element + * name. + */ + public Element(final String name) { + this(name, (Namespace) null); + } + + /** + * Creates a new element with the supplied (local) name and a namespace + * given by a URI. The element will be put into the unprefixed (default) + * namespace. + * + * @param name name of the element + * @param uri namespace URI for the element + * @throws IllegalNameException if the given name is illegal as an element + * name or the given URI is illegal as a + * namespace URI + */ + public Element(final String name, final String uri) { + this(name, Namespace.getNamespace("", uri)); + } + + /** + * Creates a new element with the supplied (local) name and a namespace + * given by the supplied prefix and URI combination. + * + * @param name local name of the element + * @param prefix namespace prefix + * @param uri namespace URI for the element + * @throws IllegalNameException if the given name is illegal as an element + * name, the given prefix is illegal as a + * namespace prefix, or the given URI is + * illegal as a namespace URI + */ + public Element(final String name, final String prefix, final String uri) { + this(name, Namespace.getNamespace(prefix, uri)); + } + + /** + * Returns the (local) name of the element (without any namespace prefix). + * + * @return local element name + */ + public String getName() { + return name; + } + + /** + * Sets the (local) name of the element. + * + * @param name the new (local) name of the element + * @return the target element + * @throws IllegalNameException if the given name is illegal as an Element + * name + */ + public Element setName(final String name) { + final String reason = Verifier.checkElementName(name); + if (reason != null) { + throw new IllegalNameException(name, "element", reason); + } + this.name = name; + return this; + } + + /** + * Returns the element's {@link Namespace}. + * + * @return the element's namespace + */ + public Namespace getNamespace() { + return namespace; + } + + /** + * Sets the element's {@link Namespace}. If the provided namespace is null, + * the element will have no namespace. + * + * @param namespace the new namespace + * @return the target element + */ + public Element setNamespace(Namespace namespace) { + if (namespace == null) { + namespace = Namespace.NO_NAMESPACE; + } + + this.namespace = namespace; + return this; + } + + /** + * Returns the namespace prefix of the element or an empty string if none + * exists. + * + * @return the namespace prefix + */ + public String getNamespacePrefix() { + return namespace.getPrefix(); + } + + /** + * Returns the namespace URI mapped to this element's prefix (or the + * in-scope default namespace URI if no prefix). If no mapping is found, an + * empty string is returned. + * + * @return the namespace URI for this element + */ + public String getNamespaceURI() { + return namespace.getURI(); + } + + /** + * Returns the {@link Namespace} corresponding to the given prefix in scope + * for this element. This involves searching up the tree, so the results + * depend on the current location of the element. Returns null if there is + * no namespace in scope with the given prefix at this point in the + * document. + * + * @param prefix namespace prefix to look up + * @return the Namespace for this prefix at this + * location, or null if none + */ + public Namespace getNamespace(final String prefix) { + if (prefix == null) { + return null; + } + + if ("xml".equals(prefix)) { + // Namespace "xml" is always bound. + return Namespace.XML_NAMESPACE; + } + + // Check if the prefix is the prefix for this element + if (prefix.equals(getNamespacePrefix())) { + return getNamespace(); + } + + // Scan the additional namespaces + if (additionalNamespaces != null) { + for (int i = 0; i < additionalNamespaces.size(); i++) { + final Namespace ns = (Namespace) additionalNamespaces.get(i); + if (prefix.equals(ns.getPrefix())) { + return ns; + } + } + } + + // If we still don't have a match, ask the parent + if (parent instanceof Element) { + return ((Element)parent).getNamespace(prefix); + } + + return null; + } + + /** + * Returns the full name of the element, in the form + * [namespacePrefix]:[localName]. If the element does not have a namespace + * prefix, then the local name is returned. + * + * @return qualified name of the element (including + * namespace prefix) + */ + public String getQualifiedName() { + // Note: Any changes here should be reflected in + // XMLOutputter.printQualifiedName() + if ("".equals(namespace.getPrefix())) { + return getName(); + } + + return new StringBuffer(namespace.getPrefix()) + .append(':') + .append(name) + .toString(); + } + + /** + * Adds a namespace declarations to this element. This should not be + * used to add the declaration for this element itself; that should be + * assigned in the construction of the element. Instead, this is for adding + * namespace declarations on the element not relating directly to itself. + * It's used during output to for stylistic reasons move namespace + * declarations higher in the tree than they would have to be. + * + * @param additionalNamespace namespace to add + * @throws IllegalAddException if the namespace prefix collides with another + * namespace prefix on the element + */ + public void addNamespaceDeclaration(final Namespace additionalNamespace) { + + // Verify the new namespace prefix doesn't collide with another + // declared namespace, an attribute prefix, or this element's prefix + final String reason = Verifier.checkNamespaceCollision(additionalNamespace, this); + if (reason != null) { + throw new IllegalAddException(this, additionalNamespace, reason); + } + + if (additionalNamespaces == null) { + additionalNamespaces = new ArrayList(INITIAL_ARRAY_SIZE); + } + + additionalNamespaces.add(additionalNamespace); + } + + /** + * Removes an additional namespace declarations from this element. This + * should not be used to remove the declaration for this element + * itself; that should be handled in the construction of the element. + * Instead, this is for removing namespace declarations on the element not + * relating directly to itself. If the declaration is not present, this + * method does nothing. + * + * @param additionalNamespace namespace to remove + */ + public void removeNamespaceDeclaration(final Namespace additionalNamespace) { + if (additionalNamespaces == null) { + return; + } + additionalNamespaces.remove(additionalNamespace); + } + + /** + * Returns a list of the additional namespace declarations on this element. + * This includes only additional namespace, not the namespace of the element + * itself, which can be obtained through {@link #getNamespace()}. If there + * are no additional declarations, this returns an empty list. Note, the + * returned list is unmodifiable. + * + * @return a List of the additional namespace + * declarations + */ + public List getAdditionalNamespaces() { + // Not having the returned list be live allows us to avoid creating a + // new list object when XMLOutputter calls this method on an element + // with an empty list. + if (additionalNamespaces == null) { + return Collections.EMPTY_LIST; + } + return Collections.unmodifiableList(additionalNamespaces); + } + + /** + * Returns the XPath 1.0 string value of this element, which is the + * complete, ordered content of all text node descendants of this element + * (i.e. the text that's left after all references are resolved + * and all other markup is stripped out.) + * + * @return a concatentation of all text node descendants + */ + public String getValue() { + final StringBuffer buffer = new StringBuffer(); + + final Iterator iter = getContent().iterator(); + while (iter.hasNext()) { + final Content child = (Content) iter.next(); + if (child instanceof Element || child instanceof Text) { + buffer.append(child.getValue()); + } + } + return buffer.toString(); + } + + /** + * Returns whether this element is a root element. This can be used in + * tandem with {@link #getParent} to determine if an element has any + * "attachments" to a parent element or document. + * + * @return whether this is a root element + */ + public boolean isRootElement() { + return parent instanceof Document; + } + + public int getContentSize() { + return content.size(); + } + + public int indexOf(final Content child) { + return content.indexOf(child); + } + +// private int indexOf(int start, Filter filter) { +// int size = getContentSize(); +// for (int i = start; i < size; i++) { +// if (filter.matches(getContent(i))) { +// return i; +// } +// } +// return -1; +// } + + + /** + * Returns the textual content directly held under this element as a string. + * This includes all text within this single element, including whitespace + * and CDATA sections if they exist. It's essentially the concatenation of + * all {@link Text} and {@link CDATA} nodes returned by {@link #getContent}. + * The call does not recurse into child elements. If no textual value exists + * for the element, an empty string is returned. + * + * @return text content for this element, or empty + * string if none + */ + public String getText() { + if (content.size() == 0) { + return ""; + } + + // If we hold only a Text or CDATA, return it directly + if (content.size() == 1) { + final Object obj = content.get(0); + if (obj instanceof Text) { + return ((Text) obj).getText(); + } + else { + return ""; + } + } + + // Else build String up + final StringBuffer textContent = new StringBuffer(); + boolean hasText = false; + + for (int i = 0; i < content.size(); i++) { + final Object obj = content.get(i); + if (obj instanceof Text) { + textContent.append(((Text) obj).getText()); + hasText = true; + } + } + + if (!hasText) { + return ""; + } + else { + return textContent.toString(); + } + } + + /** + * Returns the textual content of this element with all surrounding + * whitespace removed. If no textual value exists for the element, or if + * only whitespace exists, the empty string is returned. + * + * @return trimmed text content for this element, or + * empty string if none + */ + public String getTextTrim() { + return getText().trim(); + } + + /** + * Returns the textual content of this element with all surrounding + * whitespace removed and internal whitespace normalized to a single space. + * If no textual value exists for the element, or if only whitespace exists, + * the empty string is returned. + * + * @return normalized text content for this element, or + * empty string if none + */ + public String getTextNormalize() { + return Text.normalizeString(getText()); + } + + /** + * Returns the textual content of the named child element, or null if + * there's no such child. This method is a convenience because calling + * getChild().getText() can throw a NullPointerException. + * + * @param name the name of the child + * @return text content for the named child, or null if + * no such child + */ + public String getChildText(final String name) { + final Element child = getChild(name); + if (child == null) { + return null; + } + return child.getText(); + } + + /** + * Returns the trimmed textual content of the named child element, or null + * if there's no such child. See {@link #getTextTrim()} for + * details of text trimming. + * + * @param name the name of the child + * @return trimmed text content for the named child, or + * null if no such child + */ + public String getChildTextTrim(final String name) { + final Element child = getChild(name); + if (child == null) { + return null; + } + return child.getTextTrim(); + } + + /** + * Returns the normalized textual content of the named child element, or + * null if there's no such child. See {@link + * #getTextNormalize()} for details of text normalizing. + * + * @param name the name of the child + * @return normalized text content for the named child, + * or null if no such child + */ + public String getChildTextNormalize(final String name) { + final Element child = getChild(name); + if (child == null) { + return null; + } + return child.getTextNormalize(); + } + + /** + * Returns the textual content of the named child element, or null if + * there's no such child. + * + * @param name the name of the child + * @param ns the namespace of the child + * @return text content for the named child, or null if + * no such child + */ + public String getChildText(final String name, final Namespace ns) { + final Element child = getChild(name, ns); + if (child == null) { + return null; + } + return child.getText(); + } + + /** + * Returns the trimmed textual content of the named child element, or null + * if there's no such child. + * + * @param name the name of the child + * @param ns the namespace of the child + * @return trimmed text content for the named child, or + * null if no such child + */ + public String getChildTextTrim(final String name, final Namespace ns) { + final Element child = getChild(name, ns); + if (child == null) { + return null; + } + return child.getTextTrim(); + } + + /** + * Returns the normalized textual content of the named child element, or + * null if there's no such child. + * + * @param name the name of the child + * @param ns the namespace of the child + * @return normalized text content for the named child, + * or null if no such child + */ + public String getChildTextNormalize(final String name, final Namespace ns) { + final Element child = getChild(name, ns); + if (child == null) { + return null; + } + return child.getTextNormalize(); + } + + /** + * Sets the content of the element to be the text given. All existing text + * content and non-text context is removed. If this element should have both + * textual content and nested elements, use {@link #setContent} + * instead. Setting a null text value is equivalent to setting an empty + * string value. + * + * @param text new text content for the element + * @return the target element + * @throws IllegalDataException if the assigned text contains an illegal + * character such as a vertical tab (as + * determined by {@link + * org.jdom.Verifier#checkCharacterData}) + */ + public Element setText(final String text) { + content.clear(); + + if (text != null) { + addContent(new Text(text)); + } + + return this; + } + + /** + * This returns the full content of the element as a List which + * may contain objects of type Text, Element, + * Comment, ProcessingInstruction, + * CDATA, and EntityRef. + * The List returned is "live" in document order and modifications + * to it affect the element's actual contents. Whitespace content is + * returned in its entirety. + * + *

+ * Sequential traversal through the List is best done with an Iterator + * since the underlying implement of List.size() may require walking the + * entire list. + *

+ * + * @return a List containing the mixed content of the + * element: may contain Text, + * {@link Element}, {@link Comment}, + * {@link ProcessingInstruction}, + * {@link CDATA}, and + * {@link EntityRef} objects. + */ + public List getContent() { + return content; + } + + /** + * Return a filter view of this Element's content. + * + *

+ * Sequential traversal through the List is best done with a Iterator + * since the underlying implement of List.size() may require walking the + * entire list. + *

+ * + * @param filter Filter to apply + * @return List - filtered Element content + */ + public List getContent(final Filter filter) { + return content.getView(filter); + } + + /** + * Removes all child content from this parent. + * + * @return list of the old children detached from this parent + */ + public List removeContent() { + final List old = new ArrayList(content); + content.clear(); + return old; + } + + /** + * Remove all child content from this parent matching the supplied filter. + * + * @param filter filter to select which content to remove + * @return list of the old children detached from this parent + */ + public List removeContent(final Filter filter) { + final List old = new ArrayList(); + final Iterator iter = content.getView(filter).iterator(); + while (iter.hasNext()) { + final Content child = (Content) iter.next(); + old.add(child); + iter.remove(); + } + return old; + } + + /** + * This sets the content of the element. The supplied List should + * contain only objects of type Element, Text, + * CDATA, Comment, + * ProcessingInstruction, and EntityRef. + * + *

+ * When all objects in the supplied List are legal and before the new + * content is added, all objects in the old content will have their + * parentage set to null (no parent) and the old content list will be + * cleared. This has the effect that any active list (previously obtained + * with a call to {@link #getContent} or {@link #getChildren}) will also + * change to reflect the new content. In addition, all objects in the + * supplied List will have their parentage set to this element, but the + * List itself will not be "live" and further removals and additions will + * have no effect on this elements content. If the user wants to continue + * working with a "live" list, then a call to setContent should be + * followed by a call to {@link #getContent} or {@link #getChildren} to + * obtain a "live" version of the content. + *

+ * + *

+ * Passing a null or empty List clears the existing content. + *

+ * + *

+ * In event of an exception the original content will be unchanged and + * the objects in the supplied content will be unaltered. + *

+ * + * @param newContent Collection of content to set + * @return this element modified + * @throws IllegalAddException if the List contains objects of + * illegal types or with existing parentage. + */ + public Element setContent(final Collection newContent) { + content.clearAndSet(newContent); + return this; + } + + /** + * Replace the current child the given index with the supplied child. + *

+ * In event of an exception the original content will be unchanged and + * the supplied child will be unaltered. + *

+ * + * @param index - index of child to replace. + * @param child - child to add. + * @return element on which this method was invoked + * @throws IllegalAddException if the supplied child is already attached + * or not legal content for this parent. + * @throws IndexOutOfBoundsException if index is negative or greater + * than the current number of children. + */ + public Element setContent(final int index, final Content child) { + content.set(index, child); + return this; + } + + /** + * Replace the child at the given index whith the supplied + * collection. + *

+ * In event of an exception the original content will be unchanged and + * the content in the supplied collection will be unaltered. + *

+ * + * @param index - index of child to replace. + * @param newContent - Collection of content to replace child. + * @return object on which this method was invoked + * @throws IllegalAddException if the collection contains objects of + * illegal types. + * @throws IndexOutOfBoundsException if index is negative or greater + * than the current number of children. + */ + public Parent setContent(final int index, final Collection newContent) { + content.remove(index); + content.addAll(index, newContent); + return this; + } + + /** + * This adds text content to this element. It does not replace the + * existing content as does setText(). + * + * @param str String to add + * @return this element modified + * @throws IllegalDataException if str contains an + * illegal character such as a vertical tab (as determined + * by {@link org.jdom.Verifier#checkCharacterData}) + */ + public Element addContent(final String str) { + return addContent(new Text(str)); + } + + /** + * Appends the child to the end of the element's content list. + * + * @param child child to append to end of content list + * @return the element on which the method was called + * @throws IllegalAddException if the given child already has a parent. */ + public Element addContent(final Content child) { + content.add(child); + return this; + } + + /** + * Appends all children in the given collection to the end of + * the content list. In event of an exception during add the + * original content will be unchanged and the objects in the supplied + * collection will be unaltered. + * + * @param newContent Collection of content to append + * @return the element on which the method was called + * @throws IllegalAddException if any item in the collection + * already has a parent or is of an inappropriate type. + */ + public Element addContent(final Collection newContent) { + content.addAll(newContent); + return this; + } + + /** + * Inserts the child into the content list at the given index. + * + * @param index location for adding the collection + * @param child child to insert + * @return the parent on which the method was called + * @throws IndexOutOfBoundsException if index is negative or beyond + * the current number of children + * @throws IllegalAddException if the given child already has a parent. + */ + public Element addContent(final int index, final Content child) { + content.add(index, child); + return this; + } + + /** + * Inserts the content in a collection into the content list + * at the given index. In event of an exception the original content + * will be unchanged and the objects in the supplied collection will be + * unaltered. + * + * @param index location for adding the collection + * @param newContent Collection of content to insert + * @return the parent on which the method was called + * @throws IndexOutOfBoundsException if index is negative or beyond + * the current number of children + * @throws IllegalAddException if any item in the collection + * already has a parent or is of an inappropriate type. + */ + public Element addContent(final int index, final Collection newContent) { + content.addAll(index, newContent); + return this; + } + + public List cloneContent() { + final int size = getContentSize(); + final List list = new ArrayList(size); + for (int i = 0; i < size; i++) { + final Content child = getContent(i); + list.add(child.clone()); + } + return list; + } + + public Content getContent(final int index) { + return (Content) content.get(index); + } + +// public Content getChild(Filter filter) { +// int i = indexOf(0, filter); +// return (i < 0) ? null : getContent(i); +// } + + public boolean removeContent(final Content child) { + return content.remove(child); + } + + public Content removeContent(final int index) { + return (Content) content.remove(index); + } + + /** + * Set this element's content to be the supplied child. + *

+ * If the supplied child is legal content for this parent and before + * it is added, all content in the current content list will + * be cleared and all current children will have their parentage set to + * null. + *

+ * This has the effect that any active list (previously obtained with + * a call to one of the {@link #getContent} methods will also change + * to reflect the new content. In addition, all content in the supplied + * collection will have their parentage set to this parent. If the user + * wants to continue working with a "live" list of this parent's + * child, then a call to setContent should be followed by a call to one + * of the {@link #getContent} methods to obtain a "live" + * version of the children. + *

+ * Passing a null child clears the existing content. + *

+ * In event of an exception the original content will be unchanged and + * the supplied child will be unaltered. + * + * @param child new content to replace existing content + * @return the parent on which the method was called + * @throws IllegalAddException if the supplied child is already attached + * or not legal content for an Element + */ + public Element setContent(final Content child) { + content.clear(); + content.add(child); + return this; + } + + + /** + * Determines if this element is the ancestor of another element. + * + * @param element Element to check against + * @return true if this element is the ancestor of the + * supplied element + */ + public boolean isAncestor(final Element element) { + Parent p = element.getParent(); + while (p instanceof Element) { + if (p == this) { + return true; + } + p = p.getParent(); + } + return false; + } + + /** + *

+ * This returns the complete set of attributes for this element, as a + * List of Attribute objects in no particular + * order, or an empty list if there are none. + * The returned list is "live" and changes to it affect the + * element's actual attributes. + *

+ * + * @return attributes for the element + */ + public List getAttributes() { + return attributes; + } + + /** + *

+ * This returns the attribute for this element with the given name + * and within no namespace, or null if no such attribute exists. + *

+ * + * @param name name of the attribute to return + * @return attribute for the element + */ + public Attribute getAttribute(final String name) { + return getAttribute(name, Namespace.NO_NAMESPACE); + } + + /** + *

+ * This returns the attribute for this element with the given name + * and within the given Namespace, or null if no such attribute exists. + *

+ * + * @param name name of the attribute to return + * @param ns Namespace to search within + * @return attribute for the element + */ + public Attribute getAttribute(final String name, final Namespace ns) { + return (Attribute) attributes.get(name, ns); + } + + /** + *

+ * This returns the attribute value for the attribute with the given name + * and within no namespace, null if there is no such attribute, and the + * empty string if the attribute value is empty. + *

+ * + * @param name name of the attribute whose value to be returned + * @return the named attribute's value, or null if no such attribute + */ + public String getAttributeValue(final String name) { + return getAttributeValue(name, Namespace.NO_NAMESPACE); + } + + /** + *

+ * This returns the attribute value for the attribute with the given name + * and within no namespace, or the passed-in default if there is no + * such attribute. + *

+ * + * @param name name of the attribute whose value to be returned + * @param def a default value to return if the attribute does not exist + * @return the named attribute's value, or the default if no such attribute + */ + public String getAttributeValue(final String name, final String def) { + return getAttributeValue(name, Namespace.NO_NAMESPACE, def); + } + + /** + *

+ * This returns the attribute value for the attribute with the given name + * and within the given Namespace, null if there is no such attribute, and + * the empty string if the attribute value is empty. + *

+ * + * @param name name of the attribute whose valud is to be returned + * @param ns Namespace to search within + * @return the named attribute's value, or null if no such attribute + */ + public String getAttributeValue(final String name, final Namespace ns) { + return getAttributeValue(name, ns, null); + } + + /** + *

+ * This returns the attribute value for the attribute with the given name + * and within the given Namespace, or the passed-in default if there is no + * such attribute. + *

+ * + * @param name name of the attribute whose valud is to be returned + * @param ns Namespace to search within + * @param def a default value to return if the attribute does not exist + * @return the named attribute's value, or the default if no such attribute + */ + public String getAttributeValue(final String name, final Namespace ns, final String def) { + final Attribute attribute = (Attribute) attributes.get(name, ns); + if (attribute == null) { + return def; + } + + return attribute.getValue(); + } + + /** + *

+ * This sets the attributes of the element. The supplied Collection should + * contain only objects of type Attribute. + *

+ * + *

+ * When all objects in the supplied List are legal and before the new + * attributes are added, all old attributes will have their + * parentage set to null (no parent) and the old attribute list will be + * cleared. This has the effect that any active attribute list (previously + * obtained with a call to {@link #getAttributes}) will also change to + * reflect the new attributes. In addition, all attributes in the supplied + * List will have their parentage set to this element, but the List itself + * will not be "live" and further removals and additions will have no + * effect on this elements attributes. If the user wants to continue + * working with a "live" attribute list, then a call to setAttributes + * should be followed by a call to {@link #getAttributes} to obtain a + * "live" version of the attributes. + *

+ * + *

+ * Passing a null or empty List clears the existing attributes. + *

+ * + *

+ * In cases where the List contains duplicate attributes, only the last + * one will be retained. This has the same effect as calling + * {@link #setAttribute(Attribute)} sequentially. + *

+ * + *

+ * In event of an exception the original attributes will be unchanged and + * the attributes in the supplied attributes will be unaltered. + *

+ * + * @param newAttributes Collection of attributes to set + * @return this element modified + * @throws IllegalAddException if the List contains objects + * that are not instances of Attribute, + * or if any of the Attribute objects have + * conflicting namespace prefixes. + */ + public Element setAttributes(final Collection newAttributes) { + attributes.clearAndSet(newAttributes); + return this; + } + + /** + *

+ * This sets the attributes of the element. It's an alternate form of + * the method, accepting a List instead of a + * Collection, for backward compatibility. + *

+ */ + public Element setAttributes(final List newAttributes) { + return setAttributes((Collection)newAttributes); + } + + /** + *

+ * This sets an attribute value for this element. Any existing attribute + * with the same name and namespace URI is removed. + *

+ * + * @param name name of the attribute to set + * @param value value of the attribute to set + * @return this element modified + * @throws IllegalNameException if the given name is illegal as an + * attribute name. + * @throws IllegalDataException if the given attribute value is + * illegal character data (as determined by + * {@link org.jdom.Verifier#checkCharacterData}). + */ + public Element setAttribute(final String name, final String value) { + final Attribute attribute = getAttribute(name); + if (attribute == null) { + final Attribute newAttribute = new Attribute(name, value); + setAttribute(newAttribute); + } else { + attribute.setValue(value); + } + + return this; + } + + /** + *

+ * This sets an attribute value for this element. Any existing attribute + * with the same name and namespace URI is removed. + *

+ * + * @param name name of the attribute to set + * @param value value of the attribute to set + * @param ns namespace of the attribute to set + * @return this element modified + * @throws IllegalNameException if the given name is illegal as an + * attribute name, or if the namespace is an unprefixed default + * namespace + * @throws IllegalDataException if the given attribute value is + * illegal character data (as determined by + * {@link org.jdom.Verifier#checkCharacterData}). + * @throws IllegalAddException if the attribute namespace prefix + * collides with another namespace prefix on the element. + */ + public Element setAttribute(final String name, final String value, final Namespace ns) { + final Attribute attribute = getAttribute(name, ns); + if (attribute == null) { + final Attribute newAttribute = new Attribute(name, value, ns); + setAttribute(newAttribute); + } else { + attribute.setValue(value); + } + + return this; + } + + /** + *

+ * This sets an attribute value for this element. Any existing attribute + * with the same name and namespace URI is removed. + *

+ * + * @param attribute Attribute to set + * @return this element modified + * @throws IllegalAddException if the attribute being added already has a + * parent or if the attribute namespace prefix collides with another + * namespace prefix on the element. + */ + public Element setAttribute(final Attribute attribute) { + attributes.add(attribute); + return this; + } + + /** + *

+ * This removes the attribute with the given name and within no + * namespace. If no such attribute exists, this method does nothing. + *

+ * + * @param name name of attribute to remove + * @return whether the attribute was removed + */ + public boolean removeAttribute(final String name) { + return removeAttribute(name, Namespace.NO_NAMESPACE); + } + + /** + *

+ * This removes the attribute with the given name and within the + * given Namespace. If no such attribute exists, this method does + * nothing. + *

+ * + * @param name name of attribute to remove + * @param ns namespace URI of attribute to remove + * @return whether the attribute was removed + */ + public boolean removeAttribute(final String name, final Namespace ns) { + return attributes.remove(name, ns); + } + + /** + *

+ * This removes the supplied Attribute should it exist. + *

+ * + * @param attribute Reference to the attribute to be removed. + * @return whether the attribute was removed + */ + public boolean removeAttribute(final Attribute attribute) { + return attributes.remove(attribute); + } + + /** + *

+ * This returns a String representation of the + * Element, suitable for debugging. If the XML + * representation of the Element is desired, + * {@link org.jdom.output.XMLOutputter#outputString(Element)} + * should be used. + *

+ * + * @return String - information about the + * Element + */ + public String toString() { + final StringBuffer stringForm = new StringBuffer(64) + .append("[Element: <") + .append(getQualifiedName()); + + final String nsuri = getNamespaceURI(); + if (!"".equals(nsuri)) { + stringForm + .append(" [Namespace: ") + .append(nsuri) + .append("]"); + } + stringForm.append("/>]"); + + return stringForm.toString(); + } + + /** + *

+ * This returns a deep clone of this element. + * The new element is detached from its parent, and getParent() + * on the clone will return null. + *

+ * + * @return the clone of this element + */ + public Object clone() { + + // Ken Rune Helland is our local clone() guru + + final Element element = (Element) super.clone(); + + // name and namespace are references to immutable objects + // so super.clone() handles them ok + + // Reference to parent is copied by super.clone() + // (Object.clone()) so we have to remove it + // Actually, super is a Content, which has already detached in the + // clone(). + // element.parent = null; + + // Reference to content list and attribute lists are copyed by + // super.clone() so we set it new lists if the original had lists + element.content = new ContentList(element); + element.attributes = new AttributeList(element); + + // Cloning attributes + if (attributes != null) { + for(int i = 0; i < attributes.size(); i++) { + final Attribute attribute = (Attribute) attributes.get(i); + element.attributes.add(attribute.clone()); + } + } + + // Cloning additional namespaces + if (additionalNamespaces != null) { + element.additionalNamespaces = new ArrayList(additionalNamespaces); + } + + // Cloning content + if (content != null) { + for(int i = 0; i < content.size(); i++) { + final Content c = (Content) content.get(i); + element.content.add(c.clone()); + } + } + + return element; + } + + + // Support a custom Namespace serialization so no two namespace + // object instances may exist for the same prefix/uri pair + private void writeObject(final ObjectOutputStream out) throws IOException { + + out.defaultWriteObject(); + + // We use writeObject() and not writeUTF() to minimize space + // This allows for writing pointers to already written strings + out.writeObject(namespace.getPrefix()); + out.writeObject(namespace.getURI()); + + if (additionalNamespaces == null) { + out.write(0); + } + else { + final int size = additionalNamespaces.size(); + out.write(size); + for (int i = 0; i < size; i++) { + final Namespace additional = (Namespace) additionalNamespaces.get(i); + out.writeObject(additional.getPrefix()); + out.writeObject(additional.getURI()); + } + } + } + + private void readObject(final ObjectInputStream in) + throws IOException, ClassNotFoundException { + + in.defaultReadObject(); + + namespace = Namespace.getNamespace( + (String)in.readObject(), (String)in.readObject()); + + final int size = in.read(); + + if (size != 0) { + additionalNamespaces = new ArrayList(size); + for (int i = 0; i < size; i++) { + final Namespace additional = Namespace.getNamespace( + (String)in.readObject(), (String)in.readObject()); + additionalNamespaces.add(additional); + } + } + } + + /** + * Returns an iterator that walks over all descendants in document order. + * + * @return an iterator to walk descendants + */ + public Iterator getDescendants() { + return new DescendantIterator(this); + } + + /** + * Returns an iterator that walks over all descendants in document order + * applying the Filter to return only elements that match the filter rule. + * With filters you can match only Elements, only Comments, Elements or + * Comments, only Elements with a given name and/or prefix, and so on. + * + * @param filter filter to select which descendants to see + * @return an iterator to walk descendants within a filter + */ + public Iterator getDescendants(final Filter filter) { + final Iterator iterator = new DescendantIterator(this); + return new FilterIterator(iterator, filter); + } + + + + /** + * This returns a List of all the child elements + * nested directly (one level deep) within this element, as + * Element objects. If this target element has no nested + * elements, an empty List is returned. The returned list is "live" + * in document order and changes to it affect the element's actual + * contents. + * + *

+ * Sequential traversal through the List is best done with a Iterator + * since the underlying implement of List.size() may not be the most + * efficient. + *

+ * + *

+ * No recursion is performed, so elements nested two levels deep + * would have to be obtained with: + * 

+     * 
+     *   Iterator itr = (currentElement.getChildren()).iterator();
+     *   while(itr.hasNext()) {
+     *     Element oneLevelDeep = (Element)itr.next();
+     *     List twoLevelsDeep = oneLevelDeep.getChildren();
+     *     // Do something with these children
+     *   }
+     * 
+     *
+ *

+ * + * @return list of child Element objects for this element + */ + public List getChildren() { + return content.getView(new ElementFilter()); + } + + /** + * This returns a List of all the child elements + * nested directly (one level deep) within this element with the given + * local name and belonging to no namespace, returned as + * Element objects. If this target element has no nested + * elements with the given name outside a namespace, an empty List + * is returned. The returned list is "live" in document order + * and changes to it affect the element's actual contents. + *

+ * Please see the notes for {@link #getChildren} + * for a code example. + *

+ * + * @param name local name for the children to match + * @return all matching child elements + */ + public List getChildren(final String name) { + return getChildren(name, Namespace.NO_NAMESPACE); + } + + /** + * This returns a List of all the child elements + * nested directly (one level deep) within this element with the given + * local name and belonging to the given Namespace, returned as + * Element objects. If this target element has no nested + * elements with the given name in the given Namespace, an empty List + * is returned. The returned list is "live" in document order + * and changes to it affect the element's actual contents. + *

+ * Please see the notes for {@link #getChildren} + * for a code example. + *

+ * + * @param name local name for the children to match + * @param ns Namespace to search within + * @return all matching child elements + */ + public List getChildren(final String name, final Namespace ns) { + return content.getView(new ElementFilter(name, ns)); + } + + /** + * This returns the first child element within this element with the + * given local name and belonging to the given namespace. + * If no elements exist for the specified name and namespace, null is + * returned. + * + * @param name local name of child element to match + * @param ns Namespace to search within + * @return the first matching child element, or null if not found + */ + public Element getChild(final String name, final Namespace ns) { + final List elements = content.getView(new ElementFilter(name, ns)); + final Iterator iter = elements.iterator(); + if (iter.hasNext()) { + return (Element) iter.next(); + } + return null; + } + + /** + * This returns the first child element within this element with the + * given local name and belonging to no namespace. + * If no elements exist for the specified name and namespace, null is + * returned. + * + * @param name local name of child element to match + * @return the first matching child element, or null if not found + */ + public Element getChild(final String name) { + return getChild(name, Namespace.NO_NAMESPACE); + } + + /** + *

+ * This removes the first child element (one level deep) with the + * given local name and belonging to no namespace. + * Returns true if a child was removed. + *

+ * + * @param name the name of child elements to remove + * @return whether deletion occurred + */ + public boolean removeChild(final String name) { + return removeChild(name, Namespace.NO_NAMESPACE); + } + + /** + *

+ * This removes the first child element (one level deep) with the + * given local name and belonging to the given namespace. + * Returns true if a child was removed. + *

+ * + * @param name the name of child element to remove + * @param ns Namespace to search within + * @return whether deletion occurred + */ + public boolean removeChild(final String name, final Namespace ns) { + final Filter filter = new ElementFilter(name, ns); + final List old = content.getView(filter); + final Iterator iter = old.iterator(); + if (iter.hasNext()) { + iter.next(); + iter.remove(); + return true; + } + + return false; + } + + /** + *

+ * This removes all child elements (one level deep) with the + * given local name and belonging to no namespace. + * Returns true if any were removed. + *

+ * + * @param name the name of child elements to remove + * @return whether deletion occurred + */ + public boolean removeChildren(final String name) { + return removeChildren(name, Namespace.NO_NAMESPACE); + } + + /** + *

+ * This removes all child elements (one level deep) with the + * given local name and belonging to the given namespace. + * Returns true if any were removed. + *

+ * + * @param name the name of child elements to remove + * @param ns Namespace to search within + * @return whether deletion occurred + */ + public boolean removeChildren(final String name, final Namespace ns) { + boolean deletedSome = false; + + final Filter filter = new ElementFilter(name, ns); + final List old = content.getView(filter); + final Iterator iter = old.iterator(); + while (iter.hasNext()) { + iter.next(); + iter.remove(); + deletedSome = true; + } + + return deletedSome; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/EntityRef.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/EntityRef.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,239 @@ +/*-- + + $Id: EntityRef.java,v 1.22 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * An XML entity reference. Methods allow the user to manage its name, public + * id, and system id. + * + * @version $Revision: 1.22 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Philip Nelson + */ +public class EntityRef extends Content { + + private static final String CVS_ID = + "@(#) $RCSfile: EntityRef.java,v $ $Revision: 1.22 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** The name of the EntityRef */ + protected String name; + + /** The PublicID of the EntityRef */ + protected String publicID; + + /** The SystemID of the EntityRef */ + protected String systemID; + + /** + * Default, no-args constructor for implementations to use if needed. + */ + protected EntityRef() {} + + /** + * This will create a new EntityRef with the supplied name. + * + * @param name String name of element. + * @throws IllegalNameException if the given name is not a legal + * XML name. + */ + public EntityRef(String name) { + this(name, null, null); + } + + /** + * This will create a new EntityRef + * with the supplied name and system id. + * + * @param name String name of element. + * @param systemID system id of the entity reference being constructed + * @throws IllegalNameException if the given name is not a legal + * XML name. + * @throws IllegalDataException if the given system ID is not a legal + * system literal. + */ + public EntityRef(String name, String systemID) { + this(name, null, systemID); + } + + /** + * This will create a new EntityRef + * with the supplied name, public id, and system id. + * + * @param name String name of element. + * @param publicID public id of the entity reference being constructed + * @param systemID system id of the entity reference being constructed + * @throws IllegalDataException if the given system ID is not a legal + * system literal or the the given public ID is not a + * legal public ID + * @throws IllegalNameException if the given name is not a legal + * XML name. + */ + public EntityRef(String name, String publicID, String systemID) { + setName(name); + setPublicID(publicID); + setSystemID(systemID); + } + + /** + * This returns the name of the EntityRef. + * + * @return String - entity name. + */ + public String getName() { + return name; + } + + /** + * Returns the empty string since entity references don't have an XPath + * 1.0 string value. + * @return the empty string + */ + public String getValue() { + return ""; // entity references don't have XPath string values + } + + /** + * This will return the publid ID of this EntityRef. + * If there is no public ID, then this returns null. + * + * @return public ID of this EntityRef + */ + public String getPublicID() { + return publicID; + } + + /** + * This will return the system ID of this EntityRef. + * If there is no system ID, then this returns null. + * + * @return system ID of this EntityRef + */ + public String getSystemID() { + return systemID; + } + + /** + * This will set the name of this EntityRef. + * + * @param name new name of the entity + * @return this EntityRef modified. + * @throws IllegalNameException if the given name is not a legal + * XML name. + */ + public EntityRef setName(String name) { + // This can contain a colon so we use checkXMLName() + // instead of checkElementName() + String reason = Verifier.checkXMLName(name); + if (reason != null) { + throw new IllegalNameException(name, "EntityRef", reason); + } + this.name = name; + return this; + } + + /** + * This will set the public ID of this EntityRef. + * + * @param publicID new public id + * @return this EntityRef modified. + * @throws IllegalDataException if the given public ID is not a legal + * public ID. + */ + public EntityRef setPublicID(String publicID) { + String reason = Verifier.checkPublicID(publicID); + if (reason != null) { + throw new IllegalDataException(publicID, "EntityRef", reason); + } + this.publicID = publicID; + return this; + } + + /** + * This will set the system ID of this EntityRef. + * + * @param systemID new system id + * @throws IllegalDataException if the given system ID is not a legal + * system literal. + * @return this EntityRef modified. + */ + public EntityRef setSystemID(String systemID) { + String reason = Verifier.checkSystemLiteral(systemID); + if (reason != null) { + throw new IllegalDataException(systemID, "EntityRef", reason); + } + this.systemID = systemID; + return this; + } + + /** + * This returns a String representation of the + * EntityRef, suitable for debugging. + * + * @return String - information about the + * EntityRef + */ + public String toString() { + return new StringBuffer() + .append("[EntityRef: ") + .append("&") + .append(name) + .append(";") + .append("]") + .toString(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/FilterIterator.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/FilterIterator.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,115 @@ +/*-- + + $Id: FilterIterator.java,v 1.6 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; +import org.jdom.filter.*; + +/** + * Traverse a parent's children that match the supplied filter. + * + * @author Bradley S. Huffman + * @version $Revision: 1.6 $, $Date: 2007/11/10 05:28:59 $ + */ +class FilterIterator implements Iterator { + + private Iterator iterator; + private Filter filter; + private Object nextObject; + + private static final String CVS_ID = + "@(#) $RCSfile: FilterIterator.java,v $ $Revision: 1.6 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + public FilterIterator(Iterator iterator, Filter filter) { + if ((iterator == null) || (filter == null)) { + throw new IllegalArgumentException("null parameter"); + } + this.iterator = iterator; + this.filter = filter; + } + + public boolean hasNext() { + if (nextObject != null) { + return true; + } + + while (iterator.hasNext()) { + Object obj = iterator.next(); + if (filter.matches(obj)) { + nextObject = obj; + return true; + } + } + return false; + } + + public Object next() { + if (!hasNext()) { + throw new NoSuchElementException(); + } + + Object obj = nextObject; + nextObject = null; + return obj; + } + + public void remove() { + // XXX Could cause probs for sure if hasNext() is + // called before the remove(), although that's unlikely. + iterator.remove(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/IllegalAddException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/IllegalAddException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,323 @@ +/*-- + + $Id: IllegalAddException.java,v 1.26 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * Thrown when trying to add a illegal object to a JDOM construct. + * + * @version $Revision: 1.26 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public class IllegalAddException extends IllegalArgumentException { + + private static final String CVS_ID = + "@(#) $RCSfile: IllegalAddException.java,v $ $Revision: 1.26 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This will create an Exception indicating + * that the addition of the {@link Attribute} + * to the {@link Element} is illegal. + * + * @param base Element that Attribute + * couldn't be added to + * @param added Attribute that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element base, Attribute added, String reason) { + super(new StringBuffer() + .append("The attribute \"") + .append(added.getQualifiedName()) + .append("\" could not be added to the element \"") + .append(base.getQualifiedName()) + .append("\": ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link Element} + * to parent is illegal. + * + * @param base Element that the child + * couldn't be added to + * @param added Element that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element base, Element added, String reason) { + super(new StringBuffer() + .append("The element \"") + .append(added.getQualifiedName()) + .append("\" could not be added as a child of \"") + .append(base.getQualifiedName()) + .append("\": ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link Element} + * to the {@link Document} is illegal. + * + * @param added Element that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element added, String reason) { + super(new StringBuffer() + .append("The element \"") + .append(added.getQualifiedName()) + .append("\" could not be added as the root of the document: ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link ProcessingInstruction} + * to the {@link Element} is illegal. + * + * @param base Element that the + * ProcessingInstruction couldn't be added to + * @param added ProcessingInstruction that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element base, ProcessingInstruction added, + String reason) { + super(new StringBuffer() + .append("The PI \"") + .append(added.getTarget()) + .append("\" could not be added as content to \"") + .append(base.getQualifiedName()) + .append("\": ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link ProcessingInstruction} + * to the {@link Document} is illegal. + * + * @param added ProcessingInstruction that could not be added + * @param reason cause of the problem + */ + IllegalAddException(ProcessingInstruction added, + String reason) { + super(new StringBuffer() + .append("The PI \"") + .append(added.getTarget()) + .append("\" could not be added to the top level of the document: ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link Comment} + * to the {@link Element} is illegal. + * + * @param base Element that the Comment + * couldn't be added to + * @param added Comment that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element base, Comment added, String reason) { + super(new StringBuffer() + .append("The comment \"") + .append(added.getText()) + .append("\" could not be added as content to \"") + .append(base.getQualifiedName()) + .append("\": ") + .append(reason) + .toString()); + } + + + /** + * This will create an Exception indicating + * that the addition of the {@link CDATA} + * + * @param base Element that the CDATA + * couldn't be added to + * @param added CDATA that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element base, CDATA added, String reason) { + super(new StringBuffer() + .append("The CDATA \"") + .append(added.getText()) + .append("\" could not be added as content to \"") + .append(base.getQualifiedName()) + .append("\": ") + .append(reason) + .toString()); + } + + + /** + * This will create an Exception indicating + * that the addition of the {@link Text} + * to the {@link Element} is illegal. + * + * @param base Element that the Comment + * couldn't be added to + * @param added Text that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element base, Text added, String reason) { + super(new StringBuffer() + .append("The Text \"") + .append(added.getText()) + .append("\" could not be added as content to \"") + .append(base.getQualifiedName()) + .append("\": ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link Comment} + * to the {@link Document} is illegal. + * + * @param added Comment that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Comment added, String reason) { + super(new StringBuffer() + .append("The comment \"") + .append(added.getText()) + .append("\" could not be added to the top level of the document: ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link EntityRef} + * to the {@link Element} is illegal. + * + * @param base Element that the EntityRef + * couldn't be added to + * @param added EntityRef reference that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element base, EntityRef added, String reason) { + super(new StringBuffer() + .append("The entity reference\"") + .append(added.getName()) + .append("\" could not be added as content to \"") + .append(base.getQualifiedName()) + .append("\": ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link Namespace} + * to the {@link Element} is illegal. + * + * @param base Element that the Namespace + * couldn't be added to + * @param added Namespace that could not be added + * @param reason cause of the problem + */ + IllegalAddException(Element base, Namespace added, String reason) { + super(new StringBuffer() + .append("The namespace xmlns") + .append((added.getPrefix() == null || + added.getPrefix().equals("")) ? "=" + : ":" + added.getPrefix() + "=") + .append("\"") + .append(added.getURI()) + .append("\" could not be added as a namespace to \"") + .append(base.getQualifiedName()) + .append("\": ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception indicating + * that the addition of the {@link DocType} + * to the {@link Document} is illegal. + * + * @param added DocType that could not be added + * @param reason cause of the problem + */ + IllegalAddException(DocType added, String reason) { + super(new StringBuffer() + .append("The DOCTYPE ") + .append(added.toString()) + .append(" could not be added to the document: ") + .append(reason) + .toString()); + } + + /** + * This will create an Exception with the specified + * error message. + * + * @param reason cause of the problem + */ + public IllegalAddException(String reason) { + super(reason); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/IllegalDataException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/IllegalDataException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,118 @@ +/*-- + + $Id: IllegalDataException.java,v 1.14 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * Thrown when illegal text is supplied to a JDOM construct. + * + * @version $Revision: 1.14 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Elliotte Rusty Harold + */ +public class IllegalDataException extends IllegalArgumentException { + + private static final String CVS_ID = + "@(#) $RCSfile: IllegalDataException.java,v $ $Revision: 1.14 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This will create an Exception indicating + * that the specified data is illegal for the construct + * it was supplied to. + * + * @param data String data that breaks rules. + * @param construct String construct that data is illegal for. + * @param reason String message or reason data is illegal. + */ + IllegalDataException(String data, String construct, String reason) { + super(new StringBuffer() + .append("The data \"") + .append(data) + .append("\" is not legal for a JDOM ") + .append(construct) + .append(": ") + .append(reason) + .append(".") + .toString()); + } + + /** + * This will create an Exception indicating + * that the specified data is illegal for the construct + * it was supplied to. + * + * @param data String data that breaks rules. + * @param construct String construct that data is illegal for. + */ + IllegalDataException(String data, String construct) { + super(new StringBuffer() + .append("The data \"") + .append(data) + .append("\" is not legal for a JDOM ") + .append(construct) + .append(".") + .toString()); + } + + /** + * This will create an exceptoin with the specified error message. + * + * @param reason cause of the problem + */ + public IllegalDataException(String reason) { + super(reason); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/IllegalNameException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/IllegalNameException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,121 @@ +/*-- + + $Id: IllegalNameException.java,v 1.14 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * Thrown when a name is supplied in construction of a JDOM construct whose + * where the name breaks XML naming conventions. + * + * @version $Revision: 1.14 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Elliotte Rusty Harold + */ +public class IllegalNameException extends IllegalArgumentException { + + private static final String CVS_ID = + "@(#) $RCSfile: IllegalNameException.java,v $ $Revision: 1.14 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This will create an Exception indicating + * that the specified name is illegal for the construct + * it was supplied to. + * + * @param name String name that breaks rules. + * @param construct String name of JDOM construct + * that name was supplied to. + * @param reason String message or reason name is illegal. + */ + IllegalNameException(String name, String construct, String reason) { + super(new StringBuffer() + .append("The name \"") + .append(name) + .append("\" is not legal for JDOM/XML ") + .append(construct) + .append("s: ") + .append(reason) + .append(".") + .toString()); + } + + /** + * This will create an Exception indicating + * that the specified name is illegal for the construct + * it was supplied to. + * + * @param name String name that breaks rules. + * @param construct String name of JDOM construct + * that name was supplied to. + */ + IllegalNameException(String name, String construct) { + super(new StringBuffer() + .append("The name \"") + .append(name) + .append("\" is not legal for JDOM/XML ") + .append(construct) + .append("s.") + .toString()); + } + + /** + * Creates an exception with the specified error message. + * + * @param reason cause of the problem + */ + public IllegalNameException(String reason) { + super(reason); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/IllegalTargetException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/IllegalTargetException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,97 @@ +/*-- + + $Id: IllegalTargetException.java,v 1.15 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * Thrown when a target is supplied in construction of a JDOM {@link + * ProcessingInstruction}, and that name breaks XML naming conventions. + * + * @version $Revision: 1.15 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + */ +public class IllegalTargetException extends IllegalArgumentException { + + private static final String CVS_ID = + "@(#) $RCSfile: IllegalTargetException.java,v $ $Revision: 1.15 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This will create an Exception indicating + * that the specified target is illegal for the + * {@link ProcessingInstruction} it was supplied to. + * + * @param target String target that breaks rules. + * @param reason String message or reason target is illegal. + */ + IllegalTargetException(String target, String reason) { + super(new StringBuffer() + .append("The target \"") + .append(target) + .append("\" is not legal for JDOM/XML Processing Instructions: ") + .append(reason) + .append(".") + .toString()); + } + + /** + * Creates an exception with the specified error message. + * + * @param reason cause of the problem + */ + public IllegalTargetException(String reason) { + super(reason); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/JDOMException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/JDOMException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,367 @@ +/*-- + + $Id: JDOMException.java,v 1.26 2008/12/10 00:59:51 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.io.*; +import java.lang.reflect.*; +import java.sql.*; + +import org.xml.sax.*; + +/** + * The top level exception that JDOM classes can throw. Its subclasses add + * specificity to the problems that can occur using JDOM. This single exception + * can be caught to handle all JDOM specific problems (some methods may throw + * {@link java.io.IOException} and such). + * + * @version $Revision: 1.26 $, $Date: 2008/12/10 00:59:51 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public class JDOMException extends Exception { + + private static final String CVS_ID = + "@(#) $RCSfile: JDOMException.java,v $ $Revision: 1.26 $ $Date: 2008/12/10 00:59:51 $ $Name: jdom_1_1_1 $"; + + /** A wrapped Throwable */ + private Throwable cause; + + /** + * This will create an Exception. + */ + public JDOMException() { + super("Error occurred in JDOM application."); + } + + /** + * This will create an Exception with the given message. + * + * @param message String message indicating + * the problem that occurred. + */ + public JDOMException(String message) { + super(message); + } + + /** + * This will create an Exception with the given message + * and wrap another Exception. This is useful when + * the originating Exception should be held on to. + * + * @param message String message indicating + * the problem that occurred. + * @param cause Throwable that caused this + * to be thrown. + */ + public JDOMException(String message, Throwable cause) { + super(message); + this.cause = cause; + } + + /** + * Intializes the cause of this exception to be the specified value. + * + * @param cause Throwable that caused this + * to be thrown. + * @return a pointer to this throwable + */ + // Created to match the JDK 1.4 Throwable method. + public Throwable initCause(Throwable cause) { + this.cause = cause; + return this; + } + + /** + * This returns the message for the Exception. If + * there are one or more nested exceptions, their messages + * are appended. + * + * @return String - message for Exception. + */ + public String getMessage() { + // Get this exception's message. + String msg = super.getMessage(); + + Throwable parent = this; + Throwable child; + + // Look for nested exceptions. + while((child = getNestedException(parent)) != null) { + // Get the child's message. + String msg2 = child.getMessage(); + + // Special case: If a SAXException has no message of its own, but has a + // nested exception, then it returns the nested exception's message as its + // message. We don't want to add that message twice. + if (child instanceof SAXException) { + Throwable grandchild = ((SAXException)child).getException(); + // If the SAXException tells us that it's message is identical to + // its nested exception's message, then we skip it, so we don't + // add it twice. + if (grandchild != null && msg2 != null && msg2.equals(grandchild.getMessage())) { + msg2 = null; + } + } + + // If we found a message for the child exception, we append it. + if (msg2 != null) { + if (msg != null) { + msg += ": " + msg2; + } else { + msg = msg2; + } + } + + // Any nested JDOMException will append its own children, + // so we need to break out of here. + if (child instanceof JDOMException) { + break; + } + parent = child; + } + + // Return the completed message. + return msg; + } + + /** + * This prints the stack trace of the Exception. If + * there is a root cause, the stack trace of the root + * Exception is printed right after. + */ + public void printStackTrace() { + // Print the stack trace for this exception. + super.printStackTrace(); + + Throwable parent = this; + Throwable child; + + // Print the stack trace for each nested exception. + while((child = getNestedException(parent)) != null) { + System.err.print("Caused by: "); + child.printStackTrace(); + // Any nested JDOMException will print its own children, + // so we need to break out of here. + if (child instanceof JDOMException) { + break; + } + parent = child; + } + } + + /** + * Prints the stack trace of the Exception to the given + * PrintStream. If there is a root cause, the stack trace of the root + * Exception is printed right after. + * + * @param s PrintStream to print to + */ + public void printStackTrace(PrintStream s) { + // Print the stack trace for this exception. + super.printStackTrace(s); + + Throwable parent = this; + Throwable child; + + // Print the stack trace for each nested exception. + while((child = getNestedException(parent)) != null) { + s.print("Caused by: "); + child.printStackTrace(s); + // Any nested JDOMException will print its own children, + // so we need to break out of here. + if (child instanceof JDOMException) { + break; + } + parent = child; + } + } + + /** + * Prints the stack trace of the Exception to the given + * PrintWriter. If there is a root cause, the stack trace of the root + * Exception is printed right after. + * + * @param w PrintWriter to print to + */ + public void printStackTrace(PrintWriter w) { + // Print the stack trace for this exception. + super.printStackTrace(w); + + Throwable parent = this; + Throwable child; + + // Print the stack trace for each nested exception. + while((child = getNestedException(parent)) != null) { + w.print("Caused by: "); + child.printStackTrace(w); + // Any nested JDOMException will print its own children, + // so we need to break out of here. + if (child instanceof JDOMException) { + break; + } + parent = child; + } + } + + /** + * This will return the root cause Throwable, or null + * if one does not exist. + * + * @return Throwable - the wrapped Throwable. + */ + public Throwable getCause() { + return cause; + } + + // If this Throwable has a nested (child) exception, then we return it. + // Otherwise we return null. + private static Throwable getNestedException(Throwable parent) { + if (parent instanceof JDOMException) { + return ((JDOMException)parent).getCause(); + } + + if (parent instanceof SAXException) { + return ((SAXException)parent).getException(); + } + + if (parent instanceof SQLException) { + return ((SQLException)parent).getNextException(); + } + + if (parent instanceof InvocationTargetException) { + return ((InvocationTargetException)parent).getTargetException(); + } + + if (parent instanceof ExceptionInInitializerError) { + return ((ExceptionInInitializerError)parent).getException(); + } + + // The RMI classes are not present in Android's Dalvik VM, so we use reflection to access them. + + Throwable nestedException = getNestedExceptionFromField(parent, "java.rmi.RemoteException", "detail"); + if (nestedException != null) { + return nestedException; + } + + // These classes are not part of standard JDK 1.1 or 1.2, so again we use reflection to access them. + + nestedException = getNestedException(parent, "javax.naming.NamingException", "getRootCause"); + if (nestedException != null) { + return nestedException; + } + + nestedException = getNestedException(parent, "javax.servlet.ServletException", "getRootCause"); + if (nestedException != null) { + return nestedException; + } + + return null; + } + + // This method uses reflection to obtain the nest exception of a Throwable. We use reflection + // because the desired class may not exist in the currently-running VM. + private static Throwable getNestedException( + Throwable parent, String className, String methodName) { + try { + // See if this Throwable is of the desired type, by using isAssignableFrom(). + Class testClass = Class.forName(className); + Class objectClass = parent.getClass(); + if (testClass.isAssignableFrom(objectClass)) { + // Use reflection to call the specified method. + Class[] argClasses = new Class[0]; + Method method = testClass.getMethod(methodName, argClasses); + Object[] args = new Object[0]; + return (Throwable)method.invoke(parent, args); + } + } + catch(Exception ex) { + // Most likely, the desired class is not available in this VM. That's fine. + // Even if it's caused by something else, we don't want to display an error + // here, since we're already in the process of trying to display the original + // error - another error here will just confuse things. + } + + return null; + } + + // This method is similar to getNestedException() except it looks for a field instead + // of a method. + private static Throwable getNestedExceptionFromField( + Throwable parent, String className, String fieldName) { + try { + // See if this Throwable is of the desired type, by using isAssignableFrom(). + Class testClass = Class.forName(className); + Class objectClass = parent.getClass(); + if (testClass.isAssignableFrom(objectClass)) { + // Use reflection to call the specified method. + Class[] argClasses = new Class[0]; + Field field = testClass.getField(fieldName); + return (Throwable)field.get(parent); + } + } + catch(Exception ex) { + // Most likely, the desired class is not available in this VM. That's fine. + // Could be that the named field isn't of type Throwable, but that should happen + // with proper call usage. + // Even if it's caused by something else, we don't want to display an error + // here, since we're already in the process of trying to display the original + // error - another error here will just confuse things. + } + + return null; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/JDOMFactory.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/JDOMFactory.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,338 @@ +/*-- + + $Id: JDOMFactory.java,v 1.9 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +/** + * An interface to be used by builders when constructing JDOM objects. The + * DefaultJDOMFactory creates the standard top-level JDOM classes + * (Element, Document, Comment, etc). Another implementation of this factory + * could be used to create custom classes. + * + * @version $Revision: 1.9 $, $Date: 2007/11/10 05:28:59 $ + * @author Ken Rune Holland + * @author Phil Nelson + * @author Bradley S. Huffman + */ +public interface JDOMFactory { + + // **** constructing Attributes **** + + /** + *

+ * This will create a new Attribute with the + * specified (local) name and value, and in the provided + * {@link org.jdom.Namespace}. + *

+ * + * @param name String name of Attribute. + * @param value String value for new attribute. + */ + public Attribute attribute(String name, String value, Namespace namespace); + + /** + * This will create a new Attribute with the + * specified (local) name, value, and type, and in the provided + * {@link org.jdom.Namespace}. + * + * @param name String name of Attribute. + * @param value String value for new attribute. + * @param type int type for new attribute. + * @param namespace Namespace namespace for new attribute. + */ + public Attribute attribute(String name, String value, + int type, Namespace namespace); + + /** + * This will create a new Attribute with the + * specified (local) name and value, and does not place + * the attribute in a {@link org.jdom.Namespace}. + *

+ * Note: This actually explicitly puts the + * Attribute in the "empty" Namespace + * ({@link org.jdom.Namespace#NO_NAMESPACE}). + *

+ * + * @param name String name of Attribute. + * @param value String value for new attribute. + */ + public Attribute attribute(String name, String value); + + /** + * This will create a new Attribute with the + * specified (local) name, value and type, and does not place + * the attribute in a {@link org.jdom.Namespace}. + *

+ * Note: This actually explicitly puts the + * Attribute in the "empty" Namespace + * ({@link org.jdom.Namespace#NO_NAMESPACE}). + *

+ * + * @param name String name of Attribute. + * @param value String value for new attribute. + * @param type int type for new attribute. + */ + public Attribute attribute(String name, String value, int type); + + // **** constructing CDATA **** + + /** + * This creates the CDATA with the supplied text. + * + * @param str String content of CDATA. + */ + public CDATA cdata(String str); + + // **** constructing Text **** + + /** + * This creates the Text with the supplied text. + * + * @param str String content of Text. + */ + public Text text(String str); + + // **** constructing Comment **** + + /** + * This creates the comment with the supplied text. + * + * @param text String content of comment. + */ + public Comment comment(String text); + + // **** constructing DocType + + /** + * This will create the DocType with + * the specified element name and a reference to an + * external DTD. + * + * @param elementName String name of + * element being constrained. + * @param publicID String public ID of + * referenced DTD + * @param systemID String system ID of + * referenced DTD + */ + public DocType docType(String elementName, + String publicID, String systemID); + + /** + * This will create the DocType with + * the specified element name and reference to an + * external DTD. + * + * @param elementName String name of + * element being constrained. + * @param systemID String system ID of + * referenced DTD + */ + public DocType docType(String elementName, String systemID); + + /** + * This will create the DocType with + * the specified element name + * + * @param elementName String name of + * element being constrained. + */ + public DocType docType(String elementName); + + // **** constructing Document + + /** + * This will create a new Document, + * with the supplied {@link org.jdom.Element} + * as the root element and the supplied + * {@link org.jdom.DocType} declaration. + * + * @param rootElement Element for document root. + * @param docType DocType declaration. + */ + public Document document(Element rootElement, DocType docType); + + /** + * This will create a new Document, + * with the supplied {@link org.jdom.Element} + * as the root element and the supplied + * {@link org.jdom.DocType} declaration. + * + * @param rootElement Element for document root. + * @param docType DocType declaration. + * @param baseURI the URI from which this doucment was loaded. + */ + public Document document(Element rootElement, DocType docType, String baseURI); + + /** + * This will create a new Document, + * with the supplied {@link org.jdom.Element} + * as the root element, and no {@link org.jdom.DocType} + * declaration. + * + * @param rootElement Element for document root + */ + public Document document(Element rootElement); + + // **** constructing Elements **** + + /** + * This will create a new Element + * with the supplied (local) name, and define + * the {@link org.jdom.Namespace} to be used. + * + * @param name String name of element. + * @param namespace Namespace to put element in. + */ + public Element element(String name, Namespace namespace); + + /** + * This will create an Element in no + * {@link org.jdom.Namespace}. + * + * @param name String name of element. + */ + public Element element(String name); + + /** + * This will create a new Element with + * the supplied (local) name, and specifies the URI + * of the {@link org.jdom.Namespace} the Element + * should be in, resulting it being unprefixed (in the default + * namespace). + * + * @param name String name of element. + * @param uri String URI for Namespace element + * should be in. + */ + public Element element(String name, String uri); + + /** + * This will create a new Element with + * the supplied (local) name, and specifies the prefix and URI + * of the {@link org.jdom.Namespace} the Element + * should be in. + * + * @param name String name of element. + * @param uri String URI for Namespace element + * should be in. + */ + public Element element(String name, String prefix, String uri); + + // **** constructing ProcessingInstruction **** + + /** + * This will create a new ProcessingInstruction + * with the specified target and data. + * + * @param target String target of PI. + * @param data Map data for PI, in + * name/value pairs + */ + public ProcessingInstruction processingInstruction(String target, + Map data); + + /** + * This will create a new ProcessingInstruction + * with the specified target and data. + * + * @param target String target of PI. + * @param data String data for PI. + */ + public ProcessingInstruction processingInstruction(String target, + String data); + + // **** constructing EntityRef **** + + /** + * This will create a new EntityRef + * with the supplied name. + * + * @param name String name of element. + */ + public EntityRef entityRef(String name); + + /** + * This will create a new EntityRef + * with the supplied name, public ID, and system ID. + * + * @param name String name of element. + * @param publicID String public ID of element. + * @param systemID String system ID of element. + */ + public EntityRef entityRef(String name, String publicID, String systemID); + + /** + * This will create a new EntityRef + * with the supplied name and system ID. + * + * @param name String name of element. + * @param systemID String system ID of element. + */ + public EntityRef entityRef(String name, String systemID); + + // ===================================================================== + // List manipulation + // ===================================================================== + + public void addContent(Parent parent, Content content); + + public void setAttribute(Element element, Attribute a); + + public void addNamespaceDeclaration(Element element, Namespace additional); +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Namespace.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Namespace.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,276 @@ +/*-- + + $Id: Namespace.java,v 1.44 2008/12/17 23:22:48 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +/** + * An XML namespace representation, as well as a factory for creating XML + * namespace objects. Namespaces are not Serializable, however objects that use + * namespaces have special logic to handle serialization manually. These classes + * call the getNamespace() method on deserialization to ensure there is one + * unique Namespace object for any unique prefix/uri pair. + * + * @version $Revision: 1.44 $, $Date: 2008/12/17 23:22:48 $ + * @author Brett McLaughlin + * @author Elliotte Rusty Harold + * @author Jason Hunter + * @author Wesley Biggs + */ +public final class Namespace { + + // XXX May want to use weak references to keep the maps from growing + // large with extended use + + private static final String CVS_ID = + "@(#) $RCSfile: Namespace.java,v $ $Revision: 1.44 $ $Date: 2008/12/17 23:22:48 $ $Name: jdom_1_1_1 $"; + + /** + * Factory list of namespaces. + * Keys are prefix&URI. + * Values are Namespace objects + */ + private static HashMap namespaces; + + /** Define a Namespace for when not in a namespace */ + public static final Namespace NO_NAMESPACE = new Namespace("", ""); + + /** Define a Namespace for the standard xml prefix. */ + public static final Namespace XML_NAMESPACE = + new Namespace("xml", "http://www.w3.org/XML/1998/namespace"); + + /** The prefix mapped to this namespace */ + private String prefix; + + /** The URI for this namespace */ + private String uri; + + /** + * This static initializer acts as a factory contructor. + * It sets up storage and required initial values. + */ + static { + namespaces = new HashMap(16); + + // Add the "empty" namespace + namespaces.put(new NamespaceKey(NO_NAMESPACE), NO_NAMESPACE); + namespaces.put(new NamespaceKey(XML_NAMESPACE), XML_NAMESPACE); + } + + /** + * This will retrieve (if in existence) or create (if not) a + * Namespace for the supplied prefix and URI. + * + * @param prefix String prefix to map to + * Namespace. + * @param uri String URI of new Namespace. + * @return Namespace - ready to use namespace. + * @throws IllegalNameException if the given prefix and uri make up + * an illegal namespace name. + */ + public static Namespace getNamespace(String prefix, String uri) { + // Sanity checking + if ((prefix == null) || (prefix.trim().equals(""))) { + // Short-cut out for common case of no namespace + if ((uri == null) || (uri.trim().equals(""))) { + return NO_NAMESPACE; + } + prefix = ""; + } + else if ((uri == null) || (uri.trim().equals(""))) { + uri = ""; + } + + // Return existing namespace if found. The preexisting namespaces + // should all be legal. In other words, an illegal namespace won't + // have been placed in this. Thus we can do this test before + // verifying the URI and prefix. + NamespaceKey lookup = new NamespaceKey(prefix, uri); + Namespace preexisting; + synchronized (namespaces) { + preexisting = (Namespace) namespaces.get(lookup); + } + if (preexisting != null) { + return preexisting; + } + + // Ensure proper naming + String reason; + if ((reason = Verifier.checkNamespacePrefix(prefix)) != null) { + throw new IllegalNameException(prefix, "Namespace prefix", reason); + } + if ((reason = Verifier.checkNamespaceURI(uri)) != null) { + throw new IllegalNameException(uri, "Namespace URI", reason); + } + + // Unless the "empty" Namespace (no prefix and no URI), require a URI + if ((!prefix.equals("")) && (uri.equals(""))) { + throw new IllegalNameException("", "namespace", + "Namespace URIs must be non-null and non-empty Strings"); + } + + // Handle XML namespace mislabels. If the user requested the correct + // namespace and prefix -- xml, http://www.w3.org/XML/1998/namespace + // -- then it was already returned from the preexisting namespaces. + // Thus any use of the xml prefix or the + // http://www.w3.org/XML/1998/namespace URI at this point must be + // incorrect. + if (prefix.equals("xml")) { + throw new IllegalNameException(prefix, "Namespace prefix", + "The xml prefix can only be bound to " + + "http://www.w3.org/XML/1998/namespace"); + } + + // The erratum to Namespaces in XML 1.0 that suggests this + // next check is controversial. Not everyone accepts it. + if (uri.equals("http://www.w3.org/XML/1998/namespace")) { + throw new IllegalNameException(uri, "Namespace URI", + "The http://www.w3.org/XML/1998/namespace must be bound to " + + "the xml prefix."); + } + + // Finally, store and return + Namespace ns = new Namespace(prefix, uri); + synchronized (namespaces) { + namespaces.put(lookup, ns); + } + return ns; + } + + /** + * This will retrieve (if in existence) or create (if not) a + * Namespace for the supplied URI, and make it usable + * as a default namespace, as no prefix is supplied. + * + * @param uri String URI of new Namespace. + * @return Namespace - ready to use namespace. + */ + public static Namespace getNamespace(String uri) { + return getNamespace("", uri); + } + + /** + * This constructor handles creation of a Namespace object + * with a prefix and URI; it is intentionally left private + * so that it cannot be invoked by external programs/code. + * + * @param prefix String prefix to map to this namespace. + * @param uri String URI for namespace. + */ + private Namespace(String prefix, String uri) { + this.prefix = prefix; + this.uri = uri; + } + + /** + * This returns the prefix mapped to this Namespace. + * + * @return String - prefix for this Namespace. + */ + public String getPrefix() { + return prefix; + } + + /** + * This returns the namespace URI for this Namespace. + * + * @return String - URI for this Namespace. + */ + public String getURI() { + return uri; + } + + /** + * This tests for equality - Two Namespaces + * are equal if and only if their URIs are byte-for-byte equals. + * + * @param ob Object to compare to this Namespace. + * @return boolean - whether the supplied object is equal to + * this Namespace. + */ + public boolean equals(Object ob) { + if (this == ob) { + return true; + } + if (ob instanceof Namespace) { // instanceof returns false if null + return uri.equals(((Namespace)ob).uri); + } + return false; + } + + /** + * This returns a String representation of this + * Namespace, suitable for use in debugging. + * + * @return String - information about this instance. + */ + public String toString() { + return "[Namespace: prefix \"" + prefix + "\" is mapped to URI \"" + + uri + "\"]"; + } + + /** + * This returns a probably unique hash code for the Namespace. + * If two namespaces have the same URI, they are equal and have the same + * hash code, even if they have different prefixes. + * + * @return int - hash code for this Namespace. + */ + public int hashCode() { + return uri.hashCode(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/NamespaceKey.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/NamespaceKey.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,108 @@ +/*-- + + $Id: NamespaceKey.java,v 1.2 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +/** + * Key for storing a namespace representation in a map. + * + * @version $Revision: 1.2 $, $Date: 2007/11/10 05:28:59 $ + * @author Tatu Saloranta + * @author Bradley S. Huffman + */ +final class NamespaceKey { + + private static final String CVS_ID = + "@(#) $RCSfile: NamespaceKey.java,v $ $Revision: 1.2 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + private String prefix; + private String uri; + private int hash; + + public NamespaceKey(String prefix, String uri) { + this.prefix = prefix; + this.uri = uri; + this.hash = prefix.hashCode(); + } + + public NamespaceKey(Namespace namespace) { + this(namespace.getPrefix(), namespace.getURI()); + } + + public boolean equals(Object ob) { + if (this == ob) { + return true; + } + else if (ob instanceof NamespaceKey) { + NamespaceKey other = (NamespaceKey) ob; + return prefix.equals(other.prefix) && uri.equals(other.uri); + } + else { + return false; + } + } + + public int hashCode() { + return hash; + } + + public String toString() { + return "[NamespaceKey: prefix \"" + prefix + + "\" is mapped to URI \"" + uri + "\"]"; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Parent.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Parent.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,239 @@ +/*-- + + $Id: Parent.java,v 1.13 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.io.Serializable; +import java.util.*; +import org.jdom.filter.Filter; + +/** + * Superclass for JDOM objects which are allowed to contain + * {@link Content} content. + * + * @see org.jdom.Content + * @see org.jdom.Document + * @see org.jdom.Element + * + * @author Bradley S. Huffman + * @author Jason Hunter + * @version $Revision: 1.13 $, $Date: 2007/11/10 05:28:59 $ + */ +public interface Parent extends Cloneable, Serializable { + + /** + * Returns the number of children in this parent's content list. + * Children may be any {@link Content} type. + * + * @return number of children + */ + int getContentSize(); + + /** + * Returns the index of the supplied child in the content list, + * or -1 if not a child of this parent. + * + * @param child child to search for + * @return index of child, or -1 if not found + */ + int indexOf(Content child); + +// /** +// * Starting at the given index (inclusive), returns the index of +// * the first child matching the supplied filter, or -1 +// * if none is found. +// * +// * @return index of child, or -1 if none found +// */ +// int indexOf(int index, Filter filter); + + /** + * Returns a list containing detached clones of this parent's content list. + * + * @return list of cloned child content + */ + List cloneContent(); + + /** + * Returns the child at the given index. + * + * @param index location of desired child + * @return child at the given index + * @throws IndexOutOfBoundsException if index is negative or beyond + * the current number of children + * @throws IllegalStateException if parent is a Document + * and the root element is not set + */ + Content getContent(int index); + + /** + * Returns the full content of this parent as a {@link java.util.List} + * which contains objects of type {@link Content}. The returned list is + * "live" and in document order. Any modifications + * to it affect the element's actual contents. Modifications are checked + * for conformance to XML 1.0 rules. + *

+ * Sequential traversal through the List is best done with an Iterator + * since the underlying implement of {@link java.util.List#size} may + * require walking the entire list and indexed lookups may require + * starting at the beginning each time. + * + * @return a list of the content of the parent + * @throws IllegalStateException if parent is a Document + * and the root element is not set + */ + List getContent(); + + /** + * Returns as a {@link java.util.List} the content of + * this parent that matches the supplied filter. The returned list is + * "live" and in document order. Any modifications to it affect + * the element's actual contents. Modifications are checked for + * conformance to XML 1.0 rules. + *

+ * Sequential traversal through the List is best done with an Iterator + * since the underlying implement of {@link java.util.List#size} may + * require walking the entire list and indexed lookups may require + * starting at the beginning each time. + * + * @param filter filter to apply + * @return a list of the content of the parent matching the filter + * @throws IllegalStateException if parent is a Document + * and the root element is not set + */ + List getContent(Filter filter); + + /** + * Removes all content from this parent and returns the detached + * children. + * + * @return list of the old content detached from this parent + */ + List removeContent(); + + /** + * Removes from this parent all child content matching the given filter + * and returns a list of the detached children. + * + * @param filter filter to apply + * @return list of the detached children matching the filter + */ + List removeContent(Filter filter); + + /** + * Removes a single child node from the content list. + * + * @param child child to remove + * @return whether the removal occurred + */ + boolean removeContent(Content child); + + /** + * Removes and returns the child at the given + * index, or returns null if there's no such child. + * + * @param index index of child to remove + * @return detached child at given index or null if no + * @throws IndexOutOfBoundsException if index is negative or beyond + * the current number of children + */ + Content removeContent(int index); + + /** + * Obtain a deep, unattached copy of this parent and it's children. + * + * @return a deep copy of this parent and it's children. + */ + Object clone(); + + /** + * Returns an {@link java.util.Iterator} that walks over all descendants + * in document order. + * + * @return an iterator to walk descendants + */ + Iterator getDescendants(); + + /** + * Returns an {@link java.util.Iterator} that walks over all descendants + * in document order applying the Filter to return only elements that + * match the filter rule. With filters you can match only Elements, + * only Comments, Elements or Comments, only Elements with a given name + * and/or prefix, and so on. + * + * @param filter filter to select which descendants to see + * @return an iterator to walk descendants that match a filter + */ + Iterator getDescendants(Filter filter); + + /** + * Return this parent's parent, or null if this parent is currently + * not attached to another parent. This is the same method as in Content but + * also added to Parent to allow more easy up-the-tree walking. + * + * @return this parent's parent or null if none + */ + Parent getParent(); + + /** + * Return this parent's owning document or null if the branch containing + * this parent is currently not attached to a document. + * + * @return this child's owning document or null if none + */ + Document getDocument(); + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/ProcessingInstruction.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/ProcessingInstruction.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,473 @@ +/*-- + + $Id: ProcessingInstruction.java,v 1.47 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +/** + * An XML processing instruction. Methods allow the user to obtain the target of + * the PI as well as its data. The data can always be accessed as a String or, + * if the data appears akin to an attribute list, can be retrieved as name/value + * pairs. + * + * @version $Revision: 1.47 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Steven Gould + */ + +public class ProcessingInstruction extends Content { + + private static final String CVS_ID = + "@(#) $RCSfile: ProcessingInstruction.java,v $ $Revision: 1.47 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** The target of the PI */ + protected String target; + + /** The data for the PI as a String */ + protected String rawData; + + /** The data for the PI in name/value pairs */ + protected Map mapData; + + /** + * Default, no-args constructor for implementations + * to use if needed. + */ + protected ProcessingInstruction() { } + + /** + * This will create a new ProcessingInstruction + * with the specified target and data. + * + * @param target String target of PI. + * @param data Map data for PI, in + * name/value pairs + * @throws IllegalTargetException if the given target is illegal + * as a processing instruction name. + */ + public ProcessingInstruction(String target, Map data) { + setTarget(target); + setData(data); + } + + /** + * This will create a new ProcessingInstruction + * with the specified target and data. + * + * @param target String target of PI. + * @param data String data for PI. + * @throws IllegalTargetException if the given target is illegal + * as a processing instruction name. + */ + public ProcessingInstruction(String target, String data) { + setTarget(target); + setData(data); + } + + /** + * This will set the target for the PI. + * + * @param newTarget String new target of PI. + * @return ProcessingInstruction - this PI modified. + */ + public ProcessingInstruction setTarget(String newTarget) { + String reason; + if ((reason = Verifier.checkProcessingInstructionTarget(newTarget)) + != null) { + throw new IllegalTargetException(newTarget, reason); + } + + target = newTarget; + return this; + } + + /** + * Returns the XPath 1.0 string value of this element, which is the + * data of this PI. + * + * @return the data of this PI + */ + public String getValue() { + return rawData; + } + + + /** + * This will retrieve the target of the PI. + * + * @return String - target of PI. + */ + public String getTarget() { + return target; + } + + /** + * This will return the raw data from all instructions. + * + * @return String - data of PI. + */ + public String getData() { + return rawData; + } + + /** + * This will return a List containing the names of the + * "attribute" style pieces of name/value pairs in this PI's data. + * + * @return List - the List containing the + * "attribute" names. + */ + public List getPseudoAttributeNames() { + Set mapDataSet = mapData.entrySet(); + List nameList = new ArrayList(); + for (Iterator i = mapDataSet.iterator(); i.hasNext();) { + String wholeSet = (i.next()).toString(); + String attrName = wholeSet.substring(0,(wholeSet.indexOf("="))); + nameList.add(attrName); + } + return nameList; + } + + /** + * This will set the raw data for the PI. + * + * @param data String data of PI. + * @return ProcessingInstruction - this PI modified. + */ + public ProcessingInstruction setData(String data) { + String reason = Verifier.checkProcessingInstructionData(data); + if (reason != null) { + throw new IllegalDataException(data, reason); + } + + this.rawData = data; + this.mapData = parseData(data); + return this; + } + + /** + * This will set the name/value pairs within the passed + * Map as the pairs for the data of + * this PI. The keys should be the pair name + * and the values should be the pair values. + * + * @param data new map data to use + * @return ProcessingInstruction - modified PI. + */ + public ProcessingInstruction setData(Map data) { + String temp = toString(data); + + String reason = Verifier.checkProcessingInstructionData(temp); + if (reason != null) { + throw new IllegalDataException(temp, reason); + } + + this.rawData = temp; + this.mapData = data; + return this; + } + + + /** + * This will return the value for a specific + * name/value pair on the PI. If no such pair is + * found for this PI, null is returned. + * + * @param name String name of name/value pair + * to lookup value for. + * @return String - value of name/value pair. + */ + public String getPseudoAttributeValue(String name) { + return (String)mapData.get(name); + } + + /** + * This will set a pseudo attribute with the given name and value. + * If the PI data is not already in a pseudo-attribute format, this will + * replace the existing data. + * + * @param name String name of pair. + * @param value String value for pair. + * @return ProcessingInstruction this PI modified. + */ + public ProcessingInstruction setPseudoAttribute(String name, String value) { + String reason = Verifier.checkProcessingInstructionData(name); + if (reason != null) { + throw new IllegalDataException(name, reason); + } + + reason = Verifier.checkProcessingInstructionData(value); + if (reason != null) { + throw new IllegalDataException(value, reason); + } + + this.mapData.put(name, value); + this.rawData = toString(mapData); + return this; + } + + + /** + * This will remove the pseudo attribute with the specified name. + * + * @param name name of pseudo attribute to remove + * @return boolean - whether the requested + * instruction was removed. + */ + public boolean removePseudoAttribute(String name) { + if ((mapData.remove(name)) != null) { + rawData = toString(mapData); + return true; + } + + return false; + } + + /** + * This will convert the Map to a string representation. + * + * @param mapData Map PI data to convert + * @return a string representation of the Map as appropriate for a PI + */ + private String toString(Map mapData) { + StringBuffer rawData = new StringBuffer(); + + Iterator i = mapData.keySet().iterator(); + while (i.hasNext()) { + String name = (String)i.next(); + String value = (String)mapData.get(name); + rawData.append(name) + .append("=\"") + .append(value) + .append("\" "); + } + // Remove last space, if we did any appending + if (rawData.length() > 0) { + rawData.setLength(rawData.length() - 1); + } + + return rawData.toString(); + } + + /** + * This will parse and load the instructions for the PI. + * This is separated to allow it to occur once and then be reused. + */ + private Map parseData(String rawData) { + // The parsing here is done largely "by hand" which means the code + // gets a little tricky/messy. The following conditions should + // now be handled correctly: + // Reads OK + // Reads OK + // Reads OK + // Reads OK + // Empty Map + // Empty Map + // Empty Map + + Map data = new HashMap(); + + // System.out.println("rawData: " + rawData); + + // The inputData variable holds the part of rawData left to parse + String inputData = rawData.trim(); + + // Iterate through the remaining inputData string + while (!inputData.trim().equals("")) { + //System.out.println("parseData() looking at: " + inputData); + + // Search for "name =", "name=" or "name1 name2..." + String name = ""; + String value = ""; + int startName = 0; + char previousChar = inputData.charAt(startName); + int pos = 1; + for (; pos 0 && value != null) { + //if (data.containsKey(name)) { + // A repeat, that's a parse error, so return a null map + //return new HashMap(); + //} + //else { + data.put(name, value); + //} + } + } + + return data; + } + + /** + * This is a helper routine, only used by parseData, to extract a + * quoted String from the input parameter, rawData. A quoted string + * can use either single or double quotes, but they must match up. + * A singly quoted string can contain an unbalanced amount of double + * quotes, or vice versa. For example, the String "JDOM's the best" + * is legal as is 'JDOM"s the best'. + * + * @param rawData the input string from which a quoted string is to + * be extracted. + * @return the first quoted string encountered in the input data. If + * no quoted string is found, then the empty string, "", is + * returned. + * @see #parseData + */ + private static int[] extractQuotedString(String rawData) { + // Remembers whether we're actually in a quoted string yet + boolean inQuotes = false; + + // Remembers which type of quoted string we're in + char quoteChar = '"'; + + // Stores the position of the first character inside + // the quoted string (i.e. the start of the return string) + int start = 0; + + // Iterate through the input string looking for the start + // and end of the quoted string + for (int pos=0; pos < rawData.length(); pos++) { + char currentChar = rawData.charAt(pos); + if (currentChar=='"' || currentChar=='\'') { + if (!inQuotes) { + // We're entering a quoted string + quoteChar = currentChar; + inQuotes = true; + start = pos+1; + } + else if (quoteChar == currentChar) { + // We're leaving a quoted string + inQuotes = false; + return new int[] { start, pos }; + } + // Otherwise we've encountered a quote + // inside a quote, so just continue + } + } + + return null; + } + + /** + * This returns a String representation of the + * ProcessingInstruction, suitable for debugging. If the XML + * representation of the ProcessingInstruction is desired, + * {@link org.jdom.output.XMLOutputter#outputString(ProcessingInstruction)} + * should be used. + * + * @return String - information about the + * ProcessingInstruction + */ + public String toString() { + return new StringBuffer() + .append("[ProcessingInstruction: ") + .append(new org.jdom.output.XMLOutputter().outputString(this)) + .append("]") + .toString(); + } + + /** + * This will return a clone of this ProcessingInstruction. + * + * @return Object - clone of this + * ProcessingInstruction. + */ + public Object clone() { + ProcessingInstruction pi = (ProcessingInstruction) super.clone(); + + // target and rawdata are immutable and references copied by + // Object.clone() + + // Create a new Map object for the clone (since Map isn't Cloneable) + if (mapData != null) { + pi.mapData = parseData(rawData); + } + return pi; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Text.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Text.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,271 @@ +/*-- + + $Id: Text.java,v 1.25 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +/** + * Character-based XML content. Provides a modular, parentable method of + * representing text. Text makes no guarantees about the underlying textual + * representation of character data, but does expose that data as a Java String. + * + * @version $Revision: 1.25 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Bradley S. Huffman + */ +public class Text extends Content { + + private static final String CVS_ID = + "@(#) $RCSfile: Text.java,v $ $Revision: 1.25 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + static final String EMPTY_STRING = ""; + + /** The actual character content */ + // XXX See http://www.servlets.com/archive/servlet/ReadMsg?msgId=8612 + // from elharo for a description of why Java characters may not suffice + // long term + protected String value; + + /** + * This is the protected, no-args constructor standard in all JDOM + * classes. It allows subclassers to get a raw instance with no + * initialization. + */ + protected Text() { } + + /** + * This constructor creates a new Text node, with the + * supplied string value as it's character content. + * + * @param str the node's character content. + * @throws IllegalDataException if str contains an + * illegal character such as a vertical tab (as determined + * by {@link org.jdom.Verifier#checkCharacterData}) + */ + public Text(String str) { + setText(str); + } + + /** + * This returns the value of this Text node as a Java + * String. + * + * @return String - character content of this node. + */ + public String getText() { + return value; + } + + /** + * This returns the textual content with all surrounding whitespace + * removed. If only whitespace exists, the empty string is returned. + * + * @return trimmed text content or empty string + */ + public String getTextTrim() { + return getText().trim(); + } + + /** + * This returns the textual content with all surrounding whitespace + * removed and internal whitespace normalized to a single space. If + * only whitespace exists, the empty string is returned. + * + * @return normalized text content or empty string + */ + public String getTextNormalize() { + return normalizeString(getText()); + } + + /** + * This returns a new string with all surrounding whitespace + * removed and internal whitespace normalized to a single space. If + * only whitespace exists, the empty string is returned. + *

+ * Per XML 1.0 Production 3 whitespace includes: #x20, #x9, #xD, #xA + *

+ * + * @param str string to be normalized. + * @return normalized string or empty string + */ + public static String normalizeString(String str) { + if (str == null) + return EMPTY_STRING; + + char[] c = str.toCharArray(); + char[] n = new char[c.length]; + boolean white = true; + int pos = 0; + for (int i = 0; i < c.length; i++) { + if (" \t\n\r".indexOf(c[i]) != -1) { + if (!white) { + n[pos++] = ' '; + white = true; + } + } + else { + n[pos++] = c[i]; + white = false; + } + } + if (white && pos > 0) { + pos--; + } + return new String(n, 0, pos); + } + + /** + * This will set the value of this Text node. + * + * @param str value for node's content. + * @return the object on which the method was invoked + * @throws IllegalDataException if str contains an + * illegal character such as a vertical tab (as determined + * by {@link org.jdom.Verifier#checkCharacterData}) + */ + public Text setText(String str) { + String reason; + + if (str == null) { + value = EMPTY_STRING; + return this; + } + + if ((reason = Verifier.checkCharacterData(str)) != null) { + throw new IllegalDataException(str, "character content", reason); + } + value = str; + return this; + } + + /** + * This will append character content to whatever content already + * exists within this Text node. + * + * @param str character content to append. + * @throws IllegalDataException if str contains an + * illegal character such as a vertical tab (as determined + * by {@link org.jdom.Verifier#checkCharacterData}) + */ + public void append(String str) { + String reason; + + if (str == null) { + return; + } + if ((reason = Verifier.checkCharacterData(str)) != null) { + throw new IllegalDataException(str, "character content", reason); + } + + if (str == EMPTY_STRING) + value = str; + else value += str; + } + + /** + * This will append the content of another Text node + * to this node. + * + * @param text Text node to append. + */ + public void append(Text text) { + if (text == null) { + return; + } + value += text.getText(); + } + + /** + * Returns the XPath 1.0 string value of this element, which is the + * text itself. + * + * @return the text + */ + public String getValue() { + return value; + } + + /** + * This returns a String representation of the + * Text node, suitable for debugging. If the XML + * representation of the Text node is desired, + * either {@link #getText} or + * {@link org.jdom.output.XMLOutputter#outputString(Text)} + * should be used. + * + * @return String - information about this node. + */ + public String toString() { + return new StringBuffer(64) + .append("[Text: ") + .append(getText()) + .append("]") + .toString(); + } + + /** + * This will return a clone of this Text node, with the + * same character content, but no parent. + * + * @return Text - cloned node. + */ + public Object clone() { + Text text = (Text)super.clone(); + text.value = value; + return text; + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/UncheckedJDOMFactory.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/UncheckedJDOMFactory.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,287 @@ +/*-- + + $Id: UncheckedJDOMFactory.java,v 1.4 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +/** + * Special factory for building documents without any content or structure + * checking. This should only be used when you are 100% positive that the + * input is absolutely correct. This factory can speed builds, but any + * problems in the input will be uncaught until later when they could cause + * infinite loops, malformed XML, or worse. Use with extreme caution. + */ +public class UncheckedJDOMFactory implements JDOMFactory { + + // ===================================================================== + // Element Factory + // ===================================================================== + + public Element element(String name, Namespace namespace) { + Element e = new Element(); + e.name = name; + if (namespace == null) { + namespace = Namespace.NO_NAMESPACE; + } + e.namespace = namespace; + return e; + } + + public Element element(String name) { + Element e = new Element(); + e.name = name; + e.namespace = Namespace.NO_NAMESPACE; + return e; + } + + public Element element(String name, String uri) { + return element(name, Namespace.getNamespace("", uri)); + } + + public Element element(String name, String prefix, String uri) { + return element(name, Namespace.getNamespace(prefix, uri)); + } + + // ===================================================================== + // Attribute Factory + // ===================================================================== + + public Attribute attribute(String name, String value, Namespace namespace) { + Attribute a = new Attribute(); + a.name = name; + a.value = value; + if (namespace == null) { + namespace = Namespace.NO_NAMESPACE; + } + a.namespace = namespace; + return a; + } + + public Attribute attribute(String name, String value, int type, Namespace namespace) { + Attribute a = new Attribute(); + a.name = name; + a.type = type; + a.value = value; + if (namespace == null) { + namespace = Namespace.NO_NAMESPACE; + } + a.namespace = namespace; + return a; + } + + public Attribute attribute(String name, String value) { + Attribute a = new Attribute(); + a.name = name; + a.value = value; + a.namespace = Namespace.NO_NAMESPACE; + return a; + } + + public Attribute attribute(String name, String value, int type) { + Attribute a = new Attribute(); + a.name = name; + a.type = type; + a.value = value; + a.namespace = Namespace.NO_NAMESPACE; + return a; + } + + // ===================================================================== + // Text Factory + // ===================================================================== + + public Text text(String str) { + Text t = new Text(); + t.value = str; + return t; + } + + // ===================================================================== + // CDATA Factory + // ===================================================================== + + public CDATA cdata(String str) { + CDATA c = new CDATA(); + c.value = str; + return c; + } + + // ===================================================================== + // Comment Factory + // ===================================================================== + + public Comment comment(String str) { + Comment c = new Comment(); + c.text = str; + return c; + } + + // ===================================================================== + // Processing Instruction Factory + // ===================================================================== + + public ProcessingInstruction processingInstruction(String target, Map data) { + ProcessingInstruction p = new ProcessingInstruction(); + p.target = target; + p.setData(data); + return p; + } + + public ProcessingInstruction processingInstruction(String target, String data) { + ProcessingInstruction p = new ProcessingInstruction(); + p.target = target; + p.setData(data); + return p; + } + + // ===================================================================== + // Entity Ref Factory + // ===================================================================== + + public EntityRef entityRef(String name) { + EntityRef e = new org.jdom.EntityRef(); + e.name = name; + return e; + } + + public EntityRef entityRef(String name, String systemID) { + EntityRef e = new EntityRef(); + e.name = name; + e.systemID = systemID; + return e; + } + + public EntityRef entityRef(String name, String publicID, String systemID) { + EntityRef e = new EntityRef(); + e.name = name; + e.publicID = publicID; + e.systemID = systemID; + return e; + } + + // ===================================================================== + // DocType Factory + // ===================================================================== + + public DocType docType(String elementName, String publicID, String systemID) { + DocType d = new DocType(); + d.elementName = elementName; + d.publicID = publicID; + d.systemID = systemID; + return d; + } + + public DocType docType(String elementName, String systemID) { + return docType(elementName, null, systemID); + } + + public DocType docType(String elementName) { + return docType(elementName, null, null); + } + + // ===================================================================== + // Document Factory + // ===================================================================== + + public Document document(Element rootElement, DocType docType, String baseURI) { + Document d = new Document(); + if (docType != null) { + addContent(d, docType); + } + if (rootElement != null) { + addContent(d, rootElement); + } + if (baseURI != null) { + d.baseURI = baseURI; + } + return d; + } + + public Document document(Element rootElement, DocType docType) { + return document(rootElement, docType, null); + } + + public Document document(Element rootElement) { + return document(rootElement, null, null); + } + + // ===================================================================== + // List manipulation + // ===================================================================== + + public void addContent(Parent parent, Content child) { + if (parent instanceof Element) { + Element elt = (Element) parent; + elt.content.uncheckedAddContent(child); + } + else { + Document doc = (Document) parent; + doc.content.uncheckedAddContent(child); + } + } + + public void setAttribute(Element parent, Attribute a) { + parent.attributes.uncheckedAddAttribute(a); + } + + public void addNamespaceDeclaration(Element parent, Namespace additional) { + if (parent.additionalNamespaces == null) { + parent.additionalNamespaces = new ArrayList(5); //Element.INITIAL_ARRAY_SIZE + } + parent.additionalNamespaces.add(additional); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Verifier.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/Verifier.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,1271 @@ +/*-- + + $Id: Verifier.java,v 1.57 2009/07/23 05:54:23 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom; + +import java.util.*; + +/** + * A utility class to handle well-formedness checks on names, data, and other + * verification tasks for JDOM. The class is final and may not be subclassed. + * + * @version $Revision: 1.57 $, $Date: 2009/07/23 05:54:23 $ + * @author Brett McLaughlin + * @author Elliotte Rusty Harold + * @author Jason Hunter + * @author Bradley S. Huffman + */ +final public class Verifier { + + private static final String CVS_ID = + "@(#) $RCSfile: Verifier.java,v $ $Revision: 1.57 $ $Date: 2009/07/23 05:54:23 $ $Name: jdom_1_1_1 $"; + + /** + * Ensure instantation cannot occur. + */ + private Verifier() { } + + /** + * This will check the supplied name to see if it is legal for use as + * a JDOM {@link Element} name. + * + * @param name String name to check. + * @return String reason name is illegal, or + * null if name is OK. + */ + public static String checkElementName(String name) { + // Check basic XML name rules first + String reason; + if ((reason = checkXMLName(name)) != null) { + return reason; + } + + // No colons allowed, since elements handle this internally + if (name.indexOf(":") != -1) { + return "Element names cannot contain colons"; + } + + // If we got here, everything is OK + return null; + } + + /** + * This will check the supplied name to see if it is legal for use as + * a JDOM {@link Attribute} name. + * + * @param name String name to check. + * @return String reason name is illegal, or + * null if name is OK. + */ + public static String checkAttributeName(String name) { + // Check basic XML name rules first + String reason; + if ((reason = checkXMLName(name)) != null) { + return reason; + } + + // No colons are allowed, since attributes handle this internally + if (name.indexOf(":") != -1) { + return "Attribute names cannot contain colons"; + } + + // Attribute names may not be xmlns since we do this internally too + if (name.equals("xmlns")) { + return "An Attribute name may not be \"xmlns\"; " + + "use the Namespace class to manage namespaces"; + } + + // If we got here, everything is OK + return null; + } + + /** + * This will check the supplied string to see if it only contains + * characters allowed by the XML 1.0 specification. The C0 controls + * (e.g. null, vertical tab, formfeed, etc.) are specifically excluded + * except for carriage return, linefeed, and the horizontal tab. + * Surrogates are also excluded. + *

+ * This method is useful for checking element content and attribute + * values. Note that characters + * like " and < are allowed in attribute values and element content. + * They will simply be escaped as " or < + * when the value is serialized. + *

+ * + * @param text String value to check. + * @return String reason name is illegal, or + * null if name is OK. + */ + public static String checkCharacterData(String text) { + if (text == null) { + return "A null is not a legal XML value"; + } + + // Do check + for (int i = 0, len = text.length(); i{@link CDATA}. + * + * @param data String data to check. + * @return String reason data is illegal, or + * null is name is OK. + */ + public static String checkCDATASection(String data) { + String reason = null; + if ((reason = checkCharacterData(data)) != null) { + return reason; + } + + if (data.indexOf("]]>") != -1) { + return "CDATA cannot internally contain a CDATA ending " + + "delimiter (]]>)"; + } + + // If we got here, everything is OK + return null; + } + + /** + * This will check the supplied name to see if it is legal for use as + * a JDOM {@link Namespace} prefix. + * + * @param prefix String prefix to check. + * @return String reason name is illegal, or + * null if name is OK. + */ + public static String checkNamespacePrefix(String prefix) { + // Manually do rules, since URIs can be null or empty + if ((prefix == null) || (prefix.equals(""))) { + return null; + } + + // Cannot start with a number + char first = prefix.charAt(0); + if (isXMLDigit(first)) { + return "Namespace prefixes cannot begin with a number"; + } + // Cannot start with a $ + if (first == '$') { + return "Namespace prefixes cannot begin with a dollar sign ($)"; + } + // Cannot start with a - + if (first == '-') { + return "Namespace prefixes cannot begin with a hyphen (-)"; + } + // Cannot start with a . + if (first == '.') { + return "Namespace prefixes cannot begin with a period (.)"; + } + // Cannot start with "xml" in any character case + if (prefix.toLowerCase().startsWith("xml")) { + return "Namespace prefixes cannot begin with " + + "\"xml\" in any combination of case"; + } + + // Ensure legal content + for (int i=0, len = prefix.length(); i{@link Namespace} URI. + * + * @param uri String URI to check. + * @return String reason name is illegal, or + * null if name is OK. + */ + public static String checkNamespaceURI(String uri) { + // Manually do rules, since URIs can be null or empty + if ((uri == null) || (uri.equals(""))) { + return null; + } + + // Cannot start with a number + char first = uri.charAt(0); + if (Character.isDigit(first)) { + return "Namespace URIs cannot begin with a number"; + } + // Cannot start with a $ + if (first == '$') { + return "Namespace URIs cannot begin with a dollar sign ($)"; + } + // Cannot start with a - + if (first == '-') { + return "Namespace URIs cannot begin with a hyphen (-)"; + } + + // If we got here, everything is OK + return null; + } + + /** + * Check if two namespaces collide. + * + * @param namespace Namespace to check. + * @param other Namespace to check against. + * @return String reason for collision, or + * null if no collision. + */ + public static String checkNamespaceCollision(Namespace namespace, + Namespace other) { + String p1,p2,u1,u2,reason; + + reason = null; + p1 = namespace.getPrefix(); + u1 = namespace.getURI(); + p2 = other.getPrefix(); + u2 = other.getURI(); + if (p1.equals(p2) && !u1.equals(u2)) { + reason = "The namespace prefix \"" + p1 + "\" collides"; + } + return reason; + } + + /** + * Check if {@link Attribute}'s namespace collides with a + * {@link Element}'s namespace. + * + * @param attribute Attribute to check. + * @param element Element to check against. + * @return String reason for collision, or + * null if no collision. + */ + public static String checkNamespaceCollision(Attribute attribute, + Element element) { + Namespace namespace = attribute.getNamespace(); + String prefix = namespace.getPrefix(); + if ("".equals(prefix)) { + return null; + } + + return checkNamespaceCollision(namespace, element); + } + + /** + * Check if a {@link Namespace} collides with a + * {@link Element}'s namespace. + * + * @param namespace Namespace to check. + * @param element Element to check against. + * @return String reason for collision, or + * null if no collision. + */ + public static String checkNamespaceCollision(Namespace namespace, + Element element) { + String reason = checkNamespaceCollision(namespace, + element.getNamespace()); + if (reason != null) { + return reason + " with the element namespace prefix"; + } + + reason = checkNamespaceCollision(namespace, + element.getAdditionalNamespaces()); + if (reason != null) { + return reason; + } + + reason = checkNamespaceCollision(namespace, element.getAttributes()); + if (reason != null) { + return reason; + } + + return null; + } + + /** + * Check if a {@link Namespace} collides with a + * {@link Attribute}'s namespace. + * + * @param namespace Namespace to check. + * @param attribute Attribute to check against. + * @return String reason for collision, or + * null if no collision. + */ + public static String checkNamespaceCollision(Namespace namespace, + Attribute attribute) { + String reason = null; + if (!attribute.getNamespace().equals(Namespace.NO_NAMESPACE)) { + reason = checkNamespaceCollision(namespace, + attribute.getNamespace()); + if (reason != null) { + reason += " with an attribute namespace prefix on the element"; + } + } + return reason; + } + + /** + * Check if a {@link Namespace} collides with any namespace + * from a list of objects. + * + * @param namespace Namespace to check. + * @param list List to check against. + * @return String reason for collision, or + * null if no collision. + */ + public static String checkNamespaceCollision(Namespace namespace, + List list) { + if (list == null) { + return null; + } + + String reason = null; + Iterator i = list.iterator(); + while ((reason == null) && i.hasNext()) { + Object obj = i.next(); + if (obj instanceof Attribute) { + reason = checkNamespaceCollision(namespace, (Attribute) obj); + } + else if (obj instanceof Element) { + reason = checkNamespaceCollision(namespace, (Element) obj); + } + else if (obj instanceof Namespace) { + reason = checkNamespaceCollision(namespace, (Namespace) obj); + if (reason != null) { + reason += " with an additional namespace declared" + + " by the element"; + } + } + } + return reason; + } + + /** + * This will check the supplied data to see if it is legal for use as + * a JDOM {@link ProcessingInstruction} target. + * + * @param target String target to check. + * @return String reason target is illegal, or + * null if target is OK. + */ + public static String checkProcessingInstructionTarget(String target) { + // Check basic XML name rules first + String reason; + if ((reason = checkXMLName(target)) != null) { + return reason; + } + + // No colons allowed, per Namespace Specification Section 6 + if (target.indexOf(":") != -1) { + return "Processing instruction targets cannot contain colons"; + } + + // Cannot begin with 'xml' in any case + if (target.equalsIgnoreCase("xml")) { + return "Processing instructions cannot have a target of " + + "\"xml\" in any combination of case. (Note that the " + + "\"\" declaration at the beginning of a " + + "document is not a processing instruction and should not " + + "be added as one; it is written automatically during " + + "output, e.g. by XMLOutputter.)"; + } + + // If we got here, everything is OK + return null; + } + + /** + * This will check the supplied data to see if it is legal for use as + * {@link ProcessingInstruction} data. Besides checking that + * all the characters are allowed in XML, this also checks + * that the data does not contain the PI end-string "?>". + * + * @param data String data to check. + * @return String reason data is illegal, or + * null if data is OK. + */ + public static String checkProcessingInstructionData(String data) { + // Check basic XML name rules first + String reason = checkCharacterData(data); + + if (reason == null) { + if (data.indexOf("?>") >= 0) { + return "Processing instructions cannot contain " + + "the string \"?>\""; + } + } + + return reason; + } + + /** + * This will check the supplied data to see if it is legal for use as + * JDOM {@link Comment} data. + * + * @param data String data to check. + * @return String reason data is illegal, or + * null if data is OK. + */ + public static String checkCommentData(String data) { + String reason = null; + if ((reason = checkCharacterData(data)) != null) { + return reason; + } + + if (data.indexOf("--") != -1) { + return "Comments cannot contain double hyphens (--)"; + } + if (data.endsWith("-")) { + return "Comment data cannot end with a hyphen."; + } + + // If we got here, everything is OK + return null; + } + /** + * This is a utility function to decode a non-BMP + * UTF-16 surrogate pair. + * @param high high 16 bits + * @param low low 16 bits + * @return decoded character + */ + public static int decodeSurrogatePair(char high, char low) { + return 0x10000 + (high - 0xD800) * 0x400 + (low - 0xDC00); + } + + // [13] PubidChar ::= #x20 | #xD | #xA | [a-zA-Z0-9] | + // [-'()+,./:=?;*#@$_%] + public static boolean isXMLPublicIDCharacter(char c) { + + if (c >= 'a' && c <= 'z') return true; + if (c >= '?' && c <= 'Z') return true; + if (c >= '\'' && c <= ';') return true; + + if (c == ' ') return true; + if (c == '!') return true; + if (c == '=') return true; + if (c == '#') return true; + if (c == '$') return true; + if (c == '_') return true; + if (c == '%') return true; + if (c == '\n') return true; + if (c == '\r') return true; + if (c == '\t') return true; + + return false; + } + + /** + * This will ensure that the data for a public identifier + * is legal. + * + * @param publicID String public ID to check. + * @return String reason public ID is illegal, or + * null if public ID is OK. + */ + public static String checkPublicID(String publicID) { + String reason = null; + + if (publicID == null) return null; + // This indicates there is no public ID + + for (int i = 0; i < publicID.length(); i++) { + char c = publicID.charAt(i); + if (!isXMLPublicIDCharacter(c)) { + reason = c + " is not a legal character in public IDs"; + break; + } + } + + return reason; + } + + + /** + * This will ensure that the data for a system literal + * is legal. + * + * @param systemLiteral String system literal to check. + * @return String reason system literal is illegal, or + * null if system literal is OK. + */ + public static String checkSystemLiteral(String systemLiteral) { + String reason = null; + + if (systemLiteral == null) return null; + // This indicates there is no system ID + + if (systemLiteral.indexOf('\'') != -1 + && systemLiteral.indexOf('"') != -1) { + reason = + "System literals cannot simultaneously contain both single and double quotes."; + } + else { + reason = checkCharacterData(systemLiteral); + } + + return reason; + } + + /** + * This is a utility function for sharing the base process of checking + * any XML name. + * + * @param name String to check for XML name compliance. + * @return String reason the name is illegal, or + * null if OK. + */ + public static String checkXMLName(String name) { + // Cannot be empty or null + if ((name == null) || (name.length() == 0) + || (name.trim().equals(""))) { + return "XML names cannot be null or empty"; + } + + + // Cannot start with a number + char first = name.charAt(0); + if (!isXMLNameStartCharacter(first)) { + return "XML names cannot begin with the character \"" + + first + "\""; + } + // Ensure legal content for non-first chars + for (int i=1, len = name.length(); i + * Checks a string to see if it is a legal RFC 2396 URI. + * Both absolute and relative URIs are supported. + *

+ * + * @param uri String to check. + * @return String reason the URI is illegal, or + * null if OK. + */ + public static String checkURI(String uri) { + // URIs can be null or empty + if ((uri == null) || (uri.equals(""))) { + return null; + } + + for (int i = 0; i < uri.length(); i++) { + char test = uri.charAt(i); + if (!isURICharacter(test)) { + String msgNumber = "0x" + Integer.toHexString(test); + if (test <= 0x09) msgNumber = "0x0" + Integer.toHexString(test); + return "URIs cannot contain " + msgNumber; + } // end if + if (test == '%') { // must be followed by two hexadecimal digits + try { + char firstDigit = uri.charAt(i+1); + char secondDigit = uri.charAt(i+2); + if (!isHexDigit(firstDigit) || + !isHexDigit(secondDigit)) { + return "Percent signs in URIs must be followed by " + + "exactly two hexadecimal digits."; + } + + } + catch (StringIndexOutOfBoundsException e) { + return "Percent signs in URIs must be followed by " + + "exactly two hexadecimal digits."; + } + } + } // end for + + // If we got here, everything is OK + return null; + } + + /** + *

+ * This is a utility function for determining whether a specified + * Unicode character is a hexadecimal digit as defined in RFC 2396; + * that is, one of the ASCII characters 0-9, a-f, or A-F. + *

+ * + * @param c to check for hex digit. + * @return true if it's allowed, false otherwise. + */ + public static boolean isHexDigit(char c) { + + // I suspect most characters passed to this method will be + // correct hexadecimal digits, so I test for the true cases + // first. If this proves to be a performance bottleneck + // a switch statement or lookup table + // might optimize this. + if (c >= '0' && c <= '9') return true; + if (c >= 'A' && c <= 'F') return true; + if (c >= 'a' && c <= 'f') return true; + + return false; + } + + /** + * This is a function for determining whether the + * specified character is the high 16 bits in a + * UTF-16 surrogate pair. + * @param ch character to check + * @return true if the character is a high surrogate, false otherwise + */ + public static boolean isHighSurrogate(char ch) { + return (ch >= 0xD800 && ch <= 0xDBFF); + } + + /** + * This is a function for determining whether the + * specified character is the low 16 bits in a + * UTF-16 surrogate pair. + * @param ch character to check + * @return true if the character is a low surrogate, false otherwise. + */ + public static boolean isLowSurrogate(char ch) { + return (ch >= 0xDC00 && ch <= 0xDFFF); + } + + /** + *

+ * This is a utility function for determining whether + * a specified Unicode character is legal in URI references + * as determined by RFC 2396. + *

+ * + * @param c char to check for URI reference compliance. + * @return true if it's allowed, false otherwise. + */ + public static boolean isURICharacter(char c) { + if (c >= 'a' && c <= 'z') return true; + if (c >= 'A' && c <= 'Z') return true; + if (c >= '0' && c <= '9') return true; + if (c == '/') return true; + if (c == '-') return true; + if (c == '.') return true; + if (c == '?') return true; + if (c == ':') return true; + if (c == '@') return true; + if (c == '&') return true; + if (c == '=') return true; + if (c == '+') return true; + if (c == '$') return true; + if (c == ',') return true; + if (c == '%') return true; + + if (c == '_') return true; + if (c == '!') return true; + if (c == '~') return true; + if (c == '*') return true; + if (c == '\'') return true; + if (c == '(') return true; + if (c == ')') return true; + return false; + } + + /** + * This is a utility function for determining whether a specified + * character is a character according to production 2 of the + * XML 1.0 specification. + * + * @param c char to check for XML compliance + * @return boolean true if it's a character, + * false otherwise + */ + public static boolean isXMLCharacter(int c) { + + if (c == '\n') return true; + if (c == '\r') return true; + if (c == '\t') return true; + + if (c < 0x20) return false; if (c <= 0xD7FF) return true; + if (c < 0xE000) return false; if (c <= 0xFFFD) return true; + if (c < 0x10000) return false; if (c <= 0x10FFFF) return true; + + return false; + } + + + /** + * This is a utility function for determining whether a specified + * character is a name character according to production 4 of the + * XML 1.0 specification. + * + * @param c char to check for XML name compliance. + * @return boolean true if it's a name character, + * false otherwise. + */ + public static boolean isXMLNameCharacter(char c) { + + return (isXMLLetter(c) || isXMLDigit(c) || c == '.' || c == '-' + || c == '_' || c == ':' || isXMLCombiningChar(c) + || isXMLExtender(c)); + } + + /** + * This is a utility function for determining whether a specified + * character is a legal name start character according to production 5 + * of the XML 1.0 specification. This production does allow names + * to begin with colons which the Namespaces in XML Recommendation + * disallows. + * + * @param c char to check for XML name start compliance. + * @return boolean true if it's a name start character, + * false otherwise. + */ + public static boolean isXMLNameStartCharacter(char c) { + + return (isXMLLetter(c) || c == '_' || c ==':'); + + } + + /** + * This is a utility function for determining whether a specified + * character is a letter or digit according to productions 84 and 88 + * of the XML 1.0 specification. + * + * @param c char to check. + * @return boolean true if it's letter or digit, + * false otherwise. + */ + public static boolean isXMLLetterOrDigit(char c) { + + return (isXMLLetter(c) || isXMLDigit(c)); + + } + + /** + * This is a utility function for determining whether a specified character + * is a letter according to production 84 of the XML 1.0 specification. + * + * @param c char to check for XML name compliance. + * @return String true if it's a letter, false otherwise. + */ + public static boolean isXMLLetter(char c) { + // Note that order is very important here. The search proceeds + // from lowest to highest values, so that no searching occurs + // above the character's value. BTW, the first line is equivalent to: + // if (c >= 0x0041 && c <= 0x005A) return true; + + if (c < 0x0041) return false; if (c <= 0x005a) return true; + if (c < 0x0061) return false; if (c <= 0x007A) return true; + if (c < 0x00C0) return false; if (c <= 0x00D6) return true; + if (c < 0x00D8) return false; if (c <= 0x00F6) return true; + if (c < 0x00F8) return false; if (c <= 0x00FF) return true; + if (c < 0x0100) return false; if (c <= 0x0131) return true; + if (c < 0x0134) return false; if (c <= 0x013E) return true; + if (c < 0x0141) return false; if (c <= 0x0148) return true; + if (c < 0x014A) return false; if (c <= 0x017E) return true; + if (c < 0x0180) return false; if (c <= 0x01C3) return true; + if (c < 0x01CD) return false; if (c <= 0x01F0) return true; + if (c < 0x01F4) return false; if (c <= 0x01F5) return true; + if (c < 0x01FA) return false; if (c <= 0x0217) return true; + if (c < 0x0250) return false; if (c <= 0x02A8) return true; + if (c < 0x02BB) return false; if (c <= 0x02C1) return true; + if (c == 0x0386) return true; + if (c < 0x0388) return false; if (c <= 0x038A) return true; + if (c == 0x038C) return true; + if (c < 0x038E) return false; if (c <= 0x03A1) return true; + if (c < 0x03A3) return false; if (c <= 0x03CE) return true; + if (c < 0x03D0) return false; if (c <= 0x03D6) return true; + if (c == 0x03DA) return true; + if (c == 0x03DC) return true; + if (c == 0x03DE) return true; + if (c == 0x03E0) return true; + if (c < 0x03E2) return false; if (c <= 0x03F3) return true; + if (c < 0x0401) return false; if (c <= 0x040C) return true; + if (c < 0x040E) return false; if (c <= 0x044F) return true; + if (c < 0x0451) return false; if (c <= 0x045C) return true; + if (c < 0x045E) return false; if (c <= 0x0481) return true; + if (c < 0x0490) return false; if (c <= 0x04C4) return true; + if (c < 0x04C7) return false; if (c <= 0x04C8) return true; + if (c < 0x04CB) return false; if (c <= 0x04CC) return true; + if (c < 0x04D0) return false; if (c <= 0x04EB) return true; + if (c < 0x04EE) return false; if (c <= 0x04F5) return true; + if (c < 0x04F8) return false; if (c <= 0x04F9) return true; + if (c < 0x0531) return false; if (c <= 0x0556) return true; + if (c == 0x0559) return true; + if (c < 0x0561) return false; if (c <= 0x0586) return true; + if (c < 0x05D0) return false; if (c <= 0x05EA) return true; + if (c < 0x05F0) return false; if (c <= 0x05F2) return true; + if (c < 0x0621) return false; if (c <= 0x063A) return true; + if (c < 0x0641) return false; if (c <= 0x064A) return true; + if (c < 0x0671) return false; if (c <= 0x06B7) return true; + if (c < 0x06BA) return false; if (c <= 0x06BE) return true; + if (c < 0x06C0) return false; if (c <= 0x06CE) return true; + if (c < 0x06D0) return false; if (c <= 0x06D3) return true; + if (c == 0x06D5) return true; + if (c < 0x06E5) return false; if (c <= 0x06E6) return true; + if (c < 0x0905) return false; if (c <= 0x0939) return true; + if (c == 0x093D) return true; + if (c < 0x0958) return false; if (c <= 0x0961) return true; + if (c < 0x0985) return false; if (c <= 0x098C) return true; + if (c < 0x098F) return false; if (c <= 0x0990) return true; + if (c < 0x0993) return false; if (c <= 0x09A8) return true; + if (c < 0x09AA) return false; if (c <= 0x09B0) return true; + if (c == 0x09B2) return true; + if (c < 0x09B6) return false; if (c <= 0x09B9) return true; + if (c < 0x09DC) return false; if (c <= 0x09DD) return true; + if (c < 0x09DF) return false; if (c <= 0x09E1) return true; + if (c < 0x09F0) return false; if (c <= 0x09F1) return true; + if (c < 0x0A05) return false; if (c <= 0x0A0A) return true; + if (c < 0x0A0F) return false; if (c <= 0x0A10) return true; + if (c < 0x0A13) return false; if (c <= 0x0A28) return true; + if (c < 0x0A2A) return false; if (c <= 0x0A30) return true; + if (c < 0x0A32) return false; if (c <= 0x0A33) return true; + if (c < 0x0A35) return false; if (c <= 0x0A36) return true; + if (c < 0x0A38) return false; if (c <= 0x0A39) return true; + if (c < 0x0A59) return false; if (c <= 0x0A5C) return true; + if (c == 0x0A5E) return true; + if (c < 0x0A72) return false; if (c <= 0x0A74) return true; + if (c < 0x0A85) return false; if (c <= 0x0A8B) return true; + if (c == 0x0A8D) return true; + if (c < 0x0A8F) return false; if (c <= 0x0A91) return true; + if (c < 0x0A93) return false; if (c <= 0x0AA8) return true; + if (c < 0x0AAA) return false; if (c <= 0x0AB0) return true; + if (c < 0x0AB2) return false; if (c <= 0x0AB3) return true; + if (c < 0x0AB5) return false; if (c <= 0x0AB9) return true; + if (c == 0x0ABD) return true; + if (c == 0x0AE0) return true; + if (c < 0x0B05) return false; if (c <= 0x0B0C) return true; + if (c < 0x0B0F) return false; if (c <= 0x0B10) return true; + if (c < 0x0B13) return false; if (c <= 0x0B28) return true; + if (c < 0x0B2A) return false; if (c <= 0x0B30) return true; + if (c < 0x0B32) return false; if (c <= 0x0B33) return true; + if (c < 0x0B36) return false; if (c <= 0x0B39) return true; + if (c == 0x0B3D) return true; + if (c < 0x0B5C) return false; if (c <= 0x0B5D) return true; + if (c < 0x0B5F) return false; if (c <= 0x0B61) return true; + if (c < 0x0B85) return false; if (c <= 0x0B8A) return true; + if (c < 0x0B8E) return false; if (c <= 0x0B90) return true; + if (c < 0x0B92) return false; if (c <= 0x0B95) return true; + if (c < 0x0B99) return false; if (c <= 0x0B9A) return true; + if (c == 0x0B9C) return true; + if (c < 0x0B9E) return false; if (c <= 0x0B9F) return true; + if (c < 0x0BA3) return false; if (c <= 0x0BA4) return true; + if (c < 0x0BA8) return false; if (c <= 0x0BAA) return true; + if (c < 0x0BAE) return false; if (c <= 0x0BB5) return true; + if (c < 0x0BB7) return false; if (c <= 0x0BB9) return true; + if (c < 0x0C05) return false; if (c <= 0x0C0C) return true; + if (c < 0x0C0E) return false; if (c <= 0x0C10) return true; + if (c < 0x0C12) return false; if (c <= 0x0C28) return true; + if (c < 0x0C2A) return false; if (c <= 0x0C33) return true; + if (c < 0x0C35) return false; if (c <= 0x0C39) return true; + if (c < 0x0C60) return false; if (c <= 0x0C61) return true; + if (c < 0x0C85) return false; if (c <= 0x0C8C) return true; + if (c < 0x0C8E) return false; if (c <= 0x0C90) return true; + if (c < 0x0C92) return false; if (c <= 0x0CA8) return true; + if (c < 0x0CAA) return false; if (c <= 0x0CB3) return true; + if (c < 0x0CB5) return false; if (c <= 0x0CB9) return true; + if (c == 0x0CDE) return true; + if (c < 0x0CE0) return false; if (c <= 0x0CE1) return true; + if (c < 0x0D05) return false; if (c <= 0x0D0C) return true; + if (c < 0x0D0E) return false; if (c <= 0x0D10) return true; + if (c < 0x0D12) return false; if (c <= 0x0D28) return true; + if (c < 0x0D2A) return false; if (c <= 0x0D39) return true; + if (c < 0x0D60) return false; if (c <= 0x0D61) return true; + if (c < 0x0E01) return false; if (c <= 0x0E2E) return true; + if (c == 0x0E30) return true; + if (c < 0x0E32) return false; if (c <= 0x0E33) return true; + if (c < 0x0E40) return false; if (c <= 0x0E45) return true; + if (c < 0x0E81) return false; if (c <= 0x0E82) return true; + if (c == 0x0E84) return true; + if (c < 0x0E87) return false; if (c <= 0x0E88) return true; + if (c == 0x0E8A) return true; + if (c == 0x0E8D) return true; + if (c < 0x0E94) return false; if (c <= 0x0E97) return true; + if (c < 0x0E99) return false; if (c <= 0x0E9F) return true; + if (c < 0x0EA1) return false; if (c <= 0x0EA3) return true; + if (c == 0x0EA5) return true; + if (c == 0x0EA7) return true; + if (c < 0x0EAA) return false; if (c <= 0x0EAB) return true; + if (c < 0x0EAD) return false; if (c <= 0x0EAE) return true; + if (c == 0x0EB0) return true; + if (c < 0x0EB2) return false; if (c <= 0x0EB3) return true; + if (c == 0x0EBD) return true; + if (c < 0x0EC0) return false; if (c <= 0x0EC4) return true; + if (c < 0x0F40) return false; if (c <= 0x0F47) return true; + if (c < 0x0F49) return false; if (c <= 0x0F69) return true; + if (c < 0x10A0) return false; if (c <= 0x10C5) return true; + if (c < 0x10D0) return false; if (c <= 0x10F6) return true; + if (c == 0x1100) return true; + if (c < 0x1102) return false; if (c <= 0x1103) return true; + if (c < 0x1105) return false; if (c <= 0x1107) return true; + if (c == 0x1109) return true; + if (c < 0x110B) return false; if (c <= 0x110C) return true; + if (c < 0x110E) return false; if (c <= 0x1112) return true; + if (c == 0x113C) return true; + if (c == 0x113E) return true; + if (c == 0x1140) return true; + if (c == 0x114C) return true; + if (c == 0x114E) return true; + if (c == 0x1150) return true; + if (c < 0x1154) return false; if (c <= 0x1155) return true; + if (c == 0x1159) return true; + if (c < 0x115F) return false; if (c <= 0x1161) return true; + if (c == 0x1163) return true; + if (c == 0x1165) return true; + if (c == 0x1167) return true; + if (c == 0x1169) return true; + if (c < 0x116D) return false; if (c <= 0x116E) return true; + if (c < 0x1172) return false; if (c <= 0x1173) return true; + if (c == 0x1175) return true; + if (c == 0x119E) return true; + if (c == 0x11A8) return true; + if (c == 0x11AB) return true; + if (c < 0x11AE) return false; if (c <= 0x11AF) return true; + if (c < 0x11B7) return false; if (c <= 0x11B8) return true; + if (c == 0x11BA) return true; + if (c < 0x11BC) return false; if (c <= 0x11C2) return true; + if (c == 0x11EB) return true; + if (c == 0x11F0) return true; + if (c == 0x11F9) return true; + if (c < 0x1E00) return false; if (c <= 0x1E9B) return true; + if (c < 0x1EA0) return false; if (c <= 0x1EF9) return true; + if (c < 0x1F00) return false; if (c <= 0x1F15) return true; + if (c < 0x1F18) return false; if (c <= 0x1F1D) return true; + if (c < 0x1F20) return false; if (c <= 0x1F45) return true; + if (c < 0x1F48) return false; if (c <= 0x1F4D) return true; + if (c < 0x1F50) return false; if (c <= 0x1F57) return true; + if (c == 0x1F59) return true; + if (c == 0x1F5B) return true; + if (c == 0x1F5D) return true; + if (c < 0x1F5F) return false; if (c <= 0x1F7D) return true; + if (c < 0x1F80) return false; if (c <= 0x1FB4) return true; + if (c < 0x1FB6) return false; if (c <= 0x1FBC) return true; + if (c == 0x1FBE) return true; + if (c < 0x1FC2) return false; if (c <= 0x1FC4) return true; + if (c < 0x1FC6) return false; if (c <= 0x1FCC) return true; + if (c < 0x1FD0) return false; if (c <= 0x1FD3) return true; + if (c < 0x1FD6) return false; if (c <= 0x1FDB) return true; + if (c < 0x1FE0) return false; if (c <= 0x1FEC) return true; + if (c < 0x1FF2) return false; if (c <= 0x1FF4) return true; + if (c < 0x1FF6) return false; if (c <= 0x1FFC) return true; + if (c == 0x2126) return true; + if (c < 0x212A) return false; if (c <= 0x212B) return true; + if (c == 0x212E) return true; + if (c < 0x2180) return false; if (c <= 0x2182) return true; + if (c == 0x3007) return true; // ideographic + if (c < 0x3021) return false; if (c <= 0x3029) return true; // ideo + if (c < 0x3041) return false; if (c <= 0x3094) return true; + if (c < 0x30A1) return false; if (c <= 0x30FA) return true; + if (c < 0x3105) return false; if (c <= 0x312C) return true; + if (c < 0x4E00) return false; if (c <= 0x9FA5) return true; // ideo + if (c < 0xAC00) return false; if (c <= 0xD7A3) return true; + + return false; + + } + + /** + * This is a utility function for determining whether a specified character + * is a combining character according to production 87 + * of the XML 1.0 specification. + * + * @param c char to check. + * @return boolean true if it's a combining character, + * false otherwise. + */ + public static boolean isXMLCombiningChar(char c) { + // CombiningChar + if (c < 0x0300) return false; if (c <= 0x0345) return true; + if (c < 0x0360) return false; if (c <= 0x0361) return true; + if (c < 0x0483) return false; if (c <= 0x0486) return true; + if (c < 0x0591) return false; if (c <= 0x05A1) return true; + + if (c < 0x05A3) return false; if (c <= 0x05B9) return true; + if (c < 0x05BB) return false; if (c <= 0x05BD) return true; + if (c == 0x05BF) return true; + if (c < 0x05C1) return false; if (c <= 0x05C2) return true; + + if (c == 0x05C4) return true; + if (c < 0x064B) return false; if (c <= 0x0652) return true; + if (c == 0x0670) return true; + if (c < 0x06D6) return false; if (c <= 0x06DC) return true; + + if (c < 0x06DD) return false; if (c <= 0x06DF) return true; + if (c < 0x06E0) return false; if (c <= 0x06E4) return true; + if (c < 0x06E7) return false; if (c <= 0x06E8) return true; + + if (c < 0x06EA) return false; if (c <= 0x06ED) return true; + if (c < 0x0901) return false; if (c <= 0x0903) return true; + if (c == 0x093C) return true; + if (c < 0x093E) return false; if (c <= 0x094C) return true; + + if (c == 0x094D) return true; + if (c < 0x0951) return false; if (c <= 0x0954) return true; + if (c < 0x0962) return false; if (c <= 0x0963) return true; + if (c < 0x0981) return false; if (c <= 0x0983) return true; + + if (c == 0x09BC) return true; + if (c == 0x09BE) return true; + if (c == 0x09BF) return true; + if (c < 0x09C0) return false; if (c <= 0x09C4) return true; + if (c < 0x09C7) return false; if (c <= 0x09C8) return true; + + if (c < 0x09CB) return false; if (c <= 0x09CD) return true; + if (c == 0x09D7) return true; + if (c < 0x09E2) return false; if (c <= 0x09E3) return true; + if (c == 0x0A02) return true; + if (c == 0x0A3C) return true; + + if (c == 0x0A3E) return true; + if (c == 0x0A3F) return true; + if (c < 0x0A40) return false; if (c <= 0x0A42) return true; + if (c < 0x0A47) return false; if (c <= 0x0A48) return true; + + if (c < 0x0A4B) return false; if (c <= 0x0A4D) return true; + if (c < 0x0A70) return false; if (c <= 0x0A71) return true; + if (c < 0x0A81) return false; if (c <= 0x0A83) return true; + if (c == 0x0ABC) return true; + + if (c < 0x0ABE) return false; if (c <= 0x0AC5) return true; + if (c < 0x0AC7) return false; if (c <= 0x0AC9) return true; + if (c < 0x0ACB) return false; if (c <= 0x0ACD) return true; + + if (c < 0x0B01) return false; if (c <= 0x0B03) return true; + if (c == 0x0B3C) return true; + if (c < 0x0B3E) return false; if (c <= 0x0B43) return true; + if (c < 0x0B47) return false; if (c <= 0x0B48) return true; + + if (c < 0x0B4B) return false; if (c <= 0x0B4D) return true; + if (c < 0x0B56) return false; if (c <= 0x0B57) return true; + if (c < 0x0B82) return false; if (c <= 0x0B83) return true; + + if (c < 0x0BBE) return false; if (c <= 0x0BC2) return true; + if (c < 0x0BC6) return false; if (c <= 0x0BC8) return true; + if (c < 0x0BCA) return false; if (c <= 0x0BCD) return true; + if (c == 0x0BD7) return true; + + if (c < 0x0C01) return false; if (c <= 0x0C03) return true; + if (c < 0x0C3E) return false; if (c <= 0x0C44) return true; + if (c < 0x0C46) return false; if (c <= 0x0C48) return true; + + if (c < 0x0C4A) return false; if (c <= 0x0C4D) return true; + if (c < 0x0C55) return false; if (c <= 0x0C56) return true; + if (c < 0x0C82) return false; if (c <= 0x0C83) return true; + + if (c < 0x0CBE) return false; if (c <= 0x0CC4) return true; + if (c < 0x0CC6) return false; if (c <= 0x0CC8) return true; + if (c < 0x0CCA) return false; if (c <= 0x0CCD) return true; + + if (c < 0x0CD5) return false; if (c <= 0x0CD6) return true; + if (c < 0x0D02) return false; if (c <= 0x0D03) return true; + if (c < 0x0D3E) return false; if (c <= 0x0D43) return true; + + if (c < 0x0D46) return false; if (c <= 0x0D48) return true; + if (c < 0x0D4A) return false; if (c <= 0x0D4D) return true; + if (c == 0x0D57) return true; + if (c == 0x0E31) return true; + + if (c < 0x0E34) return false; if (c <= 0x0E3A) return true; + if (c < 0x0E47) return false; if (c <= 0x0E4E) return true; + if (c == 0x0EB1) return true; + if (c < 0x0EB4) return false; if (c <= 0x0EB9) return true; + + if (c < 0x0EBB) return false; if (c <= 0x0EBC) return true; + if (c < 0x0EC8) return false; if (c <= 0x0ECD) return true; + if (c < 0x0F18) return false; if (c <= 0x0F19) return true; + if (c == 0x0F35) return true; + + if (c == 0x0F37) return true; + if (c == 0x0F39) return true; + if (c == 0x0F3E) return true; + if (c == 0x0F3F) return true; + if (c < 0x0F71) return false; if (c <= 0x0F84) return true; + + if (c < 0x0F86) return false; if (c <= 0x0F8B) return true; + if (c < 0x0F90) return false; if (c <= 0x0F95) return true; + if (c == 0x0F97) return true; + if (c < 0x0F99) return false; if (c <= 0x0FAD) return true; + + if (c < 0x0FB1) return false; if (c <= 0x0FB7) return true; + if (c == 0x0FB9) return true; + if (c < 0x20D0) return false; if (c <= 0x20DC) return true; + if (c == 0x20E1) return true; + + if (c < 0x302A) return false; if (c <= 0x302F) return true; + if (c == 0x3099) return true; + if (c == 0x309A) return true; + + return false; + + } + + /** + * This is a utility function for determining whether a specified + * character is an extender according to production 88 of the XML 1.0 + * specification. + * + * @param c char to check. + * @return String true if it's an extender, false otherwise. + */ + public static boolean isXMLExtender(char c) { + + if (c < 0x00B6) return false; // quick short circuit + + // Extenders + if (c == 0x00B7) return true; + if (c == 0x02D0) return true; + if (c == 0x02D1) return true; + if (c == 0x0387) return true; + if (c == 0x0640) return true; + if (c == 0x0E46) return true; + if (c == 0x0EC6) return true; + if (c == 0x3005) return true; + + if (c < 0x3031) return false; if (c <= 0x3035) return true; + if (c < 0x309D) return false; if (c <= 0x309E) return true; + if (c < 0x30FC) return false; if (c <= 0x30FE) return true; + + return false; + + } + + /** + * This is a utility function for determining whether a specified + * Unicode character + * is a digit according to production 88 of the XML 1.0 specification. + * + * @param c char to check for XML digit compliance + * @return boolean true if it's a digit, false otherwise + */ + public static boolean isXMLDigit(char c) { + + if (c < 0x0030) return false; if (c <= 0x0039) return true; + if (c < 0x0660) return false; if (c <= 0x0669) return true; + if (c < 0x06F0) return false; if (c <= 0x06F9) return true; + if (c < 0x0966) return false; if (c <= 0x096F) return true; + + if (c < 0x09E6) return false; if (c <= 0x09EF) return true; + if (c < 0x0A66) return false; if (c <= 0x0A6F) return true; + if (c < 0x0AE6) return false; if (c <= 0x0AEF) return true; + + if (c < 0x0B66) return false; if (c <= 0x0B6F) return true; + if (c < 0x0BE7) return false; if (c <= 0x0BEF) return true; + if (c < 0x0C66) return false; if (c <= 0x0C6F) return true; + + if (c < 0x0CE6) return false; if (c <= 0x0CEF) return true; + if (c < 0x0D66) return false; if (c <= 0x0D6F) return true; + if (c < 0x0E50) return false; if (c <= 0x0E59) return true; + + if (c < 0x0ED0) return false; if (c <= 0x0ED9) return true; + if (c < 0x0F20) return false; if (c <= 0x0F29) return true; + + return false; + } + + /** + * This is a utility function for determining whether a specified + * Unicode character is a whitespace character according to production 3 + * of the XML 1.0 specification. + * + * @param c char to check for XML whitespace compliance + * @return boolean true if it's a whitespace, false otherwise + */ + public static boolean isXMLWhitespace(char c) { + if (c==' ' || c=='\n' || c=='\t' || c=='\r' ){ + return true; + } + return false; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/AbstractDOMAdapter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/AbstractDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,172 @@ +/*-- + + $Id: AbstractDOMAdapter.java,v 1.21 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.adapters; + +import java.io.*; +import java.lang.reflect.*; + +import org.jdom.*; +import org.w3c.dom.*; +import org.w3c.dom.Document; + +/** + * A DOMAdapter utility abstract base class. + * + * @version $Revision: 1.21 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public abstract class AbstractDOMAdapter implements DOMAdapter { + + private static final String CVS_ID = + "@(#) $RCSfile: AbstractDOMAdapter.java,v $ $Revision: 1.21 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This creates a new {@link Document} from an + * existing InputStream by letting a DOM + * parser handle parsing using the supplied stream. + * + * @param filename file to parse. + * @param validate boolean to indicate if validation should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(File filename, boolean validate) + throws IOException, JDOMException { + + return getDocument(new FileInputStream(filename), validate); + } + + /** + * This creates a new {@link Document} from an + * existing InputStream by letting a DOM + * parser handle parsing using the supplied stream. + * + * @param in InputStream to parse. + * @param validate boolean to indicate if validation should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public abstract Document getDocument(InputStream in, boolean validate) + throws IOException, JDOMException; + + /** + * This creates an empty Document object based + * on a specific parser implementation. + * + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public abstract Document createDocument() throws JDOMException; + + /** + * This creates an empty Document object based + * on a specific parser implementation with the given DOCTYPE. + * If the doctype parameter is null, the behavior is the same as + * calling createDocument(). + * + * @param doctype Initial DocType of the document. + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public Document createDocument(DocType doctype) throws JDOMException { + if (doctype == null) { + return createDocument(); + } + + DOMImplementation domImpl = createDocument().getImplementation(); + DocumentType domDocType = domImpl.createDocumentType( + doctype.getElementName(), + doctype.getPublicID(), + doctype.getSystemID()); + + // Set the internal subset if possible + setInternalSubset(domDocType, doctype.getInternalSubset()); + + return domImpl.createDocument("http://temporary", + doctype.getElementName(), + domDocType); + } + + /** + * This attempts to change the DocumentType to have the given internal DTD + * subset value. This is not a standard ability in DOM, so it's only + * available with some parsers. Subclasses can alter the mechanism by + * which the attempt is made to set the value. + * + * @param dt DocumentType to be altered + * @param s String to use as the internal DTD subset + */ + protected void setInternalSubset(DocumentType dt, String s) { + if (dt == null || s == null) return; + + // Default behavior is to attempt a setInternalSubset() call using + // reflection. This method is not part of the DOM spec, but it's + // available on Xerces 1.4.4+. It's not currently in Crimson. + try { + Class dtclass = dt.getClass(); + Method setInternalSubset = dtclass.getMethod( + "setInternalSubset", new Class[] {java.lang.String.class}); + setInternalSubset.invoke(dt, new Object[] {s}); + } + catch (Exception e) { + // ignore + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/CrimsonDOMAdapter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/CrimsonDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,146 @@ +/*-- + + $Id: CrimsonDOMAdapter.java,v 1.17 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.adapters; + +import java.io.*; +import java.lang.reflect.*; + +import org.jdom.*; +import org.w3c.dom.Document; +import org.xml.sax.*; + +/** + * An adapter for the Apache Crimson DOM parser. + * + * @version $Revision: 1.17 $, $Date: 2007/11/10 05:28:59 $ + * @author Jason Hunter + */ +public class CrimsonDOMAdapter extends AbstractDOMAdapter { + + private static final String CVS_ID = + "@(#) $RCSfile: CrimsonDOMAdapter.java,v $ $Revision: 1.17 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This creates a new {@link Document} from an + * existing InputStream by letting a DOM + * parser handle parsing using the supplied stream. + * + * @param in InputStream to parse. + * @param validate boolean to indicate if validation should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(InputStream in, boolean validate) + throws IOException, JDOMException { + + try { + Class[] parameterTypes = new Class[2]; + parameterTypes[0] = Class.forName("java.io.InputStream"); + parameterTypes[1] = boolean.class; + + Object[] args = new Object[2]; + args[0] = in; + args[1] = new Boolean(false); + + // Load the parser class and invoke the parse method + Class parserClass = Class.forName("org.apache.crimson.tree.XmlDocument"); + Method createXmlDocument = + parserClass.getMethod("createXmlDocument", parameterTypes); + Document doc = + (Document)createXmlDocument.invoke(null, args); + + return doc; + + } catch (InvocationTargetException e) { + Throwable targetException = e.getTargetException(); + if (targetException instanceof org.xml.sax.SAXParseException) { + SAXParseException parseException = (SAXParseException)targetException; + throw new JDOMException("Error on line " + parseException.getLineNumber() + + " of XML document: " + parseException.getMessage(), parseException); + } else if (targetException instanceof IOException) { + IOException ioException = (IOException) targetException; + throw ioException; + } else { + throw new JDOMException(targetException.getMessage(), targetException); + } + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage(), e); + } + } + + /** + * This creates an empty Document object based + * on a specific parser implementation. + * + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public Document createDocument() throws JDOMException { + try { + return + (Document)Class.forName( + "org.apache.crimson.tree.XmlDocument") + .newInstance(); + + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage() + " when creating document", e); + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/DOMAdapter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/DOMAdapter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,123 @@ +/*-- + + $Id: DOMAdapter.java,v 1.22 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.adapters; + +import java.io.*; + +import org.jdom.*; +import org.w3c.dom.Document; + +/** + * Defines a standard set of adapter methods for interfacing with a DOM parser + * and obtaining a DOM {@link org.w3c.dom.Document org.w3c.dom.Document} object. + * Implementing classes map these calls to DOM parser-specific calls, allowing + * any third-party parser to be used with JDOM. + * + * @version $Revision: 1.22 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public interface DOMAdapter { + + /** + * This creates a new Document from a + * given filename by letting a DOM parser handle parsing from the file. + * + * @param filename file to parse. + * @param validate boolean to indicate if validation + * should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(File filename, boolean validate) + throws IOException, JDOMException; + + /** + * This creates a new Document from an + * existing InputStream by letting a DOM + * parser handle parsing using the supplied stream. + * + * @param in InputStream to parse. + * @param validate boolean to indicate if validation + * should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(InputStream in, boolean validate) + throws IOException, JDOMException; + + /** + * This creates an empty Document object based + * on a specific parser implementation. + * + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public Document createDocument() throws JDOMException; + + /** + * This creates an empty Document object based + * on a specific parser implementation with the given DOCTYPE. + * + * @param doctype Initial DocType of the document. + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public Document createDocument(DocType doctype) throws JDOMException; +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/JAXPDOMAdapter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/JAXPDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,195 @@ +/*-- + + $Id: JAXPDOMAdapter.java,v 1.13 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.adapters; + +import java.io.*; +import java.lang.reflect.*; + +import org.jdom.*; +import org.jdom.input.*; +import org.w3c.dom.Document; + +/** + * An adapter for any parser supporting the Sun JAXP APIs. + * + * @version $Revision: 1.13 $, $Date: 2007/11/10 05:28:59 $ + * @author Jason Hunter + */ +public class JAXPDOMAdapter extends AbstractDOMAdapter { + + private static final String CVS_ID = + "@(#) $RCSfile: JAXPDOMAdapter.java,v $ $Revision: 1.13 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This creates a new {@link Document} from an + * existing InputStream by letting a JAXP + * parser handle parsing using the supplied stream. + * + * @param in InputStream to parse. + * @param validate boolean to indicate if validation + * should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(InputStream in, boolean validate) + throws IOException, JDOMException { + + try { + // Try using JAXP... + // Note we need DOM Level 2 and thus JAXP 1.1. + Class.forName("javax.xml.transform.Transformer"); + + // Try JAXP 1.1 calls to build the document + Class factoryClass = + Class.forName("javax.xml.parsers.DocumentBuilderFactory"); + + // factory = DocumentBuilderFactory.newInstance(); + Method newParserInstance = + factoryClass.getMethod("newInstance", null); + Object factory = newParserInstance.invoke(null, null); + + // factory.setValidating(validate); + Method setValidating = + factoryClass.getMethod("setValidating", + new Class[]{boolean.class}); + setValidating.invoke(factory, + new Object[]{new Boolean(validate)}); + + // factory.setNamespaceAware(true); + Method setNamespaceAware = + factoryClass.getMethod("setNamespaceAware", + new Class[]{boolean.class}); + setNamespaceAware.invoke(factory, + new Object[]{Boolean.TRUE}); + + // jaxpParser = factory.newDocumentBuilder(); + Method newDocBuilder = + factoryClass.getMethod("newDocumentBuilder", null); + Object jaxpParser = newDocBuilder.invoke(factory, null); + + // jaxpParser.setErrorHandler(null); + Class parserClass = jaxpParser.getClass(); + Method setErrorHandler = + parserClass.getMethod("setErrorHandler", + new Class[]{org.xml.sax.ErrorHandler.class}); + setErrorHandler.invoke(jaxpParser, + new Object[]{new BuilderErrorHandler()}); + + // domDoc = jaxpParser.parse(in); + Method parse = parserClass.getMethod( + "parse", new Class[]{InputStream.class}); + org.w3c.dom.Document domDoc = (org.w3c.dom.Document) + parse.invoke(jaxpParser, new Object[]{in}); + + return domDoc; + } catch (InvocationTargetException e) { + Throwable targetException = e.getTargetException(); + if (targetException instanceof IOException) { + throw (IOException) targetException; + } else { + throw new JDOMException(targetException.getMessage(), targetException); + } + } catch (Exception e) { + throw new JDOMException("Reflection failed while parsing a document with JAXP", e); + } + + // Allow all exceptions to pass through + } + + /** + * This creates an empty Document object based + * on a specific parser implementation. + * + * @return Document - created DOM Document. + * @throws JDOMException when errors occur in parsing. + */ + public Document createDocument() + throws JDOMException { + + try { + // We need DOM Level 2 and thus JAXP 1.1. + // If JAXP 1.0 is all that's available then we error out. + Class.forName("javax.xml.transform.Transformer"); + + // Try JAXP 1.1 calls to build the document + Class factoryClass = + Class.forName("javax.xml.parsers.DocumentBuilderFactory"); + + // factory = DocumentBuilderFactory.newInstance(); + Method newParserInstance = + factoryClass.getMethod("newInstance", null); + Object factory = newParserInstance.invoke(null, null); + + // jaxpParser = factory.newDocumentBuilder(); + Method newDocBuilder = + factoryClass.getMethod("newDocumentBuilder", null); + Object jaxpParser = newDocBuilder.invoke(factory, null); + + // domDoc = jaxpParser.newDocument(); + Class parserClass = jaxpParser.getClass(); + Method newDoc = parserClass.getMethod("newDocument", null); + org.w3c.dom.Document domDoc = + (org.w3c.dom.Document) newDoc.invoke(jaxpParser, null); + + return domDoc; + } catch (Exception e) { + throw new JDOMException("Reflection failed while creating new JAXP document", e); + } + + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/OracleV1DOMAdapter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/OracleV1DOMAdapter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,145 @@ +/*-- + + $Id: OracleV1DOMAdapter.java,v 1.20 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.adapters; + +import java.io.*; +import java.lang.reflect.*; + +import org.jdom.*; +import org.w3c.dom.Document; +import org.xml.sax.*; + +/** + * An adapter for the Oracle Version 1 DOM parser. + * + * @version $Revision: 1.20 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public class OracleV1DOMAdapter extends AbstractDOMAdapter { + + private static final String CVS_ID = + "@(#) $RCSfile: OracleV1DOMAdapter.java,v $ $Revision: 1.20 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This creates a new {@link Document} from an + * existing InputStream by letting a DOM + * parser handle parsing using the supplied stream. + * + * @param in InputStream to parse. + * @param validate boolean to indicate if validation should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(InputStream in, boolean validate) + throws IOException, JDOMException { + + try { + // Load the parser class + Class parserClass = Class.forName("oracle.xml.parser.XMLParser"); + Object parser = parserClass.newInstance(); + + // Parse the document + Method parse = + parserClass.getMethod("parse", + new Class[] {org.xml.sax.InputSource.class}); + parse.invoke(parser, new Object[] {new InputSource(in)}); + + // Get the Document object + Method getDocument = parserClass.getMethod("getDocument", null); + Document doc = (Document)getDocument.invoke(parser, null); + + return doc; + } catch (InvocationTargetException e) { + Throwable targetException = e.getTargetException(); + if (targetException instanceof org.xml.sax.SAXParseException) { + SAXParseException parseException = (SAXParseException) targetException; + throw new JDOMException("Error on line " + parseException.getLineNumber() + + " of XML document: " + parseException.getMessage(), parseException); + } else if (targetException instanceof IOException) { + IOException ioException = (IOException) targetException; + throw ioException; + } else { + throw new JDOMException(targetException.getMessage(), targetException); + } + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage(), e); + } + } + + /** + * This creates an empty Document object based + * on a specific parser implementation. + * + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public Document createDocument() throws JDOMException { + try { + return + (Document)Class.forName( + "oracle.xml.parser.XMLDocument") + .newInstance(); + + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage() + " when creating document", e); + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/OracleV2DOMAdapter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/OracleV2DOMAdapter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,145 @@ +/*-- + + $Id: OracleV2DOMAdapter.java,v 1.19 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.adapters; + +import java.io.*; +import java.lang.reflect.*; + +import org.jdom.*; +import org.w3c.dom.Document; +import org.xml.sax.*; + +/** + * An adapter for the Oracle Version 2 DOM parser. + * + * @version $Revision: 1.19 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public class OracleV2DOMAdapter extends AbstractDOMAdapter { + + private static final String CVS_ID = + "@(#) $RCSfile: OracleV2DOMAdapter.java,v $ $Revision: 1.19 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This creates a new {@link Document} from an + * existing InputStream by letting a DOM + * parser handle parsing using the supplied stream. + * + * @param in InputStream to parse. + * @param validate boolean to indicate if validation should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(InputStream in, boolean validate) + throws IOException, JDOMException { + + try { + // Load the parser class + Class parserClass = Class.forName("oracle.xml.parser.v2.DOMParser"); + Object parser = parserClass.newInstance(); + + // Parse the document + Method parse = + parserClass.getMethod("parse", + new Class[] {org.xml.sax.InputSource.class}); + parse.invoke(parser, new Object[] {new InputSource(in)}); + + // Get the Document object + Method getDocument = parserClass.getMethod("getDocument", null); + Document doc = (Document)getDocument.invoke(parser, null); + + return doc; + } catch (InvocationTargetException e) { + Throwable targetException = e.getTargetException(); + if (targetException instanceof org.xml.sax.SAXParseException) { + SAXParseException parseException = (SAXParseException)targetException; + throw new JDOMException("Error on line " + parseException.getLineNumber() + + " of XML document: " + parseException.getMessage(), parseException); + } else if (targetException instanceof IOException) { + IOException ioException = (IOException) targetException; + throw ioException; + } else { + throw new JDOMException(targetException.getMessage(), targetException); + } + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage(), e); + } + } + + /** + * This creates an empty Document object based + * on a specific parser implementation. + * + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public Document createDocument() throws JDOMException { + try { + return + (Document)Class.forName( + "oracle.xml.parser.v2.XMLDocument") + .newInstance(); + + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage() + " when creating document", e); + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/XML4JDOMAdapter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/XML4JDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,171 @@ +/*-- + + $Id: XML4JDOMAdapter.java,v 1.18 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.adapters; + +import java.io.*; +import java.lang.reflect.*; + +import org.jdom.*; +import org.jdom.input.*; +import org.w3c.dom.Document; +import org.xml.sax.*; + +/** + * An adapter for the IBM XML4J DOM parser. + * + * @version $Revision: 1.18 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public class XML4JDOMAdapter extends AbstractDOMAdapter { + + private static final String CVS_ID = + "@(#) $RCSfile: XML4JDOMAdapter.java,v $ $Revision: 1.18 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This creates a new {@link Document} from an + * existing InputStream by letting a DOM + * parser handle parsing using the supplied stream. + * + * @param in InputStream to parse. + * @param validate boolean to indicate if validation should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(InputStream in, boolean validate) + throws IOException, JDOMException { + + try { + /* + * IBM XML4J actually uses the Xerces parser, so this is + * all Xerces specific code. + */ + + // Load the parser class + Class parserClass = Class.forName("org.apache.xerces.parsers.DOMParser"); + Object parser = parserClass.newInstance(); + + // Set validation + Method setFeature = + parserClass.getMethod("setFeature", + new Class[] {java.lang.String.class, + boolean.class}); + setFeature.invoke(parser, new Object[] {"http://xml.org/sax/features/validation", + new Boolean(validate)}); + + // Set namespaces + setFeature.invoke(parser, new Object[] {"http://xml.org/sax/features/namespaces", + new Boolean(false)}); + + // Set the error handler + if (validate) { + Method setErrorHandler = + parserClass.getMethod("setErrorHandler", + new Class[] {ErrorHandler.class}); + setErrorHandler.invoke(parser, new Object[] {new BuilderErrorHandler()}); + } + + // Parse the document + Method parse = + parserClass.getMethod("parse", + new Class[] {org.xml.sax.InputSource.class}); + parse.invoke(parser, new Object[]{new InputSource(in)}); + + // Get the Document object + Method getDocument = parserClass.getMethod("getDocument", null); + Document doc = (Document)getDocument.invoke(parser, null); + + return doc; + } catch (InvocationTargetException e) { + Throwable targetException = e.getTargetException(); + if (targetException instanceof org.xml.sax.SAXParseException) { + SAXParseException parseException = (SAXParseException)targetException; + throw new JDOMException("Error on line " + parseException.getLineNumber() + + " of XML document: " + parseException.getMessage(), parseException); + } else if (targetException instanceof IOException) { + IOException ioException = (IOException) targetException; + throw ioException; + } else { + throw new JDOMException(targetException.getMessage(), targetException); + } + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage(), e); + } + } + + /** + * This creates an empty Document object based + * on a specific parser implementation. + * + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public Document createDocument() throws JDOMException { + try { + return + (Document)Class.forName( + "org.apache.xerces.dom.DocumentImpl") + .newInstance(); + + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage() + " while creating document", e); + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/XercesDOMAdapter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/XercesDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,170 @@ +/*-- + + $Id: XercesDOMAdapter.java,v 1.19 2007/11/10 05:28:59 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.adapters; + +import java.io.*; +import java.lang.reflect.*; + +import org.jdom.*; +import org.jdom.input.*; +import org.w3c.dom.Document; +import org.xml.sax.*; + +/** + * An adapter for the Apache Xerces DOM parser. + * + * @version $Revision: 1.19 $, $Date: 2007/11/10 05:28:59 $ + * @author Brett McLaughlin + * @author Jason Hunter + */ +public class XercesDOMAdapter extends AbstractDOMAdapter { + + private static final String CVS_ID = + "@(#) $RCSfile: XercesDOMAdapter.java,v $ $Revision: 1.19 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $"; + + /** + * This creates a new {@link Document} from an + * existing InputStream by letting a DOM + * parser handle parsing using the supplied stream. + * + * @param in InputStream to parse. + * @param validate boolean to indicate if validation + * should occur. + * @return Document - instance ready for use. + * @throws IOException when I/O error occurs. + * @throws JDOMException when errors occur in parsing. + */ + public Document getDocument(InputStream in, boolean validate) + throws IOException, JDOMException { + + try { + // Load the parser class + Class parserClass = + Class.forName("org.apache.xerces.parsers.DOMParser"); + Object parser = parserClass.newInstance(); + + // Set validation + Method setFeature = parserClass.getMethod( + "setFeature", + new Class[] {java.lang.String.class, boolean.class}); + setFeature.invoke(parser, + new Object[] {"http://xml.org/sax/features/validation", + new Boolean(validate)}); + + // Set namespaces true + setFeature.invoke(parser, + new Object[] {"http://xml.org/sax/features/namespaces", + new Boolean(true)}); + + // Set the error handler + if (validate) { + Method setErrorHandler = parserClass.getMethod( + "setErrorHandler", + new Class[] {ErrorHandler.class}); + setErrorHandler.invoke(parser, + new Object[] {new BuilderErrorHandler()}); + } + + // Parse the document + Method parse = parserClass.getMethod( + "parse", + new Class[] {org.xml.sax.InputSource.class}); + parse.invoke(parser, new Object[]{new InputSource(in)}); + + // Get the Document object + Method getDocument = parserClass.getMethod("getDocument", null); + Document doc = (Document)getDocument.invoke(parser, null); + + return doc; + } catch (InvocationTargetException e) { + Throwable targetException = e.getTargetException(); + if (targetException instanceof org.xml.sax.SAXParseException) { + SAXParseException parseException = + (SAXParseException)targetException; + throw new JDOMException("Error on line " + + parseException.getLineNumber() + + " of XML document: " + + parseException.getMessage(), e); + } else if (targetException instanceof IOException) { + IOException ioException = (IOException) targetException; + throw ioException; + } else { + throw new JDOMException(targetException.getMessage(), e); + } + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage(), e); + } + } + + /** + * This creates an empty Document object based + * on a specific parser implementation. + * + * @return Document - created DOM Document. + * @throws JDOMException when errors occur. + */ + public Document createDocument() throws JDOMException { + try { + return (Document)Class.forName( + "org.apache.xerces.dom.DocumentImpl").newInstance(); + } catch (Exception e) { + throw new JDOMException(e.getClass().getName() + ": " + + e.getMessage() + " when creating document", e); + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/adapters/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,7 @@ + + +Classes to interface with various DOM implementations. Not generally +needed except in truly advanced situations. JAXPDOMAdapter is most commonly +used. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/AbstractFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/filter/AbstractFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,82 @@ +/*-- + + $Id: AbstractFilter.java,v 1.6 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.filter; + +/** + * Partial implementation of {@link Filter}. + * + * @author Bradley S. Huffman + * @version $Revision: 1.6 $, $Date: 2007/11/10 05:29:00 $ + */ +public abstract class AbstractFilter implements Filter { + + private static final String CVS_ID = + "@(#) $RCSfile: AbstractFilter.java,v $ $Revision: 1.6 $ $Date: 2007/11/10 05:29:00 $"; + + public Filter negate() { + return new NegateFilter(this); + } + + public Filter or(Filter filter) { + return new OrFilter(this, filter); + } + + public Filter and(Filter filter) { + return new AndFilter(this, filter); + } + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/AndFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/filter/AndFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,125 @@ +/*-- + + $Id: AndFilter.java,v 1.4 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.filter; + +/** + * Allow two filters to be chained together with a logical + * and operation. + * + * @author Bradley S. Huffman + * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:00 $ + */ +final class AndFilter extends AbstractFilter { + + private static final String CVS_ID = + "@(#) $RCSfile: AndFilter.java,v $ $Revision: 1.4 $ $Date: 2007/11/10 05:29:00 $"; + + // Filter for left side of logical and. + private Filter left; + + // Filter for right side of logical and. + private Filter right; + + /** + * Match if only both supplied filters match. + * + * @param left left side of logical and + * @param right right side of logical and + * @throws IllegalArgumentException if either supplied filter is null + */ + public AndFilter(Filter left, Filter right) { + if ((left == null) || (right == null)) { + throw new IllegalArgumentException("null filter not allowed"); + } + this.left = left; + this.right = right; + } + + public boolean matches(Object obj) { + return left.matches(obj) && right.matches(obj); + } + + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + + if (obj instanceof AndFilter) { + AndFilter filter = (AndFilter) obj; + if ((left.equals(filter.left) && right.equals(filter.right)) || + (left.equals(filter.right) && right.equals(filter.left))) { + return true; + } + } + return false; + } + + public int hashCode() { + return (31 * left.hashCode()) + right.hashCode(); + } + + public String toString() { + return new StringBuffer(64) + .append("[AndFilter: ") + .append(left.toString()) + .append(",\n") + .append(" ") + .append(right.toString()) + .append("]") + .toString(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/ContentFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/filter/ContentFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,356 @@ +/*-- + + $Id: ContentFilter.java,v 1.15 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.filter; + +import org.jdom.*; + +/** + * A general purpose Filter able to represent all legal JDOM objects or a + * specific subset. Filtering is accomplished by way of a filtering mask in + * which each bit represents whether a JDOM object is visible or not. + * For example to view all Text and CDATA nodes in the content of element x. + * 

+ *      Filter filter = new ContentFilter(ContentFilter.TEXT |
+ *                                        ContentFilter.CDATA);
+ *      List content = x.getContent(filter);
+ *
+ *

+ * For those who don't like bit-masking, set methods are provided as an + * alternative. For example to allow everything except Comment nodes. + * 


+ *      Filter filter =  new ContentFilter();
+ *      filter.setCommentVisible(false);
+ *      List content = x.getContent(filter);
+ *
+ *

+ * The default is to allow all valid JDOM objects. + * + * @version $Revision: 1.15 $, $Date: 2007/11/10 05:29:00 $ + * @author Bradley S. Huffman + */ +public class ContentFilter extends AbstractFilter { + + private static final String CVS_ID = + "@(#) $RCSfile: ContentFilter.java,v $ $Revision: 1.15 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $"; + + /** Mask for JDOM {@link Element} objects */ + public static final int ELEMENT = 1; + + /** Mask for JDOM {@link CDATA} objects */ + public static final int CDATA = 2; + + /** Mask for JDOM {@link Text} objects */ + public static final int TEXT = 4; + + /** Mask for JDOM {@link Comment} objects */ + public static final int COMMENT = 8; + + /** Mask for JDOM {@link ProcessingInstruction} objects */ + public static final int PI = 16; + + /** Mask for JDOM {@link EntityRef} objects */ + public static final int ENTITYREF = 32; + + /** Mask for JDOM {@link Document} object */ + public static final int DOCUMENT = 64; + + /** Mask for JDOM {@link DocType} object */ + public static final int DOCTYPE = 128; + + /** The JDOM object mask */ + private int filterMask; + + /** + * Default constructor that allows any legal JDOM objects. + */ + public ContentFilter() { + setDefaultMask(); + } + + /** + * Set whether all JDOM objects are visible or not. + * + * @param allVisible true all JDOM objects are visible, + * false all JDOM objects are hidden. + */ + public ContentFilter(boolean allVisible) { + if (allVisible) { + setDefaultMask(); + } + else { + filterMask &= ~filterMask; + } + } + + /** + * Filter out JDOM objects according to a filtering mask. + * + * @param mask Mask of JDOM objects to allow. + */ + public ContentFilter(int mask) { + setFilterMask(mask); + } + + /** + * Return current filtering mask. + * + * @return the current filtering mask + */ + public int getFilterMask() { + return filterMask; + } + + /** + * Set filtering mask. + * + * @param mask the new filtering mask + */ + public void setFilterMask(int mask) { + setDefaultMask(); + filterMask &= mask; + } + + /** + * Set this filter to allow all legal JDOM objects. + */ + public void setDefaultMask() { + filterMask = ELEMENT | CDATA | TEXT | COMMENT | + PI | ENTITYREF | DOCUMENT | DOCTYPE; + } + + /** + * Set filter to match only JDOM objects that are legal + * document content. + */ + public void setDocumentContent() { + filterMask = ELEMENT | COMMENT | PI | DOCTYPE; + } + + /** + * Set filter to match only JDOM objects that are legal + * element content. + */ + public void setElementContent() { + filterMask = ELEMENT | CDATA | TEXT | + COMMENT | PI | ENTITYREF; + } + + /** + * Set visiblity of Element objects. + * + * @param visible whether Elements are visible, true + * if yes, false if not + */ + public void setElementVisible(boolean visible) { + if (visible) { + filterMask |= ELEMENT; + } + else { + filterMask &= ~ELEMENT; + } + } + + /** + * Set visiblity of CDATA objects. + * + * @param visible whether CDATA nodes are visible, true + * if yes, false if not + */ + public void setCDATAVisible(boolean visible) { + if (visible) { + filterMask |= CDATA; + } + else { + filterMask &= ~CDATA; + } + } + + /** + * Set visiblity of Text objects. + * + * @param visible whether Text nodes are visible, true + * if yes, false if not + */ + public void setTextVisible(boolean visible) { + if (visible) { + filterMask |= TEXT; + } + else { + filterMask &= ~TEXT; + } + } + + /** + * Set visiblity of Comment objects. + * + * @param visible whether Comments are visible, true + * if yes, false if not + */ + public void setCommentVisible(boolean visible) { + if (visible) { + filterMask |= COMMENT; + } + else { + filterMask &= ~COMMENT; + } + } + + /** + * Set visiblity of ProcessingInstruction objects. + * + * @param visible whether ProcessingInstructions are visible, + * true if yes, false if not + */ + public void setPIVisible(boolean visible) { + if (visible) { + filterMask |= PI; + } + else { + filterMask &= ~PI; + } + } + + /** + * Set visiblity of EntityRef objects. + * + * @param visible whether EntityRefs are visible, true + * if yes, false if not + */ + public void setEntityRefVisible(boolean visible) { + if (visible) { + filterMask |= ENTITYREF; + } + else { + filterMask &= ~ENTITYREF; + } + } + + /** + * Set visiblity of DocType objects. + * + * @param visible whether the DocType is visible, true + * if yes, false if not + */ + public void setDocTypeVisible(boolean visible) { + if (visible) { + filterMask |= DOCTYPE; + } + else { + filterMask &= ~DOCTYPE; + } + } + + /** + * Check to see if the object matches according to the filter mask. + * + * @param obj The object to verify. + * @return true if the objected matched a predfined + * set of rules. + */ + public boolean matches(Object obj) { + if (obj instanceof Element) { + return (filterMask & ELEMENT) != 0; + } + else if (obj instanceof CDATA) { // must come before Text check + return (filterMask & CDATA) != 0; + } + else if (obj instanceof Text) { + return (filterMask & TEXT) != 0; + } + else if (obj instanceof Comment) { + return (filterMask & COMMENT) != 0; + } + else if (obj instanceof ProcessingInstruction) { + return (filterMask & PI) != 0; + } + else if (obj instanceof EntityRef) { + return (filterMask & ENTITYREF) != 0; + } + else if (obj instanceof Document) { + return (filterMask & DOCUMENT) != 0; + } + else if (obj instanceof DocType) { + return (filterMask & DOCTYPE) != 0; + } + + return false; + } + + /** + * Returns whether the two filters are equivalent (i.e. the + * matching mask values are identical). + * + * @param obj the object to compare against + * @return whether the two filters are equal + */ + public boolean equals(Object obj) { + // Generated by IntelliJ + if (this == obj) return true; + if (!(obj instanceof ContentFilter)) return false; + + final ContentFilter filter = (ContentFilter) obj; + + if (filterMask != filter.filterMask) return false; + + return true; + } + + public int hashCode() { + // Generated by IntelliJ + return filterMask; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/ElementFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/filter/ElementFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,189 @@ +/*-- + + $Id: ElementFilter.java,v 1.20 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.filter; + +import java.io.*; +import org.jdom.*; + +/** + * A Filter that only matches {@link org.jdom.Element} objects. + * + * @version $Revision: 1.20 $, $Date: 2007/11/10 05:29:00 $ + * @author Jools Enticknap + * @author Bradley S. Huffman + */ +public class ElementFilter extends AbstractFilter { + + private static final String CVS_ID = + "@(#) $RCSfile: ElementFilter.java,v $ $Revision: 1.20 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $"; + + /** The element name */ + private String name; + + /** The element namespace */ + private transient Namespace namespace; + + /** + * Select only the Elements. + */ + public ElementFilter() {} + + /** + * Select only the Elements with the supplied name in any Namespace. + * + * @param name The name of the Element. + */ + public ElementFilter(String name) { + this.name = name; + } + + /** + * Select only the Elements with the supplied Namespace. + * + * @param namespace The namespace the Element lives in. + */ + public ElementFilter(Namespace namespace) { + this.namespace = namespace; + } + + /** + * Select only the Elements with the supplied name and Namespace. + * + * @param name The name of the Element. + * @param namespace The namespace the Element lives in. + */ + public ElementFilter(String name, Namespace namespace) { + this.name = name; + this.namespace = namespace; + } + + /** + * Check to see if the object matches a predefined set of rules. + * + * @param obj The object to verify. + * @return true if the objected matched a predfined + * set of rules. + */ + public boolean matches(Object obj) { + if (obj instanceof Element) { + Element el = (Element) obj; + return + (this.name == null || this.name.equals(el.getName())) && + (this.namespace == null || this.namespace.equals(el.getNamespace())); + } + return false; + } + + /** + * Returns whether the two filters are equivalent (i.e. the + * matching names and namespace are equivalent). + * + * @param obj the object to compare against + * @return whether the two filters are equal + */ + public boolean equals(Object obj) { + // Generated by IntelliJ + if (this == obj) return true; + if (!(obj instanceof ElementFilter)) return false; + + final ElementFilter filter = (ElementFilter) obj; + + if (name != null ? !name.equals(filter.name) : filter.name != null) return false; + if (namespace != null ? !namespace.equals(filter.namespace) : filter.namespace != null) return false; + + return true; + } + + public int hashCode() { + // Generated by IntelliJ + int result; + result = (name != null ? name.hashCode() : 0); + result = 29 * result + (namespace != null ? namespace.hashCode() : 0); + return result; + } + + // Support a custom Namespace serialization so no two namespace + // object instances may exist for the same prefix/uri pair + private void writeObject(ObjectOutputStream out) throws IOException { + + out.defaultWriteObject(); + + // We use writeObject() and not writeUTF() to minimize space + // This allows for writing pointers to already written strings + if (namespace != null) { + out.writeObject(namespace.getPrefix()); + out.writeObject(namespace.getURI()); + } + else { + out.writeObject(null); + out.writeObject(null); + } + } + + private void readObject(ObjectInputStream in) + throws IOException, ClassNotFoundException { + + in.defaultReadObject(); + + Object prefix = in.readObject(); + Object uri = in.readObject(); + + if (prefix != null) { // else leave namespace null here + namespace = Namespace.getNamespace((String) prefix, (String) uri); + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/Filter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/filter/Filter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,76 @@ +/*-- + + $Id: Filter.java,v 1.10 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.filter; + + +/** + * A generalized filter to restrict visibility or mutability on a list. + * + * @version $Revision: 1.10 $, $Date: 2007/11/10 05:29:00 $ + * @author Jools Enticknap + * @author Bradley S. Huffman + */ +public interface Filter extends java.io.Serializable { + /** + * Check to see if the object matches a predefined set of rules. + * + * @param obj The object to verify. + * @return true if the object matches a predfined + * set of rules. + */ + public boolean matches(Object obj); +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/NegateFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/filter/NegateFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,113 @@ +/*-- + + $Id: NegateFilter.java,v 1.4 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.filter; + +/** + * Filter that is the logical negation operation of another filter. + * + * + * @author Bradley S. Huffman + * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:00 $ + */ +final class NegateFilter extends AbstractFilter { + + private static final String CVS_ID = + "@(#) $RCSfile: NegateFilter.java,v $ $Revision: 1.4 $ $Date: 2007/11/10 05:29:00 $"; + + // Underlying filter. + private Filter filter; + + /** + * Match if the supplied filter does not match. + * + * @param filter filter to use. + */ + public NegateFilter(Filter filter) { + this.filter = filter; + } + + public boolean matches(Object obj) { + return !filter.matches(obj); + } + + public Filter negate() { + return filter; + } + + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + + if (obj instanceof NegateFilter) { + return filter.equals(((NegateFilter) obj).filter); + } + return false; + } + + public int hashCode() { + return ~filter.hashCode(); + } + + public String toString() { + return new StringBuffer(64) + .append("[NegateFilter: ") + .append(filter.toString()) + .append("]") + .toString(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/OrFilter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/filter/OrFilter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,125 @@ +/*-- + + $Id: OrFilter.java,v 1.5 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.filter; + +/** + * Allow two filters to be chained together with a logical + * or operation. + * + * @author Bradley S. Huffman + * @version $Revision: 1.5 $, $Date: 2007/11/10 05:29:00 $ + */ +final class OrFilter extends AbstractFilter { + + private static final String CVS_ID = + "@(#) $RCSfile: OrFilter.java,v $ $Revision: 1.5 $ $Date: 2007/11/10 05:29:00 $"; + + /** Filter for left side of logical or */ + private Filter left; + + /** Filter for right side of logical or */ + private Filter right; + + /** + * Match if either of the supplied filters. + * + * @param left left side of logical or + * @param right right side of logical or + * @throws IllegalArgumentException if either supplied filter is null + */ + public OrFilter(Filter left, Filter right) { + if ((left == null) || (right == null)) { + throw new IllegalArgumentException("null filter not allowed"); + } + this.left = left; + this.right = right; + } + + public boolean matches(Object obj) { + return left.matches(obj) || right.matches(obj); + } + + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + + if (obj instanceof OrFilter) { + OrFilter filter = (OrFilter) obj; + if ((left.equals(filter.left) && right.equals(filter.right)) || + (left.equals(filter.right) && right.equals(filter.left))) { + return true; + } + } + return false; + } + + public int hashCode() { + return (31 * left.hashCode()) + right.hashCode(); + } + + public String toString() { + return new StringBuffer(64) + .append("[OrFilter: ") + .append(left.toString()) + .append(",\n") + .append(" ") + .append(right.toString()) + .append("]") + .toString(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/filter/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,9 @@ + + +Classes to programmatically filter nodes of a document based on type, name, +value, or other aspects and to boolean and/or/negate these rules. Filters can +be used in methods like getContent(Filter) and getDescendants(Filter). A +sampling of generally useful filters are provided here. Alternate filters can +be user defined. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/BuilderErrorHandler.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/input/BuilderErrorHandler.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,111 @@ +/*-- + + $Id: BuilderErrorHandler.java,v 1.13 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.input; + +import org.xml.sax.*; + +/** + * The standard JDOM error handler implementation. + * + * @author Jason Hunter + * @version $Revision: 1.13 $, $Date: 2007/11/10 05:29:00 $ + */ + +public class BuilderErrorHandler implements ErrorHandler { + + private static final String CVS_ID = + "@(#) $RCSfile: BuilderErrorHandler.java,v $ $Revision: 1.13 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $"; + + /** + * This method is called when a warning has occurred; this indicates + * that while no XML rules were broken, something appears to be + * incorrect or missing. + * The implementation of this method here is a "no op". + * + * @param exception SAXParseException that occurred. + * @throws SAXException when things go wrong + */ + public void warning(SAXParseException exception) throws SAXException { + // nothing + } + + /** + * This method is called in response to an error that has occurred; + * this indicates that a rule was broken, typically in validation, but + * that parsing could reasonably continue. + * The implementation of this method here is to rethrow the exception. + * + * @param exception SAXParseException that occurred. + * @throws SAXException when things go wrong + */ + public void error(SAXParseException exception) throws SAXException { + throw exception; + } + + /** + * This method is called in response to a fatal error; this indicates that + * a rule has been broken that makes continued parsing either impossible + * or an almost certain waste of time. + * The implementation of this method here is to rethrow the exception. + * + * @param exception SAXParseException that occurred. + * @throws SAXException when things go wrong + */ + public void fatalError(SAXParseException exception) throws SAXException { + throw exception; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/DOMBuilder.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/input/DOMBuilder.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,341 @@ +/*-- + + $Id: DOMBuilder.java,v 1.60 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.input; + +import org.jdom.*; +import org.jdom.Document; +import org.jdom.Element; +import org.w3c.dom.*; + +/** + * Builds a JDOM {@link org.jdom.Document org.jdom.Document} from a pre-existing + * DOM {@link org.w3c.dom.Document org.w3c.dom.Document}. Also handy for testing + * builds from files to sanity check {@link SAXBuilder}. + * + * @version $Revision: 1.60 $, $Date: 2007/11/10 05:29:00 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Philip Nelson + * @author Kevin Regan + * @author Yusuf Goolamabbas + * @author Dan Schaffer + * @author Bradley S. Huffman + */ +public class DOMBuilder { + + private static final String CVS_ID = + "@(#) $RCSfile: DOMBuilder.java,v $ $Revision: 1.60 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $"; + + /** Adapter class to use */ + private String adapterClass; + + /** The factory for creating new JDOM objects */ + private JDOMFactory factory = new DefaultJDOMFactory(); + + /** + * This creates a new DOMBuilder which will attempt to first locate + * a parser via JAXP, then will try to use a set of default parsers. + * The underlying parser will not validate. + */ + public DOMBuilder() { + } + + /** + * This creates a new DOMBuilder using the specified DOMAdapter + * implementation as a way to choose the underlying parser. + * The underlying parser will not validate. + * + * @param adapterClass String name of class + * to use for DOM building. + */ + public DOMBuilder(String adapterClass) { + this.adapterClass = adapterClass; + } + + /* + * This sets a custom JDOMFactory for the builder. Use this to build + * the tree with your own subclasses of the JDOM classes. + * + * @param factory JDOMFactory to use + */ + public void setFactory(JDOMFactory factory) { + this.factory = factory; + } + + /** + * Returns the current {@link org.jdom.JDOMFactory} in use. + * @return the factory in use + */ + public JDOMFactory getFactory() { + return factory; + } + + /** + * This will build a JDOM tree from an existing DOM tree. + * + * @param domDocument org.w3c.dom.Document object + * @return Document - JDOM document object. + */ + public Document build(org.w3c.dom.Document domDocument) { + Document doc = factory.document(null); + buildTree(domDocument, doc, null, true); + return doc; + } + + /** + * This will build a JDOM Element from an existing DOM Element + * + * @param domElement org.w3c.dom.Element object + * @return Element - JDOM Element object + */ + public org.jdom.Element build(org.w3c.dom.Element domElement) { + Document doc = factory.document(null); + buildTree(domElement, doc, null, true); + return doc.getRootElement(); + } + + /** + * This takes a DOM Node and builds up + * a JDOM tree, recursing until the DOM tree is exhausted + * and the JDOM tree results. + * + * @param node Code to examine. + * @param doc JDOM Document being built. + * @param current Element that is current parent. + * @param atRoot boolean indicating whether at root level. + */ + private void buildTree(Node node, + Document doc, + Element current, + boolean atRoot) { + // Recurse through the tree + switch (node.getNodeType()) { + case Node.DOCUMENT_NODE: + NodeList nodes = node.getChildNodes(); + for (int i=0, size=nodes.getLength(); i= 0) { + prefix = nodeName.substring(0, colon); + localName = nodeName.substring(colon + 1); + } + + // Get element's namespace + Namespace ns = null; + String uri = node.getNamespaceURI(); + if (uri == null) { + ns = (current == null) ? Namespace.NO_NAMESPACE + : current.getNamespace(prefix); + } + else { + ns = Namespace.getNamespace(prefix, uri); + } + + Element element = factory.element(localName, ns); + + if (atRoot) { + // If at root, set as document root + doc.setRootElement(element); // XXX should we use a factory call? + } else { + // else add to parent element + factory.addContent(current, element); + } + + // Add namespaces + NamedNodeMap attributeList = node.getAttributes(); + int attsize = attributeList.getLength(); + + for (int i = 0; i < attsize; i++) { + Attr att = (Attr) attributeList.item(i); + + String attname = att.getName(); + if (attname.startsWith("xmlns")) { + String attPrefix = ""; + colon = attname.indexOf(':'); + if (colon >= 0) { + attPrefix = attname.substring(colon + 1); + } + + String attvalue = att.getValue(); + + Namespace declaredNS = + Namespace.getNamespace(attPrefix, attvalue); + + // Add as additional namespaces if it's different + // than this element's namespace (perhaps we should + // also have logic not to mark them as additional if + // it's been done already, but it probably doesn't + // matter) + if (prefix.equals(attPrefix)) { + element.setNamespace(declaredNS); + } + else { + factory.addNamespaceDeclaration(element, declaredNS); + } + } + } + + // Add attributes + for (int i = 0; i < attsize; i++) { + Attr att = (Attr) attributeList.item(i); + + String attname = att.getName(); + + if ( !attname.startsWith("xmlns")) { + String attPrefix = ""; + String attLocalName = attname; + colon = attname.indexOf(':'); + if (colon >= 0) { + attPrefix = attname.substring(0, colon); + attLocalName = attname.substring(colon + 1); + } + + String attvalue = att.getValue(); + + // Get attribute's namespace + Namespace attns = null; + if ("".equals(attPrefix)) { + attns = Namespace.NO_NAMESPACE; + } + else { + attns = element.getNamespace(attPrefix); + } + + Attribute attribute = + factory.attribute(attLocalName, attvalue, attns); + factory.setAttribute(element, attribute); + } + } + + // Recurse on child nodes + // The list should never be null nor should it ever contain + // null nodes, but some DOM impls are broken + NodeList children = node.getChildNodes(); + if (children != null) { + int size = children.getLength(); + for (int i = 0; i < size; i++) { + Node item = children.item(i); + if (item != null) { + buildTree(item, doc, element, false); + } + } + } + break; + + case Node.TEXT_NODE: + String data = node.getNodeValue(); + factory.addContent(current, factory.text(data)); + break; + + case Node.CDATA_SECTION_NODE: + String cdata = node.getNodeValue(); + factory.addContent(current, factory.cdata(cdata)); + break; + + + case Node.PROCESSING_INSTRUCTION_NODE: + if (atRoot) { + factory.addContent(doc, + factory.processingInstruction(node.getNodeName(), + node.getNodeValue())); + } else { + factory.addContent(current, + factory.processingInstruction(node.getNodeName(), + node.getNodeValue())); + } + break; + + case Node.COMMENT_NODE: + if (atRoot) { + factory.addContent(doc, factory.comment(node.getNodeValue())); + } else { + factory.addContent(current, factory.comment(node.getNodeValue())); + } + break; + + case Node.ENTITY_REFERENCE_NODE: + EntityRef entity = factory.entityRef(node.getNodeName()); + factory.addContent(current, entity); + break; + + case Node.ENTITY_NODE: + // ?? + break; + + case Node.DOCUMENT_TYPE_NODE: + DocumentType domDocType = (DocumentType)node; + String publicID = domDocType.getPublicId(); + String systemID = domDocType.getSystemId(); + String internalDTD = domDocType.getInternalSubset(); + + DocType docType = factory.docType(domDocType.getName()); + docType.setPublicID(publicID); + docType.setSystemID(systemID); + docType.setInternalSubset(internalDTD); + + factory.addContent(doc, docType); + break; + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/JAXPParserFactory.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/input/JAXPParserFactory.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,179 @@ +/*-- + + $Id: JAXPParserFactory.java,v 1.6 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.input; + +import java.util.*; + +import javax.xml.parsers.*; + +import org.jdom.*; +import org.xml.sax.*; + +/** + * A non-public utility class to allocate JAXP SAX parsers. + * + * @version $Revision: 1.6 $, $Date: 2007/11/10 05:29:00 $ + * @author Laurent Bihanic + */ +class JAXPParserFactory { // package protected + + private static final String CVS_ID = + "@(#) $RCSfile: JAXPParserFactory.java,v $ $Revision: 1.6 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $"; + + /** JAXP 1.2 schema language property id. */ + private static final String JAXP_SCHEMA_LANGUAGE_PROPERTY = + "http://java.sun.com/xml/jaxp/properties/schemaLanguage"; + + /** JAXP 1.2 schema location property id. */ + private static final String JAXP_SCHEMA_LOCATION_PROPERTY = + "http://java.sun.com/xml/jaxp/properties/schemaSource"; + + /** + * Private constructor to forbid allocating instances of this utility + * class. + */ + private JAXPParserFactory() { + // Never called. + } + + /* Implementor's note regarding createParser() design: The features and + properties are normally set in SAXBuilder, but we take them in + createParser() as well because some features or properties may need to be + applied during the JAXP parser construction. Today, for example, properties + is used as it's the only way to configure schema validation: JAXP defines + schema validation properties but SAX does not. This reflects in the Apache + Xerces implementation where the SAXParser implementation supports the JAXP + properties but the XMLReader does not. Hence, configuring schema validation + must be done on the SAXParser object which is only visible in + JAXParserFactory. Features is also passed in case some future JAXP release + defines JAXP-specific features. + */ + + /** + * Creates a SAX parser allocated through the configured JAXP SAX + * parser factory. + * + * @param validating whether a validating parser is requested. + * @param features the user-defined SAX features. + * @param properties the user-defined SAX properties. + * + * @return a configured XMLReader. + * + * @throws JDOMException if any error occurred when allocating or + * configuring the JAXP SAX parser. + */ + public static XMLReader createParser(boolean validating, + Map features, Map properties) throws JDOMException { + try { + SAXParser parser = null; + + // Allocate and configure JAXP SAX parser factory. + SAXParserFactory factory = SAXParserFactory.newInstance(); + factory.setValidating(validating); + factory.setNamespaceAware(true); + + try { + // Allocate parser. + parser = factory.newSAXParser(); + } + catch (ParserConfigurationException e) { + throw new JDOMException("Could not allocate JAXP SAX Parser", e); + } + + // Set user-defined JAXP properties (if any) + setProperty(parser, properties, JAXP_SCHEMA_LANGUAGE_PROPERTY); + setProperty(parser, properties, JAXP_SCHEMA_LOCATION_PROPERTY); + + // Return configured SAX XMLReader. + return parser.getXMLReader(); + } + catch (SAXException e) { + throw new JDOMException("Could not allocate JAXP SAX Parser", e); + } + } + + /** + * Sets a property on a JAXP SAX parser object if and only if it + * is declared in the user-defined properties. + * + * @param parser the JAXP SAX parser to configure. + * @param properties the user-defined SAX properties. + * @param name the name of the property to set. + * + * @throws JDOMException if any error occurred while configuring + * the property. + */ + private static void setProperty(SAXParser parser, + Map properties, String name) throws JDOMException { + try { + if (properties.containsKey(name)) { + parser.setProperty(name, properties.get(name)); + } + } + catch (SAXNotSupportedException e) { + throw new JDOMException( + name + " property not supported for JAXP parser " + + parser.getClass().getName()); + } + catch (SAXNotRecognizedException e) { + throw new JDOMException( + name + " property not recognized for JAXP parser " + + parser.getClass().getName()); + } + } +} + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/JDOMParseException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/input/JDOMParseException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,175 @@ +/*-- + + $Id: JDOMParseException.java,v 1.8 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.input; + +import org.jdom.*; +import org.xml.sax.*; + +/** + * Thrown during parse errors, with information about where the parse error + * occurred as well as access to the partially built document. + * + * @version $Revision: 1.8 $, $Date: 2007/11/10 05:29:00 $ + * @author Laurent Bihanic + */ +public class JDOMParseException extends JDOMException { + + private static final String CVS_ID = + "@(#) $RCSfile: JDOMParseException.java,v $ $Revision: 1.8 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $"; + + /** + * The portion of the document that was successfully built before + * the parse error occurred. + */ + private final Document partialDocument; + + /** + * This will create a parse Exception with the given + * message and wrap the Exception that cause a document + * parse to fail. + * + * @param message String message indicating + * the problem that occurred. + * @param cause Throwable that caused this + * to be thrown. + */ + public JDOMParseException(String message, Throwable cause) { + this(message, cause, null); + } + + /** + * This will create a parse Exception with the given + * message and the partial document and wrap the + * Exception that cause a document parse to fail. + * + * @param message String message indicating + * the problem that occurred. + * @param cause Throwable that caused this + * to be thrown. + * @param partialDocument Document the portion of + * the input XML document that was + * successfully built. + */ + public JDOMParseException(String message, Throwable cause, + Document partialDocument) { + super(message, cause); + this.partialDocument = partialDocument; + } + + /** + * Returns the partial document that was successfully built before + * the error occurred. + * + * @return the partial document or null if none. + */ + public Document getPartialDocument() { + return partialDocument; + } + + /** + * Returns the public identifier of the entity where the + * parse error occurred. + * + * @return a string containing the public identifier, or + * null if the information is not available. + */ + public String getPublicId() { + return (getCause() instanceof SAXParseException)? + ((SAXParseException)getCause()).getPublicId(): null; + } + + /** + * Returns the system identifier of the entity where the + * parse error occurred. + * + * @return a string containing the system identifier, or + * null if the information is not available. + */ + public String getSystemId() { + return (getCause() instanceof SAXParseException)? + ((SAXParseException)getCause()).getSystemId(): null; + } + + /** + * Returns the line number of the end of the text where the + * parse error occurred. + *

+ * The first line in the document is line 1.

+ * + * @return an integer representing the line number, or -1 + * if the information is not available. + */ + public int getLineNumber() { + return (getCause() instanceof SAXParseException)? + ((SAXParseException)getCause()).getLineNumber(): -1; + } + + /** + * Returns the column number of the end of the text where the + * parse error occurred. + *

+ * The first column in a line is position 1.

+ * + * @return an integer representing the column number, or -1 + * if the information is not available. + */ + public int getColumnNumber() { + return (getCause() instanceof SAXParseException)? + ((SAXParseException)getCause()).getColumnNumber(): -1; + } +} + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/SAXBuilder.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/input/SAXBuilder.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,1105 @@ +/*-- + + $Id: SAXBuilder.java,v 1.93 2009/07/23 06:26:26 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.input; + +import java.io.*; +import java.lang.reflect.*; +import java.net.*; +import java.util.*; + +import org.jdom.*; + +import org.xml.sax.*; +import org.xml.sax.helpers.XMLReaderFactory; + +/** + * Builds a JDOM document from files, streams, readers, URLs, or a SAX {@link + * org.xml.sax.InputSource} instance using a SAX parser. The builder uses a + * third-party SAX parser (chosen by JAXP by default, or you can choose + * manually) to handle the parsing duties and simply listens to the SAX events + * to construct a document. Details which SAX does not provide, such as + * whitespace outside the root element, are not represented in the JDOM + * document. Information about SAX can be found at http://www.saxproject.org. + *

+ * Known issues: Relative paths for a {@link DocType} or {@link EntityRef} may + * be converted by the SAX parser into absolute paths. + * + * @version $Revision: 1.93 $, $Date: 2009/07/23 06:26:26 $ + * @author Jason Hunter + * @author Brett McLaughlin + * @author Dan Schaffer + * @author Philip Nelson + * @author Alex Rosen + */ +public class SAXBuilder { + + private static final String CVS_ID = + "@(#) $RCSfile: SAXBuilder.java,v $ $Revision: 1.93 $ $Date: 2009/07/23 06:26:26 $ $Name: jdom_1_1_1 $"; + + /** + * Default parser class to use. This is used when no other parser + * is given and JAXP isn't available. + */ + private static final String DEFAULT_SAX_DRIVER = + "org.apache.xerces.parsers.SAXParser"; + + /** Whether validation should occur */ + private boolean validate; + + /** Whether expansion of entities should occur */ + private boolean expand = true; + + /** Adapter class to use */ + private String saxDriverClass; + + /** ErrorHandler class to use */ + private ErrorHandler saxErrorHandler = null; + + /** EntityResolver class to use */ + private EntityResolver saxEntityResolver = null; + + /** DTDHandler class to use */ + private DTDHandler saxDTDHandler = null; + + /** XMLFilter instance to use */ + private XMLFilter saxXMLFilter = null; + + /** The factory for creating new JDOM objects */ + private JDOMFactory factory = new DefaultJDOMFactory(); + + /** Whether to ignore ignorable whitespace */ + private boolean ignoringWhite = false; + + /** Whether to ignore all whitespace content */ + private boolean ignoringBoundaryWhite = false; + + /** User-specified features to be set on the SAX parser */ + private HashMap features = new HashMap(5); + + /** User-specified properties to be set on the SAX parser */ + private HashMap properties = new HashMap(5); + + /** Whether to use fast parser reconfiguration */ + private boolean fastReconfigure = false; + + /** Whether to try lexical reporting in fast parser reconfiguration */ + private boolean skipNextLexicalReportingConfig = false; + + /** Whether to to try entity expansion in fast parser reconfiguration */ + private boolean skipNextEntityExpandConfig = false; + + /** + * Whether parser reuse is allowed. + *

Default: true

+ */ + private boolean reuseParser = true; + + /** The current SAX parser, if parser reuse has been activated. */ + private XMLReader saxParser = null; + + /** + * Creates a new SAXBuilder which will attempt to first locate + * a parser via JAXP, then will try to use a set of default + * SAX Drivers. The underlying parser will not validate. + */ + public SAXBuilder() { + this(false); + } + + /** + * Creates a new SAXBuilder which will attempt to first locate + * a parser via JAXP, then will try to use a set of default + * SAX Drivers. The underlying parser will validate or not + * according to the given parameter. + * + * @param validate boolean indicating if + * validation should occur. + */ + public SAXBuilder(boolean validate) { + this.validate = validate; + } + + /** + * Creates a new SAXBuilder using the specified SAX parser. + * The underlying parser will not validate. + * + * @param saxDriverClass String name of SAX Driver + * to use for parsing. + */ + public SAXBuilder(String saxDriverClass) { + this(saxDriverClass, false); + } + + /** + * Creates a new SAXBuilder using the specified SAX parser. + * The underlying parser will validate or not + * according to the given parameter. + * + * @param saxDriverClass String name of SAX Driver + * to use for parsing. + * @param validate boolean indicating if + * validation should occur. + */ + public SAXBuilder(String saxDriverClass, boolean validate) { + this.saxDriverClass = saxDriverClass; + this.validate = validate; + } + + /** + * Returns the driver class assigned in the constructor, or null if none. + * + * @return the driver class assigned in the constructor + */ + public String getDriverClass() { + return saxDriverClass; + } + + /** + * Returns the current {@link org.jdom.JDOMFactory} in use. + * @return the factory in use + */ + public JDOMFactory getFactory() { + return factory; + } + + /** + * This sets a custom JDOMFactory for the builder. Use this to build + * the tree with your own subclasses of the JDOM classes. + * + * @param factory JDOMFactory to use + */ + public void setFactory(JDOMFactory factory) { + this.factory = factory; + } + + /** + * Returns whether validation is to be performed during the build. + * + * @return whether validation is to be performed during the build + */ + public boolean getValidation() { + return validate; + } + + /** + * This sets validation for the builder. + * + * @param validate boolean indicating whether validation + * should occur. + */ + public void setValidation(boolean validate) { + this.validate = validate; + } + + /** + * Returns the {@link ErrorHandler} assigned, or null if none. + * @return the ErrorHandler assigned, or null if none + */ + public ErrorHandler getErrorHandler() { + return saxErrorHandler; + } + + /** + * This sets custom ErrorHandler for the Builder. + * + * @param errorHandler ErrorHandler + */ + public void setErrorHandler(ErrorHandler errorHandler) { + saxErrorHandler = errorHandler; + } + + /** + * Returns the {@link EntityResolver} assigned, or null if none. + * + * @return the EntityResolver assigned + */ + public EntityResolver getEntityResolver() { + return saxEntityResolver; + } + + /** + * This sets custom EntityResolver for the Builder. + * + * @param entityResolver EntityResolver + */ + public void setEntityResolver(EntityResolver entityResolver) { + saxEntityResolver = entityResolver; + } + + /** + * Returns the {@link DTDHandler} assigned, or null if none. + * + * @return the DTDHandler assigned + */ + public DTDHandler getDTDHandler() { + return saxDTDHandler; + } + + /** + * This sets custom DTDHandler for the Builder. + * + * @param dtdHandler DTDHandler + */ + public void setDTDHandler(DTDHandler dtdHandler) { + saxDTDHandler = dtdHandler; + } + + /** + * Returns the {@link XMLFilter} used during parsing, or null if none. + * + * @return the XMLFilter used during parsing + */ + public XMLFilter getXMLFilter() { + return saxXMLFilter; + } + + /** + * This sets a custom {@link org.xml.sax.XMLFilter} for the builder. + * + * @param xmlFilter the filter to use + */ + public void setXMLFilter(XMLFilter xmlFilter) { + saxXMLFilter = xmlFilter; + } + + /** + * Returns whether element content whitespace is to be ignored during the + * build. + * + * @return whether element content whitespace is to be ignored during the + * build + */ + public boolean getIgnoringElementContentWhitespace() { + return ignoringWhite; + } + + /** + * Specifies whether or not the parser should elminate whitespace in + * element content (sometimes known as "ignorable whitespace") when + * building the document. Only whitespace which is contained within + * element content that has an element only content model will be + * eliminated (see XML Rec 3.2.1). For this setting to take effect + * requires that validation be turned on. The default value of this + * setting is false. + * + * @param ignoringWhite Whether to ignore ignorable whitespace + */ + public void setIgnoringElementContentWhitespace(boolean ignoringWhite) { + this.ignoringWhite = ignoringWhite; + } + + /** + * Returns whether or not the parser will elminate element content + * containing only whitespace. + * + * @return boolean - whether only whitespace content will + * be ignored during build. + * + * @see #setIgnoringBoundaryWhitespace + */ + public boolean getIgnoringBoundaryWhitespace() { + return ignoringBoundaryWhite; + } + + /** + * Specifies whether or not the parser should elminate boundary whitespace, + * a term that indicates whitespace-only text between element tags. This + * feature is a lot like {@link #setIgnoringElementContentWhitespace(boolean)} + * but this feature is more aggressive and doesn't require validation be + * turned on. The {@link #setIgnoringElementContentWhitespace(boolean)} + * call impacts the SAX parse process while this method impacts the JDOM + * build process, so it can be beneficial to turn both on for efficiency. + * For implementation efficiency, this method actually removes all + * whitespace-only text() nodes. That can, in some cases (like beteween an + * element tag and a comment), include whitespace that isn't just boundary + * whitespace. The default is false. + * + * @param ignoringBoundaryWhite Whether to ignore whitespace-only text + * noes + */ + public void setIgnoringBoundaryWhitespace(boolean ignoringBoundaryWhite) { + this.ignoringBoundaryWhite = ignoringBoundaryWhite; + } + + /** + * Returns whether the contained SAX parser instance is reused across + * multiple parses. The default is true. + * + * @return whether the contained SAX parser instance is reused across + * multiple parses + */ + public boolean getReuseParser() { + return reuseParser; + } + + /** + * Specifies whether this builder shall reuse the same SAX parser + * when performing subsequent parses or allocate a new parser for + * each parse. The default value of this setting is + * true (parser reuse). + *

+ * Note: As SAX parser instances are not thread safe, + * the parser reuse feature should not be used with SAXBuilder instances + * shared among threads.

+ * + * @param reuseParser Whether to reuse the SAX parser. + */ + public void setReuseParser(boolean reuseParser) { + this.reuseParser = reuseParser; + this.saxParser = null; + } + + /** + * Specifies whether this builder will do fast reconfiguration of the + * underlying SAX parser when reuseParser is true. This improves + * performance in cases where SAXBuilders are reused and lots of small + * documents are frequently parsed. This avoids attempting to set features + * on the SAX parser each time build() is called which result in + * SaxNotRecognizedExceptions. This should ONLY be set for builders where + * this specific case is an issue. The default value of this setting is + * false (no fast reconfiguration). If reuseParser is false, + * calling this has no effect. + * + * @param fastReconfigure Whether to do a fast reconfiguration of the parser + */ + public void setFastReconfigure(boolean fastReconfigure) { + if (this.reuseParser) { + this.fastReconfigure = fastReconfigure; + } + } + + /** + * This sets a feature on the SAX parser. See the SAX documentation for . + * more information. + *

+ *

+ * NOTE: SAXBuilder requires that some particular features of the SAX parser be + * set up in certain ways for it to work properly. The list of such features + * may change in the future. Therefore, the use of this method may cause + * parsing to break, and even if it doesn't break anything today it might + * break parsing in a future JDOM version, because what JDOM parsers require + * may change over time. Use with caution. + *

+ * + * @param name The feature name, which is a fully-qualified URI. + * @param value The requested state of the feature (true or false). + */ + public void setFeature(String name, boolean value) { + // Save the specified feature for later. + features.put(name, value ? Boolean.TRUE : Boolean.FALSE); + } + + /** + * This sets a property on the SAX parser. See the SAX documentation for + * more information. + *

+ * NOTE: SAXBuilder requires that some particular properties of the SAX parser be + * set up in certain ways for it to work properly. The list of such properties + * may change in the future. Therefore, the use of this method may cause + * parsing to break, and even if it doesn't break anything today it might + * break parsing in a future JDOM version, because what JDOM parsers require + * may change over time. Use with caution. + *

+ * + * @param name The property name, which is a fully-qualified URI. + * @param value The requested value for the property. + */ + public void setProperty(String name, Object value) { + // Save the specified property for later. + properties.put(name, value); + } + + /** + * This builds a document from the supplied + * input source. + * + * @param in InputSource to read from + * @return Document resultant Document object + * @throws JDOMException when errors occur in parsing + * @throws IOException when an I/O error prevents a document + * from being fully parsed + */ + public Document build(InputSource in) + throws JDOMException, IOException { + SAXHandler contentHandler = null; + + try { + // Create and configure the content handler. + contentHandler = createContentHandler(); + configureContentHandler(contentHandler); + + XMLReader parser = this.saxParser; + if (parser == null) { + // Create and configure the parser. + parser = createParser(); + + // Install optional filter + if (saxXMLFilter != null) { + // Connect filter chain to parser + XMLFilter root = saxXMLFilter; + while (root.getParent() instanceof XMLFilter) { + root = (XMLFilter)root.getParent(); + } + root.setParent(parser); + + // Read from filter + parser = saxXMLFilter; + } + + // Configure parser + configureParser(parser, contentHandler); + + if (reuseParser) { + this.saxParser = parser; + } + } + else { + // Reset content handler as SAXHandler instances cannot + // be reused + configureParser(parser, contentHandler); + } + + // Parse the document. + parser.parse(in); + + return contentHandler.getDocument(); + } + catch (SAXParseException e) { + Document doc = contentHandler.getDocument(); + if (doc.hasRootElement() == false) { + doc = null; + } + + String systemId = e.getSystemId(); + if (systemId != null) { + throw new JDOMParseException("Error on line " + + e.getLineNumber() + " of document " + systemId, e, doc); + } else { + throw new JDOMParseException("Error on line " + + e.getLineNumber(), e, doc); + } + } + catch (SAXException e) { + throw new JDOMParseException("Error in building: " + + e.getMessage(), e, contentHandler.getDocument()); + } + finally { + // Explicitly nullify the handler to encourage GC + // It's a stack var so this shouldn't be necessary, but it + // seems to help on some JVMs + contentHandler = null; + } + } + + /** + * This creates the SAXHandler that will be used to build the Document. + * + * @return SAXHandler - resultant SAXHandler object. + */ + protected SAXHandler createContentHandler() { + SAXHandler contentHandler = new SAXHandler(factory); + return contentHandler; + } + + /** + * This configures the SAXHandler that will be used to build the Document. + *

+ * The default implementation simply passes through some configuration + * settings that were set on the SAXBuilder: setExpandEntities() and + * setIgnoringElementContentWhitespace(). + *

+ * @param contentHandler The SAXHandler to configure + */ + protected void configureContentHandler(SAXHandler contentHandler) { + // Setup pass through behavior + contentHandler.setExpandEntities(expand); + contentHandler.setIgnoringElementContentWhitespace(ignoringWhite); + contentHandler.setIgnoringBoundaryWhitespace(ignoringBoundaryWhite); + } + + /** + * This creates the XMLReader to be used for reading the XML document. + *

+ * The default behavior is to (1) use the saxDriverClass, if it has been + * set, (2) try to obtain a parser from JAXP, if it is available, and + * (3) if all else fails, use a hard-coded default parser (currently + * the Xerces parser). Subclasses may override this method to determine + * the parser to use in a different way. + *

+ * + * @return XMLReader - resultant XMLReader object. + * @throws org.jdom.JDOMException + */ + protected XMLReader createParser() throws JDOMException { + XMLReader parser = null; + if (saxDriverClass != null) { + // The user knows that they want to use a particular class + try { + parser = XMLReaderFactory.createXMLReader(saxDriverClass); + + // Configure parser + setFeaturesAndProperties(parser, true); + } + catch (SAXException e) { + throw new JDOMException("Could not load " + saxDriverClass, e); + } + } else { + // Try using JAXP... + // Note we need JAXP 1.1, and if JAXP 1.0 is all that's + // available then the getXMLReader call fails and we skip + // to the hard coded default parser + try { + // Get factory class and method. + Class factoryClass = + Class.forName("org.jdom.input.JAXPParserFactory"); + + Method createParser = + factoryClass.getMethod("createParser", + new Class[] { boolean.class, Map.class, Map.class }); + + // Create SAX parser. + parser = (XMLReader)createParser.invoke(null, + new Object[] { validate ? Boolean.TRUE : Boolean.FALSE, + features, properties }); + + // Configure parser + setFeaturesAndProperties(parser, false); + } + catch (JDOMException e) { + throw e; + } + catch (NoClassDefFoundError e) { + // The class loader failed to resolve the dependencies + // of org.jdom.input.JAXPParserFactory. This probably means + // that no JAXP parser is present in its class path. + // => Ignore and try allocating default SAX parser instance. + } + catch (Exception e) { + // Ignore and try allocating default SAX parser instance. + } + } + + // Check to see if we got a parser yet, if not, try to use a + // hard coded default + if (parser == null) { + try { + parser = XMLReaderFactory.createXMLReader(DEFAULT_SAX_DRIVER); + // System.out.println("using default " + DEFAULT_SAX_DRIVER); + saxDriverClass = parser.getClass().getName(); + + // Configure parser + setFeaturesAndProperties(parser, true); + } + catch (SAXException e) { + throw new JDOMException("Could not load default SAX parser: " + + DEFAULT_SAX_DRIVER, e); + } + } + + return parser; + } + + /** + * This configures the XMLReader to be used for reading the XML document. + *

+ * The default implementation sets various options on the given XMLReader, + * such as validation, DTD resolution, entity handlers, etc., according + * to the options that were set (e.g. via setEntityResolver) + * and set various SAX properties and features that are required for JDOM + * internals. These features may change in future releases, so change this + * behavior at your own risk. + *

+ * @param parser + * @param contentHandler + * @throws org.jdom.JDOMException + */ + protected void configureParser(XMLReader parser, SAXHandler contentHandler) + throws JDOMException { + + // Setup SAX handlers. + + parser.setContentHandler(contentHandler); + + if (saxEntityResolver != null) { + parser.setEntityResolver(saxEntityResolver); + } + + if (saxDTDHandler != null) { + parser.setDTDHandler(saxDTDHandler); + } else { + parser.setDTDHandler(contentHandler); + } + + if (saxErrorHandler != null) { + parser.setErrorHandler(saxErrorHandler); + } else { + parser.setErrorHandler(new BuilderErrorHandler()); + } + + // If fastReconfigure is enabled and we failed in the previous attempt + // in configuring lexical reporting, then we skip this step. This + // saves the work of repeated exception handling on each parse. + if (!skipNextLexicalReportingConfig) { + boolean success = false; + + try { + parser.setProperty("http://xml.org/sax/handlers/LexicalHandler", + contentHandler); + success = true; + } catch (SAXNotSupportedException e) { + // No lexical reporting available + } catch (SAXNotRecognizedException e) { + // No lexical reporting available + } + + // Some parsers use alternate property for lexical handling (grr...) + if (!success) { + try { + parser.setProperty("http://xml.org/sax/properties/lexical-handler", + contentHandler); + success = true; + } catch (SAXNotSupportedException e) { + // No lexical reporting available + } catch (SAXNotRecognizedException e) { + // No lexical reporting available + } + } + + // If unable to configure this property and fastReconfigure is + // enabled, then setup to avoid this code path entirely next time. + if (!success && fastReconfigure) { + skipNextLexicalReportingConfig = true; + } + } + + // If fastReconfigure is enabled and we failed in the previous attempt + // in configuring entity expansion, then skip this step. This + // saves the work of repeated exception handling on each parse. + if (!skipNextEntityExpandConfig) { + boolean success = false; + + // Try setting the DeclHandler if entity expansion is off + if (!expand) { + try { + parser.setProperty("http://xml.org/sax/properties/declaration-handler", + contentHandler); + success = true; + } catch (SAXNotSupportedException e) { + // No lexical reporting available + } catch (SAXNotRecognizedException e) { + // No lexical reporting available + } + } + + /* If unable to configure this property and fastReconfigure is + * enabled, then setup to avoid this code path entirely next time. + */ + if (!success && fastReconfigure) { + skipNextEntityExpandConfig = true; + } + } + } + + private void setFeaturesAndProperties(XMLReader parser, + boolean coreFeatures) + throws JDOMException { + // Set any user-specified features on the parser. + Iterator iter = features.keySet().iterator(); + while (iter.hasNext()) { + String name = (String)iter.next(); + Boolean value = (Boolean)features.get(name); + internalSetFeature(parser, name, value.booleanValue(), name); + } + + // Set any user-specified properties on the parser. + iter = properties.keySet().iterator(); + while (iter.hasNext()) { + String name = (String)iter.next(); + internalSetProperty(parser, name, properties.get(name), name); + } + + if (coreFeatures) { + // Set validation. + try { + internalSetFeature(parser, + "http://xml.org/sax/features/validation", + validate, "Validation"); + } catch (JDOMException e) { + // If validation is not supported, and the user is requesting + // that we don't validate, that's fine - don't throw an + // exception. + if (validate) + throw e; + } + + // Setup some namespace features. + internalSetFeature(parser, + "http://xml.org/sax/features/namespaces", + true, "Namespaces"); + internalSetFeature(parser, + "http://xml.org/sax/features/namespace-prefixes", + true, "Namespace prefixes"); + } + + // Set entity expansion + // Note SAXHandler can work regardless of how this is set, but when + // entity expansion it's worth it to try to tell the parser not to + // even bother with external general entities. + // Apparently no parsers yet support this feature. + // XXX It might make sense to setEntityResolver() with a resolver + // that simply ignores external general entities + try { + if (parser.getFeature("http://xml.org/sax/features/external-general-entities") != expand) { + parser.setFeature("http://xml.org/sax/features/external-general-entities", expand); + } + } + catch (SAXNotRecognizedException e) { /* Ignore... */ } + catch (SAXNotSupportedException e) { /* Ignore... */ } + } + + /** + * Tries to set a feature on the parser. If the feature cannot be set, + * throws a JDOMException describing the problem. + */ + private void internalSetFeature(XMLReader parser, String feature, + boolean value, String displayName) throws JDOMException { + try { + parser.setFeature(feature, value); + } catch (SAXNotSupportedException e) { + throw new JDOMException( + displayName + " feature not supported for SAX driver " + parser.getClass().getName()); + } catch (SAXNotRecognizedException e) { + throw new JDOMException( + displayName + " feature not recognized for SAX driver " + parser.getClass().getName()); + } + } + + /** + *

+ * Tries to set a property on the parser. If the property cannot be set, + * throws a JDOMException describing the problem. + *

+ */ + private void internalSetProperty(XMLReader parser, String property, + Object value, String displayName) throws JDOMException { + try { + parser.setProperty(property, value); + } catch (SAXNotSupportedException e) { + throw new JDOMException( + displayName + " property not supported for SAX driver " + parser.getClass().getName()); + } catch (SAXNotRecognizedException e) { + throw new JDOMException( + displayName + " property not recognized for SAX driver " + parser.getClass().getName()); + } + } + + /** + *

+ * This builds a document from the supplied + * input stream. + *

+ * + * @param in InputStream to read from + * @return Document resultant Document object + * @throws JDOMException when errors occur in parsing + * @throws IOException when an I/O error prevents a document + * from being fully parsed. + */ + public Document build(InputStream in) + throws JDOMException, IOException { + return build(new InputSource(in)); + } + + /** + *

+ * This builds a document from the supplied + * filename. + *

+ * + * @param file File to read from + * @return Document resultant Document object + * @throws JDOMException when errors occur in parsing + * @throws IOException when an I/O error prevents a document + * from being fully parsed + */ + public Document build(File file) + throws JDOMException, IOException { + try { + URL url = fileToURL(file); + return build(url); + } catch (MalformedURLException e) { + throw new JDOMException("Error in building", e); + } + } + + /** + *

+ * This builds a document from the supplied + * URL. + *

+ * + * @param url URL to read from. + * @return Document - resultant Document object. + * @throws JDOMException when errors occur in parsing + * @throws IOException when an I/O error prevents a document + * from being fully parsed. + */ + public Document build(URL url) + throws JDOMException, IOException { + String systemID = url.toExternalForm(); + return build(new InputSource(systemID)); + } + + /** + *

+ * This builds a document from the supplied + * input stream. + *

+ * + * @param in InputStream to read from. + * @param systemId base for resolving relative URIs + * @return Document resultant Document object + * @throws JDOMException when errors occur in parsing + * @throws IOException when an I/O error prevents a document + * from being fully parsed + */ + public Document build(InputStream in, String systemId) + throws JDOMException, IOException { + + InputSource src = new InputSource(in); + src.setSystemId(systemId); + return build(src); + } + + /** + *

+ * This builds a document from the supplied + * Reader. It's the programmer's responsibility to make sure + * the reader matches the encoding of the file. It's often easier + * and safer to use an InputStream rather than a Reader, and to let the + * parser auto-detect the encoding from the XML declaration. + *

+ * + * @param characterStream Reader to read from + * @return Document resultant Document object + * @throws JDOMException when errors occur in parsing + * @throws IOException when an I/O error prevents a document + * from being fully parsed + */ + public Document build(Reader characterStream) + throws JDOMException, IOException { + return build(new InputSource(characterStream)); + } + + /** + *

+ * This builds a document from the supplied + * Reader. It's the programmer's responsibility to make sure + * the reader matches the encoding of the file. It's often easier + * and safer to use an InputStream rather than a Reader, and to let the + * parser auto-detect the encoding from the XML declaration. + *

+ * + * @param characterStream Reader to read from. + * @param systemId base for resolving relative URIs + * @return Document resultant Document object + * @throws JDOMException when errors occur in parsing + * @throws IOException when an I/O error prevents a document + * from being fully parsed + */ + public Document build(Reader characterStream, String systemId) + throws JDOMException, IOException { + + InputSource src = new InputSource(characterStream); + src.setSystemId(systemId); + return build(src); + } + + /** + *

+ * This builds a document from the supplied + * URI. + *

+ * @param systemId URI for the input + * @return Document resultant Document object + * @throws JDOMException when errors occur in parsing + * @throws IOException when an I/O error prevents a document + * from being fully parsed + */ + public Document build(String systemId) + throws JDOMException, IOException { + return build(new InputSource(systemId)); + } + +// /** +// * Imitation of File.toURL(), a JDK 1.2 method, reimplemented +// * here to work with JDK 1.1. +// * +// * @see java.io.File +// * +// * @param f the file to convert +// * @return the file path converted to a file: URL +// */ +// protected URL fileToURL(File f) throws MalformedURLException { +// String path = f.getAbsolutePath(); +// if (File.separatorChar != '/') { +// path = path.replace(File.separatorChar, '/'); +// } +// if (!path.startsWith("/")) { +// path = "/" + path; +// } +// if (!path.endsWith("/") && f.isDirectory()) { +// path = path + "/"; +// } +// return new URL("file", "", path); +// } + + /** Custom File.toUrl() implementation to handle special chars in file names + * + * @param file file object whose path will be converted + * @return URL form of the file, with special characters handled + * @throws MalformedURLException if there's a problem constructing a URL + */ + private static URL fileToURL(File file) throws MalformedURLException { + StringBuffer buffer = new StringBuffer(); + String path = file.getAbsolutePath(); + + // Convert non-URL style file separators + if (File.separatorChar != '/') { + path = path.replace(File.separatorChar, '/'); + } + + // Make sure it starts at root + if (!path.startsWith("/")) { + buffer.append('/'); + } + + // Copy, converting URL special characters as we go + int len = path.length(); + for (int i = 0; i < len; i++) { + char c = path.charAt(i); + if (c == ' ') + buffer.append("%20"); + else if (c == '#') + buffer.append("%23"); + else if (c == '%') + buffer.append("%25"); + else if (c == '&') + buffer.append("%26"); + else if (c == ';') + buffer.append("%3B"); + else if (c == '<') + buffer.append("%3C"); + else if (c == '=') + buffer.append("%3D"); + else if (c == '>') + buffer.append("%3E"); + else if (c == '?') + buffer.append("%3F"); + else if (c == '~') + buffer.append("%7E"); + else + buffer.append(c); + } + + // Make sure directories end with slash + if (!path.endsWith("/") && file.isDirectory()) { + buffer.append('/'); + } + + // Return URL + return new URL("file", "", buffer.toString()); + } + + /** + * Returns whether or not entities are being expanded into normal text + * content. + * + * @return whether entities are being expanded + */ + public boolean getExpandEntities() { + return expand; + } + + /** + *

+ * This sets whether or not to expand entities for the builder. + * A true means to expand entities as normal content. A false means to + * leave entities unexpanded as EntityRef objects. The + * default is true. + *

+ *

+ * When this setting is false, the internal DTD subset is retained; when + * this setting is true, the internal DTD subset is not retained. + *

+ *

+ * Note that Xerces (at least up to 1.4.4) has a bug where entities + * in attribute values will be misreported if this flag is turned off, + * resulting in entities to appear within element content. When turning + * entity expansion off either avoid entities in attribute values, or + * use another parser like Crimson. + * http://nagoya.apache.org/bugzilla/show_bug.cgi?id=6111 + *

+ * + * @param expand boolean indicating whether entity expansion + * should occur. + */ + public void setExpandEntities(boolean expand) { + this.expand = expand; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/SAXHandler.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/input/SAXHandler.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,1018 @@ +/*-- + + $Id: SAXHandler.java,v 1.73 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.input; + +import java.util.*; + +import org.jdom.*; +import org.xml.sax.*; +import org.xml.sax.ext.*; +import org.xml.sax.helpers.*; + +/** + * A support class for {@link SAXBuilder}. + * + * @version $Revision: 1.73 $, $Date: 2007/11/10 05:29:00 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Philip Nelson + * @author Bradley S. Huffman + * @author phil@triloggroup.com + */ +public class SAXHandler extends DefaultHandler implements LexicalHandler, + DeclHandler, + DTDHandler { + + private static final String CVS_ID = + "@(#) $RCSfile: SAXHandler.java,v $ $Revision: 1.73 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $"; + + /** Hash table to map SAX attribute type names to JDOM attribute types. */ + private static final Map attrNameToTypeMap = new HashMap(13); + + /** Document object being built */ + private Document document; + + /** Element object being built */ + private Element currentElement; + + /** Indicator of where in the document we are */ + private boolean atRoot; + + /** Indicator of whether we are in the DocType. Note that the DTD consists + * of both the internal subset (inside the tag) and the + * external subset (in a separate .dtd file). */ + private boolean inDTD = false; + + /** Indicator of whether we are in the internal subset */ + private boolean inInternalSubset = false; + + /** Indicator of whether we previously were in a CDATA */ + private boolean previousCDATA = false; + + /** Indicator of whether we are in a CDATA */ + private boolean inCDATA = false; + + /** Indicator of whether we should expand entities */ + private boolean expand = true; + + /** Indicator of whether we are actively suppressing (non-expanding) a + current entity */ + private boolean suppress = false; + + /** How many nested entities we're currently within */ + private int entityDepth = 0; // XXX may not be necessary anymore? + + /** Temporary holder for namespaces that have been declared with + * startPrefixMapping, but are not yet available on the element */ + private List declaredNamespaces; + + /** Temporary holder for the internal subset */ + private StringBuffer internalSubset = new StringBuffer(); + + /** Temporary holder for Text and CDATA */ + private TextBuffer textBuffer = new TextBuffer(); + + /** The external entities defined in this document */ + private Map externalEntities; + + /** The JDOMFactory used for JDOM object creation */ + private JDOMFactory factory; + + /** Whether to ignore ignorable whitespace */ + private boolean ignoringWhite = false; + + /** Whether to ignore text containing all whitespace */ + private boolean ignoringBoundaryWhite = false; + + /** The SAX Locator object provided by the parser */ + private Locator locator; + + /** + * Class initializer: Populate a table to translate SAX attribute + * type names into JDOM attribute type value (integer). + *

+ * Note that all the mappings defined below are compliant with + * the SAX 2.0 specification exception for "ENUMERATION" with is + * specific to Crimson 1.1.X and Xerces 2.0.0-betaX which report + * attributes of enumerated types with a type "ENUMERATION" + * instead of the expected "NMTOKEN". + *

+ *

+ * Note also that Xerces 1.4.X is not SAX 2.0 compliant either + * but handling its case requires + * {@link #getAttributeType specific code}. + *

+ */ + static { + attrNameToTypeMap.put("CDATA", + new Integer(Attribute.CDATA_TYPE)); + attrNameToTypeMap.put("ID", + new Integer(Attribute.ID_TYPE)); + attrNameToTypeMap.put("IDREF", + new Integer(Attribute.IDREF_TYPE)); + attrNameToTypeMap.put("IDREFS", + new Integer(Attribute.IDREFS_TYPE)); + attrNameToTypeMap.put("ENTITY", + new Integer(Attribute.ENTITY_TYPE)); + attrNameToTypeMap.put("ENTITIES", + new Integer(Attribute.ENTITIES_TYPE)); + attrNameToTypeMap.put("NMTOKEN", + new Integer(Attribute.NMTOKEN_TYPE)); + attrNameToTypeMap.put("NMTOKENS", + new Integer(Attribute.NMTOKENS_TYPE)); + attrNameToTypeMap.put("NOTATION", + new Integer(Attribute.NOTATION_TYPE)); + attrNameToTypeMap.put("ENUMERATION", + new Integer(Attribute.ENUMERATED_TYPE)); + } + + /** + * This will create a new SAXHandler that listens to SAX + * events and creates a JDOM Document. The objects will be constructed + * using the default factory. + */ + public SAXHandler() { + this(null); + } + + /** + * This will create a new SAXHandler that listens to SAX + * events and creates a JDOM Document. The objects will be constructed + * using the provided factory. + * + * @param factory JDOMFactory to be used for constructing + * objects + */ + public SAXHandler(JDOMFactory factory) { + if (factory != null) { + this.factory = factory; + } else { + this.factory = new DefaultJDOMFactory(); + } + + atRoot = true; + declaredNamespaces = new ArrayList(); + externalEntities = new HashMap(); + + document = this.factory.document(null); + } + + /** + * Pushes an element onto the tree under construction. Allows subclasses + * to put content under a dummy root element which is useful for building + * content that would otherwise be a non-well formed document. + * + * @param element root element under which content will be built + */ + protected void pushElement(Element element) { + if (atRoot) { + document.setRootElement(element); // XXX should we use a factory call? + atRoot = false; + } + else { + factory.addContent(currentElement, element); + } + currentElement = element; + } + + /** + * Returns the document. Should be called after parsing is complete. + * + * @return Document - Document that was built + */ + public Document getDocument() { + return document; + } + + /** + * Returns the factory used for constructing objects. + * + * @return JDOMFactory - the factory used for + * constructing objects. + * + * @see #SAXHandler(org.jdom.JDOMFactory) + */ + public JDOMFactory getFactory() { + return factory; + } + + /** + * This sets whether or not to expand entities during the build. + * A true means to expand entities as normal content. A false means to + * leave entities unexpanded as EntityRef objects. The + * default is true. + * + * @param expand boolean indicating whether entity expansion + * should occur. + */ + public void setExpandEntities(boolean expand) { + this.expand = expand; + } + + /** + * Returns whether or not entities will be expanded during the + * build. + * + * @return boolean - whether entity expansion + * will occur during build. + * + * @see #setExpandEntities + */ + public boolean getExpandEntities() { + return expand; + } + + /** + * Specifies whether or not the parser should elminate whitespace in + * element content (sometimes known as "ignorable whitespace") when + * building the document. Only whitespace which is contained within + * element content that has an element only content model will be + * eliminated (see XML Rec 3.2.1). For this setting to take effect + * requires that validation be turned on. The default value of this + * setting is false. + * + * @param ignoringWhite Whether to ignore ignorable whitespace + */ + public void setIgnoringElementContentWhitespace(boolean ignoringWhite) { + this.ignoringWhite = ignoringWhite; + } + + /** + * Specifies whether or not the parser should elminate text() nodes + * containing only whitespace when building the document. See + * {@link SAXBuilder#setIgnoringBoundaryWhitespace(boolean)}. + * + * @param ignoringBoundaryWhite Whether to ignore only whitespace content + */ + public void setIgnoringBoundaryWhitespace(boolean ignoringBoundaryWhite) { + this.ignoringBoundaryWhite = ignoringBoundaryWhite; + } + + /** + * Returns whether or not the parser will elminate element content + * containing only whitespace. + * + * @return boolean - whether only whitespace content will + * be ignored during build. + * + * @see #setIgnoringBoundaryWhitespace + */ + public boolean getIgnoringBoundaryWhitespace() { + return ignoringBoundaryWhite; + } + + /** + * Returns whether or not the parser will elminate whitespace in + * element content (sometimes known as "ignorable whitespace") when + * building the document. + * + * @return boolean - whether ignorable whitespace will + * be ignored during build. + * + * @see #setIgnoringElementContentWhitespace + */ + public boolean getIgnoringElementContentWhitespace() { + return ignoringWhite; + } + + public void startDocument() { + if (locator != null) { + document.setBaseURI(locator.getSystemId()); + } + } + + /** + * This is called when the parser encounters an external entity + * declaration. + * + * @param name entity name + * @param publicID public id + * @param systemID system id + * @throws SAXException when things go wrong + */ + public void externalEntityDecl(String name, + String publicID, String systemID) + throws SAXException { + // Store the public and system ids for the name + externalEntities.put(name, new String[]{publicID, systemID}); + + if (!inInternalSubset) return; + + internalSubset.append(" \n"); + } + + /** + * This handles an attribute declaration in the internal subset. + * + * @param eName String element name of attribute + * @param aName String attribute name + * @param type String attribute type + * @param valueDefault String default value of attribute + * @param value String value of attribute + * @throws SAXException + */ + public void attributeDecl(String eName, String aName, String type, + String valueDefault, String value) + throws SAXException { + + if (!inInternalSubset) return; + + internalSubset.append(" \n"); + } + + /** + * Handle an element declaration in a DTD. + * + * @param name String name of element + * @param model String model of the element in DTD syntax + * @throws SAXException + */ + public void elementDecl(String name, String model) throws SAXException { + // Skip elements that come from the external subset + if (!inInternalSubset) return; + + internalSubset.append(" \n"); + } + + /** + * Handle an internal entity declaration in a DTD. + * + * @param name String name of entity + * @param value String value of the entity + * @throws SAXException + */ + public void internalEntityDecl(String name, String value) + throws SAXException { + + // Skip entities that come from the external subset + if (!inInternalSubset) return; + + internalSubset.append(" \n"); + } + + /** + * This will indicate that a processing instruction has been encountered. + * (The XML declaration is not a processing instruction and will not + * be reported.) + * + * @param target String target of PI + * @param data String containing all data sent to the PI. + * This typically looks like one or more attribute value + * pairs. + * @throws SAXException when things go wrong + */ + public void processingInstruction(String target, String data) + throws SAXException { + + if (suppress) return; + + flushCharacters(); + + if (atRoot) { + factory.addContent(document, factory.processingInstruction(target, data)); + } else { + factory.addContent(getCurrentElement(), + factory.processingInstruction(target, data)); + } + } + + /** + * This indicates that an unresolvable entity reference has been + * encountered, normally because the external DTD subset has not been + * read. + * + * @param name String name of entity + * @throws SAXException when things go wrong + */ + public void skippedEntity(String name) + throws SAXException { + + // We don't handle parameter entity references. + if (name.startsWith("%")) return; + + flushCharacters(); + + factory.addContent(getCurrentElement(), factory.entityRef(name)); + } + + /** + * This will add the prefix mapping to the JDOM + * Document object. + * + * @param prefix String namespace prefix. + * @param uri String namespace URI. + */ + public void startPrefixMapping(String prefix, String uri) + throws SAXException { + + if (suppress) return; + + Namespace ns = Namespace.getNamespace(prefix, uri); + declaredNamespaces.add(ns); + } + + /** + * This reports the occurrence of an actual element. It will include + * the element's attributes, with the exception of XML vocabulary + * specific attributes, such as + * xmlns:[namespace prefix] and + * xsi:schemaLocation. + * + * @param namespaceURI String namespace URI this element + * is associated with, or an empty + * String + * @param localName String name of element (with no + * namespace prefix, if one is present) + * @param qName String XML 1.0 version of element name: + * [namespace prefix]:[localName] + * @param atts Attributes list for this element + * @throws SAXException when things go wrong + */ + public void startElement(String namespaceURI, String localName, + String qName, Attributes atts) + throws SAXException { + if (suppress) return; + + Element element = null; + + if ((namespaceURI != null) && (!namespaceURI.equals(""))) { + String prefix = ""; + + // Determine any prefix on the Element + if (!qName.equals(localName)) { + int split = qName.indexOf(":"); + prefix = qName.substring(0, split); + } + Namespace elementNamespace = + Namespace.getNamespace(prefix, namespaceURI); + element = factory.element(localName, elementNamespace); + } else { + element = factory.element(localName); + } + + // Take leftover declared namespaces and add them to this element's + // map of namespaces + if (declaredNamespaces.size() > 0) { + transferNamespaces(element); + } + + // Handle attributes + for (int i=0, len=atts.getLength(); i{@link Element} and + * transfer its namespaces to the global namespace storage. + * + * @param element Element to read namespaces from. + */ + private void transferNamespaces(Element element) { + Iterator i = declaredNamespaces.iterator(); + while (i.hasNext()) { + Namespace ns = (Namespace)i.next(); + if (ns != element.getNamespace()) { + element.addNamespaceDeclaration(ns); + } + } + declaredNamespaces.clear(); + } + + /** + * This will report character data (within an element). + * + * @param ch char[] character array with character data + * @param start int index in array where data starts. + * @param length int length of data. + * @throws SAXException + */ + public void characters(char[] ch, int start, int length) + throws SAXException { + + if (suppress || (length == 0)) + return; + + if (previousCDATA != inCDATA) { + flushCharacters(); + } + + textBuffer.append(ch, start, length); + } + + /** + * Capture ignorable whitespace as text. If + * setIgnoringElementContentWhitespace(true) has been called then this + * method does nothing. + * + * @param ch [] - char array of ignorable whitespace + * @param start int - starting position within array + * @param length int - length of whitespace after start + * @throws SAXException when things go wrong + */ + public void ignorableWhitespace(char[] ch, int start, int length) + throws SAXException { + if (!ignoringWhite) { + characters(ch, start, length); + } + } + + /** + * This will flush any characters from SAX character calls we've + * been buffering. + * + * @throws SAXException when things go wrong + */ + protected void flushCharacters() throws SAXException { + if (ignoringBoundaryWhite) { + if (!textBuffer.isAllWhitespace()) { + flushCharacters(textBuffer.toString()); + } + } + else { + flushCharacters(textBuffer.toString()); + } + textBuffer.clear(); + } + + /** + * Flush the given string into the document. This is a protected method + * so subclassers can control text handling without knowledge of the + * internals of this class. + * + * @param data string to flush + */ + protected void flushCharacters(String data) throws SAXException { + if (data.length() == 0) { + previousCDATA = inCDATA; + return; + } + +/** + * This is commented out because of some problems with + * the inline DTDs that Xerces seems to have. +if (!inDTD) { + if (inEntity) { + getCurrentElement().setContent(factory.text(data)); + } else { + getCurrentElement().addContent(factory.text(data)); +} +*/ + + if (previousCDATA) { + factory.addContent(getCurrentElement(), factory.cdata(data)); + } + else { + factory.addContent(getCurrentElement(), factory.text(data)); + } + + previousCDATA = inCDATA; + } + + /** + * Indicates the end of an element + * (</[element name]>) is reached. Note that + * the parser does not distinguish between empty + * elements and non-empty elements, so this will occur uniformly. + * + * @param namespaceURI String URI of namespace this + * element is associated with + * @param localName String name of element without prefix + * @param qName String name of element in XML 1.0 form + * @throws SAXException when things go wrong + */ + public void endElement(String namespaceURI, String localName, + String qName) throws SAXException { + + if (suppress) return; + + flushCharacters(); + + if (!atRoot) { + Parent p = currentElement.getParent(); + if (p instanceof Document) { + atRoot = true; + } + else { + currentElement = (Element) p; + } + } + else { + throw new SAXException( + "Ill-formed XML document (missing opening tag for " + + localName + ")"); + } + } + + /** + * This will signify that a DTD is being parsed, and can be + * used to ensure that comments and other lexical structures + * in the DTD are not added to the JDOM Document + * object. + * + * @param name String name of element listed in DTD + * @param publicID String public ID of DTD + * @param systemID String system ID of DTD + */ + public void startDTD(String name, String publicID, String systemID) + throws SAXException { + + flushCharacters(); // Is this needed here? + + factory.addContent(document, factory.docType(name, publicID, systemID)); + inDTD = true; + inInternalSubset = true; + } + + /** + * This signifies that the reading of the DTD is complete. + * + * @throws SAXException + */ + public void endDTD() throws SAXException { + + document.getDocType().setInternalSubset(internalSubset.toString()); + inDTD = false; + inInternalSubset = false; + } + + public void startEntity(String name) throws SAXException { + entityDepth++; + + if (expand || entityDepth > 1) { + // Short cut out if we're expanding or if we're nested + return; + } + + // A "[dtd]" entity indicates the beginning of the external subset + if (name.equals("[dtd]")) { + inInternalSubset = false; + return; + } + + // Ignore DTD references, and translate the standard 5 + if ((!inDTD) && + (!name.equals("amp")) && + (!name.equals("lt")) && + (!name.equals("gt")) && + (!name.equals("apos")) && + (!name.equals("quot"))) { + + if (!expand) { + String pub = null; + String sys = null; + String[] ids = (String[]) externalEntities.get(name); + if (ids != null) { + pub = ids[0]; // may be null, that's OK + sys = ids[1]; // may be null, that's OK + } + /** + * if no current element, this entity belongs to an attribute + * in these cases, it is an error on the part of the parser + * to call startEntity but this will help in some cases. + * See org/xml/sax/ext/LexicalHandler.html#startEntity(java.lang.String) + * for more information + */ + if (!atRoot) { + flushCharacters(); + EntityRef entity = factory.entityRef(name, pub, sys); + + // no way to tell if the entity was from an attribute or element so just assume element + factory.addContent(getCurrentElement(), entity); + } + suppress = true; + } + } + } + + public void endEntity(String name) throws SAXException { + entityDepth--; + if (entityDepth == 0) { + // No way are we suppressing if not in an entity, + // regardless of the "expand" value + suppress = false; + } + if (name.equals("[dtd]")) { + inInternalSubset = true; + } + } + + /** + * Report a CDATA section + * + * @throws SAXException + */ + public void startCDATA() throws SAXException { + if (suppress) return; + + inCDATA = true; + } + + /** + * Report a CDATA section + */ + public void endCDATA() throws SAXException { + if (suppress) return; + + previousCDATA = true; + inCDATA = false; + } + + /** + * This reports that a comments is parsed. If not in the + * DTD, this comment is added to the current JDOM + * Element, or the Document itself + * if at that level. + * + * @param ch ch[] array of comment characters. + * @param start int index to start reading from. + * @param length int length of data. + * @throws SAXException + */ + public void comment(char[] ch, int start, int length) + throws SAXException { + + if (suppress) return; + + flushCharacters(); + + String commentText = new String(ch, start, length); + if (inDTD && inInternalSubset && (expand == false)) { + internalSubset.append(" \n"); + return; + } + if ((!inDTD) && (!commentText.equals(""))) { + if (atRoot) { + factory.addContent(document, factory.comment(commentText)); + } else { + factory.addContent(getCurrentElement(), factory.comment(commentText)); + } + } + } + + /** + * Handle the declaration of a Notation in a DTD + * + * @param name name of the notation + * @param publicID the public ID of the notation + * @param systemID the system ID of the notation + */ + public void notationDecl(String name, String publicID, String systemID) + throws SAXException { + + if (!inInternalSubset) return; + + internalSubset.append(" \n"); + } + + /** + * Handler for unparsed entity declarations in the DTD + * + * @param name String of the unparsed entity decl + * @param publicID String of the unparsed entity decl + * @param systemID String of the unparsed entity decl + * @param notationName String of the unparsed entity decl + */ + public void unparsedEntityDecl(String name, String publicID, + String systemID, String notationName) + throws SAXException { + + if (!inInternalSubset) return; + + internalSubset.append(" \n"); + } + + /** + * Appends an external ID to the internal subset buffer. Either publicID + * or systemID may be null, but not both. + * + * @param publicID the public ID + * @param systemID the system ID + */ + private void appendExternalId(String publicID, String systemID) { + if (publicID != null) { + internalSubset.append(" PUBLIC \"") + .append(publicID) + .append('\"'); + } + if (systemID != null) { + if (publicID == null) { + internalSubset.append(" SYSTEM "); + } + else { + internalSubset.append(' '); + } + internalSubset.append('\"') + .append(systemID) + .append('\"'); + } + } + + /** + * Returns the being-parsed element. + * + * @return Element - element being built. + * @throws SAXException + */ + public Element getCurrentElement() throws SAXException { + if (currentElement == null) { + throw new SAXException( + "Ill-formed XML document (multiple root elements detected)"); + } + return currentElement; + } + + /** + * Returns the the JDOM Attribute type value from the SAX 2.0 + * attribute type string provided by the parser. + * + * @param typeName String the SAX 2.0 attribute + * type string. + * + * @return int the JDOM attribute type. + * + * @see Attribute#setAttributeType + * @see Attributes#getType + */ + private static int getAttributeType(String typeName) { + Integer type = (Integer)(attrNameToTypeMap.get(typeName)); + if (type == null) { + if (typeName != null && typeName.length() > 0 && + typeName.charAt(0) == '(') { + // Xerces 1.4.X reports attributes of enumerated type with + // a type string equals to the enumeration definition, i.e. + // starting with a parenthesis. + return Attribute.ENUMERATED_TYPE; + } + else { + return Attribute.UNDECLARED_TYPE; + } + } else { + return type.intValue(); + } + } + + /** + * Receives an object for locating the origin of SAX document + * events. This method is invoked by the SAX parser. + *

+ * {@link org.jdom.JDOMFactory} implementations can use the + * {@link #getDocumentLocator} method to get access to the + * {@link Locator} during parse. + *

+ * + * @param locator Locator an object that can return + * the location of any SAX document event. + */ + public void setDocumentLocator(Locator locator) { + this.locator = locator; + } + + /** + * Provides access to the {@link Locator} object provided by the + * SAX parser. + * + * @return Locator an object that can return + * the location of any SAX document event. + */ + public Locator getDocumentLocator() { + return locator; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/TextBuffer.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/input/TextBuffer.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,186 @@ +/*-- + + $Id: TextBuffer.java,v 1.10 2007/11/10 05:29:00 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.input; + +import org.jdom.*; + +/** + * A non-public utility class similar to StringBuffer but optimized for XML + * parsing where the common case is that you get only one chunk of characters + * per text section. TextBuffer stores the first chunk of characters in a + * String, which can just be returned directly if no second chunk is received. + * Subsequent chunks are stored in a supplemental char array (like StringBuffer + * uses). In this case, the returned text will be the first String chunk, + * concatenated with the subsequent chunks stored in the char array. This + * provides optimal performance in the common case, while still providing very + * good performance in the uncommon case. Furthermore, avoiding StringBuffer + * means that no extra unused char array space will be kept around after parsing + * is through. + * + * @version $Revision: 1.10 $, $Date: 2007/11/10 05:29:00 $ + * @author Bradley S. Huffman + * @author Alex Rosen + */ +class TextBuffer { + + private static final String CVS_ID = + "@(#) $RCSfile: TextBuffer.java,v $ $Revision: 1.10 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $"; + + /** The first part of the text value (the "prefix"). If null, the + * text value is the empty string. */ + private String prefixString; + + /** The rest of the text value (the "suffix"). Only the first + * code>arraySize characters are valid. */ + private char[] array; + + /** The size of the rest of the text value. If zero, then only + * code>prefixString contains the text value. */ + private int arraySize; + + /** Constructor */ + TextBuffer() { + array = new char[4096]; // initial capacity + arraySize = 0; + } + + /** Append the specified text to the text value of this buffer. */ + void append(char[] source, int start, int count) { + if (prefixString == null) { + // This is the first chunk, so we'll store it in the prefix string + prefixString = new String(source, start, count); + } + else { + // This is a subsequent chunk, so we'll add it to the char array + ensureCapacity(arraySize + count); + System.arraycopy(source, start, array, arraySize, count); + arraySize += count; + } + } + + /** Returns the size of the text value. */ + int size() { + if (prefixString == null) { + return 0; + } + else { + return prefixString.length() + arraySize; + } + } + + /** Clears the text value and prepares the TextBuffer for reuse. */ + void clear() { + arraySize = 0; + prefixString = null; + } + + boolean isAllWhitespace() { + if ((prefixString == null) || (prefixString.length() == 0)) { + return true; + } + + int size = prefixString.length(); + for(int i = 0; i < size; i++) { + if ( !Verifier.isXMLWhitespace(prefixString.charAt(i))) { + return false; + } + } + + for(int i = 0; i < arraySize; i++) { + if ( !Verifier.isXMLWhitespace(array[i])) { + return false; + } + } + return true; + } + + /** Returns the text value stored in the buffer. */ + public String toString() { + if (prefixString == null) { + return ""; + } + + String str = ""; + if (arraySize == 0) { + // Char array is empty, so the text value is just prefixString. + str = prefixString; + } + else { + // Char array is not empty, so the text value is prefixString + // plus the char array. + str = new StringBuffer(prefixString.length() + arraySize) + .append(prefixString) + .append(array, 0, arraySize) + .toString(); + } + return str; + } + + // Ensure that the char array has room for at least "csize" characters. + private void ensureCapacity(int csize) { + int capacity = array.length; + if (csize > capacity) { + char[] old = array; + int nsize = capacity; + while (csize > nsize) { + nsize += (capacity/2); + } + array = new char[nsize]; + System.arraycopy(old, 0, array, 0, arraySize); + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/input/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,10 @@ + + +Classes to build JDOM documents from various sources. The most common builder +class is SAXBuilder which constructs a JDOM document using a SAX parser and +can pull content from files, streams, sockets, readers, and so on. It can use +any underlying SAX parser to handle the parsing chores. SAXHandler provides +support for SAXBuilder. DOMBuilder lets you build from a pre-existing DOM +tree. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/DOMOutputter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/output/DOMOutputter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,454 @@ +/*-- + + $Id: DOMOutputter.java,v 1.43 2007/11/10 05:29:01 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + + +package org.jdom.output; + +import java.util.*; + +import org.jdom.*; +import org.jdom.adapters.*; + + +/** + * Outputs a JDOM {@link org.jdom.Document org.jdom.Document} as a DOM {@link + * org.w3c.dom.Document org.w3c.dom.Document}. + * + * @version $Revision: 1.43 $, $Date: 2007/11/10 05:29:01 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Matthew Merlo + * @author Dan Schaffer + * @author Yusuf Goolamabbas + * @author Bradley S. Huffman + */ +public class DOMOutputter { + + private static final String CVS_ID = + "@(#) $RCSfile: DOMOutputter.java,v $ $Revision: 1.43 $ $Date: 2007/11/10 05:29:01 $ $Name: jdom_1_1_1 $"; + + /** Default adapter class */ + private static final String DEFAULT_ADAPTER_CLASS = + "org.jdom.adapters.XercesDOMAdapter"; + + /** Adapter to use for interfacing with the DOM implementation */ + private String adapterClass; + + /** Output a DOM with namespaces but just the empty namespace */ + private boolean forceNamespaceAware; + + /** + * This creates a new DOMOutputter which will attempt to first locate + * a DOM implementation to use via JAXP, and if JAXP does not exist or + * there's a problem, will fall back to the default parser. + */ + public DOMOutputter() { + // nothing + } + + /** + * This creates a new DOMOutputter using the specified DOMAdapter + * implementation as a way to choose the underlying parser. + * + * @param adapterClass String name of class + * to use for DOM output + */ + public DOMOutputter(String adapterClass) { + this.adapterClass = adapterClass; + } + + /** + * Controls how NO_NAMESPACE nodes are handeled. If true the outputter + * always creates a namespace aware DOM. + * @param flag + */ + public void setForceNamespaceAware(boolean flag) { + this.forceNamespaceAware = flag; + } + + /** + * Returns whether DOMs will be constructed with namespaces even when + * the source document has elements all in the empty namespace. + * @return the forceNamespaceAware flag value + */ + public boolean getForceNamespaceAware() { + return forceNamespaceAware; + } + + /** + * This converts the JDOM Document parameter to a + * DOM Document, returning the DOM version. The DOM implementation + * is the one chosen in the constructor. + * + * @param document Document to output. + * @return an org.w3c.dom.Document version + */ + public org.w3c.dom.Document output(Document document) + throws JDOMException { + NamespaceStack namespaces = new NamespaceStack(); + + org.w3c.dom.Document domDoc = null; + try { + // Assign DOCTYPE during construction + DocType dt = document.getDocType(); + domDoc = createDOMDocument(dt); + + // Add content + Iterator itr = document.getContent().iterator(); + while (itr.hasNext()) { + Object node = itr.next(); + + if (node instanceof Element) { + Element element = (Element) node; + org.w3c.dom.Element domElement = + output(element, domDoc, namespaces); + // Add the root element, first check for existing root + org.w3c.dom.Element root = domDoc.getDocumentElement(); + if (root == null) { + // Normal case + domDoc.appendChild(domElement); // normal case + } + else { + // Xerces 1.3 creates new docs with a + // XXX: Need to address DOCTYPE mismatch still + domDoc.replaceChild(domElement, root); + } + } + else if (node instanceof Comment) { + Comment comment = (Comment) node; + org.w3c.dom.Comment domComment = + domDoc.createComment(comment.getText()); + domDoc.appendChild(domComment); + } + else if (node instanceof ProcessingInstruction) { + ProcessingInstruction pi = + (ProcessingInstruction) node; + org.w3c.dom.ProcessingInstruction domPI = + domDoc.createProcessingInstruction( + pi.getTarget(), pi.getData()); + domDoc.appendChild(domPI); + } + else if (node instanceof DocType) { + // We already dealt with the DocType above + } + else { + throw new JDOMException( + "Document contained top-level content with type:" + + node.getClass().getName()); + } + } + } + catch (Throwable e) { + throw new JDOMException("Exception outputting Document", e); + } + + return domDoc; + } + + private org.w3c.dom.Document createDOMDocument(DocType dt) + throws JDOMException { + if (adapterClass != null) { + // The user knows that they want to use a particular impl + try { + DOMAdapter adapter = + (DOMAdapter)Class.forName(adapterClass).newInstance(); + // System.out.println("using specific " + adapterClass); + return adapter.createDocument(dt); + } + catch (ClassNotFoundException e) { + // e.printStackTrace(); + } + catch (IllegalAccessException e) { + // e.printStackTrace(); + } + catch (InstantiationException e) { + // e.printStackTrace(); + } + } + else { + // Try using JAXP... + try { + DOMAdapter adapter = + (DOMAdapter)Class.forName( + "org.jdom.adapters.JAXPDOMAdapter").newInstance(); + // System.out.println("using JAXP"); + return adapter.createDocument(dt); + } + catch (ClassNotFoundException e) { + // e.printStackTrace(); + } + catch (IllegalAccessException e) { + // e.printStackTrace(); + } + catch (InstantiationException e) { + // e.printStackTrace(); + } + } + + // If no DOM doc yet, try to use a hard coded default + try { + DOMAdapter adapter = (DOMAdapter) + Class.forName(DEFAULT_ADAPTER_CLASS).newInstance(); + return adapter.createDocument(dt); + // System.out.println("Using default " + + // DEFAULT_ADAPTER_CLASS); + } + catch (ClassNotFoundException e) { + // e.printStackTrace(); + } + catch (IllegalAccessException e) { + // e.printStackTrace(); + } + catch (InstantiationException e) { + // e.printStackTrace(); + } + + throw new JDOMException("No JAXP or default parser available"); + + } + + private org.w3c.dom.Element output(Element element, + org.w3c.dom.Document domDoc, + NamespaceStack namespaces) + throws JDOMException { + try { + int previouslyDeclaredNamespaces = namespaces.size(); + + org.w3c.dom.Element domElement = null; + if (element.getNamespace() == Namespace.NO_NAMESPACE) { + // No namespace, use createElement + domElement = forceNamespaceAware ? + domDoc.createElementNS(null, element.getQualifiedName()) + : domDoc.createElement(element.getQualifiedName()); } + else { + domElement = domDoc.createElementNS( + element.getNamespaceURI(), + element.getQualifiedName()); + } + + // Add namespace attributes, beginning with the element's own + // Do this only if it's not the XML namespace and it's + // not the NO_NAMESPACE with the prefix "" not yet mapped + // (we do output xmlns="" if the "" prefix was already used + // and we need to reclaim it for the NO_NAMESPACE) + Namespace ns = element.getNamespace(); + if (ns != Namespace.XML_NAMESPACE && + !(ns == Namespace.NO_NAMESPACE && + namespaces.getURI("") == null)) { + String prefix = ns.getPrefix(); + String uri = namespaces.getURI(prefix); + if (!ns.getURI().equals(uri)) { // output a new namespace decl + namespaces.push(ns); + String attrName = getXmlnsTagFor(ns); + domElement.setAttribute(attrName, ns.getURI()); + } + } + + // Add additional namespaces also + Iterator itr = element.getAdditionalNamespaces().iterator(); + while (itr.hasNext()) { + Namespace additional = (Namespace)itr.next(); + String prefix = additional.getPrefix(); + String uri = namespaces.getURI(prefix); + if (!additional.getURI().equals(uri)) { + String attrName = getXmlnsTagFor(additional); + domElement.setAttribute(attrName, additional.getURI()); + namespaces.push(additional); + } + } + + // Add attributes to the DOM element + itr = element.getAttributes().iterator(); + while (itr.hasNext()) { + Attribute attribute = (Attribute) itr.next(); + domElement.setAttributeNode(output(attribute, domDoc)); + Namespace ns1 = attribute.getNamespace(); + if ((ns1 != Namespace.NO_NAMESPACE) && + (ns1 != Namespace.XML_NAMESPACE)) { + String prefix = ns1.getPrefix(); + String uri = namespaces.getURI(prefix); + if (!ns1.getURI().equals(uri)) { // output a new decl + String attrName = getXmlnsTagFor(ns1); + domElement.setAttribute(attrName, ns1.getURI()); + namespaces.push(ns1); + } + } + // Crimson doesn't like setAttributeNS() for non-NS attribs + if (attribute.getNamespace() == Namespace.NO_NAMESPACE) { + // No namespace, use setAttribute + if (forceNamespaceAware) { + domElement.setAttributeNS(null, + attribute.getQualifiedName(), + attribute.getValue()); + } else { + domElement.setAttribute(attribute.getQualifiedName(), + attribute.getValue()); + } + } + else { + domElement.setAttributeNS(attribute.getNamespaceURI(), + attribute.getQualifiedName(), + attribute.getValue()); + } + } + + // Add content to the DOM element + itr = element.getContent().iterator(); + while (itr.hasNext()) { + Object node = itr.next(); + + if (node instanceof Element) { + Element e = (Element) node; + org.w3c.dom.Element domElt = output(e, domDoc, namespaces); + domElement.appendChild(domElt); + } + else if (node instanceof String) { + String str = (String) node; + org.w3c.dom.Text domText = domDoc.createTextNode(str); + domElement.appendChild(domText); + } + else if (node instanceof CDATA) { + CDATA cdata = (CDATA) node; + org.w3c.dom.CDATASection domCdata = + domDoc.createCDATASection(cdata.getText()); + domElement.appendChild(domCdata); + } + else if (node instanceof Text) { + Text text = (Text) node; + org.w3c.dom.Text domText = + domDoc.createTextNode(text.getText()); + domElement.appendChild(domText); + } + else if (node instanceof Comment) { + Comment comment = (Comment) node; + org.w3c.dom.Comment domComment = + domDoc.createComment(comment.getText()); + domElement.appendChild(domComment); + } + else if (node instanceof ProcessingInstruction) { + ProcessingInstruction pi = + (ProcessingInstruction) node; + org.w3c.dom.ProcessingInstruction domPI = + domDoc.createProcessingInstruction( + pi.getTarget(), pi.getData()); + domElement.appendChild(domPI); + } + else if (node instanceof EntityRef) { + EntityRef entity = (EntityRef) node; + org.w3c.dom.EntityReference domEntity = + domDoc.createEntityReference(entity.getName()); + domElement.appendChild(domEntity); + } + else { + throw new JDOMException( + "Element contained content with type:" + + node.getClass().getName()); + } + } + + // Remove declared namespaces from stack + while (namespaces.size() > previouslyDeclaredNamespaces) { + namespaces.pop(); + } + + return domElement; + } + catch (Exception e) { + throw new JDOMException("Exception outputting Element " + + element.getQualifiedName(), e); + } + } + + private org.w3c.dom.Attr output(Attribute attribute, + org.w3c.dom.Document domDoc) + throws JDOMException { + org.w3c.dom.Attr domAttr = null; + try { + if (attribute.getNamespace() == Namespace.NO_NAMESPACE) { + // No namespace, use createAttribute + if (forceNamespaceAware) { + domAttr = domDoc.createAttributeNS(null, attribute.getQualifiedName()); + } else { + domAttr = domDoc.createAttribute(attribute.getQualifiedName()); + } + } + else { + domAttr = domDoc.createAttributeNS(attribute.getNamespaceURI(), + attribute.getQualifiedName()); + } + domAttr.setValue(attribute.getValue()); + } catch (Exception e) { + throw new JDOMException("Exception outputting Attribute " + + attribute.getQualifiedName(), e); + } + return domAttr; + } + + /** + * This will handle adding any {@link Namespace} + * attributes to the DOM tree. + * + * @param ns Namespace to add definition of + */ + private static String getXmlnsTagFor(Namespace ns) { + String attrName = "xmlns"; + if (!ns.getPrefix().equals("")) { + attrName += ":"; + attrName += ns.getPrefix(); + } + return attrName; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/EscapeStrategy.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/output/EscapeStrategy.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,76 @@ +/*-- + + $Id: EscapeStrategy.java,v 1.4 2007/11/10 05:29:01 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.output; + +/** + * Logic to determine which characters should be formatted as character + * entities. + * + * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:01 $ + * @author Alex Rosen + * @author Bradley S. Huffman + * @author Jason Hunter + */ +public interface EscapeStrategy { + + /** + * Test whether the supplied character should be formatted literally + * or as a character entity. + */ + public boolean shouldEscape(char ch); +} + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/Format.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/output/Format.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,615 @@ +/*-- + + $Id: Format.java,v 1.14 2009/07/23 05:54:23 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.output; + +import java.lang.reflect.Method; +import org.jdom.Verifier; + +/** + * Class to encapsulate XMLOutputter format options. + * Typical users can use the standard format configurations obtained by + * {@link #getRawFormat} (no whitespace changes), + * {@link #getPrettyFormat} (whitespace beautification), and + * {@link #getCompactFormat} (whitespace normalization). + *

+ * Several modes are available to effect the way textual content is printed. + * See the documentation for {@link TextMode} for details. + * + * @version $Revision: 1.14 $, $Date: 2009/07/23 05:54:23 $ + * @author Jason Hunter + */ +public class Format implements Cloneable { + + private static final String CVS_ID = + "@(#) $RCSfile: Format.java,v $ $Revision: 1.14 $ $Date: 2009/07/23 05:54:23 $ $Name: jdom_1_1_1 $"; + + /** + * Returns a new Format object that performs no whitespace changes, uses + * the UTF-8 encoding, doesn't expand empty elements, includes the + * declaration and encoding, and uses the default entity escape strategy. + * Tweaks can be made to the returned Format instance without affecting + * other instances. + + * @return a Format with no whitespace changes + */ + public static Format getRawFormat() { + return new Format(); + } + + /** + * Returns a new Format object that performs whitespace beautification with + * 2-space indents, uses the UTF-8 encoding, doesn't expand empty elements, + * includes the declaration and encoding, and uses the default entity + * escape strategy. + * Tweaks can be made to the returned Format instance without affecting + * other instances. + * + * @return a Format with whitespace beautification + */ + public static Format getPrettyFormat() { + Format f = new Format(); + f.setIndent(STANDARD_INDENT); + f.setTextMode(TextMode.TRIM); + return f; + } + + /** + * Returns a new Format object that performs whitespace normalization, uses + * the UTF-8 encoding, doesn't expand empty elements, includes the + * declaration and encoding, and uses the default entity escape strategy. + * Tweaks can be made to the returned Format instance without affecting + * other instances. + * + * @return a Format with whitespace normalization + */ + public static Format getCompactFormat() { + Format f = new Format(); + f.setTextMode(TextMode.NORMALIZE); + return f; + } + + /** standard value to indent by, if we are indenting */ + private static final String STANDARD_INDENT = " "; + + /** standard string with which to end a line */ + private static final String STANDARD_LINE_SEPARATOR = "\r\n"; + + /** standard encoding */ + private static final String STANDARD_ENCODING = "UTF-8"; + + + /** The default indent is no spaces (as original document) */ + String indent = null; + + /** New line separator */ + String lineSeparator = STANDARD_LINE_SEPARATOR; + + /** The encoding format */ + String encoding = STANDARD_ENCODING; + + /** Whether or not to output the XML declaration + * - default is false */ + boolean omitDeclaration = false; + + /** Whether or not to output the encoding in the XML declaration + * - default is false */ + boolean omitEncoding = false; + + /** Whether or not to expand empty elements to + * <tagName></tagName> - default is false */ + boolean expandEmptyElements = false; + + /** Whether TrAX output escaping disabling/enabling PIs are ignored + * or processed - default is false */ + boolean ignoreTrAXEscapingPIs = false; + + /** text handling mode */ + TextMode mode = TextMode.PRESERVE; + + /** entity escape logic */ + EscapeStrategy escapeStrategy = new DefaultEscapeStrategy(encoding); + + /** + * Creates a new Format instance with default (raw) behavior. + */ + private Format() { } + + /** + * Sets the {@link EscapeStrategy} to use for character escaping. + * + * @param strategy the EscapeStrategy to use + * @return a pointer to this Format for chaining + */ + public Format setEscapeStrategy(EscapeStrategy strategy) { + escapeStrategy = strategy; + return this; + } + + /** + * Returns the current escape strategy + * + * @return the current escape strategy + */ + public EscapeStrategy getEscapeStrategy() { + return escapeStrategy; + } + + /** + * This will set the newline separator (lineSeparator). + * The default is \r\n. To make it output + * the system default line ending string, call + * setLineSeparator(System.getProperty("line.separator")). + * + *

+ * To output "UNIX-style" documents, call + * setLineSeparator("\n"). To output "Mac-style" + * documents, call setLineSeparator("\r"). DOS-style + * documents use CR-LF ("\r\n"), which is the default. + *

+ * + *

+ * Note that this only applies to newlines generated by the + * outputter. If you parse an XML document that contains newlines + * embedded inside a text node, and you do not set TextMode.NORMALIZE, + * then the newlines will be output + * verbatim, as "\n" which is how parsers normalize them. + *

+ * + *

+ * If the format's "indent" property is null (as is the default + * for the Raw and Compact formats), then this value only effects the + * newlines written after the declaration and doctype. + *

+ * + * @see #setTextMode + * + * @param separator String line separator to use. + * @return a pointer to this Format for chaining + */ + public Format setLineSeparator(String separator) { + this.lineSeparator = separator; + return this; + } + + /** + * Returns the current line separator. + * + * @return the current line separator + */ + public String getLineSeparator() { + return lineSeparator; + } + + /** + * This will set whether the XML declaration + * (<?xml version="1.0" + * encoding="UTF-8"?>) + * includes the encoding of the document. It is common to omit + * this in uses such as WML and other wireless device protocols. + * + * @param omitEncoding boolean indicating whether or not + * the XML declaration should indicate the document encoding. + * @return a pointer to this Format for chaining + */ + public Format setOmitEncoding(boolean omitEncoding) { + this.omitEncoding = omitEncoding; + return this; + } + + /** + * Returns whether the XML declaration encoding will be omitted. + * + * @return whether the XML declaration encoding will be omitted + */ + public boolean getOmitEncoding() { + return omitEncoding; + } + + /** + * This will set whether the XML declaration + * (<?xml version="1.0"?gt;) + * will be omitted or not. It is common to omit this in uses such + * as SOAP and XML-RPC calls. + * + * @param omitDeclaration boolean indicating whether or not + * the XML declaration should be omitted. + * @return a pointer to this Format for chaining + */ + public Format setOmitDeclaration(boolean omitDeclaration) { + this.omitDeclaration = omitDeclaration; + return this; + } + + /** + * Returns whether the XML declaration will be omitted. + * + * @return whether the XML declaration will be omitted + */ + public boolean getOmitDeclaration() { + return omitDeclaration; + } + + /** + * This will set whether empty elements are expanded from + * <tagName/> to + * <tagName></tagName>. + * + * @param expandEmptyElements boolean indicating whether or not + * empty elements should be expanded. + * @return a pointer to this Format for chaining + */ + public Format setExpandEmptyElements(boolean expandEmptyElements) { + this.expandEmptyElements = expandEmptyElements; + return this; + } + + /** + * Returns whether empty elements are expanded. + * + * @return whether empty elements are expanded + */ + public boolean getExpandEmptyElements() { + return expandEmptyElements; + } + + /** + * This will set whether JAXP TrAX processing instructions for + * disabling/enabling output escaping are ignored. Disabling + * output escaping allows using XML text as element content and + * outputing it verbatim, i.e. as element children would be. + *

+ * When processed, these processing instructions are removed from + * the generated XML text and control whether the element text + * content is output verbatim or with escaping of the pre-defined + * entities in XML 1.0. The text to be output verbatim shall be + * surrounded by the + * <?javax.xml.transform.disable-output-escaping ?> + * and <?javax.xml.transform.enable-output-escaping ?> + * PIs.

+ *

+ * When ignored, the processing instructions are present in the + * generated XML text and the pre-defined entities in XML 1.0 are + * escaped. + *

+ * Default: false.

+ * + * @param ignoreTrAXEscapingPIs boolean indicating + * whether or not TrAX ouput escaping PIs are ignored. + * + * @see javax.xml.transform.Result#PI_ENABLE_OUTPUT_ESCAPING + * @see javax.xml.transform.Result#PI_DISABLE_OUTPUT_ESCAPING + */ + public void setIgnoreTrAXEscapingPIs(boolean ignoreTrAXEscapingPIs) { + this.ignoreTrAXEscapingPIs = ignoreTrAXEscapingPIs; + } + + /** + * Returns whether JAXP TrAX processing instructions for + * disabling/enabling output escaping are ignored. + * + * @return whether or not TrAX ouput escaping PIs are ignored. + */ + public boolean getIgnoreTrAXEscapingPIs() { + return ignoreTrAXEscapingPIs; + } + + /** + * This sets the text output style. Options are available as static + * {@link TextMode} instances. The default is {@link TextMode#PRESERVE}. + * + * @return a pointer to this Format for chaining + */ + public Format setTextMode(Format.TextMode mode) { + this.mode = mode; + return this; + } + + /** + * Returns the current text output style. + * + * @return the current text output style + */ + public Format.TextMode getTextMode() { + return mode; + } + + /** + * This will set the indent String to use; this + * is usually a String of empty spaces. If you pass + * the empty string (""), then no indentation will happen but newlines + * will still be generated. Passing null will result in no indentation + * and no newlines generated. Default: none (null) + * + * @param indent String to use for indentation. + * @return a pointer to this Format for chaining + */ + public Format setIndent(String indent) { + this.indent = indent; + return this; + } + + /** + * Returns the indent string in use. + * + * @return the indent string in use + */ + public String getIndent() { + return indent; + } + + /** + * Sets the output encoding. The name should be an accepted XML + * encoding. + * + * @param encoding the encoding format. Use XML-style names like + * "UTF-8" or "ISO-8859-1" or "US-ASCII" + * @return a pointer to this Format for chaining + */ + public Format setEncoding(String encoding) { + this.encoding = encoding; + escapeStrategy = new DefaultEscapeStrategy(encoding); + return this; + } + + /** + * Returns the configured output encoding. + * + * @return the output encoding + */ + public String getEncoding() { + return encoding; + } + + protected Object clone() { + Format format = null; + + try { + format = (Format) super.clone(); + } + catch (CloneNotSupportedException ce) { + } + + return format; + } + + + /** + * Handle common charsets quickly and easily. Use reflection + * to query the JDK 1.4 CharsetEncoder class for unknown charsets. + * If JDK 1.4 isn't around, default to no special encoding. + */ + class DefaultEscapeStrategy implements EscapeStrategy { + private int bits; + Object encoder; + Method canEncode; + + public DefaultEscapeStrategy(String encoding) { + if ("UTF-8".equalsIgnoreCase(encoding) || + "UTF-16".equalsIgnoreCase(encoding)) { + bits = 16; + } + else if ("ISO-8859-1".equalsIgnoreCase(encoding) || + "Latin1".equalsIgnoreCase(encoding)) { + bits = 8; + } + else if ("US-ASCII".equalsIgnoreCase(encoding) || + "ASCII".equalsIgnoreCase(encoding)) { + bits = 7; + } + else { + bits = 0; + //encoder = Charset.forName(encoding).newEncoder(); + try { + Class charsetClass = Class.forName("java.nio.charset.Charset"); + Class encoderClass = Class.forName("java.nio.charset.CharsetEncoder"); + Method forName = charsetClass.getMethod("forName", new Class[]{String.class}); + Object charsetObj = forName.invoke(null, new Object[]{encoding}); + Method newEncoder = charsetClass.getMethod("newEncoder", null); + encoder = newEncoder.invoke(charsetObj, null); + canEncode = encoderClass.getMethod("canEncode", new Class[]{char.class}); + } + catch (Exception ignored) { + } + } + } + + public boolean shouldEscape(char ch) { + if (bits == 16) { + if (Verifier.isHighSurrogate(ch)) + return true; // Safer this way per http://unicode.org/faq/utf_bom.html#utf8-4 + else + return false; + } + if (bits == 8) { + if ((int) ch > 255) + return true; + else + return false; + } + if (bits == 7) { + if ((int) ch > 127) + return true; + else + return false; + } + else { + if (Verifier.isHighSurrogate(ch)) + return true; // Safer this way per http://unicode.org/faq/utf_bom.html#utf8-4 + + if (canEncode != null && encoder != null) { + try { + Boolean val = (Boolean) canEncode.invoke(encoder, new Object[]{new Character(ch)}); + return !val.booleanValue(); + } + catch (Exception ignored) { + } + } + // Return false if we don't know. This risks not escaping + // things which should be escaped, but also means people won't + // start getting loads of unnecessary escapes. + return false; + } + } + } + + + /** + * Class to signify how text should be handled on output. The following + * table provides details. + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
+ * Text Mode + * + * Resulting behavior. + *
+ * PRESERVE (Default) + * + * All content is printed in the format it was created, no whitespace + * or line separators are are added or removed. + *
+ * TRIM_FULL_WHITE + * + * Content between tags consisting of all whitespace is not printed. + * If the content contains even one non-whitespace character, it is + * printed verbatim, whitespace and all. + *
+ * TRIM + * + * Same as TrimAllWhite, plus leading/trailing whitespace are + * trimmed. + *
+ * NORMALIZE + * + * Same as TextTrim, plus addition interior whitespace is compressed + * to a single space. + *
+ * + * In most cases textual content is aligned with the surrounding tags + * (after the appropriate text mode is applied). In the case where the only + * content between the start and end tags is textual, the start tag, text, + * and end tag are all printed on the same line. If the document being + * output already has whitespace, it's wise to turn on TRIM mode so the + * pre-existing whitespace can be trimmed before adding new whitespace. + *

+ * When a element has a xml:space attribute with the value of "preserve", + * all formating is turned off and reverts back to the default until the + * element and its contents have been printed. If a nested element contains + * another xml:space with the value "default" formatting is turned back on + * for the child element and then off for the remainder of the parent + * element. + */ + public static class TextMode { + /** + * Mode for literal text preservation. + */ + public static final TextMode PRESERVE = new TextMode("PRESERVE"); + + /** + * Mode for text trimming (left and right trim). + */ + public static final TextMode TRIM = new TextMode("TRIM"); + + /** + * Mode for text normalization (left and right trim plus internal + * whitespace is normalized to a single space. + * @see org.jdom.Element#getTextNormalize + */ + public static final TextMode NORMALIZE = new TextMode("NORMALIZE"); + + /** + * Mode for text trimming of content consisting of nothing but + * whitespace but otherwise not changing output. + */ + public static final TextMode TRIM_FULL_WHITE = + new TextMode("TRIM_FULL_WHITE"); + + private final String name; + + private TextMode(String name) { + this.name = name; + } + + public String toString() { + return name; + } + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/JDOMLocator.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/output/JDOMLocator.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,118 @@ +/*-- + + $Id: JDOMLocator.java,v 1.4 2007/11/10 05:29:01 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.output; + +import org.xml.sax.*; +import org.xml.sax.helpers.*; + +/** + * An implementation of the SAX {@link Locator} interface that + * exposes the JDOM node being processed by SAXOutputter. + * + * @author Laurent Bihanic + * + * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:01 $ + */ +public class JDOMLocator extends LocatorImpl { + + private static final String CVS_ID = + "@(#) $RCSfile: JDOMLocator.java,v $ $Revision: 1.4 $ $Date: 2007/11/10 05:29:01 $ $Name: jdom_1_1_1 $"; + + /** The JDOM node being processed by SAXOutputter. */ + private Object node; + + /** + * Default no-arg constructor. + */ + JDOMLocator() { // package protected + super(); + } + + /** + * Copy contructor. + * + * @param locator Locator to copy location + * information from. + */ + JDOMLocator(Locator locator) { // package protected + super(locator); + + if (locator instanceof JDOMLocator) { + this.setNode(((JDOMLocator)locator).getNode()); + } + } + + /** + * Returns the JDOM node being processed by SAXOutputter. + * + * @return the JDOM node being processed by SAXOutputter. + */ + public Object getNode() { + return this.node; + } + + /** + * Sets the being-processed node. + * + * @param node Object node currently processed + * by SAXOutputter. + */ + void setNode(Object node) { // package protected + this.node = node; + } +} + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/NamespaceStack.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/output/NamespaceStack.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,154 @@ +/*-- + + $Id: NamespaceStack.java,v 1.14 2007/11/10 05:29:01 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ +package org.jdom.output; + +import java.util.*; + +import org.jdom.Namespace; + +/** + * A non-public utility class used by both {@link XMLOutputter} and + * {@link SAXOutputter} to manage namespaces in a JDOM Document + * during output. + * + * @version $Revision: 1.14 $, $Date: 2007/11/10 05:29:01 $ + * @author Elliotte Rusty Harolde + * @author Fred Trimble + * @author Brett McLaughlin + */ +class NamespaceStack { + + private static final String CVS_ID = + "@(#) $RCSfile: NamespaceStack.java,v $ $Revision: 1.14 $ $Date: 2007/11/10 05:29:01 $ $Name: jdom_1_1_1 $"; + + /** The prefixes available */ + private Stack prefixes; + + /** The URIs available */ + private Stack uris; + + /** + * This creates the needed storage. + */ + NamespaceStack() { + prefixes = new Stack(); + uris = new Stack(); + } + + /** + * This will add a new {@link Namespace} + * to those currently available. + * + * @param ns Namespace to add. + */ + public void push(Namespace ns) { + prefixes.push(ns.getPrefix()); + uris.push(ns.getURI()); + } + + /** + * This will remove the topmost (most recently added) + * {@link Namespace}, and return its prefix. + * + * @return String - the popped namespace prefix. + */ + public String pop() { + String prefix = (String)prefixes.pop(); + uris.pop(); + + return prefix; + } + + /** + * This returns the number of available namespaces. + * + * @return int - size of the namespace stack. + */ + public int size() { + return prefixes.size(); + } + + /** + * Given a prefix, this will return the namespace URI most + * rencently (topmost) associated with that prefix. + * + * @param prefix String namespace prefix. + * @return String - the namespace URI for that prefix. + */ + public String getURI(String prefix) { + int index = prefixes.lastIndexOf(prefix); + if (index == -1) { + return null; + } + String uri = (String)uris.elementAt(index); + return uri; + } + + /** + * This will print out the size and current stack, from the + * most recently added {@link Namespace} to + * the "oldest," all to System.out. + */ + public String toString() { + StringBuffer buf = new StringBuffer(); + String sep = System.getProperty("line.separator"); + buf.append("Stack: " + prefixes.size() + sep); + for (int i = 0; i < prefixes.size(); i++) { + buf.append(prefixes.elementAt(i) + "&" + uris.elementAt(i) + sep); + } + return buf.toString(); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/SAXOutputter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/output/SAXOutputter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,1439 @@ +/*-- + + $Id: SAXOutputter.java,v 1.40 2007/11/10 05:29:01 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.output; + +import java.io.*; +import java.lang.reflect.*; +import java.util.*; + +import org.jdom.*; +import org.xml.sax.*; +import org.xml.sax.ext.*; +import org.xml.sax.helpers.*; + +/** + * Outputs a JDOM document as a stream of SAX2 events. + *

+ * Most ContentHandler callbacks are supported. Both + * ignorableWhitespace() and skippedEntity() have not + * been implemented. The {@link JDOMLocator} class returned by + * {@link #getLocator} exposes the current node being operated + * upon. + *

+ * At this time, it is not possible to access notations and unparsed entity + * references in a DTD from JDOM. Therefore, DTDHandler callbacks + * have not been implemented yet. + *

+ * The ErrorHandler callbacks have not been implemented, since + * these are supposed to be invoked when the document is parsed and at this + * point the document exists in memory and is known to have no errors.

+ * + * @version $Revision: 1.40 $, $Date: 2007/11/10 05:29:01 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Fred Trimble + * @author Bradley S. Huffman + */ +public class SAXOutputter { + + private static final String CVS_ID = + "@(#) $RCSfile: SAXOutputter.java,v $ $Revision: 1.40 $ $Date: 2007/11/10 05:29:01 $ $Name: jdom_1_1_1 $"; + + /** Shortcut for SAX namespaces core feature */ + private static final String NAMESPACES_SAX_FEATURE = + "http://xml.org/sax/features/namespaces"; + + /** Shortcut for SAX namespace-prefixes core feature */ + private static final String NS_PREFIXES_SAX_FEATURE = + "http://xml.org/sax/features/namespace-prefixes"; + + /** Shortcut for SAX validation core feature */ + private static final String VALIDATION_SAX_FEATURE = + "http://xml.org/sax/features/validation"; + + /** Shortcut for SAX-ext. lexical handler property */ + private static final String LEXICAL_HANDLER_SAX_PROPERTY = + "http://xml.org/sax/properties/lexical-handler"; + + /** Shortcut for SAX-ext. declaration handler property */ + private static final String DECL_HANDLER_SAX_PROPERTY = + "http://xml.org/sax/properties/declaration-handler"; + + /** + * Shortcut for SAX-ext. lexical handler alternate property. + * Although this property URI is not the one defined by the SAX + * "standard", some parsers use it instead of the official one. + */ + private static final String LEXICAL_HANDLER_ALT_PROPERTY = + "http://xml.org/sax/handlers/LexicalHandler"; + + /** Shortcut for SAX-ext. declaration handler alternate property */ + private static final String DECL_HANDLER_ALT_PROPERTY = + "http://xml.org/sax/handlers/DeclHandler"; + + /** + * Array to map JDOM attribute type (as entry index) to SAX + * attribute type names. + */ + private static final String[] attrTypeToNameMap = new String[] { + "CDATA", // Attribute.UNDEFINED_ATTRIBUTE, as per SAX 2.0 spec. + "CDATA", // Attribute.CDATA_TYPE + "ID", // Attribute.ID_TYPE + "IDREF", // Attribute.IDREF_TYPE + "IDREFS", // Attribute.IDREFS_TYPE + "ENTITY", // Attribute.ENTITY_TYPE + "ENTITIES", // Attribute.ENTITIES_TYPE + "NMTOKEN", // Attribute.NMTOKEN_TYPE + "NMTOKENS", // Attribute.NMTOKENS_TYPE + "NOTATION", // Attribute.NOTATION_TYPE + "NMTOKEN", // Attribute.ENUMERATED_TYPE, as per SAX 2.0 spec. + }; + + /** registered ContentHandler */ + private ContentHandler contentHandler; + + /** registered ErrorHandler */ + private ErrorHandler errorHandler; + + /** registered DTDHandler */ + private DTDHandler dtdHandler; + + /** registered EntityResolver */ + private EntityResolver entityResolver; + + /** registered LexicalHandler */ + private LexicalHandler lexicalHandler; + + /** registered DeclHandler */ + private DeclHandler declHandler; + + /** + * Whether to report attribute namespace declarations as xmlns attributes. + * Defaults to false as per SAX specifications. + * + * @see + * SAX namespace specifications + */ + private boolean declareNamespaces = false; + + /** + * Whether to report DTD events to DeclHandlers and LexicalHandlers. + * Defaults to true. + */ + private boolean reportDtdEvents = true; + + /** + * A SAX Locator that points at the JDOM node currently being + * outputted. + */ + private JDOMLocator locator = null; + + /** + * This will create a SAXOutputter without any + * registered handler. The application is then responsible for + * registering them using the setXxxHandler() methods. + */ + public SAXOutputter() { + } + + /** + * This will create a SAXOutputter with the + * specified ContentHandler. + * + * @param contentHandler contains ContentHandler + * callback methods + */ + public SAXOutputter(ContentHandler contentHandler) { + this(contentHandler, null, null, null, null); + } + + /** + * This will create a SAXOutputter with the + * specified SAX2 handlers. At this time, only ContentHandler + * and EntityResolver are supported. + * + * @param contentHandler contains ContentHandler + * callback methods + * @param errorHandler contains ErrorHandler callback methods + * @param dtdHandler contains DTDHandler callback methods + * @param entityResolver contains EntityResolver + * callback methods + */ + public SAXOutputter(ContentHandler contentHandler, + ErrorHandler errorHandler, + DTDHandler dtdHandler, + EntityResolver entityResolver) { + this(contentHandler, errorHandler, dtdHandler, entityResolver, null); + } + + /** + * This will create a SAXOutputter with the + * specified SAX2 handlers. At this time, only ContentHandler + * and EntityResolver are supported. + * + * @param contentHandler contains ContentHandler + * callback methods + * @param errorHandler contains ErrorHandler callback methods + * @param dtdHandler contains DTDHandler callback methods + * @param entityResolver contains EntityResolver + * callback methods + * @param lexicalHandler contains LexicalHandler callbacks. + */ + public SAXOutputter(ContentHandler contentHandler, + ErrorHandler errorHandler, + DTDHandler dtdHandler, + EntityResolver entityResolver, + LexicalHandler lexicalHandler) { + this.contentHandler = contentHandler; + this.errorHandler = errorHandler; + this.dtdHandler = dtdHandler; + this.entityResolver = entityResolver; + this.lexicalHandler = lexicalHandler; + } + + /** + * This will set the ContentHandler. + * + * @param contentHandler contains ContentHandler + * callback methods. + */ + public void setContentHandler(ContentHandler contentHandler) { + this.contentHandler = contentHandler; + } + + /** + * Returns the registered ContentHandler. + * + * @return the current ContentHandler or + * null if none was registered. + */ + public ContentHandler getContentHandler() { + return this.contentHandler; + } + + /** + * This will set the ErrorHandler. + * + * @param errorHandler contains ErrorHandler callback methods. + */ + public void setErrorHandler(ErrorHandler errorHandler) { + this.errorHandler = errorHandler; + } + + /** + * Return the registered ErrorHandler. + * + * @return the current ErrorHandler or + * null if none was registered. + */ + public ErrorHandler getErrorHandler() { + return this.errorHandler; + } + + /** + * This will set the DTDHandler. + * + * @param dtdHandler contains DTDHandler callback methods. + */ + public void setDTDHandler(DTDHandler dtdHandler) { + this.dtdHandler = dtdHandler; + } + + /** + * Return the registered DTDHandler. + * + * @return the current DTDHandler or + * null if none was registered. + */ + public DTDHandler getDTDHandler() { + return this.dtdHandler; + } + + /** + * This will set the EntityResolver. + * + * @param entityResolver contains EntityResolver callback methods. + */ + public void setEntityResolver(EntityResolver entityResolver) { + this.entityResolver = entityResolver; + } + + /** + * Return the registered EntityResolver. + * + * @return the current EntityResolver or + * null if none was registered. + */ + public EntityResolver getEntityResolver() { + return this.entityResolver; + } + + /** + * This will set the LexicalHandler. + * + * @param lexicalHandler contains lexical callback methods. + */ + public void setLexicalHandler(LexicalHandler lexicalHandler) { + this.lexicalHandler = lexicalHandler; + } + + /** + * Return the registered LexicalHandler. + * + * @return the current LexicalHandler or + * null if none was registered. + */ + public LexicalHandler getLexicalHandler() { + return this.lexicalHandler; + } + + /** + * This will set the DeclHandler. + * + * @param declHandler contains declaration callback methods. + */ + public void setDeclHandler(DeclHandler declHandler) { + this.declHandler = declHandler; + } + + /** + * Return the registered DeclHandler. + * + * @return the current DeclHandler or + * null if none was registered. + */ + public DeclHandler getDeclHandler() { + return this.declHandler; + } + + /** + * Returns whether attribute namespace declarations shall be reported as + * "xmlns" attributes. + * + * @return whether attribute namespace declarations shall be reported as + * "xmlns" attributes. + */ + public boolean getReportNamespaceDeclarations() { + return declareNamespaces; + } + + /** + * This will define whether attribute namespace declarations shall be + * reported as "xmlns" attributes. This flag defaults to false + * and behaves as the "namespace-prefixes" SAX core feature. + * + * @param declareNamespaces whether attribute namespace declarations + * shall be reported as "xmlns" attributes. + */ + public void setReportNamespaceDeclarations(boolean declareNamespaces) { + this.declareNamespaces = declareNamespaces; + } + + /** + * Returns whether DTD events will be reported. + * + * @return whether DTD events will be reported + */ + public boolean getReportDTDEvents() { + return reportDtdEvents; + } + + /** + * This will define whether to report DTD events to SAX DeclHandlers + * and LexicalHandlers if these handlers are registered and the + * document to output includes a DocType declaration. + * + * @param reportDtdEvents whether to notify DTD events. + */ + public void setReportDTDEvents(boolean reportDtdEvents) { + this.reportDtdEvents = reportDtdEvents; + } + + /** + * This will set the state of a SAX feature. + *

+ * All XMLReaders are required to support setting to true and to false. + *

+ *

+ * SAXOutputter currently supports the following SAX core features: + *

+ *
http://xml.org/sax/features/namespaces
+ *
description: true indicates + * namespace URIs and unprefixed local names for element and + * attribute names will be available
+ *
access: read/write, but always + * true!
+ *
http://xml.org/sax/features/namespace-prefixes
+ *
description: true indicates + * XML 1.0 names (with prefixes) and attributes (including xmlns* + * attributes) will be available
+ *
access: read/write
+ *
http://xml.org/sax/features/validation
+ *
description: controls whether SAXOutputter + * is reporting DTD-related events; if true, the + * DocType internal subset will be parsed to fire DTD events
+ *
access: read/write, defaults to + * true
+ *
+ *

+ * + * @param name String the feature name, which is a + * fully-qualified URI. + * @param value boolean the requested state of the + * feature (true or false). + * + * @throws SAXNotRecognizedException when SAXOutputter does not + * recognize the feature name. + * @throws SAXNotSupportedException when SAXOutputter recognizes + * the feature name but cannot set the requested value. + */ + public void setFeature(String name, boolean value) + throws SAXNotRecognizedException, SAXNotSupportedException { + if (NS_PREFIXES_SAX_FEATURE.equals(name)) { + // Namespace prefix declarations. + this.setReportNamespaceDeclarations(value); + } + else { + if (NAMESPACES_SAX_FEATURE.equals(name)) { + if (value != true) { + // Namespaces feature always supported by SAXOutputter. + throw new SAXNotSupportedException(name); + } + // Else: true is OK! + } + else { + if (VALIDATION_SAX_FEATURE.equals(name)) { + // Report DTD events. + this.setReportDTDEvents(value); + } + else { + // Not a supported feature. + throw new SAXNotRecognizedException(name); + } + } + } + } + + /** + * This will look up the value of a SAX feature. + * + * @param name String the feature name, which is a + * fully-qualified URI. + * @return boolean the current state of the feature + * (true or false). + * + * @throws SAXNotRecognizedException when SAXOutputter does not + * recognize the feature name. + * @throws SAXNotSupportedException when SAXOutputter recognizes + * the feature name but determine its value at this time. + */ + public boolean getFeature(String name) + throws SAXNotRecognizedException, SAXNotSupportedException { + if (NS_PREFIXES_SAX_FEATURE.equals(name)) { + // Namespace prefix declarations. + return (this.declareNamespaces); + } + else { + if (NAMESPACES_SAX_FEATURE.equals(name)) { + // Namespaces feature always supported by SAXOutputter. + return (true); + } + else { + if (VALIDATION_SAX_FEATURE.equals(name)) { + // Report DTD events. + return (this.reportDtdEvents); + } + else { + // Not a supported feature. + throw new SAXNotRecognizedException(name); + } + } + } + } + + /** + * This will set the value of a SAX property. + * This method is also the standard mechanism for setting extended + * handlers. + *

+ * SAXOutputter currently supports the following SAX properties: + *

+ *
http://xml.org/sax/properties/lexical-handler
+ *
data type: + * org.xml.sax.ext.LexicalHandler
+ *
description: An optional extension handler for + * lexical events like comments.
+ *
access: read/write
+ *
http://xml.org/sax/properties/declaration-handler
+ *
data type: + * org.xml.sax.ext.DeclHandler
+ *
description: An optional extension handler for + * DTD-related events other than notations and unparsed entities.
+ *
access: read/write
+ *
+ *

+ * + * @param name String the property name, which is a + * fully-qualified URI. + * @param value Object the requested value for the property. + * + * @throws SAXNotRecognizedException when SAXOutputter does not recognize + * the property name. + * @throws SAXNotSupportedException when SAXOutputter recognizes the + * property name but cannot set the requested value. + */ + public void setProperty(String name, Object value) + throws SAXNotRecognizedException, SAXNotSupportedException { + if ((LEXICAL_HANDLER_SAX_PROPERTY.equals(name)) || + (LEXICAL_HANDLER_ALT_PROPERTY.equals(name))) { + this.setLexicalHandler((LexicalHandler)value); + } + else { + if ((DECL_HANDLER_SAX_PROPERTY.equals(name)) || + (DECL_HANDLER_ALT_PROPERTY.equals(name))) { + this.setDeclHandler((DeclHandler)value); + } + else { + throw new SAXNotRecognizedException(name); + } + } + } + + /** + * This will look up the value of a SAX property. + * + * @param name String the property name, which is a + * fully-qualified URI. + * @return Object the current value of the property. + * + * @throws SAXNotRecognizedException when SAXOutputter does not recognize + * the property name. + * @throws SAXNotSupportedException when SAXOutputter recognizes the + * property name but cannot determine its value at this time. + */ + public Object getProperty(String name) + throws SAXNotRecognizedException, SAXNotSupportedException { + if ((LEXICAL_HANDLER_SAX_PROPERTY.equals(name)) || + (LEXICAL_HANDLER_ALT_PROPERTY.equals(name))) { + return this.getLexicalHandler(); + } + else { + if ((DECL_HANDLER_SAX_PROPERTY.equals(name)) || + (DECL_HANDLER_ALT_PROPERTY.equals(name))) { + return this.getDeclHandler(); + } + else { + throw new SAXNotRecognizedException(name); + } + } + } + + + /** + * This will output the JDOM Document, firing off the + * SAX events that have been registered. + * + * @param document JDOM Document to output. + * + * @throws JDOMException if any error occurred. + */ + public void output(Document document) throws JDOMException { + if (document == null) { + return; + } + + // contentHandler.setDocumentLocator() + documentLocator(document); + + // contentHandler.startDocument() + startDocument(); + + // Fire DTD events + if (this.reportDtdEvents) { + dtdEvents(document); + } + + // Handle root element, as well as any root level + // processing instructions and comments + Iterator i = document.getContent().iterator(); + while (i.hasNext()) { + Object obj = i.next(); + + // update locator + locator.setNode(obj); + + if (obj instanceof Element) { + // process root element and its content + element(document.getRootElement(), new NamespaceStack()); + } + else if (obj instanceof ProcessingInstruction) { + // contentHandler.processingInstruction() + processingInstruction((ProcessingInstruction) obj); + } + else if (obj instanceof Comment) { + // lexicalHandler.comment() + comment(((Comment) obj).getText()); + } + } + + // contentHandler.endDocument() + endDocument(); + } + + /** + * This will output a list of JDOM nodes as a document, firing + * off the SAX events that have been registered. + *

+ * Warning: This method may output ill-formed XML + * documents if the list contains top-level objects that are not + * legal at the document level (e.g. Text or CDATA nodes, multiple + * Element nodes, etc.). Thus, it should only be used to output + * document portions towards ContentHandlers capable of accepting + * such ill-formed documents (such as XSLT processors).

+ * + * @param nodes List of JDOM nodes to output. + * + * @throws JDOMException if any error occurred. + * + * @see #output(org.jdom.Document) + */ + public void output(List nodes) throws JDOMException { + if ((nodes == null) || (nodes.size() == 0)) { + return; + } + + // contentHandler.setDocumentLocator() + documentLocator(null); + + // contentHandler.startDocument() + startDocument(); + + // Process node list. + elementContent(nodes, new NamespaceStack()); + + // contentHandler.endDocument() + endDocument(); + } + + /** + * This will output a single JDOM element as a document, firing + * off the SAX events that have been registered. + * + * @param node the Element node to output. + * + * @throws JDOMException if any error occurred. + */ + public void output(Element node) throws JDOMException { + if (node == null) { + return; + } + + // contentHandler.setDocumentLocator() + documentLocator(null); + + // contentHandler.startDocument() + startDocument(); + + // Output node. + elementContent(node, new NamespaceStack()); + + // contentHandler.endDocument() + endDocument(); + } + + /** + * This will output a list of JDOM nodes as a fragment of an XML + * document, firing off the SAX events that have been registered. + *

+ * Warning: This method does not call the + * {@link ContentHandler#setDocumentLocator}, + * {@link ContentHandler#startDocument} and + * {@link ContentHandler#endDocument} callbacks on the + * {@link #setContentHandler ContentHandler}. The user shall + * invoke these methods directly prior/after outputting the + * document fragments.

+ * + * @param nodes List of JDOM nodes to output. + * + * @throws JDOMException if any error occurred. + * + * @see #outputFragment(org.jdom.Content) + */ + public void outputFragment(List nodes) throws JDOMException { + if ((nodes == null) || (nodes.size() == 0)) { + return; + } + + // Output node list as a document fragment. + elementContent(nodes, new NamespaceStack()); + } + + /** + * This will output a single JDOM nodes as a fragment of an XML + * document, firing off the SAX events that have been registered. + *

+ * Warning: This method does not call the + * {@link ContentHandler#setDocumentLocator}, + * {@link ContentHandler#startDocument} and + * {@link ContentHandler#endDocument} callbacks on the + * {@link #setContentHandler ContentHandler}. The user shall + * invoke these methods directly prior/after outputting the + * document fragments.

+ * + * @param node the Content node to output. + * + * @throws JDOMException if any error occurred. + * + * @see #outputFragment(java.util.List) + */ + public void outputFragment(Content node) throws JDOMException { + if (node == null) { + return; + } + + // Output single node as a document fragment. + elementContent(node, new NamespaceStack()); + } + + /** + * This parses a DTD declaration to fire the related events towards + * the registered handlers. + * + * @param document JDOM Document the DocType is to + * process. + */ + private void dtdEvents(Document document) throws JDOMException { + DocType docType = document.getDocType(); + + // Fire DTD-related events only if handlers have been registered. + if ((docType != null) && + ((dtdHandler != null) || (declHandler != null))) { + + // Build a dummy XML document that only references the DTD... + String dtdDoc = new XMLOutputter().outputString(docType); + + try { + // And parse it to fire DTD events. + createDTDParser().parse(new InputSource( + new StringReader(dtdDoc))); + + // We should never reach this point as the document is + // ill-formed; it does not have any root element. + } + catch (SAXParseException e) { + // Expected exception: There's no root element in document. + } + catch (SAXException e) { + throw new JDOMException("DTD parsing error", e); + } + catch (IOException e) { + throw new JDOMException("DTD parsing error", e); + } + } + } + + /** + *

+ * This method tells you the line of the XML file being parsed. + * For an in-memory document, it's meaningless. The location + * is only valid for the current parsing lifecycle, but + * the document has already been parsed. Therefore, it returns + * -1 for both line and column numbers. + *

+ * + * @param document JDOM Document. + */ + private void documentLocator(Document document) { + locator = new JDOMLocator(); + String publicID = null; + String systemID = null; + + if (document != null) { + DocType docType = document.getDocType(); + if (docType != null) { + publicID = docType.getPublicID(); + systemID = docType.getSystemID(); + } + } + locator.setPublicId(publicID); + locator.setSystemId(systemID); + locator.setLineNumber(-1); + locator.setColumnNumber(-1); + + contentHandler.setDocumentLocator(locator); + } + + /** + *

+ * This method is always the second method of all callbacks in + * all handlers to be invoked (setDocumentLocator is always first). + *

+ */ + private void startDocument() throws JDOMException { + try { + contentHandler.startDocument(); + } + catch (SAXException se) { + throw new JDOMException("Exception in startDocument", se); + } + } + + /** + *

+ * Always the last method of all callbacks in all handlers + * to be invoked. + *

+ */ + private void endDocument() throws JDOMException { + try { + contentHandler.endDocument(); + + // reset locator + locator = null; + } + catch (SAXException se) { + throw new JDOMException("Exception in endDocument", se); + } + } + + /** + *

+ * This will invoke the ContentHandler.processingInstruction + * callback when a processing instruction is encountered. + *

+ * + * @param pi ProcessingInstruction containing target and data. + */ + private void processingInstruction(ProcessingInstruction pi) + throws JDOMException { + if (pi != null) { + String target = pi.getTarget(); + String data = pi.getData(); + try { + contentHandler.processingInstruction(target, data); + } + catch (SAXException se) { + throw new JDOMException( + "Exception in processingInstruction", se); + } + } + } + + /** + *

+ * This will recursively invoke all of the callbacks for a particular + * element. + *

+ * + * @param element Element used in callbacks. + * @param namespaces List stack of Namespaces in scope. + */ + private void element(Element element, NamespaceStack namespaces) + throws JDOMException { + // used to check endPrefixMapping + int previouslyDeclaredNamespaces = namespaces.size(); + + // contentHandler.startPrefixMapping() + Attributes nsAtts = startPrefixMapping(element, namespaces); + + // contentHandler.startElement() + startElement(element, nsAtts); + + // handle content in the element + elementContent(element.getContent(), namespaces); + + // update locator + if (locator != null) { + locator.setNode(element); + } + + // contentHandler.endElement() + endElement(element); + + // contentHandler.endPrefixMapping() + endPrefixMapping(namespaces, previouslyDeclaredNamespaces); + } + + /** + *

+ * This will invoke the ContentHandler.startPrefixMapping + * callback + * when a new namespace is encountered in the Document. + *

+ * + * @param element Element used in callbacks. + * @param namespaces List stack of Namespaces in scope. + * + * @return Attributes declaring the namespaces local to + * element or null. + */ + private Attributes startPrefixMapping(Element element, + NamespaceStack namespaces) + throws JDOMException { + AttributesImpl nsAtts = null; // The namespaces as xmlns attributes + + Namespace ns = element.getNamespace(); + if (ns != Namespace.XML_NAMESPACE) { + String prefix = ns.getPrefix(); + String uri = namespaces.getURI(prefix); + if (!ns.getURI().equals(uri)) { + namespaces.push(ns); + nsAtts = this.addNsAttribute(nsAtts, ns); + try { + contentHandler.startPrefixMapping(prefix, ns.getURI()); + } + catch (SAXException se) { + throw new JDOMException( + "Exception in startPrefixMapping", se); + } + } + } + + // Fire additional namespace declarations + List additionalNamespaces = element.getAdditionalNamespaces(); + if (additionalNamespaces != null) { + Iterator itr = additionalNamespaces.iterator(); + while (itr.hasNext()) { + ns = (Namespace)itr.next(); + String prefix = ns.getPrefix(); + String uri = namespaces.getURI(prefix); + if (!ns.getURI().equals(uri)) { + namespaces.push(ns); + nsAtts = this.addNsAttribute(nsAtts, ns); + try { + contentHandler.startPrefixMapping(prefix, ns.getURI()); + } + catch (SAXException se) { + throw new JDOMException( + "Exception in startPrefixMapping", se); + } + } + } + } + return nsAtts; + } + + /** + *

+ * This will invoke the endPrefixMapping callback in the + * ContentHandler when a namespace is goes out of scope + * in the Document. + *

+ * + * @param namespaces List stack of Namespaces in scope. + * @param previouslyDeclaredNamespaces number of previously declared + * namespaces + */ + private void endPrefixMapping(NamespaceStack namespaces, + int previouslyDeclaredNamespaces) + throws JDOMException { + while (namespaces.size() > previouslyDeclaredNamespaces) { + String prefix = namespaces.pop(); + try { + contentHandler.endPrefixMapping(prefix); + } + catch (SAXException se) { + throw new JDOMException("Exception in endPrefixMapping", se); + } + } + } + + /** + *

+ * This will invoke the startElement callback + * in the ContentHandler. + *

+ * + * @param element Element used in callbacks. + * @param nsAtts List of namespaces to declare with + * the element or null. + */ + private void startElement(Element element, Attributes nsAtts) + throws JDOMException { + String namespaceURI = element.getNamespaceURI(); + String localName = element.getName(); + String rawName = element.getQualifiedName(); + + // Allocate attribute list. + AttributesImpl atts = (nsAtts != null)? + new AttributesImpl(nsAtts): new AttributesImpl(); + + List attributes = element.getAttributes(); + Iterator i = attributes.iterator(); + while (i.hasNext()) { + Attribute a = (Attribute) i.next(); + atts.addAttribute(a.getNamespaceURI(), + a.getName(), + a.getQualifiedName(), + getAttributeTypeName(a.getAttributeType()), + a.getValue()); + } + + try { + contentHandler.startElement(namespaceURI, localName, rawName, atts); + } + catch (SAXException se) { + throw new JDOMException("Exception in startElement", se); + } + } + + /** + *

+ * This will invoke the endElement callback + * in the ContentHandler. + *

+ * + * @param element Element used in callbacks. + */ + private void endElement(Element element) throws JDOMException { + String namespaceURI = element.getNamespaceURI(); + String localName = element.getName(); + String rawName = element.getQualifiedName(); + + try { + contentHandler.endElement(namespaceURI, localName, rawName); + } + catch (SAXException se) { + throw new JDOMException("Exception in endElement", se); + } + } + + /** + *

+ * This will invoke the callbacks for the content of an element. + *

+ * + * @param content element content as a List of nodes. + * @param namespaces List stack of Namespaces in scope. + */ + private void elementContent(List content, NamespaceStack namespaces) + throws JDOMException { + for (Iterator i=content.iterator(); i.hasNext(); ) { + Object obj = i.next(); + + if (obj instanceof Content) { + this.elementContent((Content)obj, namespaces); + } + else { + // Not a valid element child. This could happen with + // application-provided lists which may contain non + // JDOM objects. + handleError(new JDOMException( + "Invalid element content: " + obj)); + } + } + } + + /** + *

+ * This will invoke the callbacks for the content of an element. + *

+ * + * @param node a Content node. + * @param namespaces List stack of Namespaces in scope. + */ + private void elementContent(Content node, NamespaceStack namespaces) + throws JDOMException { + // update locator + if (locator != null) { + locator.setNode(node); + } + + if (node instanceof Element) { + element((Element) node, namespaces); + } + else if (node instanceof CDATA) { + cdata(((CDATA) node).getText()); + } + else if (node instanceof Text) { + // contentHandler.characters() + characters(((Text) node).getText()); + } + else if (node instanceof ProcessingInstruction) { + // contentHandler.processingInstruction() + processingInstruction((ProcessingInstruction) node); + } + else if (node instanceof Comment) { + // lexicalHandler.comment() + comment(((Comment) node).getText()); + } + else if (node instanceof EntityRef) { + // contentHandler.skippedEntity() + entityRef((EntityRef) node); + } + else { + // Not a valid element child. This could happen with + // application-provided lists which may contain non + // JDOM objects. + handleError(new JDOMException("Invalid element content: " + node)); + } + } + + /** + *

+ * This will be called for each chunk of CDATA section encountered. + *

+ * + * @param cdataText all text in the CDATA section, including whitespace. + */ + private void cdata(String cdataText) throws JDOMException { + try { + if (lexicalHandler != null) { + lexicalHandler.startCDATA(); + characters(cdataText); + lexicalHandler.endCDATA(); + } + else { + characters(cdataText); + } + } + catch (SAXException se) { + throw new JDOMException("Exception in CDATA", se); + } + } + + /** + *

+ * This will be called for each chunk of character data encountered. + *

+ * + * @param elementText all text in an element, including whitespace. + */ + private void characters(String elementText) throws JDOMException { + char[] c = elementText.toCharArray(); + try { + contentHandler.characters(c, 0, c.length); + } + catch (SAXException se) { + throw new JDOMException("Exception in characters", se); + } + } + + /** + *

+ * This will be called for each chunk of comment data encontered. + *

+ * + * @param commentText all text in a comment, including whitespace. + */ + private void comment(String commentText) throws JDOMException { + if (lexicalHandler != null) { + char[] c = commentText.toCharArray(); + try { + lexicalHandler.comment(c, 0, c.length); + } catch (SAXException se) { + throw new JDOMException("Exception in comment", se); + } + } + } + + /** + *

+ * This will invoke the ContentHandler.skippedEntity + * callback when an entity reference is encountered. + *

+ * + * @param entity EntityRef. + */ + private void entityRef(EntityRef entity) throws JDOMException { + if (entity != null) { + try { + // No need to worry about appending a '%' character as + // we do not support parameter entities + contentHandler.skippedEntity(entity.getName()); + } + catch (SAXException se) { + throw new JDOMException("Exception in entityRef", se); + } + } + } + + + /** + *

+ * Appends a namespace declaration in the form of a xmlns attribute to + * an attribute list, crerating this latter if needed. + *

+ * + * @param atts AttributeImpl where to add the attribute. + * @param ns Namespace the namespace to declare. + * + * @return AttributeImpl the updated attribute list. + */ + private AttributesImpl addNsAttribute(AttributesImpl atts, Namespace ns) { + if (this.declareNamespaces) { + if (atts == null) { + atts = new AttributesImpl(); + } + + String prefix = ns.getPrefix(); + if (prefix.equals("")) { + atts.addAttribute("", // namespace + "", // local name + "xmlns", // qualified name + "CDATA", // type + ns.getURI()); // value + } + else { + atts.addAttribute("", // namespace + "", // local name + "xmlns:" + ns.getPrefix(), // qualified name + "CDATA", // type + ns.getURI()); // value + } + } + return atts; + } + + /** + *

+ * Returns the SAX 2.0 attribute type string from the type of + * a JDOM Attribute. + *

+ * + * @param type int the type of the JDOM attribute. + * + * @return String the SAX 2.0 attribute type string. + * + * @see org.jdom.Attribute#getAttributeType + * @see org.xml.sax.Attributes#getType + */ + private static String getAttributeTypeName(int type) { + if ((type < 0) || (type >= attrTypeToNameMap.length)) { + type = Attribute.UNDECLARED_TYPE; + } + return attrTypeToNameMap[type]; + } + + /** + *

+ * Notifies the registered {@link ErrorHandler SAX error handler} + * (if any) of an input processing error. The error handler can + * choose to absorb the error and let the processing continue. + *

+ * + * @param exception JDOMException containing the + * error information; will be wrapped in a + * {@link SAXParseException} when reported to + * the SAX error handler. + * + * @throws JDOMException if no error handler has been registered + * or if the error handler fired a + * {@link SAXException}. + */ + private void handleError(JDOMException exception) throws JDOMException { + if (errorHandler != null) { + try { + errorHandler.error(new SAXParseException( + exception.getMessage(), null, exception)); + } + catch (SAXException se) { + if (se.getException() instanceof JDOMException) { + throw (JDOMException)(se.getException()); + } + else { + throw new JDOMException(se.getMessage(), se); + } + } + } + else { + throw exception; + } + } + + /** + *

+ * Creates a SAX XMLReader. + *

+ * + * @return XMLReader a SAX2 parser. + * + * @throws Exception if no parser can be created. + */ + protected XMLReader createParser() throws Exception { + XMLReader parser = null; + + // Try using JAXP... + // Note we need JAXP 1.1, and if JAXP 1.0 is all that's + // available then the getXMLReader call fails and we skip + // to the hard coded default parser + try { + Class factoryClass = + Class.forName("javax.xml.parsers.SAXParserFactory"); + + // factory = SAXParserFactory.newInstance(); + Method newParserInstance = + factoryClass.getMethod("newInstance", null); + Object factory = newParserInstance.invoke(null, null); + + // jaxpParser = factory.newSAXParser(); + Method newSAXParser = factoryClass.getMethod("newSAXParser", null); + Object jaxpParser = newSAXParser.invoke(factory, null); + + // parser = jaxpParser.getXMLReader(); + Class parserClass = jaxpParser.getClass(); + Method getXMLReader = + parserClass.getMethod("getXMLReader", null); + parser = (XMLReader)getXMLReader.invoke(jaxpParser, null); + } catch (ClassNotFoundException e) { + //e.printStackTrace(); + } catch (InvocationTargetException e) { + //e.printStackTrace(); + } catch (NoSuchMethodException e) { + //e.printStackTrace(); + } catch (IllegalAccessException e) { + //e.printStackTrace(); + } + + // Check to see if we got a parser yet, if not, try to use a + // hard coded default + if (parser == null) { + parser = XMLReaderFactory.createXMLReader( + "org.apache.xerces.parsers.SAXParser"); + } + return parser; + } + + /** + *

+ * This will create a SAX XMLReader capable of parsing a DTD and + * configure it so that the DTD parsing events are routed to the + * handlers registered onto this SAXOutputter. + *

+ * + * @return XMLReader a SAX2 parser. + * + * @throws JDOMException if no parser can be created. + */ + private XMLReader createDTDParser() throws JDOMException { + XMLReader parser = null; + + // Get a parser instance + try + { + parser = createParser(); + } + catch (Exception ex1) { + throw new JDOMException("Error in SAX parser allocation", ex1); + } + + // Register handlers + if (this.getDTDHandler() != null) { + parser.setDTDHandler(this.getDTDHandler()); + } + if (this.getEntityResolver() != null) { + parser.setEntityResolver(this.getEntityResolver()); + } + if (this.getLexicalHandler() != null) { + try { + parser.setProperty(LEXICAL_HANDLER_SAX_PROPERTY, + this.getLexicalHandler()); + } + catch (SAXException ex1) { + try { + parser.setProperty(LEXICAL_HANDLER_ALT_PROPERTY, + this.getLexicalHandler()); + } catch (SAXException ex2) { + // Forget it! + } + } + } + if (this.getDeclHandler() != null) { + try { + parser.setProperty(DECL_HANDLER_SAX_PROPERTY, + this.getDeclHandler()); + } + catch (SAXException ex1) { + try { + parser.setProperty(DECL_HANDLER_ALT_PROPERTY, + this.getDeclHandler()); + } catch (SAXException ex2) { + // Forget it! + } + } + } + + // Absorb errors as much as possible, per Laurent + parser.setErrorHandler(new DefaultHandler()); + + return parser; + } + + /** + * Returns a JDOMLocator object referencing the node currently + * being processed by this outputter. The returned object is a + * snapshot of the location information and can thus safely be + * memorized for later use. + *

+ * This method allows direct access to the location information + * maintained by SAXOutputter without requiring to implement + * XMLFilter. (In SAX, locators are only available + * though the ContentHandler interface).

+ *

+ * Note that location information is only available while + * SAXOutputter is outputting nodes. Hence this method should + * only be used by objects taking part in the output processing + * such as ErrorHandlers. + * + * @return a JDOMLocator object referencing the node currently + * being processed or null if no output + * operation is being performed. + */ + public JDOMLocator getLocator() { + return (locator != null)? new JDOMLocator(locator): null; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/XMLOutputter.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/output/XMLOutputter.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,1640 @@ +/*-- + + $Id: XMLOutputter.java,v 1.117 2009/07/23 05:54:23 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.output; + +import java.io.*; +import java.util.*; + +import javax.xml.transform.Result; + +import org.jdom.*; + +/** + * Outputs a JDOM document as a stream of bytes. The outputter can manage many + * styles of document formatting, from untouched to pretty printed. The default + * is to output the document content exactly as created, but this can be changed + * by setting a new Format object. For pretty-print output, use + * {@link Format#getPrettyFormat()}. For whitespace-normalized + * output, use {@link Format#getCompactFormat()}. + *

+ * There are {@link #output output(...)} methods to print any of + * the standard JDOM classes, including Document and Element, to either a Writer + * or an OutputStream. Warning: When outputting to a Writer, make sure + * the writer's encoding matches the encoding setting in the Format object. This + * ensures the encoding in which the content is written (controlled by the + * Writer configuration) matches the encoding placed in the document's XML + * declaration (controlled by the XMLOutputter). Because a Writer cannot be + * queried for its encoding, the information must be passed to the Format + * manually in its constructor or via the + * {@link Format#setEncoding} method. The default encoding is + * UTF-8. + *

+ * The methods {@link #outputString outputString(...)} are for + * convenience only; for top performance you should call one of the {@link + * #output output(...)} methods and pass in your own Writer or + * OutputStream if possible. + *

+ * XML declarations are always printed on their own line followed by a line + * seperator (this doesn't change the semantics of the document). To omit + * printing of the declaration use + * {@link Format#setOmitDeclaration}. To omit printing of the + * encoding in the declaration use {@link Format#setOmitEncoding}. + * Unfortunatly there is currently no way to know the original encoding of the + * document. + *

+ * Empty elements are by default printed as <empty/>, but this can be + * configured with {@link Format#setExpandEmptyElements} to cause + * them to be expanded to <empty></empty>. + * + * @version $Revision: 1.117 $, $Date: 2009/07/23 05:54:23 $ + * @author Brett McLaughlin + * @author Jason Hunter + * @author Jason Reid + * @author Wolfgang Werner + * @author Elliotte Rusty Harold + * @author David & Will (from Post Tool Design) + * @author Dan Schaffer + * @author Alex Chaffee + * @author Bradley S. Huffman + */ + +public class XMLOutputter implements Cloneable { + + private static final String CVS_ID = + "@(#) $RCSfile: XMLOutputter.java,v $ $Revision: 1.117 $ $Date: 2009/07/23 05:54:23 $ $Name: jdom_1_1_1 $"; + + // For normal output + private Format userFormat = Format.getRawFormat(); + + // For xml:space="preserve" + protected static final Format preserveFormat = Format.getRawFormat(); + + // What's currently in use + protected Format currentFormat = userFormat; + + /** Whether output escaping is enabled for the being processed + * Element - default is true */ + private boolean escapeOutput = true; + + // * * * * * * * * * * Constructors * * * * * * * * * * + // * * * * * * * * * * Constructors * * * * * * * * * * + + /** + * This will create an XMLOutputter with the default + * {@link Format} matching {@link Format#getRawFormat}. + */ + public XMLOutputter() { + } + + /** + * This will create an XMLOutputter with the specified + * format characteristics. Note the format object is cloned internally + * before use. + */ + public XMLOutputter(Format format) { + userFormat = (Format) format.clone(); + currentFormat = userFormat; + } + + /** + * This will create an XMLOutputter with all the + * options as set in the given XMLOutputter. Note + * that XMLOutputter two = (XMLOutputter)one.clone(); + * would work equally well. + * + * @param that the XMLOutputter to clone + */ + public XMLOutputter(XMLOutputter that) { + this.userFormat = (Format) that.userFormat.clone(); + currentFormat = userFormat; + } + + // * * * * * * * * * * Set parameters methods * * * * * * * * * * + // * * * * * * * * * * Set parameters methods * * * * * * * * * * + + /** + * Sets the new format logic for the outputter. Note the Format + * object is cloned internally before use. + * + * @param newFormat the format to use for output + */ + public void setFormat(Format newFormat) { + this.userFormat = (Format) newFormat.clone(); + this.currentFormat = userFormat; + } + + /** + * Returns the current format in use by the outputter. Note the + * Format object returned is a clone of the one used internally. + */ + public Format getFormat() { + return (Format) userFormat.clone(); + } + + // * * * * * * * * * * Output to a OutputStream * * * * * * * * * * + // * * * * * * * * * * Output to a OutputStream * * * * * * * * * * + + /** + * This will print the Document to the given output stream. + * The characters are printed using the encoding specified in the + * constructor, or a default of UTF-8. + * + * @param doc Document to format. + * @param out OutputStream to use. + * @throws IOException - if there's any problem writing. + */ + public void output(Document doc, OutputStream out) + throws IOException { + Writer writer = makeWriter(out); + output(doc, writer); // output() flushes + } + + /** + * Print out the {@link DocType}. + * + * @param doctype DocType to output. + * @param out OutputStream to use. + */ + public void output(DocType doctype, OutputStream out) throws IOException { + Writer writer = makeWriter(out); + output(doctype, writer); // output() flushes + } + + /** + * Print out an {@link Element}, including + * its {@link Attribute}s, and all + * contained (child) elements, etc. + * + * @param element Element to output. + * @param out Writer to use. + */ + public void output(Element element, OutputStream out) throws IOException { + Writer writer = makeWriter(out); + output(element, writer); // output() flushes + } + + /** + * This will handle printing out an {@link + * Element}'s content only, not including its tag, and + * attributes. This can be useful for printing the content of an + * element that contains HTML, like "<description>JDOM is + * <b>fun>!</description>". + * + * @param element Element to output. + * @param out OutputStream to use. + */ + public void outputElementContent(Element element, OutputStream out) + throws IOException { + Writer writer = makeWriter(out); + outputElementContent(element, writer); // output() flushes + } + + /** + * This will handle printing out a list of nodes. + * This can be useful for printing the content of an element that + * contains HTML, like "<description>JDOM is + * <b>fun>!</description>". + * + * @param list List of nodes. + * @param out OutputStream to use. + */ + public void output(List list, OutputStream out) + throws IOException { + Writer writer = makeWriter(out); + output(list, writer); // output() flushes + } + + /** + * Print out a {@link CDATA} node. + * + * @param cdata CDATA to output. + * @param out OutputStream to use. + */ + public void output(CDATA cdata, OutputStream out) throws IOException { + Writer writer = makeWriter(out); + output(cdata, writer); // output() flushes + } + + /** + * Print out a {@link Text} node. Perfoms + * the necessary entity escaping and whitespace stripping. + * + * @param text Text to output. + * @param out OutputStream to use. + */ + public void output(Text text, OutputStream out) throws IOException { + Writer writer = makeWriter(out); + output(text, writer); // output() flushes + } + + /** + * Print out a {@link Comment}. + * + * @param comment Comment to output. + * @param out OutputStream to use. + */ + public void output(Comment comment, OutputStream out) throws IOException { + Writer writer = makeWriter(out); + output(comment, writer); // output() flushes + } + + /** + * Print out a {@link ProcessingInstruction}. + * + * @param pi ProcessingInstruction to output. + * @param out OutputStream to use. + */ + public void output(ProcessingInstruction pi, OutputStream out) + throws IOException { + Writer writer = makeWriter(out); + output(pi, writer); // output() flushes + } + + /** + * Print out a {@link EntityRef}. + * + * @param entity EntityRef to output. + * @param out OutputStream to use. + */ + public void output(EntityRef entity, OutputStream out) throws IOException { + Writer writer = makeWriter(out); + output(entity, writer); // output() flushes + } + + /** + * Get an OutputStreamWriter, using prefered encoding + * (see {@link Format#setEncoding}). + */ + private Writer makeWriter(OutputStream out) + throws java.io.UnsupportedEncodingException { + return makeWriter(out, userFormat.encoding); + } + + /** + * Get an OutputStreamWriter, use specified encoding. + */ + private static Writer makeWriter(OutputStream out, String enc) + throws java.io.UnsupportedEncodingException { + // "UTF-8" is not recognized before JDK 1.1.6, so we'll translate + // into "UTF8" which works with all JDKs. + if ("UTF-8".equals(enc)) { + enc = "UTF8"; + } + + Writer writer = new BufferedWriter( + (new OutputStreamWriter( + new BufferedOutputStream(out), enc) + )); + return writer; + } + + // * * * * * * * * * * Output to a Writer * * * * * * * * * * + // * * * * * * * * * * Output to a Writer * * * * * * * * * * + + /** + * This will print the Document to the given Writer. + * + *

+ * Warning: using your own Writer may cause the outputter's + * preferred character encoding to be ignored. If you use + * encodings other than UTF-8, we recommend using the method that + * takes an OutputStream instead. + *

+ * + * @param doc Document to format. + * @param out Writer to use. + * @throws IOException - if there's any problem writing. + */ + public void output(Document doc, Writer out) throws IOException { + + printDeclaration(out, doc, userFormat.encoding); + + // Print out root element, as well as any root level + // comments and processing instructions, + // starting with no indentation + List content = doc.getContent(); + int size = content.size(); + for (int i = 0; i < size; i++) { + Object obj = content.get(i); + + if (obj instanceof Element) { + printElement(out, doc.getRootElement(), 0, + createNamespaceStack()); + } + else if (obj instanceof Comment) { + printComment(out, (Comment) obj); + } + else if (obj instanceof ProcessingInstruction) { + printProcessingInstruction(out, (ProcessingInstruction) obj); + } + else if (obj instanceof DocType) { + printDocType(out, doc.getDocType()); + // Always print line separator after declaration, helps the + // output look better and is semantically inconsequential + out.write(currentFormat.lineSeparator); + } + else { + // XXX if we get here then we have a illegal content, for + // now we'll just ignore it + } + + newline(out); + indent(out, 0); + } + + // Output final line separator + // We output this no matter what the newline flags say + out.write(currentFormat.lineSeparator); + + out.flush(); + } + + /** + * Print out the {@link DocType}. + * + * @param doctype DocType to output. + * @param out Writer to use. + */ + public void output(DocType doctype, Writer out) throws IOException { + printDocType(out, doctype); + out.flush(); + } + + /** + * Print out an {@link Element}, including + * its {@link Attribute}s, and all + * contained (child) elements, etc. + * + * @param element Element to output. + * @param out Writer to use. + */ + public void output(Element element, Writer out) throws IOException { + // If this is the root element we could pre-initialize the + // namespace stack with the namespaces + printElement(out, element, 0, createNamespaceStack()); + out.flush(); + } + + /** + * This will handle printing out an {@link + * Element}'s content only, not including its tag, and + * attributes. This can be useful for printing the content of an + * element that contains HTML, like "<description>JDOM is + * <b>fun>!</description>". + * + * @param element Element to output. + * @param out Writer to use. + */ + public void outputElementContent(Element element, Writer out) + throws IOException { + List content = element.getContent(); + printContentRange(out, content, 0, content.size(), + 0, createNamespaceStack()); + out.flush(); + } + + /** + * This will handle printing out a list of nodes. + * This can be useful for printing the content of an element that + * contains HTML, like "<description>JDOM is + * <b>fun>!</description>". + * + * @param list List of nodes. + * @param out Writer to use. + */ + public void output(List list, Writer out) + throws IOException { + printContentRange(out, list, 0, list.size(), + 0, createNamespaceStack()); + out.flush(); + } + + /** + * Print out a {@link CDATA} node. + * + * @param cdata CDATA to output. + * @param out Writer to use. + */ + public void output(CDATA cdata, Writer out) throws IOException { + printCDATA(out, cdata); + out.flush(); + } + + /** + * Print out a {@link Text} node. Perfoms + * the necessary entity escaping and whitespace stripping. + * + * @param text Text to output. + * @param out Writer to use. + */ + public void output(Text text, Writer out) throws IOException { + printText(out, text); + out.flush(); + } + + /** + * Print out a {@link Comment}. + * + * @param comment Comment to output. + * @param out Writer to use. + */ + public void output(Comment comment, Writer out) throws IOException { + printComment(out, comment); + out.flush(); + } + + /** + * Print out a {@link ProcessingInstruction}. + * + * @param pi ProcessingInstruction to output. + * @param out Writer to use. + */ + public void output(ProcessingInstruction pi, Writer out) + throws IOException { + boolean currentEscapingPolicy = currentFormat.ignoreTrAXEscapingPIs; + + // Output PI verbatim, disregarding TrAX escaping PIs. + currentFormat.setIgnoreTrAXEscapingPIs(true); + printProcessingInstruction(out, pi); + currentFormat.setIgnoreTrAXEscapingPIs(currentEscapingPolicy); + + out.flush(); + } + + /** + * Print out a {@link EntityRef}. + * + * @param entity EntityRef to output. + * @param out Writer to use. + */ + public void output(EntityRef entity, Writer out) throws IOException { + printEntityRef(out, entity); + out.flush(); + } + + // * * * * * * * * * * Output to a String * * * * * * * * * * + // * * * * * * * * * * Output to a String * * * * * * * * * * + + /** + * Return a string representing a document. Uses an internal + * StringWriter. Warning: a String is Unicode, which may not match + * the outputter's specified encoding. + * + * @param doc Document to format. + */ + public String outputString(Document doc) { + StringWriter out = new StringWriter(); + try { + output(doc, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + /** + * Return a string representing a DocType. Warning: a String is + * Unicode, which may not match the outputter's specified + * encoding. + * + * @param doctype DocType to format. + */ + public String outputString(DocType doctype) { + StringWriter out = new StringWriter(); + try { + output(doctype, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + /** + * Return a string representing an element. Warning: a String is + * Unicode, which may not match the outputter's specified + * encoding. + * + * @param element Element to format. + */ + public String outputString(Element element) { + StringWriter out = new StringWriter(); + try { + output(element, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + /** + * Return a string representing a list of nodes. The list is + * assumed to contain legal JDOM nodes. + * + * @param list List to format. + */ + public String outputString(List list) { + StringWriter out = new StringWriter(); + try { + output(list, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + /** + * Return a string representing a CDATA node. Warning: a String is + * Unicode, which may not match the outputter's specified + * encoding. + * + * @param cdata CDATA to format. + */ + public String outputString(CDATA cdata) { + StringWriter out = new StringWriter(); + try { + output(cdata, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + /** + * Return a string representing a Text node. Warning: a String is + * Unicode, which may not match the outputter's specified + * encoding. + * + * @param text Text to format. + */ + public String outputString(Text text) { + StringWriter out = new StringWriter(); + try { + output(text, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + + /** + * Return a string representing a comment. Warning: a String is + * Unicode, which may not match the outputter's specified + * encoding. + * + * @param comment Comment to format. + */ + public String outputString(Comment comment) { + StringWriter out = new StringWriter(); + try { + output(comment, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + /** + * Return a string representing a PI. Warning: a String is + * Unicode, which may not match the outputter's specified + * encoding. + * + * @param pi ProcessingInstruction to format. + */ + public String outputString(ProcessingInstruction pi) { + StringWriter out = new StringWriter(); + try { + output(pi, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + /** + * Return a string representing an entity. Warning: a String is + * Unicode, which may not match the outputter's specified + * encoding. + * + * @param entity EntityRef to format. + */ + public String outputString(EntityRef entity) { + StringWriter out = new StringWriter(); + try { + output(entity, out); // output() flushes + } catch (IOException e) { } + return out.toString(); + } + + // * * * * * * * * * * Internal printing methods * * * * * * * * * * + // * * * * * * * * * * Internal printing methods * * * * * * * * * * + + /** + * This will handle printing of the declaration. + * Assumes XML version 1.0 since we don't directly know. + * + * @param doc Document whose declaration to write. + * @param out Writer to use. + * @param encoding The encoding to add to the declaration + */ + protected void printDeclaration(Writer out, Document doc, + String encoding) throws IOException { + + // Only print the declaration if it's not being omitted + if (!userFormat.omitDeclaration) { + // Assume 1.0 version + out.write(""); + + // Print new line after decl always, even if no other new lines + // Helps the output look better and is semantically + // inconsequential + out.write(currentFormat.lineSeparator); + } + } + + /** + * This handle printing the DOCTYPE declaration if one exists. + * + * @param docType Document whose declaration to write. + * @param out Writer to use. + */ + protected void printDocType(Writer out, DocType docType) + throws IOException { + + String publicID = docType.getPublicID(); + String systemID = docType.getSystemID(); + String internalSubset = docType.getInternalSubset(); + boolean hasPublic = false; + + out.write(""); + } + + /** + * This will handle printing of comments. + * + * @param comment Comment to write. + * @param out Writer to use. + */ + protected void printComment(Writer out, Comment comment) + throws IOException { + out.write(""); + } + + /** + * This will handle printing of processing instructions. + * + * @param pi ProcessingInstruction to write. + * @param out Writer to use. + */ + protected void printProcessingInstruction(Writer out, ProcessingInstruction pi + ) throws IOException { + String target = pi.getTarget(); + boolean piProcessed = false; + + if (currentFormat.ignoreTrAXEscapingPIs == false) { + if (target.equals(Result.PI_DISABLE_OUTPUT_ESCAPING)) { + escapeOutput = false; + piProcessed = true; + } + else if (target.equals(Result.PI_ENABLE_OUTPUT_ESCAPING)) { + escapeOutput = true; + piProcessed = true; + } + } + if (piProcessed == false) { + String rawData = pi.getData(); + + // Write or if no data then just + if (!"".equals(rawData)) { + out.write(""); + } + else { + out.write(""); + } + } + } + + /** + * This will handle printing a {@link EntityRef}. + * Only the entity reference such as &entity; + * will be printed. However, subclasses are free to override + * this method to print the contents of the entity instead. + * + * @param entity EntityRef to output. + * @param out Writer to use. */ + protected void printEntityRef(Writer out, EntityRef entity) + throws IOException { + out.write("&"); + out.write(entity.getName()); + out.write(";"); + } + + /** + * This will handle printing of {@link CDATA} text. + * + * @param cdata CDATA to output. + * @param out Writer to use. + */ + protected void printCDATA(Writer out, CDATA cdata) throws IOException { + String str = (currentFormat.mode == Format.TextMode.NORMALIZE) + ? cdata.getTextNormalize() + : ((currentFormat.mode == Format.TextMode.TRIM) ? + cdata.getText().trim() : cdata.getText()); + out.write(""); + } + + /** + * This will handle printing of {@link Text} strings. + * + * @param text Text to write. + * @param out Writer to use. + */ + protected void printText(Writer out, Text text) throws IOException { + String str = (currentFormat.mode == Format.TextMode.NORMALIZE) + ? text.getTextNormalize() + : ((currentFormat.mode == Format.TextMode.TRIM) ? + text.getText().trim() : text.getText()); + out.write(escapeElementEntities(str)); + } + + /** + * This will handle printing a string. Escapes the element entities, + * trims interior whitespace, etc. if necessary. + */ + private void printString(Writer out, String str) throws IOException { + if (currentFormat.mode == Format.TextMode.NORMALIZE) { + str = Text.normalizeString(str); + } + else if (currentFormat.mode == Format.TextMode.TRIM) { + str = str.trim(); + } + out.write(escapeElementEntities(str)); + } + + /** + * This will handle printing of a {@link Element}, + * its {@link Attribute}s, and all contained (child) + * elements, etc. + * + * @param element Element to output. + * @param out Writer to use. + * @param level int level of indention. + * @param namespaces List stack of Namespaces in scope. + */ + protected void printElement(Writer out, Element element, + int level, NamespaceStack namespaces) + throws IOException { + + List attributes = element.getAttributes(); + List content = element.getContent(); + + // Check for xml:space and adjust format settings + String space = null; + if (attributes != null) { + space = element.getAttributeValue("space", + Namespace.XML_NAMESPACE); + } + + Format previousFormat = currentFormat; + + if ("default".equals(space)) { + currentFormat = userFormat; + } + else if ("preserve".equals(space)) { + currentFormat = preserveFormat; + } + + // Print the beginning of the tag plus attributes and any + // necessary namespace declarations + out.write("<"); + printQualifiedName(out, element); + + // Mark our namespace starting point + int previouslyDeclaredNamespaces = namespaces.size(); + + // Print the element's namespace, if appropriate + printElementNamespace(out, element, namespaces); + + // Print out additional namespace declarations + printAdditionalNamespaces(out, element, namespaces); + + // Print out attributes + if (attributes != null) + printAttributes(out, attributes, element, namespaces); + + // Depending on the settings (newlines, textNormalize, etc), we may + // or may not want to print all of the content, so determine the + // index of the start of the content we're interested + // in based on the current settings. + + int start = skipLeadingWhite(content, 0); + int size = content.size(); + if (start >= size) { + // Case content is empty or all insignificant whitespace + if (currentFormat.expandEmptyElements) { + out.write(">"); + } + else { + out.write(" />"); + } + } + else { + out.write(">"); + + // For a special case where the content is only CDATA + // or Text we don't want to indent after the start or + // before the end tag. + + if (nextNonText(content, start) < size) { + // Case Mixed Content - normal indentation + newline(out); + printContentRange(out, content, start, size, + level + 1, namespaces); + newline(out); + indent(out, level); + } + else { + // Case all CDATA or Text - no indentation + printTextRange(out, content, start, size); + } + out.write(""); + } + + // remove declared namespaces from stack + while (namespaces.size() > previouslyDeclaredNamespaces) { + namespaces.pop(); + } + + // Restore our format settings + currentFormat = previousFormat; + } + + /** + * This will handle printing of content within a given range. + * The range to print is specified in typical Java fashion; the + * starting index is inclusive, while the ending index is + * exclusive. + * + * @param content List of content to output + * @param start index of first content node (inclusive. + * @param end index of last content node (exclusive). + * @param out Writer to use. + * @param level int level of indentation. + * @param namespaces List stack of Namespaces in scope. + */ + private void printContentRange(Writer out, List content, + int start, int end, int level, + NamespaceStack namespaces) + throws IOException { + boolean firstNode; // Flag for 1st node in content + Object next; // Node we're about to print + int first, index; // Indexes into the list of content + + index = start; + while (index < end) { + firstNode = (index == start) ? true : false; + next = content.get(index); + + // + // Handle consecutive CDATA, Text, and EntityRef nodes all at once + // + if ((next instanceof Text) || (next instanceof EntityRef)) { + first = skipLeadingWhite(content, index); + // Set index to next node for loop + index = nextNonText(content, first); + + // If it's not all whitespace - print it! + if (first < index) { + if (!firstNode) + newline(out); + indent(out, level); + printTextRange(out, content, first, index); + } + continue; + } + + // + // Handle other nodes + // + if (!firstNode) { + newline(out); + } + + indent(out, level); + + if (next instanceof Comment) { + printComment(out, (Comment)next); + } + else if (next instanceof Element) { + printElement(out, (Element)next, level, namespaces); + } + else if (next instanceof ProcessingInstruction) { + printProcessingInstruction(out, (ProcessingInstruction)next); + } + else { + // XXX if we get here then we have a illegal content, for + // now we'll just ignore it (probably should throw + // a exception) + } + + index++; + } /* while */ + } + + /** + * This will handle printing of a sequence of {@link CDATA} + * or {@link Text} nodes. It is an error to have any other + * pass this method any other type of node. + * + * @param content List of content to output + * @param start index of first content node (inclusive). + * @param end index of last content node (exclusive). + * @param out Writer to use. + */ + private void printTextRange(Writer out, List content, int start, int end + ) throws IOException { + String previous; // Previous text printed + Object node; // Next node to print + String next; // Next text to print + + previous = null; + + // Remove leading whitespace-only nodes + start = skipLeadingWhite(content, start); + + int size = content.size(); + if (start < size) { + // And remove trialing whitespace-only nodes + end = skipTrailingWhite(content, end); + + for (int i = start; i < end; i++) { + node = content.get(i); + + // Get the unmangled version of the text + // we are about to print + if (node instanceof Text) { + next = ((Text) node).getText(); + } + else if (node instanceof EntityRef) { + next = "&" + ((EntityRef) node).getValue() + ";"; + } + else { + throw new IllegalStateException("Should see only " + + "CDATA, Text, or EntityRef"); + } + + // This may save a little time + if (next == null || "".equals(next)) { + continue; + } + + // Determine if we need to pad the output (padding is + // only need in trim or normalizing mode) + if (previous != null) { // Not 1st node + if (currentFormat.mode == Format.TextMode.NORMALIZE || + currentFormat.mode == Format.TextMode.TRIM) { + if ((endsWithWhite(previous)) || + (startsWithWhite(next))) { + out.write(" "); + } + } + } + + // Print the node + if (node instanceof CDATA) { + printCDATA(out, (CDATA) node); + } + else if (node instanceof EntityRef) { + printEntityRef(out, (EntityRef) node); + } + else { + printString(out, next); + } + + previous = next; + } + } + } + + /** + * This will handle printing of any needed {@link Namespace} + * declarations. + * + * @param ns Namespace to print definition of + * @param out Writer to use. + */ + private void printNamespace(Writer out, Namespace ns, + NamespaceStack namespaces) + throws IOException { + String prefix = ns.getPrefix(); + String uri = ns.getURI(); + + // Already printed namespace decl? + if (uri.equals(namespaces.getURI(prefix))) { + return; + } + + out.write(" xmlns"); + if (!prefix.equals("")) { + out.write(":"); + out.write(prefix); + } + out.write("=\""); + out.write(escapeAttributeEntities(uri)); + out.write("\""); + namespaces.push(ns); + } + + /** + * This will handle printing of a {@link Attribute} list. + * + * @param attributes List of Attribute objcts + * @param out Writer to use + */ + protected void printAttributes(Writer out, List attributes, Element parent, + NamespaceStack namespaces) + throws IOException { + + // I do not yet handle the case where the same prefix maps to + // two different URIs. For attributes on the same element + // this is illegal; but as yet we don't throw an exception + // if someone tries to do this + // Set prefixes = new HashSet(); + for (int i = 0; i < attributes.size(); i++) { + Attribute attribute = (Attribute) attributes.get(i); + Namespace ns = attribute.getNamespace(); + if ((ns != Namespace.NO_NAMESPACE) && + (ns != Namespace.XML_NAMESPACE)) { + printNamespace(out, ns, namespaces); + } + + out.write(" "); + printQualifiedName(out, attribute); + out.write("="); + + out.write("\""); + out.write(escapeAttributeEntities(attribute.getValue())); + out.write("\""); + } + } + + private void printElementNamespace(Writer out, Element element, + NamespaceStack namespaces) + throws IOException { + // Add namespace decl only if it's not the XML namespace and it's + // not the NO_NAMESPACE with the prefix "" not yet mapped + // (we do output xmlns="" if the "" prefix was already used and we + // need to reclaim it for the NO_NAMESPACE) + Namespace ns = element.getNamespace(); + if (ns == Namespace.XML_NAMESPACE) { + return; + } + if ( !((ns == Namespace.NO_NAMESPACE) && + (namespaces.getURI("") == null))) { + printNamespace(out, ns, namespaces); + } + } + + private void printAdditionalNamespaces(Writer out, Element element, + NamespaceStack namespaces) + throws IOException { + List list = element.getAdditionalNamespaces(); + if (list != null) { + for (int i = 0; i < list.size(); i++) { + Namespace additional = (Namespace)list.get(i); + printNamespace(out, additional, namespaces); + } + } + } + + // * * * * * * * * * * Support methods * * * * * * * * * * + // * * * * * * * * * * Support methods * * * * * * * * * * + + /** + * This will print a newline only if indent is not null. + * + * @param out Writer to use + */ + private void newline(Writer out) throws IOException { + if (currentFormat.indent != null) { + out.write(currentFormat.lineSeparator); + } + } + + /** + * This will print indents only if indent is not null or the empty string. + * + * @param out Writer to use + * @param level current indent level + */ + private void indent(Writer out, int level) throws IOException { + if (currentFormat.indent == null || + currentFormat.indent.equals("")) { + return; + } + + for (int i = 0; i < level; i++) { + out.write(currentFormat.indent); + } + } + + // Returns the index of the first non-all-whitespace CDATA or Text, + // index = content.size() is returned if content contains + // all whitespace. + // @param start index to begin search (inclusive) + private int skipLeadingWhite(List content, int start) { + if (start < 0) { + start = 0; + } + + int index = start; + int size = content.size(); + if (currentFormat.mode == Format.TextMode.TRIM_FULL_WHITE + || currentFormat.mode == Format.TextMode.NORMALIZE + || currentFormat.mode == Format.TextMode.TRIM) { + while (index < size) { + if (!isAllWhitespace(content.get(index))) { + return index; + } + index++; + } + } + return index; + } + + // Return the index + 1 of the last non-all-whitespace CDATA or + // Text node, index < 0 is returned + // if content contains all whitespace. + // @param start index to begin search (exclusive) + private int skipTrailingWhite(List content, int start) { + int size = content.size(); + if (start > size) { + start = size; + } + + int index = start; + if (currentFormat.mode == Format.TextMode.TRIM_FULL_WHITE + || currentFormat.mode == Format.TextMode.NORMALIZE + || currentFormat.mode == Format.TextMode.TRIM) { + while (index >= 0) { + if (!isAllWhitespace(content.get(index - 1))) + break; + --index; + } + } + return index; + } + + // Return the next non-CDATA, non-Text, or non-EntityRef node, + // index = content.size() is returned if there is no more non-CDATA, + // non-Text, or non-EntiryRef nodes + // @param start index to begin search (inclusive) + private static int nextNonText(List content, int start) { + if (start < 0) { + start = 0; + } + + int index = start; + int size = content.size(); + while (index < size) { + Object node = content.get(index); + if (!((node instanceof Text) || (node instanceof EntityRef))) { + return index; + } + index++; + } + return size; + } + + // Determine if a Object is all whitespace + private boolean isAllWhitespace(Object obj) { + String str = null; + + if (obj instanceof String) { + str = (String) obj; + } + else if (obj instanceof Text) { + str = ((Text) obj).getText(); + } + else if (obj instanceof EntityRef) { + return false; + } + else { + return false; + } + + for (int i = 0; i < str.length(); i++) { + if (!Verifier.isXMLWhitespace(str.charAt(i))) + return false; + } + return true; + } + + // Determine if a string starts with a XML whitespace. + private boolean startsWithWhite(String str) { + if ((str != null) && + (str.length() > 0) && + Verifier.isXMLWhitespace(str.charAt(0))) { + return true; + } + return false; + } + + // Determine if a string ends with a XML whitespace. + private boolean endsWithWhite(String str) { + if ((str != null) && + (str.length() > 0) && + Verifier.isXMLWhitespace(str.charAt(str.length() - 1))) { + return true; + } + return false; + } + + /** + * This will take the pre-defined entities in XML 1.0 and + * convert their character representation to the appropriate + * entity reference, suitable for XML attributes. It does not convert + * the single quote (') because it's not necessary as the outputter + * writes attributes surrounded by double-quotes. + * + * @param str String input to escape. + * @return String with escaped content. + * @throws IllegalArgumentException if an entity can not be escaped + */ + public String escapeAttributeEntities(String str) { + StringBuffer buffer; + int ch, pos; + String entity; + EscapeStrategy strategy = currentFormat.escapeStrategy; + + buffer = null; + for (int i = 0; i < str.length(); i++) { + ch = str.charAt(i); + pos = i; + switch(ch) { + case '<' : + entity = "<"; + break; + case '>' : + entity = ">"; + break; +/* + case '\'' : + entity = "'"; + break; +*/ + case '\"' : + entity = """; + break; + case '&' : + entity = "&"; + break; + case '\r' : + entity = " "; + break; + case '\t' : + entity = " "; + break; + case '\n' : + entity = " "; + break; + default : + + if (strategy.shouldEscape((char) ch)) { + // Make sure what we are escaping is not the + // Beginning of a multi-byte character. + if (Verifier.isHighSurrogate((char) ch)) { + // This is a the high of a surrogate pair + i++; + if (i < str.length()) { + char low = str.charAt(i); + if(!Verifier.isLowSurrogate(low)) { + throw new IllegalDataException("Could not decode surrogate pair 0x" + + Integer.toHexString(ch) + " / 0x" + Integer.toHexString(low)); + } + ch = Verifier.decodeSurrogatePair((char) ch, low); + } else { + throw new IllegalDataException("Surrogate pair 0x" + + Integer.toHexString(ch) + " truncated"); + } + } + entity = "&#x" + Integer.toHexString(ch) + ";"; + } + else { + entity = null; + } + break; + } + if (buffer == null) { + if (entity != null) { + // An entity occurred, so we'll have to use StringBuffer + // (allocate room for it plus a few more entities). + buffer = new StringBuffer(str.length() + 20); + // Copy previous skipped characters and fall through + // to pickup current character + buffer.append(str.substring(0, pos)); + buffer.append(entity); + } + } + else { + if (entity == null) { + buffer.append((char) ch); + } + else { + buffer.append(entity); + } + } + } + + // If there were any entities, return the escaped characters + // that we put in the StringBuffer. Otherwise, just return + // the unmodified input string. + return (buffer == null) ? str : buffer.toString(); + } + + + /** + * This will take the three pre-defined entities in XML 1.0 + * (used specifically in XML elements) and convert their character + * representation to the appropriate entity reference, suitable for + * XML element content. + * + * @param str String input to escape. + * @return String with escaped content. + * @throws IllegalArgumentException if an entity can not be escaped + */ + public String escapeElementEntities(String str) { + if (escapeOutput == false) return str; + + StringBuffer buffer; + int ch, pos; + String entity; + EscapeStrategy strategy = currentFormat.escapeStrategy; + + buffer = null; + for (int i = 0; i < str.length(); i++) { + ch = str.charAt(i); + pos = i; + switch(ch) { + case '<' : + entity = "<"; + break; + case '>' : + entity = ">"; + break; + case '&' : + entity = "&"; + break; + case '\r' : + entity = " "; + break; + case '\n' : + entity = currentFormat.lineSeparator; + break; + default : + + if (strategy.shouldEscape((char) ch)) { + + //make sure what we are escaping is not the + //beginning of a multi-byte character. + if(Verifier.isHighSurrogate((char) ch)) { + //this is a the high of a surrogate pair + i++; + if (i < str.length()) { + char low = str.charAt(i); + if(!Verifier.isLowSurrogate(low)) { + throw new IllegalDataException("Could not decode surrogate pair 0x" + + Integer.toHexString(ch) + " / 0x" + Integer.toHexString(low)); + } + ch = Verifier.decodeSurrogatePair((char) ch, low); + } else { + throw new IllegalDataException("Surrogate pair 0x" + + Integer.toHexString(ch) + " truncated"); + } + } + entity = "&#x" + Integer.toHexString(ch) + ";"; + } + else { + entity = null; + } + break; + } + if (buffer == null) { + if (entity != null) { + // An entity occurred, so we'll have to use StringBuffer + // (allocate room for it plus a few more entities). + buffer = new StringBuffer(str.length() + 20); + // Copy previous skipped characters and fall through + // to pickup current character + buffer.append(str.substring(0, pos)); + buffer.append(entity); + } + } + else { + if (entity == null) { + buffer.append((char) ch); + } + else { + buffer.append(entity); + } + } + } + + // If there were any entities, return the escaped characters + // that we put in the StringBuffer. Otherwise, just return + // the unmodified input string. + return (buffer == null) ? str : buffer.toString(); + } + + /** + * Returns a copy of this XMLOutputter. + */ + public Object clone() { + // Implementation notes: Since all state of an XMLOutputter is + // embodied in simple private instance variables, Object.clone + // can be used. Note that since Object.clone is totally + // broken, we must catch an exception that will never be + // thrown. + try { + return super.clone(); + } + catch (java.lang.CloneNotSupportedException e) { + // even though this should never ever happen, it's still + // possible to fool Java into throwing a + // CloneNotSupportedException. If that happens, we + // shouldn't swallow it. + throw new RuntimeException(e.toString()); + } + } + + /** + * Return a string listing of the settings for this + * XMLOutputter instance. + * + * @return a string listing the settings for this XMLOutputter instance + */ + public String toString() { + StringBuffer buffer = new StringBuffer(); + for (int i = 0; i < userFormat.lineSeparator.length(); i++) { + char ch = userFormat.lineSeparator.charAt(i); + switch (ch) { + case '\r': buffer.append("\\r"); + break; + case '\n': buffer.append("\\n"); + break; + case '\t': buffer.append("\\t"); + break; + default: buffer.append("[" + ((int)ch) + "]"); + break; + } + } + + return ( + "XMLOutputter[omitDeclaration = " + userFormat.omitDeclaration + ", " + + "encoding = " + userFormat.encoding + ", " + + "omitEncoding = " + userFormat.omitEncoding + ", " + + "indent = '" + userFormat.indent + "'" + ", " + + "expandEmptyElements = " + userFormat.expandEmptyElements + ", " + + "lineSeparator = '" + buffer.toString() + "', " + + "textMode = " + userFormat.mode + "]" + ); + } + + /** + * Factory for making new NamespaceStack objects. The NamespaceStack + * created is actually an inner class extending the package protected + * NamespaceStack, as a way to make NamespaceStack "friendly" toward + * subclassers. + */ + private NamespaceStack createNamespaceStack() { + // actually returns a XMLOutputter.NamespaceStack (see below) + return new NamespaceStack(); + } + + /** + * Our own null subclass of NamespaceStack. This plays a little + * trick with Java access protection. We want subclasses of + * XMLOutputter to be able to override protected methods that + * declare a NamespaceStack parameter, but we don't want to + * declare the parent NamespaceStack class as public. + */ + protected class NamespaceStack + extends org.jdom.output.NamespaceStack + { + } + + // Support method to print a name without using elt.getQualifiedName() + // and thus avoiding a StringBuffer creation and memory churn + private void printQualifiedName(Writer out, Element e) throws IOException { + if (e.getNamespace().getPrefix().length() == 0) { + out.write(e.getName()); + } + else { + out.write(e.getNamespace().getPrefix()); + out.write(':'); + out.write(e.getName()); + } + } + + // Support method to print a name without using att.getQualifiedName() + // and thus avoiding a StringBuffer creation and memory churn + private void printQualifiedName(Writer out, Attribute a) throws IOException { + String prefix = a.getNamespace().getPrefix(); + if ((prefix != null) && (!prefix.equals(""))) { + out.write(prefix); + out.write(':'); + out.write(a.getName()); + } + else { + out.write(a.getName()); + } + } + + // * * * * * * * * * * Deprecated methods * * * * * * * * * * + + /* The methods below here are deprecations of protected methods. We + * don't usually deprecate protected methods, so they're commented out. + * They're left here in case this mass deprecation causes people trouble. + * Since we're getting close to 1.0 it's actually better for people to + * raise issues early though. + */ + +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/output/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,15 @@ + + +Classes to output JDOM documents to various destinations. The most common +outputter class is XMLOutputter which outputs a document (or part of a +document) as a stream of bytes. Format and EscapeStrategy support the +XMLOutputter in letting you choose how the output should be formatted and how +special characters should be escaped. + +SAXOutputter lets you output as a stream of SAX events (handy especially in +transformations). JDOMLocator supports SAXOutputter and helps you observe the +SAX output process. + +DOMOutputter lets you output a JDOM document as a DOM tree. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,13 @@ + + +Classes to represent the components of an XML document. The Verifier is a +special class useful in ensuring well-formedness of documents. The Parent +interface is implemented by Document and Element exposing their commonality. +The Content abstract class is extended by all the node types of a document +except Document itself. + +The JDOMFactory interface and DefaultJDOMFactory standard implementation +provide advanced users with the ability to create subtypes of the org.jdom +classes. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/JDOMResult.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/transform/JDOMResult.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,670 @@ +/*-- + + $Id: JDOMResult.java,v 1.24 2007/11/10 05:29:02 jhunter Exp $ + + Copyright (C) 2001-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.transform; + +import java.util.*; + +import javax.xml.transform.sax.*; + +import org.jdom.*; +import org.jdom.input.*; +import org.xml.sax.*; +import org.xml.sax.ext.*; +import org.xml.sax.helpers.*; + +/** + * A holder for an XSL Transformation result, generally a list of nodes + * although it can be a JDOM Document also. As stated by the XSLT 1.0 + * specification, the result tree generated by an XSL transformation is not + * required to be a well-formed XML document. The result tree may have "any + * sequence of nodes as children that would be possible for an + * element node". + *

+ * The following example shows how to apply an XSL Transformation + * to a JDOM document and get the transformation result in the form + * of a list of JDOM nodes: + * 


+ *   public static List transform(Document doc, String stylesheet)
+ *                                        throws JDOMException {
+ *     try {
+ *       Transformer transformer = TransformerFactory.newInstance()
+ *                             .newTransformer(new StreamSource(stylesheet));
+ *       JDOMSource in = new JDOMSource(doc);
+ *       JDOMResult out = new JDOMResult();
+ *       transformer.transform(in, out);
+ *       return out.getResult();
+ *     }
+ *     catch (TransformerException e) {
+ *       throw new JDOMException("XSLT Transformation failed", e);
+ *     }
+ *   }
+ *
+ * + * @see org.jdom.transform.JDOMSource + * + * @version $Revision: 1.24 $, $Date: 2007/11/10 05:29:02 $ + * @author Laurent Bihanic + * @author Jason Hunter + */ +public class JDOMResult extends SAXResult { + + private static final String CVS_ID = + "@(#) $RCSfile: JDOMResult.java,v $ $Revision: 1.24 $ $Date: 2007/11/10 05:29:02 $ $Name: jdom_1_1_1 $"; + + /** + * If {@link javax.xml.transform.TransformerFactory#getFeature} + * returns true when passed this value as an + * argument, the Transformer natively supports JDOM. + *

+ * Note: This implementation does not override + * the {@link SAXResult#FEATURE} value defined by its superclass + * to be considered as a SAXResult by Transformer implementations + * not natively supporting JDOM.

+ */ + public final static String JDOM_FEATURE = + "http://org.jdom.transform.JDOMResult/feature"; + + /** + * The result of a transformation, as set by Transformer + * implementations that natively support JDOM, as a JDOM document + * or a list of JDOM nodes. + */ + private Object result = null; + + /** + * Whether the application queried the result (as a list or a + * document) since it was last set. + */ + private boolean queried = false; + + /** + * The custom JDOM factory to use when building the transformation + * result or null to use the default JDOM classes. + */ + private JDOMFactory factory = null; + + /** + * Public default constructor. + */ + public JDOMResult() { + // Allocate custom builder object... + DocumentBuilder builder = new DocumentBuilder(); + + // And use it as ContentHandler and LexicalHandler. + super.setHandler(builder); + super.setLexicalHandler(builder); + } + + /** + * Sets the object(s) produced as result of an XSL Transformation. + *

+ * Note: This method shall be used by the + * {@link javax.xml.transform.Transformer} implementations that + * natively support JDOM to directly set the transformation + * result rather than considering this object as a + * {@link SAXResult}. Applications should not use this + * method.

+ * + * @param result the result of a transformation as a + * {@link java.util.List list} of JDOM nodes + * (Elements, Texts, Comments, PIs...). + * + * @see #getResult + */ + public void setResult(List result) { + this.result = result; + this.queried = false; + } + + /** + * Returns the result of an XSL Transformation as a list of JDOM + * nodes. + *

+ * If the result of the transformation is a JDOM document, + * this method converts it into a list of JDOM nodes; any + * subsequent call to {@link #getDocument} will return + * null.

+ * + * @return the transformation result as a (possibly empty) list of + * JDOM nodes (Elements, Texts, Comments, PIs...). + */ + public List getResult() { + List nodes = Collections.EMPTY_LIST; + + // Retrieve result from the document builder if not set. + this.retrieveResult(); + + if (result instanceof List) { + nodes = (List)result; + } + else { + if ((result instanceof Document) && (queried == false)) { + List content = ((Document)result).getContent(); + nodes = new ArrayList(content.size()); + + while (content.size() != 0) + { + Object o = content.remove(0); + nodes.add(o); + } + result = nodes; + } + } + queried = true; + + return (nodes); + } + + /** + * Sets the document produced as result of an XSL Transformation. + *

+ * Note: This method shall be used by the + * {@link javax.xml.transform.Transformer} implementations that + * natively support JDOM to directly set the transformation + * result rather than considering this object as a + * {@link SAXResult}. Applications should not use this + * method.

+ * + * @param document the JDOM document result of a transformation. + * + * @see #setResult + * @see #getDocument + */ + public void setDocument(Document document) { + this.result = document; + this.queried = false; + } + + /** + * Returns the result of an XSL Transformation as a JDOM document. + *

+ * If the result of the transformation is a list of nodes, + * this method attempts to convert it into a JDOM document. If + * successful, any subsequent call to {@link #getResult} will + * return an empty list.

+ *

+ * Warning: The XSLT 1.0 specification states that + * the output of an XSL transformation is not a well-formed XML + * document but a list of nodes. Applications should thus use + * {@link #getResult} instead of this method or at least expect + * null documents to be returned. + * + * @return the transformation result as a JDOM document or + * null if the result of the transformation + * can not be converted into a well-formed document. + * + * @see #getResult + */ + public Document getDocument() { + Document doc = null; + + // Retrieve result from the document builder if not set. + this.retrieveResult(); + + if (result instanceof Document) { + doc = (Document)result; + } + else { + if ((result instanceof List) && (queried == false)) { + // Try to create a document from the result nodes + try { + JDOMFactory f = this.getFactory(); + if (f == null) { f = new DefaultJDOMFactory(); } + + doc = f.document(null); + doc.setContent((List)result); + + result = doc; + } + catch (RuntimeException ex1) { + // Some of the result nodes are not valid children of a + // Document node. => return null. + } + } + } + queried = true; + + return (doc); + } + + /** + * Sets a custom JDOMFactory to use when building the + * transformation result. Use a custom factory to build the tree + * with your own subclasses of the JDOM classes. + * + * @param factory the custom JDOMFactory to use or + * null to use the default JDOM + * classes. + * + * @see #getFactory + */ + public void setFactory(JDOMFactory factory) { + this.factory = factory; + } + + /** + * Returns the custom JDOMFactory used to build the transformation + * result. + * + * @return the custom JDOMFactory used to build the + * transformation result or null if the + * default JDOM classes are being used. + * + * @see #setFactory + */ + public JDOMFactory getFactory() { + return this.factory; + } + + /** + * Checks whether a transformation result has been set and, if not, + * retrieves the result tree being built by the document builder. + */ + private void retrieveResult() { + if (result == null) { + this.setResult(((DocumentBuilder)this.getHandler()).getResult()); + } + } + + //------------------------------------------------------------------------- + // SAXResult overwritten methods + //------------------------------------------------------------------------- + + /** + * Sets the target to be a SAX2 ContentHandler. + * + * @param handler Must be a non-null ContentHandler reference. + */ + public void setHandler(ContentHandler handler) { } + + /** + * Sets the SAX2 LexicalHandler for the output. + *

+ * This is needed to handle XML comments and the like. If the + * lexical handler is not set, an attempt should be made by the + * transformer to cast the ContentHandler to a LexicalHandler.

+ * + * @param handler A non-null LexicalHandler for + * handling lexical parse events. + */ + public void setLexicalHandler(LexicalHandler handler) { } + + + //========================================================================= + // FragmentHandler nested class + //========================================================================= + + private static class FragmentHandler extends SAXHandler { + /** + * A dummy root element required by SAXHandler that can only + * cope with well-formed documents. + */ + private Element dummyRoot = new Element("root", null, null); + + /** + * Public constructor. + */ + public FragmentHandler(JDOMFactory factory) { + super(factory); + + // Add a dummy root element to the being-built document as XSL + // transformation can output node lists instead of well-formed + // documents. + this.pushElement(dummyRoot); + } + + /** + * Returns the result of an XSL Transformation. + * + * @return the transformation result as a (possibly empty) list of + * JDOM nodes (Elements, Texts, Comments, PIs...). + */ + public List getResult() { + // Flush remaining text content in case the last text segment is + // outside an element. + try { + this.flushCharacters(); + } + catch (SAXException e) { /* Ignore... */ } + return this.getDetachedContent(dummyRoot); + } + + /** + * Returns the content of a JDOM Element detached from it. + * + * @param elt the element to get the content from. + * + * @return a (possibly empty) list of JDOM nodes, detached from + * their parent. + */ + private List getDetachedContent(Element elt) { + List content = elt.getContent(); + List nodes = new ArrayList(content.size()); + + while (content.size() != 0) + { + Object o = content.remove(0); + nodes.add(o); + } + return (nodes); + } + } + + //========================================================================= + // DocumentBuilder inner class + //========================================================================= + + private class DocumentBuilder extends XMLFilterImpl + implements LexicalHandler { + /** + * The actual JDOM document builder. + */ + private FragmentHandler saxHandler = null; + + /** + * Whether the startDocument event was received. Some XSLT + * processors such as Oracle's do not fire this event. + */ + private boolean startDocumentReceived = false; + + /** + * Public default constructor. + */ + public DocumentBuilder() { } + + /** + * Returns the result of an XSL Transformation. + * + * @return the transformation result as a (possibly empty) list of + * JDOM nodes (Elements, Texts, Comments, PIs...) or + * null if no new transformation occurred + * since the result of the previous one was returned. + */ + public List getResult() { + List result = null; + + if (this.saxHandler != null) { + // Retrieve result from SAX content handler. + result = this.saxHandler.getResult(); + + // Detach the (non-reusable) SAXHandler instance. + this.saxHandler = null; + + // And get ready for the next transformation. + this.startDocumentReceived = false; + } + return result; + } + + private void ensureInitialization() throws SAXException { + // Trigger document initialization if XSLT processor failed to + // fire the startDocument event. + if (this.startDocumentReceived == false) { + this.startDocument(); + } + } + + //----------------------------------------------------------------------- + // XMLFilterImpl overwritten methods + //----------------------------------------------------------------------- + + /** + * [SAX ContentHandler interface support] Processes a + * start of document event. + *

+ * This implementation creates a new JDOM document builder and + * marks the current result as "under construction".

+ * + * @throws SAXException if any error occurred while creating + * the document builder. + */ + public void startDocument() throws SAXException { + this.startDocumentReceived = true; + + // Reset any previously set result. + setResult(null); + + // Create the actual JDOM document builder and register it as + // ContentHandler on the superclass (XMLFilterImpl): this + // implementation will take care of propagating the LexicalHandler + // events. + this.saxHandler = new FragmentHandler(getFactory()); + super.setContentHandler(this.saxHandler); + + // And propagate event. + super.startDocument(); + } + + /** + * [SAX ContentHandler interface support] Receives + * notification of the beginning of an element. + *

+ * This implementation ensures that startDocument() has been + * called prior processing an element. + * + * @param nsURI the Namespace URI, or the empty string if + * the element has no Namespace URI or if + * Namespace processing is not being performed. + * @param localName the local name (without prefix), or the + * empty string if Namespace processing is + * not being performed. + * @param qName the qualified name (with prefix), or the + * empty string if qualified names are not + * available. + * @param atts The attributes attached to the element. If + * there are no attributes, it shall be an + * empty Attributes object. + * + * @throws SAXException if any error occurred while creating + * the document builder. + */ + public void startElement(String nsURI, String localName, String qName, + Attributes atts) throws SAXException + { + this.ensureInitialization(); + super.startElement(nsURI, localName, qName, atts); + } + + /** + * [SAX ContentHandler interface support] Begins the + * scope of a prefix-URI Namespace mapping. + */ + public void startPrefixMapping(String prefix, String uri) + throws SAXException { + this.ensureInitialization(); + super.startPrefixMapping(prefix, uri); + } + + /** + * [SAX ContentHandler interface support] Receives + * notification of character data. + */ + public void characters(char ch[], int start, int length) + throws SAXException { + this.ensureInitialization(); + super.characters(ch, start, length); + } + + /** + * [SAX ContentHandler interface support] Receives + * notification of ignorable whitespace in element content. + */ + public void ignorableWhitespace(char ch[], int start, int length) + throws SAXException { + this.ensureInitialization(); + super.ignorableWhitespace(ch, start, length); + } + + /** + * [SAX ContentHandler interface support] Receives + * notification of a processing instruction. + */ + public void processingInstruction(String target, String data) + throws SAXException { + this.ensureInitialization(); + super.processingInstruction(target, data); + } + + /** + * [SAX ContentHandler interface support] Receives + * notification of a skipped entity. + */ + public void skippedEntity(String name) throws SAXException { + this.ensureInitialization(); + super.skippedEntity(name); + } + + //----------------------------------------------------------------------- + // LexicalHandler interface support + //----------------------------------------------------------------------- + + /** + * [SAX LexicalHandler interface support] Reports the + * start of DTD declarations, if any. + * + * @param name the document type name. + * @param publicId the declared public identifier for the + * external DTD subset, or null + * if none was declared. + * @param systemId the declared system identifier for the + * external DTD subset, or null + * if none was declared. + * + * @throws SAXException The application may raise an exception. + */ + public void startDTD(String name, String publicId, String systemId) + throws SAXException { + this.ensureInitialization(); + this.saxHandler.startDTD(name, publicId, systemId); + } + + /** + * [SAX LexicalHandler interface support] Reports the end + * of DTD declarations. + * + * @throws SAXException The application may raise an exception. + */ + public void endDTD() throws SAXException { + this.saxHandler.endDTD(); + } + + /** + * [SAX LexicalHandler interface support] Reports the + * beginning of some internal and external XML entities. + * + * @param name the name of the entity. If it is a parameter + * entity, the name will begin with '%', and if it + * is the external DTD subset, it will be "[dtd]". + * + * @throws SAXException The application may raise an exception. + */ + public void startEntity(String name) throws SAXException { + this.ensureInitialization(); + this.saxHandler.startEntity(name); + } + + /** + * [SAX LexicalHandler interface support] Reports the end + * of an entity. + * + * @param name the name of the entity that is ending. + * + * @throws SAXException The application may raise an exception. + */ + public void endEntity(String name) throws SAXException { + this.saxHandler.endEntity(name); + } + + /** + * [SAX LexicalHandler interface support] Reports the + * start of a CDATA section. + * + * @throws SAXException The application may raise an exception. + */ + public void startCDATA() throws SAXException { + this.ensureInitialization(); + this.saxHandler.startCDATA(); + } + + /** + * [SAX LexicalHandler interface support] Reports the end + * of a CDATA section. + * + * @throws SAXException The application may raise an exception. + */ + public void endCDATA() throws SAXException { + this.saxHandler.endCDATA(); + } + + /** + * [SAX LexicalHandler interface support] Reports an XML + * comment anywhere in the document. + * + * @param ch an array holding the characters in the comment. + * @param start the starting position in the array. + * @param length the number of characters to use from the array. + * + * @throws SAXException The application may raise an exception. + */ + public void comment(char ch[], int start, int length) + throws SAXException { + this.ensureInitialization(); + this.saxHandler.comment(ch, start, length); + } + } +} + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/JDOMSource.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/transform/JDOMSource.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,535 @@ +/*-- + + $Id: JDOMSource.java,v 1.20 2007/11/10 05:29:02 jhunter Exp $ + + Copyright (C) 2001-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.transform; + +import java.io.*; +import java.util.*; + +import javax.xml.transform.sax.*; + +import org.jdom.*; +import org.jdom.output.*; +import org.xml.sax.*; + +/** + * A holder for an XML Transformation source: a Document, Element, or list of + * nodes. + *

+ * The is provides input to a + * {@link javax.xml.transform.Transformer JAXP TrAX Transformer}. + *

+ * The following example shows how to apply an XSL Transformation + * to a JDOM document and get the transformation result in the form + * of a list of JDOM nodes: + * 


+ *   public static List transform(Document doc, String stylesheet)
+ *                                        throws JDOMException {
+ *     try {
+ *       Transformer transformer = TransformerFactory.newInstance()
+ *                             .newTransformer(new StreamSource(stylesheet));
+ *       JDOMSource in = new JDOMSource(doc);
+ *       JDOMResult out = new JDOMResult();
+ *       transformer.transform(in, out);
+ *       return out.getResult();
+ *     }
+ *     catch (TransformerException e) {
+ *       throw new JDOMException("XSLT Transformation failed", e);
+ *     }
+ *   }
+ *
+ * + * @see org.jdom.transform.JDOMResult + * + * @version $Revision: 1.20 $, $Date: 2007/11/10 05:29:02 $ + * @author Laurent Bihanic + * @author Jason Hunter + */ +public class JDOMSource extends SAXSource { + + private static final String CVS_ID = + "@(#) $RCSfile: JDOMSource.java,v $ $Revision: 1.20 $ $Date: 2007/11/10 05:29:02 $ $Name: jdom_1_1_1 $"; + + /** + * If {@link javax.xml.transform.TransformerFactory#getFeature} + * returns true when passed this value as an + * argument, the Transformer natively supports JDOM. + *

+ * Note: This implementation does not override + * the {@link SAXSource#FEATURE} value defined by its superclass + * to be considered as a SAXSource by Transformer implementations + * not natively supporting JDOM. + *

+ */ + public final static String JDOM_FEATURE = + "http://org.jdom.transform.JDOMSource/feature"; + + /** + * The XMLReader object associated to this source or + * null if no XMLReader has yet been requested. + * + * @see #getXMLReader + */ + private XMLReader xmlReader = null; + + /** + * Optional entity resolver associated to the source of + * this document or null if no EntityResolver + * was supplied with this JDOMSource. + * + * @see #buildDocumentReader() + */ + private EntityResolver resolver = null; + + /** + * Creates a JDOM TrAX source wrapping a JDOM document. + * + * @param source the JDOM document to use as source for the + * transformations + * + * @throws IllegalArgumentException if source is + * null. + */ + public JDOMSource(Document source) { + setDocument(source); + } + + /** + * Creates a JDOM TrAX source wrapping a list of JDOM nodes. + * + * @param source the JDOM nodes to use as source for the + * transformations + * + * @throws IllegalArgumentException if source is + * null. + */ + public JDOMSource(List source) { + setNodes(source); + } + + /** + * Creates a JDOM TrAX source wrapping a JDOM element. + * + * @param source the JDOM element to use as source for the + * transformations + * + * @throws IllegalArgumentException if source is + * null. + */ + public JDOMSource(Element source) { + List nodes = new ArrayList(); + nodes.add(source); + + setNodes(nodes); + } + + /** + * Creates a JDOM TrAX source wrapping a JDOM element with an + * associated EntityResolver to resolve external entities. + * + * @param source The JDOM Element to use as source for the + * transformations + * + * @param resolver Entity resolver to use for the source + * transformation + * + * @throws IllegalArgumentException ifsource is + * null + */ + public JDOMSource(Document source, EntityResolver resolver) { + setDocument(source); + this.resolver = resolver; + } + +/** + * Sets the source document used by this TrAX source. + * + * @param source the JDOM document to use as source for the + * transformations + * + * @throws IllegalArgumentException if source is + * null. + * + * @see #getDocument + */ + public void setDocument(Document source) { + super.setInputSource(new JDOMInputSource(source)); + } + + /** + * Returns the source document used by this TrAX source. + * + * @return the source document used by this TrAX source or + * null if the source is a node list. + * + * @see #setDocument + */ + public Document getDocument() { + Object src = ((JDOMInputSource)getInputSource()).getSource(); + Document doc = null; + + if (src instanceof Document) { + doc = (Document)src; + } + return doc; + } + + /** + * Sets the source node list used by this TrAX source. + * + * @param source the JDOM nodes to use as source for the + * transformations + * + * @throws IllegalArgumentException if source is + * null. + * + * @see #getNodes + */ + public void setNodes(List source) { + super.setInputSource(new JDOMInputSource(source)); + } + + /** + * Returns the source node list used by this TrAX source. + * + * @return the source node list used by this TrAX source or + * null if the source is a JDOM document. + * + * @see #setDocument + */ + public List getNodes() { + Object src = ((JDOMInputSource)getInputSource()).getSource(); + List nodes = null; + + if (src instanceof List) { + nodes = (List)src; + } + return nodes; + } + + + //------------------------------------------------------------------------- + // SAXSource overwritten methods + //------------------------------------------------------------------------- + + /** + * Sets the SAX InputSource to be used for the Source. + *

+ * As this implementation only supports JDOM document as data + * source, this method always throws an + * {@link UnsupportedOperationException}. + *

+ * + * @param inputSource a valid InputSource reference. + * + * @throws UnsupportedOperationException always! + */ + public void setInputSource(InputSource inputSource) + throws UnsupportedOperationException { + throw new UnsupportedOperationException(); + } + + /** + * Set the XMLReader to be used for the Source. + *

+ * As this implementation only supports JDOM document as data + * source, this method throws an + * {@link UnsupportedOperationException} if the provided reader + * object does not implement the SAX {@link XMLFilter} + * interface. Otherwise, the JDOM document reader will be + * attached as parent of the filter chain.

+ * + * @param reader a valid XMLReader or XMLFilter reference. + * + * @throws UnsupportedOperationException if reader + * is not a SAX + * {@link XMLFilter}. + * @see #getXMLReader + */ + public void setXMLReader(XMLReader reader) + throws UnsupportedOperationException { + if (reader instanceof XMLFilter) { + // Connect the filter chain to a document reader. + XMLFilter filter = (XMLFilter)reader; + while (filter.getParent() instanceof XMLFilter) { + filter = (XMLFilter)(filter.getParent()); + } + filter.setParent(buildDocumentReader()); + + // Read XML data from filter chain. + this.xmlReader = reader; + } + else { + throw new UnsupportedOperationException(); + } + } + + /** + * Returns the XMLReader to be used for the Source. + *

+ * This implementation returns a specific XMLReader reading + * the XML data from the source JDOM document. + *

+ * + * @return an XMLReader reading the XML data from the source + * JDOM document. + */ + public XMLReader getXMLReader() { + if (this.xmlReader == null) { + this.xmlReader = buildDocumentReader(); + } + return this.xmlReader; + } + + /** + * Build an XMLReader to be used for the source. This will + * create a new instance of DocumentReader with an + * EntityResolver instance if available. + * + * @return XMLReader reading the XML data from the source + * JDOM document with an optional EntityResolver + */ + private XMLReader buildDocumentReader() { + DocumentReader reader = new DocumentReader(); + if (resolver != null) + reader.setEntityResolver(resolver); + return reader; + } + + //========================================================================= + // JDOMInputSource nested class + //========================================================================= + + /** + * A subclass of the SAX InputSource interface that wraps a JDOM + * Document. + *

+ * This class is nested in JDOMSource as it is not intented to + * be used independently of its friend: DocumentReader. + *

+ * + * @see org.jdom.Document + */ + private static class JDOMInputSource extends InputSource { + /** + * The source as a JDOM document or a list of JDOM nodes. + */ + private Object source = null; + + /** + * Builds a InputSource wrapping the specified JDOM Document. + * + * @param document the source document. + */ + public JDOMInputSource(Document document) { + this.source = document; + } + + /** + * Builds a InputSource wrapping a list of JDOM nodes. + * + * @param nodes the source JDOM nodes. + */ + public JDOMInputSource(List nodes) { + this.source = nodes; + } + + /** + * Returns the source. + * + * @return the source as a JDOM document or a list of JDOM nodes. + */ + public Object getSource() { + return source; + } + + //------------------------------------------------------------------------- + // InputSource overwritten methods + //------------------------------------------------------------------------- + + /** + * Sets the character stream for this input source. + *

+ * This implementation always throws an + * {@link UnsupportedOperationException} as the only source + * stream supported is the source JDOM document. + *

+ * + * @param characterStream a character stream containing + * an XML document. + * + * @throws UnsupportedOperationException always! + */ + public void setCharacterStream(Reader characterStream) + throws UnsupportedOperationException { + throw new UnsupportedOperationException(); + } + + /** + * Gets the character stream for this input source. + *

+ * Note that this method is only provided to make this + * InputSource implementation acceptable by any XML + * parser. As it generates an in-memory string representation + * of the JDOM document, it is quite inefficient from both + * speed and memory consumption points of view. + *

+ * + * @return a Reader to a string representation of the + * source JDOM document. + */ + public Reader getCharacterStream() { + Object src = this.getSource(); + Reader reader = null; + + if (src instanceof Document) { + // Get an in-memory string representation of the document + // and return a reader on it. + reader = new StringReader( + new XMLOutputter().outputString((Document)src)); + } + else { + if (src instanceof List) { + reader = new StringReader( + new XMLOutputter().outputString((List)src)); + } + // Else: No source, no reader! + } + return reader; + } + } + + //========================================================================= + // DocumentReader nested class + //========================================================================= + + /** + * An implementation of the SAX2 XMLReader interface that presents + * a SAX view of a JDOM Document. The actual generation of the + * SAX events is delegated to JDOM's SAXOutputter. + * + * @see org.jdom.Document + * @see org.jdom.output.SAXOutputter + */ + private static class DocumentReader extends SAXOutputter + implements XMLReader { + /** + * Public default constructor. + */ + public DocumentReader() { + super(); + } + + //---------------------------------------------------------------------- + // SAX XMLReader interface support + //---------------------------------------------------------------------- + + /** + * Parses an XML document from a system identifier (URI). + *

+ * This implementation does not support reading XML data from + * system identifiers, only from JDOM documents. Hence, + * this method always throws a {@link SAXNotSupportedException}. + *

+ * + * @param systemId the system identifier (URI). + * + * @throws SAXNotSupportedException always! + */ + public void parse(String systemId) throws SAXNotSupportedException { + throw new SAXNotSupportedException( + "Only JDOM Documents are supported as input"); + } + + /** + * Parses an XML document. + *

+ * The methods accepts only JDOMInputSources + * instances as input sources. + *

+ * + * @param input the input source for the top-level of the + * XML document. + * + * @throws SAXException any SAX exception, + * possibly wrapping + * another exception. + * @throws SAXNotSupportedException if the input source does + * not wrap a JDOM document. + */ + public void parse(InputSource input) throws SAXException { + if (input instanceof JDOMInputSource) { + try { + Object source = ((JDOMInputSource)input).getSource(); + if (source instanceof Document) { + this.output((Document)source); + } + else { + this.output((List)source); + } + } + catch (JDOMException e) { + throw new SAXException(e.getMessage(), e); + } + } + else { + throw new SAXNotSupportedException( + "Only JDOM Documents are supported as input"); + } + } + } +} + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/XSLTransformException.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/transform/XSLTransformException.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,82 @@ +/*-- + + $Id: XSLTransformException.java,v 1.4 2007/11/10 05:29:02 jhunter Exp $ + + Copyright (C) 2003-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.transform; + +import org.jdom.JDOMException; + +/** + * Thrown when an XSL stylesheet fails to compile or an XSL transform fails + * + * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:02 $ + * @author Jason Hunter + */ +public class XSLTransformException extends JDOMException { + + private static final String CVS_ID = + "@(#) $RCSfile: XSLTransformException.java,v $ $Revision: 1.4 $ $Date: 2007/11/10 05:29:02 $ $Name: jdom_1_1_1 $"; + + public XSLTransformException() { + } + + public XSLTransformException(String message) { + super(message); + } + + public XSLTransformException(String message, Exception cause) { + super(message, cause); + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/XSLTransformer.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/transform/XSLTransformer.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,291 @@ +/*-- + + $Id: XSLTransformer.java,v 1.5 2007/11/14 04:36:54 jhunter Exp $ + + Copyright (C) 2001-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.transform; + +import java.util.*; +import java.io.*; +import javax.xml.transform.*; +import javax.xml.transform.stream.StreamSource; +import org.jdom.*; +import org.xml.sax.EntityResolver; + +/** + * A convenience class to handle simple transformations. The JAXP TrAX classes + * have more bells and whistles and can be used with {@link JDOMSource} and + * {@link JDOMResult} for advanced uses. This class handles the common case and + * presents a simple interface. XSLTransformer is thread safe and may be + * used from multiple threads. + * + * 

+ * XSLTransformer transformer = new XSLTransformer("file.xsl");
+ *
+ * Document x2 = transformer.transform(x);  // x is a Document
+ * Document y2 = transformer.transform(y);  // y is a Document
+ *
+ * + * JDOM relies on TrAX to perform the transformation. + * The javax.xml.transform.TransformerFactory Java system property + * determines which XSLT engine TrAX uses. Its value should be + * the fully qualified name of the implementation of the abstract + * javax.xml.transform.TransformerFactory class. + * Values of this property for popular XSLT processors include: + *

+ *
  • Saxon 6.x: com.icl.saxon.TransformerFactoryImpl
    • + *
  • Saxon 7.x: net.sf.saxon.TransformerFactoryImpl
    • + *
  • Xalan: org.apache.xalan.processor.TransformerFactoryImpl
    • + *
  • jd.xslt: jd.xml.xslt.trax.TransformerFactoryImpl
    • + *
  • Oracle: oracle.xml.jaxp.JXSAXTransformerFactory
    • + *
+ *

+ * This property can be set in all the usual ways a Java system property + * can be set. TrAX picks from them in this order:

+ *
    + *
  1. Invoking System.setProperty( "javax.xml.transform.TransformerFactory", + * "classname")
    2. + *
  2. The value specified at the command line using the + * -Djavax.xml.transform.TransformerFactory=classname + * option to the java interpreter
    3. + *
  3. The class named in the lib/jaxp.properties properties file + * in the JRE directory, in a line like this one: + * 
    javax.xml.parsers.DocumentBuilderFactory=classname
    4. + *
  4. The class named in the + * META-INF/services/javax.xml.transform.TransformerFactory file + * in the JAR archives available to the runtime
    5. + *
  5. Finally, if all of the above options fail, + * a default implementation is chosen. In Sun's JDK 1.4, this is + * Xalan 2.2d10.
    6. + *
+ + * @version $Revision: 1.5 $, $Date: 2007/11/14 04:36:54 $ + * @author Jason Hunter + * @author Elliotte Rusty Harold + */ +public class XSLTransformer { + + private static final String CVS_ID = + "@(#) $RCSfile: XSLTransformer.java,v $ $Revision: 1.5 $ $Date: 2007/11/14 04:36:54 $ $Name: jdom_1_1_1 $"; + + private Templates templates; + + /** + * The custom JDOM factory to use when building the transformation + * result or null to use the default JDOM classes. + */ + private JDOMFactory factory = null; + + // Internal constructor to support the other constructors + private XSLTransformer(Source stylesheet) throws XSLTransformException { + try { + templates = TransformerFactory.newInstance() + .newTemplates(stylesheet); + } + catch (TransformerException e) { + throw new XSLTransformException("Could not construct XSLTransformer", e); + } + } + + /** + * Creates a transformer for a given stylesheet system id. + * + * @param stylesheetSystemId source stylesheet as a Source object + * @throws XSLTransformException if there's a problem in the TrAX back-end + */ + public XSLTransformer(String stylesheetSystemId) throws XSLTransformException { + this(new StreamSource(stylesheetSystemId)); + } + + /** + *

+ * This will create a new XSLTransformer by + * reading the stylesheet from the specified + * InputStream. + *

+ * + * @param stylesheet InputStream from which the stylesheet is read. + * @throws XSLTransformException when an IOException, format error, or + * something else prevents the stylesheet from being compiled + */ + public XSLTransformer(InputStream stylesheet) throws XSLTransformException { + this(new StreamSource(stylesheet)); + } + + /** + *

+ * This will create a new XSLTransformer by + * reading the stylesheet from the specified + * Reader. + *

+ * + * @param stylesheet Reader from which the stylesheet is read. + * @throws XSLTransformException when an IOException, format error, or + * something else prevents the stylesheet from being compiled + */ + public XSLTransformer(Reader stylesheet) throws XSLTransformException { + this(new StreamSource(stylesheet)); + } + + /** + *

+ * This will create a new XSLTransformer by + * reading the stylesheet from the specified + * File. + *

+ * + * @param stylesheet File from which the stylesheet is read. + * @throws XSLTransformException when an IOException, format error, or + * something else prevents the stylesheet from being compiled + */ + public XSLTransformer(File stylesheet) throws XSLTransformException { + this(new StreamSource(stylesheet)); + } + + /** + *

+ * This will create a new XSLTransformer by + * reading the stylesheet from the specified + * Document. + *

+ * + * @param stylesheet Document containing the stylesheet. + * @throws XSLTransformException when the supplied Document + * is not syntactically correct XSLT + */ + public XSLTransformer(Document stylesheet) throws XSLTransformException { + this(new JDOMSource(stylesheet)); + } + + /** + * Transforms the given input nodes to a list of output nodes. + * + * @param inputNodes input nodes + * @return transformed output nodes + * @throws XSLTransformException if there's a problem in the transformation + */ + public List transform(List inputNodes) throws XSLTransformException { + JDOMSource source = new JDOMSource(inputNodes); + JDOMResult result = new JDOMResult(); + result.setFactory(factory); // null ok + try { + templates.newTransformer().transform(source, result); + return result.getResult(); + } + catch (TransformerException e) { + throw new XSLTransformException("Could not perform transformation", e); + } + } + + /** + * Transforms the given document to an output document. + * + * @param inputDoc input document + * @return transformed output document + * @throws XSLTransformException if there's a problem in the transformation + */ + public Document transform(Document inputDoc) throws XSLTransformException { + return transform(inputDoc, null); + } + + /** + * Transforms the given document to an output document. + * + * @param inputDoc input document + * @param resolver entity resolver for the input document + * @return transformed output document + * @throws XSLTransformException if there's a problem in the transformation + */ + public Document transform(Document inputDoc, EntityResolver resolver) throws XSLTransformException { + JDOMSource source = new JDOMSource(inputDoc, resolver); + JDOMResult result = new JDOMResult(); + result.setFactory(factory); // null ok + try { + templates.newTransformer().transform(source, result); + return result.getDocument(); + } + catch (TransformerException e) { + throw new XSLTransformException("Could not perform transformation", e); + } + } + + /** + * Sets a custom JDOMFactory to use when building the + * transformation result. Use a custom factory to build the tree + * with your own subclasses of the JDOM classes. + * + * @param factory the custom JDOMFactory to use or + * null to use the default JDOM + * classes. + * + * @see #getFactory + */ + public void setFactory(JDOMFactory factory) { + this.factory = factory; + } + + /** + * Returns the custom JDOMFactory used to build the transformation + * result. + * + * @return the custom JDOMFactory used to build the + * transformation result or null if the + * default JDOM classes are being used. + * + * @see #setFactory + */ + public JDOMFactory getFactory() { + return this.factory; + } +} diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/transform/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,8 @@ + + +Classes to help with transformations, based on the JAXP TrAX classes. +JDOMTransformer supports simple transformations with one line of code. +Advanced features are available with the JDOMSource and JDOMResult classes +that interface with TrAX. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/xpath/JaxenXPath.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/xpath/JaxenXPath.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,356 @@ +///*-- +// +// $Id: JaxenXPath.java,v 1.20 2007/11/10 05:29:02 jhunter Exp $ +// +// Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions +// are met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions, and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions, and the disclaimer that follows +// these conditions in the documentation and/or other materials +// provided with the distribution. +// +// 3. The name "JDOM" must not be used to endorse or promote products +// derived from this software without prior written permission. For +// written permission, please contact . +// +// 4. Products derived from this software may not be called "JDOM", nor +// may "JDOM" appear in their name, without prior written permission +// from the JDOM Project Management . +// +// In addition, we request (but do not require) that you include in the +// end-user documentation provided with the redistribution and/or in the +// software itself an acknowledgement equivalent to the following: +// "This product includes software developed by the +// JDOM Project (http://www.jdom.org/)." +// Alternatively, the acknowledgment may be graphical using the logos +// available at http://www.jdom.org/images/logos. +// +// THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED +// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES +// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +// DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF +// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND +// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT +// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF +// SUCH DAMAGE. +// +// This software consists of voluntary contributions made by many +// individuals on behalf of the JDOM Project and was originally +// created by Jason Hunter and +// Brett McLaughlin . For more information +// on the JDOM Project, please see . +// +// */ +// +//package org.jdom.xpath; +// +// +//import java.util.*; +// +//import org.jaxen.*; +//import org.jaxen.jdom.*; +//import org.jdom.*; +// +// +///** +// * A non-public concrete XPath implementation for Jaxen. +// * +// * @version $Revision: 1.20 $, $Date: 2007/11/10 05:29:02 $ +// * @author Laurent Bihanic +// */ +//class JaxenXPath extends XPath { // package protected +// +// private static final String CVS_ID = +// "@(#) $RCSfile: JaxenXPath.java,v $ $Revision: 1.20 $ $Date: 2007/11/10 05:29:02 $ $Name: jdom_1_1_1 $"; +// +// /** +// * The compiled XPath object to select nodes. This attribute can +// * not be made final as it needs to be set upon object +// * deserialization. +// */ +// private transient JDOMXPath xPath; +// +// /** +// * The current context for XPath expression evaluation. +// */ +// private Object currentContext; +// +// /** +// * Creates a new XPath wrapper object, compiling the specified +// * XPath expression. +// * +// * @param expr the XPath expression to wrap. +// * +// * @throws JDOMException if the XPath expression is invalid. +// */ +// public JaxenXPath(String expr) throws JDOMException { +// setXPath(expr); +// } +// +// /** +// * Evaluates the wrapped XPath expression and returns the list +// * of selected items. +// * +// * @param context the node to use as context for evaluating +// * the XPath expression. +// * +// * @return the list of selected items, which may be of types: {@link Element}, +// * {@link Attribute}, {@link Text}, {@link CDATA}, +// * {@link Comment}, {@link ProcessingInstruction}, Boolean, +// * Double, or String. +// * +// * @throws JDOMException if the evaluation of the XPath +// * expression on the specified context +// * failed. +// */ +// public List selectNodes(Object context) throws JDOMException { +// try { +// currentContext = context; +// +// return xPath.selectNodes(context); +// } +// catch (JaxenException ex1) { +// throw new JDOMException("XPath error while evaluating \"" + +// xPath.toString() + "\": " + ex1.getMessage(), ex1); +// } +// finally { +// currentContext = null; +// } +// } +// +// /** +// * Evaluates the wrapped XPath expression and returns the first +// * entry in the list of selected nodes (or atomics). +// * +// * @param context the node to use as context for evaluating +// * the XPath expression. +// * +// * @return the first selected item, which may be of types: {@link Element}, +// * {@link Attribute}, {@link Text}, {@link CDATA}, +// * {@link Comment}, {@link ProcessingInstruction}, Boolean, +// * Double, String, or null if no item was selected. +// * +// * @throws JDOMException if the evaluation of the XPath +// * expression on the specified context +// * failed. +// */ +// public Object selectSingleNode(Object context) throws JDOMException { +// try { +// currentContext = context; +// +// return xPath.selectSingleNode(context); +// } +// catch (JaxenException ex1) { +// throw new JDOMException("XPath error while evaluating \"" + +// xPath.toString() + "\": " + ex1.getMessage(), ex1); +// } +// finally { +// currentContext = null; +// } +// } +// +// /** +// * Returns the string value of the first node selected by applying +// * the wrapped XPath expression to the given context. +// * +// * @param context the element to use as context for evaluating +// * the XPath expression. +// * +// * @return the string value of the first node selected by applying +// * the wrapped XPath expression to the given context. +// * +// * @throws JDOMException if the XPath expression is invalid or +// * its evaluation on the specified context +// * failed. +// */ +// public String valueOf(Object context) throws JDOMException { +// try { +// currentContext = context; +// +// return xPath.stringValueOf(context); +// } +// catch (JaxenException ex1) { +// throw new JDOMException("XPath error while evaluating \"" + +// xPath.toString() + "\": " + ex1.getMessage(), ex1); +// } +// finally { +// currentContext = null; +// } +// } +// +// /** +// * Returns the number value of the first item selected by applying +// * the wrapped XPath expression to the given context. +// * +// * @param context the element to use as context for evaluating +// * the XPath expression. +// * +// * @return the number value of the first item selected by applying +// * the wrapped XPath expression to the given context, +// * null if no node was selected or the +// * special value {@link java.lang.Double#NaN} +// * (Not-a-Number) if the selected value can not be +// * converted into a number value. +// * +// * @throws JDOMException if the XPath expression is invalid or +// * its evaluation on the specified context +// * failed. +// */ +// public Number numberValueOf(Object context) throws JDOMException { +// try { +// currentContext = context; +// +// return xPath.numberValueOf(context); +// } +// catch (JaxenException ex1) { +// throw new JDOMException("XPath error while evaluating \"" + +// xPath.toString() + "\": " + ex1.getMessage(), ex1); +// } +// finally { +// currentContext = null; +// } +// } +// +// /** +// * Defines an XPath variable and sets its value. +// * +// * @param name the variable name. +// * @param value the variable value. +// * +// * @throws IllegalArgumentException if name is not +// * a valid XPath variable name +// * or if the value type is not +// * supported by the underlying +// * implementation +// */ +// public void setVariable(String name, Object value) +// throws IllegalArgumentException { +// Object o = xPath.getVariableContext(); +// if (o instanceof SimpleVariableContext) { +// ((SimpleVariableContext)o).setVariableValue(null, name, value); +// } +// } +// +// /** +// * Adds a namespace definition to the list of namespaces known of +// * this XPath expression. +// *

+// * Note: In XPath, there is no such thing as a +// * 'default namespace'. The empty prefix always resolves +// * to the empty namespace URI.

+// * +// * @param namespace the namespace. +// */ +// public void addNamespace(Namespace namespace) { +// try { +// xPath.addNamespace(namespace.getPrefix(), namespace.getURI()); +// } +// catch (JaxenException ex1) { /* Can't happen here. */ } +// } +// +// /** +// * Returns the wrapped XPath expression as a string. +// * +// * @return the wrapped XPath expression as a string. +// */ +// public String getXPath() { +// return (xPath.toString()); +// } +// +// /** +// * Compiles and sets the XPath expression wrapped by this object. +// * +// * @param expr the XPath expression to wrap. +// * +// * @throws JDOMException if the XPath expression is invalid. +// */ +// private void setXPath(String expr) throws JDOMException { +// try { +// xPath = new JDOMXPath(expr); +// xPath.setNamespaceContext(new NSContext()); +// } +// catch (Exception ex1) { +// throw new JDOMException( +// "Invalid XPath expression: \"" + expr + "\"", ex1); +// } +// } +// +// public String toString() { +// return (xPath.toString()); +// } +// +// public boolean equals(Object o) { +// if (o instanceof JaxenXPath) { +// JaxenXPath x = (JaxenXPath)o; +// +// return (super.equals(o) && +// xPath.toString().equals(x.xPath.toString())); +// } +// return false; +// } +// +// public int hashCode() { +// return xPath.hashCode(); +// } +// +// private class NSContext extends SimpleNamespaceContext { +// public NSContext() { +// super(); +// } +// +// /** +// * [Jaxen NamespaceContext interface support] Translates +// * the provided namespace prefix into the matching bound +// * namespace URI. +// * +// * @param prefix the namespace prefix to resolve. +// * +// * @return the namespace URI matching the prefix. +// */ +// public String translateNamespacePrefixToUri(String prefix) { +// if ((prefix == null) || (prefix.length() == 0)) { +// return null; +// } +// +// String uri = super.translateNamespacePrefixToUri(prefix); +// if (uri == null) { +// Object ctx = currentContext; +// if (ctx != null) { +// Element elt = null; +// +// // Get closer element node +// if (ctx instanceof Element) { +// elt = (Element)ctx; +// } else if (ctx instanceof Attribute) { +// elt = ((Attribute)ctx).getParent(); +// } else if (ctx instanceof Content) { +// elt = ((Content) ctx).getParentElement(); +// } else if (ctx instanceof Document) { +// elt = ((Document)ctx).getRootElement(); +// } +// +// if (elt != null) { +// Namespace ns = elt.getNamespace(prefix); +// if (ns != null) { +// uri = ns.getURI(); +// } +// } +// } +// } +// return uri; +// } +// } +//} + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/xpath/XPath.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/xpath/XPath.java Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,453 @@ +/*-- + + $Id: XPath.java,v 1.17 2007/11/10 05:29:02 jhunter Exp $ + + Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin. + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions, and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions, and the disclaimer that follows + these conditions in the documentation and/or other materials + provided with the distribution. + + 3. The name "JDOM" must not be used to endorse or promote products + derived from this software without prior written permission. For + written permission, please contact . + + 4. Products derived from this software may not be called "JDOM", nor + may "JDOM" appear in their name, without prior written permission + from the JDOM Project Management . + + In addition, we request (but do not require) that you include in the + end-user documentation provided with the redistribution and/or in the + software itself an acknowledgement equivalent to the following: + "This product includes software developed by the + JDOM Project (http://www.jdom.org/)." + Alternatively, the acknowledgment may be graphical using the logos + available at http://www.jdom.org/images/logos. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + This software consists of voluntary contributions made by many + individuals on behalf of the JDOM Project and was originally + created by Jason Hunter and + Brett McLaughlin . For more information + on the JDOM Project, please see . + + */ + +package org.jdom.xpath; + + +import java.io.*; +import java.lang.reflect.*; +import java.util.*; + +import org.jdom.*; + + +/** + * A utility class for performing XPath calls on JDOM nodes, with a factory + * interface for obtaining a first XPath instance. Users operate against this + * class while XPath vendors can plug-in implementations underneath. Users + * can choose an implementation using either {@link #setXPathClass} or + * the system property "org.jdom.xpath.class". + * + * @version $Revision: 1.17 $, $Date: 2007/11/10 05:29:02 $ + * @author Laurent Bihanic + */ +public abstract class XPath implements Serializable { + + private static final String CVS_ID = + "@(#) $RCSfile: XPath.java,v $ $Revision: 1.17 $ $Date: 2007/11/10 05:29:02 $ $Name: jdom_1_1_1 $"; + + /** + * The name of the system property from which to retrieve the + * name of the implementation class to use. + *

+ * The property name is: + * "org.jdom.xpath.class".

+ */ + private final static String XPATH_CLASS_PROPERTY = "org.jdom.xpath.class"; + + /** + * The default implementation class to use if none was configured. + */ + private final static String DEFAULT_XPATH_CLASS = + "org.jdom.xpath.JaxenXPath"; + + /** + * The string passable to the JAXP 1.3 XPathFactory isObjectModelSupported() + * method to query an XPath engine regarding its support for JDOM. Defined + * to be the well-known URI "http://jdom.org/jaxp/xpath/jdom". + */ + public final static String JDOM_OBJECT_MODEL_URI = + "http://jdom.org/jaxp/xpath/jdom"; + + /** + * The constructor to instanciate a new XPath concrete + * implementation. + * + * @see #newInstance + */ + private static Constructor constructor = null; + + /** + * Creates a new XPath wrapper object, compiling the specified + * XPath expression. + * + * @param path the XPath expression to wrap. + * + * @throws JDOMException if the XPath expression is invalid. + */ + public static XPath newInstance(String path) throws JDOMException { + try { + if (constructor == null) { + // First call => Determine implementation. + String className; + try { + className = System.getProperty(XPATH_CLASS_PROPERTY, + DEFAULT_XPATH_CLASS); + } + catch (SecurityException ex1) { + // Access to system property denied. => Use default impl. + className = DEFAULT_XPATH_CLASS; + } + setXPathClass(Class.forName(className)); + } + // Allocate and return new implementation instance. + return (XPath)constructor.newInstance(new Object[] { path }); + } + catch (JDOMException ex1) { + throw ex1; + } + catch (InvocationTargetException ex2) { + // Constructor threw an error on invocation. + Throwable t = ex2.getTargetException(); + + throw (t instanceof JDOMException)? (JDOMException)t: + new JDOMException(t.toString(), t); + } + catch (Exception ex3) { + // Any reflection error (probably due to a configuration mistake). + throw new JDOMException(ex3.toString(), ex3); + } + } + + /** + * Sets the concrete XPath subclass to use when allocating XPath + * instances. + * + * @param aClass the concrete subclass of XPath. + * + * @throws IllegalArgumentException if aClass is + * null. + * @throws JDOMException if aClass is + * not a concrete subclass + * of XPath. + */ + public static void setXPathClass(Class aClass) throws JDOMException { + if (aClass == null) { + throw new IllegalArgumentException("aClass"); + } + + try { + if ((XPath.class.isAssignableFrom(aClass)) && + (Modifier.isAbstract(aClass.getModifiers()) == false)) { + // Concrete subclass of XPath => Get constructor + constructor = aClass.getConstructor(new Class[] { String.class }); + } + else { + throw new JDOMException(aClass.getName() + + " is not a concrete JDOM XPath implementation"); + } + } + catch (JDOMException ex1) { + throw ex1; + } + catch (Exception ex2) { + // Any reflection error (probably due to a configuration mistake). + throw new JDOMException(ex2.toString(), ex2); + } + } + + /** + * Evaluates the wrapped XPath expression and returns the list + * of selected items. + * + * @param context the node to use as context for evaluating + * the XPath expression. + * + * @return the list of selected items, which may be of types: {@link Element}, + * {@link Attribute}, {@link Text}, {@link CDATA}, + * {@link Comment}, {@link ProcessingInstruction}, Boolean, + * Double, or String. + * + * @throws JDOMException if the evaluation of the XPath + * expression on the specified context + * failed. + */ + abstract public List selectNodes(Object context) throws JDOMException; + + /** + * Evaluates the wrapped XPath expression and returns the first + * entry in the list of selected nodes (or atomics). + * + * @param context the node to use as context for evaluating + * the XPath expression. + * + * @return the first selected item, which may be of types: {@link Element}, + * {@link Attribute}, {@link Text}, {@link CDATA}, + * {@link Comment}, {@link ProcessingInstruction}, Boolean, + * Double, String, or null if no item was selected. + * + * @throws JDOMException if the evaluation of the XPath + * expression on the specified context + * failed. + */ + abstract public Object selectSingleNode(Object context) throws JDOMException; + + /** + * Returns the string value of the first node selected by applying + * the wrapped XPath expression to the given context. + * + * @param context the element to use as context for evaluating + * the XPath expression. + * + * @return the string value of the first node selected by applying + * the wrapped XPath expression to the given context. + * + * @throws JDOMException if the XPath expression is invalid or + * its evaluation on the specified context + * failed. + */ + abstract public String valueOf(Object context) throws JDOMException; + + /** + * Returns the number value of the first node selected by applying + * the wrapped XPath expression to the given context. + * + * @param context the element to use as context for evaluating + * the XPath expression. + * + * @return the number value of the first node selected by applying + * the wrapped XPath expression to the given context, + * null if no node was selected or the + * special value {@link java.lang.Double#NaN} + * (Not-a-Number) if the selected value can not be + * converted into a number value. + * + * @throws JDOMException if the XPath expression is invalid or + * its evaluation on the specified context + * failed. + */ + abstract public Number numberValueOf(Object context) throws JDOMException; + + /** + * Defines an XPath variable and sets its value. + * + * @param name the variable name. + * @param value the variable value. + * + * @throws IllegalArgumentException if name is not + * a valid XPath variable name + * or if the value type is not + * supported by the underlying + * implementation + */ + abstract public void setVariable(String name, Object value); + + /** + * Adds a namespace definition to the list of namespaces known of + * this XPath expression. + *

+ * Note: In XPath, there is no such thing as a + * 'default namespace'. The empty prefix always resolves + * to the empty namespace URI.

+ * + * @param namespace the namespace. + */ + abstract public void addNamespace(Namespace namespace); + + /** + * Adds a namespace definition (prefix and URI) to the list of + * namespaces known of this XPath expression. + *

+ * Note: In XPath, there is no such thing as a + * 'default namespace'. The empty prefix always resolves + * to the empty namespace URI.

+ * + * @param prefix the namespace prefix. + * @param uri the namespace URI. + * + * @throws IllegalNameException if the prefix or uri are null or + * empty strings or if they contain + * illegal characters. + */ + public void addNamespace(String prefix, String uri) { + addNamespace(Namespace.getNamespace(prefix, uri)); + } + + /** + * Returns the wrapped XPath expression as a string. + * + * @return the wrapped XPath expression as a string. + */ + abstract public String getXPath(); + + + /** + * Evaluates an XPath expression and returns the list of selected + * items. + *

+ * Note: This method should not be used when the + * same XPath expression needs to be applied several times (on the + * same or different contexts) as it requires the expression to be + * compiled before being evaluated. In such cases, + * {@link #newInstance allocating} an XPath wrapper instance and + * {@link #selectNodes(java.lang.Object) evaluating} it several + * times is way more efficient. + *

+ * + * @param context the node to use as context for evaluating + * the XPath expression. + * @param path the XPath expression to evaluate. + * + * @return the list of selected items, which may be of types: {@link Element}, + * {@link Attribute}, {@link Text}, {@link CDATA}, + * {@link Comment}, {@link ProcessingInstruction}, Boolean, + * Double, or String. + * + * @throws JDOMException if the XPath expression is invalid or + * its evaluation on the specified context + * failed. + */ + public static List selectNodes(Object context, String path) + throws JDOMException { + return newInstance(path).selectNodes(context); + } + + /** + * Evaluates the wrapped XPath expression and returns the first + * entry in the list of selected nodes (or atomics). + *

+ * Note: This method should not be used when the + * same XPath expression needs to be applied several times (on the + * same or different contexts) as it requires the expression to be + * compiled before being evaluated. In such cases, + * {@link #newInstance allocating} an XPath wrapper instance and + * {@link #selectSingleNode(java.lang.Object) evaluating} it + * several times is way more efficient. + *

+ * + * @param context the element to use as context for evaluating + * the XPath expression. + * @param path the XPath expression to evaluate. + * + * @return the first selected item, which may be of types: {@link Element}, + * {@link Attribute}, {@link Text}, {@link CDATA}, + * {@link Comment}, {@link ProcessingInstruction}, Boolean, + * Double, String, or null if no item was selected. + * + * @throws JDOMException if the XPath expression is invalid or + * its evaluation on the specified context + * failed. + */ + public static Object selectSingleNode(Object context, String path) + throws JDOMException { + return newInstance(path).selectSingleNode(context); + } + + + //------------------------------------------------------------------------- + // Serialization support + //------------------------------------------------------------------------- + + /** + * [Serialization support] Returns the alternative object + * to write to the stream when serializing this object. This + * method returns an instance of a dedicated nested class to + * serialize XPath expressions independently of the concrete + * implementation being used. + *

+ * Note: Subclasses are not allowed to override + * this method to ensure valid serialization of all + * implementations.

+ * + * @return an XPathString instance configured with the wrapped + * XPath expression. + * + * @throws ObjectStreamException never. + */ + protected final Object writeReplace() throws ObjectStreamException { + return new XPathString(this.getXPath()); + } + + /** + * The XPathString is dedicated to serialize instances of + * XPath subclasses in a implementation-independent manner. + *

+ * XPathString ensures that only string data are serialized. Upon + * deserialization, XPathString relies on XPath factory method to + * to create instances of the concrete XPath wrapper currently + * configured.

+ */ + private final static class XPathString implements Serializable { + /** + * The XPath expression as a string. + */ + private String xPath = null; + + /** + * Creates a new XPathString instance from the specified + * XPath expression. + * + * @param xpath the XPath expression. + */ + public XPathString(String xpath) { + super(); + + this.xPath = xpath; + } + + /** + * [Serialization support] Resolves the read XPathString + * objects into XPath implementations. + * + * @return an instance of a concrete implementation of + * XPath. + * + * @throws ObjectStreamException if no XPath could be built + * from the read object. + */ + private Object readResolve() throws ObjectStreamException { + try { + return XPath.newInstance(this.xPath); + } + catch (JDOMException ex1) { + throw new InvalidObjectException( + "Can't create XPath object for expression \"" + + this.xPath + "\": " + ex1.toString()); + } + } + } +} + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/xpath/package.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/org/jdom/xpath/package.html Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,6 @@ + + +Support for XPath from within JDOM. XPath provides a common interface with a +pluggable back-end. The default back end is Jaxen. + + diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/xmlFilePattern.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/src/xmlFilePattern.xml Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,62 @@ + + + 1 + + name + 0 + 0 + 0 + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + 0 + 0 + + + + \ No newline at end of file diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/anoGam1.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/anoGam1.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/bosTau4.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/bosTau4.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/cb3.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/cb3.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/ce4.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/ce4.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/ce6.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/ce6.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/danRer5.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/danRer5.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/danRer6.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/danRer6.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/danRer7.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/danRer7.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/dm2.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/dm2.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/dm3.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/dm3.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/galGal2.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/galGal2.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/galGal3.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/galGal3.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/hg18.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/hg18.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/hg19.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/hg19.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/mm8.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/mm8.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/mm9.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/mm9.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/panTro3.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/panTro3.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/rn3.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/rn3.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/rn4.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/rn4.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/backup-files/susScr2.txt.gz Binary file NGSrich_0.5.5/thirdparty/backup-files/susScr2.txt.gz has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/anoGam1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/anoGam1.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,7 @@ +chr2L 48795086 /gbdb/anoGam1/nib/chr2L.nib +chr2R 62725911 /gbdb/anoGam1/nib/chr2R.nib +chr3L 41284009 /gbdb/anoGam1/nib/chr3L.nib +chr3R 53272125 /gbdb/anoGam1/nib/chr3R.nib +chrM 15363 /gbdb/anoGam1/nib/chrM.nib +chrU 59568033 /gbdb/anoGam1/nib/chrU.nib +chrX 22145176 /gbdb/anoGam1/nib/chrX.nib diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/bosTau4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/bosTau4.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,11900 @@ +chr1 161106243 /gbdb/bosTau4/bosTau4.2bit +chr2 140800416 /gbdb/bosTau4/bosTau4.2bit +chr3 127923604 /gbdb/bosTau4/bosTau4.2bit +chr5 125847759 /gbdb/bosTau4/bosTau4.2bit +chr4 124454208 /gbdb/bosTau4/bosTau4.2bit +chr6 122561022 /gbdb/bosTau4/bosTau4.2bit +chr8 116942821 /gbdb/bosTau4/bosTau4.2bit +chr7 112078216 /gbdb/bosTau4/bosTau4.2bit +chr11 110171769 /gbdb/bosTau4/bosTau4.2bit +chr9 108145351 /gbdb/bosTau4/bosTau4.2bit +chr10 106383598 /gbdb/bosTau4/bosTau4.2bit +chrX 88516663 /gbdb/bosTau4/bosTau4.2bit +chr12 85358539 /gbdb/bosTau4/bosTau4.2bit +chr15 84633453 /gbdb/bosTau4/bosTau4.2bit +chr13 84419198 /gbdb/bosTau4/bosTau4.2bit +chr14 81345643 /gbdb/bosTau4/bosTau4.2bit +chr16 77906053 /gbdb/bosTau4/bosTau4.2bit +chr17 76506943 /gbdb/bosTau4/bosTau4.2bit +chr20 75796353 /gbdb/bosTau4/bosTau4.2bit +chr21 69173390 /gbdb/bosTau4/bosTau4.2bit +chr18 66141439 /gbdb/bosTau4/bosTau4.2bit +chr19 65312493 /gbdb/bosTau4/bosTau4.2bit +chr24 65020233 /gbdb/bosTau4/bosTau4.2bit +chr22 61848140 /gbdb/bosTau4/bosTau4.2bit +chr23 53376148 /gbdb/bosTau4/bosTau4.2bit +chr29 51998940 /gbdb/bosTau4/bosTau4.2bit +chr26 51750746 /gbdb/bosTau4/bosTau4.2bit +chr27 48749334 /gbdb/bosTau4/bosTau4.2bit +chr28 46084206 /gbdb/bosTau4/bosTau4.2bit +chr25 44060403 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1 3546887 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2 2346095 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.3 2196958 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.4 1827879 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.5 1667370 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.6 1456232 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.7 1284506 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.8 1221492 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.9 1190529 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.10 1137730 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11 1114776 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.12 998484 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.13 870761 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.14 855941 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.15 834570 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.16 832387 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.17 829265 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.18 814724 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.19 812995 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.20 789248 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.21 763971 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.22 738377 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.23 698114 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.24 691804 /gbdb/bosTau4/bosTau4.2bit 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/gbdb/bosTau4/bosTau4.2bit +chrUn.004.1900 27544 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1901 27516 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1902 27512 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1903 27510 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1904 27481 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1905 27447 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1906 27429 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1907 27422 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1908 27384 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1909 27377 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1910 27358 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1911 27257 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1912 27240 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1913 27237 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1914 27229 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1915 27227 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1916 27223 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1917 27192 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1918 27138 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1919 27120 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1920 27083 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1921 27068 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1922 27067 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1923 27063 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1924 27025 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1925 27022 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1926 26998 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1927 26948 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1928 26944 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1929 26939 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1930 26931 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1931 26931 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1932 26833 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1933 26830 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1934 26783 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1935 26779 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1936 26771 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1937 26771 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1938 26764 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1939 26726 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1940 26721 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1941 26608 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1942 26578 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1943 26565 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1944 26553 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1945 26528 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1946 26516 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1947 26505 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1948 26499 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1949 26454 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1950 26428 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1951 26414 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1952 26411 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1953 26383 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1954 26377 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1955 26335 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1956 26327 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1957 26300 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1958 26290 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1959 26287 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1960 26282 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1961 26278 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1962 26273 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1963 26256 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1964 26246 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1965 26238 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1966 26236 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1967 26226 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1968 26225 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1969 26215 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1970 26214 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1971 26188 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1972 26185 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1973 26178 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1974 26170 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1975 26167 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1976 26141 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1977 26138 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1978 26123 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1979 26115 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1980 26106 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1981 26089 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1982 26086 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1983 26080 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1984 26031 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1985 26022 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1986 26020 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1987 26018 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1988 26008 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1989 26002 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1990 25996 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1991 25955 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1992 25947 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1993 25946 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1994 25945 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1995 25915 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1996 25898 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1997 25880 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1998 25842 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.1999 25837 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2000 25833 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2001 25824 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2002 25809 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2003 25762 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2004 25742 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2005 25699 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2006 25692 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2007 25684 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2008 25668 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2009 25635 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2010 25625 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2011 25624 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2012 25597 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2013 25571 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2014 25546 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2015 25538 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2016 25531 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2017 25525 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2018 25504 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2019 25488 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2020 25460 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2021 25422 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2022 25363 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2023 25350 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2024 25349 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2025 25332 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2026 25308 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2027 25305 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2028 25300 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2029 25300 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2030 25294 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2031 25280 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2032 25275 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2033 25235 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2034 25233 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2035 25229 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2036 25216 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2037 25207 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2038 25197 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2039 25195 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2040 25181 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2041 25178 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2042 25172 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2043 25162 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2044 25160 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2045 25148 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2046 25143 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2047 25142 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2048 25132 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2049 25123 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2050 25122 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2051 25114 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2052 25109 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2053 25094 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2054 25042 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2055 25041 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2056 25002 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2057 24977 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2058 24962 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2059 24926 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2060 24922 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2061 24922 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2062 24913 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2063 24905 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2064 24875 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2065 24873 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2066 24868 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2067 24813 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2068 24808 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2069 24800 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2070 24788 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2071 24788 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2072 24788 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2073 24779 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2074 24779 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2075 24746 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2076 24741 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2077 24708 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2078 24706 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2079 24667 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2080 24664 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2081 24644 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2082 24623 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2083 24610 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2084 24608 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2085 24606 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2086 24598 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2087 24587 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2088 24560 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2089 24555 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2090 24526 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2091 24525 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2092 24498 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2093 24491 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2094 24430 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2095 24407 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2096 24405 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2097 24398 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2098 24392 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2099 24373 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2100 24370 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2101 24319 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2102 24311 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2103 24293 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2104 24278 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2105 24268 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2106 24259 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2107 24222 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2108 24220 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2109 24203 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2110 24195 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2111 24192 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2112 24189 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2113 24176 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2114 24150 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2115 24103 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2116 24092 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2117 24088 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2118 24076 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2119 24041 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2120 24033 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2121 24024 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2122 24019 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2123 24002 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2124 23877 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2125 23856 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2126 23853 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2127 23844 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2128 23838 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2129 23833 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2130 23806 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2131 23805 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2132 23773 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2133 23770 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2134 23761 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2135 23740 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2136 23737 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2137 23736 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2138 23730 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2139 23730 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2140 23718 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2141 23681 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2142 23681 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2143 23667 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2144 23654 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2145 23641 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2146 23641 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2147 23619 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2148 23612 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2149 23598 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2150 23552 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2151 23545 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2152 23543 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2153 23505 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2154 23503 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2155 23501 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2156 23465 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2157 23464 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2158 23451 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2159 23449 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2160 23415 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2161 23404 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2162 23381 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2163 23378 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2164 23373 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2165 23351 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2166 23350 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2167 23337 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2168 23330 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2169 23328 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2170 23296 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2171 23270 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2172 23269 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2173 23255 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2174 23219 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2175 23193 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2176 23175 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2177 23150 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2178 23140 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2179 23122 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2180 23120 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2181 23093 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2182 23092 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2183 23084 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2184 23084 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2185 23065 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2186 23029 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2187 22982 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2188 22971 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2189 22970 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2190 22968 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2191 22963 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2192 22953 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2193 22947 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2194 22945 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2195 22940 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2196 22929 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2197 22904 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2198 22877 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.2199 22853 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/gbdb/bosTau4/bosTau4.2bit +chrUn.004.11725 1034 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11726 1034 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11727 1033 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11728 1033 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11729 1033 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11730 1033 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11731 1033 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11732 1032 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11733 1032 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11734 1032 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11735 1032 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11736 1031 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11737 1031 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11738 1031 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11739 1030 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11740 1030 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11741 1030 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11742 1030 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11743 1030 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11744 1030 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11745 1030 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11746 1030 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11747 1029 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11748 1029 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11749 1028 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11750 1028 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11751 1027 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11752 1027 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11753 1026 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11754 1026 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11755 1026 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11756 1026 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11757 1026 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11758 1026 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11759 1025 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11760 1024 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11761 1024 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11762 1023 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11763 1023 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11764 1023 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11765 1023 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11766 1023 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11767 1023 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11768 1023 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11769 1022 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11770 1021 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11771 1021 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11772 1021 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11773 1021 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11774 1021 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11775 1021 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11776 1020 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11777 1019 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11778 1018 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11779 1017 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11780 1017 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11781 1016 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11782 1016 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11783 1016 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11784 1016 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11785 1015 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11786 1015 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11787 1014 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11788 1013 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11789 1013 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11790 1013 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11791 1013 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11792 1012 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11793 1012 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11794 1012 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11795 1012 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11796 1011 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11797 1011 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11798 1011 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11799 1010 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11800 1009 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11801 1009 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11802 1009 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11803 1009 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11804 1008 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11805 1008 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11806 1006 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11807 1006 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11808 1006 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11809 1006 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11810 1006 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11811 1005 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11812 1005 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11813 1005 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11814 1004 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11815 1004 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11816 1003 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11817 1003 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11818 1003 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11819 1002 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11820 1002 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11821 1001 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11822 1001 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11823 1000 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11824 1000 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11825 1000 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11826 999 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11827 999 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11828 999 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11829 999 /gbdb/bosTau4/bosTau4.2bit +chrUn.004.11830 999 /gbdb/bosTau4/bosTau4.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/cb3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/cb3.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,13 @@ +chrI 11274843 /gbdb/cb3/cb3.2bit +chrII 14512975 /gbdb/cb3/cb3.2bit +chrIII 13544562 /gbdb/cb3/cb3.2bit +chrIII_random 864856 /gbdb/cb3/cb3.2bit +chrII_random 2252910 /gbdb/cb3/cb3.2bit +chrIV 15290274 /gbdb/cb3/cb3.2bit +chrIV_random 751081 /gbdb/cb3/cb3.2bit +chrI_random 3509021 /gbdb/cb3/cb3.2bit +chrUn 7311690 /gbdb/cb3/cb3.2bit +chrV 16004101 /gbdb/cb3/cb3.2bit +chrV_random 2554181 /gbdb/cb3/cb3.2bit +chrX 20608032 /gbdb/cb3/cb3.2bit +chrM 14420 /gbdb/cb3/cb3.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/ce4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/ce4.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,7 @@ +chrI 15072419 /gbdb/ce4/ce4.2bit +chrII 15279316 /gbdb/ce4/ce4.2bit +chrIII 13783681 /gbdb/ce4/ce4.2bit +chrIV 17493784 /gbdb/ce4/ce4.2bit +chrM 13794 /gbdb/ce4/ce4.2bit +chrV 20919398 /gbdb/ce4/ce4.2bit +chrX 17718852 /gbdb/ce4/ce4.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/ce6.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/ce6.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,7 @@ +chrV 20919568 /gbdb/ce6/ce6.2bit +chrX 17718854 /gbdb/ce6/ce6.2bit +chrIV 17493785 /gbdb/ce6/ce6.2bit +chrII 15279323 /gbdb/ce6/ce6.2bit +chrI 15072421 /gbdb/ce6/ce6.2bit +chrIII 13783681 /gbdb/ce6/ce6.2bit +chrM 13794 /gbdb/ce6/ce6.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/danRer5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/danRer5.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,5036 @@ +chr5 70371393 /gbdb/danRer5/danRer5.2bit +chr7 70262009 /gbdb/danRer5/danRer5.2bit +chr3 62931207 /gbdb/danRer5/danRer5.2bit +chr6 59200669 /gbdb/danRer5/danRer5.2bit +chr20 56528676 /gbdb/danRer5/danRer5.2bit +chr14 56522864 /gbdb/danRer5/danRer5.2bit +chr8 56456705 /gbdb/danRer5/danRer5.2bit +chr1 56204684 /gbdb/danRer5/danRer5.2bit +chr2 54366722 /gbdb/danRer5/danRer5.2bit +chr13 53547397 /gbdb/danRer5/danRer5.2bit +chr16 53070661 /gbdb/danRer5/danRer5.2bit +chr17 52310423 /gbdb/danRer5/danRer5.2bit +chr9 51490918 /gbdb/danRer5/danRer5.2bit +chr18 49281368 /gbdb/danRer5/danRer5.2bit +chr12 47523734 /gbdb/danRer5/danRer5.2bit +chr15 46629432 /gbdb/danRer5/danRer5.2bit +chr23 46388020 /gbdb/danRer5/danRer5.2bit +chr19 46181231 /gbdb/danRer5/danRer5.2bit +chr21 46057314 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/gbdb/danRer5/danRer5.2bit +Zv7_NA2731 2008 /gbdb/danRer5/danRer5.2bit +Zv7_NA1937 2007 /gbdb/danRer5/danRer5.2bit +Zv7_NA2440 2007 /gbdb/danRer5/danRer5.2bit +Zv7_NA5765 2007 /gbdb/danRer5/danRer5.2bit +Zv7_NA6991 2007 /gbdb/danRer5/danRer5.2bit +Zv7_NA3686 2006 /gbdb/danRer5/danRer5.2bit +Zv7_NA4025 2006 /gbdb/danRer5/danRer5.2bit +Zv7_NA4956 2006 /gbdb/danRer5/danRer5.2bit +Zv7_NA5550 2006 /gbdb/danRer5/danRer5.2bit +Zv7_NA7269 2006 /gbdb/danRer5/danRer5.2bit +Zv7_NA7382 2006 /gbdb/danRer5/danRer5.2bit +Zv7_NA7682 2006 /gbdb/danRer5/danRer5.2bit +Zv7_NA3720 2005 /gbdb/danRer5/danRer5.2bit +Zv7_NA4776 2005 /gbdb/danRer5/danRer5.2bit +Zv7_NA2705 2004 /gbdb/danRer5/danRer5.2bit +Zv7_NA3538 2004 /gbdb/danRer5/danRer5.2bit +Zv7_NA1234 2003 /gbdb/danRer5/danRer5.2bit +Zv7_NA2544 2003 /gbdb/danRer5/danRer5.2bit +Zv7_NA2627 2003 /gbdb/danRer5/danRer5.2bit +Zv7_NA2720 2003 /gbdb/danRer5/danRer5.2bit +Zv7_NA4748 2003 /gbdb/danRer5/danRer5.2bit +Zv7_NA1523 2002 /gbdb/danRer5/danRer5.2bit +Zv7_NA1533 2002 /gbdb/danRer5/danRer5.2bit +Zv7_NA2719 2002 /gbdb/danRer5/danRer5.2bit +Zv7_NA2729 2001 /gbdb/danRer5/danRer5.2bit +Zv7_NA1247 2000 /gbdb/danRer5/danRer5.2bit +Zv7_NA5415 2000 /gbdb/danRer5/danRer5.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/danRer6.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/danRer6.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,11724 @@ +chr7 76918211 /gbdb/danRer6/danRer6.2bit +chr5 74451498 /gbdb/danRer6/danRer6.2bit +chr4 71658100 /gbdb/danRer6/danRer6.2bit +chr6 61647013 /gbdb/danRer6/danRer6.2bit +chr3 60907308 /gbdb/danRer6/danRer6.2bit +chr1 59305620 /gbdb/danRer6/danRer6.2bit +chr2 58009534 /gbdb/danRer6/danRer6.2bit +chr8 55568185 /gbdb/danRer6/danRer6.2bit +chr9 54736511 /gbdb/danRer6/danRer6.2bit +chr14 52930158 /gbdb/danRer6/danRer6.2bit +chr16 51890894 /gbdb/danRer6/danRer6.2bit +chr20 51884995 /gbdb/danRer6/danRer6.2bit +chr13 50748729 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/gbdb/danRer6/danRer6.2bit +Zv8_NA6090 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA6924 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA7204 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA7870 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA8173 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA8183 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA8193 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA8225 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA8301 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA8791 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA9068 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA9122 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA9604 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA9751 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA9892 2000 /gbdb/danRer6/danRer6.2bit +Zv8_NA9916 2000 /gbdb/danRer6/danRer6.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/danRer7.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/danRer7.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,1133 @@ +chr7 77276063 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/gbdb/danRer7/danRer7.2bit +Zv9_NA7 5401 /gbdb/danRer7/danRer7.2bit +Zv9_NA539 5114 /gbdb/danRer7/danRer7.2bit +Zv9_NA884 4454 /gbdb/danRer7/danRer7.2bit +Zv9_NA18 4371 /gbdb/danRer7/danRer7.2bit +Zv9_NA987 4206 /gbdb/danRer7/danRer7.2bit +Zv9_NA978 3784 /gbdb/danRer7/danRer7.2bit +Zv9_NA157 3679 /gbdb/danRer7/danRer7.2bit +Zv9_NA334 3679 /gbdb/danRer7/danRer7.2bit +Zv9_NA891 3607 /gbdb/danRer7/danRer7.2bit +Zv9_NA902 3484 /gbdb/danRer7/danRer7.2bit +Zv9_NA920 3455 /gbdb/danRer7/danRer7.2bit +Zv9_NA877 3381 /gbdb/danRer7/danRer7.2bit +Zv9_NA796 3298 /gbdb/danRer7/danRer7.2bit +Zv9_NA945 3228 /gbdb/danRer7/danRer7.2bit +Zv9_NA946 3086 /gbdb/danRer7/danRer7.2bit +Zv9_NA949 3033 /gbdb/danRer7/danRer7.2bit +Zv9_NA933 3012 /gbdb/danRer7/danRer7.2bit +Zv9_NA951 2975 /gbdb/danRer7/danRer7.2bit +Zv9_NA957 2866 /gbdb/danRer7/danRer7.2bit +Zv9_NA971 2865 /gbdb/danRer7/danRer7.2bit +Zv9_NA960 2671 /gbdb/danRer7/danRer7.2bit +Zv9_NA954 2620 /gbdb/danRer7/danRer7.2bit +Zv9_NA912 2460 /gbdb/danRer7/danRer7.2bit +Zv9_NA712 2434 /gbdb/danRer7/danRer7.2bit +Zv9_NA961 2357 /gbdb/danRer7/danRer7.2bit +Zv9_NA988 2311 /gbdb/danRer7/danRer7.2bit +Zv9_NA977 2246 /gbdb/danRer7/danRer7.2bit +Zv9_NA932 2185 /gbdb/danRer7/danRer7.2bit +Zv9_NA993 2100 /gbdb/danRer7/danRer7.2bit +Zv9_NA943 2065 /gbdb/danRer7/danRer7.2bit +Zv9_NA462 2052 /gbdb/danRer7/danRer7.2bit +Zv9_NA919 2001 /gbdb/danRer7/danRer7.2bit +Zv9_NA165 1990 /gbdb/danRer7/danRer7.2bit +Zv9_NA955 1989 /gbdb/danRer7/danRer7.2bit +Zv9_NA956 1989 /gbdb/danRer7/danRer7.2bit +Zv9_NA989 1920 /gbdb/danRer7/danRer7.2bit +Zv9_NA982 1919 /gbdb/danRer7/danRer7.2bit +Zv9_NA983 1919 /gbdb/danRer7/danRer7.2bit +Zv9_NA909 1916 /gbdb/danRer7/danRer7.2bit +Zv9_NA980 1872 /gbdb/danRer7/danRer7.2bit +Zv9_NA969 1853 /gbdb/danRer7/danRer7.2bit +Zv9_NA981 1813 /gbdb/danRer7/danRer7.2bit +Zv9_NA901 1786 /gbdb/danRer7/danRer7.2bit +Zv9_NA950 1755 /gbdb/danRer7/danRer7.2bit +Zv9_NA984 1745 /gbdb/danRer7/danRer7.2bit +Zv9_NA962 1732 /gbdb/danRer7/danRer7.2bit +Zv9_NA935 1714 /gbdb/danRer7/danRer7.2bit +Zv9_NA976 1692 /gbdb/danRer7/danRer7.2bit +Zv9_NA986 1639 /gbdb/danRer7/danRer7.2bit +Zv9_NA953 1633 /gbdb/danRer7/danRer7.2bit +Zv9_NA941 1591 /gbdb/danRer7/danRer7.2bit +Zv9_NA929 1577 /gbdb/danRer7/danRer7.2bit +Zv9_NA936 1530 /gbdb/danRer7/danRer7.2bit +Zv9_NA975 1452 /gbdb/danRer7/danRer7.2bit +Zv9_NA958 1428 /gbdb/danRer7/danRer7.2bit +Zv9_NA212 1347 /gbdb/danRer7/danRer7.2bit +Zv9_NA979 1346 /gbdb/danRer7/danRer7.2bit +Zv9_NA952 1326 /gbdb/danRer7/danRer7.2bit +Zv9_NA934 1266 /gbdb/danRer7/danRer7.2bit +Zv9_NA944 1251 /gbdb/danRer7/danRer7.2bit +Zv9_NA745 1198 /gbdb/danRer7/danRer7.2bit +Zv9_NA968 1173 /gbdb/danRer7/danRer7.2bit +Zv9_NA959 1142 /gbdb/danRer7/danRer7.2bit +Zv9_NA937 1137 /gbdb/danRer7/danRer7.2bit +Zv9_NA802 1126 /gbdb/danRer7/danRer7.2bit +Zv9_NA1000 942 /gbdb/danRer7/danRer7.2bit +Zv9_NA997 650 /gbdb/danRer7/danRer7.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/dm2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/dm2.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,13 @@ +chr4 1281640 /gbdb/dm2/nib/chr4.nib +chrM 19517 /gbdb/dm2/nib/chrM.nib +chrU 8724946 /gbdb/dm2/nib/chrU.nib +chrX 22224390 /gbdb/dm2/nib/chrX.nib +chr2L 22407834 /gbdb/dm2/nib/chr2L.nib +chr2R 20766785 /gbdb/dm2/nib/chr2R.nib +chr2h 1694122 /gbdb/dm2/nib/chr2h.nib +chr3L 23771897 /gbdb/dm2/nib/chr3L.nib +chr3R 27905053 /gbdb/dm2/nib/chr3R.nib +chr3h 2955737 /gbdb/dm2/nib/chr3h.nib +chr4h 88110 /gbdb/dm2/nib/chr4h.nib +chrXh 359526 /gbdb/dm2/nib/chrXh.nib +chrYh 396896 /gbdb/dm2/nib/chrYh.nib diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/dm3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/dm3.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,15 @@ +chr2L 23011544 /gbdb/dm3/dm3.2bit +chr2LHet 368872 /gbdb/dm3/dm3.2bit +chr2R 21146708 /gbdb/dm3/dm3.2bit +chr2RHet 3288761 /gbdb/dm3/dm3.2bit +chr3L 24543557 /gbdb/dm3/dm3.2bit +chr3LHet 2555491 /gbdb/dm3/dm3.2bit +chr3R 27905053 /gbdb/dm3/dm3.2bit +chr3RHet 2517507 /gbdb/dm3/dm3.2bit +chr4 1351857 /gbdb/dm3/dm3.2bit +chrU 10049037 /gbdb/dm3/dm3.2bit +chrUextra 29004656 /gbdb/dm3/dm3.2bit +chrX 22422827 /gbdb/dm3/dm3.2bit +chrXHet 204112 /gbdb/dm3/dm3.2bit +chrYHet 347038 /gbdb/dm3/dm3.2bit +chrM 19517 /gbdb/dm3/dm3.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/galGal2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/galGal2.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,54 @@ +chr1 188239860 /gbdb/galGal2/nib/chr1.nib +chr1_random 1356957 /gbdb/galGal2/nib/chr1_random.nib +chr10 20909726 /gbdb/galGal2/nib/chr10.nib +chr10_random 3871218 /gbdb/galGal2/nib/chr10_random.nib +chr11 19020054 /gbdb/galGal2/nib/chr11.nib +chr11_random 1153135 /gbdb/galGal2/nib/chr11_random.nib +chr12 19821895 /gbdb/galGal2/nib/chr12.nib +chr13 17279963 /gbdb/galGal2/nib/chr13.nib +chr13_random 1219686 /gbdb/galGal2/nib/chr13_random.nib +chr14 20603938 /gbdb/galGal2/nib/chr14.nib +chr15 12438626 /gbdb/galGal2/nib/chr15.nib +chr16 239457 /gbdb/galGal2/nib/chr16.nib +chr16_random 1085578 /gbdb/galGal2/nib/chr16_random.nib +chr17 10632206 /gbdb/galGal2/nib/chr17.nib +chr18 8919268 /gbdb/galGal2/nib/chr18.nib +chr19 9463882 /gbdb/galGal2/nib/chr19.nib +chr2 147590765 /gbdb/galGal2/nib/chr2.nib +chr2_random 125104 /gbdb/galGal2/nib/chr2_random.nib +chr20 13506680 /gbdb/galGal2/nib/chr20.nib +chr21 6202554 /gbdb/galGal2/nib/chr21.nib +chr22 2228820 /gbdb/galGal2/nib/chr22.nib +chr23 5666127 /gbdb/galGal2/nib/chr23.nib +chr24 5910111 /gbdb/galGal2/nib/chr24.nib +chr24_random 149561 /gbdb/galGal2/nib/chr24_random.nib +chr26 4255270 /gbdb/galGal2/nib/chr26.nib +chr27 2668888 /gbdb/galGal2/nib/chr27.nib +chr27_random 721164 /gbdb/galGal2/nib/chr27_random.nib +chr28 4731479 /gbdb/galGal2/nib/chr28.nib +chr28_random 6240 /gbdb/galGal2/nib/chr28_random.nib +chr3 108638738 /gbdb/galGal2/nib/chr3.nib +chr3_random 1636275 /gbdb/galGal2/nib/chr3_random.nib +chr32 1018878 /gbdb/galGal2/nib/chr32.nib +chr32_random 61160 /gbdb/galGal2/nib/chr32_random.nib +chr4 90634903 /gbdb/galGal2/nib/chr4.nib +chr4_random 1174127 /gbdb/galGal2/nib/chr4_random.nib +chr5 56310377 /gbdb/galGal2/nib/chr5.nib +chr5_random 54865 /gbdb/galGal2/nib/chr5_random.nib +chr6 33893787 /gbdb/galGal2/nib/chr6.nib +chr6_random 3628 /gbdb/galGal2/nib/chr6_random.nib +chr7 37338262 /gbdb/galGal2/nib/chr7.nib +chr7_random 2315 /gbdb/galGal2/nib/chr7_random.nib +chr8 30024636 /gbdb/galGal2/nib/chr8.nib +chr8_random 15783 /gbdb/galGal2/nib/chr8_random.nib +chr9 23409228 /gbdb/galGal2/nib/chr9.nib +chrE22C19W28 70504 /gbdb/galGal2/nib/chrE22C19W28.nib +chrE26C13 231937 /gbdb/galGal2/nib/chrE26C13.nib +chrE50C23 21569 /gbdb/galGal2/nib/chrE50C23.nib +chrE64 1525 /gbdb/galGal2/nib/chrE64.nib +chrM 16775 /gbdb/galGal2/nib/chrM.nib +chrUn 165033910 /gbdb/galGal2/nib/chrUn.nib +chrW 4916845 /gbdb/galGal2/nib/chrW.nib +chrW_random 455598 /gbdb/galGal2/nib/chrW_random.nib +chrZ 33651169 /gbdb/galGal2/nib/chrZ.nib +chrZ_random 14994570 /gbdb/galGal2/nib/chrZ_random.nib diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/galGal3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/galGal3.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,57 @@ +chr1 200994015 /gbdb/galGal3/galGal3.2bit +chr1_random 222095 /gbdb/galGal3/galGal3.2bit +chr10 22556432 /gbdb/galGal3/galGal3.2bit +chr10_random 13679 /gbdb/galGal3/galGal3.2bit +chr11 21928095 /gbdb/galGal3/galGal3.2bit +chr11_random 72667 /gbdb/galGal3/galGal3.2bit +chr12 20536687 /gbdb/galGal3/galGal3.2bit +chr12_random 7060 /gbdb/galGal3/galGal3.2bit +chr13 18911934 /gbdb/galGal3/galGal3.2bit +chr13_random 35775 /gbdb/galGal3/galGal3.2bit +chr14 15819469 /gbdb/galGal3/galGal3.2bit +chr15 12968165 /gbdb/galGal3/galGal3.2bit +chr16 432983 /gbdb/galGal3/galGal3.2bit +chr16_random 246252 /gbdb/galGal3/galGal3.2bit +chr17 11182526 /gbdb/galGal3/galGal3.2bit +chr17_random 2911 /gbdb/galGal3/galGal3.2bit +chr18 10925261 /gbdb/galGal3/galGal3.2bit +chr18_random 11891 /gbdb/galGal3/galGal3.2bit +chr19 9939723 /gbdb/galGal3/galGal3.2bit +chr2 154873767 /gbdb/galGal3/galGal3.2bit +chr2_random 142837 /gbdb/galGal3/galGal3.2bit +chr20 13986235 /gbdb/galGal3/galGal3.2bit +chr20_random 75095 /gbdb/galGal3/galGal3.2bit +chr21 6959642 /gbdb/galGal3/galGal3.2bit +chr22 3936574 /gbdb/galGal3/galGal3.2bit +chr22_random 156216 /gbdb/galGal3/galGal3.2bit +chr23 6042217 /gbdb/galGal3/galGal3.2bit +chr24 6400109 /gbdb/galGal3/galGal3.2bit +chr25 2031799 /gbdb/galGal3/galGal3.2bit +chr25_random 80372 /gbdb/galGal3/galGal3.2bit +chr26 5102438 /gbdb/galGal3/galGal3.2bit +chr27 4841970 /gbdb/galGal3/galGal3.2bit +chr28 4512026 /gbdb/galGal3/galGal3.2bit +chr28_random 105415 /gbdb/galGal3/galGal3.2bit +chr3 113657789 /gbdb/galGal3/galGal3.2bit +chr32 1028 /gbdb/galGal3/galGal3.2bit +chr4 94230402 /gbdb/galGal3/galGal3.2bit +chr4_random 180706 /gbdb/galGal3/galGal3.2bit +chr5 62238931 /gbdb/galGal3/galGal3.2bit +chr5_random 27907 /gbdb/galGal3/galGal3.2bit +chr6 37400442 /gbdb/galGal3/galGal3.2bit +chr6_random 34212 /gbdb/galGal3/galGal3.2bit +chr7 38384769 /gbdb/galGal3/galGal3.2bit +chr7_random 104000 /gbdb/galGal3/galGal3.2bit +chr8 30671729 /gbdb/galGal3/galGal3.2bit +chr8_random 420759 /gbdb/galGal3/galGal3.2bit +chr9 25554352 /gbdb/galGal3/galGal3.2bit +chrE22C19W28_E50C23 895237 /gbdb/galGal3/galGal3.2bit +chrE22C19W28_E50C23_random 191099 /gbdb/galGal3/galGal3.2bit +chrE64 49846 /gbdb/galGal3/galGal3.2bit +chrE64_random 557643 /gbdb/galGal3/galGal3.2bit +chrM 16775 /gbdb/galGal3/galGal3.2bit +chrUn_random 63870806 /gbdb/galGal3/galGal3.2bit +chrW 259642 /gbdb/galGal3/galGal3.2bit +chrW_random 729481 /gbdb/galGal3/galGal3.2bit +chrZ 74602320 /gbdb/galGal3/galGal3.2bit +chrZ_random 346234 /gbdb/galGal3/galGal3.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/hg18.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/hg18.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,49 @@ +chr1 247249719 /gbdb/hg18/nib/chr1.nib +chr1_random 1663265 /gbdb/hg18/nib/chr1_random.nib +chr10 135374737 /gbdb/hg18/nib/chr10.nib +chr10_random 113275 /gbdb/hg18/nib/chr10_random.nib +chr11 134452384 /gbdb/hg18/nib/chr11.nib +chr11_random 215294 /gbdb/hg18/nib/chr11_random.nib +chr12 132349534 /gbdb/hg18/nib/chr12.nib +chr13 114142980 /gbdb/hg18/nib/chr13.nib +chr13_random 186858 /gbdb/hg18/nib/chr13_random.nib +chr14 106368585 /gbdb/hg18/nib/chr14.nib +chr15 100338915 /gbdb/hg18/nib/chr15.nib +chr15_random 784346 /gbdb/hg18/nib/chr15_random.nib +chr16 88827254 /gbdb/hg18/nib/chr16.nib +chr16_random 105485 /gbdb/hg18/nib/chr16_random.nib +chr17 78774742 /gbdb/hg18/nib/chr17.nib +chr17_random 2617613 /gbdb/hg18/nib/chr17_random.nib +chr18 76117153 /gbdb/hg18/nib/chr18.nib +chr18_random 4262 /gbdb/hg18/nib/chr18_random.nib +chr19 63811651 /gbdb/hg18/nib/chr19.nib +chr19_random 301858 /gbdb/hg18/nib/chr19_random.nib +chr2 242951149 /gbdb/hg18/nib/chr2.nib +chr2_random 185571 /gbdb/hg18/nib/chr2_random.nib +chr20 62435964 /gbdb/hg18/nib/chr20.nib +chr21 46944323 /gbdb/hg18/nib/chr21.nib +chr21_random 1679693 /gbdb/hg18/nib/chr21_random.nib +chr22 49691432 /gbdb/hg18/nib/chr22.nib +chr22_random 257318 /gbdb/hg18/nib/chr22_random.nib +chr22_h2_hap1 63661 /gbdb/hg18/nib/chr22_h2_hap1.nib +chr3 199501827 /gbdb/hg18/nib/chr3.nib +chr3_random 749256 /gbdb/hg18/nib/chr3_random.nib +chr4 191273063 /gbdb/hg18/nib/chr4.nib +chr4_random 842648 /gbdb/hg18/nib/chr4_random.nib +chr5 180857866 /gbdb/hg18/nib/chr5.nib +chr5_random 143687 /gbdb/hg18/nib/chr5_random.nib +chr5_h2_hap1 1794870 /gbdb/hg18/nib/chr5_h2_hap1.nib +chr6 170899992 /gbdb/hg18/nib/chr6.nib +chr6_random 1875562 /gbdb/hg18/nib/chr6_random.nib +chr6_cox_hap1 4731698 /gbdb/hg18/nib/chr6_cox_hap1.nib +chr6_qbl_hap2 4565931 /gbdb/hg18/nib/chr6_qbl_hap2.nib +chr7 158821424 /gbdb/hg18/nib/chr7.nib +chr7_random 549659 /gbdb/hg18/nib/chr7_random.nib +chr8 146274826 /gbdb/hg18/nib/chr8.nib +chr8_random 943810 /gbdb/hg18/nib/chr8_random.nib +chr9 140273252 /gbdb/hg18/nib/chr9.nib +chr9_random 1146434 /gbdb/hg18/nib/chr9_random.nib +chrM 16571 /gbdb/hg18/nib/chrM.nib +chrX 154913754 /gbdb/hg18/nib/chrX.nib +chrX_random 1719168 /gbdb/hg18/nib/chrX_random.nib +chrY 57772954 /gbdb/hg18/nib/chrY.nib diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/hg19.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/hg19.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,93 @@ +chr1 249250621 /gbdb/hg19/hg19.2bit +chr2 243199373 /gbdb/hg19/hg19.2bit +chr3 198022430 /gbdb/hg19/hg19.2bit +chr4 191154276 /gbdb/hg19/hg19.2bit +chr5 180915260 /gbdb/hg19/hg19.2bit +chr6 171115067 /gbdb/hg19/hg19.2bit +chr7 159138663 /gbdb/hg19/hg19.2bit +chrX 155270560 /gbdb/hg19/hg19.2bit +chr8 146364022 /gbdb/hg19/hg19.2bit +chr9 141213431 /gbdb/hg19/hg19.2bit +chr10 135534747 /gbdb/hg19/hg19.2bit +chr11 135006516 /gbdb/hg19/hg19.2bit +chr12 133851895 /gbdb/hg19/hg19.2bit +chr13 115169878 /gbdb/hg19/hg19.2bit +chr14 107349540 /gbdb/hg19/hg19.2bit +chr15 102531392 /gbdb/hg19/hg19.2bit +chr16 90354753 /gbdb/hg19/hg19.2bit +chr17 81195210 /gbdb/hg19/hg19.2bit +chr18 78077248 /gbdb/hg19/hg19.2bit +chr20 63025520 /gbdb/hg19/hg19.2bit +chrY 59373566 /gbdb/hg19/hg19.2bit +chr19 59128983 /gbdb/hg19/hg19.2bit +chr22 51304566 /gbdb/hg19/hg19.2bit +chr21 48129895 /gbdb/hg19/hg19.2bit +chr6_ssto_hap7 4928567 /gbdb/hg19/hg19.2bit +chr6_mcf_hap5 4833398 /gbdb/hg19/hg19.2bit +chr6_cox_hap2 4795371 /gbdb/hg19/hg19.2bit +chr6_mann_hap4 4683263 /gbdb/hg19/hg19.2bit +chr6_apd_hap1 4622290 /gbdb/hg19/hg19.2bit +chr6_qbl_hap6 4611984 /gbdb/hg19/hg19.2bit +chr6_dbb_hap3 4610396 /gbdb/hg19/hg19.2bit +chr17_ctg5_hap1 1680828 /gbdb/hg19/hg19.2bit +chr4_ctg9_hap1 590426 /gbdb/hg19/hg19.2bit +chr1_gl000192_random 547496 /gbdb/hg19/hg19.2bit +chrUn_gl000225 211173 /gbdb/hg19/hg19.2bit +chr4_gl000194_random 191469 /gbdb/hg19/hg19.2bit +chr4_gl000193_random 189789 /gbdb/hg19/hg19.2bit +chr9_gl000200_random 187035 /gbdb/hg19/hg19.2bit +chrUn_gl000222 186861 /gbdb/hg19/hg19.2bit +chrUn_gl000212 186858 /gbdb/hg19/hg19.2bit +chr7_gl000195_random 182896 /gbdb/hg19/hg19.2bit +chrUn_gl000223 180455 /gbdb/hg19/hg19.2bit +chrUn_gl000224 179693 /gbdb/hg19/hg19.2bit +chrUn_gl000219 179198 /gbdb/hg19/hg19.2bit +chr17_gl000205_random 174588 /gbdb/hg19/hg19.2bit +chrUn_gl000215 172545 /gbdb/hg19/hg19.2bit +chrUn_gl000216 172294 /gbdb/hg19/hg19.2bit +chrUn_gl000217 172149 /gbdb/hg19/hg19.2bit +chr9_gl000199_random 169874 /gbdb/hg19/hg19.2bit +chrUn_gl000211 166566 /gbdb/hg19/hg19.2bit +chrUn_gl000213 164239 /gbdb/hg19/hg19.2bit +chrUn_gl000220 161802 /gbdb/hg19/hg19.2bit +chrUn_gl000218 161147 /gbdb/hg19/hg19.2bit +chr19_gl000209_random 159169 /gbdb/hg19/hg19.2bit +chrUn_gl000221 155397 /gbdb/hg19/hg19.2bit +chrUn_gl000214 137718 /gbdb/hg19/hg19.2bit +chrUn_gl000228 129120 /gbdb/hg19/hg19.2bit +chrUn_gl000227 128374 /gbdb/hg19/hg19.2bit +chr1_gl000191_random 106433 /gbdb/hg19/hg19.2bit +chr19_gl000208_random 92689 /gbdb/hg19/hg19.2bit +chr9_gl000198_random 90085 /gbdb/hg19/hg19.2bit +chr17_gl000204_random 81310 /gbdb/hg19/hg19.2bit +chrUn_gl000233 45941 /gbdb/hg19/hg19.2bit +chrUn_gl000237 45867 /gbdb/hg19/hg19.2bit +chrUn_gl000230 43691 /gbdb/hg19/hg19.2bit +chrUn_gl000242 43523 /gbdb/hg19/hg19.2bit +chrUn_gl000243 43341 /gbdb/hg19/hg19.2bit +chrUn_gl000241 42152 /gbdb/hg19/hg19.2bit +chrUn_gl000236 41934 /gbdb/hg19/hg19.2bit +chrUn_gl000240 41933 /gbdb/hg19/hg19.2bit +chr17_gl000206_random 41001 /gbdb/hg19/hg19.2bit +chrUn_gl000232 40652 /gbdb/hg19/hg19.2bit +chrUn_gl000234 40531 /gbdb/hg19/hg19.2bit +chr11_gl000202_random 40103 /gbdb/hg19/hg19.2bit +chrUn_gl000238 39939 /gbdb/hg19/hg19.2bit +chrUn_gl000244 39929 /gbdb/hg19/hg19.2bit +chrUn_gl000248 39786 /gbdb/hg19/hg19.2bit +chr8_gl000196_random 38914 /gbdb/hg19/hg19.2bit +chrUn_gl000249 38502 /gbdb/hg19/hg19.2bit +chrUn_gl000246 38154 /gbdb/hg19/hg19.2bit +chr17_gl000203_random 37498 /gbdb/hg19/hg19.2bit +chr8_gl000197_random 37175 /gbdb/hg19/hg19.2bit +chrUn_gl000245 36651 /gbdb/hg19/hg19.2bit +chrUn_gl000247 36422 /gbdb/hg19/hg19.2bit +chr9_gl000201_random 36148 /gbdb/hg19/hg19.2bit +chrUn_gl000235 34474 /gbdb/hg19/hg19.2bit +chrUn_gl000239 33824 /gbdb/hg19/hg19.2bit +chr21_gl000210_random 27682 /gbdb/hg19/hg19.2bit +chrUn_gl000231 27386 /gbdb/hg19/hg19.2bit +chrUn_gl000229 19913 /gbdb/hg19/hg19.2bit +chrM 16571 /gbdb/hg19/hg19.2bit +chrUn_gl000226 15008 /gbdb/hg19/hg19.2bit +chr18_gl000207_random 4262 /gbdb/hg19/hg19.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/mm8.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/mm8.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,34 @@ +chr1 197069962 /gbdb/mm8/mm8.2bit +chr2 181976762 /gbdb/mm8/mm8.2bit +chr3 159872112 /gbdb/mm8/mm8.2bit +chr4 155029701 /gbdb/mm8/mm8.2bit +chr5 152003063 /gbdb/mm8/mm8.2bit +chr6 149525685 /gbdb/mm8/mm8.2bit +chr7 145134094 /gbdb/mm8/mm8.2bit +chr8 132085098 /gbdb/mm8/mm8.2bit +chr9 124000669 /gbdb/mm8/mm8.2bit +chrM 16299 /gbdb/mm8/mm8.2bit +chrX 165556469 /gbdb/mm8/mm8.2bit +chrY 16029404 /gbdb/mm8/mm8.2bit +chr10 129959148 /gbdb/mm8/mm8.2bit +chr11 121798632 /gbdb/mm8/mm8.2bit +chr12 120463159 /gbdb/mm8/mm8.2bit +chr13 120614378 /gbdb/mm8/mm8.2bit +chr14 123978870 /gbdb/mm8/mm8.2bit +chr15 103492577 /gbdb/mm8/mm8.2bit +chr16 98252459 /gbdb/mm8/mm8.2bit +chr17 95177420 /gbdb/mm8/mm8.2bit +chr18 90736837 /gbdb/mm8/mm8.2bit +chr19 61321190 /gbdb/mm8/mm8.2bit +chr1_random 172274 /gbdb/mm8/mm8.2bit +chr5_random 2921247 /gbdb/mm8/mm8.2bit +chr7_random 243910 /gbdb/mm8/mm8.2bit +chr8_random 206961 /gbdb/mm8/mm8.2bit +chr9_random 17232 /gbdb/mm8/mm8.2bit +chrX_random 39696 /gbdb/mm8/mm8.2bit +chrY_random 14577732 /gbdb/mm8/mm8.2bit +chr10_random 10781 /gbdb/mm8/mm8.2bit +chr13_random 436191 /gbdb/mm8/mm8.2bit +chr15_random 105932 /gbdb/mm8/mm8.2bit +chr17_random 89091 /gbdb/mm8/mm8.2bit +chrUn_random 1540053 /gbdb/mm8/mm8.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/mm9.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/mm9.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,35 @@ +chr1 197195432 /gbdb/mm9/mm9.2bit +chr2 181748087 /gbdb/mm9/mm9.2bit +chr3 159599783 /gbdb/mm9/mm9.2bit +chr4 155630120 /gbdb/mm9/mm9.2bit +chr5 152537259 /gbdb/mm9/mm9.2bit +chr6 149517037 /gbdb/mm9/mm9.2bit +chr7 152524553 /gbdb/mm9/mm9.2bit +chr8 131738871 /gbdb/mm9/mm9.2bit +chr9 124076172 /gbdb/mm9/mm9.2bit +chr10 129993255 /gbdb/mm9/mm9.2bit +chr11 121843856 /gbdb/mm9/mm9.2bit +chr12 121257530 /gbdb/mm9/mm9.2bit +chr13 120284312 /gbdb/mm9/mm9.2bit +chr14 125194864 /gbdb/mm9/mm9.2bit +chr15 103494974 /gbdb/mm9/mm9.2bit +chr16 98319150 /gbdb/mm9/mm9.2bit +chr17 95272651 /gbdb/mm9/mm9.2bit +chr18 90772031 /gbdb/mm9/mm9.2bit +chr19 61342430 /gbdb/mm9/mm9.2bit +chrX 166650296 /gbdb/mm9/mm9.2bit +chrY 15902555 /gbdb/mm9/mm9.2bit +chrM 16299 /gbdb/mm9/mm9.2bit +chr13_random 400311 /gbdb/mm9/mm9.2bit +chr16_random 3994 /gbdb/mm9/mm9.2bit +chr17_random 628739 /gbdb/mm9/mm9.2bit +chr1_random 1231697 /gbdb/mm9/mm9.2bit +chr3_random 41899 /gbdb/mm9/mm9.2bit +chr4_random 160594 /gbdb/mm9/mm9.2bit +chr5_random 357350 /gbdb/mm9/mm9.2bit +chr7_random 362490 /gbdb/mm9/mm9.2bit +chr8_random 849593 /gbdb/mm9/mm9.2bit +chr9_random 449403 /gbdb/mm9/mm9.2bit +chrUn_random 5900358 /gbdb/mm9/mm9.2bit +chrX_random 1785075 /gbdb/mm9/mm9.2bit +chrY_random 58682461 /gbdb/mm9/mm9.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/panTro3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/panTro3.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,24132 @@ +chr2B 247518478 /gbdb/panTro3/panTro3.2bit +chr1 228333871 /gbdb/panTro3/panTro3.2bit +chr3 202329955 /gbdb/panTro3/panTro3.2bit +chr4 193495092 /gbdb/panTro3/panTro3.2bit +chr5 182651097 /gbdb/panTro3/panTro3.2bit +chr6 172623881 /gbdb/panTro3/panTro3.2bit +chr7 161824586 /gbdb/panTro3/panTro3.2bit +chrX 156848144 /gbdb/panTro3/panTro3.2bit +chr8 143986469 /gbdb/panTro3/panTro3.2bit +chr9 137840987 /gbdb/panTro3/panTro3.2bit +chr12 134246214 /gbdb/panTro3/panTro3.2bit +chr10 133524379 /gbdb/panTro3/panTro3.2bit +chr11 133121534 /gbdb/panTro3/panTro3.2bit +chr13 115123233 /gbdb/panTro3/panTro3.2bit +chr2A 113622374 /gbdb/panTro3/panTro3.2bit +chr14 106544938 /gbdb/panTro3/panTro3.2bit +chr15 99548318 /gbdb/panTro3/panTro3.2bit +chr16 89983829 /gbdb/panTro3/panTro3.2bit +chr17 82630442 /gbdb/panTro3/panTro3.2bit +chr18 76611499 /gbdb/panTro3/panTro3.2bit +chr19 63644993 /gbdb/panTro3/panTro3.2bit +chr20 61729293 /gbdb/panTro3/panTro3.2bit +chr22 49737984 /gbdb/panTro3/panTro3.2bit +chr21 32799110 /gbdb/panTro3/panTro3.2bit +chrY 23952694 /gbdb/panTro3/panTro3.2bit +chr13_GL392075_random 7510047 /gbdb/panTro3/panTro3.2bit +chr11_GL391837_random 5442033 /gbdb/panTro3/panTro3.2bit +chr6_GL390389_random 4046914 /gbdb/panTro3/panTro3.2bit +chr8_GL390916_random 3851136 /gbdb/panTro3/panTro3.2bit +chr10_GL391668_random 2614554 /gbdb/panTro3/panTro3.2bit +chrUn_GL393505 1195001 /gbdb/panTro3/panTro3.2bit +chr17_GL392652_random 1012752 /gbdb/panTro3/panTro3.2bit +chr19_GL392890_random 922365 /gbdb/panTro3/panTro3.2bit +chr4_GL389982_random 806427 /gbdb/panTro3/panTro3.2bit +chr9_GL391077_random 720526 /gbdb/panTro3/panTro3.2bit +chr15_GL392258_random 711350 /gbdb/panTro3/panTro3.2bit +chr17_GL392680_random 691484 /gbdb/panTro3/panTro3.2bit +chrUn_GL393516 597384 /gbdb/panTro3/panTro3.2bit +chrUn_GL393518 573897 /gbdb/panTro3/panTro3.2bit +chrUn_GL393522 458469 /gbdb/panTro3/panTro3.2bit +chr20_GL393023_random 436282 /gbdb/panTro3/panTro3.2bit +chr2A_GL389368_random 417915 /gbdb/panTro3/panTro3.2bit +chrUn_GL393519 413329 /gbdb/panTro3/panTro3.2bit +chr16_GL392457_random 408961 /gbdb/panTro3/panTro3.2bit +chrUn_GL393523 405060 /gbdb/panTro3/panTro3.2bit +chr7_GL390650_random 398731 /gbdb/panTro3/panTro3.2bit +chrUn_GL393524 393793 /gbdb/panTro3/panTro3.2bit +chr18_GL392798_random 373489 /gbdb/panTro3/panTro3.2bit +chrUn_GL393525 371432 /gbdb/panTro3/panTro3.2bit +chr16_GL392524_random 370847 /gbdb/panTro3/panTro3.2bit +chrX_GL393313_random 364597 /gbdb/panTro3/panTro3.2bit +chr20_GL393019_random 358895 /gbdb/panTro3/panTro3.2bit +chrUn_GL393530 355541 /gbdb/panTro3/panTro3.2bit +chrUn_GL393527 341619 /gbdb/panTro3/panTro3.2bit +chrUn_GL393542 339612 /gbdb/panTro3/panTro3.2bit +chrY_DP000056_random 331329 /gbdb/panTro3/panTro3.2bit +chr22_GL393078_random 277661 /gbdb/panTro3/panTro3.2bit +chrY_DP000055_random 276070 /gbdb/panTro3/panTro3.2bit +chr16_GL392506_random 257012 /gbdb/panTro3/panTro3.2bit +chrUn_GL393533 243864 /gbdb/panTro3/panTro3.2bit +chrUn_GL393535 241809 /gbdb/panTro3/panTro3.2bit +chr8_GL390880_random 230064 /gbdb/panTro3/panTro3.2bit +chr7_GL390654_random 229574 /gbdb/panTro3/panTro3.2bit +chrUn_GL393532 223908 /gbdb/panTro3/panTro3.2bit +chr14_GL392151_random 223111 /gbdb/panTro3/panTro3.2bit +chrUn_GL393534 222311 /gbdb/panTro3/panTro3.2bit +chr9_GL391203_random 222250 /gbdb/panTro3/panTro3.2bit +chr7_GL390752_random 218097 /gbdb/panTro3/panTro3.2bit +chrUn_GL393539 212451 /gbdb/panTro3/panTro3.2bit +chr17_GL392651_random 209936 /gbdb/panTro3/panTro3.2bit +chrUn_GL393541 207381 /gbdb/panTro3/panTro3.2bit +chrUn_GL393537 206612 /gbdb/panTro3/panTro3.2bit +chrUn_GL396822 202225 /gbdb/panTro3/panTro3.2bit +chrX_GL393375_random 197187 /gbdb/panTro3/panTro3.2bit +chrUn_GL393540 192064 /gbdb/panTro3/panTro3.2bit +chr1_GL389174_random 191010 /gbdb/panTro3/panTro3.2bit +chr10_GL391667_random 190155 /gbdb/panTro3/panTro3.2bit +chr17_GL392675_random 188176 /gbdb/panTro3/panTro3.2bit +chr15_GL392289_random 187897 /gbdb/panTro3/panTro3.2bit +chrUn_GL393544 186290 /gbdb/panTro3/panTro3.2bit +chr1_GL389091_random 179278 /gbdb/panTro3/panTro3.2bit +chr7_GL390665_random 176004 /gbdb/panTro3/panTro3.2bit +chrUn_GL393538 175724 /gbdb/panTro3/panTro3.2bit +chrUn_GL393536 173658 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149435_random 173505 /gbdb/panTro3/panTro3.2bit +chr13_GL392067_random 165683 /gbdb/panTro3/panTro3.2bit +chrY_GL393448_random 165288 /gbdb/panTro3/panTro3.2bit +chr16_GL392511_random 163909 /gbdb/panTro3/panTro3.2bit +chrUn_GL393529 163501 /gbdb/panTro3/panTro3.2bit +chr9_GL391240_random 153714 /gbdb/panTro3/panTro3.2bit +chrUn_GL393543 152085 /gbdb/panTro3/panTro3.2bit +chrUn_GL393548 149198 /gbdb/panTro3/panTro3.2bit +chrUn_GL393554 149188 /gbdb/panTro3/panTro3.2bit +chrUn_GL396923 147389 /gbdb/panTro3/panTro3.2bit +chr9_GL391093_random 147359 /gbdb/panTro3/panTro3.2bit +chrUn_GL393547 147173 /gbdb/panTro3/panTro3.2bit +chrUn_GL393531 146349 /gbdb/panTro3/panTro3.2bit +chr2B_GL389466_random 142960 /gbdb/panTro3/panTro3.2bit +chrUn_GL393546 140033 /gbdb/panTro3/panTro3.2bit +chrUn_GL397061 138811 /gbdb/panTro3/panTro3.2bit +chr5_GL390139_random 133348 /gbdb/panTro3/panTro3.2bit +chr17_GL392646_random 132219 /gbdb/panTro3/panTro3.2bit +chr14_GL392180_random 129696 /gbdb/panTro3/panTro3.2bit +chrUn_GL393453 129653 /gbdb/panTro3/panTro3.2bit +chrX_GL393432_random 129432 /gbdb/panTro3/panTro3.2bit +chrUn_GL393549 127063 /gbdb/panTro3/panTro3.2bit +chr9_GL391132_random 126499 /gbdb/panTro3/panTro3.2bit +chr1_GL389178_random 125691 /gbdb/panTro3/panTro3.2bit +chr9_GL391184_random 120749 /gbdb/panTro3/panTro3.2bit +chr6_GL390401_random 118306 /gbdb/panTro3/panTro3.2bit +chrUn_GL393583 117592 /gbdb/panTro3/panTro3.2bit +chrUn_GL393551 116345 /gbdb/panTro3/panTro3.2bit +chrUn_GL393550 115532 /gbdb/panTro3/panTro3.2bit +chr1_GL389150_random 113811 /gbdb/panTro3/panTro3.2bit +chr9_GL391076_random 111641 /gbdb/panTro3/panTro3.2bit +chr1_GL389083_random 110799 /gbdb/panTro3/panTro3.2bit +chrUn_GL397034 110431 /gbdb/panTro3/panTro3.2bit +chr16_GL392517_random 109449 /gbdb/panTro3/panTro3.2bit +chrUn_GL397015 108654 /gbdb/panTro3/panTro3.2bit +chr17_GL392695_random 108041 /gbdb/panTro3/panTro3.2bit +chr1_GL389157_random 107878 /gbdb/panTro3/panTro3.2bit +chrUn_GL393553 107211 /gbdb/panTro3/panTro3.2bit +chr7_GL390634_random 105805 /gbdb/panTro3/panTro3.2bit +chrUn_GL396741 104653 /gbdb/panTro3/panTro3.2bit +chr3_GL389630_random 103936 /gbdb/panTro3/panTro3.2bit +chr4_GL389940_random 103824 /gbdb/panTro3/panTro3.2bit +chrUn_GL393668 101613 /gbdb/panTro3/panTro3.2bit +chr4_GL389941_random 101566 /gbdb/panTro3/panTro3.2bit +chr8_GL390911_random 101433 /gbdb/panTro3/panTro3.2bit +chr7_GL390657_random 101353 /gbdb/panTro3/panTro3.2bit +chr10_GL391666_random 99606 /gbdb/panTro3/panTro3.2bit +chr1_GL389166_random 98911 /gbdb/panTro3/panTro3.2bit +chrUn_GL396999 98448 /gbdb/panTro3/panTro3.2bit +chr16_GL392406_random 98210 /gbdb/panTro3/panTro3.2bit +chrUn_GL393616 97347 /gbdb/panTro3/panTro3.2bit +chrUn_GL393459 94400 /gbdb/panTro3/panTro3.2bit +chr16_GL392405_random 94394 /gbdb/panTro3/panTro3.2bit +chr7_GL390732_random 93158 /gbdb/panTro3/panTro3.2bit +chr6_GL390393_random 92248 /gbdb/panTro3/panTro3.2bit +chr1_GL389238_random 90913 /gbdb/panTro3/panTro3.2bit +chr1_GL389196_random 90822 /gbdb/panTro3/panTro3.2bit +chr7_GL390754_random 89795 /gbdb/panTro3/panTro3.2bit +chr7_GL390641_random 89471 /gbdb/panTro3/panTro3.2bit +chrUn_GL393449 86740 /gbdb/panTro3/panTro3.2bit +chrUn_GL393450 85570 /gbdb/panTro3/panTro3.2bit +chr12_GL391951_random 84773 /gbdb/panTro3/panTro3.2bit +chr6_GL390400_random 84532 /gbdb/panTro3/panTro3.2bit +chr1_GL389173_random 83479 /gbdb/panTro3/panTro3.2bit +chrUn_GL394095 83109 /gbdb/panTro3/panTro3.2bit +chr7_GL390741_random 80601 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr4_GL389841_random 64713 /gbdb/panTro3/panTro3.2bit +chr7_GL390633_random 64443 /gbdb/panTro3/panTro3.2bit +chr6_GL390390_random 64356 /gbdb/panTro3/panTro3.2bit +chr1_GL389176_random 64349 /gbdb/panTro3/panTro3.2bit +chr16_GL392409_random 64049 /gbdb/panTro3/panTro3.2bit +chrUn_GL393462 63192 /gbdb/panTro3/panTro3.2bit +chr9_GL391127_random 62557 /gbdb/panTro3/panTro3.2bit +chr6_GL390396_random 62537 /gbdb/panTro3/panTro3.2bit +chr9_GL391222_random 62439 /gbdb/panTro3/panTro3.2bit +chrUn_GL394407 61854 /gbdb/panTro3/panTro3.2bit +chrUn_GL394083 61222 /gbdb/panTro3/panTro3.2bit +chrUn_GL393552 60998 /gbdb/panTro3/panTro3.2bit +chr1_GL388981_random 60209 /gbdb/panTro3/panTro3.2bit +chrUn_GL393820 59557 /gbdb/panTro3/panTro3.2bit +chr2A_GL389312_random 59088 /gbdb/panTro3/panTro3.2bit +chr5_GL390140_random 58975 /gbdb/panTro3/panTro3.2bit +chr9_GL391118_random 58555 /gbdb/panTro3/panTro3.2bit +chr10_GL391633_random 58487 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_GL391209_random 49066 /gbdb/panTro3/panTro3.2bit +chrUn_GL396958 48594 /gbdb/panTro3/panTro3.2bit +chrUn_GL394672 48567 /gbdb/panTro3/panTro3.2bit +chr16_GL392552_random 48465 /gbdb/panTro3/panTro3.2bit +chrUn_GL394248 48380 /gbdb/panTro3/panTro3.2bit +chrUn_GL394193 48297 /gbdb/panTro3/panTro3.2bit +chrUn_GL394105 48067 /gbdb/panTro3/panTro3.2bit +chr4_GL389870_random 47972 /gbdb/panTro3/panTro3.2bit +chr6_GL390403_random 47816 /gbdb/panTro3/panTro3.2bit +chr3_GL389628_random 47029 /gbdb/panTro3/panTro3.2bit +chr16_GL392510_random 46956 /gbdb/panTro3/panTro3.2bit +chrUn_GL393461 46931 /gbdb/panTro3/panTro3.2bit +chr1_GL388997_random 46833 /gbdb/panTro3/panTro3.2bit +chr9_GL391032_random 46589 /gbdb/panTro3/panTro3.2bit +chr2B_GL389463_random 46347 /gbdb/panTro3/panTro3.2bit +chrUn_GL394261 46220 /gbdb/panTro3/panTro3.2bit +chr4_GL389861_random 46175 /gbdb/panTro3/panTro3.2bit +chr6_GL390444_random 45881 /gbdb/panTro3/panTro3.2bit +chr1_GL389167_random 45780 /gbdb/panTro3/panTro3.2bit +chr7_GL390720_random 45705 /gbdb/panTro3/panTro3.2bit +chr10_GL391684_random 45627 /gbdb/panTro3/panTro3.2bit +chr11_GL391849_random 45333 /gbdb/panTro3/panTro3.2bit +chrUn_GL394206 44811 /gbdb/panTro3/panTro3.2bit +chrUn_GL394845 44796 /gbdb/panTro3/panTro3.2bit +chr9_GL391117_random 44772 /gbdb/panTro3/panTro3.2bit +chrUn_GL393454 44724 /gbdb/panTro3/panTro3.2bit +chr9_GL391144_random 44587 /gbdb/panTro3/panTro3.2bit +chrUn_GL394418 44536 /gbdb/panTro3/panTro3.2bit +chr1_GL389237_random 44129 /gbdb/panTro3/panTro3.2bit +chr6_GL390388_random 43739 /gbdb/panTro3/panTro3.2bit +chr1_GL389043_random 43593 /gbdb/panTro3/panTro3.2bit +chr9_GL391078_random 43582 /gbdb/panTro3/panTro3.2bit +chr1_GL389096_random 43246 /gbdb/panTro3/panTro3.2bit +chrUn_GL394013 43206 /gbdb/panTro3/panTro3.2bit +chrUn_GL394447 43126 /gbdb/panTro3/panTro3.2bit +chrUn_GL394354 42715 /gbdb/panTro3/panTro3.2bit +chr4_GL389885_random 42303 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394411 40212 /gbdb/panTro3/panTro3.2bit +chr16_GL392361_random 40209 /gbdb/panTro3/panTro3.2bit +chrUn_GL394404 40157 /gbdb/panTro3/panTro3.2bit +chr15_GL392250_random 40146 /gbdb/panTro3/panTro3.2bit +chrUn_GL394571 40048 /gbdb/panTro3/panTro3.2bit +chr2A_GL389315_random 40043 /gbdb/panTro3/panTro3.2bit +chr17_GL392640_random 40021 /gbdb/panTro3/panTro3.2bit +chrUn_GL394734 39932 /gbdb/panTro3/panTro3.2bit +chr14_GL392181_random 39925 /gbdb/panTro3/panTro3.2bit +chrUn_GL394264 39729 /gbdb/panTro3/panTro3.2bit +chr14_GL392176_random 39665 /gbdb/panTro3/panTro3.2bit +chr16_GL392541_random 39650 /gbdb/panTro3/panTro3.2bit +chr1_GL389138_random 39610 /gbdb/panTro3/panTro3.2bit +chr4_GL389859_random 39508 /gbdb/panTro3/panTro3.2bit +chr1_GL389088_random 39481 /gbdb/panTro3/panTro3.2bit +chrUn_GL394436 39339 /gbdb/panTro3/panTro3.2bit +chr9_GL391174_random 39229 /gbdb/panTro3/panTro3.2bit +chr1_GL389060_random 39207 /gbdb/panTro3/panTro3.2bit 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36562 /gbdb/panTro3/panTro3.2bit +chr1_GL389079_random 36561 /gbdb/panTro3/panTro3.2bit +chr7_GL390658_random 36550 /gbdb/panTro3/panTro3.2bit +chr9_GL391148_random 36444 /gbdb/panTro3/panTro3.2bit +chr9_GL391091_random 36381 /gbdb/panTro3/panTro3.2bit +chrUn_GL394250 36107 /gbdb/panTro3/panTro3.2bit +chr9_GL391095_random 36059 /gbdb/panTro3/panTro3.2bit +chr3_GL389663_random 36053 /gbdb/panTro3/panTro3.2bit +chr9_GL391219_random 35981 /gbdb/panTro3/panTro3.2bit +chrUn_GL394446 35969 /gbdb/panTro3/panTro3.2bit +chr16_GL392520_random 35952 /gbdb/panTro3/panTro3.2bit +chr7_GL390569_random 35897 /gbdb/panTro3/panTro3.2bit +chrUn_GL394756 35789 /gbdb/panTro3/panTro3.2bit +chr8_GL390770_random 35647 /gbdb/panTro3/panTro3.2bit +chrX_GL393353_random 35602 /gbdb/panTro3/panTro3.2bit +chr4_GL389703_random 35369 /gbdb/panTro3/panTro3.2bit +chrUn_GL394860 35314 /gbdb/panTro3/panTro3.2bit +chr8_GL390883_random 35271 /gbdb/panTro3/panTro3.2bit +chrUn_GL394572 34861 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_GL391082_random 33770 /gbdb/panTro3/panTro3.2bit +chr2A_GL389369_random 33678 /gbdb/panTro3/panTro3.2bit +chrUn_GL395311 33660 /gbdb/panTro3/panTro3.2bit +chr1_GL389059_random 33608 /gbdb/panTro3/panTro3.2bit +chr17_GL392674_random 33528 /gbdb/panTro3/panTro3.2bit +chr9_GL390942_random 33519 /gbdb/panTro3/panTro3.2bit +chr2A_GL389321_random 33451 /gbdb/panTro3/panTro3.2bit +chr8_GL390882_random 33402 /gbdb/panTro3/panTro3.2bit +chr4_GL389921_random 33376 /gbdb/panTro3/panTro3.2bit +chr9_GL391166_random 33325 /gbdb/panTro3/panTro3.2bit +chr15_GL392232_random 33231 /gbdb/panTro3/panTro3.2bit +chrUn_GL394462 33170 /gbdb/panTro3/panTro3.2bit +chr9_GL390965_random 33151 /gbdb/panTro3/panTro3.2bit +chrUn_GL394217 32943 /gbdb/panTro3/panTro3.2bit +chrUn_GL394800 32871 /gbdb/panTro3/panTro3.2bit +chr7_GL390695_random 32744 /gbdb/panTro3/panTro3.2bit +chrUn_GL394471 32731 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149418_random 32711 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr20_GL393020_random 31450 /gbdb/panTro3/panTro3.2bit +chrUn_GL394876 31434 /gbdb/panTro3/panTro3.2bit +chr15_GL392262_random 31425 /gbdb/panTro3/panTro3.2bit +chr7_GL390664_random 31331 /gbdb/panTro3/panTro3.2bit +chrUn_GL395239 31206 /gbdb/panTro3/panTro3.2bit +chrUn_GL394002 31153 /gbdb/panTro3/panTro3.2bit +chr9_GL391218_random 31134 /gbdb/panTro3/panTro3.2bit +chr1_GL389002_random 31115 /gbdb/panTro3/panTro3.2bit +chrUn_GL393466 31024 /gbdb/panTro3/panTro3.2bit +chr18_GL392797_random 30988 /gbdb/panTro3/panTro3.2bit +chr15_GL392268_random 30966 /gbdb/panTro3/panTro3.2bit +chr9_GL391135_random 30965 /gbdb/panTro3/panTro3.2bit +chrUn_GL394010 30965 /gbdb/panTro3/panTro3.2bit +chr9_GL391085_random 30952 /gbdb/panTro3/panTro3.2bit +chr6_GL390372_random 30938 /gbdb/panTro3/panTro3.2bit +chr1_GL389128_random 30935 /gbdb/panTro3/panTro3.2bit +chr18_GL392801_random 30865 /gbdb/panTro3/panTro3.2bit +chr6_GL390413_random 30839 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr4_GL389747_random 30316 /gbdb/panTro3/panTro3.2bit +chrUn_GL393473 30310 /gbdb/panTro3/panTro3.2bit +chrUn_GL393931 30285 /gbdb/panTro3/panTro3.2bit +chrUn_GL393918 30123 /gbdb/panTro3/panTro3.2bit +chrUn_GL393460 30089 /gbdb/panTro3/panTro3.2bit +chr11_GL391827_random 30066 /gbdb/panTro3/panTro3.2bit +chr7_GL390603_random 30034 /gbdb/panTro3/panTro3.2bit +chrUn_GL395595 30030 /gbdb/panTro3/panTro3.2bit +chr4_GL389905_random 29975 /gbdb/panTro3/panTro3.2bit +chr16_GL392368_random 29964 /gbdb/panTro3/panTro3.2bit +chrUn_GL394547 29955 /gbdb/panTro3/panTro3.2bit +chr16_GL392403_random 29912 /gbdb/panTro3/panTro3.2bit +chr1_GL388992_random 29903 /gbdb/panTro3/panTro3.2bit +chrUn_GL394903 29784 /gbdb/panTro3/panTro3.2bit +chr10_GL391679_random 29755 /gbdb/panTro3/panTro3.2bit +chrUn_GL394072 29730 /gbdb/panTro3/panTro3.2bit +chr5_GL390134_random 29715 /gbdb/panTro3/panTro3.2bit +chrUn_GL394651 29654 /gbdb/panTro3/panTro3.2bit +chr4_GL389856_random 29644 /gbdb/panTro3/panTro3.2bit +chr4_GL389917_random 29641 /gbdb/panTro3/panTro3.2bit +chrUn_GL394560 29550 /gbdb/panTro3/panTro3.2bit +chr22_GL393067_random 29542 /gbdb/panTro3/panTro3.2bit +chrUn_GL394258 29504 /gbdb/panTro3/panTro3.2bit +chr2A_GL389314_random 29467 /gbdb/panTro3/panTro3.2bit +chrUn_GL395296 29393 /gbdb/panTro3/panTro3.2bit +chr2A_GL389301_random 29387 /gbdb/panTro3/panTro3.2bit +chr7_GL390662_random 29386 /gbdb/panTro3/panTro3.2bit +chr18_GL392794_random 29355 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174263_random 29332 /gbdb/panTro3/panTro3.2bit +chr2A_GL389373_random 29202 /gbdb/panTro3/panTro3.2bit +chr1_GL389041_random 29201 /gbdb/panTro3/panTro3.2bit +chr3_GL389662_random 29201 /gbdb/panTro3/panTro3.2bit +chr11_GL391860_random 29192 /gbdb/panTro3/panTro3.2bit +chr17_GL392657_random 29170 /gbdb/panTro3/panTro3.2bit +chrUn_GL394328 29097 /gbdb/panTro3/panTro3.2bit +chr14_GL392141_random 29070 /gbdb/panTro3/panTro3.2bit +chrUn_GL395215 29026 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395238 28198 /gbdb/panTro3/panTro3.2bit +chr9_GL391150_random 28128 /gbdb/panTro3/panTro3.2bit +chrUn_GL394803 28033 /gbdb/panTro3/panTro3.2bit +chr9_GL391119_random 28022 /gbdb/panTro3/panTro3.2bit +chrUn_GL395158 27910 /gbdb/panTro3/panTro3.2bit +chr7_GL390745_random 27902 /gbdb/panTro3/panTro3.2bit +chr7_GL390660_random 27875 /gbdb/panTro3/panTro3.2bit +chrUn_GL393472 27871 /gbdb/panTro3/panTro3.2bit +chr1_GL389010_random 27867 /gbdb/panTro3/panTro3.2bit +chrUn_GL394655 27864 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03163896_random 27832 /gbdb/panTro3/panTro3.2bit +chrUn_GL393477 27802 /gbdb/panTro3/panTro3.2bit +chr4_GL389907_random 27764 /gbdb/panTro3/panTro3.2bit +chr1_GL389095_random 27740 /gbdb/panTro3/panTro3.2bit +chrUn_GL393468 27735 /gbdb/panTro3/panTro3.2bit +chr6_GL390414_random 27665 /gbdb/panTro3/panTro3.2bit +chr4_GL389863_random 27607 /gbdb/panTro3/panTro3.2bit +chrUn_GL394954 27559 /gbdb/panTro3/panTro3.2bit +chrUn_GL394915 27558 /gbdb/panTro3/panTro3.2bit +chr16_GL392391_random 27541 /gbdb/panTro3/panTro3.2bit +chr6_GL390223_random 27516 /gbdb/panTro3/panTro3.2bit +chr16_GL392392_random 27492 /gbdb/panTro3/panTro3.2bit +chrUn_GL394842 27463 /gbdb/panTro3/panTro3.2bit +chrUn_GL394486 27435 /gbdb/panTro3/panTro3.2bit +chr7_GL390719_random 27427 /gbdb/panTro3/panTro3.2bit +chr7_GL390748_random 27418 /gbdb/panTro3/panTro3.2bit +chrUn_GL395308 27414 /gbdb/panTro3/panTro3.2bit +chrUn_GL394216 27383 /gbdb/panTro3/panTro3.2bit +chr9_GL391121_random 27378 /gbdb/panTro3/panTro3.2bit +chr16_GL392387_random 27359 /gbdb/panTro3/panTro3.2bit +chr9_GL391165_random 27358 /gbdb/panTro3/panTro3.2bit +chrUn_GL394006 27296 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03179779 27261 /gbdb/panTro3/panTro3.2bit +chr9_GL391232_random 27259 /gbdb/panTro3/panTro3.2bit +chr17_GL392654_random 27228 /gbdb/panTro3/panTro3.2bit +chrUn_GL394925 27224 /gbdb/panTro3/panTro3.2bit +chr16_GL392521_random 27194 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395483 25256 /gbdb/panTro3/panTro3.2bit +chrUn_GL394130 25229 /gbdb/panTro3/panTro3.2bit +chr1_GL389008_random 25217 /gbdb/panTro3/panTro3.2bit +chr16_GL392442_random 25204 /gbdb/panTro3/panTro3.2bit +chr2B_GL389416_random 25203 /gbdb/panTro3/panTro3.2bit +chr1_GL389086_random 25160 /gbdb/panTro3/panTro3.2bit +chrUn_GL394524 25152 /gbdb/panTro3/panTro3.2bit +chrUn_GL395405 25135 /gbdb/panTro3/panTro3.2bit +chr16_GL392498_random 25108 /gbdb/panTro3/panTro3.2bit +chr16_GL392414_random 25051 /gbdb/panTro3/panTro3.2bit +chrX_GL393424_random 25045 /gbdb/panTro3/panTro3.2bit +chrUn_GL394122 25043 /gbdb/panTro3/panTro3.2bit +chrUn_GL394608 25039 /gbdb/panTro3/panTro3.2bit +chrUn_GL395407 25011 /gbdb/panTro3/panTro3.2bit +chr7_GL390724_random 24998 /gbdb/panTro3/panTro3.2bit +chrUn_GL396045 24952 /gbdb/panTro3/panTro3.2bit +chr2A_GL389302_random 24946 /gbdb/panTro3/panTro3.2bit +chrUn_GL394859 24944 /gbdb/panTro3/panTro3.2bit +chrUn_GL395234 24903 /gbdb/panTro3/panTro3.2bit +chrUn_GL394828 24885 /gbdb/panTro3/panTro3.2bit +chr6_GL390238_random 24852 /gbdb/panTro3/panTro3.2bit +chrUn_GL394920 24804 /gbdb/panTro3/panTro3.2bit +chrUn_GL394401 24800 /gbdb/panTro3/panTro3.2bit +chr4_GL389909_random 24762 /gbdb/panTro3/panTro3.2bit +chr17_GL392660_random 24750 /gbdb/panTro3/panTro3.2bit +chrUn_GL394272 24708 /gbdb/panTro3/panTro3.2bit +chr4_GL389840_random 24706 /gbdb/panTro3/panTro3.2bit +chrX_GL393214_random 24706 /gbdb/panTro3/panTro3.2bit +chrUn_GL394643 24694 /gbdb/panTro3/panTro3.2bit +chrUn_GL395257 24689 /gbdb/panTro3/panTro3.2bit +chrUn_GL394995 24682 /gbdb/panTro3/panTro3.2bit +chrUn_GL395216 24680 /gbdb/panTro3/panTro3.2bit +chrUn_GL393491 24655 /gbdb/panTro3/panTro3.2bit +chr2A_GL389376_random 24627 /gbdb/panTro3/panTro3.2bit +chr2B_GL389468_random 24602 /gbdb/panTro3/panTro3.2bit +chr1_GL389006_random 24589 /gbdb/panTro3/panTro3.2bit +chr1_GL389222_random 24558 /gbdb/panTro3/panTro3.2bit +chrUn_GL395769 24525 /gbdb/panTro3/panTro3.2bit +chr2A_GL389313_random 24478 /gbdb/panTro3/panTro3.2bit +chr10_GL391412_random 24463 /gbdb/panTro3/panTro3.2bit +chr5_GL390123_random 24451 /gbdb/panTro3/panTro3.2bit +chr7_GL390689_random 24446 /gbdb/panTro3/panTro3.2bit +chr8_GL390885_random 24388 /gbdb/panTro3/panTro3.2bit +chr16_GL392534_random 24387 /gbdb/panTro3/panTro3.2bit +chr1_GL389057_random 24381 /gbdb/panTro3/panTro3.2bit +chr9_GL391190_random 24362 /gbdb/panTro3/panTro3.2bit +chrUn_GL395480 24356 /gbdb/panTro3/panTro3.2bit +chrUn_GL394910 24352 /gbdb/panTro3/panTro3.2bit +chrUn_GL395224 24345 /gbdb/panTro3/panTro3.2bit +chr9_GL390962_random 24338 /gbdb/panTro3/panTro3.2bit +chrUn_GL395072 24333 /gbdb/panTro3/panTro3.2bit +chr2A_GL389377_random 24288 /gbdb/panTro3/panTro3.2bit +chrUn_GL394578 24274 /gbdb/panTro3/panTro3.2bit +chr1_GL389024_random 24245 /gbdb/panTro3/panTro3.2bit +chrUn_GL394450 24234 /gbdb/panTro3/panTro3.2bit +chr15_GL392279_random 24228 /gbdb/panTro3/panTro3.2bit +chr11_GL391708_random 24189 /gbdb/panTro3/panTro3.2bit +chrUn_GL395316 24170 /gbdb/panTro3/panTro3.2bit +chrUn_GL395613 24144 /gbdb/panTro3/panTro3.2bit +chr7_GL390655_random 24082 /gbdb/panTro3/panTro3.2bit +chrUn_GL394776 24070 /gbdb/panTro3/panTro3.2bit +chr16_GL392419_random 24069 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03179787 24035 /gbdb/panTro3/panTro3.2bit +chrUn_GL395122 24017 /gbdb/panTro3/panTro3.2bit +chr9_GL391183_random 24011 /gbdb/panTro3/panTro3.2bit +chr1_GL389076_random 24008 /gbdb/panTro3/panTro3.2bit +chr9_GL391194_random 23985 /gbdb/panTro3/panTro3.2bit +chrUn_GL394230 23978 /gbdb/panTro3/panTro3.2bit +chr4_GL389914_random 23975 /gbdb/panTro3/panTro3.2bit +chr5_GL390132_random 23944 /gbdb/panTro3/panTro3.2bit +chrUn_GL394989 23941 /gbdb/panTro3/panTro3.2bit +chrUn_GL395056 23934 /gbdb/panTro3/panTro3.2bit +chr16_GL392505_random 23931 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03179823 23930 /gbdb/panTro3/panTro3.2bit +chrUn_GL395350 23855 /gbdb/panTro3/panTro3.2bit 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23556 /gbdb/panTro3/panTro3.2bit +chrUn_GL394899 23532 /gbdb/panTro3/panTro3.2bit +chrUn_GL395038 23513 /gbdb/panTro3/panTro3.2bit +chr7_GL390570_random 23512 /gbdb/panTro3/panTro3.2bit +chr9_GL391192_random 23507 /gbdb/panTro3/panTro3.2bit +chr2A_GL389374_random 23500 /gbdb/panTro3/panTro3.2bit +chr7_GL390701_random 23496 /gbdb/panTro3/panTro3.2bit +chr19_GL392887_random 23484 /gbdb/panTro3/panTro3.2bit +chr9_GL391211_random 23463 /gbdb/panTro3/panTro3.2bit +chr6_GL390411_random 23433 /gbdb/panTro3/panTro3.2bit +chrUn_GL395123 23431 /gbdb/panTro3/panTro3.2bit +chr18_GL392764_random 23413 /gbdb/panTro3/panTro3.2bit +chrUn_GL393498 23412 /gbdb/panTro3/panTro3.2bit +chrUn_GL394885 23390 /gbdb/panTro3/panTro3.2bit +chrUn_GL394941 23358 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171822_random 23304 /gbdb/panTro3/panTro3.2bit +chrUn_GL395029 23304 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03163820_random 23266 /gbdb/panTro3/panTro3.2bit +chrUn_GL394908 23248 /gbdb/panTro3/panTro3.2bit 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22439 /gbdb/panTro3/panTro3.2bit +chr2B_GL389464_random 22432 /gbdb/panTro3/panTro3.2bit +chrUn_GL395084 22426 /gbdb/panTro3/panTro3.2bit +chr16_GL392495_random 22421 /gbdb/panTro3/panTro3.2bit +chrUn_GL394091 22410 /gbdb/panTro3/panTro3.2bit +chrUn_GL395360 22406 /gbdb/panTro3/panTro3.2bit +chr3_GL389556_random 22405 /gbdb/panTro3/panTro3.2bit +chrUn_GL395890 22353 /gbdb/panTro3/panTro3.2bit +chrUn_GL394413 22332 /gbdb/panTro3/panTro3.2bit +chr3_GL389636_random 22329 /gbdb/panTro3/panTro3.2bit +chr4_GL389759_random 22272 /gbdb/panTro3/panTro3.2bit +chrUn_GL395357 22242 /gbdb/panTro3/panTro3.2bit +chr1_GL388870_random 22233 /gbdb/panTro3/panTro3.2bit +chrUn_GL393968 22214 /gbdb/panTro3/panTro3.2bit +chrUn_GL395615 22199 /gbdb/panTro3/panTro3.2bit +chr16_GL392338_random 22187 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03163856_random 22181 /gbdb/panTro3/panTro3.2bit +chrUn_GL394496 22180 /gbdb/panTro3/panTro3.2bit +chr4_GL389832_random 22175 /gbdb/panTro3/panTro3.2bit +chr17_GL392666_random 22135 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174286_random 22133 /gbdb/panTro3/panTro3.2bit +chrUn_GL394601 22129 /gbdb/panTro3/panTro3.2bit +chrUn_GL395425 22124 /gbdb/panTro3/panTro3.2bit +chrUn_GL393478 22115 /gbdb/panTro3/panTro3.2bit +chr2B_GL389433_random 22107 /gbdb/panTro3/panTro3.2bit +chrUn_GL395583 22092 /gbdb/panTro3/panTro3.2bit +chrUn_GL395524 22081 /gbdb/panTro3/panTro3.2bit +chr6_GL390408_random 22063 /gbdb/panTro3/panTro3.2bit +chr2A_GL389367_random 22056 /gbdb/panTro3/panTro3.2bit +chr16_GL392435_random 22046 /gbdb/panTro3/panTro3.2bit +chrUn_GL394704 22039 /gbdb/panTro3/panTro3.2bit +chrUn_GL395220 22014 /gbdb/panTro3/panTro3.2bit +chrUn_GL394850 22007 /gbdb/panTro3/panTro3.2bit +chr1_GL389040_random 21997 /gbdb/panTro3/panTro3.2bit +chr7_GL390723_random 21979 /gbdb/panTro3/panTro3.2bit +chr9_GL391111_random 21972 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03179784 21968 /gbdb/panTro3/panTro3.2bit +chrUn_GL395182 21962 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395558 21586 /gbdb/panTro3/panTro3.2bit +chr4_GL389918_random 21553 /gbdb/panTro3/panTro3.2bit +chrUn_GL395635 21537 /gbdb/panTro3/panTro3.2bit +chr16_GL392426_random 21511 /gbdb/panTro3/panTro3.2bit +chr1_GL389125_random 21494 /gbdb/panTro3/panTro3.2bit +chrUn_GL394416 21443 /gbdb/panTro3/panTro3.2bit +chrUn_GL395091 21432 /gbdb/panTro3/panTro3.2bit +chr9_GL391129_random 21429 /gbdb/panTro3/panTro3.2bit +chr11_GL391863_random 21415 /gbdb/panTro3/panTro3.2bit +chrUn_GL395636 21390 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180790 21384 /gbdb/panTro3/panTro3.2bit +chrUn_GL395748 21329 /gbdb/panTro3/panTro3.2bit +chr11_GL391859_random 21304 /gbdb/panTro3/panTro3.2bit +chr15_GL392238_random 21299 /gbdb/panTro3/panTro3.2bit +chrUn_GL394685 21282 /gbdb/panTro3/panTro3.2bit +chr3_GL389567_random 21277 /gbdb/panTro3/panTro3.2bit +chr22_GL393064_random 21273 /gbdb/panTro3/panTro3.2bit +chr10_GL391409_random 21265 /gbdb/panTro3/panTro3.2bit +chr1_GL389067_random 21241 /gbdb/panTro3/panTro3.2bit +chr9_GL391114_random 21240 /gbdb/panTro3/panTro3.2bit +chrUn_GL395294 21238 /gbdb/panTro3/panTro3.2bit +chr1_GL389208_random 21229 /gbdb/panTro3/panTro3.2bit +chrUn_GL395252 21228 /gbdb/panTro3/panTro3.2bit +chrUn_GL393486 21227 /gbdb/panTro3/panTro3.2bit +chrX_GL393171_random 21224 /gbdb/panTro3/panTro3.2bit +chrUn_GL394771 21222 /gbdb/panTro3/panTro3.2bit +chr7_GL390711_random 21166 /gbdb/panTro3/panTro3.2bit +chrUn_GL395173 21148 /gbdb/panTro3/panTro3.2bit +chr2A_GL389383_random 21094 /gbdb/panTro3/panTro3.2bit +chrUn_GL395937 21063 /gbdb/panTro3/panTro3.2bit +chrUn_GL395798 21051 /gbdb/panTro3/panTro3.2bit +chrUn_GL394558 21015 /gbdb/panTro3/panTro3.2bit +chr9_GL391043_random 21010 /gbdb/panTro3/panTro3.2bit +chr2B_GL389457_random 20995 /gbdb/panTro3/panTro3.2bit +chrUn_GL395520 20987 /gbdb/panTro3/panTro3.2bit +chr16_GL392550_random 20977 /gbdb/panTro3/panTro3.2bit +chr20_GL392992_random 20964 /gbdb/panTro3/panTro3.2bit +chrUn_GL396089 20959 /gbdb/panTro3/panTro3.2bit +chr3_GL389608_random 20957 /gbdb/panTro3/panTro3.2bit +chr4_GL389771_random 20946 /gbdb/panTro3/panTro3.2bit +chrUn_GL395593 20933 /gbdb/panTro3/panTro3.2bit +chrUn_GL395043 20893 /gbdb/panTro3/panTro3.2bit +chr16_GL392459_random 20872 /gbdb/panTro3/panTro3.2bit +chrUn_GL394843 20872 /gbdb/panTro3/panTro3.2bit +chrUn_GL395550 20866 /gbdb/panTro3/panTro3.2bit +chrUn_GL395320 20853 /gbdb/panTro3/panTro3.2bit +chrUn_GL395717 20843 /gbdb/panTro3/panTro3.2bit +chr3_GL389540_random 20828 /gbdb/panTro3/panTro3.2bit +chr15_GL392202_random 20826 /gbdb/panTro3/panTro3.2bit +chrUn_GL394853 20824 /gbdb/panTro3/panTro3.2bit +chrX_GL393407_random 20802 /gbdb/panTro3/panTro3.2bit +chr4_GL389702_random 20796 /gbdb/panTro3/panTro3.2bit +chr7_GL390718_random 20796 /gbdb/panTro3/panTro3.2bit +chrUn_GL395075 20783 /gbdb/panTro3/panTro3.2bit +chrUn_GL395179 20720 /gbdb/panTro3/panTro3.2bit +chrUn_GL395150 20711 /gbdb/panTro3/panTro3.2bit +chr4_GL389766_random 20699 /gbdb/panTro3/panTro3.2bit +chrUn_GL395456 20675 /gbdb/panTro3/panTro3.2bit +chrUn_GL395446 20673 /gbdb/panTro3/panTro3.2bit +chr15_GL392233_random 20670 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149711_random 20664 /gbdb/panTro3/panTro3.2bit +chr18_GL392795_random 20658 /gbdb/panTro3/panTro3.2bit +chr6_GL390256_random 20639 /gbdb/panTro3/panTro3.2bit +chr16_GL392462_random 20618 /gbdb/panTro3/panTro3.2bit +chr17_GL392613_random 20613 /gbdb/panTro3/panTro3.2bit +chrUn_GL394883 20612 /gbdb/panTro3/panTro3.2bit +chrUn_GL395671 20604 /gbdb/panTro3/panTro3.2bit +chrUn_GL395401 20598 /gbdb/panTro3/panTro3.2bit +chr1_GL389108_random 20594 /gbdb/panTro3/panTro3.2bit +chrUn_GL393678 20588 /gbdb/panTro3/panTro3.2bit +chrUn_GL395903 20577 /gbdb/panTro3/panTro3.2bit +chrX_GL393399_random 20570 /gbdb/panTro3/panTro3.2bit +chr1_GL389065_random 20560 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03179890 20559 /gbdb/panTro3/panTro3.2bit +chr15_GL392263_random 20549 /gbdb/panTro3/panTro3.2bit +chrUn_GL394737 20541 /gbdb/panTro3/panTro3.2bit +chr2A_GL389323_random 20539 /gbdb/panTro3/panTro3.2bit +chr16_GL392421_random 20522 /gbdb/panTro3/panTro3.2bit +chr19_GL392897_random 20490 /gbdb/panTro3/panTro3.2bit +chrUn_GL395210 20490 /gbdb/panTro3/panTro3.2bit +chr1_GL389066_random 20489 /gbdb/panTro3/panTro3.2bit +chr10_GL391647_random 20488 /gbdb/panTro3/panTro3.2bit +chr16_GL392388_random 20485 /gbdb/panTro3/panTro3.2bit +chrUn_GL393496 20471 /gbdb/panTro3/panTro3.2bit +chrUn_GL393601 20471 /gbdb/panTro3/panTro3.2bit +chr16_GL392397_random 20440 /gbdb/panTro3/panTro3.2bit +chr9_GL391205_random 20408 /gbdb/panTro3/panTro3.2bit +chr16_GL392429_random 20391 /gbdb/panTro3/panTro3.2bit +chr2A_GL389345_random 20376 /gbdb/panTro3/panTro3.2bit +chrUn_GL395684 20327 /gbdb/panTro3/panTro3.2bit +chr4_GL389950_random 20296 /gbdb/panTro3/panTro3.2bit +chr5_GL390125_random 20274 /gbdb/panTro3/panTro3.2bit +chr9_GL391177_random 20264 /gbdb/panTro3/panTro3.2bit +chr1_GL389236_random 20247 /gbdb/panTro3/panTro3.2bit +chr7_GL390564_random 20237 /gbdb/panTro3/panTro3.2bit +chr1_GL389016_random 20236 /gbdb/panTro3/panTro3.2bit +chrUn_GL395823 20233 /gbdb/panTro3/panTro3.2bit +chrUn_GL394968 20217 /gbdb/panTro3/panTro3.2bit +chrUn_GL395081 20211 /gbdb/panTro3/panTro3.2bit +chrUn_GL395330 20205 /gbdb/panTro3/panTro3.2bit +chr10_GL391646_random 20127 /gbdb/panTro3/panTro3.2bit +chrUn_GL394877 20119 /gbdb/panTro3/panTro3.2bit +chrUn_GL394738 20117 /gbdb/panTro3/panTro3.2bit +chr1_GL388985_random 20114 /gbdb/panTro3/panTro3.2bit +chrUn_GL395515 20108 /gbdb/panTro3/panTro3.2bit +chrUn_GL395138 20107 /gbdb/panTro3/panTro3.2bit +chr11_GL391748_random 20101 /gbdb/panTro3/panTro3.2bit +chr14_GL392155_random 20084 /gbdb/panTro3/panTro3.2bit +chr15_GL392213_random 20062 /gbdb/panTro3/panTro3.2bit +chrUn_GL394979 20042 /gbdb/panTro3/panTro3.2bit +chr12_GL391969_random 19991 /gbdb/panTro3/panTro3.2bit +chrUn_GL394187 19991 /gbdb/panTro3/panTro3.2bit +chr16_GL392399_random 19988 /gbdb/panTro3/panTro3.2bit +chr1_GL389036_random 19984 /gbdb/panTro3/panTro3.2bit +chr7_GL390612_random 19981 /gbdb/panTro3/panTro3.2bit +chrX_GL393162_random 19979 /gbdb/panTro3/panTro3.2bit +chrUn_GL395174 19973 /gbdb/panTro3/panTro3.2bit +chr1_GL389045_random 19972 /gbdb/panTro3/panTro3.2bit +chr11_GL391867_random 19960 /gbdb/panTro3/panTro3.2bit +chrUn_GL393502 19960 /gbdb/panTro3/panTro3.2bit +chr9_GL391153_random 19940 /gbdb/panTro3/panTro3.2bit +chrUn_GL395264 19934 /gbdb/panTro3/panTro3.2bit +chr2A_GL389384_random 19929 /gbdb/panTro3/panTro3.2bit +chrUn_GL395770 19928 /gbdb/panTro3/panTro3.2bit +chrUn_GL395599 19921 /gbdb/panTro3/panTro3.2bit +chrUn_GL395324 19917 /gbdb/panTro3/panTro3.2bit +chrUn_GL395298 19913 /gbdb/panTro3/panTro3.2bit +chr10_GL391363_random 19910 /gbdb/panTro3/panTro3.2bit +chr10_GL391650_random 19908 /gbdb/panTro3/panTro3.2bit +chrUn_GL393987 19908 /gbdb/panTro3/panTro3.2bit +chrUn_GL395420 19899 /gbdb/panTro3/panTro3.2bit +chrUn_GL394865 19874 /gbdb/panTro3/panTro3.2bit +chrUn_GL395485 19874 /gbdb/panTro3/panTro3.2bit +chrUn_GL395118 19866 /gbdb/panTro3/panTro3.2bit +chrUn_GL394636 19862 /gbdb/panTro3/panTro3.2bit +chr9_GL391147_random 19856 /gbdb/panTro3/panTro3.2bit +chr1_GL389209_random 19855 /gbdb/panTro3/panTro3.2bit +chrUn_GL395358 19853 /gbdb/panTro3/panTro3.2bit +chr7_GL390509_random 19840 /gbdb/panTro3/panTro3.2bit +chrUn_GL395393 19830 /gbdb/panTro3/panTro3.2bit +chr6_GL390222_random 19826 /gbdb/panTro3/panTro3.2bit +chr9_GL391123_random 19821 /gbdb/panTro3/panTro3.2bit +chr9_GL391176_random 19818 /gbdb/panTro3/panTro3.2bit +chr9_GL391206_random 19815 /gbdb/panTro3/panTro3.2bit +chrUn_GL396014 19814 /gbdb/panTro3/panTro3.2bit +chrUn_GL394963 19803 /gbdb/panTro3/panTro3.2bit +chr9_GL391098_random 19761 /gbdb/panTro3/panTro3.2bit +chr1_GL389011_random 19759 /gbdb/panTro3/panTro3.2bit +chrUn_GL395039 19737 /gbdb/panTro3/panTro3.2bit +chr1_GL389179_random 19725 /gbdb/panTro3/panTro3.2bit +chr9_GL391104_random 19722 /gbdb/panTro3/panTro3.2bit +chrUn_GL395915 19711 /gbdb/panTro3/panTro3.2bit +chrUn_GL394951 19708 /gbdb/panTro3/panTro3.2bit +chr6_GL390341_random 19703 /gbdb/panTro3/panTro3.2bit +chr17_GL392655_random 19694 /gbdb/panTro3/panTro3.2bit +chr3_GL389661_random 19678 /gbdb/panTro3/panTro3.2bit +chrUn_GL395486 19672 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171840_random 19650 /gbdb/panTro3/panTro3.2bit +chr11_GL391866_random 19620 /gbdb/panTro3/panTro3.2bit +chrUn_GL394872 19618 /gbdb/panTro3/panTro3.2bit +chr16_GL392472_random 19615 /gbdb/panTro3/panTro3.2bit +chrUn_GL393488 19594 /gbdb/panTro3/panTro3.2bit +chrUn_GL396052 19548 /gbdb/panTro3/panTro3.2bit +chrUn_GL394723 19532 /gbdb/panTro3/panTro3.2bit +chrUn_GL395812 19529 /gbdb/panTro3/panTro3.2bit +chrUn_GL394561 19505 /gbdb/panTro3/panTro3.2bit +chrUn_GL395544 19498 /gbdb/panTro3/panTro3.2bit +chrUn_GL395441 19483 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165421_random 19472 /gbdb/panTro3/panTro3.2bit +chrUn_GL395742 19463 /gbdb/panTro3/panTro3.2bit +chrUn_GL394721 19450 /gbdb/panTro3/panTro3.2bit +chr10_GL391420_random 19449 /gbdb/panTro3/panTro3.2bit +chrUn_GL396044 19425 /gbdb/panTro3/panTro3.2bit +chrUn_GL395905 19419 /gbdb/panTro3/panTro3.2bit +chrUn_GL395010 19409 /gbdb/panTro3/panTro3.2bit +chr10_GL391410_random 19404 /gbdb/panTro3/panTro3.2bit +chr7_GL390686_random 19395 /gbdb/panTro3/panTro3.2bit +chrUn_GL394488 19394 /gbdb/panTro3/panTro3.2bit +chrUn_GL395484 19378 /gbdb/panTro3/panTro3.2bit +chr9_GL391208_random 19368 /gbdb/panTro3/panTro3.2bit +chr2A_GL389379_random 19360 /gbdb/panTro3/panTro3.2bit +chrUn_GL395522 19354 /gbdb/panTro3/panTro3.2bit +chr16_GL392470_random 19315 /gbdb/panTro3/panTro3.2bit +chrUn_GL395329 19298 /gbdb/panTro3/panTro3.2bit +chr15_GL392218_random 19295 /gbdb/panTro3/panTro3.2bit +chr10_GL391418_random 19288 /gbdb/panTro3/panTro3.2bit +chrUn_GL394509 19284 /gbdb/panTro3/panTro3.2bit +chrUn_GL394730 19253 /gbdb/panTro3/panTro3.2bit +chrUn_GL395202 19247 /gbdb/panTro3/panTro3.2bit +chrUn_GL394099 19242 /gbdb/panTro3/panTro3.2bit +chr16_GL392433_random 19240 /gbdb/panTro3/panTro3.2bit +chr16_GL392477_random 19240 /gbdb/panTro3/panTro3.2bit +chrUn_GL394770 19224 /gbdb/panTro3/panTro3.2bit +chr7_GL390688_random 19218 /gbdb/panTro3/panTro3.2bit +chr16_GL392545_random 19216 /gbdb/panTro3/panTro3.2bit +chr16_GL392378_random 19198 /gbdb/panTro3/panTro3.2bit +chr16_GL392340_random 19194 /gbdb/panTro3/panTro3.2bit +chr7_GL390728_random 19191 /gbdb/panTro3/panTro3.2bit +chr16_GL392522_random 19189 /gbdb/panTro3/panTro3.2bit +chr17_GL392606_random 19159 /gbdb/panTro3/panTro3.2bit +chrUn_GL395792 19154 /gbdb/panTro3/panTro3.2bit +chrUn_GL395629 19124 /gbdb/panTro3/panTro3.2bit +chr3_GL389555_random 19120 /gbdb/panTro3/panTro3.2bit +chrUn_GL394745 19119 /gbdb/panTro3/panTro3.2bit +chrUn_GL395511 19090 /gbdb/panTro3/panTro3.2bit +chr17_GL392618_random 19088 /gbdb/panTro3/panTro3.2bit +chrUn_GL395612 19078 /gbdb/panTro3/panTro3.2bit +chr3_GL389538_random 19070 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158580_random 19064 /gbdb/panTro3/panTro3.2bit +chr5_GL390146_random 19061 /gbdb/panTro3/panTro3.2bit +chr1_GL389078_random 19053 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155434_random 19042 /gbdb/panTro3/panTro3.2bit +chrX_GL393247_random 19036 /gbdb/panTro3/panTro3.2bit +chr9_GL391089_random 19021 /gbdb/panTro3/panTro3.2bit +chr7_GL390651_random 19011 /gbdb/panTro3/panTro3.2bit +chrUn_GL394268 19011 /gbdb/panTro3/panTro3.2bit +chr9_GL390968_random 19003 /gbdb/panTro3/panTro3.2bit +chr1_GL388900_random 18973 /gbdb/panTro3/panTro3.2bit +chr6_GL390249_random 18966 /gbdb/panTro3/panTro3.2bit +chrUn_GL395208 18962 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03163818_random 18961 /gbdb/panTro3/panTro3.2bit +chr15_GL392256_random 18960 /gbdb/panTro3/panTro3.2bit +chr1_GL388991_random 18934 /gbdb/panTro3/panTro3.2bit +chr15_GL392239_random 18933 /gbdb/panTro3/panTro3.2bit +chrUn_GL394658 18924 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395893 18769 /gbdb/panTro3/panTro3.2bit +chrUn_GL395121 18756 /gbdb/panTro3/panTro3.2bit +chr16_GL392450_random 18742 /gbdb/panTro3/panTro3.2bit +chr15_GL392285_random 18731 /gbdb/panTro3/panTro3.2bit +chrUn_GL393494 18728 /gbdb/panTro3/panTro3.2bit +chrUn_GL395537 18695 /gbdb/panTro3/panTro3.2bit +chr16_GL392488_random 18692 /gbdb/panTro3/panTro3.2bit +chr16_GL392425_random 18673 /gbdb/panTro3/panTro3.2bit +chr10_GL391392_random 18648 /gbdb/panTro3/panTro3.2bit +chr3_GL389665_random 18632 /gbdb/panTro3/panTro3.2bit +chr17_GL392642_random 18628 /gbdb/panTro3/panTro3.2bit +chrUn_GL393509 18615 /gbdb/panTro3/panTro3.2bit +chrUn_GL395289 18612 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03172866_random 18606 /gbdb/panTro3/panTro3.2bit +chrUn_GL395641 18597 /gbdb/panTro3/panTro3.2bit +chrUn_GL395189 18587 /gbdb/panTro3/panTro3.2bit +chr7_GL390502_random 18571 /gbdb/panTro3/panTro3.2bit +chr10_GL391648_random 18562 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr7_GL390583_random 18334 /gbdb/panTro3/panTro3.2bit +chr10_GL391649_random 18331 /gbdb/panTro3/panTro3.2bit +chr4_GL389946_random 18326 /gbdb/panTro3/panTro3.2bit +chrUn_GL394152 18321 /gbdb/panTro3/panTro3.2bit +chr14_GL392119_random 18320 /gbdb/panTro3/panTro3.2bit +chr12_GL391976_random 18311 /gbdb/panTro3/panTro3.2bit +chr9_GL391103_random 18303 /gbdb/panTro3/panTro3.2bit +chrUn_GL395555 18291 /gbdb/panTro3/panTro3.2bit +chr4_GL389935_random 18290 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158625_random 18275 /gbdb/panTro3/panTro3.2bit +chr16_GL392373_random 18274 /gbdb/panTro3/panTro3.2bit +chr4_GL389911_random 18239 /gbdb/panTro3/panTro3.2bit +chr9_GL390975_random 18239 /gbdb/panTro3/panTro3.2bit +chrUn_GL395361 18222 /gbdb/panTro3/panTro3.2bit +chrUn_GL395334 18200 /gbdb/panTro3/panTro3.2bit +chrUn_GL395688 18198 /gbdb/panTro3/panTro3.2bit +chrUn_GL395428 18184 /gbdb/panTro3/panTro3.2bit +chrUn_GL395412 18165 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr7_AACZ03160630_random 17991 /gbdb/panTro3/panTro3.2bit +chrUn_GL395200 17990 /gbdb/panTro3/panTro3.2bit +chrUn_GL394794 17989 /gbdb/panTro3/panTro3.2bit +chr7_GL390513_random 17976 /gbdb/panTro3/panTro3.2bit +chrUn_GL395921 17976 /gbdb/panTro3/panTro3.2bit +chrUn_GL395578 17972 /gbdb/panTro3/panTro3.2bit +chr5_GL390142_random 17961 /gbdb/panTro3/panTro3.2bit +chr6_GL390394_random 17960 /gbdb/panTro3/panTro3.2bit +chr4_GL389953_random 17959 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181702 17958 /gbdb/panTro3/panTro3.2bit +chrUn_GL395619 17956 /gbdb/panTro3/panTro3.2bit +chr10_GL391444_random 17955 /gbdb/panTro3/panTro3.2bit +chrUn_GL395634 17955 /gbdb/panTro3/panTro3.2bit +chrUn_GL394663 17950 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174313_random 17943 /gbdb/panTro3/panTro3.2bit +chr15_GL392205_random 17933 /gbdb/panTro3/panTro3.2bit +chrUn_GL395976 17923 /gbdb/panTro3/panTro3.2bit +chr9_GL391154_random 17915 /gbdb/panTro3/panTro3.2bit +chrUn_GL395780 17909 /gbdb/panTro3/panTro3.2bit +chr1_GL389084_random 17906 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149794_random 17900 /gbdb/panTro3/panTro3.2bit +chrUn_GL395687 17890 /gbdb/panTro3/panTro3.2bit +chr7_GL390710_random 17875 /gbdb/panTro3/panTro3.2bit +chrUn_GL395525 17871 /gbdb/panTro3/panTro3.2bit +chrUn_GL394677 17863 /gbdb/panTro3/panTro3.2bit +chr10_GL391652_random 17861 /gbdb/panTro3/panTro3.2bit +chrUn_GL396003 17855 /gbdb/panTro3/panTro3.2bit +chrUn_GL395085 17837 /gbdb/panTro3/panTro3.2bit +chr13_GL392039_random 17834 /gbdb/panTro3/panTro3.2bit +chrUn_GL394709 17820 /gbdb/panTro3/panTro3.2bit +chr10_GL391490_random 17814 /gbdb/panTro3/panTro3.2bit +chr1_GL389037_random 17813 /gbdb/panTro3/panTro3.2bit +chrUn_GL394852 17790 /gbdb/panTro3/panTro3.2bit +chr6_GL390269_random 17785 /gbdb/panTro3/panTro3.2bit +chrUn_GL395587 17753 /gbdb/panTro3/panTro3.2bit +chr8_GL390896_random 17745 /gbdb/panTro3/panTro3.2bit +chrUn_GL395221 17741 /gbdb/panTro3/panTro3.2bit +chr7_GL390648_random 17737 /gbdb/panTro3/panTro3.2bit +chr14_GL392143_random 17724 /gbdb/panTro3/panTro3.2bit +chr9_GL390998_random 17709 /gbdb/panTro3/panTro3.2bit +chr7_GL390530_random 17708 /gbdb/panTro3/panTro3.2bit +chr1_GL389074_random 17706 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03160538_random 17685 /gbdb/panTro3/panTro3.2bit +chr4_GL389844_random 17656 /gbdb/panTro3/panTro3.2bit +chr10_GL391417_random 17630 /gbdb/panTro3/panTro3.2bit +chr9_GL391216_random 17629 /gbdb/panTro3/panTro3.2bit +chrUn_GL393465 17621 /gbdb/panTro3/panTro3.2bit +chrUn_GL396062 17621 /gbdb/panTro3/panTro3.2bit +chrUn_GL395794 17615 /gbdb/panTro3/panTro3.2bit +chrUn_GL395588 17613 /gbdb/panTro3/panTro3.2bit +chr16_GL392402_random 17585 /gbdb/panTro3/panTro3.2bit +chrUn_GL394189 17580 /gbdb/panTro3/panTro3.2bit +chrUn_GL394832 17577 /gbdb/panTro3/panTro3.2bit +chrUn_GL395071 17574 /gbdb/panTro3/panTro3.2bit +chrUn_GL395141 17562 /gbdb/panTro3/panTro3.2bit +chrUn_GL395342 17559 /gbdb/panTro3/panTro3.2bit +chr6_GL390268_random 17557 /gbdb/panTro3/panTro3.2bit +chrUn_GL394854 17543 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03179827 17541 /gbdb/panTro3/panTro3.2bit +chrUn_GL396190 17538 /gbdb/panTro3/panTro3.2bit +chr17_GL392672_random 17533 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180313 17514 /gbdb/panTro3/panTro3.2bit +chr1_GL389213_random 17509 /gbdb/panTro3/panTro3.2bit +chr9_GL391156_random 17507 /gbdb/panTro3/panTro3.2bit +chrUn_GL395879 17505 /gbdb/panTro3/panTro3.2bit +chrUn_GL395940 17505 /gbdb/panTro3/panTro3.2bit +chr17_GL392644_random 17487 /gbdb/panTro3/panTro3.2bit +chrUn_GL395656 17479 /gbdb/panTro3/panTro3.2bit +chrUn_GL395277 17464 /gbdb/panTro3/panTro3.2bit +chr8_GL390906_random 17454 /gbdb/panTro3/panTro3.2bit +chrUn_GL395584 17453 /gbdb/panTro3/panTro3.2bit +chr6_GL390415_random 17452 /gbdb/panTro3/panTro3.2bit +chrUn_GL396215 17449 /gbdb/panTro3/panTro3.2bit +chr12_GL391977_random 17440 /gbdb/panTro3/panTro3.2bit +chrUn_GL394805 17432 /gbdb/panTro3/panTro3.2bit +chrUn_GL395300 17432 /gbdb/panTro3/panTro3.2bit +chrUn_GL394702 17427 /gbdb/panTro3/panTro3.2bit +chrUn_GL395373 17426 /gbdb/panTro3/panTro3.2bit +chrUn_GL395813 17420 /gbdb/panTro3/panTro3.2bit +chr14_GL392147_random 17417 /gbdb/panTro3/panTro3.2bit +chrUn_GL393480 17409 /gbdb/panTro3/panTro3.2bit +chr2A_GL389382_random 17394 /gbdb/panTro3/panTro3.2bit +chrUn_GL395321 17391 /gbdb/panTro3/panTro3.2bit +chrUn_GL396112 17391 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181370 17386 /gbdb/panTro3/panTro3.2bit +chrUn_GL395497 17383 /gbdb/panTro3/panTro3.2bit +chr10_GL391451_random 17373 /gbdb/panTro3/panTro3.2bit +chr10_GL391467_random 17355 /gbdb/panTro3/panTro3.2bit +chr10_GL391454_random 17351 /gbdb/panTro3/panTro3.2bit +chr15_GL392240_random 17348 /gbdb/panTro3/panTro3.2bit +chrUn_GL395186 17345 /gbdb/panTro3/panTro3.2bit +chr1_GL389231_random 17338 /gbdb/panTro3/panTro3.2bit +chrX_GL393169_random 17335 /gbdb/panTro3/panTro3.2bit +chr7_GL390595_random 17325 /gbdb/panTro3/panTro3.2bit +chr1_GL389080_random 17313 /gbdb/panTro3/panTro3.2bit +chrUn_GL395677 17312 /gbdb/panTro3/panTro3.2bit +chrUn_GL395175 17307 /gbdb/panTro3/panTro3.2bit +chr9_GL391113_random 17299 /gbdb/panTro3/panTro3.2bit +chr20_GL392999_random 17297 /gbdb/panTro3/panTro3.2bit +chrUn_GL395065 17284 /gbdb/panTro3/panTro3.2bit +chrUn_GL394449 17282 /gbdb/panTro3/panTro3.2bit +chrUn_GL394308 17277 /gbdb/panTro3/panTro3.2bit +chr9_GL391193_random 17274 /gbdb/panTro3/panTro3.2bit +chr19_GL392957_random 17265 /gbdb/panTro3/panTro3.2bit +chr1_GL389025_random 17265 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180487 17258 /gbdb/panTro3/panTro3.2bit +chr14_GL392144_random 17244 /gbdb/panTro3/panTro3.2bit +chr16_GL392549_random 17244 /gbdb/panTro3/panTro3.2bit +chrUn_GL395389 17235 /gbdb/panTro3/panTro3.2bit +chrUn_GL395018 17230 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174285_random 17225 /gbdb/panTro3/panTro3.2bit +chrUn_GL395331 17221 /gbdb/panTro3/panTro3.2bit +chrUn_GL395146 17217 /gbdb/panTro3/panTro3.2bit +chrUn_GL395757 17217 /gbdb/panTro3/panTro3.2bit +chrUn_GL395263 17203 /gbdb/panTro3/panTro3.2bit +chrUn_GL395825 17201 /gbdb/panTro3/panTro3.2bit +chrUn_GL395460 17197 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181659 17196 /gbdb/panTro3/panTro3.2bit +chrUn_GL395983 17194 /gbdb/panTro3/panTro3.2bit +chrUn_GL395098 17185 /gbdb/panTro3/panTro3.2bit +chr1_GL389153_random 17140 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03163954_random 17138 /gbdb/panTro3/panTro3.2bit +chrUn_GL395408 17134 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164171_random 17130 /gbdb/panTro3/panTro3.2bit +chrUn_GL395305 17128 /gbdb/panTro3/panTro3.2bit +chrUn_GL395640 17122 /gbdb/panTro3/panTro3.2bit +chr1_GL389127_random 17110 /gbdb/panTro3/panTro3.2bit +chr10_GL391642_random 17102 /gbdb/panTro3/panTro3.2bit +chr7_GL390516_random 17092 /gbdb/panTro3/panTro3.2bit +chr11_GL391864_random 17086 /gbdb/panTro3/panTro3.2bit +chrUn_GL395476 17078 /gbdb/panTro3/panTro3.2bit +chrUn_GL395697 17078 /gbdb/panTro3/panTro3.2bit +chrUn_GL395942 17078 /gbdb/panTro3/panTro3.2bit +chr16_GL392482_random 17074 /gbdb/panTro3/panTro3.2bit +chr1_GL389207_random 17063 /gbdb/panTro3/panTro3.2bit +chrUn_GL395367 17052 /gbdb/panTro3/panTro3.2bit +chrUn_GL395803 17042 /gbdb/panTro3/panTro3.2bit +chr8_GL390799_random 17028 /gbdb/panTro3/panTro3.2bit +chrUn_GL394927 17025 /gbdb/panTro3/panTro3.2bit +chrUn_GL396288 17016 /gbdb/panTro3/panTro3.2bit +chrUn_GL394939 17009 /gbdb/panTro3/panTro3.2bit +chrUn_GL395166 17002 /gbdb/panTro3/panTro3.2bit +chr1_GL389117_random 16997 /gbdb/panTro3/panTro3.2bit +chrUn_GL395073 16989 /gbdb/panTro3/panTro3.2bit +chrUn_GL395416 16988 /gbdb/panTro3/panTro3.2bit +chr3_GL389553_random 16984 /gbdb/panTro3/panTro3.2bit +chr9_GL391120_random 16981 /gbdb/panTro3/panTro3.2bit +chrUn_GL394351 16977 /gbdb/panTro3/panTro3.2bit +chr2A_GL389380_random 16973 /gbdb/panTro3/panTro3.2bit +chrUn_GL395229 16969 /gbdb/panTro3/panTro3.2bit +chrUn_GL395536 16969 /gbdb/panTro3/panTro3.2bit +chr10_GL391463_random 16967 /gbdb/panTro3/panTro3.2bit +chrUn_GL395517 16941 /gbdb/panTro3/panTro3.2bit +chrUn_GL394724 16937 /gbdb/panTro3/panTro3.2bit +chrUn_GL395209 16937 /gbdb/panTro3/panTro3.2bit +chrUn_GL395965 16919 /gbdb/panTro3/panTro3.2bit +chr7_GL390717_random 16908 /gbdb/panTro3/panTro3.2bit +chr6_GL390275_random 16899 /gbdb/panTro3/panTro3.2bit +chrUn_GL395475 16890 /gbdb/panTro3/panTro3.2bit +chr7_GL390613_random 16883 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03163899_random 16869 /gbdb/panTro3/panTro3.2bit +chr16_GL392449_random 16861 /gbdb/panTro3/panTro3.2bit +chr1_GL388897_random 16855 /gbdb/panTro3/panTro3.2bit +chrUn_GL395601 16846 /gbdb/panTro3/panTro3.2bit +chrUn_GL395372 16826 /gbdb/panTro3/panTro3.2bit +chr6_GL390352_random 16824 /gbdb/panTro3/panTro3.2bit +chrUn_GL393508 16821 /gbdb/panTro3/panTro3.2bit +chr3_GL389578_random 16801 /gbdb/panTro3/panTro3.2bit +chr16_GL392581_random 16791 /gbdb/panTro3/panTro3.2bit +chr3_GL389664_random 16788 /gbdb/panTro3/panTro3.2bit +chrUn_GL395818 16778 /gbdb/panTro3/panTro3.2bit +chrUn_GL395969 16772 /gbdb/panTro3/panTro3.2bit +chrUn_GL395385 16766 /gbdb/panTro3/panTro3.2bit +chrUn_GL395014 16762 /gbdb/panTro3/panTro3.2bit +chr10_GL391441_random 16759 /gbdb/panTro3/panTro3.2bit +chr14_GL392150_random 16758 /gbdb/panTro3/panTro3.2bit +chrUn_GL395705 16757 /gbdb/panTro3/panTro3.2bit +chrUn_GL395041 16740 /gbdb/panTro3/panTro3.2bit +chrUn_GL395054 16712 /gbdb/panTro3/panTro3.2bit +chr9_GL391169_random 16710 /gbdb/panTro3/panTro3.2bit +chrUn_GL395232 16698 /gbdb/panTro3/panTro3.2bit +chrUn_GL395419 16659 /gbdb/panTro3/panTro3.2bit +chrUn_GL395751 16623 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149634_random 16620 /gbdb/panTro3/panTro3.2bit +chrUn_GL395281 16614 /gbdb/panTro3/panTro3.2bit +chrUn_GL396011 16613 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149844_random 16610 /gbdb/panTro3/panTro3.2bit +chrUn_GL395381 16602 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168126_random 16596 /gbdb/panTro3/panTro3.2bit +chr10_GL391468_random 16590 /gbdb/panTro3/panTro3.2bit +chr10_GL391434_random 16582 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155435_random 16570 /gbdb/panTro3/panTro3.2bit +chr16_GL392501_random 16565 /gbdb/panTro3/panTro3.2bit +chrUn_GL395103 16560 /gbdb/panTro3/panTro3.2bit +chrM 16554 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03151902_random 16553 /gbdb/panTro3/panTro3.2bit +chrUn_GL394851 16546 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150093_random 16522 /gbdb/panTro3/panTro3.2bit +chrUn_GL395285 16496 /gbdb/panTro3/panTro3.2bit +chr1_GL389216_random 16480 /gbdb/panTro3/panTro3.2bit +chrUn_GL395543 16465 /gbdb/panTro3/panTro3.2bit +chr16_GL392478_random 16458 /gbdb/panTro3/panTro3.2bit +chr1_GL388938_random 16454 /gbdb/panTro3/panTro3.2bit +chr16_GL392526_random 16446 /gbdb/panTro3/panTro3.2bit +chrUn_GL393493 16446 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03172779_random 16445 /gbdb/panTro3/panTro3.2bit +chrUn_GL394916 16429 /gbdb/panTro3/panTro3.2bit +chr1_GL389003_random 16422 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394779 16286 /gbdb/panTro3/panTro3.2bit +chrUn_GL395988 16282 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03151919_random 16280 /gbdb/panTro3/panTro3.2bit +chr2A_GL389286_random 16279 /gbdb/panTro3/panTro3.2bit +chr4_GL389831_random 16270 /gbdb/panTro3/panTro3.2bit +chr6_GL390418_random 16270 /gbdb/panTro3/panTro3.2bit +chr9_GL391083_random 16267 /gbdb/panTro3/panTro3.2bit +chrUn_GL395496 16255 /gbdb/panTro3/panTro3.2bit +chr9_GL391201_random 16247 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164000_random 16239 /gbdb/panTro3/panTro3.2bit +chrUn_GL395845 16236 /gbdb/panTro3/panTro3.2bit +chr1_GL388942_random 16224 /gbdb/panTro3/panTro3.2bit +chr3_GL389648_random 16221 /gbdb/panTro3/panTro3.2bit +chrUn_GL396323 16205 /gbdb/panTro3/panTro3.2bit +chrUn_GL395445 16202 /gbdb/panTro3/panTro3.2bit +chr6_GL390406_random 16201 /gbdb/panTro3/panTro3.2bit +chrUn_GL395404 16200 /gbdb/panTro3/panTro3.2bit +chrUn_GL395967 16198 /gbdb/panTro3/panTro3.2bit +chrUn_GL395936 16190 /gbdb/panTro3/panTro3.2bit +chr4_GL389945_random 16185 /gbdb/panTro3/panTro3.2bit +chrUn_GL393483 16181 /gbdb/panTro3/panTro3.2bit +chrUn_GL395059 16181 /gbdb/panTro3/panTro3.2bit +chr2A_GL389319_random 16168 /gbdb/panTro3/panTro3.2bit +chr9_GL391158_random 16147 /gbdb/panTro3/panTro3.2bit +chrUn_GL395827 16142 /gbdb/panTro3/panTro3.2bit +chrUn_GL395674 16136 /gbdb/panTro3/panTro3.2bit +chr10_GL391450_random 16133 /gbdb/panTro3/panTro3.2bit +chrUn_GL395435 16132 /gbdb/panTro3/panTro3.2bit +chr16_GL392471_random 16122 /gbdb/panTro3/panTro3.2bit +chr9_GL391050_random 16122 /gbdb/panTro3/panTro3.2bit +chr2A_GL389364_random 16111 /gbdb/panTro3/panTro3.2bit +chr1_GL389056_random 16099 /gbdb/panTro3/panTro3.2bit +chrX_GL393384_random 16086 /gbdb/panTro3/panTro3.2bit +chr11_GL391828_random 16081 /gbdb/panTro3/panTro3.2bit +chr9_GL390989_random 16080 /gbdb/panTro3/panTro3.2bit +chr7_GL390729_random 16071 /gbdb/panTro3/panTro3.2bit +chrUn_GL395528 16070 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr4_GL389871_random 15929 /gbdb/panTro3/panTro3.2bit +chrUn_GL395864 15914 /gbdb/panTro3/panTro3.2bit +chrUn_GL396156 15914 /gbdb/panTro3/panTro3.2bit +chrUn_GL395363 15896 /gbdb/panTro3/panTro3.2bit +chr6_GL390281_random 15890 /gbdb/panTro3/panTro3.2bit +chrUn_GL395602 15875 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181884 15874 /gbdb/panTro3/panTro3.2bit +chrUn_GL395364 15872 /gbdb/panTro3/panTro3.2bit +chr16_GL392385_random 15865 /gbdb/panTro3/panTro3.2bit +chrUn_GL395947 15865 /gbdb/panTro3/panTro3.2bit +chrUn_GL395782 15853 /gbdb/panTro3/panTro3.2bit +chrUn_GL395678 15848 /gbdb/panTro3/panTro3.2bit +chr10_GL391484_random 15825 /gbdb/panTro3/panTro3.2bit +chrUn_GL395074 15806 /gbdb/panTro3/panTro3.2bit +chr9_GL391217_random 15800 /gbdb/panTro3/panTro3.2bit +chrUn_GL395477 15794 /gbdb/panTro3/panTro3.2bit +chrX_GL393191_random 15794 /gbdb/panTro3/panTro3.2bit +chrUn_GL395727 15783 /gbdb/panTro3/panTro3.2bit +chr4_GL389785_random 15774 /gbdb/panTro3/panTro3.2bit +chr6_GL390405_random 15770 /gbdb/panTro3/panTro3.2bit +chr9_GL390992_random 15764 /gbdb/panTro3/panTro3.2bit +chr1_GL389027_random 15763 /gbdb/panTro3/panTro3.2bit +chrUn_GL395306 15758 /gbdb/panTro3/panTro3.2bit +chrX_GL393377_random 15744 /gbdb/panTro3/panTro3.2bit +chr2A_GL389353_random 15740 /gbdb/panTro3/panTro3.2bit +chrUn_GL395834 15736 /gbdb/panTro3/panTro3.2bit +chrUn_GL395244 15730 /gbdb/panTro3/panTro3.2bit +chr4_GL389798_random 15726 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149767_random 15708 /gbdb/panTro3/panTro3.2bit +chrUn_GL396095 15704 /gbdb/panTro3/panTro3.2bit +chrUn_GL395237 15703 /gbdb/panTro3/panTro3.2bit +chrUn_GL395375 15702 /gbdb/panTro3/panTro3.2bit +chrUn_GL395887 15696 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181260 15690 /gbdb/panTro3/panTro3.2bit +chrUn_GL395261 15684 /gbdb/panTro3/panTro3.2bit +chr17_GL392607_random 15676 /gbdb/panTro3/panTro3.2bit +chrUn_GL395633 15676 /gbdb/panTro3/panTro3.2bit +chrUn_GL396041 15673 /gbdb/panTro3/panTro3.2bit +chrUn_GL395368 15661 /gbdb/panTro3/panTro3.2bit +chrUn_GL394625 15654 /gbdb/panTro3/panTro3.2bit +chr4_GL389777_random 15642 /gbdb/panTro3/panTro3.2bit +chr11_GL391751_random 15640 /gbdb/panTro3/panTro3.2bit +chr6_GL390369_random 15635 /gbdb/panTro3/panTro3.2bit +chr1_GL388937_random 15622 /gbdb/panTro3/panTro3.2bit +chr15_GL392222_random 15618 /gbdb/panTro3/panTro3.2bit +chr1_GL388934_random 15617 /gbdb/panTro3/panTro3.2bit +chr10_GL391439_random 15615 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149820_random 15605 /gbdb/panTro3/panTro3.2bit +chrUn_GL395534 15602 /gbdb/panTro3/panTro3.2bit +chr9_GL390984_random 15595 /gbdb/panTro3/panTro3.2bit +chr7_GL390715_random 15593 /gbdb/panTro3/panTro3.2bit +chrUn_GL395914 15590 /gbdb/panTro3/panTro3.2bit +chr6_GL390363_random 15580 /gbdb/panTro3/panTro3.2bit +chrUn_GL395997 15567 /gbdb/panTro3/panTro3.2bit +chrUn_GL395488 15560 /gbdb/panTro3/panTro3.2bit +chrUn_GL395500 15553 /gbdb/panTro3/panTro3.2bit +chrUn_GL395134 15552 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164038_random 15540 /gbdb/panTro3/panTro3.2bit +chr8_GL390824_random 15530 /gbdb/panTro3/panTro3.2bit +chr9_GL391068_random 15526 /gbdb/panTro3/panTro3.2bit +chrUn_GL394430 15518 /gbdb/panTro3/panTro3.2bit +chrUn_GL395841 15511 /gbdb/panTro3/panTro3.2bit +chrUn_GL395786 15509 /gbdb/panTro3/panTro3.2bit +chrX_GL393154_random 15497 /gbdb/panTro3/panTro3.2bit +chrUn_GL395797 15487 /gbdb/panTro3/panTro3.2bit +chr22_GL393074_random 15485 /gbdb/panTro3/panTro3.2bit +chr11_GL391807_random 15478 /gbdb/panTro3/panTro3.2bit +chr4_GL389947_random 15478 /gbdb/panTro3/panTro3.2bit +chr1_GL389038_random 15475 /gbdb/panTro3/panTro3.2bit +chr4_GL389952_random 15471 /gbdb/panTro3/panTro3.2bit +chr9_GL391080_random 15468 /gbdb/panTro3/panTro3.2bit +chr9_GL391149_random 15460 /gbdb/panTro3/panTro3.2bit +chr1_GL388918_random 15450 /gbdb/panTro3/panTro3.2bit +chrUn_GL396440 15447 /gbdb/panTro3/panTro3.2bit +chrUn_GL395284 15441 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395532 15315 /gbdb/panTro3/panTro3.2bit +chrUn_GL395594 15295 /gbdb/panTro3/panTro3.2bit +chr10_GL391687_random 15285 /gbdb/panTro3/panTro3.2bit +chrUn_GL396363 15275 /gbdb/panTro3/panTro3.2bit +chr2A_GL389378_random 15270 /gbdb/panTro3/panTro3.2bit +chrUn_GL395292 15266 /gbdb/panTro3/panTro3.2bit +chr7_GL390713_random 15265 /gbdb/panTro3/panTro3.2bit +chr2B_GL389465_random 15261 /gbdb/panTro3/panTro3.2bit +chrUn_GL395319 15251 /gbdb/panTro3/panTro3.2bit +chrUn_GL395644 15244 /gbdb/panTro3/panTro3.2bit +chr1_GL389155_random 15242 /gbdb/panTro3/panTro3.2bit +chr7_GL390567_random 15230 /gbdb/panTro3/panTro3.2bit +chrUn_GL395606 15217 /gbdb/panTro3/panTro3.2bit +chrUn_GL396414 15212 /gbdb/panTro3/panTro3.2bit +chrUn_GL394513 15204 /gbdb/panTro3/panTro3.2bit +chrUn_GL395028 15201 /gbdb/panTro3/panTro3.2bit +chrUn_GL395589 15201 /gbdb/panTro3/panTro3.2bit +chr1_GL388927_random 15198 /gbdb/panTro3/panTro3.2bit +chrUn_GL395501 15198 /gbdb/panTro3/panTro3.2bit +chr1_GL389047_random 15197 /gbdb/panTro3/panTro3.2bit +chrUn_GL395657 15194 /gbdb/panTro3/panTro3.2bit +chrUn_GL395617 15188 /gbdb/panTro3/panTro3.2bit +chrUn_GL395907 15179 /gbdb/panTro3/panTro3.2bit +chr9_GL391185_random 15176 /gbdb/panTro3/panTro3.2bit +chrUn_GL395799 15168 /gbdb/panTro3/panTro3.2bit +chrUn_GL395506 15161 /gbdb/panTro3/panTro3.2bit +chr9_GL391100_random 15158 /gbdb/panTro3/panTro3.2bit +chr4_GL389860_random 15152 /gbdb/panTro3/panTro3.2bit +chrUn_GL395464 15137 /gbdb/panTro3/panTro3.2bit +chr16_GL392454_random 15135 /gbdb/panTro3/panTro3.2bit +chrUn_GL396007 15118 /gbdb/panTro3/panTro3.2bit +chrUn_GL395167 15112 /gbdb/panTro3/panTro3.2bit +chrUn_GL394300 15109 /gbdb/panTro3/panTro3.2bit +chr9_GL391188_random 15106 /gbdb/panTro3/panTro3.2bit +chr9_GL390983_random 15095 /gbdb/panTro3/panTro3.2bit +chrUn_GL395253 15066 /gbdb/panTro3/panTro3.2bit +chr16_GL392339_random 15065 /gbdb/panTro3/panTro3.2bit +chr1_GL389130_random 15063 /gbdb/panTro3/panTro3.2bit +chrUn_GL395703 15053 /gbdb/panTro3/panTro3.2bit +chrUn_GL395198 15045 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171846_random 15037 /gbdb/panTro3/panTro3.2bit +chrUn_GL395847 15031 /gbdb/panTro3/panTro3.2bit +chr8_GL390787_random 15030 /gbdb/panTro3/panTro3.2bit +chrUn_GL396080 15021 /gbdb/panTro3/panTro3.2bit +chr1_GL389085_random 15008 /gbdb/panTro3/panTro3.2bit +chr9_GL391092_random 15002 /gbdb/panTro3/panTro3.2bit +chrUn_GL394993 14996 /gbdb/panTro3/panTro3.2bit +chrUn_GL394945 14991 /gbdb/panTro3/panTro3.2bit +chrUn_GL395886 14991 /gbdb/panTro3/panTro3.2bit +chrUn_GL395433 14988 /gbdb/panTro3/panTro3.2bit +chrUn_GL395943 14988 /gbdb/panTro3/panTro3.2bit +chr15_GL392217_random 14986 /gbdb/panTro3/panTro3.2bit +chr4_GL389835_random 14982 /gbdb/panTro3/panTro3.2bit +chrUn_GL395410 14979 /gbdb/panTro3/panTro3.2bit +chrUn_GL396058 14973 /gbdb/panTro3/panTro3.2bit +chr16_GL392577_random 14968 /gbdb/panTro3/panTro3.2bit +chr2A_GL389317_random 14968 /gbdb/panTro3/panTro3.2bit +chr1_GL389092_random 14953 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150028_random 14943 /gbdb/panTro3/panTro3.2bit +chr3_GL389673_random 14942 /gbdb/panTro3/panTro3.2bit +chr14_GL392120_random 14936 /gbdb/panTro3/panTro3.2bit +chrUn_GL393506 14936 /gbdb/panTro3/panTro3.2bit +chrUn_GL395779 14934 /gbdb/panTro3/panTro3.2bit +chrUn_GL395741 14921 /gbdb/panTro3/panTro3.2bit +chrUn_GL395666 14915 /gbdb/panTro3/panTro3.2bit +chr3_GL389643_random 14913 /gbdb/panTro3/panTro3.2bit +chrUn_GL395327 14911 /gbdb/panTro3/panTro3.2bit +chrUn_GL395978 14908 /gbdb/panTro3/panTro3.2bit +chr16_GL392480_random 14907 /gbdb/panTro3/panTro3.2bit +chr4_GL389808_random 14904 /gbdb/panTro3/panTro3.2bit +chr7_GL390684_random 14891 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180456 14890 /gbdb/panTro3/panTro3.2bit +chrUn_GL395870 14889 /gbdb/panTro3/panTro3.2bit +chr2A_GL389363_random 14887 /gbdb/panTro3/panTro3.2bit +chrUn_GL396073 14887 /gbdb/panTro3/panTro3.2bit +chrUn_GL395767 14886 /gbdb/panTro3/panTro3.2bit +chrUn_GL396459 14886 /gbdb/panTro3/panTro3.2bit +chrUn_GL395590 14878 /gbdb/panTro3/panTro3.2bit +chrUn_GL395804 14865 /gbdb/panTro3/panTro3.2bit +chr1_GL389014_random 14853 /gbdb/panTro3/panTro3.2bit +chr5_GL390062_random 14824 /gbdb/panTro3/panTro3.2bit +chr22_GL393065_random 14823 /gbdb/panTro3/panTro3.2bit +chr9_GL391099_random 14811 /gbdb/panTro3/panTro3.2bit +chr16_GL392418_random 14808 /gbdb/panTro3/panTro3.2bit +chr17_GL392678_random 14802 /gbdb/panTro3/panTro3.2bit +chrUn_GL395565 14794 /gbdb/panTro3/panTro3.2bit +chrUn_GL395356 14789 /gbdb/panTro3/panTro3.2bit +chr16_GL392436_random 14785 /gbdb/panTro3/panTro3.2bit +chrUn_GL396038 14778 /gbdb/panTro3/panTro3.2bit +chrUn_GL395510 14768 /gbdb/panTro3/panTro3.2bit +chr6_GL390283_random 14764 /gbdb/panTro3/panTro3.2bit +chr7_GL390505_random 14753 /gbdb/panTro3/panTro3.2bit +chrUn_GL394822 14746 /gbdb/panTro3/panTro3.2bit +chr16_GL392503_random 14745 /gbdb/panTro3/panTro3.2bit +chr2B_GL389471_random 14737 /gbdb/panTro3/panTro3.2bit +chrUn_GL395624 14721 /gbdb/panTro3/panTro3.2bit +chrUn_GL396009 14721 /gbdb/panTro3/panTro3.2bit +chr1_GL389093_random 14716 /gbdb/panTro3/panTro3.2bit +chr16_GL392393_random 14708 /gbdb/panTro3/panTro3.2bit +chrUn_GL396401 14707 /gbdb/panTro3/panTro3.2bit +chr4_GL389933_random 14705 /gbdb/panTro3/panTro3.2bit +chr9_GL391213_random 14701 /gbdb/panTro3/panTro3.2bit +chrUn_GL395696 14699 /gbdb/panTro3/panTro3.2bit +chrUn_GL396429 14699 /gbdb/panTro3/panTro3.2bit +chr16_GL392469_random 14669 /gbdb/panTro3/panTro3.2bit +chr10_GL391473_random 14666 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149819_random 14666 /gbdb/panTro3/panTro3.2bit +chrUn_GL395732 14663 /gbdb/panTro3/panTro3.2bit +chrUn_GL395894 14662 /gbdb/panTro3/panTro3.2bit +chrUn_GL394199 14645 /gbdb/panTro3/panTro3.2bit +chrUn_GL395665 14640 /gbdb/panTro3/panTro3.2bit +chrUn_GL396180 14636 /gbdb/panTro3/panTro3.2bit +chrUn_GL395386 14621 /gbdb/panTro3/panTro3.2bit +chr9_GL391007_random 14603 /gbdb/panTro3/panTro3.2bit +chr9_GL391175_random 14602 /gbdb/panTro3/panTro3.2bit +chrUn_GL395995 14602 /gbdb/panTro3/panTro3.2bit +chrUn_GL396074 14602 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182055 14599 /gbdb/panTro3/panTro3.2bit +chr1_GL388990_random 14596 /gbdb/panTro3/panTro3.2bit +chrUn_GL395672 14594 /gbdb/panTro3/panTro3.2bit +chr1_GL389046_random 14590 /gbdb/panTro3/panTro3.2bit +chr1_GL389132_random 14576 /gbdb/panTro3/panTro3.2bit +chrUn_GL395912 14569 /gbdb/panTro3/panTro3.2bit +chrUn_GL395611 14567 /gbdb/panTro3/panTro3.2bit +chr7_GL390473_random 14546 /gbdb/panTro3/panTro3.2bit +chr7_GL390726_random 14535 /gbdb/panTro3/panTro3.2bit +chrUn_GL394594 14531 /gbdb/panTro3/panTro3.2bit +chrUn_GL395052 14523 /gbdb/panTro3/panTro3.2bit +chrX_GL393346_random 14498 /gbdb/panTro3/panTro3.2bit +chr20_GL393011_random 14493 /gbdb/panTro3/panTro3.2bit +chr11_GL391865_random 14490 /gbdb/panTro3/panTro3.2bit +chrUn_GL395681 14469 /gbdb/panTro3/panTro3.2bit +chrUn_GL395623 14464 /gbdb/panTro3/panTro3.2bit +chrUn_GL396455 14456 /gbdb/panTro3/panTro3.2bit +chr6_GL390266_random 14448 /gbdb/panTro3/panTro3.2bit +chr6_GL390246_random 14446 /gbdb/panTro3/panTro3.2bit +chr18_GL392799_random 14444 /gbdb/panTro3/panTro3.2bit +chrUn_GL395670 14435 /gbdb/panTro3/panTro3.2bit +chr1_GL389000_random 14429 /gbdb/panTro3/panTro3.2bit +chrUn_GL395541 14429 /gbdb/panTro3/panTro3.2bit +chrUn_GL394874 14425 /gbdb/panTro3/panTro3.2bit +chrUn_GL395426 14424 /gbdb/panTro3/panTro3.2bit +chrX_GL393305_random 14422 /gbdb/panTro3/panTro3.2bit +chr16_GL392407_random 14420 /gbdb/panTro3/panTro3.2bit +chr7_GL390691_random 14415 /gbdb/panTro3/panTro3.2bit +chrUn_GL395689 14407 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03163819_random 14406 /gbdb/panTro3/panTro3.2bit +chr8_GL390907_random 14402 /gbdb/panTro3/panTro3.2bit +chrUn_GL394938 14397 /gbdb/panTro3/panTro3.2bit +chrUn_GL395313 14396 /gbdb/panTro3/panTro3.2bit +chrUn_GL395051 14394 /gbdb/panTro3/panTro3.2bit +chrUn_GL395459 14394 /gbdb/panTro3/panTro3.2bit +chrUn_GL395816 14391 /gbdb/panTro3/panTro3.2bit +chr22_GL393081_random 14387 /gbdb/panTro3/panTro3.2bit +chrX_GL393170_random 14379 /gbdb/panTro3/panTro3.2bit +chr17_GL392697_random 14375 /gbdb/panTro3/panTro3.2bit +chrUn_GL395896 14372 /gbdb/panTro3/panTro3.2bit +chr4_GL389960_random 14367 /gbdb/panTro3/panTro3.2bit +chr6_GL390270_random 14367 /gbdb/panTro3/panTro3.2bit +chrUn_GL395177 14366 /gbdb/panTro3/panTro3.2bit +chr16_GL392476_random 14349 /gbdb/panTro3/panTro3.2bit +chrUn_GL395044 14345 /gbdb/panTro3/panTro3.2bit +chrUn_GL395370 14343 /gbdb/panTro3/panTro3.2bit +chrUn_GL395924 14343 /gbdb/panTro3/panTro3.2bit +chr16_GL392474_random 14319 /gbdb/panTro3/panTro3.2bit +chrUn_GL396184 14318 /gbdb/panTro3/panTro3.2bit +chr9_GL391101_random 14314 /gbdb/panTro3/panTro3.2bit +chrUn_GL395245 14314 /gbdb/panTro3/panTro3.2bit +chrUn_GL395743 14314 /gbdb/panTro3/panTro3.2bit +chrUn_GL395783 14312 /gbdb/panTro3/panTro3.2bit +chrUn_GL395740 14308 /gbdb/panTro3/panTro3.2bit +chrX_GL393212_random 14307 /gbdb/panTro3/panTro3.2bit +chr7_GL390753_random 14300 /gbdb/panTro3/panTro3.2bit +chr9_GL391196_random 14299 /gbdb/panTro3/panTro3.2bit +chrUn_GL394891 14297 /gbdb/panTro3/panTro3.2bit +chrUn_GL395465 14290 /gbdb/panTro3/panTro3.2bit +chr19_GL392885_random 14268 /gbdb/panTro3/panTro3.2bit +chr9_GL390981_random 14267 /gbdb/panTro3/panTro3.2bit +chrUn_GL395682 14254 /gbdb/panTro3/panTro3.2bit +chr9_GL391002_random 14244 /gbdb/panTro3/panTro3.2bit +chrUn_GL395424 14234 /gbdb/panTro3/panTro3.2bit +chr14_GL392153_random 14226 /gbdb/panTro3/panTro3.2bit +chr17_GL392659_random 14221 /gbdb/panTro3/panTro3.2bit +chrUn_GL395788 14221 /gbdb/panTro3/panTro3.2bit +chr1_GL389073_random 14219 /gbdb/panTro3/panTro3.2bit +chrUn_GL395830 14219 /gbdb/panTro3/panTro3.2bit +chr18_GL392803_random 14218 /gbdb/panTro3/panTro3.2bit +chrUn_GL395648 14211 /gbdb/panTro3/panTro3.2bit +chr1_GL388868_random 14205 /gbdb/panTro3/panTro3.2bit +chr6_GL390409_random 14203 /gbdb/panTro3/panTro3.2bit +chr11_GL391781_random 14201 /gbdb/panTro3/panTro3.2bit +chrUn_GL395574 14193 /gbdb/panTro3/panTro3.2bit +chrUn_GL394987 14191 /gbdb/panTro3/panTro3.2bit +chr2B_GL389476_random 14186 /gbdb/panTro3/panTro3.2bit +chr6_GL390398_random 14186 /gbdb/panTro3/panTro3.2bit +chr2A_GL389355_random 14184 /gbdb/panTro3/panTro3.2bit +chr1_GL389180_random 14182 /gbdb/panTro3/panTro3.2bit +chrUn_GL396173 14179 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181338 14172 /gbdb/panTro3/panTro3.2bit +chr16_GL392525_random 14170 /gbdb/panTro3/panTro3.2bit +chr9_GL391157_random 14168 /gbdb/panTro3/panTro3.2bit +chr9_GL391152_random 14157 /gbdb/panTro3/panTro3.2bit +chrUn_GL396230 14150 /gbdb/panTro3/panTro3.2bit +chr4_GL389836_random 14133 /gbdb/panTro3/panTro3.2bit +chrUn_GL395922 14128 /gbdb/panTro3/panTro3.2bit +chr6_GL390427_random 14111 /gbdb/panTro3/panTro3.2bit +chrUn_GL395934 14106 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181639 14105 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395554 13890 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03163837_random 13889 /gbdb/panTro3/panTro3.2bit +chr7_GL390507_random 13871 /gbdb/panTro3/panTro3.2bit +chrUn_GL395728 13868 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174407_random 13867 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03160591_random 13857 /gbdb/panTro3/panTro3.2bit +chrUn_GL395516 13844 /gbdb/panTro3/panTro3.2bit +chr16_GL392548_random 13833 /gbdb/panTro3/panTro3.2bit +chrUn_GL395461 13833 /gbdb/panTro3/panTro3.2bit +chr16_GL392416_random 13829 /gbdb/panTro3/panTro3.2bit +chr17_GL392671_random 13820 /gbdb/panTro3/panTro3.2bit +chrUn_GL394544 13820 /gbdb/panTro3/panTro3.2bit +chr8_GL390823_random 13817 /gbdb/panTro3/panTro3.2bit +chr1_GL389240_random 13813 /gbdb/panTro3/panTro3.2bit +chr6_GL390282_random 13807 /gbdb/panTro3/panTro3.2bit +chrUn_GL396367 13807 /gbdb/panTro3/panTro3.2bit +chr15_GL392221_random 13787 /gbdb/panTro3/panTro3.2bit +chrUn_GL395336 13786 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr6_GL390399_random 13707 /gbdb/panTro3/panTro3.2bit +chr19_GL392857_random 13699 /gbdb/panTro3/panTro3.2bit +chrUn_GL396005 13696 /gbdb/panTro3/panTro3.2bit +chrUn_GL395458 13687 /gbdb/panTro3/panTro3.2bit +chr16_GL392430_random 13685 /gbdb/panTro3/panTro3.2bit +chr1_GL388999_random 13682 /gbdb/panTro3/panTro3.2bit +chrUn_GL395971 13682 /gbdb/panTro3/panTro3.2bit +chrUn_GL396071 13676 /gbdb/panTro3/panTro3.2bit +chr1_GL389051_random 13668 /gbdb/panTro3/panTro3.2bit +chrUn_GL395961 13664 /gbdb/panTro3/panTro3.2bit +chrUn_GL395954 13663 /gbdb/panTro3/panTro3.2bit +chrUn_GL396037 13654 /gbdb/panTro3/panTro3.2bit +chrUn_GL396085 13644 /gbdb/panTro3/panTro3.2bit +chr6_GL390286_random 13642 /gbdb/panTro3/panTro3.2bit +chr11_GL391753_random 13641 /gbdb/panTro3/panTro3.2bit +chr15_GL392215_random 13631 /gbdb/panTro3/panTro3.2bit +chrUn_GL395495 13630 /gbdb/panTro3/panTro3.2bit +chr18_GL392800_random 13629 /gbdb/panTro3/panTro3.2bit +chrUn_GL394478 13629 /gbdb/panTro3/panTro3.2bit +chr6_GL390262_random 13605 /gbdb/panTro3/panTro3.2bit +chrUn_GL395718 13598 /gbdb/panTro3/panTro3.2bit +chrUn_GL395241 13594 /gbdb/panTro3/panTro3.2bit +chrUn_GL396060 13588 /gbdb/panTro3/panTro3.2bit +chrUn_GL395502 13579 /gbdb/panTro3/panTro3.2bit +chr9_GL391180_random 13573 /gbdb/panTro3/panTro3.2bit +chrUn_GL395669 13569 /gbdb/panTro3/panTro3.2bit +chrUn_GL395883 13557 /gbdb/panTro3/panTro3.2bit +chrUn_GL395719 13555 /gbdb/panTro3/panTro3.2bit +chrUn_GL395820 13553 /gbdb/panTro3/panTro3.2bit +chrUn_GL395414 13551 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174363_random 13550 /gbdb/panTro3/panTro3.2bit +chrUn_GL395569 13546 /gbdb/panTro3/panTro3.2bit +chr7_GL390508_random 13538 /gbdb/panTro3/panTro3.2bit +chrUn_GL395653 13537 /gbdb/panTro3/panTro3.2bit +chr1_GL389032_random 13536 /gbdb/panTro3/panTro3.2bit +chr16_GL392461_random 13533 /gbdb/panTro3/panTro3.2bit +chr9_GL391202_random 13532 /gbdb/panTro3/panTro3.2bit +chrUn_GL395470 13526 /gbdb/panTro3/panTro3.2bit +chr11_GL391854_random 13521 /gbdb/panTro3/panTro3.2bit +chr11_GL391861_random 13519 /gbdb/panTro3/panTro3.2bit +chrUn_GL395108 13519 /gbdb/panTro3/panTro3.2bit +chr6_GL390419_random 13518 /gbdb/panTro3/panTro3.2bit +chr9_GL391125_random 13518 /gbdb/panTro3/panTro3.2bit +chrUn_GL395846 13516 /gbdb/panTro3/panTro3.2bit +chrUn_GL395603 13511 /gbdb/panTro3/panTro3.2bit +chr7_GL390500_random 13505 /gbdb/panTro3/panTro3.2bit +chrUn_GL396473 13504 /gbdb/panTro3/panTro3.2bit +chrUn_GL395977 13502 /gbdb/panTro3/panTro3.2bit +chrUn_GL395842 13497 /gbdb/panTro3/panTro3.2bit +chr4_GL389915_random 13494 /gbdb/panTro3/panTro3.2bit +chr9_GL391044_random 13482 /gbdb/panTro3/panTro3.2bit +chrUn_GL395721 13478 /gbdb/panTro3/panTro3.2bit +chrX_GL393404_random 13476 /gbdb/panTro3/panTro3.2bit +chr16_GL392514_random 13475 /gbdb/panTro3/panTro3.2bit +chr7_GL390678_random 13473 /gbdb/panTro3/panTro3.2bit +chrUn_GL396220 13465 /gbdb/panTro3/panTro3.2bit +chrUn_GL396057 13463 /gbdb/panTro3/panTro3.2bit +chr15_GL392207_random 13460 /gbdb/panTro3/panTro3.2bit +chr15_GL392214_random 13453 /gbdb/panTro3/panTro3.2bit +chr16_GL392381_random 13453 /gbdb/panTro3/panTro3.2bit +chr8_GL390893_random 13453 /gbdb/panTro3/panTro3.2bit +chrUn_GL394952 13450 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03179818 13447 /gbdb/panTro3/panTro3.2bit +chr11_GL391839_random 13446 /gbdb/panTro3/panTro3.2bit +chr1_GL389115_random 13445 /gbdb/panTro3/panTro3.2bit +chrUn_GL395314 13441 /gbdb/panTro3/panTro3.2bit +chr1_GL388930_random 13437 /gbdb/panTro3/panTro3.2bit +chr16_GL392417_random 13436 /gbdb/panTro3/panTro3.2bit +chrUn_GL396610 13425 /gbdb/panTro3/panTro3.2bit +chrUn_GL395645 13415 /gbdb/panTro3/panTro3.2bit +chrUn_GL395449 13408 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03160588_random 13406 /gbdb/panTro3/panTro3.2bit +chr8_GL390826_random 13403 /gbdb/panTro3/panTro3.2bit +chr7_GL390703_random 13398 /gbdb/panTro3/panTro3.2bit +chrUn_GL395302 13394 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr1_GL388924_random 13137 /gbdb/panTro3/panTro3.2bit +chr16_GL392468_random 13134 /gbdb/panTro3/panTro3.2bit +chrUn_GL395213 13128 /gbdb/panTro3/panTro3.2bit +chrUn_GL395557 13125 /gbdb/panTro3/panTro3.2bit +chrUn_GL396048 13125 /gbdb/panTro3/panTro3.2bit +chr6_GL390285_random 13123 /gbdb/panTro3/panTro3.2bit +chrUn_GL395110 13114 /gbdb/panTro3/panTro3.2bit +chrUn_GL396055 13111 /gbdb/panTro3/panTro3.2bit +chrUn_GL396965 13111 /gbdb/panTro3/panTro3.2bit +chrUn_GL395004 13110 /gbdb/panTro3/panTro3.2bit +chr6_GL390421_random 13105 /gbdb/panTro3/panTro3.2bit +chrUn_GL394933 13102 /gbdb/panTro3/panTro3.2bit +chr11_GL391797_random 13093 /gbdb/panTro3/panTro3.2bit +chr16_GL392574_random 13083 /gbdb/panTro3/panTro3.2bit +chrUn_GL395165 13079 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180442 13060 /gbdb/panTro3/panTro3.2bit +chr4_GL389963_random 13054 /gbdb/panTro3/panTro3.2bit +chr9_GL391161_random 13054 /gbdb/panTro3/panTro3.2bit +chrUn_GL396212 13053 /gbdb/panTro3/panTro3.2bit +chr12_GL391929_random 13052 /gbdb/panTro3/panTro3.2bit +chrUn_GL395539 13051 /gbdb/panTro3/panTro3.2bit +chr17_GL392615_random 13042 /gbdb/panTro3/panTro3.2bit +chr7_GL390528_random 13039 /gbdb/panTro3/panTro3.2bit +chrUn_GL394950 13039 /gbdb/panTro3/panTro3.2bit +chrUn_GL395114 13030 /gbdb/panTro3/panTro3.2bit +chr15_GL392211_random 13025 /gbdb/panTro3/panTro3.2bit +chrUn_GL395031 13024 /gbdb/panTro3/panTro3.2bit +chr7_GL390639_random 13023 /gbdb/panTro3/panTro3.2bit +chr7_GL390693_random 13021 /gbdb/panTro3/panTro3.2bit +chrUn_GL396263 13017 /gbdb/panTro3/panTro3.2bit +chrX_GL393251_random 13008 /gbdb/panTro3/panTro3.2bit +chr1_GL389049_random 13007 /gbdb/panTro3/panTro3.2bit +chrUn_GL394961 12996 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03160577_random 12993 /gbdb/panTro3/panTro3.2bit +chr7_GL390705_random 12993 /gbdb/panTro3/panTro3.2bit +chrUn_GL396141 12989 /gbdb/panTro3/panTro3.2bit +chr7_GL390652_random 12988 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr8_GL390834_random 12637 /gbdb/panTro3/panTro3.2bit +chrUn_GL396108 12633 /gbdb/panTro3/panTro3.2bit +chr18_GL392822_random 12632 /gbdb/panTro3/panTro3.2bit +chrUn_GL395906 12632 /gbdb/panTro3/panTro3.2bit +chrUn_GL395021 12630 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182957 12626 /gbdb/panTro3/panTro3.2bit +chrUn_GL396036 12624 /gbdb/panTro3/panTro3.2bit +chrUn_GL396540 12618 /gbdb/panTro3/panTro3.2bit +chrUn_GL395605 12612 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180441 12606 /gbdb/panTro3/panTro3.2bit +chr11_GL391832_random 12603 /gbdb/panTro3/panTro3.2bit +chrUn_GL396165 12602 /gbdb/panTro3/panTro3.2bit +chr4_GL389850_random 12581 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182644 12577 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152800_random 12562 /gbdb/panTro3/panTro3.2bit +chrUn_GL395377 12561 /gbdb/panTro3/panTro3.2bit +chrUn_GL394722 12560 /gbdb/panTro3/panTro3.2bit +chr15_GL392251_random 12548 /gbdb/panTro3/panTro3.2bit +chr2A_GL389303_random 12547 /gbdb/panTro3/panTro3.2bit +chr22_GL393072_random 12546 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149968_random 12544 /gbdb/panTro3/panTro3.2bit +chr5_GL390155_random 12528 /gbdb/panTro3/panTro3.2bit +chrUn_GL395901 12526 /gbdb/panTro3/panTro3.2bit +chr6_GL390417_random 12521 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149721_random 12517 /gbdb/panTro3/panTro3.2bit +chrUn_GL395800 12512 /gbdb/panTro3/panTro3.2bit +chrUn_GL395787 12507 /gbdb/panTro3/panTro3.2bit +chrUn_GL396120 12502 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169151_random 12492 /gbdb/panTro3/panTro3.2bit +chrUn_GL395542 12487 /gbdb/panTro3/panTro3.2bit +chr16_GL392509_random 12480 /gbdb/panTro3/panTro3.2bit +chrUn_GL396245 12472 /gbdb/panTro3/panTro3.2bit +chrUn_GL395711 12470 /gbdb/panTro3/panTro3.2bit +chrUn_GL396021 12466 /gbdb/panTro3/panTro3.2bit +chr7_GL390737_random 12460 /gbdb/panTro3/panTro3.2bit +chrUn_GL395388 12456 /gbdb/panTro3/panTro3.2bit +chrUn_GL395128 12454 /gbdb/panTro3/panTro3.2bit +chrUn_GL395580 12454 /gbdb/panTro3/panTro3.2bit +chrUn_GL395651 12440 /gbdb/panTro3/panTro3.2bit +chrUn_GL395979 12435 /gbdb/panTro3/panTro3.2bit +chrUn_GL395080 12431 /gbdb/panTro3/panTro3.2bit +chrUn_GL395863 12429 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150092_random 12420 /gbdb/panTro3/panTro3.2bit +chr9_GL391155_random 12420 /gbdb/panTro3/panTro3.2bit +chr7_GL390692_random 12401 /gbdb/panTro3/panTro3.2bit +chrUn_GL395482 12389 /gbdb/panTro3/panTro3.2bit +chr15_GL392269_random 12371 /gbdb/panTro3/panTro3.2bit +chr8_GL390873_random 12367 /gbdb/panTro3/panTro3.2bit +chrUn_GL395807 12367 /gbdb/panTro3/panTro3.2bit +chrUn_GL395429 12364 /gbdb/panTro3/panTro3.2bit +chrUn_GL396297 12358 /gbdb/panTro3/panTro3.2bit +chrUn_GL396582 12348 /gbdb/panTro3/panTro3.2bit +chr7_GL390659_random 12346 /gbdb/panTro3/panTro3.2bit +chrUn_GL394900 12341 /gbdb/panTro3/panTro3.2bit +chrUn_GL395957 12341 /gbdb/panTro3/panTro3.2bit +chr15_GL392220_random 12339 /gbdb/panTro3/panTro3.2bit +chrUn_GL396203 12339 /gbdb/panTro3/panTro3.2bit +chrUn_GL396246 12339 /gbdb/panTro3/panTro3.2bit +chrUn_GL395899 12338 /gbdb/panTro3/panTro3.2bit +chr9_GL390991_random 12335 /gbdb/panTro3/panTro3.2bit +chr7_GL390536_random 12333 /gbdb/panTro3/panTro3.2bit +chr16_GL392500_random 12329 /gbdb/panTro3/panTro3.2bit +chrUn_GL395683 12326 /gbdb/panTro3/panTro3.2bit +chrUn_GL395851 12316 /gbdb/panTro3/panTro3.2bit +chrUn_GL396150 12313 /gbdb/panTro3/panTro3.2bit +chr15_GL392223_random 12309 /gbdb/panTro3/panTro3.2bit +chrUn_GL395844 12306 /gbdb/panTro3/panTro3.2bit +chr9_GL391087_random 12303 /gbdb/panTro3/panTro3.2bit +chr15_GL392235_random 12302 /gbdb/panTro3/panTro3.2bit +chr7_GL390529_random 12298 /gbdb/panTro3/panTro3.2bit +chrUn_GL396302 12298 /gbdb/panTro3/panTro3.2bit +chr6_GL390351_random 12297 /gbdb/panTro3/panTro3.2bit +chr2B_GL389436_random 12296 /gbdb/panTro3/panTro3.2bit +chr14_GL392152_random 12288 /gbdb/panTro3/panTro3.2bit +chr7_GL390493_random 12284 /gbdb/panTro3/panTro3.2bit +chrUn_GL396175 12284 /gbdb/panTro3/panTro3.2bit +chr1_GL389248_random 12276 /gbdb/panTro3/panTro3.2bit +chr4_GL389936_random 12271 /gbdb/panTro3/panTro3.2bit +chrUn_GL395649 12271 /gbdb/panTro3/panTro3.2bit +chr9_GL391251_random 12269 /gbdb/panTro3/panTro3.2bit +chrX_GL393385_random 12258 /gbdb/panTro3/panTro3.2bit +chrUn_GL395796 12257 /gbdb/panTro3/panTro3.2bit +chr9_GL391084_random 12252 /gbdb/panTro3/panTro3.2bit +chrUn_GL395860 12251 /gbdb/panTro3/panTro3.2bit +chr1_GL388926_random 12241 /gbdb/panTro3/panTro3.2bit +chrUn_GL396254 12240 /gbdb/panTro3/panTro3.2bit +chrUn_GL396039 12232 /gbdb/panTro3/panTro3.2bit +chrUn_GL395219 12230 /gbdb/panTro3/panTro3.2bit +chrUn_GL395951 12230 /gbdb/panTro3/panTro3.2bit +chrX_GL393350_random 12228 /gbdb/panTro3/panTro3.2bit +chrUn_GL396317 12221 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168086_random 12219 /gbdb/panTro3/panTro3.2bit +chr3_GL389672_random 12218 /gbdb/panTro3/panTro3.2bit +chr9_GL391112_random 12216 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395417 12146 /gbdb/panTro3/panTro3.2bit +chrUn_GL393515 12138 /gbdb/panTro3/panTro3.2bit +chrUn_GL395432 12135 /gbdb/panTro3/panTro3.2bit +chr16_GL392408_random 12132 /gbdb/panTro3/panTro3.2bit +chr4_GL389789_random 12114 /gbdb/panTro3/panTro3.2bit +chrUn_GL395650 12113 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03151920_random 12111 /gbdb/panTro3/panTro3.2bit +chrUn_GL395926 12109 /gbdb/panTro3/panTro3.2bit +chrUn_GL396064 12108 /gbdb/panTro3/panTro3.2bit +chrX_GL393421_random 12102 /gbdb/panTro3/panTro3.2bit +chr1_GL388944_random 12097 /gbdb/panTro3/panTro3.2bit +chrUn_GL395853 12097 /gbdb/panTro3/panTro3.2bit +chrUn_GL395397 12094 /gbdb/panTro3/panTro3.2bit +chrUn_GL396238 12089 /gbdb/panTro3/panTro3.2bit +chrUn_GL393520 12088 /gbdb/panTro3/panTro3.2bit +chr6_GL390278_random 12087 /gbdb/panTro3/panTro3.2bit +chr19_GL392937_random 12074 /gbdb/panTro3/panTro3.2bit +chr15_GL392284_random 12073 /gbdb/panTro3/panTro3.2bit +chr4_GL389778_random 12070 /gbdb/panTro3/panTro3.2bit +chr16_GL392485_random 12067 /gbdb/panTro3/panTro3.2bit +chrUn_GL393500 12065 /gbdb/panTro3/panTro3.2bit +chrUn_GL395765 12065 /gbdb/panTro3/panTro3.2bit +chrUn_GL396535 12064 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164147_random 12062 /gbdb/panTro3/panTro3.2bit +chr17_GL392643_random 12061 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171821_random 12058 /gbdb/panTro3/panTro3.2bit +chrUn_GL395685 12055 /gbdb/panTro3/panTro3.2bit +chr11_GL391802_random 12050 /gbdb/panTro3/panTro3.2bit +chr9_GL391236_random 12048 /gbdb/panTro3/panTro3.2bit +chrUn_GL395707 12041 /gbdb/panTro3/panTro3.2bit +chr11_GL391840_random 12040 /gbdb/panTro3/panTro3.2bit +chrUn_GL394810 12036 /gbdb/panTro3/panTro3.2bit +chrUn_GL395658 12031 /gbdb/panTro3/panTro3.2bit +chr16_GL392427_random 12025 /gbdb/panTro3/panTro3.2bit +chr15_GL392219_random 12024 /gbdb/panTro3/panTro3.2bit +chr16_GL392543_random 12007 /gbdb/panTro3/panTro3.2bit +chr4_GL389779_random 12006 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr5_GL390141_random 11952 /gbdb/panTro3/panTro3.2bit +chr1_GL389004_random 11951 /gbdb/panTro3/panTro3.2bit +chr3_GL389601_random 11951 /gbdb/panTro3/panTro3.2bit +chrUn_GL396713 11947 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180404 11945 /gbdb/panTro3/panTro3.2bit +chrUn_GL396186 11943 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173054_random 11938 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176499_random 11929 /gbdb/panTro3/panTro3.2bit +chr10_GL391480_random 11925 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182014 11923 /gbdb/panTro3/panTro3.2bit +chr1_GL389072_random 11922 /gbdb/panTro3/panTro3.2bit +chrUn_GL395758 11922 /gbdb/panTro3/panTro3.2bit +chrUn_GL395880 11921 /gbdb/panTro3/panTro3.2bit +chrUn_GL396097 11919 /gbdb/panTro3/panTro3.2bit +chr4_GL389847_random 11916 /gbdb/panTro3/panTro3.2bit +chrUn_GL395111 11915 /gbdb/panTro3/panTro3.2bit +chr6_GL390364_random 11911 /gbdb/panTro3/panTro3.2bit +chr9_GL391191_random 11905 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395352 11724 /gbdb/panTro3/panTro3.2bit +chrUn_GL395986 11723 /gbdb/panTro3/panTro3.2bit +chr18_GL392810_random 11722 /gbdb/panTro3/panTro3.2bit +chrUn_GL395575 11722 /gbdb/panTro3/panTro3.2bit +chrUn_GL396174 11718 /gbdb/panTro3/panTro3.2bit +chr16_GL392464_random 11715 /gbdb/panTro3/panTro3.2bit +chrUn_GL395628 11712 /gbdb/panTro3/panTro3.2bit +chr16_GL392390_random 11711 /gbdb/panTro3/panTro3.2bit +chr16_GL392332_random 11704 /gbdb/panTro3/panTro3.2bit +chr5_GL390108_random 11698 /gbdb/panTro3/panTro3.2bit +chrUn_GL396590 11693 /gbdb/panTro3/panTro3.2bit +chr1_GL388943_random 11692 /gbdb/panTro3/panTro3.2bit +chrUn_GL395540 11684 /gbdb/panTro3/panTro3.2bit +chr18_GL392808_random 11683 /gbdb/panTro3/panTro3.2bit +chrUn_GL395447 11682 /gbdb/panTro3/panTro3.2bit +chr4_GL389880_random 11681 /gbdb/panTro3/panTro3.2bit +chr5_GL390128_random 11677 /gbdb/panTro3/panTro3.2bit +chrUn_GL395824 11672 /gbdb/panTro3/panTro3.2bit +chrUn_GL395949 11670 /gbdb/panTro3/panTro3.2bit +chr6_GL390370_random 11669 /gbdb/panTro3/panTro3.2bit +chr1_GL388932_random 11665 /gbdb/panTro3/panTro3.2bit +chrUn_GL395744 11665 /gbdb/panTro3/panTro3.2bit +chr16_GL392364_random 11664 /gbdb/panTro3/panTro3.2bit +chrUn_GL395143 11664 /gbdb/panTro3/panTro3.2bit +chr16_GL392529_random 11658 /gbdb/panTro3/panTro3.2bit +chrUn_GL396061 11653 /gbdb/panTro3/panTro3.2bit +chr16_GL392519_random 11650 /gbdb/panTro3/panTro3.2bit +chrUn_GL394919 11638 /gbdb/panTro3/panTro3.2bit +chr6_GL390261_random 11626 /gbdb/panTro3/panTro3.2bit +chr7_GL390514_random 11625 /gbdb/panTro3/panTro3.2bit +chrUn_GL395089 11625 /gbdb/panTro3/panTro3.2bit +chr11_GL391799_random 11624 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158627_random 11620 /gbdb/panTro3/panTro3.2bit +chr4_GL389906_random 11612 /gbdb/panTro3/panTro3.2bit +chrUn_GL395876 11610 /gbdb/panTro3/panTro3.2bit +chrUn_GL395627 11601 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181313 11589 /gbdb/panTro3/panTro3.2bit +chrUn_GL396395 11585 /gbdb/panTro3/panTro3.2bit +chr3_GL389565_random 11582 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149754_random 11573 /gbdb/panTro3/panTro3.2bit +chrX_GL393415_random 11570 /gbdb/panTro3/panTro3.2bit +chrUn_GL395387 11567 /gbdb/panTro3/panTro3.2bit +chr10_GL391486_random 11566 /gbdb/panTro3/panTro3.2bit +chrUn_GL394907 11565 /gbdb/panTro3/panTro3.2bit +chr12_GL391978_random 11558 /gbdb/panTro3/panTro3.2bit +chrUn_GL396216 11554 /gbdb/panTro3/panTro3.2bit +chrUn_GL396253 11551 /gbdb/panTro3/panTro3.2bit +chrUn_GL395828 11547 /gbdb/panTro3/panTro3.2bit +chrUn_GL396450 11544 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181651 11538 /gbdb/panTro3/panTro3.2bit +chrUn_GL396277 11538 /gbdb/panTro3/panTro3.2bit +chrUn_GL394521 11535 /gbdb/panTro3/panTro3.2bit +chrUn_GL395242 11526 /gbdb/panTro3/panTro3.2bit +chrUn_GL395673 11525 /gbdb/panTro3/panTro3.2bit +chrX_GL393445_random 11525 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181339 11518 /gbdb/panTro3/panTro3.2bit +chr16_GL392496_random 11516 /gbdb/panTro3/panTro3.2bit +chrUn_GL396164 11515 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170402_random 11508 /gbdb/panTro3/panTro3.2bit +chr7_GL390716_random 11501 /gbdb/panTro3/panTro3.2bit +chrUn_GL396195 11500 /gbdb/panTro3/panTro3.2bit +chr8_GL390812_random 11499 /gbdb/panTro3/panTro3.2bit +chrUn_GL395868 11490 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150013_random 11487 /gbdb/panTro3/panTro3.2bit +chrUn_GL396765 11485 /gbdb/panTro3/panTro3.2bit +chrUn_GL396396 11476 /gbdb/panTro3/panTro3.2bit +chr7_GL390632_random 11475 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155355_random 11474 /gbdb/panTro3/panTro3.2bit +chr4_GL389942_random 11474 /gbdb/panTro3/panTro3.2bit +chr9_GL391181_random 11466 /gbdb/panTro3/panTro3.2bit +chrUn_GL396331 11465 /gbdb/panTro3/panTro3.2bit +chr11_GL391796_random 11464 /gbdb/panTro3/panTro3.2bit +chr1_GL388939_random 11464 /gbdb/panTro3/panTro3.2bit +chrUn_GL396068 11464 /gbdb/panTro3/panTro3.2bit +chr12_GL391972_random 11463 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_AACZ03164096_random 11285 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180153 11285 /gbdb/panTro3/panTro3.2bit +chr18_GL392820_random 11284 /gbdb/panTro3/panTro3.2bit +chr7_GL390708_random 11279 /gbdb/panTro3/panTro3.2bit +chr2A_GL389299_random 11261 /gbdb/panTro3/panTro3.2bit +chrUn_GL395632 11247 /gbdb/panTro3/panTro3.2bit +chrUn_GL395133 11246 /gbdb/panTro3/panTro3.2bit +chrUn_GL396521 11239 /gbdb/panTro3/panTro3.2bit +chr1_GL389035_random 11238 /gbdb/panTro3/panTro3.2bit +chrUn_GL395993 11236 /gbdb/panTro3/panTro3.2bit +chrX_GL393220_random 11234 /gbdb/panTro3/panTro3.2bit +chrUn_GL395777 11232 /gbdb/panTro3/panTro3.2bit +chrUn_GL396274 11231 /gbdb/panTro3/panTro3.2bit +chr1_GL388941_random 11224 /gbdb/panTro3/panTro3.2bit +chrUn_GL395262 11210 /gbdb/panTro3/panTro3.2bit +chr1_GL389175_random 11204 /gbdb/panTro3/panTro3.2bit +chr16_GL392389_random 11202 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181037 11194 /gbdb/panTro3/panTro3.2bit +chr2A_GL389381_random 11184 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155288_random 11179 /gbdb/panTro3/panTro3.2bit +chr9_GL391163_random 11178 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180347 11177 /gbdb/panTro3/panTro3.2bit +chr3_GL389623_random 11164 /gbdb/panTro3/panTro3.2bit +chrUn_GL395973 11164 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182034 11163 /gbdb/panTro3/panTro3.2bit +chr16_GL392428_random 11157 /gbdb/panTro3/panTro3.2bit +chrUn_GL395802 11154 /gbdb/panTro3/panTro3.2bit +chrUn_GL395563 11153 /gbdb/panTro3/panTro3.2bit +chr20_GL393021_random 11145 /gbdb/panTro3/panTro3.2bit +chrUn_GL395927 11141 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174387_random 11136 /gbdb/panTro3/panTro3.2bit +chr2A_GL389307_random 11130 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150027_random 11127 /gbdb/panTro3/panTro3.2bit +chr8_GL390829_random 11127 /gbdb/panTro3/panTro3.2bit +chr6_GL390280_random 11125 /gbdb/panTro3/panTro3.2bit +chrUn_GL395659 11125 /gbdb/panTro3/panTro3.2bit +chrUn_GL395369 11123 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr11_GL391816_random 11067 /gbdb/panTro3/panTro3.2bit +chrUn_GL396522 11065 /gbdb/panTro3/panTro3.2bit +chrUn_GL396412 11062 /gbdb/panTro3/panTro3.2bit +chr4_GL389769_random 11061 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149932_random 11058 /gbdb/panTro3/panTro3.2bit +chrUn_GL394824 11056 /gbdb/panTro3/panTro3.2bit +chr22_GL393071_random 11054 /gbdb/panTro3/panTro3.2bit +chr9_GL391167_random 11047 /gbdb/panTro3/panTro3.2bit +chrUn_GL393511 11043 /gbdb/panTro3/panTro3.2bit +chr9_GL391122_random 11030 /gbdb/panTro3/panTro3.2bit +chrX_GL393230_random 11028 /gbdb/panTro3/panTro3.2bit +chr16_GL392336_random 11027 /gbdb/panTro3/panTro3.2bit +chrUn_GL396422 11026 /gbdb/panTro3/panTro3.2bit +chrUn_GL396501 11024 /gbdb/panTro3/panTro3.2bit +chr1_GL389033_random 11023 /gbdb/panTro3/panTro3.2bit +chr9_GL391178_random 11020 /gbdb/panTro3/panTro3.2bit +chrUn_GL396079 11020 /gbdb/panTro3/panTro3.2bit +chr9_GL391081_random 11019 /gbdb/panTro3/panTro3.2bit +chrUn_GL396415 11015 /gbdb/panTro3/panTro3.2bit +chrUn_GL395614 11014 /gbdb/panTro3/panTro3.2bit +chr9_GL391000_random 11011 /gbdb/panTro3/panTro3.2bit +chrUn_GL394918 11010 /gbdb/panTro3/panTro3.2bit +chrUn_GL395706 11006 /gbdb/panTro3/panTro3.2bit +chr9_GL391109_random 11003 /gbdb/panTro3/panTro3.2bit +chr9_GL391164_random 11003 /gbdb/panTro3/panTro3.2bit +chr16_GL392411_random 11000 /gbdb/panTro3/panTro3.2bit +chr1_GL389081_random 11000 /gbdb/panTro3/panTro3.2bit +chrUn_GL396069 10997 /gbdb/panTro3/panTro3.2bit +chrUn_GL396252 10995 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164109_random 10994 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158626_random 10982 /gbdb/panTro3/panTro3.2bit +chrUn_GL396168 10974 /gbdb/panTro3/panTro3.2bit +chr16_GL392440_random 10973 /gbdb/panTro3/panTro3.2bit +chrUn_GL396438 10967 /gbdb/panTro3/panTro3.2bit +chrUn_GL395725 10965 /gbdb/panTro3/panTro3.2bit +chrUn_GL394564 10961 /gbdb/panTro3/panTro3.2bit +chrUn_GL395392 10957 /gbdb/panTro3/panTro3.2bit +chr6_GL390420_random 10951 /gbdb/panTro3/panTro3.2bit +chr14_GL392178_random 10942 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180559 10941 /gbdb/panTro3/panTro3.2bit +chrUn_GL395737 10940 /gbdb/panTro3/panTro3.2bit +chrUn_GL395604 10938 /gbdb/panTro3/panTro3.2bit +chrUn_GL396575 10936 /gbdb/panTro3/panTro3.2bit +chr4_GL389912_random 10934 /gbdb/panTro3/panTro3.2bit +chr1_GL388996_random 10933 /gbdb/panTro3/panTro3.2bit +chrUn_GL396125 10930 /gbdb/panTro3/panTro3.2bit +chr3_GL389678_random 10926 /gbdb/panTro3/panTro3.2bit +chrUn_GL394656 10926 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03183544 10919 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164135_random 10914 /gbdb/panTro3/panTro3.2bit +chrUn_GL396105 10912 /gbdb/panTro3/panTro3.2bit +chrUn_GL396797 10911 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165489_random 10907 /gbdb/panTro3/panTro3.2bit +chrUn_GL396127 10905 /gbdb/panTro3/panTro3.2bit +chrUn_GL396405 10904 /gbdb/panTro3/panTro3.2bit +chrUn_GL396612 10903 /gbdb/panTro3/panTro3.2bit +chrX_GL393156_random 10897 /gbdb/panTro3/panTro3.2bit +chrUn_GL394974 10896 /gbdb/panTro3/panTro3.2bit +chr5_GL390157_random 10894 /gbdb/panTro3/panTro3.2bit +chrUn_GL396449 10893 /gbdb/panTro3/panTro3.2bit +chr11_GL391858_random 10890 /gbdb/panTro3/panTro3.2bit +chr4_GL389944_random 10890 /gbdb/panTro3/panTro3.2bit +chrUn_GL395318 10889 /gbdb/panTro3/panTro3.2bit +chrUn_GL395450 10889 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03172806_random 10888 /gbdb/panTro3/panTro3.2bit +chrUn_GL395162 10886 /gbdb/panTro3/panTro3.2bit +chrUn_GL395226 10885 /gbdb/panTro3/panTro3.2bit +chrUn_GL393747 10882 /gbdb/panTro3/panTro3.2bit +chrUn_GL396670 10880 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180154 10879 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150008_random 10877 /gbdb/panTro3/panTro3.2bit +chr16_GL392518_random 10875 /gbdb/panTro3/panTro3.2bit +chr1_GL389119_random 10872 /gbdb/panTro3/panTro3.2bit +chr7_GL390712_random 10869 /gbdb/panTro3/panTro3.2bit +chrUn_GL394924 10869 /gbdb/panTro3/panTro3.2bit +chrUn_GL396369 10869 /gbdb/panTro3/panTro3.2bit +chrUn_GL396162 10868 /gbdb/panTro3/panTro3.2bit +chr12_GL391940_random 10863 /gbdb/panTro3/panTro3.2bit +chrUn_GL395609 10862 /gbdb/panTro3/panTro3.2bit +chr1_GL388983_random 10854 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150059_random 10851 /gbdb/panTro3/panTro3.2bit +chrUn_GL395437 10851 /gbdb/panTro3/panTro3.2bit +chrUn_GL395974 10843 /gbdb/panTro3/panTro3.2bit +chr1_GL389054_random 10837 /gbdb/panTro3/panTro3.2bit +chrUn_GL395048 10836 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149907_random 10834 /gbdb/panTro3/panTro3.2bit +chrUn_GL395789 10834 /gbdb/panTro3/panTro3.2bit +chr16_GL392370_random 10833 /gbdb/panTro3/panTro3.2bit +chr16_GL392356_random 10827 /gbdb/panTro3/panTro3.2bit +chrUn_GL395304 10825 /gbdb/panTro3/panTro3.2bit +chrUn_GL395762 10816 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03184081 10815 /gbdb/panTro3/panTro3.2bit +chr3_GL389671_random 10809 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171892_random 10807 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrX_GL393410_random 10705 /gbdb/panTro3/panTro3.2bit +chr4_GL389788_random 10704 /gbdb/panTro3/panTro3.2bit +chr6_GL390244_random 10704 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162474_random 10700 /gbdb/panTro3/panTro3.2bit +chrUn_GL395562 10699 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150195_random 10694 /gbdb/panTro3/panTro3.2bit +chr17_GL392686_random 10687 /gbdb/panTro3/panTro3.2bit +chr17_GL392637_random 10686 /gbdb/panTro3/panTro3.2bit +chr4_GL389792_random 10685 /gbdb/panTro3/panTro3.2bit +chr10_GL391464_random 10682 /gbdb/panTro3/panTro3.2bit +chrUn_GL395916 10682 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182106 10679 /gbdb/panTro3/panTro3.2bit +chr17_GL392619_random 10676 /gbdb/panTro3/panTro3.2bit +chrUn_GL395958 10674 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03172818_random 10671 /gbdb/panTro3/panTro3.2bit +chrUn_GL395752 10671 /gbdb/panTro3/panTro3.2bit +chrUn_GL395444 10664 /gbdb/panTro3/panTro3.2bit +chr2B_GL389479_random 10663 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155483_random 10662 /gbdb/panTro3/panTro3.2bit +chrUn_GL396261 10662 /gbdb/panTro3/panTro3.2bit +chrUn_GL395932 10659 /gbdb/panTro3/panTro3.2bit +chr19_GL392963_random 10651 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149998_random 10651 /gbdb/panTro3/panTro3.2bit +chr1_GL388915_random 10650 /gbdb/panTro3/panTro3.2bit +chrUn_GL395006 10648 /gbdb/panTro3/panTro3.2bit +chr11_GL391755_random 10641 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164119_random 10641 /gbdb/panTro3/panTro3.2bit +chrUn_GL395970 10641 /gbdb/panTro3/panTro3.2bit +chr16_GL392493_random 10638 /gbdb/panTro3/panTro3.2bit +chr7_GL390606_random 10638 /gbdb/panTro3/panTro3.2bit +chrUn_GL395418 10638 /gbdb/panTro3/panTro3.2bit +chrX_GL393388_random 10635 /gbdb/panTro3/panTro3.2bit +chr14_GL392118_random 10631 /gbdb/panTro3/panTro3.2bit +chr16_GL392365_random 10626 /gbdb/panTro3/panTro3.2bit +chr16_GL392434_random 10625 /gbdb/panTro3/panTro3.2bit +chrUn_GL396035 10624 /gbdb/panTro3/panTro3.2bit 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10538 /gbdb/panTro3/panTro3.2bit +chrX_GL393204_random 10538 /gbdb/panTro3/panTro3.2bit +chrX_GL393159_random 10537 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158708_random 10535 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155354_random 10534 /gbdb/panTro3/panTro3.2bit +chr1_GL389225_random 10531 /gbdb/panTro3/panTro3.2bit +chrUn_GL395439 10531 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170401_random 10528 /gbdb/panTro3/panTro3.2bit +chr8_GL390804_random 10527 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182278 10526 /gbdb/panTro3/panTro3.2bit +chrUn_GL395944 10526 /gbdb/panTro3/panTro3.2bit +chr6_GL390288_random 10523 /gbdb/panTro3/panTro3.2bit +chrUn_GL395950 10521 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182044 10514 /gbdb/panTro3/panTro3.2bit +chrUn_GL395955 10509 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153686_random 10505 /gbdb/panTro3/panTro3.2bit +chrUn_GL396757 10503 /gbdb/panTro3/panTro3.2bit +chrUn_GL395637 10496 /gbdb/panTro3/panTro3.2bit +chr16_GL392507_random 10493 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_GL391605_random 10441 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181084 10436 /gbdb/panTro3/panTro3.2bit +chr17_GL392658_random 10421 /gbdb/panTro3/panTro3.2bit +chr8_GL390833_random 10421 /gbdb/panTro3/panTro3.2bit +chr13_GL392061_random 10420 /gbdb/panTro3/panTro3.2bit +chr11_GL391811_random 10416 /gbdb/panTro3/panTro3.2bit +chrUn_GL396301 10416 /gbdb/panTro3/panTro3.2bit +chrUn_GL396939 10416 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155584_random 10389 /gbdb/panTro3/panTro3.2bit +chr10_GL391440_random 10386 /gbdb/panTro3/panTro3.2bit +chr1_GL389241_random 10382 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164256_random 10382 /gbdb/panTro3/panTro3.2bit +chrUn_GL396271 10382 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174404_random 10380 /gbdb/panTro3/panTro3.2bit +chr2B_GL389489_random 10378 /gbdb/panTro3/panTro3.2bit +chr1_GL388914_random 10377 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175846_random 10370 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164232_random 10363 /gbdb/panTro3/panTro3.2bit +chr19_GL392909_random 10359 /gbdb/panTro3/panTro3.2bit +chr6_GL390436_random 10352 /gbdb/panTro3/panTro3.2bit +chrUn_GL395989 10351 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150003_random 10345 /gbdb/panTro3/panTro3.2bit +chrUn_GL396432 10342 /gbdb/panTro3/panTro3.2bit +chr5_GL390049_random 10337 /gbdb/panTro3/panTro3.2bit +chr10_GL391438_random 10333 /gbdb/panTro3/panTro3.2bit +chr7_GL390495_random 10328 /gbdb/panTro3/panTro3.2bit +chrUn_GL395187 10327 /gbdb/panTro3/panTro3.2bit +chrUn_GL393513 10326 /gbdb/panTro3/panTro3.2bit +chrUn_GL396282 10326 /gbdb/panTro3/panTro3.2bit +chr11_GL391833_random 10325 /gbdb/panTro3/panTro3.2bit +chr18_GL392811_random 10322 /gbdb/panTro3/panTro3.2bit +chrUn_GL396537 10321 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03183022 10317 /gbdb/panTro3/panTro3.2bit +chr8_GL390822_random 10307 /gbdb/panTro3/panTro3.2bit +chr22_GL393079_random 10300 /gbdb/panTro3/panTro3.2bit +chrUn_GL396431 10299 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr5_GL390145_random 10248 /gbdb/panTro3/panTro3.2bit +chr6_GL390300_random 10248 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177547_random 10248 /gbdb/panTro3/panTro3.2bit +chr2A_GL389371_random 10244 /gbdb/panTro3/panTro3.2bit +chr1_GL389219_random 10243 /gbdb/panTro3/panTro3.2bit +chrUn_GL395230 10243 /gbdb/panTro3/panTro3.2bit +chr22_GL393069_random 10234 /gbdb/panTro3/panTro3.2bit +chr9_GL391010_random 10233 /gbdb/panTro3/panTro3.2bit +chrUn_GL396101 10233 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158652_random 10230 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03160672_random 10230 /gbdb/panTro3/panTro3.2bit +chrUn_GL396485 10230 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164180_random 10225 /gbdb/panTro3/panTro3.2bit +chrUn_GL396034 10223 /gbdb/panTro3/panTro3.2bit +chrUn_GL396130 10221 /gbdb/panTro3/panTro3.2bit +chr2B_GL389442_random 10219 /gbdb/panTro3/panTro3.2bit +chr6_GL390361_random 10213 /gbdb/panTro3/panTro3.2bit +chrUn_GL393658 10213 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr1_GL388822_random 10148 /gbdb/panTro3/panTro3.2bit +chr12_GL391980_random 10138 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180802 10137 /gbdb/panTro3/panTro3.2bit +chrUn_GL396329 10136 /gbdb/panTro3/panTro3.2bit +chr7_GL390608_random 10134 /gbdb/panTro3/panTro3.2bit +chr9_GL391151_random 10134 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177468_random 10128 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165468_random 10127 /gbdb/panTro3/panTro3.2bit +chr1_GL388896_random 10124 /gbdb/panTro3/panTro3.2bit +chrUn_GL395892 10124 /gbdb/panTro3/panTro3.2bit +chr2A_GL389304_random 10121 /gbdb/panTro3/panTro3.2bit +chr9_GL391115_random 10118 /gbdb/panTro3/panTro3.2bit +chrUn_GL395546 10115 /gbdb/panTro3/panTro3.2bit +chr5_GL390160_random 10114 /gbdb/panTro3/panTro3.2bit +chr9_GL391106_random 10105 /gbdb/panTro3/panTro3.2bit +chrUn_GL396281 10105 /gbdb/panTro3/panTro3.2bit +chrUn_GL396352 10105 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181085 10102 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_GL391020_random 10062 /gbdb/panTro3/panTro3.2bit +chrX_GL393190_random 10060 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181726 10049 /gbdb/panTro3/panTro3.2bit +chrUn_GL395113 10044 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03183652 10029 /gbdb/panTro3/panTro3.2bit +chr4_GL389967_random 10014 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176506_random 10009 /gbdb/panTro3/panTro3.2bit +chrUn_GL396119 10009 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03160919_random 10008 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157073_random 10007 /gbdb/panTro3/panTro3.2bit +chr9_GL391237_random 10006 /gbdb/panTro3/panTro3.2bit +chrUn_GL396576 10001 /gbdb/panTro3/panTro3.2bit +chrUn_GL395897 9996 /gbdb/panTro3/panTro3.2bit +chrUn_GL395655 9986 /gbdb/panTro3/panTro3.2bit +chr5_GL390143_random 9979 /gbdb/panTro3/panTro3.2bit +chrUn_GL394986 9974 /gbdb/panTro3/panTro3.2bit +chr16_GL392412_random 9973 /gbdb/panTro3/panTro3.2bit +chrUn_GL396664 9968 /gbdb/panTro3/panTro3.2bit +chr6_GL390374_random 9967 /gbdb/panTro3/panTro3.2bit +chrUn_GL396181 9963 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158689_random 9956 /gbdb/panTro3/panTro3.2bit +chr16_GL392515_random 9954 /gbdb/panTro3/panTro3.2bit +chrUn_GL395491 9952 /gbdb/panTro3/panTro3.2bit +chr1_GL389146_random 9951 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168164_random 9947 /gbdb/panTro3/panTro3.2bit +chrUn_GL395690 9947 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182534 9942 /gbdb/panTro3/panTro3.2bit +chrX_GL393282_random 9938 /gbdb/panTro3/panTro3.2bit +chrUn_GL395347 9937 /gbdb/panTro3/panTro3.2bit +chrUn_GL395462 9930 /gbdb/panTro3/panTro3.2bit +chrUn_GL396443 9926 /gbdb/panTro3/panTro3.2bit +chr3_GL389615_random 9923 /gbdb/panTro3/panTro3.2bit +chr4_GL389802_random 9919 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181261 9916 /gbdb/panTro3/panTro3.2bit +chrUn_GL396096 9912 /gbdb/panTro3/panTro3.2bit +chrUn_GL396467 9910 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155609_random 9904 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150194_random 9901 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181058 9895 /gbdb/panTro3/panTro3.2bit +chrX_GL393307_random 9895 /gbdb/panTro3/panTro3.2bit +chr10_GL391472_random 9891 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180536 9891 /gbdb/panTro3/panTro3.2bit +chr4_GL389737_random 9889 /gbdb/panTro3/panTro3.2bit +chrUn_GL396702 9883 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155274_random 9881 /gbdb/panTro3/panTro3.2bit +chrUn_GL396247 9878 /gbdb/panTro3/panTro3.2bit +chr13_GL392076_random 9870 /gbdb/panTro3/panTro3.2bit +chr6_GL390442_random 9868 /gbdb/panTro3/panTro3.2bit +chr1_GL389139_random 9863 /gbdb/panTro3/panTro3.2bit +chr7_GL390647_random 9862 /gbdb/panTro3/panTro3.2bit +chrUn_GL396139 9862 /gbdb/panTro3/panTro3.2bit +chrUn_GL395712 9860 /gbdb/panTro3/panTro3.2bit +chr20_GL393007_random 9857 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03183030 9857 /gbdb/panTro3/panTro3.2bit +chrUn_GL395829 9855 /gbdb/panTro3/panTro3.2bit +chrUn_GL395885 9849 /gbdb/panTro3/panTro3.2bit +chrUn_GL395639 9848 /gbdb/panTro3/panTro3.2bit +chrUn_GL395664 9847 /gbdb/panTro3/panTro3.2bit +chrUn_GL396510 9846 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03183623 9845 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171934_random 9840 /gbdb/panTro3/panTro3.2bit +chr7_GL390690_random 9840 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03149798_random 9837 /gbdb/panTro3/panTro3.2bit +chr15_GL392261_random 9836 /gbdb/panTro3/panTro3.2bit +chrUn_GL396214 9836 /gbdb/panTro3/panTro3.2bit +chrUn_GL395984 9835 /gbdb/panTro3/panTro3.2bit +chr6_GL390428_random 9829 /gbdb/panTro3/panTro3.2bit +chr6_GL390298_random 9828 /gbdb/panTro3/panTro3.2bit +chrUn_GL395630 9818 /gbdb/panTro3/panTro3.2bit +chrUn_GL396206 9817 /gbdb/panTro3/panTro3.2bit +chrUn_GL395663 9816 /gbdb/panTro3/panTro3.2bit +chr19_GL392861_random 9803 /gbdb/panTro3/panTro3.2bit +chrUn_GL396092 9802 /gbdb/panTro3/panTro3.2bit +chr7_GL390517_random 9799 /gbdb/panTro3/panTro3.2bit +chr9_GL390993_random 9796 /gbdb/panTro3/panTro3.2bit +chrUn_GL396113 9790 /gbdb/panTro3/panTro3.2bit +chrUn_GL396208 9789 /gbdb/panTro3/panTro3.2bit +chr14_GL392163_random 9785 /gbdb/panTro3/panTro3.2bit +chr10_GL391461_random 9779 /gbdb/panTro3/panTro3.2bit +chrUn_GL396404 9775 /gbdb/panTro3/panTro3.2bit +chrUn_GL395772 9774 /gbdb/panTro3/panTro3.2bit +chrX_GL393406_random 9772 /gbdb/panTro3/panTro3.2bit +chrUn_GL396283 9770 /gbdb/panTro3/panTro3.2bit +chr10_GL391465_random 9769 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181545 9769 /gbdb/panTro3/panTro3.2bit +chrUn_GL393521 9760 /gbdb/panTro3/panTro3.2bit +chrUn_GL396926 9760 /gbdb/panTro3/panTro3.2bit +chr1_GL389229_random 9759 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171938_random 9757 /gbdb/panTro3/panTro3.2bit +chrUn_GL395962 9757 /gbdb/panTro3/panTro3.2bit +chrUn_GL396225 9757 /gbdb/panTro3/panTro3.2bit +chr17_GL392621_random 9755 /gbdb/panTro3/panTro3.2bit +chrUn_GL395749 9755 /gbdb/panTro3/panTro3.2bit +chr18_GL392779_random 9750 /gbdb/panTro3/panTro3.2bit +chrUn_GL396418 9749 /gbdb/panTro3/panTro3.2bit 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9601 /gbdb/panTro3/panTro3.2bit +chrUn_GL396275 9599 /gbdb/panTro3/panTro3.2bit +chr4_GL389839_random 9579 /gbdb/panTro3/panTro3.2bit +chr5_GL390101_random 9579 /gbdb/panTro3/panTro3.2bit +chrUn_GL395275 9578 /gbdb/panTro3/panTro3.2bit +chr12_GL391939_random 9574 /gbdb/panTro3/panTro3.2bit +chrUn_GL396495 9572 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181703 9568 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03184676 9561 /gbdb/panTro3/panTro3.2bit +chrUn_GL396390 9561 /gbdb/panTro3/panTro3.2bit +chrUn_GL396434 9559 /gbdb/panTro3/panTro3.2bit +chrUn_GL396513 9556 /gbdb/panTro3/panTro3.2bit +chrUn_GL396148 9554 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155608_random 9549 /gbdb/panTro3/panTro3.2bit +chr7_GL390572_random 9549 /gbdb/panTro3/panTro3.2bit +chr15_GL392247_random 9547 /gbdb/panTro3/panTro3.2bit +chrUn_GL395836 9546 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173164_random 9543 /gbdb/panTro3/panTro3.2bit +chr5_GL390099_random 9543 /gbdb/panTro3/panTro3.2bit +chrUn_GL395952 9543 /gbdb/panTro3/panTro3.2bit +chr3_GL389645_random 9537 /gbdb/panTro3/panTro3.2bit +chrUn_GL396143 9536 /gbdb/panTro3/panTro3.2bit +chrUn_GL395972 9535 /gbdb/panTro3/panTro3.2bit +chrUn_GL395190 9527 /gbdb/panTro3/panTro3.2bit +chr9_GL391047_random 9526 /gbdb/panTro3/panTro3.2bit +chrUn_GL396157 9524 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173289_random 9509 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181676 9509 /gbdb/panTro3/panTro3.2bit +chrUn_GL397063 9509 /gbdb/panTro3/panTro3.2bit +chr10_GL391505_random 9507 /gbdb/panTro3/panTro3.2bit +chrUn_GL393528 9507 /gbdb/panTro3/panTro3.2bit +chr9_GL390994_random 9506 /gbdb/panTro3/panTro3.2bit +chr13_GL392064_random 9498 /gbdb/panTro3/panTro3.2bit +chr16_GL392328_random 9497 /gbdb/panTro3/panTro3.2bit +chrUn_GL395553 9496 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181493 9491 /gbdb/panTro3/panTro3.2bit +chr10_GL391478_random 9474 /gbdb/panTro3/panTro3.2bit +chr13_GL392090_random 9471 /gbdb/panTro3/panTro3.2bit +chr6_GL390302_random 9468 /gbdb/panTro3/panTro3.2bit +chr13_GL392051_random 9460 /gbdb/panTro3/panTro3.2bit +chrUn_GL396650 9456 /gbdb/panTro3/panTro3.2bit +chr10_GL391528_random 9451 /gbdb/panTro3/panTro3.2bit +chr11_GL391760_random 9451 /gbdb/panTro3/panTro3.2bit +chrX_GL393412_random 9449 /gbdb/panTro3/panTro3.2bit +chr10_GL391474_random 9448 /gbdb/panTro3/panTro3.2bit +chrUn_GL395731 9445 /gbdb/panTro3/panTro3.2bit +chrUn_GL395873 9440 /gbdb/panTro3/panTro3.2bit +chr18_GL392766_random 9435 /gbdb/panTro3/panTro3.2bit +chrUn_GL396856 9423 /gbdb/panTro3/panTro3.2bit +chrUn_GL396077 9419 /gbdb/panTro3/panTro3.2bit +chrUn_GL396466 9417 /gbdb/panTro3/panTro3.2bit +chr11_GL391758_random 9408 /gbdb/panTro3/panTro3.2bit +chrUn_GL395661 9381 /gbdb/panTro3/panTro3.2bit +chrUn_GL396015 9374 /gbdb/panTro3/panTro3.2bit +chr4_GL389768_random 9373 /gbdb/panTro3/panTro3.2bit +chrUn_GL395339 9373 /gbdb/panTro3/panTro3.2bit +chrX_GL393417_random 9371 /gbdb/panTro3/panTro3.2bit +chrUn_GL396292 9370 /gbdb/panTro3/panTro3.2bit 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9231 /gbdb/panTro3/panTro3.2bit +chrUn_GL396249 9230 /gbdb/panTro3/panTro3.2bit +chrUn_GL395130 9225 /gbdb/panTro3/panTro3.2bit +chr11_GL391848_random 9220 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03180369 9216 /gbdb/panTro3/panTro3.2bit +chr4_GL389758_random 9204 /gbdb/panTro3/panTro3.2bit +chrUn_GL395436 9200 /gbdb/panTro3/panTro3.2bit +chr6_GL390386_random 9195 /gbdb/panTro3/panTro3.2bit +chr2A_GL389358_random 9193 /gbdb/panTro3/panTro3.2bit +chr2B_GL389482_random 9179 /gbdb/panTro3/panTro3.2bit +chrUn_GL396583 9176 /gbdb/panTro3/panTro3.2bit +chrUn_GL396500 9164 /gbdb/panTro3/panTro3.2bit +chrUn_GL396135 9150 /gbdb/panTro3/panTro3.2bit +chr8_GL390839_random 9141 /gbdb/panTro3/panTro3.2bit +chrUn_GL396132 9136 /gbdb/panTro3/panTro3.2bit +chrUn_GL396144 9136 /gbdb/panTro3/panTro3.2bit +chrUn_GL396296 9135 /gbdb/panTro3/panTro3.2bit +chrUn_GL396796 9132 /gbdb/panTro3/panTro3.2bit +chr2A_GL389288_random 9127 /gbdb/panTro3/panTro3.2bit +chrUn_GL396090 9127 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_GL391019_random 8996 /gbdb/panTro3/panTro3.2bit +chr13_GL392046_random 8994 /gbdb/panTro3/panTro3.2bit +chrUn_GL396072 8993 /gbdb/panTro3/panTro3.2bit +chrUn_GL396687 8989 /gbdb/panTro3/panTro3.2bit +chr20_GL393003_random 8986 /gbdb/panTro3/panTro3.2bit +chrUn_GL397001 8984 /gbdb/panTro3/panTro3.2bit +chrUn_GL396106 8971 /gbdb/panTro3/panTro3.2bit +chrUn_GL396559 8971 /gbdb/panTro3/panTro3.2bit +chrX_GL393211_random 8961 /gbdb/panTro3/panTro3.2bit +chr16_GL392463_random 8959 /gbdb/panTro3/panTro3.2bit +chrUn_GL396255 8952 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173325_random 8942 /gbdb/panTro3/panTro3.2bit +chr12_GL391988_random 8939 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165456_random 8938 /gbdb/panTro3/panTro3.2bit +chrUn_GL396598 8920 /gbdb/panTro3/panTro3.2bit +chr8_GL390813_random 8906 /gbdb/panTro3/panTro3.2bit +chrUn_GL396351 8898 /gbdb/panTro3/panTro3.2bit +chr6_GL390289_random 8897 /gbdb/panTro3/panTro3.2bit +chr19_GL392849_random 8895 /gbdb/panTro3/panTro3.2bit +chr2A_GL389352_random 8894 /gbdb/panTro3/panTro3.2bit +chrUn_GL396520 8894 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152020_random 8889 /gbdb/panTro3/panTro3.2bit +chrUn_GL396303 8889 /gbdb/panTro3/panTro3.2bit +chrUn_GL396243 8880 /gbdb/panTro3/panTro3.2bit +chr1_GL389106_random 8872 /gbdb/panTro3/panTro3.2bit +chrUn_GL395992 8871 /gbdb/panTro3/panTro3.2bit +chrUn_GL396149 8868 /gbdb/panTro3/panTro3.2bit +chrUn_GL396008 8860 /gbdb/panTro3/panTro3.2bit +chr13_GL392066_random 8856 /gbdb/panTro3/panTro3.2bit +chrUn_GL396355 8856 /gbdb/panTro3/panTro3.2bit +chr3_GL389651_random 8850 /gbdb/panTro3/panTro3.2bit +chr17_GL392696_random 8849 /gbdb/panTro3/panTro3.2bit +chr12_GL392002_random 8848 /gbdb/panTro3/panTro3.2bit +chrUn_GL396614 8845 /gbdb/panTro3/panTro3.2bit +chr20_GL393022_random 8841 /gbdb/panTro3/panTro3.2bit +chr4_GL389923_random 8840 /gbdb/panTro3/panTro3.2bit +chr16_GL392445_random 8836 /gbdb/panTro3/panTro3.2bit +chrUn_GL395956 8836 /gbdb/panTro3/panTro3.2bit +chrUn_GL396642 8827 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173349_random 8817 /gbdb/panTro3/panTro3.2bit +chrUn_GL396496 8817 /gbdb/panTro3/panTro3.2bit +chr13_GL392086_random 8815 /gbdb/panTro3/panTro3.2bit +chrUn_GL396311 8812 /gbdb/panTro3/panTro3.2bit +chr15_GL392234_random 8810 /gbdb/panTro3/panTro3.2bit +chr2B_GL389439_random 8807 /gbdb/panTro3/panTro3.2bit +chrUn_GL395380 8807 /gbdb/panTro3/panTro3.2bit +chr3_GL389577_random 8803 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173045_random 8799 /gbdb/panTro3/panTro3.2bit +chrUn_GL396446 8788 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165514_random 8782 /gbdb/panTro3/panTro3.2bit +chrUn_GL396133 8777 /gbdb/panTro3/panTro3.2bit +chrUn_GL395791 8776 /gbdb/panTro3/panTro3.2bit +chr9_GL391058_random 8773 /gbdb/panTro3/panTro3.2bit +chrUn_GL396033 8773 /gbdb/panTro3/panTro3.2bit +chrUn_GL396189 8763 /gbdb/panTro3/panTro3.2bit +chrUn_GL395680 8758 /gbdb/panTro3/panTro3.2bit +chrUn_GL396210 8757 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/gbdb/panTro3/panTro3.2bit +chr10_GL391540_random 8599 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155686_random 8594 /gbdb/panTro3/panTro3.2bit +chrUn_GL396461 8589 /gbdb/panTro3/panTro3.2bit +chrUn_GL396453 8587 /gbdb/panTro3/panTro3.2bit +chrUn_GL396136 8582 /gbdb/panTro3/panTro3.2bit +chr15_GL392226_random 8580 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03184944 8580 /gbdb/panTro3/panTro3.2bit +chr10_GL391514_random 8577 /gbdb/panTro3/panTro3.2bit +chr14_GL392126_random 8572 /gbdb/panTro3/panTro3.2bit +chr17_GL392711_random 8561 /gbdb/panTro3/panTro3.2bit +chrUn_GL394375 8558 /gbdb/panTro3/panTro3.2bit +chr4_GL389849_random 8556 /gbdb/panTro3/panTro3.2bit +chrUn_GL396646 8545 /gbdb/panTro3/panTro3.2bit +chr8_GL390862_random 8544 /gbdb/panTro3/panTro3.2bit +chrUn_GL396040 8544 /gbdb/panTro3/panTro3.2bit +chrUn_GL396004 8537 /gbdb/panTro3/panTro3.2bit +chr5_GL390084_random 8535 /gbdb/panTro3/panTro3.2bit +chr10_GL391675_random 8530 /gbdb/panTro3/panTro3.2bit +chr1_GL389228_random 8529 /gbdb/panTro3/panTro3.2bit +chr8_GL390910_random 8526 /gbdb/panTro3/panTro3.2bit +chr9_GL391009_random 8525 /gbdb/panTro3/panTro3.2bit +chr7_GL390532_random 8522 /gbdb/panTro3/panTro3.2bit +chr1_GL388964_random 8519 /gbdb/panTro3/panTro3.2bit +chrUn_GL393916 8512 /gbdb/panTro3/panTro3.2bit +chrUn_GL396348 8508 /gbdb/panTro3/panTro3.2bit +chr9_GL391012_random 8507 /gbdb/panTro3/panTro3.2bit +chrUn_GL396897 8499 /gbdb/panTro3/panTro3.2bit +chrX_GL393362_random 8499 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03182731 8488 /gbdb/panTro3/panTro3.2bit +chr11_GL391768_random 8486 /gbdb/panTro3/panTro3.2bit +chr9_GL391221_random 8486 /gbdb/panTro3/panTro3.2bit +chr6_GL390336_random 8470 /gbdb/panTro3/panTro3.2bit +chrUn_GL396686 8466 /gbdb/panTro3/panTro3.2bit +chrUn_GL396699 8465 /gbdb/panTro3/panTro3.2bit +chr19_GL392946_random 8461 /gbdb/panTro3/panTro3.2bit +chrUn_GL396517 8444 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03181016 8442 /gbdb/panTro3/panTro3.2bit +chrUn_GL396197 8440 /gbdb/panTro3/panTro3.2bit +chr15_GL392259_random 8436 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150132_random 8436 /gbdb/panTro3/panTro3.2bit +chr3_GL389646_random 8436 /gbdb/panTro3/panTro3.2bit +chrUn_GL396142 8435 /gbdb/panTro3/panTro3.2bit +chrUn_GL396846 8430 /gbdb/panTro3/panTro3.2bit +chr10_GL391527_random 8426 /gbdb/panTro3/panTro3.2bit +chr2A_GL389361_random 8425 /gbdb/panTro3/panTro3.2bit +chr15_GL392225_random 8420 /gbdb/panTro3/panTro3.2bit +chrUn_GL395652 8417 /gbdb/panTro3/panTro3.2bit +chr18_GL392782_random 8414 /gbdb/panTro3/panTro3.2bit +chrUn_GL396159 8413 /gbdb/panTro3/panTro3.2bit +chrUn_GL397051 8411 /gbdb/panTro3/panTro3.2bit +chr1_GL389061_random 8410 /gbdb/panTro3/panTro3.2bit +chr2B_GL389441_random 8407 /gbdb/panTro3/panTro3.2bit +chr3_GL389584_random 8407 /gbdb/panTro3/panTro3.2bit +chr4_GL389806_random 8405 /gbdb/panTro3/panTro3.2bit +chrUn_GL396176 8405 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186099 8402 /gbdb/panTro3/panTro3.2bit +chr13_GL392083_random 8398 /gbdb/panTro3/panTro3.2bit +chr6_GL390292_random 8395 /gbdb/panTro3/panTro3.2bit +chr19_GL392850_random 8394 /gbdb/panTro3/panTro3.2bit +chr14_GL392174_random 8388 /gbdb/panTro3/panTro3.2bit +chr4_GL389819_random 8388 /gbdb/panTro3/panTro3.2bit +chrUn_GL396094 8388 /gbdb/panTro3/panTro3.2bit +chr1_GL389168_random 8386 /gbdb/panTro3/panTro3.2bit +chr8_GL390831_random 8383 /gbdb/panTro3/panTro3.2bit +chrUn_GL396191 8376 /gbdb/panTro3/panTro3.2bit +chrUn_GL396332 8375 /gbdb/panTro3/panTro3.2bit +chr6_GL390325_random 8374 /gbdb/panTro3/panTro3.2bit +chrUn_GL396140 8369 /gbdb/panTro3/panTro3.2bit +chr14_GL392157_random 8367 /gbdb/panTro3/panTro3.2bit +chr18_GL392743_random 8365 /gbdb/panTro3/panTro3.2bit +chr8_GL390842_random 8361 /gbdb/panTro3/panTro3.2bit +chrUn_GL396386 8361 /gbdb/panTro3/panTro3.2bit +chr7_GL390666_random 8360 /gbdb/panTro3/panTro3.2bit +chrUn_GL395184 8358 /gbdb/panTro3/panTro3.2bit +chrUn_GL396265 8357 /gbdb/panTro3/panTro3.2bit +chr20_GL393004_random 8356 /gbdb/panTro3/panTro3.2bit +chr2B_GL389449_random 8354 /gbdb/panTro3/panTro3.2bit +chr11_GL391761_random 8353 /gbdb/panTro3/panTro3.2bit +chrUn_GL396338 8351 /gbdb/panTro3/panTro3.2bit +chr11_GL391804_random 8348 /gbdb/panTro3/panTro3.2bit +chr10_GL391496_random 8336 /gbdb/panTro3/panTro3.2bit +chrUn_GL393899 8332 /gbdb/panTro3/panTro3.2bit +chr6_GL390347_random 8326 /gbdb/panTro3/panTro3.2bit +chr19_GL392927_random 8323 /gbdb/panTro3/panTro3.2bit +chrUn_GL396192 8321 /gbdb/panTro3/panTro3.2bit +chrUn_GL396336 8321 /gbdb/panTro3/panTro3.2bit +chr3_GL389583_random 8317 /gbdb/panTro3/panTro3.2bit +chr4_GL389813_random 8317 /gbdb/panTro3/panTro3.2bit +chrX_GL393207_random 8311 /gbdb/panTro3/panTro3.2bit +chr3_GL389592_random 8309 /gbdb/panTro3/panTro3.2bit +chrUn_GL396492 8306 /gbdb/panTro3/panTro3.2bit +chr12_GL391967_random 8305 /gbdb/panTro3/panTro3.2bit +chr10_GL391476_random 8299 /gbdb/panTro3/panTro3.2bit +chr6_GL390305_random 8292 /gbdb/panTro3/panTro3.2bit +chrUn_GL395929 8292 /gbdb/panTro3/panTro3.2bit +chr4_GL389787_random 8288 /gbdb/panTro3/panTro3.2bit +chrUn_GL395774 8287 /gbdb/panTro3/panTro3.2bit +chrUn_GL396445 8283 /gbdb/panTro3/panTro3.2bit +chr8_GL390835_random 8277 /gbdb/panTro3/panTro3.2bit +chrUn_GL396827 8277 /gbdb/panTro3/panTro3.2bit +chrUn_GL397018 8277 /gbdb/panTro3/panTro3.2bit +chrUn_GL396067 8269 /gbdb/panTro3/panTro3.2bit +chr16_GL392530_random 8266 /gbdb/panTro3/panTro3.2bit +chr3_GL389613_random 8261 /gbdb/panTro3/panTro3.2bit +chrX_GL393103_random 8258 /gbdb/panTro3/panTro3.2bit +chrUn_GL396528 8257 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152053_random 8255 /gbdb/panTro3/panTro3.2bit +chr2B_GL389501_random 8255 /gbdb/panTro3/panTro3.2bit +chr7_GL390676_random 8252 /gbdb/panTro3/panTro3.2bit +chr16_GL392347_random 8245 /gbdb/panTro3/panTro3.2bit +chr2B_GL389443_random 8244 /gbdb/panTro3/panTro3.2bit +chrUn_GL393560 8241 /gbdb/panTro3/panTro3.2bit +chr10_GL391488_random 8235 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03185027 8235 /gbdb/panTro3/panTro3.2bit +chrUn_GL395866 8230 /gbdb/panTro3/panTro3.2bit +chrUn_GL396504 8228 /gbdb/panTro3/panTro3.2bit +chrUn_GL396207 8227 /gbdb/panTro3/panTro3.2bit +chr1_GL389126_random 8215 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03183927 8215 /gbdb/panTro3/panTro3.2bit +chrUn_GL396567 8215 /gbdb/panTro3/panTro3.2bit +chr11_GL391841_random 8214 /gbdb/panTro3/panTro3.2bit +chrUn_GL395709 8213 /gbdb/panTro3/panTro3.2bit +chr19_GL392961_random 8211 /gbdb/panTro3/panTro3.2bit +chr13_GL392047_random 8206 /gbdb/panTro3/panTro3.2bit +chr5_GL390068_random 8206 /gbdb/panTro3/panTro3.2bit +chr10_GL391471_random 8205 /gbdb/panTro3/panTro3.2bit +chrUn_GL395810 8205 /gbdb/panTro3/panTro3.2bit +chr13_GL392052_random 8203 /gbdb/panTro3/panTro3.2bit +chr3_GL389669_random 8203 /gbdb/panTro3/panTro3.2bit +chr11_GL391868_random 8199 /gbdb/panTro3/panTro3.2bit +chr11_GL391791_random 8192 /gbdb/panTro3/panTro3.2bit +chrUn_GL396617 8191 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169188_random 8186 /gbdb/panTro3/panTro3.2bit +chrUn_GL396392 8186 /gbdb/panTro3/panTro3.2bit +chrUn_GL396514 8179 /gbdb/panTro3/panTro3.2bit +chr19_GL392942_random 8176 /gbdb/panTro3/panTro3.2bit +chr9_GL391027_random 8175 /gbdb/panTro3/panTro3.2bit +chrUn_GL396479 8175 /gbdb/panTro3/panTro3.2bit +chrUn_GL396645 8175 /gbdb/panTro3/panTro3.2bit +chrUn_GL393845 8173 /gbdb/panTro3/panTro3.2bit +chr4_GL389853_random 8171 /gbdb/panTro3/panTro3.2bit +chr5_GL390153_random 8171 /gbdb/panTro3/panTro3.2bit +chr10_GL391653_random 8170 /gbdb/panTro3/panTro3.2bit +chr9_GL391199_random 8166 /gbdb/panTro3/panTro3.2bit +chrUn_GL396542 8161 /gbdb/panTro3/panTro3.2bit +chr1_GL388971_random 8160 /gbdb/panTro3/panTro3.2bit +chr4_GL389975_random 8155 /gbdb/panTro3/panTro3.2bit +chr13_GL392079_random 8151 /gbdb/panTro3/panTro3.2bit +chr9_GL391171_random 8150 /gbdb/panTro3/panTro3.2bit +chrX_GL393443_random 8150 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158731_random 8149 /gbdb/panTro3/panTro3.2bit +chr7_GL390552_random 8149 /gbdb/panTro3/panTro3.2bit +chrUn_GL396353 8148 /gbdb/panTro3/panTro3.2bit +chr9_GL391049_random 8147 /gbdb/panTro3/panTro3.2bit +chrUn_GL396349 8143 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164391_random 8141 /gbdb/panTro3/panTro3.2bit +chrUn_GL396310 8141 /gbdb/panTro3/panTro3.2bit +chr10_GL391592_random 8139 /gbdb/panTro3/panTro3.2bit +chrUn_GL396876 8139 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155321_random 8133 /gbdb/panTro3/panTro3.2bit +chr18_GL392791_random 8132 /gbdb/panTro3/panTro3.2bit +chrUn_GL396229 8131 /gbdb/panTro3/panTro3.2bit +chrUn_GL396834 8128 /gbdb/panTro3/panTro3.2bit +chrX_GL393440_random 8123 /gbdb/panTro3/panTro3.2bit +chr18_GL392817_random 8118 /gbdb/panTro3/panTro3.2bit +chrUn_GL396172 8111 /gbdb/panTro3/panTro3.2bit +chr8_GL390891_random 8109 /gbdb/panTro3/panTro3.2bit +chrX_GL393221_random 8101 /gbdb/panTro3/panTro3.2bit +chr10_GL391513_random 8100 /gbdb/panTro3/panTro3.2bit +chrUn_GL393708 8099 /gbdb/panTro3/panTro3.2bit +chr6_GL390297_random 8089 /gbdb/panTro3/panTro3.2bit +chrUn_GL396233 8088 /gbdb/panTro3/panTro3.2bit +chr17_GL392627_random 8084 /gbdb/panTro3/panTro3.2bit +chrUn_GL396026 8084 /gbdb/panTro3/panTro3.2bit +chrUn_GL395431 8082 /gbdb/panTro3/panTro3.2bit +chr16_GL392528_random 8069 /gbdb/panTro3/panTro3.2bit +chr13_GL392088_random 8066 /gbdb/panTro3/panTro3.2bit +chr4_GL389896_random 8065 /gbdb/panTro3/panTro3.2bit +chrUn_GL394065 8059 /gbdb/panTro3/panTro3.2bit +chrUn_GL396871 8059 /gbdb/panTro3/panTro3.2bit +chrUn_GL396967 8059 /gbdb/panTro3/panTro3.2bit +chr3_GL389634_random 8053 /gbdb/panTro3/panTro3.2bit +chrUn_GL396579 8052 /gbdb/panTro3/panTro3.2bit +chrUn_GL396865 8049 /gbdb/panTro3/panTro3.2bit +chr10_GL391566_random 8043 /gbdb/panTro3/panTro3.2bit +chrUn_GL396740 8040 /gbdb/panTro3/panTro3.2bit +chrX_GL393249_random 8040 /gbdb/panTro3/panTro3.2bit +chrUn_GL394249 8033 /gbdb/panTro3/panTro3.2bit +chrUn_GL396123 8032 /gbdb/panTro3/panTro3.2bit +chrUn_GL396946 8030 /gbdb/panTro3/panTro3.2bit +chrUn_GL393584 8029 /gbdb/panTro3/panTro3.2bit +chrUn_GL394054 8029 /gbdb/panTro3/panTro3.2bit +chr10_GL391538_random 8024 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158783_random 8023 /gbdb/panTro3/panTro3.2bit +chrUn_GL396503 8018 /gbdb/panTro3/panTro3.2bit +chrUn_GL396267 8017 /gbdb/panTro3/panTro3.2bit +chr10_GL391600_random 8013 /gbdb/panTro3/panTro3.2bit +chrUn_GL396862 8013 /gbdb/panTro3/panTro3.2bit +chrUn_GL396494 8010 /gbdb/panTro3/panTro3.2bit +chr1_GL388950_random 8005 /gbdb/panTro3/panTro3.2bit +chr12_GL391995_random 8002 /gbdb/panTro3/panTro3.2bit +chrUn_GL396935 7999 /gbdb/panTro3/panTro3.2bit +chrX_GL393178_random 7995 /gbdb/panTro3/panTro3.2bit +chr19_GL392891_random 7994 /gbdb/panTro3/panTro3.2bit +chrUn_GL396914 7994 /gbdb/panTro3/panTro3.2bit +chr11_GL391846_random 7990 /gbdb/panTro3/panTro3.2bit +chr16_GL392475_random 7989 /gbdb/panTro3/panTro3.2bit +chrUn_GL396665 7984 /gbdb/panTro3/panTro3.2bit +chrX_GL393104_random 7983 /gbdb/panTro3/panTro3.2bit +chrX_GL393177_random 7981 /gbdb/panTro3/panTro3.2bit +chr4_GL389821_random 7978 /gbdb/panTro3/panTro3.2bit +chrUn_GL396879 7975 /gbdb/panTro3/panTro3.2bit +chrUn_GL396155 7972 /gbdb/panTro3/panTro3.2bit +chr2A_GL389305_random 7971 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171152_random 7967 /gbdb/panTro3/panTro3.2bit +chr13_GL392044_random 7964 /gbdb/panTro3/panTro3.2bit +chr18_GL392821_random 7961 /gbdb/panTro3/panTro3.2bit +chr12_GL391965_random 7956 /gbdb/panTro3/panTro3.2bit +chrUn_GL393794 7953 /gbdb/panTro3/panTro3.2bit +chrUn_GL396280 7951 /gbdb/panTro3/panTro3.2bit +chrUn_GL396818 7950 /gbdb/panTro3/panTro3.2bit +chrUn_GL396321 7945 /gbdb/panTro3/panTro3.2bit +chr4_GL389804_random 7943 /gbdb/panTro3/panTro3.2bit +chr9_GL391223_random 7942 /gbdb/panTro3/panTro3.2bit +chr10_GL391501_random 7941 /gbdb/panTro3/panTro3.2bit +chr1_GL389113_random 7941 /gbdb/panTro3/panTro3.2bit +chr9_GL391071_random 7941 /gbdb/panTro3/panTro3.2bit +chrUn_GL396917 7940 /gbdb/panTro3/panTro3.2bit +chrUn_GL396940 7934 /gbdb/panTro3/panTro3.2bit +chr13_GL392073_random 7933 /gbdb/panTro3/panTro3.2bit +chr19_GL392916_random 7932 /gbdb/panTro3/panTro3.2bit +chrUn_GL393643 7930 /gbdb/panTro3/panTro3.2bit +chrUn_GL395832 7930 /gbdb/panTro3/panTro3.2bit +chr19_GL392908_random 7923 /gbdb/panTro3/panTro3.2bit +chr15_GL392194_random 7921 /gbdb/panTro3/panTro3.2bit +chr10_GL391512_random 7920 /gbdb/panTro3/panTro3.2bit +chr1_GL388965_random 7919 /gbdb/panTro3/panTro3.2bit +chrUn_GL396029 7913 /gbdb/panTro3/panTro3.2bit +chr2A_GL389344_random 7902 /gbdb/panTro3/panTro3.2bit +chr9_GL391195_random 7901 /gbdb/panTro3/panTro3.2bit +chrUn_GL393621 7894 /gbdb/panTro3/panTro3.2bit +chrUn_GL396436 7892 /gbdb/panTro3/panTro3.2bit +chr10_GL391673_random 7888 /gbdb/panTro3/panTro3.2bit +chrUn_GL396581 7887 /gbdb/panTro3/panTro3.2bit +chr20_GL393016_random 7881 /gbdb/panTro3/panTro3.2bit +chrUn_GL396364 7881 /gbdb/panTro3/panTro3.2bit +chrUn_GL394690 7870 /gbdb/panTro3/panTro3.2bit +chrUn_GL393800 7868 /gbdb/panTro3/panTro3.2bit +chr3_GL389593_random 7865 /gbdb/panTro3/panTro3.2bit +chrUn_GL396678 7856 /gbdb/panTro3/panTro3.2bit +chr4_GL389829_random 7855 /gbdb/panTro3/panTro3.2bit +chr11_GL391787_random 7850 /gbdb/panTro3/panTro3.2bit +chrUn_GL396987 7850 /gbdb/panTro3/panTro3.2bit +chrUn_GL396569 7849 /gbdb/panTro3/panTro3.2bit +chrUn_GL396117 7845 /gbdb/panTro3/panTro3.2bit +chrX_GL393245_random 7844 /gbdb/panTro3/panTro3.2bit +chrUn_GL396239 7841 /gbdb/panTro3/panTro3.2bit +chrX_GL393225_random 7837 /gbdb/panTro3/panTro3.2bit +chr19_GL392904_random 7836 /gbdb/panTro3/panTro3.2bit +chrUn_GL396075 7831 /gbdb/panTro3/panTro3.2bit +chr10_GL391588_random 7830 /gbdb/panTro3/panTro3.2bit +chr1_GL389191_random 7824 /gbdb/panTro3/panTro3.2bit +chr7_GL390584_random 7824 /gbdb/panTro3/panTro3.2bit +chrUn_GL396707 7820 /gbdb/panTro3/panTro3.2bit +chrUn_GL396185 7819 /gbdb/panTro3/panTro3.2bit +chr1_GL388955_random 7818 /gbdb/panTro3/panTro3.2bit +chr10_GL391321_random 7816 /gbdb/panTro3/panTro3.2bit +chr3_GL389509_random 7815 /gbdb/panTro3/panTro3.2bit +chrUn_GL396773 7815 /gbdb/panTro3/panTro3.2bit +chr3_GL389582_random 7811 /gbdb/panTro3/panTro3.2bit +chr12_GL391941_random 7809 /gbdb/panTro3/panTro3.2bit +chrUn_GL396383 7809 /gbdb/panTro3/panTro3.2bit +chr5_GL390083_random 7807 /gbdb/panTro3/panTro3.2bit +chr14_GL392137_random 7802 /gbdb/panTro3/panTro3.2bit +chr6_GL390338_random 7802 /gbdb/panTro3/panTro3.2bit +chrUn_GL396937 7802 /gbdb/panTro3/panTro3.2bit +chrUn_GL396556 7801 /gbdb/panTro3/panTro3.2bit +chrUn_GL396631 7799 /gbdb/panTro3/panTro3.2bit +chrUn_GL396046 7796 /gbdb/panTro3/panTro3.2bit +chr5_GL390069_random 7795 /gbdb/panTro3/panTro3.2bit +chrUn_GL393762 7792 /gbdb/panTro3/panTro3.2bit +chrUn_GL396676 7787 /gbdb/panTro3/panTro3.2bit +chrUn_GL395939 7780 /gbdb/panTro3/panTro3.2bit +chrUn_GL396683 7777 /gbdb/panTro3/panTro3.2bit +chr9_GL391029_random 7776 /gbdb/panTro3/panTro3.2bit +chrUn_GL396309 7775 /gbdb/panTro3/panTro3.2bit 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7709 /gbdb/panTro3/panTro3.2bit +chrUn_GL396722 7709 /gbdb/panTro3/panTro3.2bit +chr10_GL391296_random 7707 /gbdb/panTro3/panTro3.2bit +chr10_GL391500_random 7705 /gbdb/panTro3/panTro3.2bit +chr6_GL390431_random 7704 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153798_random 7703 /gbdb/panTro3/panTro3.2bit +chr4_GL389882_random 7699 /gbdb/panTro3/panTro3.2bit +chrUn_GL396901 7698 /gbdb/panTro3/panTro3.2bit +chr16_GL392350_random 7697 /gbdb/panTro3/panTro3.2bit +chr10_GL391475_random 7696 /gbdb/panTro3/panTro3.2bit +chr19_GL392854_random 7693 /gbdb/panTro3/panTro3.2bit +chr10_GL391563_random 7692 /gbdb/panTro3/panTro3.2bit +chr2A_GL389290_random 7688 /gbdb/panTro3/panTro3.2bit +chr6_GL390321_random 7688 /gbdb/panTro3/panTro3.2bit +chrUn_GL393772 7686 /gbdb/panTro3/panTro3.2bit +chrUn_GL396493 7683 /gbdb/panTro3/panTro3.2bit +chr8_GL390840_random 7681 /gbdb/panTro3/panTro3.2bit +chr9_GL391021_random 7675 /gbdb/panTro3/panTro3.2bit +chrUn_GL396606 7675 /gbdb/panTro3/panTro3.2bit +chrUn_GL396943 7672 /gbdb/panTro3/panTro3.2bit +chrUn_GL393795 7670 /gbdb/panTro3/panTro3.2bit +chr19_GL392851_random 7668 /gbdb/panTro3/panTro3.2bit +chrX_GL393355_random 7660 /gbdb/panTro3/panTro3.2bit +chr10_GL391638_random 7659 /gbdb/panTro3/panTro3.2bit +chrUn_GL393594 7654 /gbdb/panTro3/panTro3.2bit +chrUn_GL396649 7654 /gbdb/panTro3/panTro3.2bit +chrUn_GL393843 7653 /gbdb/panTro3/panTro3.2bit +chrUn_GL394849 7653 /gbdb/panTro3/panTro3.2bit +chrUn_GL396201 7652 /gbdb/panTro3/panTro3.2bit +chrUn_GL396563 7652 /gbdb/panTro3/panTro3.2bit +chr10_GL391598_random 7651 /gbdb/panTro3/panTro3.2bit +chr10_GL391681_random 7651 /gbdb/panTro3/panTro3.2bit +chrUn_GL396714 7650 /gbdb/panTro3/panTro3.2bit +chrUn_GL396745 7649 /gbdb/panTro3/panTro3.2bit +chr8_GL390902_random 7647 /gbdb/panTro3/panTro3.2bit +chrUn_GL396545 7647 /gbdb/panTro3/panTro3.2bit +chrUn_GL395981 7646 /gbdb/panTro3/panTro3.2bit +chr12_GL392003_random 7645 /gbdb/panTro3/panTro3.2bit +chrUn_GL394067 7645 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL396619 7600 /gbdb/panTro3/panTro3.2bit +chrUn_GL396666 7600 /gbdb/panTro3/panTro3.2bit +chr10_GL391587_random 7599 /gbdb/panTro3/panTro3.2bit +chrUn_GL393735 7596 /gbdb/panTro3/panTro3.2bit +chrUn_GL395917 7594 /gbdb/panTro3/panTro3.2bit +chr12_GL391963_random 7591 /gbdb/panTro3/panTro3.2bit +chr1_GL389019_random 7590 /gbdb/panTro3/panTro3.2bit +chrUn_GL396546 7590 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03160960_random 7587 /gbdb/panTro3/panTro3.2bit +chr5_GL390166_random 7582 /gbdb/panTro3/panTro3.2bit +chrUn_GL393558 7580 /gbdb/panTro3/panTro3.2bit +chr15_GL392227_random 7578 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186027 7577 /gbdb/panTro3/panTro3.2bit +chrUn_GL393706 7576 /gbdb/panTro3/panTro3.2bit +chrUn_GL395991 7576 /gbdb/panTro3/panTro3.2bit +chrX_GL393253_random 7573 /gbdb/panTro3/panTro3.2bit +chrUn_GL396481 7567 /gbdb/panTro3/panTro3.2bit +chrUn_GL396340 7566 /gbdb/panTro3/panTro3.2bit +chrUn_GL396878 7565 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL396604 7523 /gbdb/panTro3/panTro3.2bit +chr9_GL391136_random 7522 /gbdb/panTro3/panTro3.2bit +chrX_GL393373_random 7521 /gbdb/panTro3/panTro3.2bit +chrUn_GL393763 7519 /gbdb/panTro3/panTro3.2bit +chr4_GL389690_random 7511 /gbdb/panTro3/panTro3.2bit +chrUn_GL396892 7502 /gbdb/panTro3/panTro3.2bit +chrUn_GL394023 7499 /gbdb/panTro3/panTro3.2bit +chrUn_GL396259 7499 /gbdb/panTro3/panTro3.2bit +chrUn_GL396394 7499 /gbdb/panTro3/panTro3.2bit +chrUn_GL397006 7499 /gbdb/panTro3/panTro3.2bit +chrUn_GL394191 7496 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165455_random 7495 /gbdb/panTro3/panTro3.2bit +chrX_GL393329_random 7494 /gbdb/panTro3/panTro3.2bit +chrUn_GL396928 7492 /gbdb/panTro3/panTro3.2bit +chr19_GL392907_random 7491 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153799_random 7486 /gbdb/panTro3/panTro3.2bit +chrUn_GL393829 7486 /gbdb/panTro3/panTro3.2bit +chrUn_GL393565 7484 /gbdb/panTro3/panTro3.2bit +chrUn_GL394194 7481 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr6_GL390195_random 7442 /gbdb/panTro3/panTro3.2bit +chrUn_GL396531 7442 /gbdb/panTro3/panTro3.2bit +chr12_GL391945_random 7440 /gbdb/panTro3/panTro3.2bit +chrUn_GL396498 7440 /gbdb/panTro3/panTro3.2bit +chrUn_GL396593 7439 /gbdb/panTro3/panTro3.2bit +chr10_GL391264_random 7435 /gbdb/panTro3/panTro3.2bit +chrUn_GL393739 7435 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150295_random 7434 /gbdb/panTro3/panTro3.2bit +chrUn_GL395933 7432 /gbdb/panTro3/panTro3.2bit +chr8_GL390841_random 7431 /gbdb/panTro3/panTro3.2bit +chr9_GL391107_random 7429 /gbdb/panTro3/panTro3.2bit +chrX_GL393269_random 7423 /gbdb/panTro3/panTro3.2bit +chrUn_GL393579 7422 /gbdb/panTro3/panTro3.2bit +chrUn_GL396806 7420 /gbdb/panTro3/panTro3.2bit +chr10_GL391261_random 7419 /gbdb/panTro3/panTro3.2bit +chr5_GL390093_random 7418 /gbdb/panTro3/panTro3.2bit +chrUn_GL393655 7418 /gbdb/panTro3/panTro3.2bit +chr10_GL391526_random 7414 /gbdb/panTro3/panTro3.2bit +chr3_GL389603_random 7412 /gbdb/panTro3/panTro3.2bit +chrUn_GL393675 7408 /gbdb/panTro3/panTro3.2bit +chrUn_GL393623 7406 /gbdb/panTro3/panTro3.2bit +chrUn_GL394322 7405 /gbdb/panTro3/panTro3.2bit +chrUn_GL396211 7401 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155667_random 7400 /gbdb/panTro3/panTro3.2bit +chrUn_GL396091 7400 /gbdb/panTro3/panTro3.2bit +chr12_GL391974_random 7391 /gbdb/panTro3/panTro3.2bit +chr15_GL392257_random 7391 /gbdb/panTro3/panTro3.2bit +chrUn_GL396241 7391 /gbdb/panTro3/panTro3.2bit +chrUn_GL396709 7390 /gbdb/panTro3/panTro3.2bit +chrUn_GL393866 7387 /gbdb/panTro3/panTro3.2bit +chrUn_GL396739 7387 /gbdb/panTro3/panTro3.2bit +chrUn_GL397010 7381 /gbdb/panTro3/panTro3.2bit +chr4_GL389828_random 7379 /gbdb/panTro3/panTro3.2bit +chrUn_GL396028 7374 /gbdb/panTro3/panTro3.2bit +chr10_GL391499_random 7372 /gbdb/panTro3/panTro3.2bit +chrUn_GL396098 7371 /gbdb/panTro3/panTro3.2bit +chrUn_GL396470 7371 /gbdb/panTro3/panTro3.2bit +chr3_GL389585_random 7370 /gbdb/panTro3/panTro3.2bit +chrUn_GL393872 7370 /gbdb/panTro3/panTro3.2bit +chr16_GL392341_random 7364 /gbdb/panTro3/panTro3.2bit +chr7_GL390750_random 7364 /gbdb/panTro3/panTro3.2bit +chr1_GL388951_random 7361 /gbdb/panTro3/panTro3.2bit +chr11_GL391788_random 7358 /gbdb/panTro3/panTro3.2bit +chrUn_GL396227 7358 /gbdb/panTro3/panTro3.2bit +chr2A_GL389347_random 7354 /gbdb/panTro3/panTro3.2bit +chrUn_GL396326 7354 /gbdb/panTro3/panTro3.2bit +chr16_GL392371_random 7351 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162518_random 7351 /gbdb/panTro3/panTro3.2bit +chrUn_GL396945 7351 /gbdb/panTro3/panTro3.2bit +chrUn_GL396655 7349 /gbdb/panTro3/panTro3.2bit +chrUn_GL397050 7348 /gbdb/panTro3/panTro3.2bit +chrX_GL393324_random 7345 /gbdb/panTro3/panTro3.2bit +chrUn_GL394115 7343 /gbdb/panTro3/panTro3.2bit +chr11_GL391853_random 7342 /gbdb/panTro3/panTro3.2bit +chr6_GL390382_random 7339 /gbdb/panTro3/panTro3.2bit +chrUn_GL396688 7335 /gbdb/panTro3/panTro3.2bit +chr2B_GL389394_random 7327 /gbdb/panTro3/panTro3.2bit +chrUn_GL396525 7325 /gbdb/panTro3/panTro3.2bit +chr10_GL391519_random 7323 /gbdb/panTro3/panTro3.2bit +chr9_GL391079_random 7323 /gbdb/panTro3/panTro3.2bit +chrX_GL393113_random 7318 /gbdb/panTro3/panTro3.2bit +chrX_GL393312_random 7316 /gbdb/panTro3/panTro3.2bit +chrUn_GL396194 7315 /gbdb/panTro3/panTro3.2bit +chrUn_GL393812 7314 /gbdb/panTro3/panTro3.2bit +chrUn_GL396480 7314 /gbdb/panTro3/panTro3.2bit +chrUn_GL396759 7314 /gbdb/panTro3/panTro3.2bit +chrUn_GL396121 7312 /gbdb/panTro3/panTro3.2bit +chr2B_GL389444_random 7307 /gbdb/panTro3/panTro3.2bit +chrUn_GL396793 7307 /gbdb/panTro3/panTro3.2bit +chrUn_GL393684 7304 /gbdb/panTro3/panTro3.2bit +chr9_GL391018_random 7303 /gbdb/panTro3/panTro3.2bit +chrUn_GL396457 7301 /gbdb/panTro3/panTro3.2bit +chrUn_GL393810 7300 /gbdb/panTro3/panTro3.2bit +chr6_GL390378_random 7299 /gbdb/panTro3/panTro3.2bit +chrUn_GL396313 7296 /gbdb/panTro3/panTro3.2bit +chrUn_GL393925 7293 /gbdb/panTro3/panTro3.2bit +chr3_GL389619_random 7292 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL396786 7248 /gbdb/panTro3/panTro3.2bit +chrUn_GL396924 7248 /gbdb/panTro3/panTro3.2bit +chrUn_GL393669 7247 /gbdb/panTro3/panTro3.2bit +chrUn_GL396452 7247 /gbdb/panTro3/panTro3.2bit +chr10_GL391493_random 7241 /gbdb/panTro3/panTro3.2bit +chrUn_GL396469 7238 /gbdb/panTro3/panTro3.2bit +chrUn_GL396800 7236 /gbdb/panTro3/panTro3.2bit +chr8_GL390917_random 7231 /gbdb/panTro3/panTro3.2bit +chrUn_GL393700 7231 /gbdb/panTro3/panTro3.2bit +chr4_GL389803_random 7229 /gbdb/panTro3/panTro3.2bit +chr6_GL390312_random 7228 /gbdb/panTro3/panTro3.2bit +chrUn_GL396774 7228 /gbdb/panTro3/panTro3.2bit +chr4_GL389900_random 7220 /gbdb/panTro3/panTro3.2bit +chrUn_GL396532 7220 /gbdb/panTro3/panTro3.2bit +chr13_GL392048_random 7219 /gbdb/panTro3/panTro3.2bit +chr11_GL391773_random 7212 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03184477 7211 /gbdb/panTro3/panTro3.2bit +chr4_GL389826_random 7207 /gbdb/panTro3/panTro3.2bit +chrUn_GL393910 7204 /gbdb/panTro3/panTro3.2bit 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7063 /gbdb/panTro3/panTro3.2bit +chr12_GL391953_random 7061 /gbdb/panTro3/panTro3.2bit +chr8_GL390859_random 7051 /gbdb/panTro3/panTro3.2bit +chrUn_GL396299 7050 /gbdb/panTro3/panTro3.2bit +chrX_GL393183_random 7050 /gbdb/panTro3/panTro3.2bit +chr9_GL390928_random 7047 /gbdb/panTro3/panTro3.2bit +chr2A_GL389348_random 7045 /gbdb/panTro3/panTro3.2bit +chrUn_GL393749 7045 /gbdb/panTro3/panTro3.2bit +chrUn_GL396476 7044 /gbdb/panTro3/panTro3.2bit +chr19_GL392943_random 7043 /gbdb/panTro3/panTro3.2bit +chr6_GL390308_random 7040 /gbdb/panTro3/panTro3.2bit +chrUn_GL396777 7040 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186116 7039 /gbdb/panTro3/panTro3.2bit +chrUn_GL396236 7036 /gbdb/panTro3/panTro3.2bit +chr4_GL389848_random 7034 /gbdb/panTro3/panTro3.2bit +chrUn_GL393776 7033 /gbdb/panTro3/panTro3.2bit +chrUn_GL396736 7031 /gbdb/panTro3/panTro3.2bit +chrUn_GL396049 7029 /gbdb/panTro3/panTro3.2bit +chr8_GL390836_random 7028 /gbdb/panTro3/panTro3.2bit +chr14_GL392154_random 7022 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/gbdb/panTro3/panTro3.2bit +chrUn_GL396056 6590 /gbdb/panTro3/panTro3.2bit +chrUn_GL393834 6588 /gbdb/panTro3/panTro3.2bit +chr17_GL392620_random 6584 /gbdb/panTro3/panTro3.2bit +chr4_GL389939_random 6582 /gbdb/panTro3/panTro3.2bit +chrUn_GL393885 6581 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162517_random 6580 /gbdb/panTro3/panTro3.2bit +chr1_GL388969_random 6578 /gbdb/panTro3/panTro3.2bit +chr10_GL391258_random 6577 /gbdb/panTro3/panTro3.2bit +chr8_GL390915_random 6570 /gbdb/panTro3/panTro3.2bit +chr9_GL391048_random 6569 /gbdb/panTro3/panTro3.2bit +chrUn_GL396626 6568 /gbdb/panTro3/panTro3.2bit +chrUn_GL396909 6566 /gbdb/panTro3/panTro3.2bit +chr2A_GL389346_random 6560 /gbdb/panTro3/panTro3.2bit +chr11_GL391694_random 6558 /gbdb/panTro3/panTro3.2bit +chrUn_GL396778 6557 /gbdb/panTro3/panTro3.2bit +chr1_GL388975_random 6547 /gbdb/panTro3/panTro3.2bit +chrUn_GL396264 6543 /gbdb/panTro3/panTro3.2bit +chr10_GL391672_random 6540 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157176_random 6535 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6320 /gbdb/panTro3/panTro3.2bit +chr1_GL388952_random 6316 /gbdb/panTro3/panTro3.2bit +chrUn_GL394188 6315 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168280_random 6313 /gbdb/panTro3/panTro3.2bit +chrUn_GL393941 6310 /gbdb/panTro3/panTro3.2bit +chrUn_GL396672 6310 /gbdb/panTro3/panTro3.2bit +chr3_GL389659_random 6309 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03184791 6307 /gbdb/panTro3/panTro3.2bit +chr4_GL389699_random 6304 /gbdb/panTro3/panTro3.2bit +chr17_GL392691_random 6301 /gbdb/panTro3/panTro3.2bit +chrUn_GL393556 6297 /gbdb/panTro3/panTro3.2bit +chr1_GL388974_random 6296 /gbdb/panTro3/panTro3.2bit +chr15_GL392249_random 6293 /gbdb/panTro3/panTro3.2bit +chrUn_GL396820 6289 /gbdb/panTro3/panTro3.2bit +chr4_GL389679_random 6280 /gbdb/panTro3/panTro3.2bit +chr12_GL391983_random 6279 /gbdb/panTro3/panTro3.2bit +chr11_GL391780_random 6275 /gbdb/panTro3/panTro3.2bit +chr13_GL392054_random 6274 /gbdb/panTro3/panTro3.2bit +chrUn_GL396847 6273 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr1_GL389023_random 6198 /gbdb/panTro3/panTro3.2bit +chrUn_GL396731 6195 /gbdb/panTro3/panTro3.2bit +chrUn_GL396927 6193 /gbdb/panTro3/panTro3.2bit +chrUn_GL396970 6193 /gbdb/panTro3/panTro3.2bit +chrUn_GL393740 6192 /gbdb/panTro3/panTro3.2bit +chrUn_GL394146 6189 /gbdb/panTro3/panTro3.2bit +chr10_GL391380_random 6188 /gbdb/panTro3/panTro3.2bit +chr6_GL390190_random 6187 /gbdb/panTro3/panTro3.2bit +chr12_GL391891_random 6185 /gbdb/panTro3/panTro3.2bit +chr4_GL389686_random 6183 /gbdb/panTro3/panTro3.2bit +chr10_GL391292_random 6181 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157302_random 6181 /gbdb/panTro3/panTro3.2bit +chrUn_GL396742 6181 /gbdb/panTro3/panTro3.2bit +chr10_GL391489_random 6178 /gbdb/panTro3/panTro3.2bit +chrUn_GL393598 6178 /gbdb/panTro3/panTro3.2bit +chr5_GL389996_random 6175 /gbdb/panTro3/panTro3.2bit +chrUn_GL396959 6175 /gbdb/panTro3/panTro3.2bit +chrX_GL393106_random 6165 /gbdb/panTro3/panTro3.2bit +chr10_GL391631_random 6164 /gbdb/panTro3/panTro3.2bit +chr13_GL392074_random 6163 /gbdb/panTro3/panTro3.2bit +chrUn_GL396114 6163 /gbdb/panTro3/panTro3.2bit +chr17_GL392713_random 6162 /gbdb/panTro3/panTro3.2bit +chr4_GL389867_random 6162 /gbdb/panTro3/panTro3.2bit +chr3_GL389511_random 6161 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153850_random 6160 /gbdb/panTro3/panTro3.2bit +chrUn_GL396630 6157 /gbdb/panTro3/panTro3.2bit +chr4_GL389925_random 6156 /gbdb/panTro3/panTro3.2bit +chr18_GL392784_random 6153 /gbdb/panTro3/panTro3.2bit +chr2B_GL389445_random 6148 /gbdb/panTro3/panTro3.2bit +chr4_GL389811_random 6146 /gbdb/panTro3/panTro3.2bit +chr9_GL391030_random 6143 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150296_random 6141 /gbdb/panTro3/panTro3.2bit +chr10_GL391560_random 6138 /gbdb/panTro3/panTro3.2bit +chr10_GL391613_random 6138 /gbdb/panTro3/panTro3.2bit +chrUn_GL396968 6137 /gbdb/panTro3/panTro3.2bit +chrUn_GL394047 6126 /gbdb/panTro3/panTro3.2bit +chr1_GL388945_random 6122 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394947 5901 /gbdb/panTro3/panTro3.2bit +chrUn_GL396538 5900 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173417_random 5899 /gbdb/panTro3/panTro3.2bit +chrUn_GL396370 5899 /gbdb/panTro3/panTro3.2bit +chrUn_GL396621 5899 /gbdb/panTro3/panTro3.2bit +chrUn_GL396634 5898 /gbdb/panTro3/panTro3.2bit +chr4_GL389727_random 5897 /gbdb/panTro3/panTro3.2bit +chrUn_GL393571 5897 /gbdb/panTro3/panTro3.2bit +chrUn_GL394409 5896 /gbdb/panTro3/panTro3.2bit +chrUn_GL393563 5895 /gbdb/panTro3/panTro3.2bit +chrUn_GL396231 5895 /gbdb/panTro3/panTro3.2bit +chr12_GL391943_random 5894 /gbdb/panTro3/panTro3.2bit +chr22_GL393094_random 5894 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152064_random 5894 /gbdb/panTro3/panTro3.2bit +chrUn_GL393808 5891 /gbdb/panTro3/panTro3.2bit +chr4_GL389719_random 5889 /gbdb/panTro3/panTro3.2bit +chrUn_GL396710 5889 /gbdb/panTro3/panTro3.2bit +chr17_GL392630_random 5884 /gbdb/panTro3/panTro3.2bit +chr2A_GL389256_random 5879 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr6_GL390172_random 5846 /gbdb/panTro3/panTro3.2bit +chr2A_GL389292_random 5845 /gbdb/panTro3/panTro3.2bit +chr22_GL393063_random 5844 /gbdb/panTro3/panTro3.2bit +chr11_GL391766_random 5843 /gbdb/panTro3/panTro3.2bit +chr4_GL389887_random 5843 /gbdb/panTro3/panTro3.2bit +chrUn_GL393629 5841 /gbdb/panTro3/panTro3.2bit +chr1_GL388823_random 5840 /gbdb/panTro3/panTro3.2bit +chr1_GL388812_random 5839 /gbdb/panTro3/panTro3.2bit +chrUn_GL396854 5836 /gbdb/panTro3/panTro3.2bit +chr4_GL389687_random 5835 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187548 5833 /gbdb/panTro3/panTro3.2bit +chr4_GL389928_random 5832 /gbdb/panTro3/panTro3.2bit +chr9_GL390957_random 5831 /gbdb/panTro3/panTro3.2bit +chrUn_GL393659 5830 /gbdb/panTro3/panTro3.2bit +chr18_GL392802_random 5828 /gbdb/panTro3/panTro3.2bit +chrUn_GL393785 5828 /gbdb/panTro3/panTro3.2bit +chr10_GL391509_random 5824 /gbdb/panTro3/panTro3.2bit +chr10_GL391542_random 5824 /gbdb/panTro3/panTro3.2bit +chrUn_GL394145 5822 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159003_random 5821 /gbdb/panTro3/panTro3.2bit +chrUn_GL394570 5820 /gbdb/panTro3/panTro3.2bit +chrUn_GL396922 5820 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164532_random 5819 /gbdb/panTro3/panTro3.2bit +chrUn_GL394461 5814 /gbdb/panTro3/panTro3.2bit +chrUn_GL396411 5814 /gbdb/panTro3/panTro3.2bit +chr13_GL392077_random 5813 /gbdb/panTro3/panTro3.2bit +chrUn_GL396024 5812 /gbdb/panTro3/panTro3.2bit +chr3_GL389629_random 5811 /gbdb/panTro3/panTro3.2bit +chrUn_GL396423 5810 /gbdb/panTro3/panTro3.2bit +chr10_GL391343_random 5808 /gbdb/panTro3/panTro3.2bit +chr8_GL390874_random 5803 /gbdb/panTro3/panTro3.2bit +chr16_GL392570_random 5802 /gbdb/panTro3/panTro3.2bit +chr3_GL389522_random 5801 /gbdb/panTro3/panTro3.2bit +chr9_GL390930_random 5800 /gbdb/panTro3/panTro3.2bit +chrUn_GL393958 5800 /gbdb/panTro3/panTro3.2bit +chrUn_GL394158 5800 /gbdb/panTro3/panTro3.2bit +chrUn_GL396376 5798 /gbdb/panTro3/panTro3.2bit +chrUn_GL396475 5797 /gbdb/panTro3/panTro3.2bit +chr1_GL389247_random 5795 /gbdb/panTro3/panTro3.2bit +chr6_GL390328_random 5794 /gbdb/panTro3/panTro3.2bit +chrUn_GL396408 5794 /gbdb/panTro3/panTro3.2bit +chr4_GL389884_random 5793 /gbdb/panTro3/panTro3.2bit +chr2A_GL389259_random 5791 /gbdb/panTro3/panTro3.2bit +chrUn_GL396523 5790 /gbdb/panTro3/panTro3.2bit +chr13_GL392016_random 5788 /gbdb/panTro3/panTro3.2bit +chrUn_GL396776 5777 /gbdb/panTro3/panTro3.2bit +chr10_GL391405_random 5776 /gbdb/panTro3/panTro3.2bit +chr6_GL390309_random 5776 /gbdb/panTro3/panTro3.2bit +chr8_GL390843_random 5775 /gbdb/panTro3/panTro3.2bit +chr8_GL390845_random 5775 /gbdb/panTro3/panTro3.2bit +chr3_GL389504_random 5773 /gbdb/panTro3/panTro3.2bit +chr13_GL392081_random 5772 /gbdb/panTro3/panTro3.2bit +chr9_GL391225_random 5771 /gbdb/panTro3/panTro3.2bit +chrUn_GL396605 5768 /gbdb/panTro3/panTro3.2bit +chr6_GL390322_random 5767 /gbdb/panTro3/panTro3.2bit +chrUn_GL393939 5766 /gbdb/panTro3/panTro3.2bit +chrX_GL393102_random 5764 /gbdb/panTro3/panTro3.2bit +chr17_GL392633_random 5763 /gbdb/panTro3/panTro3.2bit +chr4_GL389707_random 5763 /gbdb/panTro3/panTro3.2bit +chr11_GL391842_random 5761 /gbdb/panTro3/panTro3.2bit +chr16_GL392567_random 5761 /gbdb/panTro3/panTro3.2bit +chrUn_GL396826 5760 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165515_random 5755 /gbdb/panTro3/panTro3.2bit +chr5_GL390064_random 5755 /gbdb/panTro3/panTro3.2bit +chrUn_GL396419 5752 /gbdb/panTro3/panTro3.2bit +chr15_GL392244_random 5751 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175168_random 5751 /gbdb/panTro3/panTro3.2bit +chrUn_GL396663 5750 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186484 5749 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186302 5747 /gbdb/panTro3/panTro3.2bit +chr15_GL392197_random 5746 /gbdb/panTro3/panTro3.2bit +chrUn_GL396782 5746 /gbdb/panTro3/panTro3.2bit +chr20_GL392977_random 5745 /gbdb/panTro3/panTro3.2bit +chrUn_GL396417 5745 /gbdb/panTro3/panTro3.2bit +chr3_GL389596_random 5744 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394727 5726 /gbdb/panTro3/panTro3.2bit +chrX_GL393115_random 5725 /gbdb/panTro3/panTro3.2bit +chr1_GL389101_random 5723 /gbdb/panTro3/panTro3.2bit +chr1_GL389206_random 5723 /gbdb/panTro3/panTro3.2bit +chr18_GL392760_random 5722 /gbdb/panTro3/panTro3.2bit +chr19_GL392868_random 5722 /gbdb/panTro3/panTro3.2bit +chrUn_GL395996 5722 /gbdb/panTro3/panTro3.2bit +chr9_GL391028_random 5719 /gbdb/panTro3/panTro3.2bit +chr16_GL392455_random 5718 /gbdb/panTro3/panTro3.2bit +chrUn_GL396698 5717 /gbdb/panTro3/panTro3.2bit +chr4_GL389756_random 5716 /gbdb/panTro3/panTro3.2bit +chr18_GL392788_random 5715 /gbdb/panTro3/panTro3.2bit +chrUn_GL393569 5715 /gbdb/panTro3/panTro3.2bit +chr10_GL391661_random 5713 /gbdb/panTro3/panTro3.2bit +chr11_GL391851_random 5713 /gbdb/panTro3/panTro3.2bit +chrUn_GL396054 5713 /gbdb/panTro3/panTro3.2bit +chrUn_GL396998 5713 /gbdb/panTro3/panTro3.2bit +chrUn_GL393595 5712 /gbdb/panTro3/panTro3.2bit +chr10_GL391572_random 5710 /gbdb/panTro3/panTro3.2bit +chr16_GL392535_random 5709 /gbdb/panTro3/panTro3.2bit +chrUn_GL396421 5709 /gbdb/panTro3/panTro3.2bit +chrUn_GL394347 5707 /gbdb/panTro3/panTro3.2bit +chrUn_GL396397 5706 /gbdb/panTro3/panTro3.2bit +chr14_GL392148_random 5705 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186568 5704 /gbdb/panTro3/panTro3.2bit +chr2B_GL389451_random 5703 /gbdb/panTro3/panTro3.2bit +chrUn_GL393705 5701 /gbdb/panTro3/panTro3.2bit +chr1_GL388961_random 5700 /gbdb/panTro3/panTro3.2bit +chrUn_GL393934 5697 /gbdb/panTro3/panTro3.2bit +chrUn_GL393980 5696 /gbdb/panTro3/panTro3.2bit +chrUn_GL394674 5696 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188291 5695 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186471 5694 /gbdb/panTro3/panTro3.2bit +chrUn_GL394215 5694 /gbdb/panTro3/panTro3.2bit +chrUn_GL393650 5692 /gbdb/panTro3/panTro3.2bit +chrUn_GL396568 5691 /gbdb/panTro3/panTro3.2bit +chr12_GL391987_random 5690 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153815_random 5689 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_GL391553_random 5664 /gbdb/panTro3/panTro3.2bit +chr16_GL392354_random 5664 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186179 5664 /gbdb/panTro3/panTro3.2bit +chr1_GL389246_random 5662 /gbdb/panTro3/panTro3.2bit +chrUn_GL396177 5661 /gbdb/panTro3/panTro3.2bit +chrUn_GL396547 5660 /gbdb/panTro3/panTro3.2bit +chr18_GL392787_random 5659 /gbdb/panTro3/panTro3.2bit +chr10_GL391546_random 5656 /gbdb/panTro3/panTro3.2bit +chrUn_GL396883 5656 /gbdb/panTro3/panTro3.2bit +chrUn_GL397049 5655 /gbdb/panTro3/panTro3.2bit +chr16_GL392536_random 5651 /gbdb/panTro3/panTro3.2bit +chr2B_GL389446_random 5651 /gbdb/panTro3/panTro3.2bit +chrUn_GL396398 5649 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152926_random 5647 /gbdb/panTro3/panTro3.2bit +chr12_GL391921_random 5646 /gbdb/panTro3/panTro3.2bit +chrUn_GL393717 5644 /gbdb/panTro3/panTro3.2bit +chr6_GL390169_random 5643 /gbdb/panTro3/panTro3.2bit +chrUn_GL396748 5641 /gbdb/panTro3/panTro3.2bit +chr6_GL390319_random 5638 /gbdb/panTro3/panTro3.2bit +chr6_GL390366_random 5637 /gbdb/panTro3/panTro3.2bit +chr5_GL390081_random 5635 /gbdb/panTro3/panTro3.2bit +chrUn_GL394454 5634 /gbdb/panTro3/panTro3.2bit +chr4_GL389681_random 5633 /gbdb/panTro3/panTro3.2bit +chrUn_GL396482 5632 /gbdb/panTro3/panTro3.2bit +chrUn_GL397054 5632 /gbdb/panTro3/panTro3.2bit +chr4_GL389883_random 5631 /gbdb/panTro3/panTro3.2bit +chr2A_GL389257_random 5627 /gbdb/panTro3/panTro3.2bit +chr7_GL390504_random 5627 /gbdb/panTro3/panTro3.2bit +chrUn_GL394121 5627 /gbdb/panTro3/panTro3.2bit +chr10_GL391256_random 5626 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168286_random 5626 /gbdb/panTro3/panTro3.2bit +chrUn_GL393637 5626 /gbdb/panTro3/panTro3.2bit +chrUn_GL396456 5625 /gbdb/panTro3/panTro3.2bit +chr5_GL390144_random 5622 /gbdb/panTro3/panTro3.2bit +chrUn_GL394504 5621 /gbdb/panTro3/panTro3.2bit +chr10_GL391260_random 5620 /gbdb/panTro3/panTro3.2bit +chrUn_GL396808 5620 /gbdb/panTro3/panTro3.2bit +chr8_GL390790_random 5618 /gbdb/panTro3/panTro3.2bit +chrUn_GL396771 5617 /gbdb/panTro3/panTro3.2bit +chr13_GL392012_random 5616 /gbdb/panTro3/panTro3.2bit +chr2B_GL389452_random 5611 /gbdb/panTro3/panTro3.2bit +chrUn_GL394541 5611 /gbdb/panTro3/panTro3.2bit +chrUn_GL396594 5611 /gbdb/panTro3/panTro3.2bit +chrUn_GL396381 5610 /gbdb/panTro3/panTro3.2bit +chr19_GL392869_random 5608 /gbdb/panTro3/panTro3.2bit +chrUn_GL394166 5608 /gbdb/panTro3/panTro3.2bit +chrUn_GL396611 5608 /gbdb/panTro3/panTro3.2bit +chr6_GL390187_random 5606 /gbdb/panTro3/panTro3.2bit +chrUn_GL393799 5606 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158974_random 5603 /gbdb/panTro3/panTro3.2bit +chrUn_GL396357 5603 /gbdb/panTro3/panTro3.2bit +chr10_GL391615_random 5601 /gbdb/panTro3/panTro3.2bit +chrUn_GL393741 5601 /gbdb/panTro3/panTro3.2bit +chrUn_GL396830 5601 /gbdb/panTro3/panTro3.2bit +chr3_GL389618_random 5599 /gbdb/panTro3/panTro3.2bit +chr6_GL390354_random 5599 /gbdb/panTro3/panTro3.2bit +chrUn_GL396938 5598 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr4_GL389683_random 5569 /gbdb/panTro3/panTro3.2bit +chr9_GL391003_random 5569 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187888 5568 /gbdb/panTro3/panTro3.2bit +chr8_GL390860_random 5566 /gbdb/panTro3/panTro3.2bit +chr11_GL391695_random 5565 /gbdb/panTro3/panTro3.2bit +chr10_GL391393_random 5563 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186449 5563 /gbdb/panTro3/panTro3.2bit +chrUn_GL395254 5562 /gbdb/panTro3/panTro3.2bit +chr5_GL390158_random 5559 /gbdb/panTro3/panTro3.2bit +chrUn_GL393651 5559 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174462_random 5557 /gbdb/panTro3/panTro3.2bit +chr18_GL392750_random 5557 /gbdb/panTro3/panTro3.2bit +chr5_GL389999_random 5557 /gbdb/panTro3/panTro3.2bit +chr10_GL391629_random 5556 /gbdb/panTro3/panTro3.2bit +chrUn_GL397023 5554 /gbdb/panTro3/panTro3.2bit +chr14_GL392098_random 5553 /gbdb/panTro3/panTro3.2bit +chrUn_GL396366 5553 /gbdb/panTro3/panTro3.2bit +chrUn_GL396553 5551 /gbdb/panTro3/panTro3.2bit +chr5_GL390154_random 5549 /gbdb/panTro3/panTro3.2bit +chr10_GL391300_random 5544 /gbdb/panTro3/panTro3.2bit +chr11_GL391696_random 5540 /gbdb/panTro3/panTro3.2bit +chrUn_GL393816 5540 /gbdb/panTro3/panTro3.2bit +chrUn_GL396289 5540 /gbdb/panTro3/panTro3.2bit +chr1_GL388813_random 5539 /gbdb/panTro3/panTro3.2bit +chrUn_GL396754 5539 /gbdb/panTro3/panTro3.2bit +chr3_GL389598_random 5537 /gbdb/panTro3/panTro3.2bit +chrUn_GL393853 5537 /gbdb/panTro3/panTro3.2bit +chrUn_GL396915 5536 /gbdb/panTro3/panTro3.2bit +chrUn_GL397045 5534 /gbdb/panTro3/panTro3.2bit +chr2B_GL389447_random 5533 /gbdb/panTro3/panTro3.2bit +chrUn_GL393582 5532 /gbdb/panTro3/panTro3.2bit +chr6_GL390353_random 5531 /gbdb/panTro3/panTro3.2bit +chrUn_GL396888 5531 /gbdb/panTro3/panTro3.2bit +chr1_GL388977_random 5530 /gbdb/panTro3/panTro3.2bit +chr4_GL389830_random 5530 /gbdb/panTro3/panTro3.2bit +chr10_GL391541_random 5529 /gbdb/panTro3/panTro3.2bit +chrUn_GL397064 5529 /gbdb/panTro3/panTro3.2bit +chr10_GL391621_random 5528 /gbdb/panTro3/panTro3.2bit +chr11_GL391770_random 5528 /gbdb/panTro3/panTro3.2bit +chr11_GL391719_random 5526 /gbdb/panTro3/panTro3.2bit +chr15_GL392252_random 5523 /gbdb/panTro3/panTro3.2bit +chr1_GL389111_random 5523 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188187 5523 /gbdb/panTro3/panTro3.2bit +chr2B_GL389454_random 5522 /gbdb/panTro3/panTro3.2bit +chr6_GL390271_random 5521 /gbdb/panTro3/panTro3.2bit +chr6_GL390209_random 5520 /gbdb/panTro3/panTro3.2bit +chrUn_GL396984 5519 /gbdb/panTro3/panTro3.2bit +chr10_GL391287_random 5518 /gbdb/panTro3/panTro3.2bit +chr2A_GL389260_random 5518 /gbdb/panTro3/panTro3.2bit +chrUn_GL396868 5518 /gbdb/panTro3/panTro3.2bit +chr2B_GL389487_random 5517 /gbdb/panTro3/panTro3.2bit +chr7_GL390447_random 5517 /gbdb/panTro3/panTro3.2bit +chr10_GL391316_random 5515 /gbdb/panTro3/panTro3.2bit +chr2B_GL389493_random 5515 /gbdb/panTro3/panTro3.2bit +chr12_GL391877_random 5514 /gbdb/panTro3/panTro3.2bit +chr5_GL389997_random 5514 /gbdb/panTro3/panTro3.2bit +chr16_GL392531_random 5513 /gbdb/panTro3/panTro3.2bit +chr4_GL389823_random 5513 /gbdb/panTro3/panTro3.2bit +chrUn_GL394266 5512 /gbdb/panTro3/panTro3.2bit +chr2B_GL389393_random 5510 /gbdb/panTro3/panTro3.2bit +chrUn_GL396747 5510 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171983_random 5507 /gbdb/panTro3/panTro3.2bit +chrUn_GL393698 5506 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03185728 5505 /gbdb/panTro3/panTro3.2bit +chrUn_GL393750 5505 /gbdb/panTro3/panTro3.2bit +chrUn_GL396137 5505 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03183955 5504 /gbdb/panTro3/panTro3.2bit +chr10_GL391662_random 5501 /gbdb/panTro3/panTro3.2bit +chr7_GL390463_random 5501 /gbdb/panTro3/panTro3.2bit +chr16_GL392294_random 5500 /gbdb/panTro3/panTro3.2bit +chr2B_GL389460_random 5500 /gbdb/panTro3/panTro3.2bit +chr15_GL392192_random 5499 /gbdb/panTro3/panTro3.2bit +chrUn_GL396812 5498 /gbdb/panTro3/panTro3.2bit +chr11_GL391733_random 5496 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158902_random 5495 /gbdb/panTro3/panTro3.2bit +chr13_GL392072_random 5493 /gbdb/panTro3/panTro3.2bit +chr2B_GL389427_random 5493 /gbdb/panTro3/panTro3.2bit +chrUn_GL394792 5493 /gbdb/panTro3/panTro3.2bit +chrUn_GL393943 5492 /gbdb/panTro3/panTro3.2bit +chrUn_GL393737 5491 /gbdb/panTro3/panTro3.2bit +chr16_GL392327_random 5489 /gbdb/panTro3/panTro3.2bit +chr1_GL388814_random 5488 /gbdb/panTro3/panTro3.2bit +chrUn_GL393873 5487 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153876_random 5485 /gbdb/panTro3/panTro3.2bit +chr3_GL389517_random 5484 /gbdb/panTro3/panTro3.2bit +chr16_GL392358_random 5482 /gbdb/panTro3/panTro3.2bit +chr20_GL392982_random 5482 /gbdb/panTro3/panTro3.2bit +chr11_GL391789_random 5480 /gbdb/panTro3/panTro3.2bit +chrUn_GL393833 5480 /gbdb/panTro3/panTro3.2bit +chr16_GL392297_random 5479 /gbdb/panTro3/panTro3.2bit +chrUn_GL393839 5479 /gbdb/panTro3/panTro3.2bit +chrUn_GL394414 5479 /gbdb/panTro3/panTro3.2bit +chrUn_GL394909 5479 /gbdb/panTro3/panTro3.2bit +chrUn_GL395258 5479 /gbdb/panTro3/panTro3.2bit +chr12_GL391907_random 5478 /gbdb/panTro3/panTro3.2bit +chr22_GL393101_random 5478 /gbdb/panTro3/panTro3.2bit +chr3_GL389518_random 5477 /gbdb/panTro3/panTro3.2bit +chr8_GL390757_random 5477 /gbdb/panTro3/panTro3.2bit +chr13_GL392009_random 5476 /gbdb/panTro3/panTro3.2bit +chr6_GL390349_random 5476 /gbdb/panTro3/panTro3.2bit +chr10_GL391312_random 5475 /gbdb/panTro3/panTro3.2bit +chr17_GL392715_random 5475 /gbdb/panTro3/panTro3.2bit +chr2A_GL389291_random 5475 /gbdb/panTro3/panTro3.2bit +chrUn_GL396632 5475 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158977_random 5474 /gbdb/panTro3/panTro3.2bit +chr5_GL390090_random 5473 /gbdb/panTro3/panTro3.2bit +chr12_GL391906_random 5472 /gbdb/panTro3/panTro3.2bit +chr12_GL391997_random 5472 /gbdb/panTro3/panTro3.2bit +chr19_GL392934_random 5472 /gbdb/panTro3/panTro3.2bit +chr20_GL393047_random 5470 /gbdb/panTro3/panTro3.2bit +chr8_GL390864_random 5470 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152052_random 5469 /gbdb/panTro3/panTro3.2bit +chr11_GL391792_random 5468 /gbdb/panTro3/panTro3.2bit +chrUn_GL393950 5468 /gbdb/panTro3/panTro3.2bit +chr7_GL390557_random 5463 /gbdb/panTro3/panTro3.2bit +chrUn_GL396589 5463 /gbdb/panTro3/panTro3.2bit +chr10_GL391277_random 5462 /gbdb/panTro3/panTro3.2bit +chr2B_GL389496_random 5462 /gbdb/panTro3/panTro3.2bit +chrUn_GL395884 5460 /gbdb/panTro3/panTro3.2bit +chr10_GL391257_random 5459 /gbdb/panTro3/panTro3.2bit +chr5_GL390039_random 5458 /gbdb/panTro3/panTro3.2bit +chrUn_GL394031 5458 /gbdb/panTro3/panTro3.2bit +chr16_GL392357_random 5457 /gbdb/panTro3/panTro3.2bit +chrUn_GL394977 5457 /gbdb/panTro3/panTro3.2bit +chr11_GL391703_random 5454 /gbdb/panTro3/panTro3.2bit +chr14_GL392097_random 5454 /gbdb/panTro3/panTro3.2bit +chr5_GL390097_random 5454 /gbdb/panTro3/panTro3.2bit +chr4_GL389817_random 5451 /gbdb/panTro3/panTro3.2bit +chrUn_GL394267 5446 /gbdb/panTro3/panTro3.2bit +chr9_GL391022_random 5445 /gbdb/panTro3/panTro3.2bit +chrUn_GL393921 5445 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152882_random 5444 /gbdb/panTro3/panTro3.2bit +chr10_GL391404_random 5443 /gbdb/panTro3/panTro3.2bit +chr6_GL390306_random 5443 /gbdb/panTro3/panTro3.2bit +chrUn_GL394275 5443 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169246_random 5442 /gbdb/panTro3/panTro3.2bit +chr10_GL391372_random 5441 /gbdb/panTro3/panTro3.2bit +chrUn_GL396657 5441 /gbdb/panTro3/panTro3.2bit +chr5_GL390017_random 5440 /gbdb/panTro3/panTro3.2bit +chrUn_GL393625 5440 /gbdb/panTro3/panTro3.2bit +chr10_GL391594_random 5438 /gbdb/panTro3/panTro3.2bit +chrUn_GL396769 5438 /gbdb/panTro3/panTro3.2bit +chr10_GL391278_random 5437 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186157 5437 /gbdb/panTro3/panTro3.2bit +chr3_GL389594_random 5436 /gbdb/panTro3/panTro3.2bit +chr2A_GL389330_random 5435 /gbdb/panTro3/panTro3.2bit +chr3_GL389523_random 5435 /gbdb/panTro3/panTro3.2bit +chrUn_GL396592 5435 /gbdb/panTro3/panTro3.2bit +chrUn_GL396691 5435 /gbdb/panTro3/panTro3.2bit +chrUn_GL393962 5434 /gbdb/panTro3/panTro3.2bit +chrX_GL393381_random 5434 /gbdb/panTro3/panTro3.2bit +chr12_GL391947_random 5433 /gbdb/panTro3/panTro3.2bit +chrUn_GL393756 5433 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173342_random 5431 /gbdb/panTro3/panTro3.2bit +chr5_GL390121_random 5431 /gbdb/panTro3/panTro3.2bit +chr1_GL388834_random 5430 /gbdb/panTro3/panTro3.2bit +chr9_GL391233_random 5429 /gbdb/panTro3/panTro3.2bit +chrUn_GL394051 5429 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175181_random 5428 /gbdb/panTro3/panTro3.2bit +chr1_GL388959_random 5427 /gbdb/panTro3/panTro3.2bit +chrUn_GL396625 5427 /gbdb/panTro3/panTro3.2bit +chr22_GL393084_random 5426 /gbdb/panTro3/panTro3.2bit +chr2A_GL389265_random 5423 /gbdb/panTro3/panTro3.2bit +chrUn_GL396648 5423 /gbdb/panTro3/panTro3.2bit +chrUn_GL394415 5421 /gbdb/panTro3/panTro3.2bit +chrUn_GL394120 5420 /gbdb/panTro3/panTro3.2bit +chrUn_GL394434 5419 /gbdb/panTro3/panTro3.2bit +chr17_GL392722_random 5418 /gbdb/panTro3/panTro3.2bit +chr8_GL390890_random 5418 /gbdb/panTro3/panTro3.2bit +chrUn_GL394148 5417 /gbdb/panTro3/panTro3.2bit +chr5_GL390152_random 5415 /gbdb/panTro3/panTro3.2bit +chr11_GL391852_random 5414 /gbdb/panTro3/panTro3.2bit +chrUn_GL396869 5414 /gbdb/panTro3/panTro3.2bit +chr6_GL390310_random 5412 /gbdb/panTro3/panTro3.2bit +chrUn_GL396824 5409 /gbdb/panTro3/panTro3.2bit +chr16_GL392315_random 5408 /gbdb/panTro3/panTro3.2bit +chr5_GL390133_random 5408 /gbdb/panTro3/panTro3.2bit +chr14_GL392094_random 5407 /gbdb/panTro3/panTro3.2bit +chrUn_GL396893 5407 /gbdb/panTro3/panTro3.2bit +chr5_GL390116_random 5406 /gbdb/panTro3/panTro3.2bit +chr1_GL388825_random 5404 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03185367 5404 /gbdb/panTro3/panTro3.2bit +chrUn_GL396932 5403 /gbdb/panTro3/panTro3.2bit +chr3_GL389562_random 5401 /gbdb/panTro3/panTro3.2bit +chr4_GL389715_random 5401 /gbdb/panTro3/panTro3.2bit +chr18_GL392759_random 5399 /gbdb/panTro3/panTro3.2bit +chrUn_GL394024 5399 /gbdb/panTro3/panTro3.2bit +chrUn_GL394084 5399 /gbdb/panTro3/panTro3.2bit +chrUn_GL396986 5399 /gbdb/panTro3/panTro3.2bit +chr17_GL392716_random 5398 /gbdb/panTro3/panTro3.2bit +chr7_GL390696_random 5398 /gbdb/panTro3/panTro3.2bit +chr11_GL391779_random 5397 /gbdb/panTro3/panTro3.2bit +chrUn_GL394160 5396 /gbdb/panTro3/panTro3.2bit +chr4_GL389807_random 5391 /gbdb/panTro3/panTro3.2bit +chr5_GL389998_random 5390 /gbdb/panTro3/panTro3.2bit +chrUn_GL395487 5389 /gbdb/panTro3/panTro3.2bit +chrUn_GL394645 5388 /gbdb/panTro3/panTro3.2bit +chrUn_GL396950 5386 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155787_random 5385 /gbdb/panTro3/panTro3.2bit +chrUn_GL394287 5384 /gbdb/panTro3/panTro3.2bit +chr18_GL392748_random 5383 /gbdb/panTro3/panTro3.2bit +chr16_GL392348_random 5380 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150340_random 5380 /gbdb/panTro3/panTro3.2bit +chrUn_GL393926 5380 /gbdb/panTro3/panTro3.2bit +chr1_GL389165_random 5379 /gbdb/panTro3/panTro3.2bit +chrUn_GL393689 5378 /gbdb/panTro3/panTro3.2bit +chr2B_GL389453_random 5377 /gbdb/panTro3/panTro3.2bit +chr6_GL390184_random 5377 /gbdb/panTro3/panTro3.2bit +chr2B_GL389396_random 5375 /gbdb/panTro3/panTro3.2bit +chr3_GL389606_random 5375 /gbdb/panTro3/panTro3.2bit +chrUn_GL396768 5375 /gbdb/panTro3/panTro3.2bit +chr2B_GL389389_random 5374 /gbdb/panTro3/panTro3.2bit +chr8_GL390763_random 5374 /gbdb/panTro3/panTro3.2bit +chrUn_GL396989 5373 /gbdb/panTro3/panTro3.2bit +chr10_GL391565_random 5371 /gbdb/panTro3/panTro3.2bit +chr18_GL392742_random 5370 /gbdb/panTro3/panTro3.2bit +chr9_GL390940_random 5369 /gbdb/panTro3/panTro3.2bit +chrUn_GL393562 5369 /gbdb/panTro3/panTro3.2bit +chrUn_GL396886 5369 /gbdb/panTro3/panTro3.2bit +chrUn_GL393993 5368 /gbdb/panTro3/panTro3.2bit +chrUn_GL394068 5368 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153797_random 5367 /gbdb/panTro3/panTro3.2bit +chr6_GL390359_random 5367 /gbdb/panTro3/panTro3.2bit +chr6_GL390387_random 5366 /gbdb/panTro3/panTro3.2bit +chrUn_GL393865 5364 /gbdb/panTro3/panTro3.2bit +chr10_GL391616_random 5361 /gbdb/panTro3/panTro3.2bit +chr2A_GL389342_random 5361 /gbdb/panTro3/panTro3.2bit +chr12_GL391993_random 5360 /gbdb/panTro3/panTro3.2bit +chrUn_GL397028 5360 /gbdb/panTro3/panTro3.2bit +chr5_GL390003_random 5359 /gbdb/panTro3/panTro3.2bit +chrUn_GL393575 5359 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164566_random 5358 /gbdb/panTro3/panTro3.2bit +chrUn_GL393730 5356 /gbdb/panTro3/panTro3.2bit +chrUn_GL394111 5356 /gbdb/panTro3/panTro3.2bit +chrUn_GL396735 5356 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165541_random 5355 /gbdb/panTro3/panTro3.2bit +chr11_GL391790_random 5355 /gbdb/panTro3/panTro3.2bit +chr4_GL389704_random 5355 /gbdb/panTro3/panTro3.2bit +chr9_GL390923_random 5353 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150462_random 5348 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153942_random 5344 /gbdb/panTro3/panTro3.2bit +chrUn_GL396872 5344 /gbdb/panTro3/panTro3.2bit +chrX_GL393358_random 5344 /gbdb/panTro3/panTro3.2bit +chr8_GL390900_random 5343 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr2A_GL389295_random 5316 /gbdb/panTro3/panTro3.2bit +chrUn_GL396798 5315 /gbdb/panTro3/panTro3.2bit +chr6_GL390367_random 5314 /gbdb/panTro3/panTro3.2bit +chr10_GL391320_random 5312 /gbdb/panTro3/panTro3.2bit +chr18_GL392757_random 5312 /gbdb/panTro3/panTro3.2bit +chr6_GL390439_random 5311 /gbdb/panTro3/panTro3.2bit +chr7_GL390596_random 5310 /gbdb/panTro3/panTro3.2bit +chrUn_GL396730 5310 /gbdb/panTro3/panTro3.2bit +chrUn_GL397065 5309 /gbdb/panTro3/panTro3.2bit +chrUn_GL396451 5308 /gbdb/panTro3/panTro3.2bit +chr12_GL391935_random 5303 /gbdb/panTro3/panTro3.2bit +chr2B_GL389483_random 5303 /gbdb/panTro3/panTro3.2bit +chr5_GL390119_random 5303 /gbdb/panTro3/panTro3.2bit +chr7_GL390470_random 5302 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162556_random 5302 /gbdb/panTro3/panTro3.2bit +chr17_GL392592_random 5301 /gbdb/panTro3/panTro3.2bit +chr8_GL390766_random 5300 /gbdb/panTro3/panTro3.2bit +chrUn_GL394029 5300 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr1_GL388973_random 5282 /gbdb/panTro3/panTro3.2bit +chrUn_GL394000 5280 /gbdb/panTro3/panTro3.2bit +chrUn_GL396787 5280 /gbdb/panTro3/panTro3.2bit +chrUn_GL396988 5280 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150475_random 5278 /gbdb/panTro3/panTro3.2bit +chr9_GL391248_random 5277 /gbdb/panTro3/panTro3.2bit +chrUn_GL394125 5277 /gbdb/panTro3/panTro3.2bit +chrUn_GL396850 5277 /gbdb/panTro3/panTro3.2bit +chr10_GL391284_random 5276 /gbdb/panTro3/panTro3.2bit +chrUn_GL396920 5276 /gbdb/panTro3/panTro3.2bit +chr16_GL392444_random 5275 /gbdb/panTro3/panTro3.2bit +chr4_GL389898_random 5275 /gbdb/panTro3/panTro3.2bit +chrUn_GL395152 5275 /gbdb/panTro3/panTro3.2bit +chrUn_GL397008 5275 /gbdb/panTro3/panTro3.2bit +chrUn_GL396973 5274 /gbdb/panTro3/panTro3.2bit +chrX_GL393186_random 5274 /gbdb/panTro3/panTro3.2bit +chr9_GL391026_random 5272 /gbdb/panTro3/panTro3.2bit +chr3_GL389513_random 5268 /gbdb/panTro3/panTro3.2bit +chr6_GL390445_random 5268 /gbdb/panTro3/panTro3.2bit +chr16_GL392352_random 5267 /gbdb/panTro3/panTro3.2bit +chrUn_GL396375 5267 /gbdb/panTro3/panTro3.2bit +chr1_GL389218_random 5266 /gbdb/panTro3/panTro3.2bit +chrUn_GL394064 5266 /gbdb/panTro3/panTro3.2bit +chrUn_GL394463 5266 /gbdb/panTro3/panTro3.2bit +chrUn_GL396882 5265 /gbdb/panTro3/panTro3.2bit +chr8_GL390849_random 5261 /gbdb/panTro3/panTro3.2bit +chrUn_GL393617 5261 /gbdb/panTro3/panTro3.2bit +chr1_GL388831_random 5260 /gbdb/panTro3/panTro3.2bit +chrUn_GL394483 5260 /gbdb/panTro3/panTro3.2bit +chrUn_GL396554 5260 /gbdb/panTro3/panTro3.2bit +chr4_GL389991_random 5259 /gbdb/panTro3/panTro3.2bit +chr3_GL389668_random 5258 /gbdb/panTro3/panTro3.2bit +chrUn_GL394075 5258 /gbdb/panTro3/panTro3.2bit +chr16_GL392452_random 5257 /gbdb/panTro3/panTro3.2bit +chr10_GL391573_random 5256 /gbdb/panTro3/panTro3.2bit +chr13_GL392015_random 5256 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189192 5256 /gbdb/panTro3/panTro3.2bit +chrUn_GL394683 5256 /gbdb/panTro3/panTro3.2bit 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5242 /gbdb/panTro3/panTro3.2bit +chrUn_GL394292 5238 /gbdb/panTro3/panTro3.2bit +chrUn_GL394403 5238 /gbdb/panTro3/panTro3.2bit +chrUn_GL395376 5238 /gbdb/panTro3/panTro3.2bit +chrUn_GL393588 5236 /gbdb/panTro3/panTro3.2bit +chrUn_GL393640 5235 /gbdb/panTro3/panTro3.2bit +chrUn_GL396821 5235 /gbdb/panTro3/panTro3.2bit +chrUn_GL396833 5235 /gbdb/panTro3/panTro3.2bit +chr10_GL391408_random 5234 /gbdb/panTro3/panTro3.2bit +chr10_GL391426_random 5231 /gbdb/panTro3/panTro3.2bit +chr10_GL391376_random 5230 /gbdb/panTro3/panTro3.2bit +chr6_GL390176_random 5230 /gbdb/panTro3/panTro3.2bit +chrUn_GL393686 5227 /gbdb/panTro3/panTro3.2bit +chrX_GL393254_random 5227 /gbdb/panTro3/panTro3.2bit +chrUn_GL396908 5225 /gbdb/panTro3/panTro3.2bit +chr2A_GL389337_random 5222 /gbdb/panTro3/panTro3.2bit +chrUn_GL394717 5222 /gbdb/panTro3/panTro3.2bit +chrUn_GL396933 5220 /gbdb/panTro3/panTro3.2bit +chrX_GL393300_random 5220 /gbdb/panTro3/panTro3.2bit +chr14_GL392183_random 5219 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr13_GL392068_random 5200 /gbdb/panTro3/panTro3.2bit +chrUn_GL393587 5200 /gbdb/panTro3/panTro3.2bit +chrX_GL393121_random 5199 /gbdb/panTro3/panTro3.2bit +chrUn_GL396912 5197 /gbdb/panTro3/panTro3.2bit +chr10_GL391276_random 5196 /gbdb/panTro3/panTro3.2bit +chr5_GL390159_random 5194 /gbdb/panTro3/panTro3.2bit +chr10_GL391597_random 5193 /gbdb/panTro3/panTro3.2bit +chr1_GL388842_random 5193 /gbdb/panTro3/panTro3.2bit +chrUn_GL394763 5193 /gbdb/panTro3/panTro3.2bit +chr12_GL391957_random 5192 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150283_random 5191 /gbdb/panTro3/panTro3.2bit +chrUn_GL394356 5191 /gbdb/panTro3/panTro3.2bit +chr11_GL391716_random 5190 /gbdb/panTro3/panTro3.2bit +chr14_GL392108_random 5190 /gbdb/panTro3/panTro3.2bit +chr16_GL392295_random 5190 /gbdb/panTro3/panTro3.2bit +chr16_GL392558_random 5190 /gbdb/panTro3/panTro3.2bit +chrUn_GL393942 5189 /gbdb/panTro3/panTro3.2bit +chrUn_GL396962 5188 /gbdb/panTro3/panTro3.2bit +chrUn_GL393707 5187 /gbdb/panTro3/panTro3.2bit +chr10_GL391347_random 5186 /gbdb/panTro3/panTro3.2bit +chr9_GL391062_random 5186 /gbdb/panTro3/panTro3.2bit +chrX_GL393109_random 5186 /gbdb/panTro3/panTro3.2bit +chr17_GL392670_random 5185 /gbdb/panTro3/panTro3.2bit +chr4_GL389712_random 5185 /gbdb/panTro3/panTro3.2bit +chrUn_GL396204 5185 /gbdb/panTro3/panTro3.2bit +chrX_GL393131_random 5185 /gbdb/panTro3/panTro3.2bit +chrUn_GL394025 5183 /gbdb/panTro3/panTro3.2bit +chrUn_GL393745 5182 /gbdb/panTro3/panTro3.2bit +chrUn_GL394549 5182 /gbdb/panTro3/panTro3.2bit +chr1_GL389183_random 5181 /gbdb/panTro3/panTro3.2bit +chrUn_GL396963 5181 /gbdb/panTro3/panTro3.2bit +chr10_GL391271_random 5180 /gbdb/panTro3/panTro3.2bit +chr16_GL392303_random 5180 /gbdb/panTro3/panTro3.2bit +chrUn_GL396766 5178 /gbdb/panTro3/panTro3.2bit +chr15_GL392230_random 5177 /gbdb/panTro3/panTro3.2bit +chrUn_GL394086 5177 /gbdb/panTro3/panTro3.2bit +chrUn_GL396975 5176 /gbdb/panTro3/panTro3.2bit +chr8_GL390761_random 5175 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5125 /gbdb/panTro3/panTro3.2bit +chr1_GL389169_random 5125 /gbdb/panTro3/panTro3.2bit +chr5_GL389994_random 5125 /gbdb/panTro3/panTro3.2bit +chr4_GL389892_random 5124 /gbdb/panTro3/panTro3.2bit +chrUn_GL394648 5124 /gbdb/panTro3/panTro3.2bit +chrUn_GL396335 5124 /gbdb/panTro3/panTro3.2bit +chrUn_GL393662 5123 /gbdb/panTro3/panTro3.2bit +chrUn_GL393748 5123 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173297_random 5122 /gbdb/panTro3/panTro3.2bit +chr4_GL389695_random 5122 /gbdb/panTro3/panTro3.2bit +chrUn_GL394197 5120 /gbdb/panTro3/panTro3.2bit +chr1_GL388847_random 5119 /gbdb/panTro3/panTro3.2bit +chr5_GL390076_random 5119 /gbdb/panTro3/panTro3.2bit +chr17_GL392595_random 5118 /gbdb/panTro3/panTro3.2bit +chr22_GL393060_random 5118 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187072 5118 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150444_random 5117 /gbdb/panTro3/panTro3.2bit +chrUn_GL393723 5117 /gbdb/panTro3/panTro3.2bit +chrUn_GL395206 5117 /gbdb/panTro3/panTro3.2bit +chr12_GL391958_random 5114 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187534 5113 /gbdb/panTro3/panTro3.2bit +chrUn_GL393835 5113 /gbdb/panTro3/panTro3.2bit +chrUn_GL396622 5113 /gbdb/panTro3/panTro3.2bit +chr4_GL389903_random 5112 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162671_random 5112 /gbdb/panTro3/panTro3.2bit +chrUn_GL395024 5111 /gbdb/panTro3/panTro3.2bit +chrUn_GL395822 5111 /gbdb/panTro3/panTro3.2bit +chr10_GL391449_random 5109 /gbdb/panTro3/panTro3.2bit +chr1_GL388820_random 5109 /gbdb/panTro3/panTro3.2bit +chr12_GL391979_random 5107 /gbdb/panTro3/panTro3.2bit +chrUn_GL393760 5106 /gbdb/panTro3/panTro3.2bit +chrUn_GL396652 5106 /gbdb/panTro3/panTro3.2bit +chrUn_GL397037 5106 /gbdb/panTro3/panTro3.2bit +chr10_GL391282_random 5105 /gbdb/panTro3/panTro3.2bit +chr12_GL391966_random 5105 /gbdb/panTro3/panTro3.2bit +chrUn_GL393944 5104 /gbdb/panTro3/panTro3.2bit +chr4_GL389814_random 5103 /gbdb/panTro3/panTro3.2bit +chr6_GL390380_random 5102 /gbdb/panTro3/panTro3.2bit +chrUn_GL396620 5101 /gbdb/panTro3/panTro3.2bit +chr4_GL389736_random 5100 /gbdb/panTro3/panTro3.2bit +chr1_GL388843_random 5098 /gbdb/panTro3/panTro3.2bit +chrUn_GL396477 5098 /gbdb/panTro3/panTro3.2bit +chrUn_GL396727 5098 /gbdb/panTro3/panTro3.2bit +chr11_GL391704_random 5097 /gbdb/panTro3/panTro3.2bit +chr12_GL391872_random 5097 /gbdb/panTro3/panTro3.2bit +chrUn_GL395467 5097 /gbdb/panTro3/panTro3.2bit +chr10_GL391544_random 5095 /gbdb/panTro3/panTro3.2bit +chr10_GL391552_random 5095 /gbdb/panTro3/panTro3.2bit +chrUn_GL393681 5095 /gbdb/panTro3/panTro3.2bit +chrUn_GL394301 5095 /gbdb/panTro3/panTro3.2bit +chr22_GL393059_random 5094 /gbdb/panTro3/panTro3.2bit +chr5_GL390020_random 5094 /gbdb/panTro3/panTro3.2bit +chrUn_GL393567 5094 /gbdb/panTro3/panTro3.2bit +chrUn_GL393978 5092 /gbdb/panTro3/panTro3.2bit +chr12_GL391950_random 5091 /gbdb/panTro3/panTro3.2bit +chrUn_GL395413 5091 /gbdb/panTro3/panTro3.2bit +chr1_GL388815_random 5090 /gbdb/panTro3/panTro3.2bit +chrUn_GL394468 5090 /gbdb/panTro3/panTro3.2bit +chr11_GL391765_random 5089 /gbdb/panTro3/panTro3.2bit +chr16_GL392451_random 5089 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153930_random 5089 /gbdb/panTro3/panTro3.2bit +chr10_GL391543_random 5088 /gbdb/panTro3/panTro3.2bit +chr1_GL389194_random 5088 /gbdb/panTro3/panTro3.2bit +chr2B_GL389474_random 5088 /gbdb/panTro3/panTro3.2bit +chr4_GL389986_random 5087 /gbdb/panTro3/panTro3.2bit +chrUn_GL393614 5087 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152939_random 5086 /gbdb/panTro3/panTro3.2bit +chr6_GL390433_random 5084 /gbdb/panTro3/panTro3.2bit +chrUn_GL396799 5083 /gbdb/panTro3/panTro3.2bit +chr11_GL391783_random 5082 /gbdb/panTro3/panTro3.2bit +chrUn_GL396638 5082 /gbdb/panTro3/panTro3.2bit +chr1_GL389071_random 5081 /gbdb/panTro3/panTro3.2bit +chr7_GL390602_random 5081 /gbdb/panTro3/panTro3.2bit +chrUn_GL394297 5081 /gbdb/panTro3/panTro3.2bit +chrUn_GL394761 5081 /gbdb/panTro3/panTro3.2bit +chr17_GL392708_random 5080 /gbdb/panTro3/panTro3.2bit +chrUn_GL396733 5080 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171153_random 5078 /gbdb/panTro3/panTro3.2bit +chr20_GL392980_random 5078 /gbdb/panTro3/panTro3.2bit +chrUn_GL394394 5078 /gbdb/panTro3/panTro3.2bit +chrUn_GL394204 5077 /gbdb/panTro3/panTro3.2bit +chr11_GL391810_random 5076 /gbdb/panTro3/panTro3.2bit +chrUn_GL393657 5075 /gbdb/panTro3/panTro3.2bit +chr14_GL392096_random 5074 /gbdb/panTro3/panTro3.2bit +chr18_GL392747_random 5074 /gbdb/panTro3/panTro3.2bit +chr5_GL390008_random 5073 /gbdb/panTro3/panTro3.2bit +chrUn_GL393634 5072 /gbdb/panTro3/panTro3.2bit +chrUn_GL395699 5072 /gbdb/panTro3/panTro3.2bit +chrX_GL393243_random 5071 /gbdb/panTro3/panTro3.2bit +chrX_GL393433_random 5071 /gbdb/panTro3/panTro3.2bit +chr19_GL392941_random 5070 /gbdb/panTro3/panTro3.2bit +chr9_GL390947_random 5070 /gbdb/panTro3/panTro3.2bit +chrUn_GL397038 5070 /gbdb/panTro3/panTro3.2bit +chr19_GL392960_random 5069 /gbdb/panTro3/panTro3.2bit +chr9_GL391133_random 5069 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr14_GL392100_random 5034 /gbdb/panTro3/panTro3.2bit +chrUn_GL394366 5034 /gbdb/panTro3/panTro3.2bit +chrUn_GL394542 5034 /gbdb/panTro3/panTro3.2bit +chrUn_GL395490 5034 /gbdb/panTro3/panTro3.2bit +chr10_GL391539_random 5032 /gbdb/panTro3/panTro3.2bit +chrUn_GL393821 5032 /gbdb/panTro3/panTro3.2bit +chrUn_GL396696 5032 /gbdb/panTro3/panTro3.2bit +chrX_GL393222_random 5030 /gbdb/panTro3/panTro3.2bit +chr13_GL392010_random 5029 /gbdb/panTro3/panTro3.2bit +chr6_GL390180_random 5029 /gbdb/panTro3/panTro3.2bit +chrUn_GL394985 5028 /gbdb/panTro3/panTro3.2bit +chr1_GL388878_random 5027 /gbdb/panTro3/panTro3.2bit +chr10_GL391537_random 5024 /gbdb/panTro3/panTro3.2bit +chrUn_GL396506 5024 /gbdb/panTro3/panTro3.2bit +chr3_GL389575_random 5022 /gbdb/panTro3/panTro3.2bit +chr16_GL392302_random 5020 /gbdb/panTro3/panTro3.2bit +chr19_GL392929_random 5020 /gbdb/panTro3/panTro3.2bit +chr8_GL390846_random 5020 /gbdb/panTro3/panTro3.2bit +chr17_GL392625_random 5019 /gbdb/panTro3/panTro3.2bit +chr2A_GL389270_random 5019 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162705_random 5019 /gbdb/panTro3/panTro3.2bit +chrUn_GL394369 5019 /gbdb/panTro3/panTro3.2bit +chrUn_GL396835 5019 /gbdb/panTro3/panTro3.2bit +chrUn_GL396956 5019 /gbdb/panTro3/panTro3.2bit +chrX_GL393124_random 5019 /gbdb/panTro3/panTro3.2bit +chr18_GL392785_random 5017 /gbdb/panTro3/panTro3.2bit +chrUn_GL393679 5017 /gbdb/panTro3/panTro3.2bit +chrUn_GL394042 5017 /gbdb/panTro3/panTro3.2bit +chrX_GL393281_random 5017 /gbdb/panTro3/panTro3.2bit +chrUn_GL396693 5016 /gbdb/panTro3/panTro3.2bit +chrUn_GL396877 5016 /gbdb/panTro3/panTro3.2bit +chrUn_GL396979 5016 /gbdb/panTro3/panTro3.2bit +chr10_GL391550_random 5014 /gbdb/panTro3/panTro3.2bit +chrUn_GL395064 5014 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170484_random 5013 /gbdb/panTro3/panTro3.2bit +chrUn_GL393797 5013 /gbdb/panTro3/panTro3.2bit +chrUn_GL394201 5013 /gbdb/panTro3/panTro3.2bit +chrUn_GL395168 5013 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL393875 4990 /gbdb/panTro3/panTro3.2bit +chr3_GL389529_random 4989 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157352_random 4989 /gbdb/panTro3/panTro3.2bit +chr6_GL390192_random 4988 /gbdb/panTro3/panTro3.2bit +chr6_GL390329_random 4987 /gbdb/panTro3/panTro3.2bit +chrX_GL393380_random 4987 /gbdb/panTro3/panTro3.2bit +chr10_GL391558_random 4986 /gbdb/panTro3/panTro3.2bit +chr15_GL392242_random 4986 /gbdb/panTro3/panTro3.2bit +chr1_GL389198_random 4986 /gbdb/panTro3/panTro3.2bit +chr10_GL391599_random 4985 /gbdb/panTro3/panTro3.2bit +chr16_GL392497_random 4984 /gbdb/panTro3/panTro3.2bit +chr8_GL390758_random 4982 /gbdb/panTro3/panTro3.2bit +chrUn_GL394212 4982 /gbdb/panTro3/panTro3.2bit +chrUn_GL394229 4982 /gbdb/panTro3/panTro3.2bit +chrUn_GL394302 4981 /gbdb/panTro3/panTro3.2bit +chr8_GL390783_random 4980 /gbdb/panTro3/panTro3.2bit +chr6_GL390173_random 4978 /gbdb/panTro3/panTro3.2bit +chrUn_GL393704 4978 /gbdb/panTro3/panTro3.2bit +chrUn_GL393892 4978 /gbdb/panTro3/panTro3.2bit +chr14_GL392166_random 4977 /gbdb/panTro3/panTro3.2bit +chr17_GL392683_random 4976 /gbdb/panTro3/panTro3.2bit +chr1_GL388956_random 4976 /gbdb/panTro3/panTro3.2bit +chr8_GL390764_random 4975 /gbdb/panTro3/panTro3.2bit +chr8_GL390870_random 4974 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152095_random 4973 /gbdb/panTro3/panTro3.2bit +chrX_GL393141_random 4973 /gbdb/panTro3/panTro3.2bit +chr17_GL392589_random 4972 /gbdb/panTro3/panTro3.2bit +chr2B_GL389473_random 4972 /gbdb/panTro3/panTro3.2bit +chr5_GL389995_random 4972 /gbdb/panTro3/panTro3.2bit +chrUn_GL394221 4972 /gbdb/panTro3/panTro3.2bit +chr10_GL391351_random 4971 /gbdb/panTro3/panTro3.2bit +chr2A_GL389349_random 4971 /gbdb/panTro3/panTro3.2bit +chrUn_GL395735 4971 /gbdb/panTro3/panTro3.2bit +chr2B_GL389475_random 4970 /gbdb/panTro3/panTro3.2bit +chrX_GL393219_random 4970 /gbdb/panTro3/panTro3.2bit +chr18_GL392736_random 4968 /gbdb/panTro3/panTro3.2bit +chrUn_GL394333 4968 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL393920 4939 /gbdb/panTro3/panTro3.2bit +chrUn_GL396894 4938 /gbdb/panTro3/panTro3.2bit +chrUn_GL394626 4937 /gbdb/panTro3/panTro3.2bit +chr11_GL391722_random 4936 /gbdb/panTro3/panTro3.2bit +chrUn_GL393870 4935 /gbdb/panTro3/panTro3.2bit +chrUn_GL394171 4935 /gbdb/panTro3/panTro3.2bit +chrUn_GL394440 4935 /gbdb/panTro3/panTro3.2bit +chr9_GL390982_random 4934 /gbdb/panTro3/panTro3.2bit +chr18_GL392790_random 4933 /gbdb/panTro3/panTro3.2bit +chr5_GL390030_random 4933 /gbdb/panTro3/panTro3.2bit +chrUn_GL396198 4933 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157264_random 4932 /gbdb/panTro3/panTro3.2bit +chrUn_GL396284 4932 /gbdb/panTro3/panTro3.2bit +chr12_GL391890_random 4931 /gbdb/panTro3/panTro3.2bit +chr1_GL388827_random 4931 /gbdb/panTro3/panTro3.2bit +chrUn_GL393957 4931 /gbdb/panTro3/panTro3.2bit +chr10_GL391345_random 4930 /gbdb/panTro3/panTro3.2bit +chrUn_GL393848 4930 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174475_random 4928 /gbdb/panTro3/panTro3.2bit +chr19_GL392932_random 4928 /gbdb/panTro3/panTro3.2bit +chrUn_GL394101 4928 /gbdb/panTro3/panTro3.2bit +chrUn_GL394361 4928 /gbdb/panTro3/panTro3.2bit +chr2B_GL389401_random 4927 /gbdb/panTro3/panTro3.2bit +chr4_GL389924_random 4927 /gbdb/panTro3/panTro3.2bit +chrUn_GL397019 4926 /gbdb/panTro3/panTro3.2bit +chrUn_GL397047 4926 /gbdb/panTro3/panTro3.2bit +chr12_GL391886_random 4925 /gbdb/panTro3/panTro3.2bit +chrUn_GL393631 4925 /gbdb/panTro3/panTro3.2bit +chrUn_GL394698 4925 /gbdb/panTro3/panTro3.2bit +chr3_GL389512_random 4924 /gbdb/panTro3/panTro3.2bit +chr6_GL390216_random 4924 /gbdb/panTro3/panTro3.2bit +chrUn_GL393559 4924 /gbdb/panTro3/panTro3.2bit +chrUn_GL396813 4924 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165723_random 4923 /gbdb/panTro3/panTro3.2bit +chr4_GL389984_random 4923 /gbdb/panTro3/panTro3.2bit +chrUn_GL395861 4923 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165564_random 4922 /gbdb/panTro3/panTro3.2bit +chr12_GL391902_random 4922 /gbdb/panTro3/panTro3.2bit +chrUn_GL393660 4922 /gbdb/panTro3/panTro3.2bit +chr10_GL391448_random 4921 /gbdb/panTro3/panTro3.2bit +chr13_GL392013_random 4921 /gbdb/panTro3/panTro3.2bit +chrUn_GL394313 4921 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175959_random 4920 /gbdb/panTro3/panTro3.2bit +chr6_GL390350_random 4920 /gbdb/panTro3/panTro3.2bit +chr11_GL391730_random 4919 /gbdb/panTro3/panTro3.2bit +chr17_GL392629_random 4918 /gbdb/panTro3/panTro3.2bit +chrUn_GL393847 4918 /gbdb/panTro3/panTro3.2bit +chrUn_GL393949 4918 /gbdb/panTro3/panTro3.2bit +chr18_GL392805_random 4916 /gbdb/panTro3/panTro3.2bit +chr1_GL389134_random 4916 /gbdb/panTro3/panTro3.2bit +chrX_GL393258_random 4916 /gbdb/panTro3/panTro3.2bit +chr18_GL392739_random 4915 /gbdb/panTro3/panTro3.2bit +chrUn_GL393973 4915 /gbdb/panTro3/panTro3.2bit +chrUn_GL394168 4915 /gbdb/panTro3/panTro3.2bit +chrUn_GL394303 4914 /gbdb/panTro3/panTro3.2bit +chr16_GL392565_random 4912 /gbdb/panTro3/panTro3.2bit +chrUn_GL397031 4911 /gbdb/panTro3/panTro3.2bit +chrUn_GL394400 4910 /gbdb/panTro3/panTro3.2bit +chr12_GL391893_random 4908 /gbdb/panTro3/panTro3.2bit +chr6_GL390168_random 4908 /gbdb/panTro3/panTro3.2bit +chr8_GL390773_random 4908 /gbdb/panTro3/panTro3.2bit +chrUn_GL395117 4908 /gbdb/panTro3/panTro3.2bit +chrUn_GL396483 4908 /gbdb/panTro3/panTro3.2bit +chrUn_GL397026 4908 /gbdb/panTro3/panTro3.2bit +chrUn_GL393628 4907 /gbdb/panTro3/panTro3.2bit +chrUn_GL393976 4907 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153910_random 4906 /gbdb/panTro3/panTro3.2bit +chrUn_GL393624 4906 /gbdb/panTro3/panTro3.2bit +chrUn_GL393758 4906 /gbdb/panTro3/panTro3.2bit +chr7_GL390682_random 4905 /gbdb/panTro3/panTro3.2bit +chr8_GL390779_random 4905 /gbdb/panTro3/panTro3.2bit +chr18_GL392819_random 4904 /gbdb/panTro3/panTro3.2bit +chr4_GL389738_random 4904 /gbdb/panTro3/panTro3.2bit +chrUn_GL393996 4904 /gbdb/panTro3/panTro3.2bit +chrUn_GL394441 4904 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168274_random 4903 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150325_random 4903 /gbdb/panTro3/panTro3.2bit +chr2A_GL389297_random 4902 /gbdb/panTro3/panTro3.2bit +chr22_GL393057_random 4901 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186823 4901 /gbdb/panTro3/panTro3.2bit +chr19_GL392973_random 4900 /gbdb/panTro3/panTro3.2bit +chr15_GL392195_random 4899 /gbdb/panTro3/panTro3.2bit +chr2B_GL389404_random 4898 /gbdb/panTro3/panTro3.2bit +chrUn_GL396511 4896 /gbdb/panTro3/panTro3.2bit +chr14_GL392170_random 4895 /gbdb/panTro3/panTro3.2bit +chrUn_GL396724 4895 /gbdb/panTro3/panTro3.2bit +chr2A_GL389255_random 4894 /gbdb/panTro3/panTro3.2bit +chrUn_GL396728 4894 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170475_random 4893 /gbdb/panTro3/panTro3.2bit +chr13_GL392008_random 4892 /gbdb/panTro3/panTro3.2bit +chr5_GL390016_random 4892 /gbdb/panTro3/panTro3.2bit +chr6_GL390207_random 4891 /gbdb/panTro3/panTro3.2bit +chrUn_GL394069 4890 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176530_random 4889 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL397062 4819 /gbdb/panTro3/panTro3.2bit +chrX_GL393210_random 4819 /gbdb/panTro3/panTro3.2bit +chr10_GL391356_random 4818 /gbdb/panTro3/panTro3.2bit +chr11_GL391697_random 4818 /gbdb/panTro3/panTro3.2bit +chr11_GL391815_random 4817 /gbdb/panTro3/panTro3.2bit +chrUn_GL394073 4817 /gbdb/panTro3/panTro3.2bit +chr13_GL392065_random 4816 /gbdb/panTro3/panTro3.2bit +chrUn_GL394825 4816 /gbdb/panTro3/panTro3.2bit +chr19_GL392870_random 4815 /gbdb/panTro3/panTro3.2bit +chr8_GL390866_random 4815 /gbdb/panTro3/panTro3.2bit +chr22_GL393049_random 4814 /gbdb/panTro3/panTro3.2bit +chr4_GL389706_random 4814 /gbdb/panTro3/panTro3.2bit +chr20_GL393039_random 4812 /gbdb/panTro3/panTro3.2bit +chr10_GL391562_random 4809 /gbdb/panTro3/panTro3.2bit +chrUn_GL393755 4809 /gbdb/panTro3/panTro3.2bit +chrUn_GL396464 4809 /gbdb/panTro3/panTro3.2bit +chr19_GL392873_random 4808 /gbdb/panTro3/panTro3.2bit +chrUn_GL393869 4808 /gbdb/panTro3/panTro3.2bit +chrUn_GL394392 4808 /gbdb/panTro3/panTro3.2bit +chrUn_GL396609 4807 /gbdb/panTro3/panTro3.2bit +chr15_GL392293_random 4805 /gbdb/panTro3/panTro3.2bit +chr4_GL389931_random 4802 /gbdb/panTro3/panTro3.2bit +chrUn_GL393792 4802 /gbdb/panTro3/panTro3.2bit +chrUn_GL394659 4802 /gbdb/panTro3/panTro3.2bit +chrUn_GL396911 4802 /gbdb/panTro3/panTro3.2bit +chr7_GL390499_random 4801 /gbdb/panTro3/panTro3.2bit +chr11_GL391808_random 4798 /gbdb/panTro3/panTro3.2bit +chrUn_GL393779 4798 /gbdb/panTro3/panTro3.2bit +chr4_GL389964_random 4796 /gbdb/panTro3/panTro3.2bit +chr1_GL388841_random 4795 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157234_random 4795 /gbdb/panTro3/panTro3.2bit +chrUn_GL394021 4795 /gbdb/panTro3/panTro3.2bit +chrUn_GL394211 4795 /gbdb/panTro3/panTro3.2bit +chrUn_GL396700 4795 /gbdb/panTro3/panTro3.2bit +chrUn_GL396864 4795 /gbdb/panTro3/panTro3.2bit +chrUn_GL396948 4795 /gbdb/panTro3/panTro3.2bit +chr6_GL390235_random 4794 /gbdb/panTro3/panTro3.2bit +chr4_GL389762_random 4792 /gbdb/panTro3/panTro3.2bit 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4749 /gbdb/panTro3/panTro3.2bit +chrUn_GL393983 4749 /gbdb/panTro3/panTro3.2bit +chr11_GL391728_random 4748 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169258_random 4748 /gbdb/panTro3/panTro3.2bit +chr17_GL392710_random 4747 /gbdb/panTro3/panTro3.2bit +chr8_GL390795_random 4747 /gbdb/panTro3/panTro3.2bit +chr2B_GL389410_random 4746 /gbdb/panTro3/panTro3.2bit +chrUn_GL394729 4746 /gbdb/panTro3/panTro3.2bit +chrX_GL393280_random 4745 /gbdb/panTro3/panTro3.2bit +chr10_GL391294_random 4744 /gbdb/panTro3/panTro3.2bit +chr10_GL391602_random 4742 /gbdb/panTro3/panTro3.2bit +chr6_GL390213_random 4742 /gbdb/panTro3/panTro3.2bit +chrUn_GL394398 4742 /gbdb/panTro3/panTro3.2bit +chrX_GL393137_random 4742 /gbdb/panTro3/panTro3.2bit +chr10_GL391609_random 4740 /gbdb/panTro3/panTro3.2bit +chrUn_GL393713 4739 /gbdb/panTro3/panTro3.2bit +chr18_GL392744_random 4738 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162796_random 4738 /gbdb/panTro3/panTro3.2bit +chr9_GL390956_random 4738 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_GL391561_random 4689 /gbdb/panTro3/panTro3.2bit +chr9_GL390922_random 4689 /gbdb/panTro3/panTro3.2bit +chrUn_GL396603 4689 /gbdb/panTro3/panTro3.2bit +chrX_GL393317_random 4688 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157244_random 4687 /gbdb/panTro3/panTro3.2bit +chrUn_GL393938 4687 /gbdb/panTro3/panTro3.2bit +chr12_GL391962_random 4686 /gbdb/panTro3/panTro3.2bit +chr22_GL393087_random 4686 /gbdb/panTro3/panTro3.2bit +chrX_GL393127_random 4686 /gbdb/panTro3/panTro3.2bit +chr10_GL391671_random 4685 /gbdb/panTro3/panTro3.2bit +chrX_GL393262_random 4685 /gbdb/panTro3/panTro3.2bit +chr4_GL389682_random 4684 /gbdb/panTro3/panTro3.2bit +chrUn_GL393982 4684 /gbdb/panTro3/panTro3.2bit +chr11_GL391869_random 4683 /gbdb/panTro3/panTro3.2bit +chrUn_GL394124 4683 /gbdb/panTro3/panTro3.2bit +chrUn_GL394422 4683 /gbdb/panTro3/panTro3.2bit +chrUn_GL394620 4683 /gbdb/panTro3/panTro3.2bit +chr16_GL392578_random 4681 /gbdb/panTro3/panTro3.2bit +chr17_GL392702_random 4681 /gbdb/panTro3/panTro3.2bit +chrUn_GL396624 4681 /gbdb/panTro3/panTro3.2bit +chr10_GL391283_random 4680 /gbdb/panTro3/panTro3.2bit +chr10_GL391591_random 4679 /gbdb/panTro3/panTro3.2bit +chr5_GL390004_random 4679 /gbdb/panTro3/panTro3.2bit +chrUn_GL393907 4679 /gbdb/panTro3/panTro3.2bit +chrUn_GL394587 4676 /gbdb/panTro3/panTro3.2bit +chrUn_GL397004 4676 /gbdb/panTro3/panTro3.2bit +chrUn_GL396966 4674 /gbdb/panTro3/panTro3.2bit +chrUn_GL394085 4673 /gbdb/panTro3/panTro3.2bit +chr11_GL391814_random 4672 /gbdb/panTro3/panTro3.2bit +chr1_GL389205_random 4672 /gbdb/panTro3/panTro3.2bit +chr9_GL390952_random 4672 /gbdb/panTro3/panTro3.2bit +chrUn_GL393789 4672 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153853_random 4671 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164479_random 4671 /gbdb/panTro3/panTro3.2bit +chrUn_GL394279 4671 /gbdb/panTro3/panTro3.2bit +chrUn_GL396977 4671 /gbdb/panTro3/panTro3.2bit +chrX_GL393314_random 4671 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152056_random 4670 /gbdb/panTro3/panTro3.2bit +chrUn_GL393570 4669 /gbdb/panTro3/panTro3.2bit +chr7_GL390485_random 4668 /gbdb/panTro3/panTro3.2bit +chr11_GL391691_random 4667 /gbdb/panTro3/panTro3.2bit +chr7_GL390458_random 4667 /gbdb/panTro3/panTro3.2bit +chrUn_GL394360 4667 /gbdb/panTro3/panTro3.2bit +chr1_GL388875_random 4666 /gbdb/panTro3/panTro3.2bit +chrUn_GL396919 4666 /gbdb/panTro3/panTro3.2bit +chr11_GL391721_random 4665 /gbdb/panTro3/panTro3.2bit +chrUn_GL393878 4665 /gbdb/panTro3/panTro3.2bit +chr10_GL391619_random 4664 /gbdb/panTro3/panTro3.2bit +chrUn_GL393852 4664 /gbdb/panTro3/panTro3.2bit +chr2A_GL389365_random 4663 /gbdb/panTro3/panTro3.2bit +chrUn_GL395266 4663 /gbdb/panTro3/panTro3.2bit +chrUn_GL397014 4663 /gbdb/panTro3/panTro3.2bit +chrUn_GL394170 4661 /gbdb/panTro3/panTro3.2bit +chrUn_GL394184 4661 /gbdb/panTro3/panTro3.2bit +chrUn_GL396472 4661 /gbdb/panTro3/panTro3.2bit +chr1_GL389149_random 4660 /gbdb/panTro3/panTro3.2bit +chr6_GL390204_random 4660 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394325 4637 /gbdb/panTro3/panTro3.2bit +chr9_GL390933_random 4636 /gbdb/panTro3/panTro3.2bit +chrUn_GL394934 4636 /gbdb/panTro3/panTro3.2bit +chrX_GL393418_random 4636 /gbdb/panTro3/panTro3.2bit +chr10_GL391269_random 4635 /gbdb/panTro3/panTro3.2bit +chr17_GL392588_random 4635 /gbdb/panTro3/panTro3.2bit +chr5_GL390024_random 4635 /gbdb/panTro3/panTro3.2bit +chr6_GL390437_random 4635 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169301_random 4634 /gbdb/panTro3/panTro3.2bit +chrUn_GL393906 4634 /gbdb/panTro3/panTro3.2bit +chrUn_GL394787 4634 /gbdb/panTro3/panTro3.2bit +chrUn_GL394789 4633 /gbdb/panTro3/panTro3.2bit +chr14_GL392129_random 4632 /gbdb/panTro3/panTro3.2bit +chr19_GL392864_random 4632 /gbdb/panTro3/panTro3.2bit +chr3_GL389649_random 4632 /gbdb/panTro3/panTro3.2bit +chr5_GL390085_random 4632 /gbdb/panTro3/panTro3.2bit +chrUn_GL394627 4632 /gbdb/panTro3/panTro3.2bit +chr17_GL392735_random 4631 /gbdb/panTro3/panTro3.2bit +chr19_GL392945_random 4631 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394114 4490 /gbdb/panTro3/panTro3.2bit +chrUn_GL396964 4490 /gbdb/panTro3/panTro3.2bit +chr11_GL391823_random 4489 /gbdb/panTro3/panTro3.2bit +chrUn_GL395271 4489 /gbdb/panTro3/panTro3.2bit +chr10_GL391358_random 4488 /gbdb/panTro3/panTro3.2bit +chrUn_GL395518 4488 /gbdb/panTro3/panTro3.2bit +chrX_GL393363_random 4488 /gbdb/panTro3/panTro3.2bit +chr5_GL390162_random 4487 /gbdb/panTro3/panTro3.2bit +chr20_GL392991_random 4486 /gbdb/panTro3/panTro3.2bit +chrUn_GL393823 4486 /gbdb/panTro3/panTro3.2bit +chrUn_GL394811 4486 /gbdb/panTro3/panTro3.2bit +chr5_GL390120_random 4485 /gbdb/panTro3/panTro3.2bit +chr11_GL391739_random 4484 /gbdb/panTro3/panTro3.2bit +chrUn_GL393841 4484 /gbdb/panTro3/panTro3.2bit +chrUn_GL395778 4484 /gbdb/panTro3/panTro3.2bit +chr10_GL391352_random 4483 /gbdb/panTro3/panTro3.2bit +chrUn_GL394100 4483 /gbdb/panTro3/panTro3.2bit +chrUn_GL395248 4483 /gbdb/panTro3/panTro3.2bit +chr6_GL390241_random 4481 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr16_GL392566_random 4464 /gbdb/panTro3/panTro3.2bit +chr12_GL391896_random 4462 /gbdb/panTro3/panTro3.2bit +chr12_GL391897_random 4462 /gbdb/panTro3/panTro3.2bit +chrUn_GL394753 4462 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165618_random 4461 /gbdb/panTro3/panTro3.2bit +chr18_GL392778_random 4461 /gbdb/panTro3/panTro3.2bit +chrUn_GL394887 4461 /gbdb/panTro3/panTro3.2bit +chr2B_GL389490_random 4460 /gbdb/panTro3/panTro3.2bit +chr9_GL391197_random 4460 /gbdb/panTro3/panTro3.2bit +chr10_GL391325_random 4459 /gbdb/panTro3/panTro3.2bit +chr11_GL391741_random 4459 /gbdb/panTro3/panTro3.2bit +chr20_GL393035_random 4459 /gbdb/panTro3/panTro3.2bit +chr10_GL391357_random 4457 /gbdb/panTro3/panTro3.2bit +chr10_GL391665_random 4457 /gbdb/panTro3/panTro3.2bit +chr1_GL388855_random 4457 /gbdb/panTro3/panTro3.2bit +chr3_GL389535_random 4457 /gbdb/panTro3/panTro3.2bit +chr6_GL390314_random 4457 /gbdb/panTro3/panTro3.2bit +chrUn_GL393822 4457 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395582 4427 /gbdb/panTro3/panTro3.2bit +chr4_GL389773_random 4426 /gbdb/panTro3/panTro3.2bit +chrUn_GL395243 4426 /gbdb/panTro3/panTro3.2bit +chrX_GL393351_random 4426 /gbdb/panTro3/panTro3.2bit +chr2A_GL389273_random 4425 /gbdb/panTro3/panTro3.2bit +chrUn_GL393699 4425 /gbdb/panTro3/panTro3.2bit +chrX_GL393205_random 4425 /gbdb/panTro3/panTro3.2bit +chr12_GL392000_random 4424 /gbdb/panTro3/panTro3.2bit +chr17_GL392719_random 4424 /gbdb/panTro3/panTro3.2bit +chrUn_GL393568 4424 /gbdb/panTro3/panTro3.2bit +chr16_GL392317_random 4423 /gbdb/panTro3/panTro3.2bit +chr1_GL388862_random 4423 /gbdb/panTro3/panTro3.2bit +chr17_GL392690_random 4422 /gbdb/panTro3/panTro3.2bit +chr10_GL391268_random 4421 /gbdb/panTro3/panTro3.2bit +chr10_GL391397_random 4420 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152082_random 4420 /gbdb/panTro3/panTro3.2bit +chr3_GL389536_random 4420 /gbdb/panTro3/panTro3.2bit +chrUn_GL397017 4420 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394286 4413 /gbdb/panTro3/panTro3.2bit +chrUn_GL394584 4413 /gbdb/panTro3/panTro3.2bit +chr12_GL391909_random 4412 /gbdb/panTro3/panTro3.2bit +chr13_GL392069_random 4411 /gbdb/panTro3/panTro3.2bit +chrUn_GL394688 4411 /gbdb/panTro3/panTro3.2bit +chrUn_GL395195 4411 /gbdb/panTro3/panTro3.2bit +chr10_GL391281_random 4410 /gbdb/panTro3/panTro3.2bit +chr12_GL391887_random 4410 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158969_random 4410 /gbdb/panTro3/panTro3.2bit +chr8_GL390794_random 4410 /gbdb/panTro3/panTro3.2bit +chr10_GL391304_random 4409 /gbdb/panTro3/panTro3.2bit +chr14_GL392110_random 4409 /gbdb/panTro3/panTro3.2bit +chr1_GL388867_random 4409 /gbdb/panTro3/panTro3.2bit +chrUn_GL393693 4409 /gbdb/panTro3/panTro3.2bit +chrUn_GL394180 4409 /gbdb/panTro3/panTro3.2bit +chrUn_GL394946 4409 /gbdb/panTro3/panTro3.2bit +chr11_GL391714_random 4407 /gbdb/panTro3/panTro3.2bit +chrUn_GL393887 4407 /gbdb/panTro3/panTro3.2bit +chrUn_GL394795 4406 /gbdb/panTro3/panTro3.2bit +chr6_GL390194_random 4405 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189231 4404 /gbdb/panTro3/panTro3.2bit +chrUn_GL393828 4404 /gbdb/panTro3/panTro3.2bit +chr13_GL392036_random 4403 /gbdb/panTro3/panTro3.2bit +chrUn_GL394514 4403 /gbdb/panTro3/panTro3.2bit +chrUn_GL394066 4401 /gbdb/panTro3/panTro3.2bit +chrUn_GL395453 4401 /gbdb/panTro3/panTro3.2bit +chrUn_GL396858 4401 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152100_random 4400 /gbdb/panTro3/panTro3.2bit +chrUn_GL394236 4400 /gbdb/panTro3/panTro3.2bit +chrUn_GL396825 4400 /gbdb/panTro3/panTro3.2bit +chr10_GL391318_random 4399 /gbdb/panTro3/panTro3.2bit +chr19_GL392836_random 4399 /gbdb/panTro3/panTro3.2bit +chrUn_GL393994 4399 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152083_random 4398 /gbdb/panTro3/panTro3.2bit +chrUn_GL394265 4398 /gbdb/panTro3/panTro3.2bit +chrUn_GL394762 4398 /gbdb/panTro3/panTro3.2bit +chr12_GL391923_random 4397 /gbdb/panTro3/panTro3.2bit +chr5_GL390164_random 4397 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/gbdb/panTro3/panTro3.2bit +chr5_GL390061_random 4390 /gbdb/panTro3/panTro3.2bit +chr7_GL390590_random 4390 /gbdb/panTro3/panTro3.2bit +chr20_GL392976_random 4389 /gbdb/panTro3/panTro3.2bit +chr6_GL390253_random 4389 /gbdb/panTro3/panTro3.2bit +chrUn_GL393661 4388 /gbdb/panTro3/panTro3.2bit +chrUn_GL394442 4388 /gbdb/panTro3/panTro3.2bit +chr10_GL391429_random 4387 /gbdb/panTro3/panTro3.2bit +chrX_GL393248_random 4387 /gbdb/panTro3/panTro3.2bit +chr14_GL392139_random 4386 /gbdb/panTro3/panTro3.2bit +chr18_GL392749_random 4386 /gbdb/panTro3/panTro3.2bit +chr2B_GL389462_random 4386 /gbdb/panTro3/panTro3.2bit +chr6_GL390265_random 4386 /gbdb/panTro3/panTro3.2bit +chrUn_GL394888 4386 /gbdb/panTro3/panTro3.2bit +chrUn_GL394901 4386 /gbdb/panTro3/panTro3.2bit +chr7_GL390456_random 4385 /gbdb/panTro3/panTro3.2bit +chr9_GL390959_random 4385 /gbdb/panTro3/panTro3.2bit +chrUn_GL393844 4385 /gbdb/panTro3/panTro3.2bit +chrUn_GL394256 4384 /gbdb/panTro3/panTro3.2bit +chrX_GL393238_random 4384 /gbdb/panTro3/panTro3.2bit +chr17_GL392732_random 4383 /gbdb/panTro3/panTro3.2bit +chr7_GL390555_random 4383 /gbdb/panTro3/panTro3.2bit +chrUn_GL395199 4383 /gbdb/panTro3/panTro3.2bit +chr1_GL389185_random 4381 /gbdb/panTro3/panTro3.2bit +chr5_GL390105_random 4381 /gbdb/panTro3/panTro3.2bit +chrUn_GL394321 4381 /gbdb/panTro3/panTro3.2bit +chr10_GL391306_random 4380 /gbdb/panTro3/panTro3.2bit +chr4_GL389710_random 4380 /gbdb/panTro3/panTro3.2bit +chr6_GL390227_random 4380 /gbdb/panTro3/panTro3.2bit +chrUn_GL394186 4379 /gbdb/panTro3/panTro3.2bit +chrUn_GL394836 4379 /gbdb/panTro3/panTro3.2bit +chr10_GL391373_random 4378 /gbdb/panTro3/panTro3.2bit +chr17_GL392717_random 4378 /gbdb/panTro3/panTro3.2bit +chr20_GL393046_random 4378 /gbdb/panTro3/panTro3.2bit +chrUn_GL394510 4378 /gbdb/panTro3/panTro3.2bit +chrUn_GL394826 4378 /gbdb/panTro3/panTro3.2bit +chr18_GL392752_random 4377 /gbdb/panTro3/panTro3.2bit +chrUn_GL393922 4377 /gbdb/panTro3/panTro3.2bit +chr1_GL388935_random 4376 /gbdb/panTro3/panTro3.2bit +chr4_GL389901_random 4376 /gbdb/panTro3/panTro3.2bit +chrUn_GL394647 4376 /gbdb/panTro3/panTro3.2bit +chr16_GL392335_random 4375 /gbdb/panTro3/panTro3.2bit +chr10_GL391339_random 4374 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169281_random 4374 /gbdb/panTro3/panTro3.2bit +chrX_GL393208_random 4374 /gbdb/panTro3/panTro3.2bit +chrX_GL393335_random 4374 /gbdb/panTro3/panTro3.2bit +chr10_GL391436_random 4373 /gbdb/panTro3/panTro3.2bit +chrUn_GL394978 4373 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168255_random 4372 /gbdb/panTro3/panTro3.2bit +chrX_GL393133_random 4372 /gbdb/panTro3/panTro3.2bit +chrX_GL393411_random 4372 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188197 4371 /gbdb/panTro3/panTro3.2bit +chrUn_GL395012 4371 /gbdb/panTro3/panTro3.2bit +chrUn_GL395231 4371 /gbdb/panTro3/panTro3.2bit +chrUn_GL397048 4371 /gbdb/panTro3/panTro3.2bit +chr3_GL389524_random 4370 /gbdb/panTro3/panTro3.2bit +chr8_GL390791_random 4370 /gbdb/panTro3/panTro3.2bit +chrUn_GL394451 4370 /gbdb/panTro3/panTro3.2bit +chr10_GL391288_random 4369 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168329_random 4369 /gbdb/panTro3/panTro3.2bit +chrUn_GL393599 4368 /gbdb/panTro3/panTro3.2bit +chrUn_GL393882 4368 /gbdb/panTro3/panTro3.2bit +chrUn_GL394207 4368 /gbdb/panTro3/panTro3.2bit +chrUn_GL394231 4368 /gbdb/panTro3/panTro3.2bit +chrUn_GL394386 4368 /gbdb/panTro3/panTro3.2bit +chrUn_GL395181 4368 /gbdb/panTro3/panTro3.2bit +chr11_GL391743_random 4367 /gbdb/panTro3/panTro3.2bit +chrUn_GL394516 4367 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174520_random 4366 /gbdb/panTro3/panTro3.2bit +chrUn_GL393786 4366 /gbdb/panTro3/panTro3.2bit +chrUn_GL393967 4366 /gbdb/panTro3/panTro3.2bit +chrUn_GL397022 4366 /gbdb/panTro3/panTro3.2bit +chr14_GL392185_random 4365 /gbdb/panTro3/panTro3.2bit +chr3_GL389599_random 4364 /gbdb/panTro3/panTro3.2bit +chrUn_GL394579 4364 /gbdb/panTro3/panTro3.2bit +chrUn_GL396597 4364 /gbdb/panTro3/panTro3.2bit +chr18_GL392770_random 4363 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr15_AACZ03171961_random 4352 /gbdb/panTro3/panTro3.2bit +chrUn_GL395211 4352 /gbdb/panTro3/panTro3.2bit +chr17_GL392667_random 4351 /gbdb/panTro3/panTro3.2bit +chr2B_GL389415_random 4350 /gbdb/panTro3/panTro3.2bit +chr6_GL390200_random 4350 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162733_random 4349 /gbdb/panTro3/panTro3.2bit +chr9_GL391059_random 4349 /gbdb/panTro3/panTro3.2bit +chr15_GL392198_random 4348 /gbdb/panTro3/panTro3.2bit +chrUn_GL393734 4348 /gbdb/panTro3/panTro3.2bit +chrUn_GL394624 4348 /gbdb/panTro3/panTro3.2bit +chrUn_GL394665 4348 /gbdb/panTro3/panTro3.2bit +chrX_GL393396_random 4348 /gbdb/panTro3/panTro3.2bit +chrX_GL393292_random 4347 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156024_random 4346 /gbdb/panTro3/panTro3.2bit +chrUn_GL394539 4346 /gbdb/panTro3/panTro3.2bit +chr10_GL391683_random 4345 /gbdb/panTro3/panTro3.2bit +chr20_GL393026_random 4345 /gbdb/panTro3/panTro3.2bit +chr7_GL390725_random 4344 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr1_GL389148_random 4314 /gbdb/panTro3/panTro3.2bit +chr5_GL390112_random 4314 /gbdb/panTro3/panTro3.2bit +chr11_GL391701_random 4313 /gbdb/panTro3/panTro3.2bit +chrUn_GL394466 4313 /gbdb/panTro3/panTro3.2bit +chr2B_GL389417_random 4312 /gbdb/panTro3/panTro3.2bit +chr2B_GL389492_random 4312 /gbdb/panTro3/panTro3.2bit +chrUn_GL394030 4312 /gbdb/panTro3/panTro3.2bit +chrUn_GL394182 4312 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158960_random 4311 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170507_random 4310 /gbdb/panTro3/panTro3.2bit +chrUn_GL394786 4310 /gbdb/panTro3/panTro3.2bit +chrUn_GL394982 4310 /gbdb/panTro3/panTro3.2bit +chrUn_GL396081 4310 /gbdb/panTro3/panTro3.2bit +chr11_GL391711_random 4309 /gbdb/panTro3/panTro3.2bit +chr1_GL389244_random 4309 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157303_random 4308 /gbdb/panTro3/panTro3.2bit +chrUn_GL394545 4308 /gbdb/panTro3/panTro3.2bit +chrUn_GL394703 4308 /gbdb/panTro3/panTro3.2bit +chrUn_GL393999 4307 /gbdb/panTro3/panTro3.2bit +chr17_GL392726_random 4306 /gbdb/panTro3/panTro3.2bit +chrUn_GL393692 4306 /gbdb/panTro3/panTro3.2bit +chr14_GL392114_random 4305 /gbdb/panTro3/panTro3.2bit +chrUn_GL397040 4304 /gbdb/panTro3/panTro3.2bit +chr10_GL391614_random 4303 /gbdb/panTro3/panTro3.2bit +chr6_GL390313_random 4303 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162577_random 4303 /gbdb/panTro3/panTro3.2bit +chrUn_GL395222 4303 /gbdb/panTro3/panTro3.2bit +chr1_GL388913_random 4301 /gbdb/panTro3/panTro3.2bit +chrUn_GL396032 4301 /gbdb/panTro3/panTro3.2bit +chr12_GL391961_random 4300 /gbdb/panTro3/panTro3.2bit +chr4_GL389749_random 4300 /gbdb/panTro3/panTro3.2bit +chr4_GL389976_random 4300 /gbdb/panTro3/panTro3.2bit +chrUn_GL394705 4300 /gbdb/panTro3/panTro3.2bit +chr20_GL392978_random 4299 /gbdb/panTro3/panTro3.2bit +chrX_GL393164_random 4299 /gbdb/panTro3/panTro3.2bit +chr10_GL391293_random 4298 /gbdb/panTro3/panTro3.2bit +chrUn_GL394395 4298 /gbdb/panTro3/panTro3.2bit +chr22_GL393089_random 4297 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188962 4297 /gbdb/panTro3/panTro3.2bit +chr16_GL392572_random 4296 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174555_random 4296 /gbdb/panTro3/panTro3.2bit +chr19_GL392903_random 4296 /gbdb/panTro3/panTro3.2bit +chr6_GL390212_random 4296 /gbdb/panTro3/panTro3.2bit +chr10_GL391262_random 4295 /gbdb/panTro3/panTro3.2bit +chr4_GL389723_random 4295 /gbdb/panTro3/panTro3.2bit +chrUn_GL394338 4295 /gbdb/panTro3/panTro3.2bit +chrUn_GL394528 4295 /gbdb/panTro3/panTro3.2bit +chrX_GL393116_random 4295 /gbdb/panTro3/panTro3.2bit +chr10_GL391370_random 4294 /gbdb/panTro3/panTro3.2bit +chrUn_GL394491 4294 /gbdb/panTro3/panTro3.2bit +chrUn_GL394814 4294 /gbdb/panTro3/panTro3.2bit +chr2A_GL389326_random 4293 /gbdb/panTro3/panTro3.2bit +chrUn_GL394603 4293 /gbdb/panTro3/panTro3.2bit +chrUn_GL395443 4293 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187658 4292 /gbdb/panTro3/panTro3.2bit +chrUn_GL396969 4292 /gbdb/panTro3/panTro3.2bit +chr9_GL391054_random 4291 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187524 4291 /gbdb/panTro3/panTro3.2bit +chrUn_GL393639 4291 /gbdb/panTro3/panTro3.2bit +chrUn_GL394550 4291 /gbdb/panTro3/panTro3.2bit +chr1_GL388908_random 4290 /gbdb/panTro3/panTro3.2bit +chr2A_GL389283_random 4290 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189238 4290 /gbdb/panTro3/panTro3.2bit +chrUn_GL394695 4290 /gbdb/panTro3/panTro3.2bit +chrUn_GL394895 4290 /gbdb/panTro3/panTro3.2bit +chr19_GL392834_random 4289 /gbdb/panTro3/panTro3.2bit +chr1_GL389122_random 4289 /gbdb/panTro3/panTro3.2bit +chrUn_GL394644 4289 /gbdb/panTro3/panTro3.2bit +chrUn_GL396870 4289 /gbdb/panTro3/panTro3.2bit +chr10_GL391416_random 4288 /gbdb/panTro3/panTro3.2bit +chr2A_GL389360_random 4288 /gbdb/panTro3/panTro3.2bit +chr4_GL389745_random 4288 /gbdb/panTro3/panTro3.2bit +chrUn_GL394930 4288 /gbdb/panTro3/panTro3.2bit +chrX_GL393288_random 4288 /gbdb/panTro3/panTro3.2bit +chr17_GL392689_random 4287 /gbdb/panTro3/panTro3.2bit +chr19_GL392823_random 4287 /gbdb/panTro3/panTro3.2bit +chr19_GL392856_random 4286 /gbdb/panTro3/panTro3.2bit +chr20_GL393010_random 4286 /gbdb/panTro3/panTro3.2bit +chrUn_GL396814 4286 /gbdb/panTro3/panTro3.2bit +chr1_GL388832_random 4285 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157237_random 4285 /gbdb/panTro3/panTro3.2bit +chr6_GL390257_random 4285 /gbdb/panTro3/panTro3.2bit +chr2B_GL389423_random 4284 /gbdb/panTro3/panTro3.2bit +chrUn_GL393850 4284 /gbdb/panTro3/panTro3.2bit +chrUn_GL394597 4284 /gbdb/panTro3/panTro3.2bit +chrUn_GL394173 4283 /gbdb/panTro3/panTro3.2bit +chr7_GL390492_random 4282 /gbdb/panTro3/panTro3.2bit +chr8_GL390810_random 4282 /gbdb/panTro3/panTro3.2bit +chrUn_GL393830 4282 /gbdb/panTro3/panTro3.2bit +chr2A_GL389272_random 4281 /gbdb/panTro3/panTro3.2bit +chrUn_GL393642 4281 /gbdb/panTro3/panTro3.2bit +chrX_GL393234_random 4281 /gbdb/panTro3/panTro3.2bit +chr10_GL391328_random 4280 /gbdb/panTro3/panTro3.2bit +chr14_GL392161_random 4280 /gbdb/panTro3/panTro3.2bit +chr2B_GL389409_random 4280 /gbdb/panTro3/panTro3.2bit +chrUn_GL393673 4280 /gbdb/panTro3/panTro3.2bit +chrUn_GL394027 4280 /gbdb/panTro3/panTro3.2bit +chrUn_GL396890 4280 /gbdb/panTro3/panTro3.2bit +chr10_GL391374_random 4279 /gbdb/panTro3/panTro3.2bit +chrUn_GL393766 4278 /gbdb/panTro3/panTro3.2bit +chrUn_GL394511 4277 /gbdb/panTro3/panTro3.2bit +chrUn_GL395002 4277 /gbdb/panTro3/panTro3.2bit +chr5_GL390027_random 4276 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159167_random 4276 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157253_random 4275 /gbdb/panTro3/panTro3.2bit +chrUn_GL394136 4275 /gbdb/panTro3/panTro3.2bit +chrUn_GL394362 4275 /gbdb/panTro3/panTro3.2bit +chr15_GL392200_random 4274 /gbdb/panTro3/panTro3.2bit +chr16_GL392337_random 4274 /gbdb/panTro3/panTro3.2bit +chrUn_GL396801 4274 /gbdb/panTro3/panTro3.2bit +chr10_GL391259_random 4273 /gbdb/panTro3/panTro3.2bit +chr10_GL391659_random 4273 /gbdb/panTro3/panTro3.2bit +chrUn_GL396679 4273 /gbdb/panTro3/panTro3.2bit +chrUn_GL397020 4273 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395448 4247 /gbdb/panTro3/panTro3.2bit +chrUn_GL395953 4247 /gbdb/panTro3/panTro3.2bit +chrX_GL393203_random 4247 /gbdb/panTro3/panTro3.2bit +chr19_GL392924_random 4246 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153921_random 4246 /gbdb/panTro3/panTro3.2bit +chr3_GL389554_random 4246 /gbdb/panTro3/panTro3.2bit +chr9_GL390973_random 4246 /gbdb/panTro3/panTro3.2bit +chrUn_GL395621 4246 /gbdb/panTro3/panTro3.2bit +chr3_GL389527_random 4245 /gbdb/panTro3/panTro3.2bit +chrUn_GL396499 4245 /gbdb/panTro3/panTro3.2bit +chrX_GL393236_random 4245 /gbdb/panTro3/panTro3.2bit +chr18_GL392753_random 4244 /gbdb/panTro3/panTro3.2bit +chr19_GL392953_random 4244 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152086_random 4244 /gbdb/panTro3/panTro3.2bit +chrUn_GL393971 4244 /gbdb/panTro3/panTro3.2bit +chr10_GL391303_random 4243 /gbdb/panTro3/panTro3.2bit +chr12_GL391915_random 4243 /gbdb/panTro3/panTro3.2bit +chrUn_GL394079 4243 /gbdb/panTro3/panTro3.2bit +chrUn_GL396715 4243 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170504_random 4242 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153886_random 4242 /gbdb/panTro3/panTro3.2bit +chr4_GL389744_random 4242 /gbdb/panTro3/panTro3.2bit +chr17_GL392700_random 4241 /gbdb/panTro3/panTro3.2bit +chr2B_GL389426_random 4241 /gbdb/panTro3/panTro3.2bit +chrUn_GL393981 4241 /gbdb/panTro3/panTro3.2bit +chrUn_GL394213 4241 /gbdb/panTro3/panTro3.2bit +chr22_GL393051_random 4240 /gbdb/panTro3/panTro3.2bit +chr2B_GL389399_random 4240 /gbdb/panTro3/panTro3.2bit +chr22_GL393056_random 4239 /gbdb/panTro3/panTro3.2bit +chr2A_GL389271_random 4239 /gbdb/panTro3/panTro3.2bit +chr9_GL391189_random 4239 /gbdb/panTro3/panTro3.2bit +chrUn_GL393914 4239 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165728_random 4238 /gbdb/panTro3/panTro3.2bit +chr10_GL391330_random 4238 /gbdb/panTro3/panTro3.2bit +chr17_GL392721_random 4238 /gbdb/panTro3/panTro3.2bit +chr2B_GL389402_random 4238 /gbdb/panTro3/panTro3.2bit +chr4_GL389965_random 4238 /gbdb/panTro3/panTro3.2bit +chr12_GL391917_random 4237 /gbdb/panTro3/panTro3.2bit +chr3_GL389534_random 4237 /gbdb/panTro3/panTro3.2bit +chr4_GL389989_random 4237 /gbdb/panTro3/panTro3.2bit +chr8_GL390803_random 4236 /gbdb/panTro3/panTro3.2bit +chrUn_GL394890 4236 /gbdb/panTro3/panTro3.2bit +chrX_GL393400_random 4236 /gbdb/panTro3/panTro3.2bit +chrUn_GL393586 4235 /gbdb/panTro3/panTro3.2bit +chrUn_GL393988 4235 /gbdb/panTro3/panTro3.2bit +chr10_GL391331_random 4234 /gbdb/panTro3/panTro3.2bit +chrUn_GL393806 4234 /gbdb/panTro3/panTro3.2bit +chrUn_GL396701 4234 /gbdb/panTro3/panTro3.2bit +chrX_GL393387_random 4234 /gbdb/panTro3/panTro3.2bit +chr2A_GL389274_random 4233 /gbdb/panTro3/panTro3.2bit +chrX_GL393272_random 4233 /gbdb/panTro3/panTro3.2bit +chr10_GL391366_random 4232 /gbdb/panTro3/panTro3.2bit +chr20_GL392994_random 4232 /gbdb/panTro3/panTro3.2bit +chr8_GL390785_random 4232 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153917_random 4231 /gbdb/panTro3/panTro3.2bit +chrUn_GL395096 4231 /gbdb/panTro3/panTro3.2bit +chr9_GL391137_random 4230 /gbdb/panTro3/panTro3.2bit +chr12_GL391901_random 4229 /gbdb/panTro3/panTro3.2bit +chrUn_GL394569 4229 /gbdb/panTro3/panTro3.2bit +chrUn_GL394780 4229 /gbdb/panTro3/panTro3.2bit +chrUn_GL395265 4229 /gbdb/panTro3/panTro3.2bit +chr9_GL391042_random 4228 /gbdb/panTro3/panTro3.2bit +chrX_GL393135_random 4228 /gbdb/panTro3/panTro3.2bit +chrUn_GL393630 4227 /gbdb/panTro3/panTro3.2bit +chrUn_GL394372 4225 /gbdb/panTro3/panTro3.2bit +chr1_GL389200_random 4224 /gbdb/panTro3/panTro3.2bit +chr2A_GL389284_random 4224 /gbdb/panTro3/panTro3.2bit +chrUn_GL396994 4224 /gbdb/panTro3/panTro3.2bit +chr15_GL392203_random 4223 /gbdb/panTro3/panTro3.2bit +chrUn_GL394505 4223 /gbdb/panTro3/panTro3.2bit +chrUn_GL394681 4223 /gbdb/panTro3/panTro3.2bit +chrUn_GL394994 4223 /gbdb/panTro3/panTro3.2bit +chr4_GL389930_random 4222 /gbdb/panTro3/panTro3.2bit +chr7_GL390738_random 4222 /gbdb/panTro3/panTro3.2bit +chrUn_GL393731 4222 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr13_GL392029_random 4210 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155765_random 4210 /gbdb/panTro3/panTro3.2bit +chr4_GL389750_random 4210 /gbdb/panTro3/panTro3.2bit +chr4_GL389968_random 4210 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187353 4210 /gbdb/panTro3/panTro3.2bit +chr11_GL391705_random 4209 /gbdb/panTro3/panTro3.2bit +chr14_GL392156_random 4209 /gbdb/panTro3/panTro3.2bit +chr18_GL392771_random 4209 /gbdb/panTro3/panTro3.2bit +chr2B_GL389411_random 4209 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162573_random 4209 /gbdb/panTro3/panTro3.2bit +chrUn_GL395013 4209 /gbdb/panTro3/panTro3.2bit +chrX_GL393200_random 4209 /gbdb/panTro3/panTro3.2bit +chr4_GL389985_random 4208 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162612_random 4208 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175938_random 4207 /gbdb/panTro3/panTro3.2bit +chr19_GL392826_random 4207 /gbdb/panTro3/panTro3.2bit +chr4_GL389969_random 4207 /gbdb/panTro3/panTro3.2bit +chr11_GL391735_random 4205 /gbdb/panTro3/panTro3.2bit +chrUn_GL394499 4205 /gbdb/panTro3/panTro3.2bit +chrUn_GL394764 4205 /gbdb/panTro3/panTro3.2bit +chr1_GL388869_random 4204 /gbdb/panTro3/panTro3.2bit +chr1_GL388940_random 4204 /gbdb/panTro3/panTro3.2bit +chr4_GL389981_random 4204 /gbdb/panTro3/panTro3.2bit +chrUn_GL394801 4204 /gbdb/panTro3/panTro3.2bit +chrUn_GL397066 4204 /gbdb/panTro3/panTro3.2bit +chr1_GL388886_random 4203 /gbdb/panTro3/panTro3.2bit +chrUn_GL393774 4203 /gbdb/panTro3/panTro3.2bit +chrUn_GL396949 4203 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150516_random 4202 /gbdb/panTro3/panTro3.2bit +chr9_GL390926_random 4202 /gbdb/panTro3/panTro3.2bit +chrUn_GL394349 4202 /gbdb/panTro3/panTro3.2bit +chrUn_GL394005 4201 /gbdb/panTro3/panTro3.2bit +chr16_GL392375_random 4200 /gbdb/panTro3/panTro3.2bit +chrUn_GL393890 4199 /gbdb/panTro3/panTro3.2bit +chrUn_GL396118 4199 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165681_random 4198 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177063_random 4198 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152119_random 4198 /gbdb/panTro3/panTro3.2bit +chrUn_GL394061 4198 /gbdb/panTro3/panTro3.2bit +chrUn_GL394942 4198 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157274_random 4197 /gbdb/panTro3/panTro3.2bit +chr5_GL390033_random 4197 /gbdb/panTro3/panTro3.2bit +chrUn_GL394195 4197 /gbdb/panTro3/panTro3.2bit +chrUn_GL394412 4197 /gbdb/panTro3/panTro3.2bit +chr5_GL390137_random 4196 /gbdb/panTro3/panTro3.2bit +chrUn_GL394327 4196 /gbdb/panTro3/panTro3.2bit +chr3_GL389532_random 4195 /gbdb/panTro3/panTro3.2bit +chrUn_GL393725 4195 /gbdb/panTro3/panTro3.2bit +chr9_GL391231_random 4194 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188462 4194 /gbdb/panTro3/panTro3.2bit +chrX_GL393229_random 4192 /gbdb/panTro3/panTro3.2bit +chr12_GL391934_random 4191 /gbdb/panTro3/panTro3.2bit +chr18_GL392812_random 4191 /gbdb/panTro3/panTro3.2bit +chrUn_GL394527 4191 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176533_random 4190 /gbdb/panTro3/panTro3.2bit +chr2B_GL389403_random 4190 /gbdb/panTro3/panTro3.2bit +chr17_GL392706_random 4189 /gbdb/panTro3/panTro3.2bit +chrUn_GL395153 4189 /gbdb/panTro3/panTro3.2bit +chrUn_GL395763 4189 /gbdb/panTro3/panTro3.2bit +chrUn_GL396845 4189 /gbdb/panTro3/panTro3.2bit +chr1_GL388923_random 4188 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155924_random 4188 /gbdb/panTro3/panTro3.2bit +chrUn_GL395035 4188 /gbdb/panTro3/panTro3.2bit +chrUn_GL395105 4188 /gbdb/panTro3/panTro3.2bit +chrUn_GL395288 4188 /gbdb/panTro3/panTro3.2bit +chr10_GL391610_random 4187 /gbdb/panTro3/panTro3.2bit +chrUn_GL393935 4187 /gbdb/panTro3/panTro3.2bit +chr18_GL392758_random 4186 /gbdb/panTro3/panTro3.2bit +chr2A_GL389280_random 4186 /gbdb/panTro3/panTro3.2bit +chr4_GL389938_random 4186 /gbdb/panTro3/panTro3.2bit +chr5_GL390043_random 4186 /gbdb/panTro3/panTro3.2bit +chrUn_GL394821 4186 /gbdb/panTro3/panTro3.2bit +chrUn_GL395451 4186 /gbdb/panTro3/panTro3.2bit +chr15_GL392286_random 4185 /gbdb/panTro3/panTro3.2bit +chrUn_GL393813 4185 /gbdb/panTro3/panTro3.2bit +chrUn_GL394650 4185 /gbdb/panTro3/panTro3.2bit +chr11_GL391736_random 4184 /gbdb/panTro3/panTro3.2bit +chrUn_GL394634 4184 /gbdb/panTro3/panTro3.2bit +chr17_GL392596_random 4183 /gbdb/panTro3/panTro3.2bit +chr19_GL392881_random 4183 /gbdb/panTro3/panTro3.2bit +chr19_GL392842_random 4182 /gbdb/panTro3/panTro3.2bit +chrUn_GL393733 4182 /gbdb/panTro3/panTro3.2bit +chr12_GL391913_random 4181 /gbdb/panTro3/panTro3.2bit +chrUn_GL394172 4181 /gbdb/panTro3/panTro3.2bit +chrUn_GL394470 4181 /gbdb/panTro3/panTro3.2bit +chrUn_GL394554 4181 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168454_random 4180 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171317_random 4180 /gbdb/panTro3/panTro3.2bit +chr20_GL392993_random 4180 /gbdb/panTro3/panTro3.2bit +chrUn_GL393656 4180 /gbdb/panTro3/panTro3.2bit +chr13_GL392033_random 4179 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174505_random 4179 /gbdb/panTro3/panTro3.2bit +chr9_GL391051_random 4179 /gbdb/panTro3/panTro3.2bit +chr9_GL391060_random 4179 /gbdb/panTro3/panTro3.2bit +chr1_GL388852_random 4178 /gbdb/panTro3/panTro3.2bit +chrUn_GL394388 4178 /gbdb/panTro3/panTro3.2bit +chrUn_GL394917 4178 /gbdb/panTro3/panTro3.2bit +chr6_GL390272_random 4177 /gbdb/panTro3/panTro3.2bit +chrUn_GL394208 4177 /gbdb/panTro3/panTro3.2bit +chr10_GL391394_random 4176 /gbdb/panTro3/panTro3.2bit +chr11_GL391725_random 4176 /gbdb/panTro3/panTro3.2bit +chr12_GL391895_random 4176 /gbdb/panTro3/panTro3.2bit +chr12_GL391919_random 4175 /gbdb/panTro3/panTro3.2bit +chrUn_GL394472 4175 /gbdb/panTro3/panTro3.2bit +chrX_GL393431_random 4175 /gbdb/panTro3/panTro3.2bit +chr5_GL390022_random 4174 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164478_random 4174 /gbdb/panTro3/panTro3.2bit +chr1_GL388910_random 4173 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177068_random 4173 /gbdb/panTro3/panTro3.2bit +chrUn_GL394353 4173 /gbdb/panTro3/panTro3.2bit +chrUn_GL395859 4173 /gbdb/panTro3/panTro3.2bit +chr14_GL392172_random 4172 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL393784 4158 /gbdb/panTro3/panTro3.2bit +chrUn_GL395638 4158 /gbdb/panTro3/panTro3.2bit +chrUn_GL396654 4158 /gbdb/panTro3/panTro3.2bit +chrUn_GL393672 4157 /gbdb/panTro3/panTro3.2bit +chrUn_GL394782 4157 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165609_random 4156 /gbdb/panTro3/panTro3.2bit +chrUn_GL393970 4156 /gbdb/panTro3/panTro3.2bit +chrUn_GL394808 4156 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156048_random 4155 /gbdb/panTro3/panTro3.2bit +chr9_GL391244_random 4155 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187683 4155 /gbdb/panTro3/panTro3.2bit +chrUn_GL394996 4155 /gbdb/panTro3/panTro3.2bit +chr12_GL391960_random 4154 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170584_random 4154 /gbdb/panTro3/panTro3.2bit +chr6_GL390346_random 4154 /gbdb/panTro3/panTro3.2bit +chrUn_GL394606 4154 /gbdb/panTro3/panTro3.2bit +chrUn_GL395440 4154 /gbdb/panTro3/panTro3.2bit +chr16_GL392448_random 4153 /gbdb/panTro3/panTro3.2bit +chr17_GL392598_random 4153 /gbdb/panTro3/panTro3.2bit +chr9_GL390970_random 4153 /gbdb/panTro3/panTro3.2bit +chrX_GL393268_random 4153 /gbdb/panTro3/panTro3.2bit +chr10_GL391333_random 4152 /gbdb/panTro3/panTro3.2bit +chr11_GL391727_random 4152 /gbdb/panTro3/panTro3.2bit +chr10_GL391421_random 4151 /gbdb/panTro3/panTro3.2bit +chr1_GL388988_random 4151 /gbdb/panTro3/panTro3.2bit +chrUn_GL394725 4151 /gbdb/panTro3/panTro3.2bit +chr10_GL391387_random 4150 /gbdb/panTro3/panTro3.2bit +chrUn_GL395359 4150 /gbdb/panTro3/panTro3.2bit +chr11_GL391817_random 4149 /gbdb/panTro3/panTro3.2bit +chr1_GL388851_random 4148 /gbdb/panTro3/panTro3.2bit +chr3_GL389548_random 4148 /gbdb/panTro3/panTro3.2bit +chrUn_GL393752 4148 /gbdb/panTro3/panTro3.2bit +chrUn_GL394246 4148 /gbdb/panTro3/panTro3.2bit +chrUn_GL395355 4148 /gbdb/panTro3/panTro3.2bit +chrX_GL393175_random 4148 /gbdb/panTro3/panTro3.2bit +chr17_GL392617_random 4147 /gbdb/panTro3/panTro3.2bit +chrUn_GL394183 4147 /gbdb/panTro3/panTro3.2bit +chr14_GL392101_random 4146 /gbdb/panTro3/panTro3.2bit +chrUn_GL394582 4146 /gbdb/panTro3/panTro3.2bit +chrUn_GL394588 4146 /gbdb/panTro3/panTro3.2bit +chrX_GL393244_random 4146 /gbdb/panTro3/panTro3.2bit +chr7_GL390482_random 4145 /gbdb/panTro3/panTro3.2bit +chrUn_GL394884 4145 /gbdb/panTro3/panTro3.2bit +chr19_GL392898_random 4144 /gbdb/panTro3/panTro3.2bit +chr20_GL392990_random 4144 /gbdb/panTro3/panTro3.2bit +chr3_GL389561_random 4144 /gbdb/panTro3/panTro3.2bit +chr5_GL390023_random 4144 /gbdb/panTro3/panTro3.2bit +chr5_GL390048_random 4144 /gbdb/panTro3/panTro3.2bit +chrUn_GL395120 4144 /gbdb/panTro3/panTro3.2bit +chrX_GL393114_random 4144 /gbdb/panTro3/panTro3.2bit +chr9_GL391074_random 4143 /gbdb/panTro3/panTro3.2bit +chrUn_GL395235 4143 /gbdb/panTro3/panTro3.2bit +chrX_GL393310_random 4143 /gbdb/panTro3/panTro3.2bit +chrX_GL393153_random 4141 /gbdb/panTro3/panTro3.2bit +chr19_GL392911_random 4140 /gbdb/panTro3/panTro3.2bit +chr5_GL390072_random 4140 /gbdb/panTro3/panTro3.2bit +chrUn_GL394227 4140 /gbdb/panTro3/panTro3.2bit +chrUn_GL394719 4140 /gbdb/panTro3/panTro3.2bit +chr7_GL390578_random 4139 /gbdb/panTro3/panTro3.2bit +chr9_GL390939_random 4139 /gbdb/panTro3/panTro3.2bit +chr12_GL391894_random 4138 /gbdb/panTro3/panTro3.2bit +chr1_GL388833_random 4138 /gbdb/panTro3/panTro3.2bit +chr10_GL391411_random 4137 /gbdb/panTro3/panTro3.2bit +chr1_GL389018_random 4137 /gbdb/panTro3/panTro3.2bit +chr4_GL389716_random 4137 /gbdb/panTro3/panTro3.2bit +chrUn_GL394071 4137 /gbdb/panTro3/panTro3.2bit +chrX_GL393180_random 4137 /gbdb/panTro3/panTro3.2bit +chr10_GL391606_random 4136 /gbdb/panTro3/panTro3.2bit +chr2A_GL389309_random 4136 /gbdb/panTro3/panTro3.2bit +chr10_GL391424_random 4135 /gbdb/panTro3/panTro3.2bit +chr15_GL392274_random 4135 /gbdb/panTro3/panTro3.2bit +chr9_GL391227_random 4135 /gbdb/panTro3/panTro3.2bit +chrUn_GL393989 4135 /gbdb/panTro3/panTro3.2bit +chrUn_GL394233 4135 /gbdb/panTro3/panTro3.2bit +chrUn_GL395966 4135 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187307 4134 /gbdb/panTro3/panTro3.2bit +chrUn_GL393664 4134 /gbdb/panTro3/panTro3.2bit +chrUn_GL394804 4134 /gbdb/panTro3/panTro3.2bit +chrX_GL393392_random 4134 /gbdb/panTro3/panTro3.2bit +chrUn_GL394632 4133 /gbdb/panTro3/panTro3.2bit +chr10_GL391458_random 4132 /gbdb/panTro3/panTro3.2bit +chr15_GL392266_random 4132 /gbdb/panTro3/panTro3.2bit +chr16_GL392320_random 4132 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162574_random 4131 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170491_random 4130 /gbdb/panTro3/panTro3.2bit +chr7_GL390506_random 4130 /gbdb/panTro3/panTro3.2bit +chrUn_GL394878 4130 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158836_random 4129 /gbdb/panTro3/panTro3.2bit +chrUn_GL395831 4128 /gbdb/panTro3/panTro3.2bit +chrUn_GL396154 4128 /gbdb/panTro3/panTro3.2bit +chr10_GL391432_random 4127 /gbdb/panTro3/panTro3.2bit +chr9_GL391138_random 4127 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187315 4127 /gbdb/panTro3/panTro3.2bit +chr10_GL391308_random 4126 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187744 4119 /gbdb/panTro3/panTro3.2bit +chrUn_GL394937 4119 /gbdb/panTro3/panTro3.2bit +chr10_GL391491_random 4118 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03184932 4118 /gbdb/panTro3/panTro3.2bit +chrUn_GL394131 4118 /gbdb/panTro3/panTro3.2bit +chr19_GL392837_random 4117 /gbdb/panTro3/panTro3.2bit +chrUn_GL394016 4117 /gbdb/panTro3/panTro3.2bit +chrX_GL393167_random 4117 /gbdb/panTro3/panTro3.2bit +chrUn_GL394943 4116 /gbdb/panTro3/panTro3.2bit +chr11_GL391776_random 4115 /gbdb/panTro3/panTro3.2bit +chr14_GL392116_random 4115 /gbdb/panTro3/panTro3.2bit +chr15_GL392276_random 4115 /gbdb/panTro3/panTro3.2bit +chr9_GL390960_random 4115 /gbdb/panTro3/panTro3.2bit +chr10_GL391625_random 4114 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174632_random 4114 /gbdb/panTro3/panTro3.2bit +chr8_GL390808_random 4114 /gbdb/panTro3/panTro3.2bit +chr4_GL389697_random 4113 /gbdb/panTro3/panTro3.2bit +chrUn_GL393654 4113 /gbdb/panTro3/panTro3.2bit +chrUn_GL394557 4113 /gbdb/panTro3/panTro3.2bit +chrUn_GL395747 4113 /gbdb/panTro3/panTro3.2bit +chrX_GL393283_random 4113 /gbdb/panTro3/panTro3.2bit +chr12_GL391928_random 4112 /gbdb/panTro3/panTro3.2bit +chr20_GL392998_random 4112 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152876_random 4112 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174461_random 4111 /gbdb/panTro3/panTro3.2bit +chr4_GL389927_random 4110 /gbdb/panTro3/panTro3.2bit +chrUn_GL394710 4110 /gbdb/panTro3/panTro3.2bit +chrUn_GL395466 4110 /gbdb/panTro3/panTro3.2bit +chr9_GL390976_random 4109 /gbdb/panTro3/panTro3.2bit +chr1_GL388880_random 4108 /gbdb/panTro3/panTro3.2bit +chrUn_GL394428 4108 /gbdb/panTro3/panTro3.2bit +chr3_GL389635_random 4107 /gbdb/panTro3/panTro3.2bit +chr6_GL390220_random 4107 /gbdb/panTro3/panTro3.2bit +chrUn_GL394059 4107 /gbdb/panTro3/panTro3.2bit +chrUn_GL394214 4107 /gbdb/panTro3/panTro3.2bit +chrUn_GL396287 4107 /gbdb/panTro3/panTro3.2bit +chr11_GL391738_random 4106 /gbdb/panTro3/panTro3.2bit +chr3_GL389579_random 4106 /gbdb/panTro3/panTro3.2bit +chrUn_GL393688 4106 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165706_random 4105 /gbdb/panTro3/panTro3.2bit +chrUn_GL394749 4105 /gbdb/panTro3/panTro3.2bit +chr1_GL388853_random 4103 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154016_random 4103 /gbdb/panTro3/panTro3.2bit +chrUn_GL394812 4103 /gbdb/panTro3/panTro3.2bit +chr22_GL393053_random 4102 /gbdb/panTro3/panTro3.2bit +chrUn_GL394235 4102 /gbdb/panTro3/panTro3.2bit +chrUn_GL395161 4102 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172041_random 4101 /gbdb/panTro3/panTro3.2bit +chr1_GL388856_random 4101 /gbdb/panTro3/panTro3.2bit +chr1_GL388874_random 4101 /gbdb/panTro3/panTro3.2bit +chrX_GL393277_random 4101 /gbdb/panTro3/panTro3.2bit +chr20_GL392995_random 4099 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169270_random 4098 /gbdb/panTro3/panTro3.2bit +chr18_GL392768_random 4098 /gbdb/panTro3/panTro3.2bit +chr1_GL388836_random 4098 /gbdb/panTro3/panTro3.2bit +chr1_GL389136_random 4098 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr16_GL392359_random 4073 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159051_random 4073 /gbdb/panTro3/panTro3.2bit +chr6_GL390255_random 4073 /gbdb/panTro3/panTro3.2bit +chrUn_GL394863 4073 /gbdb/panTro3/panTro3.2bit +chrUn_GL395552 4073 /gbdb/panTro3/panTro3.2bit +chr12_GL391964_random 4072 /gbdb/panTro3/panTro3.2bit +chr3_GL389641_random 4072 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162736_random 4072 /gbdb/panTro3/panTro3.2bit +chr10_GL391577_random 4071 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186403 4071 /gbdb/panTro3/panTro3.2bit +chrUn_GL395170 4071 /gbdb/panTro3/panTro3.2bit +chrUn_GL396772 4071 /gbdb/panTro3/panTro3.2bit +chr5_GL390050_random 4070 /gbdb/panTro3/panTro3.2bit +chrX_GL393325_random 4070 /gbdb/panTro3/panTro3.2bit +chr13_GL392063_random 4069 /gbdb/panTro3/panTro3.2bit +chr5_GL390054_random 4069 /gbdb/panTro3/panTro3.2bit +chrUn_GL396362 4069 /gbdb/panTro3/panTro3.2bit +chrUn_GL393930 4068 /gbdb/panTro3/panTro3.2bit +chrUn_GL394078 4068 /gbdb/panTro3/panTro3.2bit +chrUn_GL394610 4068 /gbdb/panTro3/panTro3.2bit +chr12_GL391910_random 4067 /gbdb/panTro3/panTro3.2bit +chr13_GL392034_random 4067 /gbdb/panTro3/panTro3.2bit +chr9_GL390938_random 4067 /gbdb/panTro3/panTro3.2bit +chrUn_GL394525 4067 /gbdb/panTro3/panTro3.2bit +chr11_GL391723_random 4066 /gbdb/panTro3/panTro3.2bit +chr1_GL388903_random 4066 /gbdb/panTro3/panTro3.2bit +chr1_GL388989_random 4066 /gbdb/panTro3/panTro3.2bit +chr2B_GL389421_random 4066 /gbdb/panTro3/panTro3.2bit +chrX_GL393359_random 4066 /gbdb/panTro3/panTro3.2bit +chrUn_GL395107 4065 /gbdb/panTro3/panTro3.2bit +chrUn_GL395771 4065 /gbdb/panTro3/panTro3.2bit +chrX_GL393261_random 4065 /gbdb/panTro3/panTro3.2bit +chrX_GL393403_random 4065 /gbdb/panTro3/panTro3.2bit +chr3_GL389604_random 4064 /gbdb/panTro3/panTro3.2bit +chr5_GL390055_random 4064 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161490_random 4064 /gbdb/panTro3/panTro3.2bit +chrUn_GL393859 4064 /gbdb/panTro3/panTro3.2bit +chrUn_GL394389 4064 /gbdb/panTro3/panTro3.2bit +chr14_GL392105_random 4063 /gbdb/panTro3/panTro3.2bit +chrUn_GL394346 4063 /gbdb/panTro3/panTro3.2bit +chr2A_GL389362_random 4062 /gbdb/panTro3/panTro3.2bit +chrUn_GL394018 4062 /gbdb/panTro3/panTro3.2bit +chr12_GL391970_random 4061 /gbdb/panTro3/panTro3.2bit +chr1_GL388854_random 4061 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162502_random 4061 /gbdb/panTro3/panTro3.2bit +chr8_GL390759_random 4061 /gbdb/panTro3/panTro3.2bit +chrUn_GL393932 4061 /gbdb/panTro3/panTro3.2bit +chrUn_GL394619 4061 /gbdb/panTro3/panTro3.2bit +chrUn_GL394123 4060 /gbdb/panTro3/panTro3.2bit +chrUn_GL394205 4060 /gbdb/panTro3/panTro3.2bit +chr12_GL391992_random 4059 /gbdb/panTro3/panTro3.2bit +chrUn_GL394423 4059 /gbdb/panTro3/panTro3.2bit +chrX_GL393118_random 4059 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172067_random 4058 /gbdb/panTro3/panTro3.2bit +chr19_GL392902_random 4058 /gbdb/panTro3/panTro3.2bit +chrUn_GL394923 4058 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169282_random 4057 /gbdb/panTro3/panTro3.2bit +chrUn_GL394687 4056 /gbdb/panTro3/panTro3.2bit +chr1_GL388916_random 4055 /gbdb/panTro3/panTro3.2bit +chrUn_GL394200 4055 /gbdb/panTro3/panTro3.2bit +chrUn_GL395061 4055 /gbdb/panTro3/panTro3.2bit +chrUn_GL395733 4055 /gbdb/panTro3/panTro3.2bit +chr3_GL389573_random 4054 /gbdb/panTro3/panTro3.2bit +chr10_GL391445_random 4053 /gbdb/panTro3/panTro3.2bit +chr13_GL392021_random 4053 /gbdb/panTro3/panTro3.2bit +chr19_GL392852_random 4053 /gbdb/panTro3/panTro3.2bit +chr9_GL391053_random 4053 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169372_random 4052 /gbdb/panTro3/panTro3.2bit +chr15_GL392275_random 4052 /gbdb/panTro3/panTro3.2bit +chr2B_GL389488_random 4052 /gbdb/panTro3/panTro3.2bit +chr6_GL390251_random 4052 /gbdb/panTro3/panTro3.2bit +chrUn_GL396860 4051 /gbdb/panTro3/panTro3.2bit +chr12_GL391899_random 4049 /gbdb/panTro3/panTro3.2bit +chr12_GL391925_random 4049 /gbdb/panTro3/panTro3.2bit +chr9_GL390949_random 4049 /gbdb/panTro3/panTro3.2bit +chrUn_GL394906 4048 /gbdb/panTro3/panTro3.2bit +chr2B_GL389430_random 4047 /gbdb/panTro3/panTro3.2bit +chr9_GL390972_random 4047 /gbdb/panTro3/panTro3.2bit +chrUn_GL394408 4047 /gbdb/panTro3/panTro3.2bit +chr1_GL388907_random 4046 /gbdb/panTro3/panTro3.2bit +chr14_GL392117_random 4045 /gbdb/panTro3/panTro3.2bit +chr18_GL392807_random 4045 /gbdb/panTro3/panTro3.2bit +chr19_GL392974_random 4045 /gbdb/panTro3/panTro3.2bit +chrUn_GL394495 4045 /gbdb/panTro3/panTro3.2bit +chrUn_GL394581 4045 /gbdb/panTro3/panTro3.2bit +chrUn_GL394586 4045 /gbdb/panTro3/panTro3.2bit +chr16_GL392579_random 4044 /gbdb/panTro3/panTro3.2bit +chr8_GL390802_random 4044 /gbdb/panTro3/panTro3.2bit +chrUn_GL395205 4044 /gbdb/panTro3/panTro3.2bit +chr10_GL391377_random 4043 /gbdb/panTro3/panTro3.2bit +chr11_GL391729_random 4043 /gbdb/panTro3/panTro3.2bit +chr9_GL390978_random 4043 /gbdb/panTro3/panTro3.2bit +chrUn_GL395564 4043 /gbdb/panTro3/panTro3.2bit +chrX_GL393189_random 4043 /gbdb/panTro3/panTro3.2bit +chr1_GL388877_random 4042 /gbdb/panTro3/panTro3.2bit +chrUn_GL395194 4042 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153928_random 4041 /gbdb/panTro3/panTro3.2bit +chr5_GL390026_random 4041 /gbdb/panTro3/panTro3.2bit +chrUn_GL394960 4041 /gbdb/panTro3/panTro3.2bit +chrX_GL393123_random 4041 /gbdb/panTro3/panTro3.2bit +chr19_GL392921_random 4040 /gbdb/panTro3/panTro3.2bit +chrX_GL393227_random 4040 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155814_random 4039 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157377_random 4039 /gbdb/panTro3/panTro3.2bit +chrUn_GL394551 4039 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166048_random 4038 /gbdb/panTro3/panTro3.2bit +chr19_GL392944_random 4038 /gbdb/panTro3/panTro3.2bit +chr4_GL389753_random 4038 /gbdb/panTro3/panTro3.2bit +chrUn_GL395811 4038 /gbdb/panTro3/panTro3.2bit +chr2A_GL389254_random 4037 /gbdb/panTro3/panTro3.2bit +chr9_GL390966_random 4037 /gbdb/panTro3/panTro3.2bit +chrX_GL393423_random 4037 /gbdb/panTro3/panTro3.2bit +chr19_GL392841_random 4036 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr8_AACZ03162557_random 4028 /gbdb/panTro3/panTro3.2bit +chr8_GL390800_random 4028 /gbdb/panTro3/panTro3.2bit +chr16_GL392564_random 4027 /gbdb/panTro3/panTro3.2bit +chr1_GL389170_random 4026 /gbdb/panTro3/panTro3.2bit +chr4_GL389725_random 4026 /gbdb/panTro3/panTro3.2bit +chrUn_GL394622 4026 /gbdb/panTro3/panTro3.2bit +chr10_GL391336_random 4025 /gbdb/panTro3/panTro3.2bit +chr19_GL392893_random 4025 /gbdb/panTro3/panTro3.2bit +chr6_GL390179_random 4025 /gbdb/panTro3/panTro3.2bit +chr10_GL391608_random 4024 /gbdb/panTro3/panTro3.2bit +chr10_GL391612_random 4024 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172040_random 4024 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173462_random 4024 /gbdb/panTro3/panTro3.2bit +chrUn_GL394192 4024 /gbdb/panTro3/panTro3.2bit +chr14_GL392112_random 4022 /gbdb/panTro3/panTro3.2bit +chrX_GL393425_random 4022 /gbdb/panTro3/panTro3.2bit +chr5_GL390042_random 4021 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188531 4021 /gbdb/panTro3/panTro3.2bit +chrUn_GL394506 4021 /gbdb/panTro3/panTro3.2bit +chrX_GL393347_random 4020 /gbdb/panTro3/panTro3.2bit +chr15_GL392216_random 4019 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155915_random 4019 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157351_random 4019 /gbdb/panTro3/panTro3.2bit +chrUn_GL394612 4019 /gbdb/panTro3/panTro3.2bit +chrUn_GL394871 4019 /gbdb/panTro3/panTro3.2bit +chr4_GL389770_random 4018 /gbdb/panTro3/panTro3.2bit +chrUn_GL395693 4018 /gbdb/panTro3/panTro3.2bit +chr10_GL391379_random 4017 /gbdb/panTro3/panTro3.2bit +chr11_GL391726_random 4017 /gbdb/panTro3/panTro3.2bit +chr1_GL388860_random 4017 /gbdb/panTro3/panTro3.2bit +chrUn_GL394523 4017 /gbdb/panTro3/panTro3.2bit +chr19_GL392875_random 4016 /gbdb/panTro3/panTro3.2bit +chr18_GL392774_random 4015 /gbdb/panTro3/panTro3.2bit +chr2B_GL389419_random 4015 /gbdb/panTro3/panTro3.2bit +chrUn_GL393960 4014 /gbdb/panTro3/panTro3.2bit +chrUn_GL394997 4014 /gbdb/panTro3/panTro3.2bit +chrUn_GL395560 4014 /gbdb/panTro3/panTro3.2bit +chr2B_GL389405_random 4013 /gbdb/panTro3/panTro3.2bit +chr3_GL389507_random 4013 /gbdb/panTro3/panTro3.2bit +chr6_GL390178_random 4013 /gbdb/panTro3/panTro3.2bit +chrX_GL393122_random 4013 /gbdb/panTro3/panTro3.2bit +chrX_GL393289_random 4013 /gbdb/panTro3/panTro3.2bit +chrUn_GL393602 4012 /gbdb/panTro3/panTro3.2bit +chrUn_GL394154 4010 /gbdb/panTro3/panTro3.2bit +chrUn_GL394260 4010 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153951_random 4009 /gbdb/panTro3/panTro3.2bit +chrUn_GL394898 4008 /gbdb/panTro3/panTro3.2bit +chrX_GL393408_random 4008 /gbdb/panTro3/panTro3.2bit +chr8_GL390801_random 4007 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187425 4007 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189668 4006 /gbdb/panTro3/panTro3.2bit +chrUn_GL393857 4005 /gbdb/panTro3/panTro3.2bit +chrUn_GL394294 4005 /gbdb/panTro3/panTro3.2bit +chrUn_GL394548 4005 /gbdb/panTro3/panTro3.2bit +chr11_GL391693_random 4004 /gbdb/panTro3/panTro3.2bit +chr19_GL392829_random 4004 /gbdb/panTro3/panTro3.2bit +chr9_GL391226_random 4004 /gbdb/panTro3/panTro3.2bit +chrUn_GL394707 4004 /gbdb/panTro3/panTro3.2bit +chrUn_GL394615 4003 /gbdb/panTro3/panTro3.2bit +chrX_GL393184_random 4003 /gbdb/panTro3/panTro3.2bit +chr1_GL389140_random 4002 /gbdb/panTro3/panTro3.2bit +chrUn_GL396524 4002 /gbdb/panTro3/panTro3.2bit +chrX_GL393136_random 4002 /gbdb/panTro3/panTro3.2bit +chr16_GL392311_random 4001 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157267_random 4001 /gbdb/panTro3/panTro3.2bit +chrUn_GL395299 4001 /gbdb/panTro3/panTro3.2bit +chr10_GL391335_random 4000 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171205_random 4000 /gbdb/panTro3/panTro3.2bit +chrUn_GL394953 4000 /gbdb/panTro3/panTro3.2bit +chr10_GL391383_random 3999 /gbdb/panTro3/panTro3.2bit +chr10_GL391385_random 3999 /gbdb/panTro3/panTro3.2bit +chr8_GL390850_random 3999 /gbdb/panTro3/panTro3.2bit +chr11_GL391747_random 3998 /gbdb/panTro3/panTro3.2bit +chr12_GL391905_random 3998 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr17_GL392604_random 3976 /gbdb/panTro3/panTro3.2bit +chrUn_GL394060 3976 /gbdb/panTro3/panTro3.2bit +chr10_GL391604_random 3975 /gbdb/panTro3/panTro3.2bit +chrUn_GL394692 3975 /gbdb/panTro3/panTro3.2bit +chrUn_GL395455 3975 /gbdb/panTro3/panTro3.2bit +chrUn_GL394772 3974 /gbdb/panTro3/panTro3.2bit +chr16_GL392324_random 3973 /gbdb/panTro3/panTro3.2bit +chr4_GL389721_random 3972 /gbdb/panTro3/panTro3.2bit +chrUn_GL393888 3972 /gbdb/panTro3/panTro3.2bit +chr1_GL389197_random 3971 /gbdb/panTro3/panTro3.2bit +chr2A_GL389332_random 3971 /gbdb/panTro3/panTro3.2bit +chrUn_GL394050 3971 /gbdb/panTro3/panTro3.2bit +chrUn_GL396898 3971 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169421_random 3970 /gbdb/panTro3/panTro3.2bit +chr1_GL388883_random 3970 /gbdb/panTro3/panTro3.2bit +chr8_GL390811_random 3970 /gbdb/panTro3/panTro3.2bit +chrUn_GL396468 3970 /gbdb/panTro3/panTro3.2bit +chrUn_GL396783 3970 /gbdb/panTro3/panTro3.2bit +chr3_GL389600_random 3969 /gbdb/panTro3/panTro3.2bit +chrUn_GL394293 3969 /gbdb/panTro3/panTro3.2bit +chrUn_GL394755 3969 /gbdb/panTro3/panTro3.2bit +chr16_GL392316_random 3968 /gbdb/panTro3/panTro3.2bit +chrUn_GL394352 3968 /gbdb/panTro3/panTro3.2bit +chrUn_GL395776 3968 /gbdb/panTro3/panTro3.2bit +chr1_GL388888_random 3967 /gbdb/panTro3/panTro3.2bit +chr7_GL390486_random 3967 /gbdb/panTro3/panTro3.2bit +chrUn_GL396685 3967 /gbdb/panTro3/panTro3.2bit +chrX_GL393360_random 3967 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150352_random 3966 /gbdb/panTro3/panTro3.2bit +chr2B_GL389408_random 3966 /gbdb/panTro3/panTro3.2bit +chr4_GL389973_random 3966 /gbdb/panTro3/panTro3.2bit +chr6_GL390232_random 3965 /gbdb/panTro3/panTro3.2bit +chrX_GL393444_random 3965 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165483_random 3964 /gbdb/panTro3/panTro3.2bit +chr19_GL392900_random 3964 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187781 3964 /gbdb/panTro3/panTro3.2bit +chr11_GL391835_random 3963 /gbdb/panTro3/panTro3.2bit 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+chr4_GL389851_random 3931 /gbdb/panTro3/panTro3.2bit +chrUn_GL395207 3931 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188031 3930 /gbdb/panTro3/panTro3.2bit +chrUn_GL394474 3930 /gbdb/panTro3/panTro3.2bit +chr10_GL391396_random 3929 /gbdb/panTro3/panTro3.2bit +chrUn_GL394817 3929 /gbdb/panTro3/panTro3.2bit +chrUn_GL395430 3929 /gbdb/panTro3/panTro3.2bit +chrX_GL393217_random 3929 /gbdb/panTro3/panTro3.2bit +chr8_GL390793_random 3928 /gbdb/panTro3/panTro3.2bit +chrUn_GL393903 3928 /gbdb/panTro3/panTro3.2bit +chrUn_GL395473 3927 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153988_random 3926 /gbdb/panTro3/panTro3.2bit +chrUn_GL394741 3925 /gbdb/panTro3/panTro3.2bit +chrUn_GL394893 3925 /gbdb/panTro3/panTro3.2bit +chrUn_GL394796 3924 /gbdb/panTro3/panTro3.2bit +chrUn_GL395008 3924 /gbdb/panTro3/panTro3.2bit +chr12_GL391908_random 3923 /gbdb/panTro3/panTro3.2bit +chr3_GL389632_random 3922 /gbdb/panTro3/panTro3.2bit +chr4_GL389774_random 3922 /gbdb/panTro3/panTro3.2bit +chr18_GL392772_random 3921 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189532 3921 /gbdb/panTro3/panTro3.2bit +chr10_GL391522_random 3920 /gbdb/panTro3/panTro3.2bit +chr16_GL392314_random 3920 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153868_random 3920 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189138 3920 /gbdb/panTro3/panTro3.2bit +chrUn_GL394330 3920 /gbdb/panTro3/panTro3.2bit +chrUn_GL396866 3920 /gbdb/panTro3/panTro3.2bit +chrX_GL393405_random 3920 /gbdb/panTro3/panTro3.2bit +chr19_GL392972_random 3919 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150362_random 3919 /gbdb/panTro3/panTro3.2bit +chrUn_GL394285 3919 /gbdb/panTro3/panTro3.2bit +chrX_GL393278_random 3918 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169308_random 3917 /gbdb/panTro3/panTro3.2bit +chrUn_GL394469 3917 /gbdb/panTro3/panTro3.2bit +chrX_GL393145_random 3917 /gbdb/panTro3/panTro3.2bit +chr4_GL389751_random 3916 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164915_random 3916 /gbdb/panTro3/panTro3.2bit +chr18_GL392780_random 3914 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_GL390980_random 3882 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187177 3882 /gbdb/panTro3/panTro3.2bit +chrX_GL393275_random 3881 /gbdb/panTro3/panTro3.2bit +chr10_GL391402_random 3880 /gbdb/panTro3/panTro3.2bit +chrUn_GL394711 3880 /gbdb/panTro3/panTro3.2bit +chrUn_GL394882 3879 /gbdb/panTro3/panTro3.2bit +chr11_GL391709_random 3878 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150512_random 3878 /gbdb/panTro3/panTro3.2bit +chr22_GL393099_random 3878 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153929_random 3878 /gbdb/panTro3/panTro3.2bit +chrUn_GL395092 3878 /gbdb/panTro3/panTro3.2bit +chr3_GL389652_random 3877 /gbdb/panTro3/panTro3.2bit +chr4_GL389732_random 3876 /gbdb/panTro3/panTro3.2bit +chr9_GL391033_random 3876 /gbdb/panTro3/panTro3.2bit +chrUn_GL393923 3876 /gbdb/panTro3/panTro3.2bit +chrUn_GL395472 3876 /gbdb/panTro3/panTro3.2bit +chrX_GL393150_random 3876 /gbdb/panTro3/panTro3.2bit +chr11_GL391843_random 3875 /gbdb/panTro3/panTro3.2bit +chr1_GL389105_random 3874 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190162 3874 /gbdb/panTro3/panTro3.2bit +chrX_GL393295_random 3874 /gbdb/panTro3/panTro3.2bit +chrX_GL393374_random 3874 /gbdb/panTro3/panTro3.2bit +chr10_GL391419_random 3873 /gbdb/panTro3/panTro3.2bit +chrUn_GL394503 3873 /gbdb/panTro3/panTro3.2bit +chr6_GL390228_random 3872 /gbdb/panTro3/panTro3.2bit +chr10_GL391354_random 3871 /gbdb/panTro3/panTro3.2bit +chr8_GL390856_random 3871 /gbdb/panTro3/panTro3.2bit +chrUn_GL395303 3871 /gbdb/panTro3/panTro3.2bit +chr16_GL392331_random 3870 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158971_random 3870 /gbdb/panTro3/panTro3.2bit +chrUn_GL395801 3870 /gbdb/panTro3/panTro3.2bit +chr19_GL392879_random 3869 /gbdb/panTro3/panTro3.2bit +chrX_GL393279_random 3869 /gbdb/panTro3/panTro3.2bit +chrUn_GL394228 3868 /gbdb/panTro3/panTro3.2bit +chrUn_GL395097 3868 /gbdb/panTro3/panTro3.2bit +chr10_GL391272_random 3867 /gbdb/panTro3/panTro3.2bit +chr19_GL392825_random 3867 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL396110 3861 /gbdb/panTro3/panTro3.2bit +chr11_GL391724_random 3860 /gbdb/panTro3/panTro3.2bit +chr5_GL390053_random 3860 /gbdb/panTro3/panTro3.2bit +chr17_GL392699_random 3859 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165654_random 3858 /gbdb/panTro3/panTro3.2bit +chr19_GL392838_random 3858 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157273_random 3857 /gbdb/panTro3/panTro3.2bit +chrUn_GL394224 3856 /gbdb/panTro3/panTro3.2bit +chr5_GL390130_random 3854 /gbdb/panTro3/panTro3.2bit +chr9_GL391134_random 3854 /gbdb/panTro3/panTro3.2bit +chrUn_GL394519 3854 /gbdb/panTro3/panTro3.2bit +chrUn_GL394809 3854 /gbdb/panTro3/panTro3.2bit +chr1_GL388850_random 3853 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162643_random 3853 /gbdb/panTro3/panTro3.2bit +chr1_GL388864_random 3852 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190593 3852 /gbdb/panTro3/panTro3.2bit +chrUn_GL394337 3852 /gbdb/panTro3/panTro3.2bit +chr1_GL389252_random 3851 /gbdb/panTro3/panTro3.2bit +chrUn_GL393561 3851 /gbdb/panTro3/panTro3.2bit +chr10_GL391455_random 3850 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162738_random 3850 /gbdb/panTro3/panTro3.2bit +chr3_GL389569_random 3849 /gbdb/panTro3/panTro3.2bit +chr3_GL389611_random 3849 /gbdb/panTro3/panTro3.2bit +chr6_GL390225_random 3849 /gbdb/panTro3/panTro3.2bit +chrUn_GL394602 3849 /gbdb/panTro3/panTro3.2bit +chrUn_GL394673 3847 /gbdb/panTro3/panTro3.2bit +chrX_GL393232_random 3847 /gbdb/panTro3/panTro3.2bit +chr10_GL391462_random 3846 /gbdb/panTro3/panTro3.2bit +chr3_GL389617_random 3846 /gbdb/panTro3/panTro3.2bit +chrUn_GL394543 3846 /gbdb/panTro3/panTro3.2bit +chrUn_GL394750 3846 /gbdb/panTro3/panTro3.2bit +chrUn_GL394043 3843 /gbdb/panTro3/panTro3.2bit +chrUn_GL395236 3843 /gbdb/panTro3/panTro3.2bit +chrUn_GL395724 3843 /gbdb/panTro3/panTro3.2bit +chrUn_GL395849 3843 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152157_random 3842 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153941_random 3842 /gbdb/panTro3/panTro3.2bit +chrUn_GL396122 3842 /gbdb/panTro3/panTro3.2bit +chrUn_GL393604 3841 /gbdb/panTro3/panTro3.2bit +chrUn_GL395027 3841 /gbdb/panTro3/panTro3.2bit +chrX_GL393140_random 3841 /gbdb/panTro3/panTro3.2bit +chr2A_GL389354_random 3840 /gbdb/panTro3/panTro3.2bit +chr4_GL389977_random 3840 /gbdb/panTro3/panTro3.2bit +chrUn_GL395069 3840 /gbdb/panTro3/panTro3.2bit +chr11_GL391742_random 3839 /gbdb/panTro3/panTro3.2bit +chr19_GL392931_random 3837 /gbdb/panTro3/panTro3.2bit +chrX_GL393439_random 3836 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173432_random 3835 /gbdb/panTro3/panTro3.2bit +chrUn_GL394669 3835 /gbdb/panTro3/panTro3.2bit +chr1_GL388936_random 3834 /gbdb/panTro3/panTro3.2bit +chrUn_GL393670 3834 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169481_random 3833 /gbdb/panTro3/panTro3.2bit +chr20_GL393001_random 3833 /gbdb/panTro3/panTro3.2bit +chrUn_GL393724 3833 /gbdb/panTro3/panTro3.2bit +chrUn_GL394966 3831 /gbdb/panTro3/panTro3.2bit +chrUn_GL394911 3830 /gbdb/panTro3/panTro3.2bit +chrUn_GL394567 3829 /gbdb/panTro3/panTro3.2bit +chrUn_GL394735 3829 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186138 3828 /gbdb/panTro3/panTro3.2bit +chrUn_GL394163 3828 /gbdb/panTro3/panTro3.2bit +chrUn_GL394345 3828 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177027_random 3827 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192675 3827 /gbdb/panTro3/panTro3.2bit +chrUn_GL394992 3827 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168323_random 3826 /gbdb/panTro3/panTro3.2bit +chr1_GL389195_random 3826 /gbdb/panTro3/panTro3.2bit +chrUn_GL395026 3825 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168292_random 3824 /gbdb/panTro3/panTro3.2bit +chr8_GL390777_random 3824 /gbdb/panTro3/panTro3.2bit +chr13_GL392041_random 3823 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152951_random 3823 /gbdb/panTro3/panTro3.2bit +chrUn_GL393793 3822 /gbdb/panTro3/panTro3.2bit +chrUn_GL394284 3822 /gbdb/panTro3/panTro3.2bit +chr16_GL392329_random 3821 /gbdb/panTro3/panTro3.2bit +chr19_GL392833_random 3821 /gbdb/panTro3/panTro3.2bit +chr2A_GL389268_random 3821 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153970_random 3820 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162635_random 3820 /gbdb/panTro3/panTro3.2bit +chr8_GL390755_random 3820 /gbdb/panTro3/panTro3.2bit +chrUn_GL393798 3820 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162719_random 3819 /gbdb/panTro3/panTro3.2bit +chrUn_GL394149 3819 /gbdb/panTro3/panTro3.2bit +chrUn_GL394534 3819 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154056_random 3818 /gbdb/panTro3/panTro3.2bit +chr7_GL390704_random 3818 /gbdb/panTro3/panTro3.2bit +chrUn_GL395131 3818 /gbdb/panTro3/panTro3.2bit +chrUn_GL395345 3818 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187285 3817 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188505 3817 /gbdb/panTro3/panTro3.2bit +chrUn_GL395214 3817 /gbdb/panTro3/panTro3.2bit +chrUn_GL395268 3817 /gbdb/panTro3/panTro3.2bit +chrUn_GL395315 3817 /gbdb/panTro3/panTro3.2bit +chr19_GL392958_random 3816 /gbdb/panTro3/panTro3.2bit +chrX_GL393369_random 3816 /gbdb/panTro3/panTro3.2bit +chrUn_GL395754 3814 /gbdb/panTro3/panTro3.2bit +chr10_GL391274_random 3813 /gbdb/panTro3/panTro3.2bit +chr17_GL392687_random 3813 /gbdb/panTro3/panTro3.2bit +chrUn_GL394225 3813 /gbdb/panTro3/panTro3.2bit +chrUn_GL393947 3812 /gbdb/panTro3/panTro3.2bit +chrUn_GL396694 3812 /gbdb/panTro3/panTro3.2bit +chr10_GL391360_random 3811 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161230_random 3811 /gbdb/panTro3/panTro3.2bit +chrUn_GL396160 3811 /gbdb/panTro3/panTro3.2bit +chr10_GL391456_random 3810 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175947_random 3810 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153861_random 3810 /gbdb/panTro3/panTro3.2bit +chrUn_GL394694 3810 /gbdb/panTro3/panTro3.2bit +chr1_GL388898_random 3809 /gbdb/panTro3/panTro3.2bit +chrUn_GL393860 3809 /gbdb/panTro3/panTro3.2bit +chrUn_GL394278 3809 /gbdb/panTro3/panTro3.2bit +chrUn_GL394288 3809 /gbdb/panTro3/panTro3.2bit +chrUn_GL395016 3809 /gbdb/panTro3/panTro3.2bit +chr13_GL392035_random 3808 /gbdb/panTro3/panTro3.2bit +chr4_GL389966_random 3808 /gbdb/panTro3/panTro3.2bit +chr7_GL390501_random 3808 /gbdb/panTro3/panTro3.2bit +chrUn_GL394932 3808 /gbdb/panTro3/panTro3.2bit +chr19_GL392922_random 3807 /gbdb/panTro3/panTro3.2bit +chr3_GL389557_random 3807 /gbdb/panTro3/panTro3.2bit +chrUn_GL394239 3806 /gbdb/panTro3/panTro3.2bit +chrUn_GL395691 3806 /gbdb/panTro3/panTro3.2bit +chrUn_GL397046 3806 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161037_random 3805 /gbdb/panTro3/panTro3.2bit +chrUn_GL393884 3805 /gbdb/panTro3/panTro3.2bit +chrUn_GL394607 3805 /gbdb/panTro3/panTro3.2bit +chr1_GL388929_random 3804 /gbdb/panTro3/panTro3.2bit +chr3_GL389568_random 3804 /gbdb/panTro3/panTro3.2bit +chr1_GL389050_random 3802 /gbdb/panTro3/panTro3.2bit +chr6_GL390229_random 3802 /gbdb/panTro3/panTro3.2bit +chrUn_GL394350 3802 /gbdb/panTro3/panTro3.2bit +chrUn_GL396183 3801 /gbdb/panTro3/panTro3.2bit +chrX_GL393256_random 3800 /gbdb/panTro3/panTro3.2bit +chr12_GL391932_random 3799 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162715_random 3799 /gbdb/panTro3/panTro3.2bit +chrUn_GL394593 3799 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177790_random 3799 /gbdb/panTro3/panTro3.2bit +chrX_GL393441_random 3799 /gbdb/panTro3/panTro3.2bit +chr1_GL389181_random 3798 /gbdb/panTro3/panTro3.2bit +chrUn_GL395001 3798 /gbdb/panTro3/panTro3.2bit +chr20_GL393043_random 3797 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159011_random 3797 /gbdb/panTro3/panTro3.2bit +chrUn_GL395343 3797 /gbdb/panTro3/panTro3.2bit +chrUn_GL395478 3797 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175191_random 3796 /gbdb/panTro3/panTro3.2bit +chr1_GL388887_random 3796 /gbdb/panTro3/panTro3.2bit +chr2A_GL389282_random 3796 /gbdb/panTro3/panTro3.2bit +chrUn_GL394518 3796 /gbdb/panTro3/panTro3.2bit +chr10_GL391265_random 3795 /gbdb/panTro3/panTro3.2bit +chrUn_GL394482 3795 /gbdb/panTro3/panTro3.2bit +chrUn_GL395270 3794 /gbdb/panTro3/panTro3.2bit +chr6_GL390208_random 3793 /gbdb/panTro3/panTro3.2bit +chrUn_GL394652 3793 /gbdb/panTro3/panTro3.2bit +chrUn_GL395785 3793 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189257 3792 /gbdb/panTro3/panTro3.2bit +chrUn_GL394242 3792 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186574 3791 /gbdb/panTro3/panTro3.2bit +chrUn_GL394126 3791 /gbdb/panTro3/panTro3.2bit +chr12_GL391931_random 3789 /gbdb/panTro3/panTro3.2bit +chr6_GL390263_random 3789 /gbdb/panTro3/panTro3.2bit +chr9_GL390945_random 3789 /gbdb/panTro3/panTro3.2bit +chrUn_GL394133 3789 /gbdb/panTro3/panTro3.2bit +chrUn_GL394999 3788 /gbdb/panTro3/panTro3.2bit +chrUn_GL395382 3788 /gbdb/panTro3/panTro3.2bit +chrX_GL393378_random 3788 /gbdb/panTro3/panTro3.2bit +chr4_GL389752_random 3786 /gbdb/panTro3/panTro3.2bit +chr5_GL390052_random 3785 /gbdb/panTro3/panTro3.2bit +chrUn_GL395547 3785 /gbdb/panTro3/panTro3.2bit +chr4_GL389775_random 3784 /gbdb/panTro3/panTro3.2bit +chr7_GL390675_random 3784 /gbdb/panTro3/panTro3.2bit +chrUn_GL395616 3784 /gbdb/panTro3/panTro3.2bit +chrX_GL393130_random 3784 /gbdb/panTro3/panTro3.2bit +chrX_GL393391_random 3784 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159146_random 3782 /gbdb/panTro3/panTro3.2bit +chr16_GL392554_random 3781 /gbdb/panTro3/panTro3.2bit +chr17_GL392693_random 3781 /gbdb/panTro3/panTro3.2bit +chrUn_GL395102 3781 /gbdb/panTro3/panTro3.2bit +chrUn_GL395471 3781 /gbdb/panTro3/panTro3.2bit +chr10_GL391381_random 3780 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172002_random 3780 /gbdb/panTro3/panTro3.2bit +chr17_GL392712_random 3780 /gbdb/panTro3/panTro3.2bit +chrUn_GL396570 3780 /gbdb/panTro3/panTro3.2bit +chrUn_GL393644 3779 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150743_random 3777 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157205_random 3777 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158885_random 3777 /gbdb/panTro3/panTro3.2bit +chr8_GL390869_random 3777 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188336 3777 /gbdb/panTro3/panTro3.2bit +chr16_GL392377_random 3776 /gbdb/panTro3/panTro3.2bit +chr19_GL392839_random 3776 /gbdb/panTro3/panTro3.2bit +chr3_GL389542_random 3776 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr13_GL392031_random 3760 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158970_random 3760 /gbdb/panTro3/panTro3.2bit +chrUn_GL394768 3760 /gbdb/panTro3/panTro3.2bit +chrX_GL393276_random 3760 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162684_random 3759 /gbdb/panTro3/panTro3.2bit +chrUn_GL394823 3759 /gbdb/panTro3/panTro3.2bit +chrUn_GL394733 3758 /gbdb/panTro3/panTro3.2bit +chr22_GL393085_random 3757 /gbdb/panTro3/panTro3.2bit +chr5_GL390114_random 3757 /gbdb/panTro3/panTro3.2bit +chrUn_GL394290 3756 /gbdb/panTro3/panTro3.2bit +chrUn_GL394431 3756 /gbdb/panTro3/panTro3.2bit +chrUn_GL395279 3756 /gbdb/panTro3/panTro3.2bit +chrUn_GL394791 3755 /gbdb/panTro3/panTro3.2bit +chrUn_GL394875 3755 /gbdb/panTro3/panTro3.2bit +chrUn_GL395156 3754 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172018_random 3753 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169259_random 3751 /gbdb/panTro3/panTro3.2bit +chrUn_GL394118 3751 /gbdb/panTro3/panTro3.2bit +chrUn_GL394492 3751 /gbdb/panTro3/panTro3.2bit +chrUn_GL394922 3751 /gbdb/panTro3/panTro3.2bit +chrUn_GL395591 3751 /gbdb/panTro3/panTro3.2bit +chrUn_GL395959 3751 /gbdb/panTro3/panTro3.2bit +chrX_GL393155_random 3750 /gbdb/panTro3/panTro3.2bit +chrUn_GL395037 3749 /gbdb/panTro3/panTro3.2bit +chr11_GL391819_random 3748 /gbdb/panTro3/panTro3.2bit +chrUn_GL395142 3746 /gbdb/panTro3/panTro3.2bit +chrUn_GL395297 3746 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165648_random 3743 /gbdb/panTro3/panTro3.2bit +chr16_GL392557_random 3743 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158899_random 3743 /gbdb/panTro3/panTro3.2bit +chr9_GL390997_random 3743 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175994_random 3742 /gbdb/panTro3/panTro3.2bit +chr5_GL390057_random 3742 /gbdb/panTro3/panTro3.2bit +chr8_GL390825_random 3742 /gbdb/panTro3/panTro3.2bit +chrUn_GL396171 3742 /gbdb/panTro3/panTro3.2bit +chrX_GL393174_random 3742 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177050_random 3740 /gbdb/panTro3/panTro3.2bit +chrUn_GL395559 3740 /gbdb/panTro3/panTro3.2bit +chrUn_GL394957 3739 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173387_random 3738 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152164_random 3738 /gbdb/panTro3/panTro3.2bit +chr16_GL392322_random 3737 /gbdb/panTro3/panTro3.2bit +chr19_GL392858_random 3737 /gbdb/panTro3/panTro3.2bit +chr1_GL388872_random 3737 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153885_random 3737 /gbdb/panTro3/panTro3.2bit +chr6_GL390260_random 3737 /gbdb/panTro3/panTro3.2bit +chr11_GL391754_random 3736 /gbdb/panTro3/panTro3.2bit +chr1_GL388928_random 3736 /gbdb/panTro3/panTro3.2bit +chr16_GL392556_random 3734 /gbdb/panTro3/panTro3.2bit +chr1_GL389052_random 3734 /gbdb/panTro3/panTro3.2bit +chr10_GL391401_random 3733 /gbdb/panTro3/panTro3.2bit +chr6_GL390226_random 3733 /gbdb/panTro3/panTro3.2bit +chr9_GL391075_random 3733 /gbdb/panTro3/panTro3.2bit +chrX_GL393255_random 3733 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165499_random 3732 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157196_random 3732 /gbdb/panTro3/panTro3.2bit +chrUn_GL394744 3732 /gbdb/panTro3/panTro3.2bit +chrUn_GL394862 3731 /gbdb/panTro3/panTro3.2bit +chrX_GL393129_random 3731 /gbdb/panTro3/panTro3.2bit +chr10_GL391311_random 3728 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169292_random 3728 /gbdb/panTro3/panTro3.2bit +chr16_GL392562_random 3728 /gbdb/panTro3/panTro3.2bit +chr1_GL389214_random 3728 /gbdb/panTro3/panTro3.2bit +chr16_GL392349_random 3726 /gbdb/panTro3/panTro3.2bit +chr5_GL390071_random 3726 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159010_random 3726 /gbdb/panTro3/panTro3.2bit +chrX_GL393401_random 3726 /gbdb/panTro3/panTro3.2bit +chr12_GL391924_random 3725 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176003_random 3725 /gbdb/panTro3/panTro3.2bit +chr8_GL390875_random 3725 /gbdb/panTro3/panTro3.2bit +chrUn_GL395019 3725 /gbdb/panTro3/panTro3.2bit +chrX_GL393297_random 3725 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175205_random 3724 /gbdb/panTro3/panTro3.2bit +chrUn_GL395620 3724 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr2B_GL389424_random 3712 /gbdb/panTro3/panTro3.2bit +chr5_GL390040_random 3712 /gbdb/panTro3/panTro3.2bit +chrUn_GL394530 3712 /gbdb/panTro3/panTro3.2bit +chr20_GL393002_random 3711 /gbdb/panTro3/panTro3.2bit +chr20_GL393042_random 3711 /gbdb/panTro3/panTro3.2bit +chr2A_GL389298_random 3711 /gbdb/panTro3/panTro3.2bit +chr6_GL390230_random 3711 /gbdb/panTro3/panTro3.2bit +chrUn_GL394222 3711 /gbdb/panTro3/panTro3.2bit +chrUn_GL394671 3711 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150505_random 3710 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188910 3710 /gbdb/panTro3/panTro3.2bit +chrUn_GL394831 3709 /gbdb/panTro3/panTro3.2bit +chrUn_GL395549 3709 /gbdb/panTro3/panTro3.2bit +chr11_GL391818_random 3708 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187684 3708 /gbdb/panTro3/panTro3.2bit +chrUn_GL394429 3708 /gbdb/panTro3/panTro3.2bit +chrUn_GL396145 3708 /gbdb/panTro3/panTro3.2bit +chrUn_GL394638 3707 /gbdb/panTro3/panTro3.2bit +chrUn_GL396885 3706 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174702_random 3705 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188510 3705 /gbdb/panTro3/panTro3.2bit +chrUn_GL394935 3705 /gbdb/panTro3/panTro3.2bit +chrUn_GL395139 3703 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153903_random 3702 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158954_random 3702 /gbdb/panTro3/panTro3.2bit +chrUn_GL395531 3702 /gbdb/panTro3/panTro3.2bit +chr11_GL391759_random 3701 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187967 3701 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190104 3701 /gbdb/panTro3/panTro3.2bit +chrUn_GL394253 3701 /gbdb/panTro3/panTro3.2bit +chrUn_GL394742 3698 /gbdb/panTro3/panTro3.2bit +chrUn_GL396737 3698 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169356_random 3697 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188402 3697 /gbdb/panTro3/panTro3.2bit +chrUn_GL395291 3696 /gbdb/panTro3/panTro3.2bit +chrUn_GL396899 3696 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169280_random 3695 /gbdb/panTro3/panTro3.2bit +chrUn_GL394343 3695 /gbdb/panTro3/panTro3.2bit +chrUn_GL394948 3695 /gbdb/panTro3/panTro3.2bit +chrUn_GL394427 3694 /gbdb/panTro3/panTro3.2bit +chrUn_GL395875 3694 /gbdb/panTro3/panTro3.2bit +chr16_GL392560_random 3693 /gbdb/panTro3/panTro3.2bit +chr3_GL389558_random 3693 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189608 3692 /gbdb/panTro3/panTro3.2bit +chrX_GL393179_random 3692 /gbdb/panTro3/panTro3.2bit +chr1_GL388919_random 3691 /gbdb/panTro3/panTro3.2bit +chr1_GL388921_random 3691 /gbdb/panTro3/panTro3.2bit +chrUn_GL396541 3690 /gbdb/panTro3/panTro3.2bit +chr13_GL392038_random 3689 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150407_random 3687 /gbdb/panTro3/panTro3.2bit +chr6_GL390182_random 3686 /gbdb/panTro3/panTro3.2bit +chrUn_GL395148 3686 /gbdb/panTro3/panTro3.2bit +chrUn_GL395494 3686 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150584_random 3685 /gbdb/panTro3/panTro3.2bit +chrUn_GL394902 3684 /gbdb/panTro3/panTro3.2bit +chrUn_GL395057 3684 /gbdb/panTro3/panTro3.2bit +chrUn_GL395963 3684 /gbdb/panTro3/panTro3.2bit +chr3_GL389572_random 3683 /gbdb/panTro3/panTro3.2bit +chr5_GL390007_random 3683 /gbdb/panTro3/panTro3.2bit +chrUn_GL394378 3683 /gbdb/panTro3/panTro3.2bit +chrUn_GL394666 3683 /gbdb/panTro3/panTro3.2bit +chrUn_GL395129 3683 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174651_random 3682 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152124_random 3682 /gbdb/panTro3/panTro3.2bit +chrUn_GL393564 3682 /gbdb/panTro3/panTro3.2bit +chrUn_GL396955 3682 /gbdb/panTro3/panTro3.2bit +chr10_GL391391_random 3681 /gbdb/panTro3/panTro3.2bit +chrUn_GL396758 3681 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174610_random 3680 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152915_random 3680 /gbdb/panTro3/panTro3.2bit +chrUn_GL394815 3679 /gbdb/panTro3/panTro3.2bit +chr19_GL392967_random 3678 /gbdb/panTro3/panTro3.2bit +chrUn_GL396810 3678 /gbdb/panTro3/panTro3.2bit +chrUn_GL394220 3676 /gbdb/panTro3/panTro3.2bit +chrUn_GL394244 3676 /gbdb/panTro3/panTro3.2bit +chrX_GL393332_random 3676 /gbdb/panTro3/panTro3.2bit +chr5_GL390032_random 3675 /gbdb/panTro3/panTro3.2bit +chr6_GL390291_random 3675 /gbdb/panTro3/panTro3.2bit +chrX_GL393158_random 3674 /gbdb/panTro3/panTro3.2bit +chr22_GL393052_random 3673 /gbdb/panTro3/panTro3.2bit +chr2B_GL389437_random 3673 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150607_random 3672 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187224 3672 /gbdb/panTro3/panTro3.2bit +chr11_GL391763_random 3671 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172062_random 3671 /gbdb/panTro3/panTro3.2bit +chrUn_GL395701 3671 /gbdb/panTro3/panTro3.2bit +chrUn_GL394456 3670 /gbdb/panTro3/panTro3.2bit +chr6_GL390237_random 3669 /gbdb/panTro3/panTro3.2bit +chrUn_GL394595 3669 /gbdb/panTro3/panTro3.2bit +chr10_GL391388_random 3668 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150533_random 3668 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153935_random 3666 /gbdb/panTro3/panTro3.2bit +chrUn_GL394426 3666 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177748_random 3666 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_GL391611_random 3642 /gbdb/panTro3/panTro3.2bit +chr12_GL391959_random 3642 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158999_random 3642 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189599 3642 /gbdb/panTro3/panTro3.2bit +chrUn_GL394237 3642 /gbdb/panTro3/panTro3.2bit +chrUn_GL395585 3640 /gbdb/panTro3/panTro3.2bit +chrUn_GL396382 3640 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175358_random 3639 /gbdb/panTro3/panTro3.2bit +chr19_GL392874_random 3639 /gbdb/panTro3/panTro3.2bit +chrUn_GL395346 3639 /gbdb/panTro3/panTro3.2bit +chrX_GL393132_random 3639 /gbdb/panTro3/panTro3.2bit +chrX_GL393149_random 3639 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169303_random 3637 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171342_random 3637 /gbdb/panTro3/panTro3.2bit +chr9_GL391039_random 3637 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190426 3637 /gbdb/panTro3/panTro3.2bit +chrUn_GL395032 3636 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165775_random 3635 /gbdb/panTro3/panTro3.2bit 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3628 /gbdb/panTro3/panTro3.2bit +chrX_GL393420_random 3628 /gbdb/panTro3/panTro3.2bit +chrUn_GL395171 3627 /gbdb/panTro3/panTro3.2bit +chrUn_GL395570 3627 /gbdb/panTro3/panTro3.2bit +chrUn_GL394476 3626 /gbdb/panTro3/panTro3.2bit +chrX_GL393327_random 3625 /gbdb/panTro3/panTro3.2bit +chr20_GL393037_random 3624 /gbdb/panTro3/panTro3.2bit +chrUn_GL394856 3624 /gbdb/panTro3/panTro3.2bit +chrUn_GL396551 3624 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175244_random 3623 /gbdb/panTro3/panTro3.2bit +chrUn_GL395925 3623 /gbdb/panTro3/panTro3.2bit +chr5_GL390067_random 3622 /gbdb/panTro3/panTro3.2bit +chr16_GL392372_random 3621 /gbdb/panTro3/panTro3.2bit +chr17_GL392688_random 3621 /gbdb/panTro3/panTro3.2bit +chrUn_GL397009 3621 /gbdb/panTro3/panTro3.2bit +chr15_GL392272_random 3620 /gbdb/panTro3/panTro3.2bit +chr16_GL392345_random 3620 /gbdb/panTro3/panTro3.2bit +chr4_GL389729_random 3618 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190014 3618 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177697_random 3618 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171343_random 3617 /gbdb/panTro3/panTro3.2bit +chrUn_GL393578 3617 /gbdb/panTro3/panTro3.2bit +chrUn_GL396361 3617 /gbdb/panTro3/panTro3.2bit +chr14_GL392123_random 3616 /gbdb/panTro3/panTro3.2bit +chrUn_GL394629 3616 /gbdb/panTro3/panTro3.2bit +chr19_GL392876_random 3615 /gbdb/panTro3/panTro3.2bit +chr19_GL392951_random 3615 /gbdb/panTro3/panTro3.2bit +chrX_GL393395_random 3615 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175229_random 3614 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188357 3614 /gbdb/panTro3/panTro3.2bit +chrX_GL393157_random 3614 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173637_random 3613 /gbdb/panTro3/panTro3.2bit +chr2B_GL389429_random 3613 /gbdb/panTro3/panTro3.2bit +chr1_GL388873_random 3612 /gbdb/panTro3/panTro3.2bit +chr12_GL391994_random 3611 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188121 3611 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172065_random 3610 /gbdb/panTro3/panTro3.2bit +chrUn_GL395137 3610 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL395078 3586 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173517_random 3585 /gbdb/panTro3/panTro3.2bit +chrUn_GL394296 3584 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159287_random 3583 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186891 3583 /gbdb/panTro3/panTro3.2bit +chr19_GL392926_random 3582 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157268_random 3581 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188839 3581 /gbdb/panTro3/panTro3.2bit +chrUn_GL395223 3581 /gbdb/panTro3/panTro3.2bit +chr2A_GL389333_random 3580 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162710_random 3580 /gbdb/panTro3/panTro3.2bit +chrUn_GL395402 3580 /gbdb/panTro3/panTro3.2bit +chr19_GL392845_random 3579 /gbdb/panTro3/panTro3.2bit +chr6_GL390340_random 3579 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187878 3579 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187936 3579 /gbdb/panTro3/panTro3.2bit +chrUn_GL396749 3579 /gbdb/panTro3/panTro3.2bit +chrX_GL393296_random 3578 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394640 3565 /gbdb/panTro3/panTro3.2bit +chrUn_GL394679 3565 /gbdb/panTro3/panTro3.2bit +chr19_GL392872_random 3564 /gbdb/panTro3/panTro3.2bit +chrUn_GL395526 3563 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168337_random 3562 /gbdb/panTro3/panTro3.2bit +chr17_GL392729_random 3561 /gbdb/panTro3/panTro3.2bit +chrUn_GL394535 3561 /gbdb/panTro3/panTro3.2bit +chrX_GL393367_random 3561 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168572_random 3560 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150531_random 3559 /gbdb/panTro3/panTro3.2bit +chr6_GL390345_random 3559 /gbdb/panTro3/panTro3.2bit +chrUn_GL395626 3558 /gbdb/panTro3/panTro3.2bit +chrUn_GL396887 3558 /gbdb/panTro3/panTro3.2bit +chr11_GL391795_random 3556 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150441_random 3555 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153989_random 3555 /gbdb/panTro3/panTro3.2bit +chrUn_GL396066 3554 /gbdb/panTro3/panTro3.2bit +chrUn_GL394113 3552 /gbdb/panTro3/panTro3.2bit +chrUn_GL395000 3552 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150637_random 3551 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156105_random 3550 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188296 3550 /gbdb/panTro3/panTro3.2bit +chrUn_GL395125 3550 /gbdb/panTro3/panTro3.2bit +chrUn_GL395197 3550 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188676 3549 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150813_random 3548 /gbdb/panTro3/panTro3.2bit +chrUn_GL393929 3548 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165638_random 3547 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177096_random 3547 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162704_random 3547 /gbdb/panTro3/panTro3.2bit +chr9_GL390974_random 3546 /gbdb/panTro3/panTro3.2bit +chrUn_GL395203 3546 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189862 3545 /gbdb/panTro3/panTro3.2bit +chr15_GL392206_random 3544 /gbdb/panTro3/panTro3.2bit +chrUn_GL393726 3544 /gbdb/panTro3/panTro3.2bit +chrUn_GL394281 3544 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150420_random 3543 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr18_GL392781_random 3525 /gbdb/panTro3/panTro3.2bit +chrUn_GL394340 3525 /gbdb/panTro3/panTro3.2bit +chr12_GL391922_random 3524 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153931_random 3524 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187110 3523 /gbdb/panTro3/panTro3.2bit +chrX_GL393147_random 3522 /gbdb/panTro3/panTro3.2bit +chrX_GL393151_random 3522 /gbdb/panTro3/panTro3.2bit +chrUn_GL393913 3521 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155900_random 3520 /gbdb/panTro3/panTro3.2bit +chr7_GL390481_random 3520 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189352 3520 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189163 3518 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176621_random 3517 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152088_random 3516 /gbdb/panTro3/panTro3.2bit +chrUn_GL393596 3516 /gbdb/panTro3/panTro3.2bit +chrUn_GL395508 3516 /gbdb/panTro3/panTro3.2bit +chrX_GL393188_random 3516 /gbdb/panTro3/panTro3.2bit +chrX_GL393354_random 3516 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr11_GL391809_random 3504 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172075_random 3504 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176552_random 3504 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152956_random 3504 /gbdb/panTro3/panTro3.2bit +chrUn_GL395119 3504 /gbdb/panTro3/panTro3.2bit +chrUn_GL395600 3504 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162751_random 3503 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172059_random 3501 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164686_random 3501 /gbdb/panTro3/panTro3.2bit +chrX_GL393139_random 3501 /gbdb/panTro3/panTro3.2bit +chr12_GL391871_random 3500 /gbdb/panTro3/panTro3.2bit +chrX_GL393144_random 3500 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150636_random 3499 /gbdb/panTro3/panTro3.2bit +chr22_GL393100_random 3499 /gbdb/panTro3/panTro3.2bit +chrUn_GL394041 3498 /gbdb/panTro3/panTro3.2bit +chrUn_GL394868 3498 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152197_random 3497 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189196 3497 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150691_random 3496 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157370_random 3496 /gbdb/panTro3/panTro3.2bit +chrX_GL393263_random 3496 /gbdb/panTro3/panTro3.2bit +chr3_GL389563_random 3495 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162714_random 3495 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191251 3495 /gbdb/panTro3/panTro3.2bit +chrUn_GL394904 3495 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162609_random 3494 /gbdb/panTro3/panTro3.2bit +chrUn_GL395920 3494 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153036_random 3492 /gbdb/panTro3/panTro3.2bit +chrUn_GL394452 3492 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171259_random 3490 /gbdb/panTro3/panTro3.2bit +chrUn_GL395489 3490 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152170_random 3489 /gbdb/panTro3/panTro3.2bit +chrUn_GL396244 3489 /gbdb/panTro3/panTro3.2bit +chrUn_GL396599 3489 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188169 3487 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189158 3486 /gbdb/panTro3/panTro3.2bit 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3474 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168309_random 3473 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159027_random 3473 /gbdb/panTro3/panTro3.2bit +chr12_GL391968_random 3472 /gbdb/panTro3/panTro3.2bit +chrUn_GL394210 3472 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162739_random 3471 /gbdb/panTro3/panTro3.2bit +chr9_GL390990_random 3471 /gbdb/panTro3/panTro3.2bit +chrUn_GL396025 3471 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155842_random 3470 /gbdb/panTro3/panTro3.2bit +chrUn_GL394135 3470 /gbdb/panTro3/panTro3.2bit +chrUn_GL395642 3470 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168378_random 3469 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150655_random 3469 /gbdb/panTro3/panTro3.2bit +chrUn_GL396002 3469 /gbdb/panTro3/panTro3.2bit +chr4_GL389754_random 3468 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169256_random 3466 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150413_random 3465 /gbdb/panTro3/panTro3.2bit +chr3_GL389541_random 3465 /gbdb/panTro3/panTro3.2bit +chrUn_GL395147 3465 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154134_random 3464 /gbdb/panTro3/panTro3.2bit +chr4_GL389786_random 3464 /gbdb/panTro3/panTro3.2bit +chr5_GL390028_random 3464 /gbdb/panTro3/panTro3.2bit +chr17_GL392616_random 3463 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177047_random 3463 /gbdb/panTro3/panTro3.2bit +chrUn_GL394701 3462 /gbdb/panTro3/panTro3.2bit +chr17_GL392681_random 3461 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162856_random 3461 /gbdb/panTro3/panTro3.2bit +chrUn_GL395295 3461 /gbdb/panTro3/panTro3.2bit +chr10_GL391403_random 3459 /gbdb/panTro3/panTro3.2bit +chrUn_GL393969 3459 /gbdb/panTro3/panTro3.2bit +chr5_GL390035_random 3458 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173464_random 3457 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152982_random 3457 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159077_random 3457 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169271_random 3456 /gbdb/panTro3/panTro3.2bit +chr6_GL390264_random 3456 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162693_random 3456 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187943 3456 /gbdb/panTro3/panTro3.2bit +chrUn_GL394489 3454 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176556_random 3453 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164601_random 3453 /gbdb/panTro3/panTro3.2bit +chrUn_GL396290 3453 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157339_random 3452 /gbdb/panTro3/panTro3.2bit +chr5_GL390103_random 3452 /gbdb/panTro3/panTro3.2bit +chrUn_GL394976 3452 /gbdb/panTro3/panTro3.2bit +chrUn_GL395212 3452 /gbdb/panTro3/panTro3.2bit +chrX_GL393160_random 3452 /gbdb/panTro3/panTro3.2bit +chrUn_GL394435 3451 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171235_random 3450 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162757_random 3450 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187758 3450 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174658_random 3449 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162794_random 3449 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187421 3449 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191057 3449 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr1_AACZ03150515_random 3416 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153123_random 3416 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191668 3416 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165859_random 3415 /gbdb/panTro3/panTro3.2bit +chrUn_GL393837 3414 /gbdb/panTro3/panTro3.2bit +chrUn_GL394972 3414 /gbdb/panTro3/panTro3.2bit +chrUn_GL394981 3413 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157723_random 3411 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177036_random 3410 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187180 3410 /gbdb/panTro3/panTro3.2bit +chr4_GL389987_random 3409 /gbdb/panTro3/panTro3.2bit +chrUn_GL393555 3409 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177848_random 3409 /gbdb/panTro3/panTro3.2bit +chr7_GL390511_random 3408 /gbdb/panTro3/panTro3.2bit +chr10_GL391427_random 3406 /gbdb/panTro3/panTro3.2bit +chrUn_GL394320 3405 /gbdb/panTro3/panTro3.2bit +chrUn_GL395172 3405 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157492_random 3404 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr6_GL390274_random 3395 /gbdb/panTro3/panTro3.2bit +chrUn_GL395898 3395 /gbdb/panTro3/panTro3.2bit +chrUn_GL394846 3394 /gbdb/panTro3/panTro3.2bit +chr6_GL390239_random 3393 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162613_random 3393 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189351 3393 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165718_random 3391 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190087 3391 /gbdb/panTro3/panTro3.2bit +chr12_GL391926_random 3390 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153912_random 3389 /gbdb/panTro3/panTro3.2bit +chrUn_GL394553 3389 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165803_random 3388 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157327_random 3388 /gbdb/panTro3/panTro3.2bit +chrUn_GL394040 3388 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152141_random 3387 /gbdb/panTro3/panTro3.2bit +chrUn_GL395902 3387 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169296_random 3385 /gbdb/panTro3/panTro3.2bit +chrUn_GL396200 3385 /gbdb/panTro3/panTro3.2bit 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3349 /gbdb/panTro3/panTro3.2bit +chrUn_GL395328 3349 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150664_random 3348 /gbdb/panTro3/panTro3.2bit +chr1_GL389114_random 3348 /gbdb/panTro3/panTro3.2bit +chrUn_GL395322 3348 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150681_random 3347 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159081_random 3347 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188903 3347 /gbdb/panTro3/panTro3.2bit +chr19_GL392886_random 3346 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153901_random 3346 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162628_random 3346 /gbdb/panTro3/panTro3.2bit +chrUn_GL395077 3346 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169530_random 3345 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157270_random 3345 /gbdb/panTro3/panTro3.2bit +chrUn_GL395116 3345 /gbdb/panTro3/panTro3.2bit +chrUn_GL395837 3344 /gbdb/panTro3/panTro3.2bit +chr8_GL390904_random 3343 /gbdb/panTro3/panTro3.2bit +chrUn_GL395076 3343 /gbdb/panTro3/panTro3.2bit +chrUn_GL396659 3342 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr15_GL392253_random 3320 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174531_random 3320 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191034 3319 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155916_random 3317 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189453 3317 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169451_random 3316 /gbdb/panTro3/panTro3.2bit +chrUn_GL394758 3315 /gbdb/panTro3/panTro3.2bit +chr10_GL391548_random 3314 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153049_random 3314 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153966_random 3312 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158933_random 3312 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162724_random 3312 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169193_random 3311 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165633_random 3310 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165894_random 3310 /gbdb/panTro3/panTro3.2bit +chr10_GL391398_random 3310 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157324_random 3310 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr5_AACZ03157279_random 3291 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162633_random 3291 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162748_random 3291 /gbdb/panTro3/panTro3.2bit +chrUn_GL395512 3291 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157417_random 3290 /gbdb/panTro3/panTro3.2bit +chr5_GL390056_random 3290 /gbdb/panTro3/panTro3.2bit +chr8_GL390912_random 3290 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189360 3290 /gbdb/panTro3/panTro3.2bit +chrUn_GL394110 3290 /gbdb/panTro3/panTro3.2bit +chr17_GL392624_random 3289 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159173_random 3289 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190112 3289 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162641_random 3287 /gbdb/panTro3/panTro3.2bit +chrUn_GL395136 3287 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175929_random 3285 /gbdb/panTro3/panTro3.2bit +chr2A_GL389278_random 3285 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170603_random 3284 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188384 3284 /gbdb/panTro3/panTro3.2bit +chrUn_GL396219 3284 /gbdb/panTro3/panTro3.2bit +chrUn_GL396695 3283 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150554_random 3281 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157322_random 3281 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192011 3281 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168562_random 3280 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168283_random 3279 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169338_random 3278 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170525_random 3277 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175201_random 3276 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190486 3276 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175272_random 3275 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176130_random 3273 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187946 3272 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156076_random 3270 /gbdb/panTro3/panTro3.2bit +chrUn_GL395068 3270 /gbdb/panTro3/panTro3.2bit +chr19_GL392830_random 3269 /gbdb/panTro3/panTro3.2bit +chrUn_GL396257 3267 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168441_random 3266 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164658_random 3265 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168438_random 3264 /gbdb/panTro3/panTro3.2bit +chr19_GL392853_random 3264 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152230_random 3264 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162825_random 3262 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187990 3262 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165694_random 3261 /gbdb/panTro3/panTro3.2bit +chrUn_GL396684 3261 /gbdb/panTro3/panTro3.2bit +chrUn_GL394419 3259 /gbdb/panTro3/panTro3.2bit +chrUn_GL393819 3258 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163064_random 3257 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173378_random 3255 /gbdb/panTro3/panTro3.2bit +chr4_GL389694_random 3255 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187115 3255 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165669_random 3253 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157582_random 3252 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174529_random 3251 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190490 3250 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171304_random 3249 /gbdb/panTro3/panTro3.2bit +chr9_GL391235_random 3249 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186880 3249 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175968_random 3248 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155993_random 3248 /gbdb/panTro3/panTro3.2bit +chrUn_GL395066 3247 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171283_random 3246 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156013_random 3246 /gbdb/panTro3/panTro3.2bit +chrUn_GL395354 3245 /gbdb/panTro3/panTro3.2bit +chrUn_GL395538 3244 /gbdb/panTro3/panTro3.2bit +chrUn_GL395100 3243 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186803 3239 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162873_random 3238 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164636_random 3238 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152996_random 3236 /gbdb/panTro3/panTro3.2bit +chrUn_GL395093 3235 /gbdb/panTro3/panTro3.2bit +chrUn_GL395290 3235 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_AACZ03164791_random 3223 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175249_random 3222 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188160 3221 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190355 3221 /gbdb/panTro3/panTro3.2bit +chr6_GL390277_random 3220 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189556 3220 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150471_random 3219 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162551_random 3219 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189962 3219 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190171 3216 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152175_random 3214 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158937_random 3213 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165843_random 3212 /gbdb/panTro3/panTro3.2bit +chrUn_GL397042 3212 /gbdb/panTro3/panTro3.2bit +chrUn_GL394967 3211 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171203_random 3209 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176053_random 3209 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159494_random 3209 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/gbdb/panTro3/panTro3.2bit +chr8_AACZ03162624_random 3185 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187896 3185 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155946_random 3184 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188999 3184 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186881 3183 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173600_random 3181 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157212_random 3181 /gbdb/panTro3/panTro3.2bit +chrUn_GL394747 3181 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173383_random 3180 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156061_random 3180 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188275 3180 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177059_random 3178 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187947 3178 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153222_random 3177 /gbdb/panTro3/panTro3.2bit +chrX_GL393239_random 3177 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159345_random 3176 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168516_random 3174 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173801_random 3174 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155894_random 3174 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03171994_random 3173 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190625 3173 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155909_random 3172 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174546_random 3171 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190388 3171 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175269_random 3168 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159427_random 3168 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161282_random 3168 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188860 3165 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153010_random 3164 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171208_random 3163 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171272_random 3163 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191501 3162 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155988_random 3161 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165848_random 3160 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150633_random 3160 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr11_AACZ03168466_random 3146 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169398_random 3146 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176620_random 3145 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156327_random 3145 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191392 3145 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165981_random 3144 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169431_random 3144 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164841_random 3144 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188554 3143 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165844_random 3142 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175180_random 3142 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155825_random 3141 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154053_random 3140 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156130_random 3140 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176531_random 3139 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189367 3138 /gbdb/panTro3/panTro3.2bit +chr11_GL391744_random 3136 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr6_AACZ03159978_random 3129 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152189_random 3128 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189622 3128 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188445 3127 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173493_random 3126 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157729_random 3126 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187138 3126 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165849_random 3125 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150686_random 3124 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171249_random 3122 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171316_random 3122 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189708 3122 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153068_random 3120 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154061_random 3120 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159182_random 3120 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152972_random 3119 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154029_random 3119 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189000 3108 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159433_random 3107 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191599 3107 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159096_random 3106 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151132_random 3105 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164543_random 3105 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190565 3105 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189935 3102 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190559 3102 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168351_random 3101 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169337_random 3101 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165935_random 3100 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150411_random 3099 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177095_random 3099 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189760 3099 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172082_random 3097 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157349_random 3097 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_AACZ03164591_random 3006 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150550_random 3005 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153911_random 3005 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172084_random 3004 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157341_random 3004 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164763_random 3004 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174476_random 3003 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157554_random 3003 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188039 3003 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190186 3003 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170556_random 3002 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162810_random 3002 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188137 3002 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169283_random 3001 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189275 3001 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150665_random 3000 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151323_random 3000 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr12_AACZ03169603_random 2988 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168377_random 2987 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168395_random 2987 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164632_random 2987 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156011_random 2986 /gbdb/panTro3/panTro3.2bit +chrUn_GL394169 2984 /gbdb/panTro3/panTro3.2bit +chr19_GL392901_random 2983 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164759_random 2983 /gbdb/panTro3/panTro3.2bit +chrUn_GL395095 2983 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168371_random 2982 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155990_random 2982 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154498_random 2981 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159775_random 2981 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164648_random 2981 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189212 2981 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169409_random 2980 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155753_random 2980 /gbdb/panTro3/panTro3.2bit 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2972 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162915_random 2972 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153051_random 2971 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188838 2971 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189826 2971 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157446_random 2970 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189241 2970 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172105_random 2969 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171305_random 2968 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155913_random 2968 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187602 2968 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150610_random 2967 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150703_random 2964 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168326_random 2963 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189386 2963 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165950_random 2962 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154074_random 2962 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150872_random 2961 /gbdb/panTro3/panTro3.2bit 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2939 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165789_random 2938 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155885_random 2938 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157316_random 2938 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190183 2938 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152105_random 2937 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154089_random 2937 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189217 2937 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170548_random 2936 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175346_random 2936 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177881_random 2936 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159116_random 2935 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175209_random 2934 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189511 2934 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191737 2934 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170517_random 2933 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175248_random 2933 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190478 2933 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr1_AACZ03150510_random 2923 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190521 2923 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172151_random 2922 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169532_random 2921 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150599_random 2921 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154043_random 2921 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159013_random 2921 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189248 2921 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175465_random 2920 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150578_random 2920 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156149_random 2920 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188902 2920 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157256_random 2919 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159723_random 2917 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152443_random 2914 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188695 2914 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159075_random 2913 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr14_AACZ03171236_random 2907 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150597_random 2907 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164811_random 2907 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162809_random 2906 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188325 2906 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155945_random 2905 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162647_random 2904 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171210_random 2903 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156182_random 2903 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188537 2903 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169293_random 2902 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150647_random 2901 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188915 2901 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190374 2899 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165766_random 2897 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150994_random 2897 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165729_random 2896 /gbdb/panTro3/panTro3.2bit 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2886 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188601 2886 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173447_random 2885 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170462_random 2884 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157345_random 2883 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169371_random 2882 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172226_random 2882 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162942_random 2882 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162968_random 2882 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153092_random 2881 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162843_random 2880 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187780 2880 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189442 2880 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152123_random 2879 /gbdb/panTro3/panTro3.2bit +chr4_GL389902_random 2879 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188565 2879 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157500_random 2878 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162900_random 2878 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189372 2807 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159487_random 2806 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172315_random 2805 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154152_random 2805 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191411 2805 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150948_random 2804 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157532_random 2804 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165079_random 2804 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191649 2804 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173774_random 2803 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175233_random 2802 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162953_random 2802 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192392 2802 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171239_random 2800 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154066_random 2800 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165886_random 2799 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165907_random 2799 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187327 2793 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190125 2793 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190541 2792 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169390_random 2791 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154025_random 2791 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156168_random 2791 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190103 2791 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174599_random 2790 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159432_random 2790 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189149 2790 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189295 2790 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159170_random 2789 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191262 2789 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164855_random 2788 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192393 2788 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168642_random 2787 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170644_random 2787 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173386_random 2787 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174948_random 2786 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176624_random 2786 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187859 2786 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178056_random 2786 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165614_random 2785 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157932_random 2785 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188608 2785 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150796_random 2784 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153101_random 2784 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159242_random 2784 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188696 2784 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150559_random 2783 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188326 2783 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163186_random 2782 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192275 2782 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155873_random 2781 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171389_random 2779 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_AACZ03166112_random 2766 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188887 2766 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173460_random 2765 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150670_random 2765 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188940 2764 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189799 2764 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150658_random 2763 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169693_random 2762 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174698_random 2762 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150776_random 2762 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190634 2762 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172034_random 2761 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172290_random 2761 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190675 2761 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173573_random 2760 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176633_random 2759 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187004 2758 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr16_AACZ03173559_random 2751 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176068_random 2751 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159295_random 2751 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164649_random 2751 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157498_random 2750 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165893_random 2749 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171240_random 2749 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188992 2749 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169305_random 2748 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174645_random 2747 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162648_random 2747 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191358 2747 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171327_random 2746 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153023_random 2746 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162749_random 2746 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190061 2746 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171348_random 2745 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154052_random 2745 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159622_random 2745 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161223_random 2744 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187887 2744 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189416 2744 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176023_random 2743 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153057_random 2743 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190064 2743 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176024_random 2742 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173419_random 2741 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151237_random 2741 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190277 2741 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169480_random 2739 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190640 2739 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188248 2738 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188956 2737 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170661_random 2736 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr4_AACZ03156000_random 2730 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165738_random 2729 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188680 2729 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191495 2729 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173544_random 2727 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154036_random 2727 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162981_random 2727 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168499_random 2726 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171397_random 2726 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159651_random 2726 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162600_random 2726 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190673 2726 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191552 2726 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178281_random 2725 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173558_random 2724 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156144_random 2724 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154140_random 2723 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr13_AACZ03170528_random 2713 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157493_random 2713 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157379_random 2712 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190256 2712 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191865 2712 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165861_random 2711 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172047_random 2711 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150580_random 2711 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177930_random 2711 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165684_random 2710 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189245 2710 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188728 2709 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190438 2709 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175213_random 2708 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153979_random 2708 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188300 2707 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165791_random 2706 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr12_AACZ03169229_random 2701 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154413_random 2700 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189424 2700 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178025_random 2700 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175195_random 2699 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152193_random 2698 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159132_random 2698 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165794_random 2697 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154462_random 2697 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186663 2697 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187812 2697 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165575_random 2696 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172158_random 2696 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152528_random 2696 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157914_random 2695 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159820_random 2695 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191211 2695 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150630_random 2694 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190019 2694 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190244 2694 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191283 2694 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150585_random 2693 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153079_random 2693 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161269_random 2693 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166162_random 2692 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156169_random 2692 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187332 2692 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190339 2692 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157323_random 2691 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172128_random 2690 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174665_random 2690 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159162_random 2690 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165783_random 2689 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169921_random 2689 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159313_random 2689 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162923_random 2689 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168530_random 2688 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153087_random 2687 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192632 2687 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175342_random 2686 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176623_random 2686 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157407_random 2686 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159130_random 2686 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174712_random 2685 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170577_random 2684 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162689_random 2684 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172193_random 2683 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190335 2683 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190896 2682 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172288_random 2681 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173474_random 2681 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190912 2681 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_AACZ03165809_random 2674 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175286_random 2674 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151328_random 2674 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176649_random 2674 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189061 2674 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165679_random 2673 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177127_random 2673 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189266 2673 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191310 2673 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152389_random 2672 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153897_random 2672 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166211_random 2671 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159172_random 2671 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189199 2671 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168412_random 2670 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152201_random 2670 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168463_random 2669 /gbdb/panTro3/panTro3.2bit 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2655 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169414_random 2654 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174602_random 2654 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154148_random 2654 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192127 2654 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150972_random 2653 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155974_random 2653 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159070_random 2653 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154327_random 2652 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157421_random 2652 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157495_random 2652 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168501_random 2651 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169324_random 2650 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170558_random 2650 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174813_random 2650 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191177 2650 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169502_random 2649 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164764_random 2649 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188317 2649 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165795_random 2648 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166002_random 2648 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173553_random 2648 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162836_random 2648 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192676 2648 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192770 2648 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168540_random 2647 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172402_random 2647 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150734_random 2647 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151133_random 2647 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161272_random 2647 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191233 2647 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169617_random 2646 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170744_random 2646 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150941_random 2646 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152176_random 2646 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_AACZ03165839_random 2617 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150671_random 2616 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188538 2616 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190997 2616 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175276_random 2615 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154406_random 2614 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159428_random 2614 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189202 2614 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190757 2614 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191776 2614 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168810_random 2613 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172048_random 2613 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173633_random 2613 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175406_random 2613 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176031_random 2613 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150769_random 2613 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150801_random 2613 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152274_random 2607 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190401 2607 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189571 2606 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168680_random 2605 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189213 2605 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189455 2605 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191840 2605 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178140_random 2605 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152173_random 2604 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152548_random 2604 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188118 2604 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190851 2604 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192112 2604 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150451_random 2603 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150682_random 2603 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151607_random 2603 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156650_random 2603 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190880 2603 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/gbdb/panTro3/panTro3.2bit +chr3_AACZ03154093_random 2572 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189956 2572 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190848 2572 /gbdb/panTro3/panTro3.2bit +chrUn_GL396251 2572 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156222_random 2571 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156576_random 2571 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159523_random 2571 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174595_random 2570 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150567_random 2570 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152198_random 2570 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159324_random 2570 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192045 2570 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166026_random 2569 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166066_random 2569 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171449_random 2569 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150848_random 2569 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190786 2569 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191097 2569 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191967 2569 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165982_random 2568 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172064_random 2568 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177117_random 2568 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157402_random 2568 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159222_random 2568 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159319_random 2568 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159383_random 2568 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168462_random 2567 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176234_random 2567 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154294_random 2567 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188423 2567 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189030 2567 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153042_random 2566 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154258_random 2566 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154510_random 2566 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159974_random 2566 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163153_random 2566 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189738 2566 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190025 2566 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165951_random 2565 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176017_random 2565 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153220_random 2565 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190594 2565 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192350 2565 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168489_random 2564 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170592_random 2564 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151135_random 2564 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157537_random 2564 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189143 2564 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172066_random 2563 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155926_random 2563 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189951 2563 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191175 2563 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165992_random 2562 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168616_random 2562 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162729_random 2562 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192700 2562 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188760 2561 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170767_random 2560 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171323_random 2560 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150541_random 2560 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190503 2560 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192373 2560 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168851_random 2559 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151021_random 2559 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159459_random 2559 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163075_random 2559 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164778_random 2559 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189723 2559 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171655_random 2557 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172136_random 2557 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151066_random 2557 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191171 2557 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176607_random 2556 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155985_random 2556 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191528 2556 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176659_random 2555 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154202_random 2555 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156325_random 2555 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189470 2555 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192071 2555 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166043_random 2554 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170685_random 2554 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151316_random 2554 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159299_random 2554 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189049 2554 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170712_random 2553 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190469 2553 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178505_random 2553 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176064_random 2552 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190330 2552 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153007_random 2551 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154186_random 2551 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170501_random 2550 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173496_random 2550 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156228_random 2550 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162814_random 2550 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177849_random 2550 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168723_random 2549 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154128_random 2549 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159560_random 2549 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162861_random 2549 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155897_random 2548 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157788_random 2548 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159210_random 2548 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189886 2548 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155952_random 2547 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157452_random 2547 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159229_random 2547 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192209 2547 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166000_random 2546 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173796_random 2546 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189894 2546 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190203 2546 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165690_random 2545 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174591_random 2545 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175401_random 2545 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152065_random 2545 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162685_random 2545 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188427 2545 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169685_random 2544 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154291_random 2544 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159133_random 2544 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189675 2544 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168465_random 2543 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176610_random 2543 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152353_random 2543 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158143_random 2543 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189089 2543 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165664_random 2542 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165987_random 2542 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150957_random 2542 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152156_random 2542 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189096 2542 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189596 2542 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189924 2542 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171349_random 2541 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190381 2541 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191334 2541 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173828_random 2540 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174976_random 2540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159255_random 2540 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189063 2540 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189508 2540 /gbdb/panTro3/panTro3.2bit +chrUn_GL394326 2540 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178002_random 2540 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173881_random 2539 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157311_random 2539 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161454_random 2539 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162711_random 2539 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156413_random 2538 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157773_random 2538 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191646 2538 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176338_random 2537 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150851_random 2537 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153185_random 2537 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154240_random 2537 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154588_random 2537 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190154 2537 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174617_random 2536 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150758_random 2536 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156232_random 2536 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161685_random 2536 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191532 2536 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166329_random 2535 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154194_random 2535 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155925_random 2535 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159446_random 2535 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159686_random 2535 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161186_random 2535 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188600 2535 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192126 2535 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168567_random 2534 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176560_random 2534 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152257_random 2534 /gbdb/panTro3/panTro3.2bit 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2530 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190221 2530 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190404 2530 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191565 2530 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172109_random 2529 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190102 2529 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190996 2529 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159282_random 2528 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190460 2528 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172133_random 2527 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174571_random 2527 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159270_random 2527 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191895 2527 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156435_random 2526 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192640 2526 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176701_random 2525 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157469_random 2525 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157931_random 2525 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151289_random 2524 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154165_random 2524 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159682_random 2524 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161339_random 2524 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153943_random 2523 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159501_random 2523 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191354 2523 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192121 2523 /gbdb/panTro3/panTro3.2bit +chr10_GL391286_random 2522 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151206_random 2522 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176642_random 2522 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186328 2522 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168384_random 2521 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152233_random 2521 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168380_random 2520 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150650_random 2520 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153116_random 2520 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157447_random 2520 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158049_random 2520 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159275_random 2520 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190431 2520 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171484_random 2519 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153062_random 2519 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154224_random 2519 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165195_random 2519 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190177 2519 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170505_random 2518 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173511_random 2518 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156488_random 2517 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159757_random 2517 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161377_random 2517 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175307_random 2516 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151007_random 2516 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151292_random 2516 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172300_random 2515 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175308_random 2515 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175327_random 2515 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154101_random 2515 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154135_random 2515 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159890_random 2515 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188906 2515 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166326_random 2514 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173703_random 2514 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156392_random 2514 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159369_random 2514 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164828_random 2514 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190566 2514 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192645 2514 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175200_random 2513 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166011_random 2512 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176254_random 2512 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164934_random 2512 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190799 2512 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156214_random 2511 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157458_random 2511 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159072_random 2511 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161520_random 2511 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189186 2511 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168493_random 2510 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192351 2510 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153089_random 2509 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165845_random 2508 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165946_random 2508 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150568_random 2508 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157376_random 2508 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189150 2508 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190013 2508 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165793_random 2507 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173614_random 2506 /gbdb/panTro3/panTro3.2bit 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2502 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166016_random 2501 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171289_random 2501 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189467 2501 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191372 2501 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166202_random 2500 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154145_random 2500 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157531_random 2500 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188352 2500 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166295_random 2499 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159488_random 2499 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164843_random 2499 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190911 2499 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166184_random 2498 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170846_random 2498 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151220_random 2498 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03152995_random 2498 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03185572 2498 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr12_AACZ03169780_random 2495 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172127_random 2495 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150849_random 2495 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154149_random 2495 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192657 2495 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166267_random 2494 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151048_random 2494 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159549_random 2494 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163279_random 2494 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188397 2494 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192083 2494 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168404_random 2493 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172247_random 2493 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159175_random 2493 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159572_random 2493 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190910 2493 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192421 2493 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr12_AACZ03169408_random 2489 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172011_random 2489 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154012_random 2489 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154484_random 2489 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157996_random 2489 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190586 2489 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190637 2489 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152534_random 2488 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159538_random 2488 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166605_random 2487 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176116_random 2487 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151236_random 2487 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159227_random 2487 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190179 2487 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168589_random 2486 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169838_random 2486 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154103_random 2486 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157428_random 2486 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159456_random 2486 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188580 2486 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157680_random 2485 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160050_random 2484 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191644 2484 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154064_random 2483 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161222_random 2483 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191945 2483 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191979 2483 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165852_random 2482 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165966_random 2482 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170632_random 2482 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171278_random 2482 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150465_random 2482 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190413 2482 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191757 2482 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192269 2482 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176720_random 2481 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172108_random 2480 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174775_random 2480 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156075_random 2480 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162754_random 2480 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156129_random 2479 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164900_random 2479 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152133_random 2478 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152280_random 2478 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154714_random 2478 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162857_random 2478 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165029_random 2478 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191172 2478 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168517_random 2477 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156417_random 2477 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159247_random 2477 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189986 2477 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173762_random 2476 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174687_random 2476 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157968_random 2476 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188574 2475 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190928 2475 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169770_random 2474 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151494_random 2474 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159460_random 2474 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189489 2474 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191694 2474 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191955 2474 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168619_random 2473 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175373_random 2473 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177131_random 2473 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155898_random 2473 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191981 2473 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192276 2473 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192027 2472 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165988_random 2471 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159302_random 2471 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186519 2471 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169584_random 2470 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169859_random 2470 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156597_random 2470 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171365_random 2469 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187603 2469 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187824 2469 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190590 2469 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190745 2469 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170877_random 2468 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159164_random 2468 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176045_random 2467 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154674_random 2467 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156072_random 2467 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158242_random 2467 /gbdb/panTro3/panTro3.2bit 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2409 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156282_random 2409 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157459_random 2409 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157527_random 2409 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168394_random 2408 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169419_random 2408 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171231_random 2408 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175954_random 2408 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151377_random 2408 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176643_random 2408 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152719_random 2408 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158978_random 2408 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159043_random 2408 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164916_random 2407 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165925_random 2406 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150861_random 2406 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176647_random 2406 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163013_random 2406 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2403 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151415_random 2403 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177160_random 2403 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187233 2403 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191258 2403 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191993 2403 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192145 2403 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172031_random 2402 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175999_random 2402 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151449_random 2402 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154592_random 2402 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157329_random 2402 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169535_random 2401 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153247_random 2401 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156042_random 2401 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156223_random 2401 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157664_random 2401 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188869 2401 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_AACZ03166064_random 2375 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176247_random 2375 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154191_random 2375 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191169 2375 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192070 2375 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172248_random 2374 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157799_random 2374 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157851_random 2374 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189583 2374 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191882 2374 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169557_random 2373 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176156_random 2373 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161793_random 2373 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163501_random 2373 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164756_random 2373 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189462 2373 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189898 2373 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr10_AACZ03165890_random 2370 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170628_random 2370 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156583_random 2370 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157623_random 2370 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162844_random 2370 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189031 2370 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191631 2370 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176580_random 2369 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169580_random 2368 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150969_random 2368 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156066_random 2368 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161232_random 2368 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189895 2368 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190949 2368 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191130 2368 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154153_random 2367 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188237 2367 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152260_random 2364 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156465_random 2364 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189570 2364 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192584 2364 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171539_random 2363 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177142_random 2363 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154139_random 2363 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166479_random 2362 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169306_random 2362 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157261_random 2362 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190914 2362 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171294_random 2361 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168456_random 2360 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168651_random 2360 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156409_random 2360 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164784_random 2359 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03185121 2359 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_AACZ03164848_random 2356 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165025_random 2356 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190123 2356 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152228_random 2355 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158092_random 2355 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192820 2355 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174686_random 2354 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175978_random 2354 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156219_random 2354 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159359_random 2354 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187584 2354 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157497_random 2353 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189735 2353 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190522 2353 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166384_random 2352 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171344_random 2352 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150936_random 2352 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189667 2348 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166097_random 2347 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169499_random 2347 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171300_random 2347 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150716_random 2347 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151530_random 2347 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152320_random 2347 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152326_random 2347 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189438 2347 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191622 2347 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166037_random 2346 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171254_random 2346 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172311_random 2346 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174823_random 2346 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159343_random 2346 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188770 2346 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190214 2346 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr3_AACZ03154827_random 2332 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159852_random 2332 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188528 2332 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173487_random 2331 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162756_random 2331 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163219_random 2331 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164871_random 2331 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168413_random 2330 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154254_random 2330 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157753_random 2330 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162944_random 2330 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150754_random 2329 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151281_random 2329 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154586_random 2329 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156189_random 2329 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156329_random 2329 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156873_random 2329 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164977_random 2329 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166113_random 2328 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169479_random 2328 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191022 2328 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191700 2328 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192791 2328 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172258_random 2327 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173647_random 2327 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191636 2327 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153854_random 2326 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190117 2326 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162877_random 2325 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163012_random 2325 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189805 2325 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190650 2325 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192345 2325 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192874 2325 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166320_random 2324 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175423_random 2324 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189642 2324 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192203 2324 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169973_random 2323 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153223_random 2323 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154167_random 2323 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159351_random 2323 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164681_random 2323 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164766_random 2323 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191610 2323 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191635 2323 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192038 2323 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192885 2323 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174767_random 2322 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174791_random 2322 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151491_random 2322 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155668_random 2322 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191478 2311 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192241 2311 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165853_random 2310 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169513_random 2310 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154138_random 2310 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157705_random 2310 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163025_random 2310 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188163 2310 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189073 2310 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189298 2310 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190476 2310 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191143 2310 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191913 2310 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170588_random 2309 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172104_random 2309 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172416_random 2309 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153463_random 2309 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159330_random 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/gbdb/panTro3/panTro3.2bit +chrUn_GL394381 2293 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165744_random 2292 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165860_random 2292 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159626_random 2292 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188309 2292 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190168 2292 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190215 2292 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175391_random 2291 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156725_random 2291 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161234_random 2291 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190191 2291 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171516_random 2290 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190341 2290 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165932_random 2289 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151212_random 2289 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190325 2289 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191210 2289 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166028_random 2288 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170717_random 2288 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152602_random 2288 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154122_random 2288 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191679 2288 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178470_random 2288 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168715_random 2287 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174633_random 2287 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175210_random 2287 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156473_random 2287 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157350_random 2287 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187968 2287 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191693 2287 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192155 2287 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171270_random 2286 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157573_random 2286 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188994 2286 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190439 2286 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189254 2282 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192776 2282 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192875 2282 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192888 2282 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165655_random 2281 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172119_random 2281 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172165_random 2281 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174648_random 2281 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175228_random 2281 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150412_random 2281 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154250_random 2281 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164747_random 2281 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188345 2281 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190716 2281 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191029 2281 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192260 2281 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166168_random 2280 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169445_random 2280 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172273_random 2280 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173388_random 2280 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173912_random 2280 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150735_random 2280 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153395_random 2280 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154268_random 2280 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157441_random 2280 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157951_random 2280 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162766_random 2280 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165842_random 2279 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168804_random 2279 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150593_random 2279 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176640_random 2279 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159448_random 2279 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159628_random 2279 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192122 2279 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192813 2279 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2266 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192449 2266 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172223_random 2265 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173951_random 2265 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158188_random 2265 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159633_random 2265 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189160 2265 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169743_random 2264 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173435_random 2264 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152383_random 2264 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162799_random 2264 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163171_random 2264 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192474 2264 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171440_random 2263 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174950_random 2263 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150683_random 2263 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154260_random 2263 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164890_random 2263 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168451_random 2262 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173283_random 2262 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151073_random 2262 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152244_random 2262 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159195_random 2262 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186206 2262 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171446_random 2261 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152496_random 2261 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153102_random 2261 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162972_random 2261 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190977 2261 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192280 2261 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170623_random 2260 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153259_random 2260 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192611 2260 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192613 2260 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165804_random 2259 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr9_AACZ03164898_random 2246 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188426 2246 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190564 2246 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191769 2246 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191843 2246 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192000 2246 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168707_random 2245 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170731_random 2245 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171301_random 2245 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156284_random 2245 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159545_random 2245 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188959 2245 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190953 2245 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191416 2245 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191516 2245 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192039 2245 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172162_random 2244 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175397_random 2244 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188783 2242 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190979 2242 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191592 2242 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162894_random 2241 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164610_random 2241 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164964_random 2241 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190065 2241 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191342 2241 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192309 2241 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192605 2241 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169663_random 2240 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172113_random 2240 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177152_random 2240 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162807_random 2240 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164973_random 2240 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191035 2240 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166192_random 2239 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176767_random 2239 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/gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189701 2125 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192099 2125 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192625 2125 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169578_random 2124 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169806_random 2124 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174752_random 2124 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174832_random 2124 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153397_random 2124 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157818_random 2124 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187572 2124 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176244_random 2123 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151684_random 2123 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153122_random 2123 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189927 2123 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190895 2123 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191293 2123 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192623 2123 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169340_random 2122 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170602_random 2122 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173662_random 2122 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174801_random 2122 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158189_random 2122 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163419_random 2122 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192087 2122 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169612_random 2121 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176671_random 2121 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176737_random 2121 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156238_random 2121 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156244_random 2121 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156668_random 2121 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157526_random 2121 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157860_random 2121 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162928_random 2121 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191089 2121 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192580 2121 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2107 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170609_random 2106 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171607_random 2106 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154867_random 2106 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163019_random 2106 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190862 2106 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191205 2106 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166397_random 2105 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168576_random 2105 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173723_random 2105 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157560_random 2105 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158165_random 2105 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162842_random 2105 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192281 2105 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192480 2105 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150622_random 2104 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150894_random 2104 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152502_random 2104 /gbdb/panTro3/panTro3.2bit 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2096 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171412_random 2096 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175594_random 2096 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154761_random 2096 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159724_random 2096 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162747_random 2096 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189038 2096 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192762 2096 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168631_random 2095 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172243_random 2095 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157396_random 2095 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157633_random 2095 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186745 2095 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191367 2095 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192284 2095 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165865_random 2094 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166268_random 2094 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168699_random 2094 /gbdb/panTro3/panTro3.2bit 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2084 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173763_random 2084 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03175998_random 2084 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156487_random 2084 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159349_random 2084 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159981_random 2084 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162886_random 2084 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164799_random 2084 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191284 2084 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191431 2084 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192204 2084 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192285 2084 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192498 2084 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192576 2084 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166539_random 2083 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168950_random 2083 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175587_random 2083 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150917_random 2083 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152343_random 2080 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189739 2080 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192040 2080 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169424_random 2079 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171497_random 2079 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154193_random 2079 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166660_random 2078 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168450_random 2078 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175515_random 2078 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151813_random 2078 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159430_random 2078 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159736_random 2078 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162997_random 2078 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191512 2078 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192550 2078 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154465_random 2077 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156358_random 2077 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr19_AACZ03176199_random 2069 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151239_random 2069 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151414_random 2069 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163228_random 2069 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191271 2069 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191533 2069 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191730 2069 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166079_random 2068 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166094_random 2068 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169592_random 2068 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177207_random 2068 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163071_random 2068 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189208 2068 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189377 2068 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190283 2068 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192407 2068 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192593 2068 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192771 2068 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2060 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192282 2060 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178182_random 2060 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165876_random 2059 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173537_random 2059 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173727_random 2059 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174736_random 2059 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152667_random 2059 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159356_random 2059 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159880_random 2059 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163202_random 2059 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165245_random 2059 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165249_random 2059 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03186607 2059 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191357 2059 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192082 2059 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178107_random 2059 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169844_random 2058 /gbdb/panTro3/panTro3.2bit 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2023 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189198 2023 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189852 2023 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190543 2023 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191741 2023 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192677 2023 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166414_random 2022 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169686_random 2022 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169755_random 2022 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151011_random 2022 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176770_random 2022 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177143_random 2022 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154459_random 2022 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154776_random 2022 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154859_random 2022 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189567 2022 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189848 2022 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190418 2022 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191116 2022 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166032_random 2021 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168607_random 2021 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169896_random 2021 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176769_random 2021 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153302_random 2021 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153304_random 2021 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154322_random 2021 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156658_random 2021 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157336_random 2021 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159367_random 2021 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163542_random 2021 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190754 2021 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190888 2021 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192367 2021 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192679 2021 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168716_random 2020 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168808_random 2020 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152360_random 2017 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157467_random 2017 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157658_random 2017 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163363_random 2017 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187575 2017 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191219 2017 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191292 2017 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191323 2017 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192501 2017 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192599 2017 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192633 2017 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192788 2017 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150573_random 2016 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151331_random 2016 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151546_random 2016 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153026_random 2016 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154555_random 2016 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156065_random 2016 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159791_random 2016 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162988_random 2016 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163466_random 2016 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191574 2016 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192042 2016 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192655 2016 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178287_random 2016 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169411_random 2015 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169717_random 2015 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150878_random 2015 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177138_random 2015 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03153975_random 2015 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154758_random 2015 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154949_random 2015 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156782_random 2015 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163047_random 2015 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188472 2015 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr3_AACZ03154235_random 2012 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154653_random 2012 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156109_random 2012 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156448_random 2012 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157720_random 2012 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157913_random 2012 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189039 2012 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192430 2012 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168849_random 2011 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169831_random 2011 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171296_random 2011 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172320_random 2011 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177113_random 2011 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157608_random 2011 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157766_random 2011 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159937_random 2011 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163474_random 2011 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189441 2011 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190738 2011 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191075 2011 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165921_random 2010 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168683_random 2010 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174749_random 2010 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150708_random 2010 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151039_random 2010 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151598_random 2010 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152340_random 2010 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153581_random 2010 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189994 2010 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190746 2010 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191965 2010 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192466 2010 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192519 2010 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178341_random 2010 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175379_random 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/gbdb/panTro3/panTro3.2bit +chr10_AACZ03166015_random 2007 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171330_random 2007 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172271_random 2007 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173877_random 2007 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174530_random 2007 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151240_random 2007 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151285_random 2007 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151770_random 2007 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153491_random 2007 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154690_random 2007 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156646_random 2007 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162845_random 2007 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163092_random 2007 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03187916 2007 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03190137 2007 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191543 2007 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165947_random 2006 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176051_random 2006 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176760_random 2006 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152526_random 2006 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154094_random 2006 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154121_random 2006 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156369_random 2006 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156706_random 2006 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161534_random 2006 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165054_random 2006 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188960 2006 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192481 2006 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192698 2006 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178196_random 2006 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169581_random 2005 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171462_random 2005 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173846_random 2005 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152361_random 2005 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154210_random 2005 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154373_random 2005 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154605_random 2005 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157510_random 2005 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158062_random 2005 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159400_random 2005 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161215_random 2005 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162952_random 2005 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163573_random 2005 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165035_random 2005 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165084_random 2005 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189097 2005 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189552 2005 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191487 2005 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192187 2005 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154813_random 2004 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157877_random 2004 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162990_random 2004 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188353 2004 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189029 2004 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165956_random 2003 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166515_random 2003 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172211_random 2003 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174663_random 2003 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159202_random 2003 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03188382 2003 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191932 2003 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170962_random 2002 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176180_random 2002 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157361_random 2002 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159666_random 2002 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159717_random 2002 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159850_random 2002 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164967_random 2002 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03189553 2002 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03191596 2002 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192865 2002 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171481_random 2001 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173907_random 2001 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174865_random 2001 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176260_random 2001 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152376_random 2001 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162803_random 2001 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192705 2001 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166392_random 2000 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151732_random 2000 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153053_random 2000 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154269_random 2000 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159113_random 2000 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161326_random 2000 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165265_random 2000 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192205 2000 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192441 2000 /gbdb/panTro3/panTro3.2bit +chrUn_AACZ03192761 2000 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168805_random 1999 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171560_random 1999 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176098_random 1999 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151231_random 1999 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176747_random 1999 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162863_random 1999 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163166_random 1999 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168702_random 1998 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169373_random 1998 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169731_random 1998 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170816_random 1998 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172292_random 1998 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173852_random 1998 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176221_random 1998 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151229_random 1998 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151646_random 1998 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152277_random 1998 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156077_random 1998 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157419_random 1998 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161522_random 1998 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162817_random 1998 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163011_random 1998 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165197_random 1998 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169449_random 1997 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171627_random 1997 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171654_random 1997 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173876_random 1997 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175582_random 1997 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176632_random 1997 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176674_random 1997 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157641_random 1997 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169879_random 1996 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171445_random 1996 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174933_random 1996 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176154_random 1996 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152338_random 1996 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154587_random 1996 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156087_random 1996 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156262_random 1996 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163063_random 1996 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164797_random 1996 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178191_random 1996 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178527_random 1996 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168528_random 1995 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170859_random 1995 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154595_random 1995 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163174_random 1995 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165734_random 1994 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166049_random 1994 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168705_random 1994 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173697_random 1994 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176243_random 1994 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150958_random 1994 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150990_random 1994 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151183_random 1994 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153286_random 1994 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154256_random 1994 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156618_random 1994 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157760_random 1994 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159453_random 1994 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169821_random 1993 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153155_random 1993 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154647_random 1993 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157983_random 1993 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158012_random 1993 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159256_random 1993 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163260_random 1993 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178247_random 1993 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178292_random 1993 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165976_random 1992 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168825_random 1992 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172233_random 1992 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172382_random 1992 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172414_random 1992 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175042_random 1992 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176793_random 1992 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153319_random 1992 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156318_random 1992 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157777_random 1992 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162838_random 1992 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168691_random 1991 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151110_random 1991 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151184_random 1991 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152495_random 1991 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160022_random 1991 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163578_random 1991 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166609_random 1990 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170936_random 1990 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152354_random 1990 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152713_random 1990 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161467_random 1990 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166519_random 1989 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168744_random 1989 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168939_random 1989 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169803_random 1989 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170621_random 1989 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176245_random 1989 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150842_random 1989 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152232_random 1989 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153335_random 1989 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154161_random 1989 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157963_random 1989 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171255_random 1988 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154017_random 1988 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154884_random 1988 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159394_random 1988 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168577_random 1987 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168862_random 1987 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171310_random 1987 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172376_random 1987 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151433_random 1987 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153076_random 1987 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153176_random 1987 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156056_random 1987 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157518_random 1987 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157975_random 1987 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159442_random 1987 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159470_random 1987 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164849_random 1987 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175568_random 1986 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176357_random 1986 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176419_random 1986 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154160_random 1986 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154271_random 1986 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154393_random 1986 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157344_random 1986 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157991_random 1986 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165330_random 1986 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165725_random 1985 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166421_random 1985 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168896_random 1985 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173811_random 1985 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156580_random 1985 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160101_random 1985 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161724_random 1985 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162932_random 1985 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163273_random 1985 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165266_random 1985 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168563_random 1984 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171430_random 1984 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175427_random 1984 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151025_random 1984 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153242_random 1984 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154567_random 1984 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156577_random 1984 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163105_random 1984 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163216_random 1984 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176192_random 1983 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150983_random 1983 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157615_random 1983 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159350_random 1983 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159811_random 1983 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166610_random 1982 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166687_random 1982 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168446_random 1982 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168717_random 1982 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171526_random 1982 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176304_random 1982 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154182_random 1982 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156349_random 1982 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157472_random 1982 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162808_random 1982 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166118_random 1981 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169544_random 1981 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169895_random 1981 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170887_random 1981 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171443_random 1981 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171555_random 1981 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174836_random 1981 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151174_random 1981 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154073_random 1981 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154247_random 1981 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154297_random 1981 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154401_random 1981 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156250_random 1981 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157640_random 1981 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159268_random 1981 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161585_random 1981 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178386_random 1981 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168704_random 1980 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173972_random 1980 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152364_random 1980 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153287_random 1980 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153580_random 1980 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157692_random 1980 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178226_random 1980 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165833_random 1979 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169450_random 1979 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171387_random 1979 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176746_random 1979 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153306_random 1979 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157792_random 1979 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158276_random 1979 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172305_random 1978 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175583_random 1978 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154997_random 1978 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157748_random 1978 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158140_random 1978 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161284_random 1978 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169760_random 1977 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170044_random 1977 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175319_random 1977 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152397_random 1977 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156899_random 1977 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156951_random 1977 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157598_random 1977 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164888_random 1977 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165238_random 1977 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166222_random 1976 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169639_random 1976 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169850_random 1976 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170013_random 1976 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173924_random 1976 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174764_random 1976 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176351_random 1976 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151022_random 1976 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153252_random 1976 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153291_random 1976 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154069_random 1976 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159617_random 1976 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178370_random 1976 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178566_random 1976 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170610_random 1975 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170875_random 1975 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173602_random 1975 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173720_random 1975 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150930_random 1975 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151446_random 1975 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151509_random 1975 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151582_random 1975 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152557_random 1975 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153516_random 1975 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156544_random 1975 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162852_random 1975 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169722_random 1974 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173943_random 1974 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174864_random 1974 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175425_random 1974 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175577_random 1974 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176125_random 1974 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151258_random 1974 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156982_random 1974 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157432_random 1974 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157557_random 1974 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162029_random 1974 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163057_random 1974 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164783_random 1974 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165064_random 1974 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156388_random 1973 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156703_random 1973 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159206_random 1973 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164678_random 1973 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166282_random 1972 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168725_random 1972 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168743_random 1972 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176000_random 1972 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154895_random 1972 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157917_random 1972 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161963_random 1972 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163177_random 1972 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165077_random 1972 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166598_random 1971 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170801_random 1971 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151569_random 1971 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152391_random 1971 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154278_random 1971 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156424_random 1971 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156655_random 1971 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159512_random 1971 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164614_random 1971 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166471_random 1970 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166656_random 1970 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170890_random 1970 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172117_random 1970 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174949_random 1970 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156038_random 1970 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156532_random 1970 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157620_random 1970 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162916_random 1970 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165231_random 1970 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166157_random 1969 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169648_random 1969 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173853_random 1969 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174719_random 1969 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175483_random 1969 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151355_random 1969 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151535_random 1969 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176712_random 1969 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176895_random 1969 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162860_random 1969 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169399_random 1968 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169944_random 1968 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170581_random 1968 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171581_random 1968 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171675_random 1968 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172085_random 1968 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173813_random 1968 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151655_random 1968 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176694_random 1968 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154445_random 1968 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166368_random 1967 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176890_random 1967 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156555_random 1967 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159874_random 1967 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165122_random 1967 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174647_random 1966 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176164_random 1966 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176802_random 1966 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157328_random 1966 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157645_random 1966 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159419_random 1966 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177878_random 1966 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165832_random 1965 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166767_random 1965 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170666_random 1965 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170667_random 1965 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171530_random 1965 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171587_random 1965 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151630_random 1965 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154560_random 1965 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156500_random 1965 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172436_random 1964 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175365_random 1964 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150659_random 1964 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151275_random 1964 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153278_random 1964 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154458_random 1964 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154545_random 1964 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157806_random 1964 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159279_random 1964 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161815_random 1964 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178511_random 1964 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168918_random 1963 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170826_random 1963 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174900_random 1963 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151439_random 1963 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156142_random 1963 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157858_random 1963 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159550_random 1963 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165342_random 1963 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178079_random 1963 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169101_random 1962 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169473_random 1962 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170551_random 1962 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173795_random 1962 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150569_random 1962 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151363_random 1962 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154543_random 1962 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158145_random 1962 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168693_random 1961 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169880_random 1961 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173791_random 1961 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174793_random 1961 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175033_random 1961 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175600_random 1961 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176348_random 1961 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154354_random 1961 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157797_random 1961 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159373_random 1961 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165914_random 1960 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175502_random 1960 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175571_random 1960 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152578_random 1960 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153342_random 1960 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154284_random 1960 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159235_random 1960 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159543_random 1960 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161802_random 1960 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178161_random 1960 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170814_random 1959 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172283_random 1959 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175484_random 1959 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150570_random 1959 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176789_random 1959 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154851_random 1959 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166243_random 1958 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168916_random 1958 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169472_random 1958 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170670_random 1958 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171424_random 1958 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175519_random 1958 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150942_random 1958 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151260_random 1958 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152281_random 1958 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157770_random 1958 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157876_random 1958 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159578_random 1958 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159804_random 1958 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178534_random 1958 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166714_random 1957 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170640_random 1957 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172385_random 1957 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173739_random 1957 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152342_random 1957 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163206_random 1957 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165251_random 1957 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166754_random 1956 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171403_random 1956 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174726_random 1956 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176120_random 1956 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157622_random 1956 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178468_random 1956 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166589_random 1955 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166675_random 1955 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174912_random 1955 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151115_random 1955 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154649_random 1955 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156212_random 1955 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156549_random 1955 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157549_random 1955 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178286_random 1955 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166719_random 1954 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169917_random 1954 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171578_random 1954 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173755_random 1954 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151603_random 1954 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152309_random 1954 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153460_random 1954 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153520_random 1954 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156517_random 1954 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156525_random 1954 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159465_random 1954 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159688_random 1954 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161762_random 1954 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163407_random 1954 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168491_random 1953 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168629_random 1953 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169631_random 1953 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170925_random 1953 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172102_random 1953 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175235_random 1953 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150803_random 1953 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154313_random 1953 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156041_random 1953 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162158_random 1953 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163131_random 1953 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164687_random 1953 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169615_random 1952 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170888_random 1952 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173961_random 1952 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176092_random 1952 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176907_random 1952 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152302_random 1952 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159429_random 1952 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159993_random 1952 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160177_random 1952 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163516_random 1952 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163527_random 1952 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165206_random 1952 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166001_random 1951 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172245_random 1951 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174605_random 1951 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152359_random 1951 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157668_random 1951 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157732_random 1951 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158219_random 1951 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163445_random 1951 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166156_random 1950 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168549_random 1950 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168979_random 1950 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169898_random 1950 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172418_random 1950 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154561_random 1950 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159801_random 1950 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159918_random 1950 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159968_random 1950 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161871_random 1950 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163119_random 1950 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168949_random 1949 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169588_random 1949 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170920_random 1949 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173664_random 1949 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173827_random 1949 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174003_random 1949 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175567_random 1949 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154963_random 1949 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159455_random 1949 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159636_random 1949 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163384_random 1949 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165075_random 1949 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168659_random 1948 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173936_random 1948 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150975_random 1948 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151772_random 1948 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156263_random 1948 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157621_random 1948 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159000_random 1948 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166093_random 1947 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169022_random 1947 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174786_random 1947 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153536_random 1947 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153537_random 1947 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159496_random 1947 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165215_random 1947 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166034_random 1946 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168534_random 1946 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168546_random 1946 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169870_random 1946 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170658_random 1946 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152630_random 1946 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153249_random 1946 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156657_random 1946 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160232_random 1946 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162045_random 1946 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174635_random 1945 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150783_random 1945 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153598_random 1945 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154279_random 1945 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154419_random 1945 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157003_random 1945 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159437_random 1945 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159773_random 1945 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165320_random 1945 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165382_random 1945 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166546_random 1944 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166616_random 1944 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168376_random 1944 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169754_random 1944 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169861_random 1944 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173833_random 1944 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177218_random 1944 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154784_random 1944 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154797_random 1944 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156286_random 1944 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156936_random 1944 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156942_random 1944 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157330_random 1944 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161731_random 1944 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164808_random 1944 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164972_random 1944 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178322_random 1944 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166188_random 1943 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166229_random 1943 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166230_random 1943 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169423_random 1943 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169641_random 1943 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173786_random 1943 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173939_random 1943 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177161_random 1943 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152619_random 1943 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154262_random 1943 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159767_random 1943 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163256_random 1943 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165155_random 1943 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168983_random 1942 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173634_random 1942 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175421_random 1942 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152434_random 1942 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153322_random 1942 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153323_random 1942 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154578_random 1942 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162813_random 1942 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178176_random 1942 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178312_random 1942 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166557_random 1941 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169901_random 1941 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173702_random 1941 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175403_random 1941 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177083_random 1941 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153183_random 1941 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157597_random 1941 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163423_random 1941 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166372_random 1940 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166670_random 1940 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169621_random 1940 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170022_random 1940 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170751_random 1940 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170992_random 1940 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173617_random 1940 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174012_random 1940 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151059_random 1940 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151742_random 1940 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152450_random 1940 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154575_random 1940 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156438_random 1940 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159032_random 1940 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159508_random 1940 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159807_random 1940 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161294_random 1940 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161327_random 1940 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166128_random 1939 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170007_random 1939 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173552_random 1939 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174016_random 1939 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176099_random 1939 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150995_random 1939 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151297_random 1939 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154350_random 1939 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154359_random 1939 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156365_random 1939 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156559_random 1939 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156644_random 1939 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156954_random 1939 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157878_random 1939 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172092_random 1938 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174667_random 1938 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176286_random 1938 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151051_random 1938 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156728_random 1938 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157805_random 1938 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159463_random 1938 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159818_random 1938 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160139_random 1938 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166671_random 1937 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168674_random 1937 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170986_random 1937 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173769_random 1937 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176806_random 1937 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153558_random 1937 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154789_random 1937 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159261_random 1937 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159294_random 1937 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164856_random 1937 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165962_random 1936 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174727_random 1936 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174904_random 1936 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151014_random 1936 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151564_random 1936 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159583_random 1936 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160002_random 1936 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163074_random 1936 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163141_random 1936 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178457_random 1936 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166394_random 1935 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171311_random 1935 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172246_random 1935 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175404_random 1935 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175464_random 1935 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175561_random 1935 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151348_random 1935 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156177_random 1935 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156637_random 1935 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156773_random 1935 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157702_random 1935 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159706_random 1935 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161773_random 1935 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161860_random 1935 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166644_random 1934 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168866_random 1934 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169794_random 1934 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170784_random 1934 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170856_random 1934 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176080_random 1934 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150836_random 1934 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176707_random 1934 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154158_random 1934 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156470_random 1934 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161983_random 1934 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166542_random 1933 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166571_random 1933 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176121_random 1933 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154361_random 1933 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156301_random 1933 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160008_random 1933 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171345_random 1932 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174828_random 1932 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156832_random 1932 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156856_random 1932 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158067_random 1932 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159744_random 1932 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163067_random 1932 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163150_random 1932 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168934_random 1931 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177085_random 1931 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157946_random 1931 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159753_random 1931 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163272_random 1931 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178188_random 1931 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170773_random 1930 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151511_random 1930 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154236_random 1930 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162922_random 1930 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164836_random 1930 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166426_random 1929 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166430_random 1929 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166596_random 1929 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169591_random 1929 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170848_random 1929 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171709_random 1929 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173456_random 1929 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173941_random 1929 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153157_random 1929 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153508_random 1929 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154429_random 1929 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156110_random 1929 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156829_random 1929 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163211_random 1929 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171414_random 1928 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172129_random 1928 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172256_random 1928 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174825_random 1928 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174987_random 1928 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152377_random 1928 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154722_random 1928 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156152_random 1928 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157418_random 1928 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159761_random 1928 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160169_random 1928 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161482_random 1928 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164943_random 1928 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168608_random 1927 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168913_random 1927 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170662_random 1927 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171426_random 1927 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173844_random 1927 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150798_random 1927 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152315_random 1927 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154718_random 1927 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156591_random 1927 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158194_random 1927 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159305_random 1927 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163416_random 1927 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166873_random 1926 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169448_random 1926 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171477_random 1926 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172155_random 1926 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174869_random 1926 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151194_random 1926 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151280_random 1926 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152433_random 1926 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153113_random 1926 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154623_random 1926 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163617_random 1926 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164960_random 1926 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178366_random 1926 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166179_random 1925 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174848_random 1925 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150932_random 1925 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153137_random 1925 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154532_random 1925 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159681_random 1925 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178424_random 1925 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165942_random 1924 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169566_random 1924 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171422_random 1924 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173665_random 1924 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150876_random 1924 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151438_random 1924 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151525_random 1924 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154455_random 1924 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154775_random 1924 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154870_random 1924 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156772_random 1924 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156881_random 1924 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162964_random 1924 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166069_random 1923 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173863_random 1923 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151301_random 1923 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152202_random 1923 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152405_random 1923 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153544_random 1923 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156172_random 1923 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157688_random 1923 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159700_random 1923 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160001_random 1923 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162893_random 1923 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175394_random 1922 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175596_random 1922 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150575_random 1922 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153243_random 1922 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156154_random 1922 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159561_random 1922 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160080_random 1922 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163301_random 1922 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168636_random 1921 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168780_random 1921 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169388_random 1921 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169620_random 1921 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170805_random 1921 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171325_random 1921 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172260_random 1921 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173837_random 1921 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175330_random 1921 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151140_random 1921 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156398_random 1921 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159858_random 1921 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166883_random 1920 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168748_random 1920 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168883_random 1920 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170591_random 1920 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174884_random 1920 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151036_random 1920 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151098_random 1920 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151508_random 1920 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152247_random 1920 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156686_random 1920 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165020_random 1920 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178089_random 1920 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165733_random 1919 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172336_random 1919 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172458_random 1919 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175049_random 1919 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176256_random 1919 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150968_random 1919 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152600_random 1919 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154535_random 1919 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156191_random 1919 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157504_random 1919 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158078_random 1919 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158171_random 1919 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159292_random 1919 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161474_random 1919 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178526_random 1919 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166608_random 1918 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171611_random 1918 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173768_random 1918 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175328_random 1918 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175597_random 1918 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176797_random 1918 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152240_random 1918 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152489_random 1918 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159635_random 1918 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166187_random 1917 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169600_random 1917 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169653_random 1917 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169715_random 1917 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174596_random 1917 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175522_random 1917 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151009_random 1917 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151147_random 1917 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152439_random 1917 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154753_random 1917 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156326_random 1917 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156407_random 1917 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158198_random 1917 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159338_random 1917 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159942_random 1917 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163540_random 1917 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165331_random 1917 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168763_random 1916 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170763_random 1916 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175660_random 1916 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151493_random 1916 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155961_random 1916 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159837_random 1916 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171535_random 1915 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173421_random 1915 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151352_random 1915 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153149_random 1915 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153254_random 1915 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154091_random 1915 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158290_random 1915 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159748_random 1915 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163122_random 1915 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166042_random 1914 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169038_random 1914 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171400_random 1914 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151248_random 1914 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154281_random 1914 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154564_random 1914 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156051_random 1914 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158032_random 1914 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161671_random 1914 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165772_random 1913 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166518_random 1913 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168709_random 1913 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170576_random 1913 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170733_random 1913 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171407_random 1913 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172475_random 1913 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175690_random 1913 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151709_random 1913 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152265_random 1913 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153179_random 1913 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156395_random 1913 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162885_random 1913 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162911_random 1913 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165060_random 1913 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165990_random 1912 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169558_random 1912 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171512_random 1912 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174794_random 1912 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174965_random 1912 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151034_random 1912 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153167_random 1912 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154642_random 1912 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163381_random 1912 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165652_random 1911 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165878_random 1911 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168876_random 1911 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175457_random 1911 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151102_random 1911 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151362_random 1911 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177101_random 1911 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153066_random 1911 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154227_random 1911 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154810_random 1911 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157864_random 1911 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159827_random 1911 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165014_random 1911 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169503_random 1910 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170795_random 1910 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171559_random 1910 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151453_random 1910 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152311_random 1910 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154397_random 1910 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156659_random 1910 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156708_random 1910 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158125_random 1910 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152441_random 1909 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154596_random 1909 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154735_random 1909 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156515_random 1909 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157814_random 1909 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159668_random 1909 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165174_random 1909 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169914_random 1908 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174907_random 1908 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152367_random 1908 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152581_random 1908 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157613_random 1908 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161673_random 1908 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163253_random 1908 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165109_random 1908 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166231_random 1907 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166526_random 1907 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168521_random 1907 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170945_random 1907 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171448_random 1907 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174662_random 1907 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175579_random 1907 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151524_random 1907 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177180_random 1907 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152113_random 1907 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153354_random 1907 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154059_random 1907 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163136_random 1907 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164961_random 1907 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166041_random 1906 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169871_random 1906 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171331_random 1906 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176166_random 1906 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151560_random 1906 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176655_random 1906 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152487_random 1906 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156451_random 1906 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159721_random 1906 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160128_random 1906 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165180_random 1906 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171358_random 1905 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171447_random 1905 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171558_random 1905 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172207_random 1905 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173923_random 1905 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175364_random 1905 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151545_random 1905 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153165_random 1905 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156057_random 1905 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163078_random 1905 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165005_random 1905 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166305_random 1904 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169789_random 1904 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170710_random 1904 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173540_random 1904 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151656_random 1904 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176830_random 1904 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153161_random 1904 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156277_random 1904 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156836_random 1904 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159315_random 1904 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159894_random 1904 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159971_random 1904 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168681_random 1903 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169862_random 1903 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171441_random 1903 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174955_random 1903 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175530_random 1903 /gbdb/panTro3/panTro3.2bit 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+chr2B_AACZ03153444_random 1902 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159708_random 1902 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168976_random 1901 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172365_random 1901 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174885_random 1901 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151116_random 1901 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151831_random 1901 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154509_random 1901 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154762_random 1901 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178314_random 1901 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178504_random 1901 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166078_random 1900 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168573_random 1900 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169900_random 1900 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173440_random 1900 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175553_random 1900 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150790_random 1900 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156067_random 1900 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157568_random 1900 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157790_random 1900 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158003_random 1900 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159730_random 1900 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165953_random 1899 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166498_random 1899 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169304_random 1899 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170673_random 1899 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171423_random 1899 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171548_random 1899 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176774_random 1899 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156493_random 1899 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160216_random 1899 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162948_random 1899 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163065_random 1899 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166439_random 1898 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168488_random 1898 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168919_random 1898 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172504_random 1898 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174880_random 1898 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174898_random 1898 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154060_random 1898 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154631_random 1898 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156252_random 1898 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156804_random 1898 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157821_random 1898 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158308_random 1898 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162920_random 1898 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163137_random 1898 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178605_random 1898 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170774_random 1897 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172110_random 1897 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176884_random 1897 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155971_random 1897 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157833_random 1897 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158050_random 1897 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159571_random 1897 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159598_random 1897 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164949_random 1897 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178192_random 1897 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166153_random 1896 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169040_random 1896 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171494_random 1896 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173898_random 1896 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175006_random 1896 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150925_random 1896 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152337_random 1896 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154773_random 1896 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157743_random 1896 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159298_random 1896 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161907_random 1896 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164779_random 1896 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165193_random 1896 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170901_random 1895 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171471_random 1895 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171604_random 1895 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171659_random 1895 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173905_random 1895 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176332_random 1895 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151391_random 1895 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153174_random 1895 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154265_random 1895 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154756_random 1895 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157850_random 1895 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157856_random 1895 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159540_random 1895 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161902_random 1895 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163359_random 1895 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163570_random 1895 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178164_random 1895 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166022_random 1894 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166532_random 1894 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168687_random 1894 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171383_random 1894 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173373_random 1894 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150775_random 1894 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176833_random 1894 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154257_random 1894 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156320_random 1894 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156489_random 1894 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158224_random 1894 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159924_random 1894 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163455_random 1894 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170612_random 1893 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170841_random 1893 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173521_random 1893 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173545_random 1893 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174668_random 1893 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174781_random 1893 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176753_random 1893 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177162_random 1893 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153420_random 1893 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154217_random 1893 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154681_random 1893 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159922_random 1893 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162077_random 1893 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162895_random 1893 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162908_random 1893 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163192_random 1893 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164806_random 1893 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168813_random 1892 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170882_random 1892 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173797_random 1892 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151734_random 1892 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177174_random 1892 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154641_random 1892 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154646_random 1892 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157828_random 1892 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166306_random 1891 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166742_random 1891 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168599_random 1891 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168846_random 1891 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168897_random 1891 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169001_random 1891 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169613_random 1891 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172096_random 1891 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176409_random 1891 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151662_random 1891 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153436_random 1891 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156170_random 1891 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157478_random 1891 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157761_random 1891 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159646_random 1891 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160089_random 1891 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169396_random 1890 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173805_random 1890 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175513_random 1890 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151307_random 1890 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176888_random 1890 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157445_random 1890 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157541_random 1890 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157588_random 1890 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158291_random 1890 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162956_random 1890 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163160_random 1890 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164798_random 1890 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169456_random 1889 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171504_random 1889 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172338_random 1889 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151124_random 1889 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154700_random 1889 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157513_random 1889 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157686_random 1889 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157937_random 1889 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158268_random 1889 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163366_random 1889 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178189_random 1889 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165646_random 1888 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166524_random 1888 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151213_random 1888 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151472_random 1888 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153310_random 1888 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154207_random 1888 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154926_random 1888 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161865_random 1888 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163024_random 1888 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163178_random 1888 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163285_random 1888 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165194_random 1888 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168669_random 1887 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170822_random 1887 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171464_random 1887 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174840_random 1887 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151830_random 1887 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154831_random 1887 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156036_random 1887 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156503_random 1887 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157826_random 1887 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159477_random 1887 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161503_random 1887 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178342_random 1887 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166027_random 1886 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166125_random 1886 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166324_random 1886 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166398_random 1886 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152368_random 1886 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152471_random 1886 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153100_random 1886 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156027_random 1886 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156760_random 1886 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157507_random 1886 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158169_random 1886 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159110_random 1886 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160071_random 1886 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166178_random 1885 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168995_random 1885 /gbdb/panTro3/panTro3.2bit 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+chr1_AACZ03151536_random 1884 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156633_random 1884 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157875_random 1884 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162837_random 1884 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166735_random 1883 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168809_random 1883 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170806_random 1883 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175043_random 1883 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175311_random 1883 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176213_random 1883 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150406_random 1883 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150956_random 1883 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176681_random 1883 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177148_random 1883 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154591_random 1883 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156221_random 1883 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156952_random 1883 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159812_random 1883 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178476_random 1883 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169109_random 1882 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154695_random 1882 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157978_random 1882 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157997_random 1882 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158196_random 1882 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163072_random 1882 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163190_random 1882 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164804_random 1882 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178252_random 1882 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178327_random 1882 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169724_random 1881 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151317_random 1881 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151712_random 1881 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152707_random 1881 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153567_random 1881 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156211_random 1881 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159699_random 1881 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165107_random 1881 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166196_random 1880 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166588_random 1880 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166634_random 1880 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170821_random 1880 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171321_random 1880 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151010_random 1880 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151784_random 1880 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176826_random 1880 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176856_random 1880 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152408_random 1880 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154216_random 1880 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156700_random 1880 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158118_random 1880 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159695_random 1880 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159742_random 1880 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163367_random 1880 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166855_random 1879 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169085_random 1879 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172179_random 1879 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151528_random 1879 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156153_random 1879 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156175_random 1879 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157731_random 1879 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166460_random 1878 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171001_random 1878 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172391_random 1878 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172410_random 1878 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173900_random 1878 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175045_random 1878 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151217_random 1878 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176685_random 1878 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176723_random 1878 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152546_random 1878 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152741_random 1878 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153208_random 1878 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153477_random 1878 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154808_random 1878 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156553_random 1878 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157457_random 1878 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165106_random 1878 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169007_random 1877 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170578_random 1877 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170823_random 1877 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171417_random 1877 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173628_random 1877 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152286_random 1877 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157935_random 1877 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159263_random 1877 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159653_random 1877 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162966_random 1877 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178518_random 1877 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166663_random 1876 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170853_random 1876 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170892_random 1876 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176421_random 1876 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150945_random 1876 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159260_random 1876 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159680_random 1876 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159755_random 1876 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161639_random 1876 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163436_random 1876 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166695_random 1875 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166707_random 1875 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168633_random 1875 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169969_random 1875 /gbdb/panTro3/panTro3.2bit 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+chr15_AACZ03172228_random 1869 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173746_random 1869 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176684_random 1869 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176708_random 1869 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152466_random 1869 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152763_random 1869 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157694_random 1869 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166881_random 1868 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169837_random 1868 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169886_random 1868 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174053_random 1868 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151411_random 1868 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154557_random 1868 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154893_random 1868 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158207_random 1868 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162133_random 1868 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165002_random 1868 /gbdb/panTro3/panTro3.2bit 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/gbdb/panTro3/panTro3.2bit +chr11_AACZ03169075_random 1669 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169919_random 1669 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170772_random 1669 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170780_random 1669 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171404_random 1669 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173735_random 1669 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175630_random 1669 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151361_random 1669 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152642_random 1669 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153181_random 1669 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153543_random 1669 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154544_random 1669 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156757_random 1669 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156896_random 1669 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158202_random 1669 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166495_random 1668 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170730_random 1668 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170897_random 1668 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173764_random 1668 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151121_random 1668 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151182_random 1668 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152530_random 1668 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153357_random 1668 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153621_random 1668 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154628_random 1668 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154703_random 1668 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156156_random 1668 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156534_random 1668 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158228_random 1668 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163083_random 1668 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163442_random 1668 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163509_random 1668 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166333_random 1667 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166793_random 1667 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172149_random 1667 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172302_random 1667 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174857_random 1667 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151611_random 1667 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151650_random 1667 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176911_random 1667 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176950_random 1667 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153196_random 1667 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157595_random 1667 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157759_random 1667 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158120_random 1667 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162170_random 1667 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162945_random 1667 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162954_random 1667 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163333_random 1667 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165354_random 1667 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166235_random 1666 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166508_random 1666 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166700_random 1666 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166774_random 1666 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166851_random 1666 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170867_random 1666 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170932_random 1666 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170943_random 1666 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170979_random 1666 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171375_random 1666 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175026_random 1666 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175052_random 1666 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175661_random 1666 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151442_random 1666 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151828_random 1666 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153355_random 1666 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156485_random 1666 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156941_random 1666 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157943_random 1666 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161634_random 1666 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163220_random 1666 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163293_random 1666 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163538_random 1666 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165156_random 1666 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166831_random 1665 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168647_random 1665 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171357_random 1665 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172282_random 1665 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174063_random 1665 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154801_random 1665 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154909_random 1665 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155042_random 1665 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156128_random 1665 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156545_random 1665 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156810_random 1665 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156944_random 1665 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156967_random 1665 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158009_random 1665 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158200_random 1665 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160033_random 1665 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163378_random 1665 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165198_random 1665 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168921_random 1664 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169976_random 1664 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170851_random 1664 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172070_random 1664 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175480_random 1664 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154643_random 1664 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156016_random 1664 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159925_random 1664 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163558_random 1664 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163575_random 1664 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163601_random 1664 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165148_random 1664 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166117_random 1663 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169957_random 1663 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170721_random 1663 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171510_random 1663 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172197_random 1663 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173970_random 1663 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174902_random 1663 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151018_random 1663 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151097_random 1663 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176696_random 1663 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177192_random 1663 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152558_random 1663 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153575_random 1663 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153611_random 1663 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154802_random 1663 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156562_random 1663 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157638_random 1663 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157919_random 1663 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158036_random 1663 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159528_random 1663 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159747_random 1663 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160161_random 1663 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163170_random 1663 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178392_random 1663 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166771_random 1662 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169695_random 1662 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169959_random 1662 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170803_random 1662 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170957_random 1662 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171406_random 1662 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173798_random 1662 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173929_random 1662 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151444_random 1662 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176749_random 1662 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177239_random 1662 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152640_random 1662 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154931_random 1662 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156184_random 1662 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156797_random 1662 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161560_random 1662 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163106_random 1662 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165288_random 1662 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178315_random 1662 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166347_random 1661 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166853_random 1661 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169554_random 1661 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169573_random 1661 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173854_random 1661 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174981_random 1661 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151327_random 1661 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153312_random 1661 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154483_random 1661 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154904_random 1661 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156670_random 1661 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156900_random 1661 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157900_random 1661 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163112_random 1661 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163328_random 1661 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165116_random 1661 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166074_random 1660 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166445_random 1660 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166757_random 1660 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168692_random 1660 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168828_random 1660 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168901_random 1660 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169522_random 1660 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171550_random 1660 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176754_random 1660 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176762_random 1660 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152552_random 1660 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153628_random 1660 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156420_random 1660 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156537_random 1660 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156599_random 1660 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157872_random 1660 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160032_random 1660 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161780_random 1660 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163116_random 1660 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165092_random 1660 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165112_random 1660 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165246_random 1660 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165287_random 1660 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165400_random 1660 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166478_random 1659 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169646_random 1659 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170990_random 1659 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171532_random 1659 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175053_random 1659 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152524_random 1659 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153384_random 1659 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154381_random 1659 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154850_random 1659 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155004_random 1659 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156684_random 1659 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156894_random 1659 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156991_random 1659 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157953_random 1659 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160237_random 1659 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165323_random 1659 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178507_random 1659 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166585_random 1658 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168945_random 1658 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169520_random 1658 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169930_random 1658 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170974_random 1658 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172135_random 1658 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172249_random 1658 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172421_random 1658 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172480_random 1658 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175505_random 1658 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151811_random 1658 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152452_random 1658 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152634_random 1658 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152739_random 1658 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152759_random 1658 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153469_random 1658 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156337_random 1658 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156433_random 1658 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156695_random 1658 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160141_random 1658 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162940_random 1658 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163521_random 1658 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166293_random 1657 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166849_random 1657 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169706_random 1657 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171006_random 1657 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172081_random 1657 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173391_random 1657 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175479_random 1657 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151148_random 1657 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151590_random 1657 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151726_random 1657 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153376_random 1657 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154201_random 1657 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154974_random 1657 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156566_random 1657 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156752_random 1657 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163120_random 1657 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166783_random 1656 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168972_random 1656 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169950_random 1656 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171669_random 1656 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172153_random 1656 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172308_random 1656 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174854_random 1656 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175691_random 1656 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151479_random 1656 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176886_random 1656 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176915_random 1656 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153610_random 1656 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154492_random 1656 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156962_random 1656 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158042_random 1656 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158047_random 1656 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158163_random 1656 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158211_random 1656 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159684_random 1656 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159959_random 1656 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160187_random 1656 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166574_random 1655 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166654_random 1655 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168832_random 1655 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168942_random 1655 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169029_random 1655 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176433_random 1655 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151473_random 1655 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153154_random 1655 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153578_random 1655 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154155_random 1655 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154708_random 1655 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154711_random 1655 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156401_random 1655 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159588_random 1655 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159692_random 1655 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159726_random 1655 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159752_random 1655 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163374_random 1655 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178500_random 1655 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178625_random 1655 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166340_random 1654 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166455_random 1654 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168638_random 1654 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173734_random 1654 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173855_random 1654 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175510_random 1654 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175573_random 1654 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176208_random 1654 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151264_random 1654 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151314_random 1654 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151430_random 1654 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151755_random 1654 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176916_random 1654 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152766_random 1654 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154319_random 1654 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154507_random 1654 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154766_random 1654 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154881_random 1654 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154890_random 1654 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154978_random 1654 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156705_random 1654 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156778_random 1654 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156947_random 1654 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157607_random 1654 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158108_random 1654 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163289_random 1654 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163316_random 1654 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178513_random 1654 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166315_random 1653 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166768_random 1653 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169828_random 1653 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170871_random 1653 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172174_random 1653 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176799_random 1653 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176933_random 1653 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152316_random 1653 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153417_random 1653 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154336_random 1653 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154725_random 1653 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154855_random 1653 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154989_random 1653 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158180_random 1653 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160127_random 1653 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162827_random 1653 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163081_random 1653 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165224_random 1653 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165279_random 1653 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166263_random 1652 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168617_random 1652 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169638_random 1652 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172441_random 1652 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176406_random 1652 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151273_random 1652 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176677_random 1652 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152449_random 1652 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153471_random 1652 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154921_random 1652 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156421_random 1652 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156482_random 1652 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156610_random 1652 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157509_random 1652 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159308_random 1652 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159594_random 1652 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163096_random 1652 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163587_random 1652 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165264_random 1652 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178418_random 1652 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166313_random 1651 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166769_random 1651 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175466_random 1651 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151008_random 1651 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151168_random 1651 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151454_random 1651 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151838_random 1651 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176820_random 1651 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153246_random 1651 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153517_random 1651 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156958_random 1651 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157957_random 1651 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158010_random 1651 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159497_random 1651 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160210_random 1651 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162064_random 1651 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163259_random 1651 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165153_random 1651 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178568_random 1651 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166691_random 1650 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169720_random 1650 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169997_random 1650 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171608_random 1650 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173851_random 1650 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176268_random 1650 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150886_random 1650 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176923_random 1650 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153626_random 1650 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154444_random 1650 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156825_random 1650 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156868_random 1650 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162032_random 1650 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162081_random 1650 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163441_random 1650 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163525_random 1650 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165045_random 1650 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178565_random 1650 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166220_random 1649 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169718_random 1649 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170895_random 1649 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173856_random 1649 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174011_random 1649 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174951_random 1649 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152266_random 1649 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153273_random 1649 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154728_random 1649 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157741_random 1649 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159920_random 1649 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163243_random 1649 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163433_random 1649 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165319_random 1649 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177983_random 1649 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166746_random 1648 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166800_random 1648 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166803_random 1648 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169785_random 1648 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170034_random 1648 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170879_random 1648 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170898_random 1648 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171513_random 1648 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171570_random 1648 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173903_random 1648 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174819_random 1648 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150656_random 1648 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151171_random 1648 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151404_random 1648 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151616_random 1648 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151806_random 1648 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176892_random 1648 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153338_random 1648 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153563_random 1648 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154075_random 1648 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156462_random 1648 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157576_random 1648 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157807_random 1648 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158099_random 1648 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162899_random 1648 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178259_random 1648 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178544_random 1648 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178572_random 1648 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166729_random 1647 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166801_random 1647 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169884_random 1647 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171569_random 1647 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171672_random 1647 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174800_random 1647 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174915_random 1647 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174930_random 1647 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150998_random 1647 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151276_random 1647 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151366_random 1647 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176934_random 1647 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/gbdb/panTro3/panTro3.2bit +chr5_AACZ03157977_random 1645 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159661_random 1645 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159926_random 1645 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160178_random 1645 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161546_random 1645 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163297_random 1645 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163606_random 1645 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178447_random 1645 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166264_random 1644 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166499_random 1644 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166788_random 1644 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168842_random 1644 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169017_random 1644 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172039_random 1644 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175609_random 1644 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175621_random 1644 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176179_random 1644 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151644_random 1644 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154947_random 1644 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155029_random 1644 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156638_random 1644 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158197_random 1644 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158243_random 1644 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159243_random 1644 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160203_random 1644 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165339_random 1644 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178574_random 1644 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166797_random 1643 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166821_random 1643 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169076_random 1643 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169657_random 1643 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174939_random 1643 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151753_random 1643 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152686_random 1643 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156722_random 1643 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158149_random 1643 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159415_random 1643 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166462_random 1642 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166667_random 1642 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166787_random 1642 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169673_random 1642 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169679_random 1642 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170854_random 1642 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172167_random 1642 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172251_random 1642 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173611_random 1642 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173906_random 1642 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151167_random 1642 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151462_random 1642 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155050_random 1642 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157998_random 1642 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158287_random 1642 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161835_random 1642 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165036_random 1642 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165221_random 1642 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166631_random 1641 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166715_random 1641 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176291_random 1641 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150897_random 1641 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151635_random 1641 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151768_random 1641 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152504_random 1641 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153289_random 1641 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156904_random 1641 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156908_random 1641 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157925_random 1641 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158129_random 1641 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160055_random 1641 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162172_random 1641 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163208_random 1641 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163589_random 1641 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165163_random 1641 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165365_random 1641 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165710_random 1640 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166750_random 1640 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166838_random 1640 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168727_random 1640 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169042_random 1640 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169113_random 1640 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170781_random 1640 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170787_random 1640 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171522_random 1640 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175012_random 1640 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176330_random 1640 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151219_random 1640 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154553_random 1640 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155001_random 1640 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156617_random 1640 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160045_random 1640 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160226_random 1640 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162093_random 1640 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162115_random 1640 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163535_random 1640 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165864_random 1639 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166845_random 1639 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169130_random 1639 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170724_random 1639 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170835_random 1639 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170850_random 1639 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171279_random 1639 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171520_random 1639 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171694_random 1639 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171697_random 1639 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173612_random 1639 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175516_random 1639 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151196_random 1639 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151541_random 1639 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151778_random 1639 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152569_random 1639 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154416_random 1639 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154755_random 1639 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156741_random 1639 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157016_random 1639 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157712_random 1639 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159665_random 1639 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163331_random 1639 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163368_random 1639 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165262_random 1639 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178202_random 1639 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/gbdb/panTro3/panTro3.2bit +chr1_AACZ03151733_random 1638 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176942_random 1638 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152182_random 1638 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152564_random 1638 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153320_random 1638 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154363_random 1638 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154403_random 1638 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154511_random 1638 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154803_random 1638 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156601_random 1638 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156901_random 1638 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157892_random 1638 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160202_random 1638 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165352_random 1638 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178412_random 1638 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166798_random 1637 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166888_random 1637 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169043_random 1637 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170775_random 1637 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170815_random 1637 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172420_random 1637 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172491_random 1637 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173512_random 1637 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173918_random 1637 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174917_random 1637 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176203_random 1637 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176331_random 1637 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176918_random 1637 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152706_random 1637 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154846_random 1637 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160051_random 1637 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162046_random 1637 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162137_random 1637 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164744_random 1637 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165158_random 1637 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165379_random 1637 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178475_random 1637 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166614_random 1636 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170040_random 1636 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171668_random 1636 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173631_random 1636 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176278_random 1636 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176845_random 1636 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152514_random 1636 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152770_random 1636 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153366_random 1636 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153426_random 1636 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154937_random 1636 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156512_random 1636 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156639_random 1636 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157709_random 1636 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157847_random 1636 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162730_random 1636 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163020_random 1636 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163505_random 1636 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165150_random 1636 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166150_random 1635 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168735_random 1635 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169835_random 1635 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170924_random 1635 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172485_random 1635 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174916_random 1635 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174977_random 1635 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175015_random 1635 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176337_random 1635 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151195_random 1635 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177251_random 1635 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152767_random 1635 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153507_random 1635 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154589_random 1635 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157687_random 1635 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160172_random 1635 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160234_random 1635 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163061_random 1635 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163201_random 1635 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163255_random 1635 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163402_random 1635 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165154_random 1635 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165280_random 1635 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166200_random 1634 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166321_random 1634 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168807_random 1634 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169766_random 1634 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169939_random 1634 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172212_random 1634 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172507_random 1634 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173626_random 1634 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175586_random 1634 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176299_random 1634 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176392_random 1634 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176408_random 1634 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151368_random 1634 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151595_random 1634 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176943_random 1634 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153582_random 1634 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154442_random 1634 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156352_random 1634 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156662_random 1634 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156843_random 1634 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156854_random 1634 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156884_random 1634 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157018_random 1634 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157961_random 1634 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158283_random 1634 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159879_random 1634 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160157_random 1634 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160184_random 1634 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161787_random 1634 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163549_random 1634 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166291_random 1633 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169046_random 1633 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171540_random 1633 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175409_random 1633 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151221_random 1633 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151339_random 1633 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151579_random 1633 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151626_random 1633 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151693_random 1633 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152592_random 1633 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152746_random 1633 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153329_random 1633 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154869_random 1633 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154886_random 1633 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155014_random 1633 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159704_random 1633 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160135_random 1633 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160138_random 1633 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163036_random 1633 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163167_random 1633 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163385_random 1633 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163567_random 1633 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166164_random 1632 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168427_random 1632 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168745_random 1632 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169887_random 1632 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171619_random 1632 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174050_random 1632 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176885_random 1632 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152545_random 1632 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153402_random 1632 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155005_random 1632 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157811_random 1632 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158278_random 1632 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165243_random 1632 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178610_random 1632 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168806_random 1631 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168874_random 1631 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169726_random 1631 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170660_random 1631 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171537_random 1631 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172397_random 1631 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172422_random 1631 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173819_random 1631 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174043_random 1631 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150895_random 1631 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153533_random 1631 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154956_random 1631 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156959_random 1631 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157916_random 1631 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157960_random 1631 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158093_random 1631 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158133_random 1631 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159843_random 1631 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159982_random 1631 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178183_random 1631 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178429_random 1631 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166252_random 1630 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166260_random 1630 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166377_random 1630 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168800_random 1630 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168911_random 1630 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169651_random 1630 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169767_random 1630 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169816_random 1630 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171658_random 1630 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172229_random 1630 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173595_random 1630 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173932_random 1630 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174031_random 1630 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175599_random 1630 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176341_random 1630 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177168_random 1630 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153593_random 1630 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154329_random 1630 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156697_random 1630 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156976_random 1630 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178348_random 1630 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178456_random 1630 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168508_random 1629 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169490_random 1629 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169576_random 1629 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169735_random 1629 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169893_random 1629 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169941_random 1629 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172190_random 1629 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174626_random 1629 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174968_random 1629 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175018_random 1629 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151537_random 1629 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176920_random 1629 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152448_random 1629 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154996_random 1629 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156561_random 1629 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163336_random 1629 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163512_random 1629 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165176_random 1629 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165232_random 1629 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165344_random 1629 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178542_random 1629 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166328_random 1628 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166753_random 1628 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168708_random 1628 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169496_random 1628 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169966_random 1628 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169987_random 1628 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171642_random 1628 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172482_random 1628 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173958_random 1628 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175048_random 1628 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176146_random 1628 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176795_random 1628 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152714_random 1628 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156649_random 1628 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158034_random 1628 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158152_random 1628 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159533_random 1628 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159845_random 1628 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160027_random 1628 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160038_random 1628 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163344_random 1628 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178458_random 1628 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178554_random 1628 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166131_random 1627 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166643_random 1627 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169045_random 1627 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170911_random 1627 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171651_random 1627 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172490_random 1627 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174944_random 1627 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175654_random 1627 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150745_random 1627 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151156_random 1627 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176861_random 1627 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177195_random 1627 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153282_random 1627 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154534_random 1627 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154627_random 1627 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155035_random 1627 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156321_random 1627 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156348_random 1627 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156579_random 1627 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156612_random 1627 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156915_random 1627 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157547_random 1627 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159989_random 1627 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160113_random 1627 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162802_random 1627 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162906_random 1627 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163425_random 1627 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166511_random 1626 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169635_random 1626 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169905_random 1626 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169913_random 1626 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170049_random 1626 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170078_random 1626 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175683_random 1626 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176190_random 1626 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151070_random 1626 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151604_random 1626 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151834_random 1626 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176864_random 1626 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154940_random 1626 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156604_random 1626 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156707_random 1626 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156886_random 1626 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156920_random 1626 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157530_random 1626 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157832_random 1626 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158095_random 1626 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159530_random 1626 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163086_random 1626 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165277_random 1626 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178229_random 1626 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178592_random 1626 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166051_random 1625 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166390_random 1625 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170081_random 1625 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174824_random 1625 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175029_random 1625 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/gbdb/panTro3/panTro3.2bit +chr13_AACZ03170910_random 1624 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171518_random 1624 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175598_random 1624 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151670_random 1624 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151738_random 1624 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176922_random 1624 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152662_random 1624 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154136_random 1624 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154733_random 1624 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158124_random 1624 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159642_random 1624 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159835_random 1624 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161969_random 1624 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163517_random 1624 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164982_random 1624 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165258_random 1624 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178246_random 1624 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178423_random 1624 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166629_random 1623 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168816_random 1623 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169574_random 1623 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173724_random 1623 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173908_random 1623 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173960_random 1623 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175040_random 1623 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175452_random 1623 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175455_random 1623 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151464_random 1623 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151486_random 1623 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151547_random 1623 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151663_random 1623 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151804_random 1623 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154392_random 1623 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154480_random 1623 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154645_random 1623 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154731_random 1623 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157690_random 1623 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157751_random 1623 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159579_random 1623 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159685_random 1623 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160145_random 1623 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160201_random 1623 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161701_random 1623 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163426_random 1623 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165387_random 1623 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166135_random 1622 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166503_random 1622 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169809_random 1622 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171007_random 1622 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172404_random 1622 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174807_random 1622 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175481_random 1622 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175611_random 1622 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175623_random 1622 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151437_random 1622 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151780_random 1622 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152445_random 1622 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153635_random 1622 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154906_random 1622 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156627_random 1622 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156798_random 1622 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157586_random 1622 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159481_random 1622 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159932_random 1622 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159947_random 1622 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161615_random 1622 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162085_random 1622 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163519_random 1622 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163526_random 1622 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166224_random 1621 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166346_random 1621 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166406_random 1621 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169599_random 1621 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175010_random 1621 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175626_random 1621 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176399_random 1621 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150770_random 1621 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151074_random 1621 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152533_random 1621 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152748_random 1621 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154688_random 1621 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156411_random 1621 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157881_random 1621 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159809_random 1621 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162071_random 1621 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163508_random 1621 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164882_random 1621 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165936_random 1620 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166304_random 1620 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166836_random 1620 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168783_random 1620 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168982_random 1620 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169455_random 1620 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169962_random 1620 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169992_random 1620 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170608_random 1620 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171468_random 1620 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173334_random 1620 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173754_random 1620 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151076_random 1620 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151621_random 1620 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153385_random 1620 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153457_random 1620 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154312_random 1620 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156924_random 1620 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158214_random 1620 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161874_random 1620 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163504_random 1620 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165089_random 1620 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165166_random 1620 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178495_random 1620 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166570_random 1619 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169063_random 1619 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169971_random 1619 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170886_random 1619 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171623_random 1619 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172352_random 1619 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176220_random 1619 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150915_random 1619 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151385_random 1619 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151501_random 1619 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152358_random 1619 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154905_random 1619 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154944_random 1619 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159576_random 1619 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160197_random 1619 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160199_random 1619 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163395_random 1619 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163449_random 1619 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165032_random 1619 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178601_random 1619 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165828_random 1618 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166509_random 1618 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166555_random 1618 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166852_random 1618 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166877_random 1618 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169982_random 1618 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171583_random 1618 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172351_random 1618 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151345_random 1618 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151632_random 1618 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152583_random 1618 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154316_random 1618 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154747_random 1618 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156687_random 1618 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156713_random 1618 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156858_random 1618 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156971_random 1618 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157719_random 1618 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157848_random 1618 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159339_random 1618 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159765_random 1618 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160147_random 1618 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164873_random 1618 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166336_random 1617 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168989_random 1617 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169070_random 1617 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171582_random 1617 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172266_random 1617 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172388_random 1617 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173638_random 1617 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173757_random 1617 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175020_random 1617 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175557_random 1617 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151636_random 1617 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176839_random 1617 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152417_random 1617 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152606_random 1617 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153478_random 1617 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154383_random 1617 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154864_random 1617 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155020_random 1617 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156468_random 1617 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157922_random 1617 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159785_random 1617 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163435_random 1617 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166058_random 1616 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166456_random 1616 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166513_random 1616 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166751_random 1616 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166889_random 1616 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168936_random 1616 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169093_random 1616 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169637_random 1616 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169985_random 1616 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171684_random 1616 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172438_random 1616 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173971_random 1616 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174028_random 1616 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175629_random 1616 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175674_random 1616 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151504_random 1616 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152574_random 1616 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153187_random 1616 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153493_random 1616 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153549_random 1616 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154382_random 1616 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155009_random 1616 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156685_random 1616 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157767_random 1616 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158258_random 1616 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161842_random 1616 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178274_random 1616 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166662_random 1615 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/gbdb/panTro3/panTro3.2bit +chr4_AACZ03156322_random 1614 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158238_random 1614 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158246_random 1614 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158267_random 1614 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159368_random 1614 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160182_random 1614 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160233_random 1614 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161760_random 1614 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164774_random 1614 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166522_random 1613 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166672_random 1613 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169118_random 1613 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169725_random 1613 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170794_random 1613 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170860_random 1613 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172354_random 1613 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176394_random 1613 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152753_random 1613 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153434_random 1613 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154608_random 1613 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154734_random 1613 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154914_random 1613 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154943_random 1613 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156732_random 1613 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156864_random 1613 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163193_random 1613 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178489_random 1613 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168922_random 1612 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169002_random 1612 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171536_random 1612 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172214_random 1612 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173772_random 1612 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151002_random 1612 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152614_random 1612 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/gbdb/panTro3/panTro3.2bit +chr15_AACZ03172444_random 1611 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175618_random 1611 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151169_random 1611 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151617_random 1611 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176775_random 1611 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176819_random 1611 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154981_random 1611 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155000_random 1611 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157619_random 1611 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157971_random 1611 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158231_random 1611 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158311_random 1611 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163261_random 1611 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163597_random 1611 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164968_random 1611 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178512_random 1611 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166096_random 1610 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/gbdb/panTro3/panTro3.2bit +chr3_AACZ03154991_random 1610 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156986_random 1610 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158048_random 1610 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160125_random 1610 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161764_random 1610 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163548_random 1610 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163581_random 1610 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165182_random 1610 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169938_random 1609 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170008_random 1609 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170799_random 1609 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172502_random 1609 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173875_random 1609 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174040_random 1609 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175415_random 1609 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176393_random 1609 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151612_random 1609 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151711_random 1609 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176688_random 1609 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152617_random 1609 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153496_random 1609 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156455_random 1609 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156754_random 1609 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156834_random 1609 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159606_random 1609 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164765_random 1609 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178410_random 1609 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178428_random 1609 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166287_random 1608 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166468_random 1608 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168834_random 1608 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171605_random 1608 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172462_random 1608 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174019_random 1608 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175640_random 1608 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151678_random 1608 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177213_random 1608 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152402_random 1608 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153158_random 1608 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153418_random 1608 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153475_random 1608 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153499_random 1608 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154300_random 1608 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156310_random 1608 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157017_random 1608 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157905_random 1608 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159952_random 1608 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160070_random 1608 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163532_random 1608 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165096_random 1608 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165228_random 1608 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178480_random 1608 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178533_random 1608 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169018_random 1607 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175314_random 1607 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151267_random 1607 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151817_random 1607 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177130_random 1607 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152697_random 1607 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152774_random 1607 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153541_random 1607 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154467_random 1607 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154660_random 1607 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155059_random 1607 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156443_random 1607 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156571_random 1607 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156593_random 1607 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156961_random 1607 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159524_random 1607 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159854_random 1607 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159911_random 1607 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163528_random 1607 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166565_random 1606 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166572_random 1606 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166674_random 1606 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166738_random 1606 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166844_random 1606 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166876_random 1606 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168908_random 1606 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170970_random 1606 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171405_random 1606 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171610_random 1606 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176851_random 1606 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154712_random 1606 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154816_random 1606 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156069_random 1606 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157539_random 1606 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157890_random 1606 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158255_random 1606 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160165_random 1606 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166792_random 1605 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168741_random 1605 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169825_random 1605 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171004_random 1605 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171588_random 1605 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171617_random 1605 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172380_random 1605 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172392_random 1605 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172469_random 1605 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150959_random 1605 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151499_random 1605 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151588_random 1605 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152501_random 1605 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152772_random 1605 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153334_random 1605 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154791_random 1605 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155027_random 1605 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156795_random 1605 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162963_random 1605 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163639_random 1605 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165057_random 1605 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165242_random 1605 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166543_random 1604 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168673_random 1604 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170771_random 1604 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171476_random 1604 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172473_random 1604 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176118_random 1604 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150960_random 1604 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151290_random 1604 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176818_random 1604 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154536_random 1604 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155036_random 1604 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160042_random 1604 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160244_random 1604 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161991_random 1604 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162951_random 1604 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162958_random 1604 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163450_random 1604 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169124_random 1603 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170080_random 1603 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170870_random 1603 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171714_random 1603 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174837_random 1603 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174874_random 1603 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176410_random 1603 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151326_random 1603 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152618_random 1603 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154285_random 1603 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154485_random 1603 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154759_random 1603 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156192_random 1603 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156853_random 1603 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157567_random 1603 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157618_random 1603 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157693_random 1603 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157885_random 1603 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158115_random 1603 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158295_random 1603 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159915_random 1603 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159919_random 1603 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159965_random 1603 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160143_random 1603 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160227_random 1603 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163511_random 1603 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164955_random 1603 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166040_random 1602 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166253_random 1602 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169099_random 1602 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169747_random 1602 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170928_random 1602 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172455_random 1602 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173886_random 1602 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173925_random 1602 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176369_random 1602 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152421_random 1602 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154932_random 1602 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157646_random 1602 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157801_random 1602 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157846_random 1602 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159105_random 1602 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163559_random 1602 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164790_random 1602 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164946_random 1602 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165360_random 1602 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178454_random 1602 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166673_random 1601 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166727_random 1601 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166765_random 1601 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168981_random 1601 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169769_random 1601 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170788_random 1601 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171595_random 1601 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171708_random 1601 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171710_random 1601 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175506_random 1601 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151441_random 1601 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151474_random 1601 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153627_random 1601 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156575_random 1601 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156846_random 1601 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158218_random 1601 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158296_random 1601 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159738_random 1601 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160011_random 1601 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165378_random 1601 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178461_random 1601 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178617_random 1601 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166217_random 1600 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168892_random 1600 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171359_random 1600 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171682_random 1600 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171719_random 1600 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174675_random 1600 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174725_random 1600 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175589_random 1600 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176122_random 1600 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150847_random 1600 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151261_random 1600 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151325_random 1600 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176650_random 1600 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153221_random 1600 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153494_random 1600 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154547_random 1600 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154872_random 1600 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156543_random 1600 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156608_random 1600 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160099_random 1600 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162106_random 1600 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169096_random 1599 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169744_random 1599 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171543_random 1599 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173895_random 1599 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175478_random 1599 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151186_random 1599 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151303_random 1599 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156784_random 1599 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157763_random 1599 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157771_random 1599 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160185_random 1599 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160198_random 1599 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163249_random 1599 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164948_random 1599 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178561_random 1599 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165980_random 1598 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166590_random 1598 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168481_random 1598 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172225_random 1598 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172356_random 1598 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172398_random 1598 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173640_random 1598 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173885_random 1598 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174960_random 1598 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151460_random 1598 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151766_random 1598 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153128_random 1598 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153160_random 1598 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153522_random 1598 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153634_random 1598 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154549_random 1598 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154742_random 1598 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154972_random 1598 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156983_random 1598 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157884_random 1598 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159713_random 1598 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159772_random 1598 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160246_random 1598 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162162_random 1598 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163494_random 1598 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166531_random 1597 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166665_random 1597 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166778_random 1597 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168728_random 1597 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169023_random 1597 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172378_random 1597 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173616_random 1597 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175547_random 1597 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156312_random 1597 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156313_random 1597 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156805_random 1597 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157804_random 1597 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158011_random 1597 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162890_random 1597 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163176_random 1597 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178199_random 1597 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166144_random 1596 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174881_random 1596 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174956_random 1596 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175060_random 1596 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175350_random 1596 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176381_random 1596 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150921_random 1596 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150973_random 1596 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151478_random 1596 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151707_random 1596 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177200_random 1596 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152577_random 1596 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154792_random 1596 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156173_random 1596 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156859_random 1596 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157985_random 1596 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158150_random 1596 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158251_random 1596 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160196_random 1596 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162068_random 1596 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162114_random 1596 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163354_random 1596 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163369_random 1596 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165059_random 1596 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165349_random 1596 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178606_random 1596 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166492_random 1595 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169664_random 1595 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169801_random 1595 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170812_random 1595 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174029_random 1595 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175051_random 1595 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175608_random 1595 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175651_random 1595 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151683_random 1595 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151723_random 1595 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177211_random 1595 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152685_random 1595 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152702_random 1595 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153219_random 1595 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154097_random 1595 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154583_random 1595 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154979_random 1595 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157012_random 1595 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157909_random 1595 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157910_random 1595 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159778_random 1595 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161979_random 1595 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163204_random 1595 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163357_random 1595 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163593_random 1595 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164962_random 1595 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166091_random 1594 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166457_random 1594 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168882_random 1594 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169655_random 1594 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169703_random 1594 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169937_random 1594 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170706_random 1594 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150710_random 1594 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150887_random 1594 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151375_random 1594 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176722_random 1594 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152500_random 1594 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154888_random 1594 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156476_random 1594 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159923_random 1594 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160040_random 1594 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160120_random 1594 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160168_random 1594 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161774_random 1594 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163239_random 1594 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165165_random 1594 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178508_random 1594 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178613_random 1594 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166052_random 1593 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166204_random 1593 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166745_random 1593 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169691_random 1593 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169928_random 1593 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169951_random 1593 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171498_random 1593 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172483_random 1593 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173657_random 1593 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173957_random 1593 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174032_random 1593 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150868_random 1593 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151507_random 1593 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176825_random 1593 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153231_random 1593 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153590_random 1593 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154680_random 1593 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155045_random 1593 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159741_random 1593 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160085_random 1593 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164980_random 1593 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165169_random 1593 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165200_random 1593 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178408_random 1593 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178563_random 1593 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178619_random 1593 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165899_random 1592 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165940_random 1592 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166182_random 1592 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168316_random 1592 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168379_random 1592 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171021_random 1592 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171032_random 1592 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171347_random 1592 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172467_random 1592 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175686_random 1592 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151485_random 1592 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151634_random 1592 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176638_random 1592 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154502_random 1592 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154698_random 1592 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157956_random 1592 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158209_random 1592 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158233_random 1592 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159992_random 1592 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160059_random 1592 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160186_random 1592 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163412_random 1592 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164903_random 1592 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165401_random 1592 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166556_random 1591 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166688_random 1591 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169008_random 1591 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169106_random 1591 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169416_random 1591 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169885_random 1591 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169952_random 1591 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171376_random 1591 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171579_random 1591 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171585_random 1591 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171701_random 1591 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173646_random 1591 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173962_random 1591 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174918_random 1591 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176153_random 1591 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176155_random 1591 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151370_random 1591 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152752_random 1591 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153237_random 1591 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153328_random 1591 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153485_random 1591 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153596_random 1591 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153608_random 1591 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154231_random 1591 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156688_random 1591 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156753_random 1591 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156807_random 1591 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158262_random 1591 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159819_random 1591 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160031_random 1591 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160043_random 1591 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161966_random 1591 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163271_random 1591 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163495_random 1591 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163568_random 1591 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165066_random 1591 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178546_random 1591 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168933_random 1590 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170869_random 1590 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170942_random 1590 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171564_random 1590 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172419_random 1590 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151384_random 1590 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151390_random 1590 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176866_random 1590 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152416_random 1590 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153484_random 1590 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154377_random 1590 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154723_random 1590 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154853_random 1590 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156518_random 1590 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156651_random 1590 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157954_random 1590 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158141_random 1590 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160020_random 1590 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160136_random 1590 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163050_random 1590 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163644_random 1590 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165134_random 1590 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178553_random 1590 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166197_random 1589 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166325_random 1589 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166635_random 1589 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168967_random 1589 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174035_random 1589 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174903_random 1589 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175385_random 1589 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175572_random 1589 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175628_random 1589 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175687_random 1589 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151503_random 1589 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176759_random 1589 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152721_random 1589 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154694_random 1589 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154741_random 1589 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154794_random 1589 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156490_random 1589 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156557_random 1589 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156821_random 1589 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156857_random 1589 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157575_random 1589 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157967_random 1589 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158023_random 1589 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160188_random 1589 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163181_random 1589 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163212_random 1589 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165355_random 1589 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178333_random 1589 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178618_random 1589 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166884_random 1588 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168765_random 1588 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169840_random 1588 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171652_random 1588 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152734_random 1588 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153602_random 1588 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153620_random 1588 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154683_random 1588 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156828_random 1588 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158040_random 1588 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158261_random 1588 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159604_random 1588 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159955_random 1588 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160090_random 1588 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160204_random 1588 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161655_random 1588 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164971_random 1588 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165012_random 1588 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165190_random 1588 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165261_random 1588 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178401_random 1588 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178541_random 1588 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178549_random 1588 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165952_random 1587 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166288_random 1587 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166650_random 1587 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166659_random 1587 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166842_random 1587 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169074_random 1587 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169989_random 1587 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172427_random 1587 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173635_random 1587 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173979_random 1587 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174892_random 1587 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175563_random 1587 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150979_random 1587 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151407_random 1587 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151765_random 1587 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151782_random 1587 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176668_random 1587 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176949_random 1587 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154192_random 1587 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154324_random 1587 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157727_random 1587 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159720_random 1587 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159795_random 1587 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160030_random 1587 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163027_random 1587 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163321_random 1587 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163342_random 1587 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163562_random 1587 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165067_random 1587 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165396_random 1587 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177931_random 1587 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178523_random 1587 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166827_random 1586 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166837_random 1586 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168817_random 1586 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169103_random 1586 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170969_random 1586 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170972_random 1586 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170991_random 1586 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171673_random 1586 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173572_random 1586 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176259_random 1586 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151417_random 1586 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151534_random 1586 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151565_random 1586 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151839_random 1586 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177235_random 1586 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177258_random 1586 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152597_random 1586 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153279_random 1586 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153382_random 1586 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156893_random 1586 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157572_random 1586 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157585_random 1586 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159719_random 1586 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159910_random 1586 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160007_random 1586 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160035_random 1586 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161896_random 1586 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161992_random 1586 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163130_random 1586 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163278_random 1586 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163372_random 1586 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163479_random 1586 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163628_random 1586 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166619_random 1585 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168898_random 1585 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168940_random 1585 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169067_random 1585 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169529_random 1585 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169533_random 1585 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169940_random 1585 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171679_random 1585 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172274_random 1585 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172453_random 1585 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172470_random 1585 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173743_random 1585 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173870_random 1585 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174062_random 1585 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175514_random 1585 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176422_random 1585 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151563_random 1585 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151627_random 1585 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152582_random 1585 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154692_random 1585 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157715_random 1585 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157865_random 1585 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158019_random 1585 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163048_random 1585 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165113_random 1585 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178197_random 1585 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178398_random 1585 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166083_random 1584 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166702_random 1584 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169719_random 1584 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169746_random 1584 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170941_random 1584 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172348_random 1584 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172366_random 1584 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172411_random 1584 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174846_random 1584 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174913_random 1584 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150904_random 1584 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151829_random 1584 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152505_random 1584 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152730_random 1584 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154635_random 1584 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154781_random 1584 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154796_random 1584 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154836_random 1584 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156756_random 1584 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156762_random 1584 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159474_random 1584 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159984_random 1584 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161649_random 1584 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161798_random 1584 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161897_random 1584 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161921_random 1584 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163143_random 1584 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163148_random 1584 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164942_random 1584 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178399_random 1584 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178559_random 1584 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166551_random 1583 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166628_random 1583 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168678_random 1583 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168812_random 1583 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168909_random 1583 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170753_random 1583 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170843_random 1583 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171002_random 1583 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171592_random 1583 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171661_random 1583 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172347_random 1583 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172451_random 1583 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174699_random 1583 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175633_random 1583 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176844_random 1583 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177256_random 1583 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152720_random 1583 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154164_random 1583 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154889_random 1583 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154897_random 1583 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154920_random 1583 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154959_random 1583 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158280_random 1583 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159779_random 1583 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165131_random 1583 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178357_random 1583 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166476_random 1582 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166655_random 1582 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166684_random 1582 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166806_random 1582 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169738_random 1582 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170714_random 1582 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171364_random 1582 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171486_random 1582 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171506_random 1582 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171713_random 1582 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173627_random 1582 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175501_random 1582 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175627_random 1582 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176921_random 1582 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152491_random 1582 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152555_random 1582 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152566_random 1582 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152744_random 1582 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153500_random 1582 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154384_random 1582 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156865_random 1582 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159683_random 1582 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159987_random 1582 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161781_random 1582 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163312_random 1582 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165371_random 1582 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165392_random 1582 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178482_random 1582 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166739_random 1581 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169116_random 1581 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172341_random 1581 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173636_random 1581 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173865_random 1581 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176265_random 1581 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151701_random 1581 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177184_random 1581 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152570_random 1581 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153358_random 1581 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154745_random 1581 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156890_random 1581 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160205_random 1581 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160252_random 1581 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161531_random 1581 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161999_random 1581 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163103_random 1581 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163411_random 1581 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163557_random 1581 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178485_random 1581 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178496_random 1581 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178558_random 1581 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166214_random 1580 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166816_random 1580 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168852_random 1580 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168960_random 1580 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169115_random 1580 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169567_random 1580 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169927_random 1580 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172440_random 1580 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173891_random 1580 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175027_random 1580 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175643_random 1580 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176430_random 1580 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151589_random 1580 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151823_random 1580 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176875_random 1580 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177225_random 1580 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152674_random 1580 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156323_random 1580 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157596_random 1580 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158007_random 1580 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160006_random 1580 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160107_random 1580 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161694_random 1580 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162120_random 1580 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163554_random 1580 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178380_random 1580 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166371_random 1579 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166869_random 1579 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171590_random 1579 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172386_random 1579 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175542_random 1579 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151149_random 1579 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151320_random 1579 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152508_random 1579 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153566_random 1579 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154777_random 1579 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154845_random 1579 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155057_random 1579 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156647_random 1579 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156835_random 1579 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157484_random 1579 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158244_random 1579 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159559_random 1579 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160163_random 1579 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160181_random 1579 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160206_random 1579 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161949_random 1579 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162111_random 1579 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165285_random 1579 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178248_random 1579 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178587_random 1579 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166693_random 1578 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168583_random 1578 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168944_random 1578 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173847_random 1578 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174022_random 1578 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174052_random 1578 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175046_random 1578 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150913_random 1578 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151313_random 1578 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151388_random 1578 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177266_random 1578 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153192_random 1578 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153300_random 1578 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154603_random 1578 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154616_random 1578 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154697_random 1578 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154998_random 1578 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156796_random 1578 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157754_random 1578 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158071_random 1578 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159567_random 1578 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159903_random 1578 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160115_random 1578 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160119_random 1578 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165072_random 1578 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178453_random 1578 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178569_random 1578 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166541_random 1577 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166867_random 1577 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166885_random 1577 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168784_random 1577 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169108_random 1577 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170028_random 1577 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170937_random 1577 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174969_random 1577 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174998_random 1577 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176325_random 1577 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151101_random 1577 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151790_random 1577 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152743_random 1577 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154568_random 1577 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154840_random 1577 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154856_random 1577 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156820_random 1577 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157938_random 1577 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158122_random 1577 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159536_random 1577 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159691_random 1577 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159857_random 1577 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159941_random 1577 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163282_random 1577 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163410_random 1577 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164717_random 1577 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165395_random 1577 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166554_random 1576 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166756_random 1576 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168789_random 1576 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169069_random 1576 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169995_random 1576 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173866_random 1576 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174810_random 1576 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175007_random 1576 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175678_random 1576 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176432_random 1576 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151710_random 1576 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176800_random 1576 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177269_random 1576 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152541_random 1576 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153570_random 1576 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154457_random 1576 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154854_random 1576 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158217_random 1576 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158289_random 1576 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160159_random 1576 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161732_random 1576 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162967_random 1576 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163451_random 1576 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163522_random 1576 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178471_random 1576 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166547_random 1575 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166567_random 1575 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168855_random 1575 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170076_random 1575 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171030_random 1575 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172342_random 1575 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172368_random 1575 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174879_random 1575 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175005_random 1575 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175592_random 1575 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150817_random 1575 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151586_random 1575 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153556_random 1575 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154969_random 1575 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156135_random 1575 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156607_random 1575 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161654_random 1575 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163032_random 1575 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163608_random 1575 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165073_random 1575 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165074_random 1575 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178417_random 1575 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166420_random 1574 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168711_random 1574 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168931_random 1574 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169039_random 1574 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169978_random 1574 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172235_random 1574 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176333_random 1574 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151645_random 1574 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151697_random 1574 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176704_random 1574 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176901_random 1574 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177267_random 1574 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153189_random 1574 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153379_random 1574 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154527_random 1574 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156442_random 1574 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156671_random 1574 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157795_random 1574 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157986_random 1574 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158293_random 1574 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159632_random 1574 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160116_random 1574 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160207_random 1574 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163044_random 1574 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166348_random 1573 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166617_random 1573 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168980_random 1573 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170690_random 1573 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170985_random 1573 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173991_random 1573 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175482_random 1573 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151306_random 1573 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151685_random 1573 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176672_random 1573 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152432_random 1573 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152689_random 1573 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154488_random 1573 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154721_random 1573 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156823_random 1573 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156866_random 1573 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156978_random 1573 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160183_random 1573 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163338_random 1573 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165260_random 1573 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178421_random 1573 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166255_random 1572 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166716_random 1572 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169730_random 1572 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169763_random 1572 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169872_random 1572 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171388_random 1572 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173427_random 1572 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173987_random 1572 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174064_random 1572 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175022_random 1572 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151822_random 1572 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176791_random 1572 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152615_random 1572 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153212_random 1572 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153364_random 1572 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154402_random 1572 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154425_random 1572 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154744_random 1572 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157886_random 1572 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158086_random 1572 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159670_random 1572 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161841_random 1572 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161994_random 1572 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163414_random 1572 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163599_random 1572 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163609_random 1572 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165143_random 1572 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178431_random 1572 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166517_random 1571 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168903_random 1571 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169024_random 1571 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169086_random 1571 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170063_random 1571 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171023_random 1571 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174876_random 1571 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175632_random 1571 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176315_random 1571 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151797_random 1571 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152731_random 1571 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152740_random 1571 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153233_random 1571 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154858_random 1571 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154862_random 1571 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154922_random 1571 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154942_random 1571 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156422_random 1571 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156711_random 1571 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156928_random 1571 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156956_random 1571 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156985_random 1571 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157020_random 1571 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157669_random 1571 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158136_random 1571 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158215_random 1571 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159600_random 1571 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160092_random 1571 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160129_random 1571 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160256_random 1571 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165016_random 1571 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166363_random 1570 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166785_random 1570 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169799_random 1570 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171026_random 1570 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171571_random 1570 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175374_random 1570 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176349_random 1570 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151042_random 1570 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151456_random 1570 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151533_random 1570 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151731_random 1570 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176867_random 1570 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152380_random 1570 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153470_random 1570 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153574_random 1570 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154330_random 1570 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155033_random 1570 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156230_random 1570 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158131_random 1570 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160086_random 1570 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163280_random 1570 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163484_random 1570 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165327_random 1570 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178497_random 1570 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166171_random 1569 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166228_random 1569 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166494_random 1569 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172476_random 1569 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151305_random 1569 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151696_random 1569 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152547_random 1569 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154505_random 1569 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155047_random 1569 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156319_random 1569 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156739_random 1569 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159674_random 1569 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159961_random 1569 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163507_random 1569 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165129_random 1569 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178194_random 1569 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178607_random 1569 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165911_random 1568 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168925_random 1568 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168951_random 1568 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169634_random 1568 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169687_random 1568 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171725_random 1568 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172240_random 1568 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175548_random 1568 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152604_random 1568 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153454_random 1568 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154326_random 1568 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154559_random 1568 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157000_random 1568 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161964_random 1568 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163598_random 1568 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165050_random 1568 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165083_random 1568 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165136_random 1568 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165340_random 1568 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178451_random 1568 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178491_random 1568 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168948_random 1567 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169795_random 1567 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169994_random 1567 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171334_random 1567 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171687_random 1567 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175023_random 1567 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175400_random 1567 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175549_random 1567 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175613_random 1567 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151416_random 1567 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151692_random 1567 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151821_random 1567 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152532_random 1567 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152625_random 1567 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152780_random 1567 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153597_random 1567 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156876_random 1567 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157803_random 1567 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158205_random 1567 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163371_random 1567 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163503_random 1567 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163514_random 1567 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165024_random 1567 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165278_random 1567 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165281_random 1567 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178560_random 1567 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166381_random 1566 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169058_random 1566 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170878_random 1566 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170899_random 1566 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171028_random 1566 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171657_random 1566 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173716_random 1566 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174002_random 1566 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175509_random 1566 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175575_random 1566 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176111_random 1566 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151369_random 1566 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151522_random 1566 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153514_random 1566 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154919_random 1566 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156667_random 1566 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156838_random 1566 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156855_random 1566 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158158_random 1566 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159895_random 1566 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169061_random 1565 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171615_random 1565 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172201_random 1565 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173952_random 1565 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175699_random 1565 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176346_random 1565 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151131_random 1565 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151771_random 1565 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152579_random 1565 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153526_random 1565 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153564_random 1565 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156973_random 1565 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162055_random 1565 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162787_random 1565 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166207_random 1564 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166645_random 1564 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166847_random 1564 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170776_random 1564 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170949_random 1564 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170971_random 1564 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172313_random 1564 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172426_random 1564 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175445_random 1564 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175647_random 1564 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176262_random 1564 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151367_random 1564 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151794_random 1564 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176881_random 1564 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152520_random 1564 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152648_random 1564 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153188_random 1564 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153455_random 1564 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153554_random 1564 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156743_random 1564 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156816_random 1564 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157982_random 1564 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157994_random 1564 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158033_random 1564 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159718_random 1564 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160228_random 1564 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163469_random 1564 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178543_random 1564 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166830_random 1563 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170068_random 1563 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172481_random 1563 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172488_random 1563 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175396_random 1563 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176353_random 1563 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176420_random 1563 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151694_random 1563 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151774_random 1563 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154446_random 1563 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154983_random 1563 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158286_random 1563 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159743_random 1563 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159853_random 1563 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159907_random 1563 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160255_random 1563 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160259_random 1563 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161697_random 1563 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163614_random 1563 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165970_random 1562 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166694_random 1562 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169105_random 1562 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170876_random 1562 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171416_random 1562 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172234_random 1562 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173915_random 1562 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174072_random 1562 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174073_random 1562 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176212_random 1562 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176340_random 1562 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176400_random 1562 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151226_random 1562 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151529_random 1562 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151844_random 1562 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177246_random 1562 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152658_random 1562 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153055_random 1562 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153111_random 1562 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153356_random 1562 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154299_random 1562 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154839_random 1562 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154994_random 1562 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156499_random 1562 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156794_random 1562 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156803_random 1562 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156979_random 1562 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157959_random 1562 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158030_random 1562 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158073_random 1562 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158234_random 1562 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159771_random 1562 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159792_random 1562 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160005_random 1562 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161908_random 1562 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164996_random 1562 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178400_random 1562 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178616_random 1562 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166036_random 1561 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166364_random 1561 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166553_random 1561 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168747_random 1561 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170026_random 1561 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170786_random 1561 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170921_random 1561 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170978_random 1561 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172489_random 1561 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173458_random 1561 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176191_random 1561 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176350_random 1561 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151274_random 1561 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151580_random 1561 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152646_random 1561 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152728_random 1561 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152773_random 1561 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153336_random 1561 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154966_random 1561 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156975_random 1561 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156997_random 1561 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157911_random 1561 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158025_random 1561 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158046_random 1561 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160041_random 1561 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164829_random 1561 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166237_random 1560 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166809_random 1560 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168992_random 1560 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170831_random 1560 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172194_random 1560 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172413_random 1560 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172499_random 1560 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174045_random 1560 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174735_random 1560 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174919_random 1560 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175550_random 1560 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175655_random 1560 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176231_random 1560 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176842_random 1560 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152635_random 1560 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154478_random 1560 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154639_random 1560 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155006_random 1560 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156625_random 1560 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156769_random 1560 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156926_random 1560 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157604_random 1560 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158259_random 1560 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158264_random 1560 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159658_random 1560 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159869_random 1560 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161924_random 1560 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163427_random 1560 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165389_random 1560 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168917_random 1559 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170739_random 1559 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170919_random 1559 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170948_random 1559 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171033_random 1559 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171386_random 1559 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172452_random 1559 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174755_random 1559 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174861_random 1559 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175671_random 1559 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151480_random 1559 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151532_random 1559 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176761_random 1559 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152476_random 1559 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153350_random 1559 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153411_random 1559 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154757_random 1559 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154771_random 1559 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155012_random 1559 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156677_random 1559 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156826_random 1559 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157005_random 1559 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157810_random 1559 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159842_random 1559 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160108_random 1559 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160218_random 1559 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161723_random 1559 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162036_random 1559 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163225_random 1559 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163400_random 1559 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163563_random 1559 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165337_random 1559 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178198_random 1559 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178326_random 1559 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178582_random 1559 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169098_random 1558 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169812_random 1558 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170056_random 1558 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171606_random 1558 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171690_random 1558 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172468_random 1558 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172492_random 1558 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173788_random 1558 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175030_random 1558 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176272_random 1558 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177228_random 1558 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152411_random 1558 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152490_random 1558 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152499_random 1558 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152717_random 1558 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154945_random 1558 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154950_random 1558 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155016_random 1558 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156530_random 1558 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156628_random 1558 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156850_random 1558 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156937_random 1558 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157929_random 1558 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160054_random 1558 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161832_random 1558 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161876_random 1558 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163123_random 1558 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163355_random 1558 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163458_random 1558 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163502_random 1558 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178603_random 1558 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166359_random 1557 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166446_random 1557 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166450_random 1557 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166562_random 1557 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166632_random 1557 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168845_random 1557 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169053_random 1557 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170807_random 1557 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171561_random 1557 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171568_random 1557 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171586_random 1557 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171613_random 1557 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172512_random 1557 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150877_random 1557 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150931_random 1557 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151395_random 1557 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151843_random 1557 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176872_random 1557 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152650_random 1557 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153349_random 1557 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153435_random 1557 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154410_random 1557 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154530_random 1557 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155058_random 1557 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157683_random 1557 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158279_random 1557 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159611_random 1557 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162881_random 1557 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163091_random 1557 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163302_random 1557 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163313_random 1557 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163345_random 1557 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163530_random 1557 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163625_random 1557 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163630_random 1557 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165205_random 1557 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165397_random 1557 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178228_random 1557 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166506_random 1556 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166568_random 1556 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168833_random 1556 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168966_random 1556 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169943_random 1556 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170001_random 1556 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173956_random 1556 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174935_random 1556 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175032_random 1556 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152231_random 1556 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158028_random 1556 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159798_random 1556 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165078_random 1556 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178455_random 1556 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166120_random 1555 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166407_random 1555 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166653_random 1555 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168790_random 1555 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169993_random 1555 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171014_random 1555 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171702_random 1555 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173959_random 1555 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174763_random 1555 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175644_random 1555 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175664_random 1555 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176056_random 1555 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176073_random 1555 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176183_random 1555 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151204_random 1555 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151272_random 1555 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151410_random 1555 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151785_random 1555 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176919_random 1555 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176945_random 1555 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153392_random 1555 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153606_random 1555 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156733_random 1555 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156938_random 1555 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157859_random 1555 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158275_random 1555 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158284_random 1555 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159905_random 1555 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159956_random 1555 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163351_random 1555 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163390_random 1555 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164785_random 1555 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165099_random 1555 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165302_random 1555 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166302_random 1554 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168971_random 1554 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169055_random 1554 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169597_random 1554 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169883_random 1554 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171646_random 1554 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174037_random 1554 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174057_random 1554 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175025_random 1554 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175035_random 1554 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175593_random 1554 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176358_random 1554 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151470_random 1554 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151639_random 1554 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151787_random 1554 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177243_random 1554 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152351_random 1554 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153502_random 1554 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154626_random 1554 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154783_random 1554 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156440_random 1554 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156510_random 1554 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156672_random 1554 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156790_random 1554 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156968_random 1554 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157868_random 1554 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165144_random 1554 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166140_random 1553 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166854_random 1553 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168675_random 1553 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169797_random 1553 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169999_random 1553 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170055_random 1553 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170077_random 1553 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170747_random 1553 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170769_random 1553 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174056_random 1553 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174894_random 1553 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150784_random 1553 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152700_random 1553 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152757_random 1553 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153388_random 1553 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153408_random 1553 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153441_random 1553 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154710_random 1553 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154748_random 1553 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154878_random 1553 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156712_random 1553 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157769_random 1553 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158053_random 1553 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159678_random 1553 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161437_random 1553 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161975_random 1553 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164911_random 1553 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166227_random 1552 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166244_random 1552 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166573_random 1552 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166606_random 1552 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169049_random 1552 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169097_random 1552 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169733_random 1552 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170020_random 1552 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172494_random 1552 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175050_random 1552 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175670_random 1552 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151394_random 1552 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151422_random 1552 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151445_random 1552 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176840_random 1552 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152527_random 1552 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153240_random 1552 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154638_random 1552 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154968_random 1552 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156729_random 1552 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156849_random 1552 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157866_random 1552 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159893_random 1552 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160004_random 1552 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160146_random 1552 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163157_random 1552 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178438_random 1552 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166625_random 1551 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166817_random 1551 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168555_random 1551 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168889_random 1551 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169035_random 1551 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169684_random 1551 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169688_random 1551 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170708_random 1551 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174008_random 1551 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175283_random 1551 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175666_random 1551 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176184_random 1551 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151351_random 1551 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151386_random 1551 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151648_random 1551 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151799_random 1551 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177220_random 1551 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153524_random 1551 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155037_random 1551 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156676_random 1551 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156724_random 1551 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156789_random 1551 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156819_random 1551 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156940_random 1551 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156943_random 1551 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159603_random 1551 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160013_random 1551 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160039_random 1551 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163139_random 1551 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163207_random 1551 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163379_random 1551 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163424_random 1551 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163463_random 1551 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163627_random 1551 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165294_random 1551 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166210_random 1550 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166875_random 1550 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168987_random 1550 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169640_random 1550 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171589_random 1550 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174926_random 1550 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176343_random 1550 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151349_random 1550 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151767_random 1550 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176951_random 1550 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152429_random 1550 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152683_random 1550 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155028_random 1550 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156624_random 1550 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156643_random 1550 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156674_random 1550 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156764_random 1550 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158181_random 1550 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159183_random 1550 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159577_random 1550 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159813_random 1550 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163571_random 1550 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165082_random 1550 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03165873_random 1549 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166270_random 1549 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169495_random 1549 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171641_random 1549 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171699_random 1549 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174025_random 1549 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176427_random 1549 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151321_random 1549 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151490_random 1549 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151760_random 1549 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176763_random 1549 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176794_random 1549 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176843_random 1549 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177237_random 1549 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152288_random 1549 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152761_random 1549 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153346_random 1549 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154806_random 1549 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156463_random 1549 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156747_random 1549 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156948_random 1549 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156995_random 1549 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157823_random 1549 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157928_random 1549 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159948_random 1549 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163169_random 1549 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163198_random 1549 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163496_random 1549 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163513_random 1549 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165127_random 1549 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165402_random 1549 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168823_random 1548 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170755_random 1548 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170975_random 1548 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171010_random 1548 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171024_random 1548 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171470_random 1548 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171603_random 1548 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171666_random 1548 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173777_random 1548 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173845_random 1548 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173860_random 1548 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152401_random 1548 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156809_random 1548 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156970_random 1548 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157995_random 1548 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160170_random 1548 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161702_random 1548 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162083_random 1548 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162169_random 1548 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163645_random 1548 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165030_random 1548 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165118_random 1548 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165345_random 1548 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166301_random 1547 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166350_random 1547 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168623_random 1547 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170053_random 1547 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171027_random 1547 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171450_random 1547 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171517_random 1547 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172183_random 1547 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172498_random 1547 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175367_random 1547 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151371_random 1547 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151492_random 1547 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151682_random 1547 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151749_random 1547 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152535_random 1547 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152598_random 1547 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152664_random 1547 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154832_random 1547 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154865_random 1547 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156294_random 1547 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156589_random 1547 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156731_random 1547 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156880_random 1547 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160215_random 1547 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163059_random 1547 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163347_random 1547 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165273_random 1547 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165373_random 1547 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178571_random 1547 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166600_random 1546 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166846_random 1546 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169129_random 1546 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169819_random 1546 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169833_random 1546 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169931_random 1546 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171650_random 1546 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172433_random 1546 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173672_random 1546 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173787_random 1546 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173965_random 1546 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174015_random 1546 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174068_random 1546 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174868_random 1546 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174920_random 1546 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175497_random 1546 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175584_random 1546 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175631_random 1546 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175681_random 1546 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150736_random 1546 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151471_random 1546 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151842_random 1546 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176832_random 1546 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152512_random 1546 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152590_random 1546 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152645_random 1546 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156513_random 1546 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156882_random 1546 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159673_random 1546 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160209_random 1546 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163319_random 1546 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163550_random 1546 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165160_random 1546 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166233_random 1545 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166277_random 1545 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166612_random 1545 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166819_random 1545 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166878_random 1545 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169123_random 1545 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170704_random 1545 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171017_random 1545 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171685_random 1545 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172301_random 1545 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173922_random 1545 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174006_random 1545 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175039_random 1545 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151137_random 1545 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151824_random 1545 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177221_random 1545 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153511_random 1545 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155007_random 1545 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156802_random 1545 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156927_random 1545 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158263_random 1545 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165239_random 1545 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165388_random 1545 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178555_random 1545 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166550_random 1544 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166638_random 1544 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166723_random 1544 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168814_random 1544 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168864_random 1544 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169059_random 1544 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169136_random 1544 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171034_random 1544 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171698_random 1544 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172156_random 1544 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174855_random 1544 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151661_random 1544 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176790_random 1544 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177172_random 1544 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153405_random 1544 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157830_random 1544 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159297_random 1544 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159507_random 1544 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159983_random 1544 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162173_random 1544 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163397_random 1544 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165293_random 1544 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178319_random 1544 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178502_random 1544 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166658_random 1543 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166805_random 1543 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166815_random 1543 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168785_random 1543 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169114_random 1543 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172432_random 1543 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172509_random 1543 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173501_random 1543 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173808_random 1543 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174953_random 1543 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151762_random 1543 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153121_random 1543 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154630_random 1543 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154636_random 1543 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154675_random 1543 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154739_random 1543 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156447_random 1543 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156584_random 1543 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156664_random 1543 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156822_random 1543 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157662_random 1543 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158182_random 1543 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158249_random 1543 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158285_random 1543 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159806_random 1543 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159933_random 1543 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163224_random 1543 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178181_random 1543 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178473_random 1543 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166374_random 1542 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166473_random 1542 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166685_random 1542 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166874_random 1542 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169912_random 1542 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169947_random 1542 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169990_random 1542 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170005_random 1542 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170931_random 1542 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171315_random 1542 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173931_random 1542 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175418_random 1542 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151759_random 1542 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176756_random 1542 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152488_random 1542 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152742_random 1542 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153347_random 1542 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153439_random 1542 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153546_random 1542 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153551_random 1542 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154682_random 1542 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154696_random 1542 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156560_random 1542 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157021_random 1542 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157749_random 1542 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159332_random 1542 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163546_random 1542 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165223_random 1542 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165234_random 1542 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166564_random 1541 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166594_random 1541 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166683_random 1541 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166686_random 1541 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169654_random 1541 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170023_random 1541 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170066_random 1541 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170929_random 1541 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171320_random 1541 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171597_random 1541 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171648_random 1541 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174731_random 1541 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176289_random 1541 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151455_random 1541 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176603_random 1541 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152442_random 1541 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152672_random 1541 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153616_random 1541 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153629_random 1541 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154414_random 1541 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154670_random 1541 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156998_random 1541 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157764_random 1541 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158043_random 1541 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158274_random 1541 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162939_random 1541 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163052_random 1541 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163515_random 1541 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163629_random 1541 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165384_random 1541 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178556_random 1541 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178557_random 1541 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166870_random 1540 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168739_random 1540 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168954_random 1540 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169818_random 1540 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170863_random 1540 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171612_random 1540 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173894_random 1540 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175014_random 1540 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175038_random 1540 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176364_random 1540 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151080_random 1540 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151750_random 1540 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152525_random 1540 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152572_random 1540 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155019_random 1540 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156136_random 1540 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156354_random 1540 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156759_random 1540 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157013_random 1540 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157883_random 1540 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158013_random 1540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159232_random 1540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159303_random 1540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159707_random 1540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159749_random 1540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160021_random 1540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160142_random 1540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160240_random 1540 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160258_random 1540 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162082_random 1540 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163373_random 1540 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163592_random 1540 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166344_random 1539 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166577_random 1539 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168786_random 1539 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168943_random 1539 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169778_random 1539 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172479_random 1539 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174000_random 1539 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174937_random 1539 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175685_random 1539 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151629_random 1539 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153510_random 1539 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154911_random 1539 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155041_random 1539 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156788_random 1539 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157927_random 1539 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159663_random 1539 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159711_random 1539 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163489_random 1539 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163610_random 1539 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178586_random 1539 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166353_random 1538 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166388_random 1538 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169848_random 1538 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170003_random 1538 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170027_random 1538 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170963_random 1538 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172196_random 1538 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172327_random 1538 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151330_random 1538 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151469_random 1538 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151698_random 1538 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151805_random 1538 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152777_random 1538 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153255_random 1538 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153390_random 1538 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153483_random 1538 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153495_random 1538 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154615_random 1538 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154982_random 1538 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155055_random 1538 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157009_random 1538 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159782_random 1538 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160200_random 1538 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163615_random 1538 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165394_random 1538 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166351_random 1537 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166812_random 1537 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166879_random 1537 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169031_random 1537 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169834_random 1537 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173850_random 1537 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174814_random 1537 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176435_random 1537 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150771_random 1537 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151215_random 1537 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152656_random 1537 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153550_random 1537 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154720_random 1537 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157974_random 1537 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158193_random 1537 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159760_random 1537 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159826_random 1537 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160076_random 1537 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160112_random 1537 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160144_random 1537 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160250_random 1537 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163248_random 1537 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163434_random 1537 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165105_random 1537 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165350_random 1537 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178268_random 1537 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178425_random 1537 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178460_random 1537 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168887_random 1536 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169012_random 1536 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169122_random 1536 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169705_random 1536 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169897_random 1536 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169933_random 1536 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170024_random 1536 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170051_random 1536 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170820_random 1536 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170917_random 1536 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171689_random 1536 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174845_random 1536 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174958_random 1536 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175688_random 1536 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175694_random 1536 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151585_random 1536 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151779_random 1536 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151803_random 1536 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176817_random 1536 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176902_random 1536 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152310_random 1536 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152560_random 1536 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153211_random 1536 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153449_random 1536 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153605_random 1536 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154952_random 1536 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156891_random 1536 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157768_random 1536 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158107_random 1536 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159841_random 1536 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163621_random 1536 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165393_random 1536 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178608_random 1536 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168640_random 1535 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168904_random 1535 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169710_random 1535 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169737_random 1535 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169858_random 1535 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170065_random 1535 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170885_random 1535 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173868_random 1535 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174018_random 1535 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174561_random 1535 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174792_random 1535 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151812_random 1535 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152580_random 1535 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153595_random 1535 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156913_random 1535 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156955_random 1535 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161813_random 1535 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164974_random 1535 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178564_random 1535 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178622_random 1535 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170042_random 1534 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170996_random 1534 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172465_random 1534 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173744_random 1534 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174044_random 1534 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175499_random 1534 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151055_random 1534 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151421_random 1534 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151751_random 1534 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151833_random 1534 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152769_random 1534 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154883_random 1534 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154898_random 1534 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154910_random 1534 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156390_random 1534 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156464_random 1534 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156504_random 1534 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157906_random 1534 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157955_random 1534 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160024_random 1534 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162152_random 1534 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165299_random 1534 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166497_random 1533 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166791_random 1533 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166826_random 1533 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170036_random 1533 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170039_random 1533 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171633_random 1533 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172244_random 1533 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173890_random 1533 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174970_random 1533 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175590_random 1533 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176898_random 1533 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153387_random 1533 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153486_random 1533 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154713_random 1533 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154730_random 1533 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156730_random 1533 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157999_random 1533 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159897_random 1533 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160066_random 1533 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163026_random 1533 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163100_random 1533 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163353_random 1533 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166583_random 1532 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169102_random 1532 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170742_random 1532 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171418_random 1532 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171664_random 1532 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173814_random 1532 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174030_random 1532 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174780_random 1532 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174788_random 1532 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174844_random 1532 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174994_random 1532 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151448_random 1532 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153433_random 1532 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153458_random 1532 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153467_random 1532 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153572_random 1532 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154387_random 1532 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154658_random 1532 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156366_random 1532 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156453_random 1532 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156960_random 1532 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157888_random 1532 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158177_random 1532 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159590_random 1532 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159750_random 1532 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162147_random 1532 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165021_random 1532 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165244_random 1532 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165286_random 1532 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178550_random 1532 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178562_random 1532 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178621_random 1532 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166451_random 1531 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169054_random 1531 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169089_random 1531 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169107_random 1531 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170021_random 1531 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171529_random 1531 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172319_random 1531 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172506_random 1531 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173940_random 1531 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174066_random 1531 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174978_random 1531 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175057_random 1531 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175684_random 1531 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151334_random 1531 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151570_random 1531 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176796_random 1531 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177183_random 1531 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153497_random 1531 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154716_random 1531 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156755_random 1531 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158245_random 1531 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159563_random 1531 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159815_random 1531 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160079_random 1531 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160167_random 1531 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160249_random 1531 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161844_random 1531 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163234_random 1531 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165071_random 1531 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166352_random 1530 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166763_random 1530 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166829_random 1530 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169127_random 1530 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170050_random 1530 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170939_random 1530 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173993_random 1530 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175663_random 1530 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175696_random 1530 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151845_random 1530 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176732_random 1530 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154665_random 1530 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156750_random 1530 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158041_random 1530 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158229_random 1530 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159650_random 1530 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159950_random 1530 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159951_random 1530 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161406_random 1530 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161704_random 1530 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162066_random 1530 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165404_random 1530 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178469_random 1530 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166358_random 1529 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166405_random 1529 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168836_random 1529 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169723_random 1529 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170069_random 1529 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172501_random 1529 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175398_random 1529 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176412_random 1529 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150902_random 1529 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151113_random 1529 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151465_random 1529 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151668_random 1529 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176798_random 1529 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176850_random 1529 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152480_random 1529 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152536_random 1529 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152591_random 1529 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153612_random 1529 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154709_random 1529 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155060_random 1529 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156921_random 1529 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158144_random 1529 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158250_random 1529 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159634_random 1529 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160082_random 1529 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160110_random 1529 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160117_random 1529 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160121_random 1529 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160239_random 1529 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163217_random 1529 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163544_random 1529 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163604_random 1529 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165372_random 1529 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166592_random 1528 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166799_random 1528 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168841_random 1528 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169032_random 1528 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169082_random 1528 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169084_random 1528 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170766_random 1528 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172463_random 1528 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174005_random 1528 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175617_random 1528 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175698_random 1528 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175701_random 1528 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151193_random 1528 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152331_random 1528 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153474_random 1528 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153613_random 1528 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154785_random 1528 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154923_random 1528 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156260_random 1528 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156925_random 1528 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158035_random 1528 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163290_random 1528 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163524_random 1528 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165313_random 1528 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165367_random 1528 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178313_random 1528 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169422_random 1527 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169626_random 1527 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169875_random 1527 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170029_random 1527 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171469_random 1527 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171594_random 1527 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171644_random 1527 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172143_random 1527 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173648_random 1527 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175624_random 1527 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151403_random 1527 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151600_random 1527 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151601_random 1527 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176814_random 1527 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176877_random 1527 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152735_random 1527 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152771_random 1527 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153265_random 1527 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154542_random 1527 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154687_random 1527 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156425_random 1527 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156726_random 1527 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156841_random 1527 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156972_random 1527 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156999_random 1527 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157816_random 1527 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157990_random 1527 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158005_random 1527 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158247_random 1527 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159586_random 1527 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162125_random 1527 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163189_random 1527 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163447_random 1527 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163580_random 1527 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178530_random 1527 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166469_random 1526 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166604_random 1526 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169462_random 1526 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169881_random 1526 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170067_random 1526 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171029_random 1526 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171483_random 1526 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171528_random 1526 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172443_random 1526 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176285_random 1526 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176387_random 1526 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151344_random 1526 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151719_random 1526 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151744_random 1526 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176705_random 1526 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176940_random 1526 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152633_random 1526 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153399_random 1526 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156933_random 1526 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158079_random 1526 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158132_random 1526 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159609_random 1526 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160236_random 1526 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160257_random 1526 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162076_random 1526 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162700_random 1526 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163618_random 1526 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163633_random 1526 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178212_random 1526 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178487_random 1526 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178493_random 1526 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178589_random 1526 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166084_random 1525 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166296_random 1525 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166449_random 1525 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169607_random 1525 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169841_random 1525 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170046_random 1525 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170072_random 1525 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171678_random 1525 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173889_random 1525 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175636_random 1525 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176224_random 1525 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150890_random 1525 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151413_random 1525 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151573_random 1525 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176852_random 1525 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152775_random 1525 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152779_random 1525 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154137_random 1525 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154593_random 1525 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155022_random 1525 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156974_random 1525 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159900_random 1525 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162122_random 1525 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163421_random 1525 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163619_random 1525 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163631_random 1525 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164872_random 1525 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178623_random 1525 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166578_random 1524 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166840_random 1524 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168726_random 1524 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169945_random 1524 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170006_random 1524 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171433_random 1524 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174049_random 1524 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174766_random 1524 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175044_random 1524 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175355_random 1524 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151227_random 1524 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151591_random 1524 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151724_random 1524 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152549_random 1524 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152654_random 1524 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153421_random 1524 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153583_random 1524 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154523_random 1524 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154726_random 1524 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154992_random 1524 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156324_random 1524 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156720_random 1524 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156931_random 1524 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157912_random 1524 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159280_random 1524 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159734_random 1524 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161990_random 1524 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162737_random 1524 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165329_random 1524 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178477_random 1524 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166537_random 1523 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166766_random 1523 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166794_random 1523 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166823_random 1523 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169027_random 1523 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169701_random 1523 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169970_random 1523 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170054_random 1523 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170981_random 1523 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171457_random 1523 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171649_random 1523 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174059_random 1523 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151513_random 1523 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151676_random 1523 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153623_random 1523 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154489_random 1523 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154918_random 1523 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154948_random 1523 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155023_random 1523 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155046_random 1523 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156648_random 1523 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158130_random 1523 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159783_random 1523 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161806_random 1523 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161995_random 1523 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163440_random 1523 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163551_random 1523 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165186_random 1523 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165309_random 1523 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178516_random 1523 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166289_random 1522 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166545_random 1522 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166593_random 1522 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166633_random 1522 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166777_random 1522 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168768_random 1522 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168824_random 1522 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169732_random 1522 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169805_random 1522 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170031_random 1522 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170993_random 1522 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171022_random 1522 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172510_random 1522 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173926_random 1522 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174811_random 1522 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174875_random 1522 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175055_random 1522 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175559_random 1522 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176089_random 1522 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151293_random 1522 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151576_random 1522 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151638_random 1522 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176828_random 1522 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176946_random 1522 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177229_random 1522 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152699_random 1522 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153440_random 1522 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153456_random 1522 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153561_random 1522 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154815_random 1522 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156098_random 1522 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156376_random 1522 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156402_random 1522 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156885_random 1522 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157569_random 1522 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162935_random 1522 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165208_random 1522 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165295_random 1522 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165374_random 1522 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166323_random 1521 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166436_random 1521 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166886_random 1521 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168570_random 1521 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171575_random 1521 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172429_random 1521 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174971_random 1521 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175036_random 1521 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151451_random 1521 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176869_random 1521 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176948_random 1521 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152588_random 1521 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153465_random 1521 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153542_random 1521 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153591_random 1521 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154238_random 1521 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154719_random 1521 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154788_random 1521 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155040_random 1521 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155054_random 1521 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156827_random 1521 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157861_random 1521 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157904_random 1521 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158175_random 1521 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159944_random 1521 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159954_random 1521 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160140_random 1521 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162030_random 1521 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162146_random 1521 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162976_random 1521 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163097_random 1521 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163475_random 1521 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163497_random 1521 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163531_random 1521 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165147_random 1521 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165398_random 1521 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178537_random 1521 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166191_random 1520 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166360_random 1520 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166481_random 1520 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168999_random 1520 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171534_random 1520 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172454_random 1520 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175570_random 1520 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176352_random 1520 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151146_random 1520 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151319_random 1520 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152426_random 1520 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152529_random 1520 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152652_random 1520 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153209_random 1520 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153506_random 1520 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153601_random 1520 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154738_random 1520 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155039_random 1520 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156375_random 1520 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156758_random 1520 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156783_random 1520 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158128_random 1520 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158153_random 1520 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158192_random 1520 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158294_random 1520 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159518_random 1520 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161666_random 1520 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161976_random 1520 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162108_random 1520 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162119_random 1520 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164815_random 1520 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169119_random 1519 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170922_random 1519 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171509_random 1519 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173781_random 1519 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173992_random 1519 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174060_random 1519 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174562_random 1519 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175540_random 1519 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176423_random 1519 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151111_random 1519 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176812_random 1519 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176905_random 1519 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176932_random 1519 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154799_random 1519 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154896_random 1519 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154917_random 1519 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156573_random 1519 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156770_random 1519 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156830_random 1519 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156984_random 1519 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157545_random 1519 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157898_random 1519 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158020_random 1519 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159876_random 1519 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160241_random 1519 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163453_random 1519 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165269_random 1519 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165289_random 1519 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165328_random 1519 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165341_random 1519 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165369_random 1519 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178483_random 1519 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178590_random 1519 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166330_random 1518 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169066_random 1518 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169877_random 1518 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170914_random 1518 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170980_random 1518 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171717_random 1518 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172383_random 1518 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173896_random 1518 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173916_random 1518 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174946_random 1518 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175058_random 1518 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176270_random 1518 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151647_random 1518 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151837_random 1518 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176928_random 1518 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152725_random 1518 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152736_random 1518 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152755_random 1518 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153509_random 1518 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153594_random 1518 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153624_random 1518 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154355_random 1518 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154563_random 1518 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154705_random 1518 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156368_random 1518 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156980_random 1518 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157784_random 1518 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159153_random 1518 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161855_random 1518 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163422_random 1518 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163465_random 1518 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163586_random 1518 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178609_random 1518 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166452_random 1517 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170839_random 1517 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171525_random 1517 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171665_random 1517 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172101_random 1517 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172332_random 1517 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172487_random 1517 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174061_random 1517 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175588_random 1517 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175673_random 1517 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176112_random 1517 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176306_random 1517 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151250_random 1517 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151599_random 1517 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151769_random 1517 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176745_random 1517 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153380_random 1517 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153498_random 1517 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154252_random 1517 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154962_random 1517 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156645_random 1517 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157007_random 1517 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157546_random 1517 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157915_random 1517 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158154_random 1517 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161967_random 1517 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163330_random 1517 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163576_random 1517 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163642_random 1517 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164845_random 1517 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165177_random 1517 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166563_random 1516 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168827_random 1516 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168840_random 1516 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169019_random 1516 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169079_random 1516 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170062_random 1516 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170891_random 1516 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171011_random 1516 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175536_random 1516 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151358_random 1516 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177181_random 1516 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177186_random 1516 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177265_random 1516 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152639_random 1516 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152661_random 1516 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152749_random 1516 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153425_random 1516 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153450_random 1516 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154366_random 1516 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156777_random 1516 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157869_random 1516 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158068_random 1516 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159838_random 1516 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159988_random 1516 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163482_random 1516 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178328_random 1516 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178419_random 1516 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166050_random 1515 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166602_random 1515 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166747_random 1515 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166776_random 1515 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169867_random 1515 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170923_random 1515 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170954_random 1515 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170956_random 1515 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171616_random 1515 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171622_random 1515 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173954_random 1515 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174972_random 1515 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174991_random 1515 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176385_random 1515 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151061_random 1515 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151423_random 1515 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151763_random 1515 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151801_random 1515 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151835_random 1515 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176938_random 1515 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152446_random 1515 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153339_random 1515 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153513_random 1515 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153562_random 1515 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156870_random 1515 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158226_random 1515 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160229_random 1515 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162131_random 1515 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163643_random 1515 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177903_random 1515 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166560_random 1514 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166775_random 1514 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168615_random 1514 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168978_random 1514 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169068_random 1514 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169110_random 1514 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169910_random 1514 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170000_random 1514 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170004_random 1514 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171562_random 1514 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171711_random 1514 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172373_random 1514 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173740_random 1514 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173759_random 1514 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173859_random 1514 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174980_random 1514 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175016_random 1514 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175659_random 1514 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151527_random 1514 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151625_random 1514 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151827_random 1514 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176758_random 1514 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176829_random 1514 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153398_random 1514 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153424_random 1514 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153464_random 1514 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154554_random 1514 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154750_random 1514 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154929_random 1514 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155056_random 1514 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156478_random 1514 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156691_random 1514 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158045_random 1514 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158100_random 1514 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158183_random 1514 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158222_random 1514 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159751_random 1514 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159973_random 1514 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160023_random 1514 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163439_random 1514 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163529_random 1514 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163590_random 1514 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165018_random 1514 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165053_random 1514 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165366_random 1514 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165380_random 1514 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166146_random 1513 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166527_random 1513 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166705_random 1513 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166726_random 1513 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166832_random 1513 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168837_random 1513 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168875_random 1513 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169041_random 1513 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170075_random 1513 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170909_random 1513 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170926_random 1513 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171600_random 1513 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173725_random 1513 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175526_random 1513 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151383_random 1513 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151608_random 1513 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151773_random 1513 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151795_random 1513 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176824_random 1513 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152425_random 1513 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152718_random 1513 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152722_random 1513 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154174_random 1513 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154984_random 1513 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156567_random 1513 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156663_random 1513 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158265_random 1513 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159597_random 1513 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160123_random 1513 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163149_random 1513 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163622_random 1513 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163632_random 1513 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166669_random 1512 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166843_random 1512 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166887_random 1512 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168799_random 1512 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169865_random 1512 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170048_random 1512 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171019_random 1512 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171035_random 1512 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171677_random 1512 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173981_random 1512 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174986_random 1512 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175037_random 1512 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175503_random 1512 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175545_random 1512 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175675_random 1512 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176436_random 1512 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150644_random 1512 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151119_random 1512 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151468_random 1512 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151747_random 1512 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176768_random 1512 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152440_random 1512 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152465_random 1512 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152701_random 1512 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154828_random 1512 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154935_random 1512 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154964_random 1512 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154986_random 1512 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159957_random 1512 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162949_random 1512 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163277_random 1512 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163291_random 1512 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165317_random 1512 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165377_random 1512 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178488_random 1512 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166376_random 1511 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166647_random 1511 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166709_random 1511 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170045_random 1511 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170790_random 1511 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170946_random 1511 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171696_random 1511 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171722_random 1511 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171724_random 1511 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172424_random 1511 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173942_random 1511 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173982_random 1511 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174967_random 1511 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175619_random 1511 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176417_random 1511 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154447_random 1511 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154476_random 1511 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154843_random 1511 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154912_random 1511 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155061_random 1511 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156594_random 1511 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156609_random 1511 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156736_random 1511 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156839_random 1511 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156905_random 1511 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157004_random 1511 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158054_random 1511 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158074_random 1511 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159800_random 1511 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159902_random 1511 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159963_random 1511 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163329_random 1511 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178365_random 1511 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178434_random 1511 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178583_random 1511 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166380_random 1510 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166749_random 1510 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166781_random 1510 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168994_random 1510 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169111_random 1510 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169117_random 1510 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169845_random 1510 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170987_random 1510 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171015_random 1510 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171503_random 1510 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175447_random 1510 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175642_random 1510 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176233_random 1510 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151640_random 1510 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152715_random 1510 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152724_random 1510 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153201_random 1510 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156877_random 1510 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156878_random 1510 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157479_random 1510 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158097_random 1510 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158208_random 1510 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159796_random 1510 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159834_random 1510 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159891_random 1510 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159962_random 1510 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160114_random 1510 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160134_random 1510 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160235_random 1510 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162070_random 1510 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163370_random 1510 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163473_random 1510 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163498_random 1510 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178416_random 1510 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166246_random 1509 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166312_random 1509 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166731_random 1509 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166789_random 1509 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166811_random 1509 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166882_random 1509 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168742_random 1509 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169028_random 1509 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169094_random 1509 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169126_random 1509 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171523_random 1509 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171700_random 1509 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171705_random 1509 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172496_random 1509 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172511_random 1509 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173878_random 1509 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175446_random 1509 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176426_random 1509 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150939_random 1509 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151255_random 1509 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151516_random 1509 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151776_random 1509 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153372_random 1509 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153530_random 1509 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154752_random 1509 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03155914_random 1509 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158060_random 1509 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158230_random 1509 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159931_random 1509 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162161_random 1509 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163467_random 1509 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165322_random 1509 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165353_random 1509 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178479_random 1509 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166795_random 1508 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168893_random 1508 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169823_random 1508 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170064_random 1508 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173861_random 1508 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173967_random 1508 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174055_random 1508 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174842_random 1508 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175637_random 1508 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150852_random 1508 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177074_random 1508 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152400_random 1508 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152593_random 1508 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153166_random 1508 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153632_random 1508 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153633_random 1508 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153636_random 1508 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154957_random 1508 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154988_random 1508 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157918_random 1508 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157947_random 1508 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158066_random 1508 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160131_random 1508 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160154_random 1508 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162151_random 1508 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163226_random 1508 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166666_random 1507 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169121_random 1507 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170930_random 1507 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171727_random 1507 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174947_random 1507 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174979_random 1507 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175648_random 1507 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176194_random 1507 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176418_random 1507 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151477_random 1507 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151561_random 1507 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151690_random 1507 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151714_random 1507 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151798_random 1507 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176752_random 1507 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177230_random 1507 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152510_random 1507 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152537_random 1507 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153622_random 1507 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154441_random 1507 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154521_random 1507 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154584_random 1507 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155025_random 1507 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158085_random 1507 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159739_random 1507 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165119_random 1507 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178305_random 1507 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168476_random 1506 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168877_random 1506 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168926_random 1506 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170657_random 1506 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170819_random 1506 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171410_random 1506 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172189_random 1506 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172323_random 1506 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172461_random 1506 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173997_random 1506 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151106_random 1506 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151543_random 1506 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151741_random 1506 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176751_random 1506 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177208_random 1506 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177270_random 1506 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153589_random 1506 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154852_random 1506 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154857_random 1506 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155003_random 1506 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156710_random 1506 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156994_random 1506 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158155_random 1506 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160018_random 1506 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160212_random 1506 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162075_random 1506 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163235_random 1506 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163605_random 1506 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165254_random 1506 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165290_random 1506 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165376_random 1506 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166624_random 1505 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168923_random 1505 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170944_random 1505 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171009_random 1505 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171662_random 1505 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172306_random 1505 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172345_random 1505 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172393_random 1505 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175665_random 1505 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176411_random 1505 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176424_random 1505 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150816_random 1505 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150950_random 1505 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151552_random 1505 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151592_random 1505 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176947_random 1505 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152603_random 1505 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152705_random 1505 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153552_random 1505 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153557_random 1505 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154391_random 1505 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154644_random 1505 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154892_random 1505 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154939_random 1505 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155049_random 1505 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156666_random 1505 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156673_random 1505 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158055_random 1505 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159916_random 1505 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159970_random 1505 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162058_random 1505 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162074_random 1505 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178499_random 1505 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166327_random 1504 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166865_random 1504 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168838_random 1504 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169768_random 1504 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169784_random 1504 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170824_random 1504 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170852_random 1504 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170884_random 1504 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171003_random 1504 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172484_random 1504 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174054_random 1504 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175634_random 1504 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176087_random 1504 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151620_random 1504 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151631_random 1504 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151826_random 1504 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151832_random 1504 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176944_random 1504 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152511_random 1504 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152703_random 1504 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153414_random 1504 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154334_random 1504 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154933_random 1504 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154955_random 1504 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155048_random 1504 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156892_random 1504 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158083_random 1504 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160029_random 1504 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161968_random 1504 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162002_random 1504 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162157_random 1504 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163183_random 1504 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163364_random 1504 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163375_random 1504 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163399_random 1504 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163404_random 1504 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166335_random 1503 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166597_random 1503 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166744_random 1503 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166772_random 1503 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166807_random 1503 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169804_random 1503 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170047_random 1503 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170874_random 1503 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171554_random 1503 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173695_random 1503 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173937_random 1503 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173938_random 1503 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174802_random 1503 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174954_random 1503 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176141_random 1503 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151364_random 1503 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151717_random 1503 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151846_random 1503 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177240_random 1503 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177244_random 1503 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177252_random 1503 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152469_random 1503 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152585_random 1503 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152587_random 1503 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152621_random 1503 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154871_random 1503 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154902_random 1503 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155034_random 1503 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156918_random 1503 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157674_random 1503 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158117_random 1503 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158186_random 1503 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159404_random 1503 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159846_random 1503 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160028_random 1503 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163315_random 1503 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164886_random 1503 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165214_random 1503 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165321_random 1503 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178494_random 1503 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166871_random 1502 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168792_random 1502 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168850_random 1502 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168937_random 1502 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170834_random 1502 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172278_random 1502 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173568_random 1502 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173977_random 1502 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175602_random 1502 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151728_random 1502 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151807_random 1502 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176855_random 1502 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177223_random 1502 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177238_random 1502 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152513_random 1502 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152563_random 1502 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152636_random 1502 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153462_random 1502 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154882_random 1502 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154938_random 1502 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156531_random 1502 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158292_random 1502 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159671_random 1502 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161888_random 1502 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163125_random 1502 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163209_random 1502 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163305_random 1502 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165282_random 1502 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03177833_random 1502 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166395_random 1501 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166773_random 1501 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166790_random 1501 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168712_random 1501 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168970_random 1501 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169064_random 1501 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169908_random 1501 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170741_random 1501 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174758_random 1501 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174945_random 1501 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175031_random 1501 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176311_random 1501 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151818_random 1501 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177140_random 1501 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177231_random 1501 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152607_random 1501 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152762_random 1501 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154398_random 1501 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154556_random 1501 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154873_random 1501 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156430_random 1501 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156781_random 1501 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158101_random 1501 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159575_random 1501 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160148_random 1501 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160158_random 1501 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162947_random 1501 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178624_random 1501 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166581_random 1500 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166786_random 1500 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166860_random 1500 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168670_random 1500 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168782_random 1500 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169092_random 1500 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170889_random 1500 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171626_random 1500 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171635_random 1500 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171707_random 1500 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175669_random 1500 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151054_random 1500 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177261_random 1500 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152317_random 1500 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152413_random 1500 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152584_random 1500 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152599_random 1500 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152670_random 1500 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153400_random 1500 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153585_random 1500 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153604_random 1500 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154261_random 1500 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154673_random 1500 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154835_random 1500 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154894_random 1500 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161959_random 1500 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163341_random 1500 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163510_random 1500 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165351_random 1500 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165390_random 1500 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178595_random 1500 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168729_random 1499 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168930_random 1499 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163310_random 1499 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163506_random 1499 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178501_random 1499 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176200_random 1498 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176389_random 1498 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154662_random 1498 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156793_random 1498 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172217_random 1497 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175527_random 1497 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168820_random 1496 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153625_random 1496 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158254_random 1496 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159967_random 1496 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163269_random 1496 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165272_random 1496 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168718_random 1495 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150649_random 1495 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153573_random 1495 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168736_random 1494 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169968_random 1494 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176695_random 1494 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153461_random 1494 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158304_random 1494 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151382_random 1493 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153437_random 1493 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156416_random 1493 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178593_random 1493 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169065_random 1492 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174993_random 1492 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151633_random 1492 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159764_random 1492 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163403_random 1492 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165346_random 1491 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175679_random 1490 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160173_random 1490 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151247_random 1489 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176880_random 1489 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176925_random 1489 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157682_random 1489 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165070_random 1489 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165226_random 1489 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173995_random 1488 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152676_random 1488 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153576_random 1488 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170967_random 1487 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175576_random 1487 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156993_random 1487 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163468_random 1487 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178521_random 1487 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174023_random 1486 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174070_random 1486 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163182_random 1486 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165358_random 1486 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169974_random 1485 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171704_random 1485 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177257_random 1485 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152616_random 1485 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153588_random 1485 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158256_random 1485 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162027_random 1485 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165275_random 1485 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169090_random 1484 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169963_random 1484 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174893_random 1484 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175652_random 1484 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152553_random 1484 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159776_random 1484 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159995_random 1484 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164992_random 1484 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168881_random 1483 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171688_random 1483 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176371_random 1483 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153393_random 1483 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153540_random 1483 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158281_random 1483 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165305_random 1483 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168953_random 1482 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170061_random 1482 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172401_random 1482 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151752_random 1482 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152472_random 1482 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153413_random 1482 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158240_random 1482 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159643_random 1482 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163490_random 1482 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168731_random 1481 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160179_random 1481 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151512_random 1480 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163477_random 1480 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169009_random 1479 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177144_random 1479 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154930_random 1479 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173998_random 1478 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163555_random 1478 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158058_random 1477 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158094_random 1477 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158307_random 1477 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163638_random 1477 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170016_random 1476 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151521_random 1476 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159870_random 1476 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174071_random 1475 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151279_random 1475 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156801_random 1475 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165283_random 1475 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165381_random 1475 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169964_random 1474 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156523_random 1474 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163572_random 1474 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165308_random 1474 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170079_random 1473 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175438_random 1473 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156481_random 1473 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159976_random 1473 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165307_random 1473 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170881_random 1472 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150811_random 1472 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154875_random 1472 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156635_random 1472 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174051_random 1471 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153235_random 1471 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154571_random 1471 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155008_random 1471 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160253_random 1471 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161935_random 1471 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170947_random 1470 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169689_random 1469 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151609_random 1469 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169965_random 1468 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155051_random 1468 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156702_random 1468 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163268_random 1468 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153584_random 1467 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153586_random 1467 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156665_random 1467 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156847_random 1467 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171541_random 1466 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171692_random 1466 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151452_random 1466 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176926_random 1466 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157022_random 1466 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159608_random 1466 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171681_random 1465 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153603_random 1465 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154541_random 1465 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154899_random 1465 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158174_random 1465 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160192_random 1465 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161958_random 1465 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163539_random 1465 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173570_random 1464 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151666_random 1464 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154793_random 1464 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178600_random 1464 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151089_random 1463 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152423_random 1463 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153407_random 1463 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154880_random 1463 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168968_random 1462 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153266_random 1462 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157661_random 1462 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176246_random 1461 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151667_random 1461 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154572_random 1461 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154829_random 1461 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162011_random 1461 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165187_random 1461 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174041_random 1460 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153332_random 1460 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178594_random 1460 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171715_random 1459 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151185_random 1459 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151800_random 1459 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163418_random 1459 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163485_random 1459 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165049_random 1459 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154469_random 1458 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157625_random 1458 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160102_random 1458 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172399_random 1456 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156405_random 1456 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158063_random 1456 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174809_random 1455 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175580_random 1455 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157962_random 1455 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168788_random 1454 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172353_random 1454 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172503_random 1454 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152576_random 1454 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156640_random 1454 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158168_random 1454 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158237_random 1454 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159863_random 1454 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03164988_random 1454 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153415_random 1453 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162142_random 1453 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169062_random 1452 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153571_random 1452 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160242_random 1452 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03150892_random 1451 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151284_random 1451 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151497_random 1451 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176813_random 1451 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157676_random 1451 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173994_random 1450 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151672_random 1450 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153182_random 1450 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154819_random 1450 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178375_random 1450 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178611_random 1450 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170894_random 1449 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169060_random 1448 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169839_random 1448 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173953_random 1448 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151737_random 1448 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160164_random 1448 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174017_random 1447 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153309_random 1447 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159996_random 1447 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156678_random 1446 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168959_random 1445 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176318_random 1445 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154562_random 1445 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165338_random 1445 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171020_random 1444 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151700_random 1443 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154818_random 1443 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172344_random 1442 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156867_random 1442 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156969_random 1442 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158090_random 1442 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177236_random 1441 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156660_random 1441 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165291_random 1441 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178585_random 1441 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171683_random 1439 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152399_random 1439 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175535_random 1438 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159625_random 1438 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175490_random 1437 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151725_random 1437 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169857_random 1436 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173756_random 1436 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177253_random 1436 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154085_random 1436 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156501_random 1436 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165361_random 1436 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169798_random 1435 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171593_random 1435 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151271_random 1435 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159613_random 1435 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160009_random 1435 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169856_random 1434 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170071_random 1434 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151810_random 1434 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176815_random 1434 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159865_random 1434 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172318_random 1433 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169854_random 1432 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174959_random 1432 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153337_random 1432 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156860_random 1432 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163431_random 1432 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152750_random 1431 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154976_random 1431 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173802_random 1430 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171693_random 1429 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151170_random 1429 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163133_random 1429 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159949_random 1428 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152711_random 1427 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154934_random 1427 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155052_random 1427 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156477_random 1427 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156953_random 1427 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172350_random 1426 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165102_random 1426 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154879_random 1425 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177222_random 1424 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157014_random 1424 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172456_random 1423 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173983_random 1423 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175461_random 1423 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156126_random 1422 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165399_random 1422 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174878_random 1421 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175525_random 1421 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155015_random 1421 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177249_random 1420 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153476_random 1419 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178612_random 1419 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151730_random 1418 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163322_random 1417 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157970_random 1416 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174001_random 1415 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154661_random 1415 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176416_random 1414 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152609_random 1414 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176787_random 1413 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152709_random 1412 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163471_random 1412 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172293_random 1410 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175574_random 1410 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153587_random 1410 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175700_random 1409 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177248_random 1409 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156484_random 1409 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169699_random 1408 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154456_random 1408 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155031_random 1407 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170038_random 1406 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151207_random 1406 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170998_random 1405 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157708_random 1405 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172370_random 1404 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159848_random 1404 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171008_random 1403 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171656_random 1403 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152663_random 1403 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157980_random 1403 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169087_random 1402 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151123_random 1402 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153617_random 1402 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158031_random 1402 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163276_random 1402 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151727_random 1400 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160166_random 1399 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157831_random 1398 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158191_random 1398 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160100_random 1398 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158185_random 1397 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160044_random 1397 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174067_random 1395 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157829_random 1394 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176301_random 1393 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03162965_random 1393 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174990_random 1392 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154965_random 1392 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172296_random 1391 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154364_random 1390 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166740_random 1388 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174830_random 1388 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158301_random 1387 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160103_random 1387 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178614_random 1387 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177247_random 1385 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152554_random 1384 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03157730_random 1384 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163460_random 1384 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156502_random 1383 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151628_random 1380 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151819_random 1380 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154970_random 1380 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158227_random 1380 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153505_random 1378 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171638_random 1377 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174905_random 1377 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151736_random 1377 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151815_random 1375 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158298_random 1375 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151373_random 1374 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159407_random 1373 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170988_random 1372 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170994_random 1371 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171363_random 1371 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176711_random 1371 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170060_random 1369 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152738_random 1369 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170995_random 1368 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170037_random 1365 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175410_random 1365 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153472_random 1365 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156963_random 1363 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154887_random 1361 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160247_random 1360 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170952_random 1359 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153539_random 1359 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158306_random 1355 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174973_random 1348 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153403_random 1348 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160251_random 1347 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171505_random 1346 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175657_random 1343 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156872_random 1343 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158223_random 1342 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160151_random 1342 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160094_random 1339 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159759_random 1338 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171721_random 1337 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158257_random 1332 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171444_random 1331 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152716_random 1328 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170778_random 1322 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169822_random 1314 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163491_random 1310 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03170976_random 1309 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151735_random 1309 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153406_random 1309 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159999_random 1306 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173888_random 1303 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173914_random 1302 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03174827_random 1294 /gbdb/panTro3/panTro3.2bit +chr10_AACZ03166294_random 1291 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158248_random 1291 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152729_random 1290 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03154990_random 1288 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168759_random 1287 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158241_random 1286 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151814_random 1285 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176697_random 1284 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170030_random 1281 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160248_random 1279 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158162_random 1272 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174046_random 1269 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160217_random 1269 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175578_random 1264 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170014_random 1261 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169125_random 1260 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151792_random 1259 /gbdb/panTro3/panTro3.2bit +chr22_AACZ03177262_random 1259 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162164_random 1259 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176236_random 1258 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163624_random 1253 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158232_random 1251 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03173973_random 1245 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156653_random 1239 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158271_random 1238 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169890_random 1235 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155038_random 1235 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165270_random 1232 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171670_random 1231 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160162_random 1224 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03161587_random 1224 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152727_random 1222 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03168998_random 1214 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151539_random 1212 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169977_random 1202 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152538_random 1201 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158225_random 1201 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153619_random 1196 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151739_random 1180 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160190_random 1178 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165271_random 1166 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175668_random 1158 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03160191_random 1143 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176425_random 1126 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170019_random 1124 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169134_random 1121 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178602_random 1120 /gbdb/panTro3/panTro3.2bit +chr20_AACZ03176904_random 1117 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03159656_random 1114 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153615_random 1113 /gbdb/panTro3/panTro3.2bit +chr19_AACZ03176437_random 1104 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155018_random 1100 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165347_random 1090 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172446_random 1079 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151783_random 1075 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151688_random 1073 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163611_random 1073 /gbdb/panTro3/panTro3.2bit +chr15_AACZ03172500_random 1070 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169120_random 1065 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151643_random 1057 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03169983_random 1038 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158305_random 1036 /gbdb/panTro3/panTro3.2bit +chr5_AACZ03158221_random 1035 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170032_random 1032 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175672_random 1016 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153607_random 1015 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171691_random 1008 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163602_random 995 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162167_random 992 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169132_random 981 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171726_random 977 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151510_random 967 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174069_random 965 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175682_random 960 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171712_random 959 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178598_random 958 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163637_random 957 /gbdb/panTro3/panTro3.2bit +chr9_AACZ03165403_random 946 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169131_random 930 /gbdb/panTro3/panTro3.2bit +chr14_AACZ03171718_random 925 /gbdb/panTro3/panTro3.2bit +chrX_AACZ03178599_random 901 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155017_random 900 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155010_random 899 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163641_random 897 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163613_random 896 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153521_random 885 /gbdb/panTro3/panTro3.2bit +chr3_AACZ03155053_random 882 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151847_random 873 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152669_random 873 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151840_random 870 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152778_random 851 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03156965_random 850 /gbdb/panTro3/panTro3.2bit +chr8_AACZ03163636_random 829 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174058_random 822 /gbdb/panTro3/panTro3.2bit +chr12_AACZ03170074_random 821 /gbdb/panTro3/panTro3.2bit +chr13_AACZ03171025_random 814 /gbdb/panTro3/panTro3.2bit +chr17_AACZ03175059_random 801 /gbdb/panTro3/panTro3.2bit +chr2A_AACZ03152776_random 801 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157024_random 796 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169133_random 778 /gbdb/panTro3/panTro3.2bit +chr4_AACZ03157023_random 773 /gbdb/panTro3/panTro3.2bit +chr7_AACZ03162166_random 764 /gbdb/panTro3/panTro3.2bit +chr11_AACZ03169135_random 762 /gbdb/panTro3/panTro3.2bit +chr18_AACZ03175702_random 741 /gbdb/panTro3/panTro3.2bit +chr6_AACZ03158310_random 740 /gbdb/panTro3/panTro3.2bit +chr2B_AACZ03153257_random 661 /gbdb/panTro3/panTro3.2bit +chr16_AACZ03174065_random 659 /gbdb/panTro3/panTro3.2bit +chr1_AACZ03151841_random 373 /gbdb/panTro3/panTro3.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/rn3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/rn3.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,44 @@ +chr1 268121971 /gbdb/rn3/nib/chr1.nib +chr2 258222147 /gbdb/rn3/nib/chr2.nib +chr3 170969371 /gbdb/rn3/nib/chr3.nib +chr4 187371129 /gbdb/rn3/nib/chr4.nib +chr5 173106704 /gbdb/rn3/nib/chr5.nib +chr6 147642806 /gbdb/rn3/nib/chr6.nib +chr7 143082968 /gbdb/rn3/nib/chr7.nib +chr8 129061546 /gbdb/rn3/nib/chr8.nib +chr9 113649943 /gbdb/rn3/nib/chr9.nib +chrX 160775580 /gbdb/rn3/nib/chrX.nib +chr1_random 3887217 /gbdb/rn3/nib/chr1_random.nib +chr2_random 4341851 /gbdb/rn3/nib/chr2_random.nib +chr3_random 1724363 /gbdb/rn3/nib/chr3_random.nib +chr4_random 2124656 /gbdb/rn3/nib/chr4_random.nib +chr5_random 2145107 /gbdb/rn3/nib/chr5_random.nib +chr6_random 1770534 /gbdb/rn3/nib/chr6_random.nib +chr7_random 1175105 /gbdb/rn3/nib/chr7_random.nib +chr8_random 887087 /gbdb/rn3/nib/chr8_random.nib +chr9_random 1166303 /gbdb/rn3/nib/chr9_random.nib +chrX_random 1977738 /gbdb/rn3/nib/chrX_random.nib +chr10 110733352 /gbdb/rn3/nib/chr10.nib +chr11 87800381 /gbdb/rn3/nib/chr11.nib +chr12 46649226 /gbdb/rn3/nib/chr12.nib +chr13 111348958 /gbdb/rn3/nib/chr13.nib +chr14 112220682 /gbdb/rn3/nib/chr14.nib +chr15 109774626 /gbdb/rn3/nib/chr15.nib +chr16 90224819 /gbdb/rn3/nib/chr16.nib +chr17 97307196 /gbdb/rn3/nib/chr17.nib +chr18 87338544 /gbdb/rn3/nib/chr18.nib +chr19 59223525 /gbdb/rn3/nib/chr19.nib +chr20 55296979 /gbdb/rn3/nib/chr20.nib +chrUn 75822765 /gbdb/rn3/nib/chrUn.nib +chr10_random 870782 /gbdb/rn3/nib/chr10_random.nib +chr11_random 1278614 /gbdb/rn3/nib/chr11_random.nib +chr12_random 953141 /gbdb/rn3/nib/chr12_random.nib +chr13_random 608348 /gbdb/rn3/nib/chr13_random.nib +chr14_random 1825095 /gbdb/rn3/nib/chr14_random.nib +chr15_random 1609635 /gbdb/rn3/nib/chr15_random.nib +chr16_random 1400107 /gbdb/rn3/nib/chr16_random.nib +chr17_random 615889 /gbdb/rn3/nib/chr17_random.nib +chr18_random 594525 /gbdb/rn3/nib/chr18_random.nib +chr19_random 984116 /gbdb/rn3/nib/chr19_random.nib +chr20_random 604928 /gbdb/rn3/nib/chr20_random.nib +chrUn_random 6862066 /gbdb/rn3/nib/chrUn_random.nib diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/rn4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/rn4.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,45 @@ +chr1 267910886 /gbdb/rn4/rn4.2bit +chr1_random 3887217 /gbdb/rn4/rn4.2bit +chr10 110718848 /gbdb/rn4/rn4.2bit +chr10_random 870782 /gbdb/rn4/rn4.2bit +chr11 87759784 /gbdb/rn4/rn4.2bit +chr11_random 1278614 /gbdb/rn4/rn4.2bit +chr12 46782294 /gbdb/rn4/rn4.2bit +chr12_random 953141 /gbdb/rn4/rn4.2bit +chr13 111154910 /gbdb/rn4/rn4.2bit +chr13_random 608348 /gbdb/rn4/rn4.2bit +chr14 112194335 /gbdb/rn4/rn4.2bit +chr14_random 1825095 /gbdb/rn4/rn4.2bit +chr15 109758846 /gbdb/rn4/rn4.2bit +chr15_random 1609635 /gbdb/rn4/rn4.2bit +chr16 90238779 /gbdb/rn4/rn4.2bit +chr16_random 1400107 /gbdb/rn4/rn4.2bit +chr17 97296363 /gbdb/rn4/rn4.2bit +chr17_random 615889 /gbdb/rn4/rn4.2bit +chr18 87265094 /gbdb/rn4/rn4.2bit +chr18_random 594525 /gbdb/rn4/rn4.2bit +chr19 59218465 /gbdb/rn4/rn4.2bit +chr19_random 984116 /gbdb/rn4/rn4.2bit +chr2 258207540 /gbdb/rn4/rn4.2bit +chr2_random 4341851 /gbdb/rn4/rn4.2bit +chr20 55268282 /gbdb/rn4/rn4.2bit +chr20_random 604928 /gbdb/rn4/rn4.2bit +chr3 171063335 /gbdb/rn4/rn4.2bit +chr3_random 1724363 /gbdb/rn4/rn4.2bit +chr4 187126005 /gbdb/rn4/rn4.2bit +chr4_random 2124656 /gbdb/rn4/rn4.2bit +chr5 173096209 /gbdb/rn4/rn4.2bit +chr5_random 2145107 /gbdb/rn4/rn4.2bit +chr6 147636619 /gbdb/rn4/rn4.2bit +chr6_random 1770534 /gbdb/rn4/rn4.2bit +chr7 143002779 /gbdb/rn4/rn4.2bit +chr7_random 1175105 /gbdb/rn4/rn4.2bit +chr8 129041809 /gbdb/rn4/rn4.2bit +chr8_random 887087 /gbdb/rn4/rn4.2bit +chr9 113440463 /gbdb/rn4/rn4.2bit +chr9_random 1166303 /gbdb/rn4/rn4.2bit +chrM 16300 /gbdb/rn4/rn4.2bit +chrUn 75822765 /gbdb/rn4/rn4.2bit +chrUn_random 6862066 /gbdb/rn4/rn4.2bit +chrX 160699376 /gbdb/rn4/rn4.2bit +chrX_random 1977738 /gbdb/rn4/rn4.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/susScr2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/chromInfo/susScr2.txt Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,20 @@ +chr1 295529705 /gbdb/susScr2/susScr2.2bit +chr14 148510138 /gbdb/susScr2/susScr2.2bit +chr13 145235301 /gbdb/susScr2/susScr2.2bit +chr2 140133492 /gbdb/susScr2/susScr2.2bit +chr7 136409062 /gbdb/susScr2/susScr2.2bit +chr4 136254946 /gbdb/susScr2/susScr2.2bit +chr15 134541103 /gbdb/susScr2/susScr2.2bit +chr9 132468591 /gbdb/susScr2/susScr2.2bit +chrX 125871292 /gbdb/susScr2/susScr2.2bit +chr3 123599780 /gbdb/susScr2/susScr2.2bit +chr6 123305171 /gbdb/susScr2/susScr2.2bit +chr8 119985671 /gbdb/susScr2/susScr2.2bit +chr5 100516970 /gbdb/susScr2/susScr2.2bit +chr11 79814395 /gbdb/susScr2/susScr2.2bit +chr16 77435658 /gbdb/susScr2/susScr2.2bit +chr10 66736929 /gbdb/susScr2/susScr2.2bit +chr17 64395339 /gbdb/susScr2/susScr2.2bit +chr12 57431344 /gbdb/susScr2/susScr2.2bit +chr18 54309914 /gbdb/susScr2/susScr2.2bit +chrM 16770 /gbdb/susScr2/susScr2.2bit diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/fetchChromSizes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NGSrich_0.5.5/thirdparty/fetchChromSizes Mon Nov 21 08:12:19 2011 -0500 @@ -0,0 +1,94 @@ +#!/bin/sh + +# fetchChromSizes - script to grab chrom.sizes from UCSC via either of: +# mysql, wget or ftp + +# "$Id: fetchChromSizes,v 1.2 2009/03/26 18:40:09 hiram Exp $" + +usage() { + echo "usage: fetchChromSizes > .chrom.sizes" + echo " used to fetch chrom.sizes information from UCSC for the given " + echo " - name of UCSC database, e.g.: hg18, mm9, etc ..." + echo "" + echo "This script expects to find one of the following commands:" + echo " wget, mysql, or ftp in order to fetch information from UCSC." + echo "Route the output to the file .chrom.sizes as indicated above." + echo "" + echo "Example: fetchChromSizes hg18 > hg18.chrom.sizes" + exit 255 +} + +DB=$1 +export DB +if [ -z "${DB}" ]; then + usage +fi + +WGET=`type wget 2> /dev/null | sed -e "s/.* is //"` +MYSQL=`type mysql 2> /dev/null | sed -e "s/.* is //"` +FTP=`type ftp 2> /dev/null | sed -e "s/.* is //"` + +if [ -z "${WGET}" -a -z "${MYSQL}" -a -z "${FTP}" ]; then + echo "ERROR: can not find any of the commands: wget mysql or ftp" + usage +fi + +DONE=0 +export DONE +if [ -n "${MYSQL}" ]; then + echo "INFO: trying MySQL ${MYSQL} for database ${DB}" 1>&2 + ${MYSQL} -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \ + "SELECT chrom,size FROM chromInfo ORDER BY size DESC;" ${DB} + if [ $? -ne 0 ]; then + echo "WARNING: mysql command failed" 1>&2 + else + DONE=1 + fi +fi + +if [ "${DONE}" -eq 1 ]; then + exit 0 +fi + +if [ -n "${WGET}" ]; then + echo "INFO: trying WGET ${WGET} for database ${DB}" 1>&2 + tmpResult=chromInfoTemp.$$.gz + ${WGET} \ +"ftp://hgdownload.cse.ucsc.edu/goldenPath/${DB}/database/chromInfo.txt.gz" \ + -O ${tmpResult} 2> /dev/null + if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then + echo "WARNING: wget command failed" 1>&2 + rm -f "${tmpResult}" + else + zcat ${tmpResult} 2> /dev/null | cut -f1,2 | sort -k2nr + rm -f "${tmpResult}" + DONE=1 + fi +fi + +if [ "${DONE}" -eq 1 ]; then + exit 0 +fi + +if [ -n "${FTP}" ]; then + echo "INFO: trying FTP ${FTP} for database ${DB}" 1>&2 + tmpFtpRsp=fetchTemp.$$ + echo "user anonymous fetchChromSizes@" > ${tmpFtpRsp} + echo "cd goldenPath/${DB}/database" >> ${tmpFtpRsp} + echo "get chromInfo.txt.gz ${tmpResult}" >> ${tmpFtpRsp} + echo "bye" >> ${tmpFtpRsp} + ${FTP} -u -n -i hgdownload.cse.ucsc.edu < ${tmpFtpRsp} > /dev/null 2>&1 + if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then + echo "ERROR: ftp command failed" 1>&2 + rm -f "${tmpFtpRsp}" "${tmpResult}" + else + zcat ${tmpResult} | cut -f1,2 | sort -k2nr + rm -f "${tmpFtpRsp}" "${tmpResult}" + DONE=1 + fi +fi + +if [ "${DONE}" -eq 0 ]; then + echo "ERROR: sorry, attempt to fetch chrom.sizes has failed ?" 1>&2 + exit 255 +fi diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/samtools/0.1.16/samtools Binary file NGSrich_0.5.5/thirdparty/samtools/0.1.16/samtools has changed diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/wigToBigWig Binary file NGSrich_0.5.5/thirdparty/wigToBigWig has changed