# HG changeset patch # User brasset_jensen # Date 1548694635 18000 # Node ID 96751292431771a38873ce1876eec32654d4a60d # Parent 11708af40030823e46092c585b315a47d502246e planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d diff -r 11708af40030 -r 967512924317 README.rst --- a/README.rst Thu Jan 24 13:09:46 2019 -0500 +++ b/README.rst Mon Jan 28 11:57:15 2019 -0500 @@ -15,7 +15,7 @@ Prerequisites ============= -1. Unix system with A Galaxy server (release july 2014 or later installed) +1. Unix system with A Galaxy server (release 16.01 or later installed) 2. Some tools are used by sRNAPipe and must be installed and added to the Path. diff -r 11708af40030 -r 967512924317 bin/Rcall.pm --- a/bin/Rcall.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,136 +0,0 @@ -package Rcall; - -use strict; -use warnings; -use Statistics::R; - -use Exporter; -our @ISA = qw(Exporter); -our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png ); - -sub histogram -{ - my ($size_hashR, $out_png, $size) = @_; - my (@abs, @ord); - my $i = 0; - foreach my $k (sort {$a <=> $b} keys %{$size_hashR}) - { - my $percentage = 0; - $percentage = $size_hashR->{$k} * 100 / $size if $size != 0; - $abs[$i] = $k ; $ord[$i] = $percentage; $i++; - } - my $abs = join (",", @abs ); - my $ord = join (",", @ord ); - if (scalar(@abs) != 0) - { - - my $R = Statistics::R->new(); - $R->startR; - $R->send( - qq`library(ggplot2) - percentage = c($ord) - size =c($abs) - min = min(size) - max = max(size) - dat = data.frame(size,percentage) - png(filename=\"$out_png\", width = 640, height = 640) - c = ggplot(dat,aes(size,percentage)) - c + geom_bar(stat="identity") + scale_x_continuous(breaks=min:max)+theme( axis.text.x = element_text(angle=90, hjust=0.5, size=20), axis.text.y = element_text( size=20 ), axis.title.x = element_text( size=25, face="bold"), axis.title.y = element_text( size=25, face="bold") ) - dev.off()`); - $R->stopR(); - - } -} - -sub bg_to_png -{ - my ( $fai, $bgP, $bgM, $dir, $sb ) = @_; - my $R = Statistics::R->new(); - $R->startR; - $R->send( - qq`library('Sushi') - fai =read.table("$fai") - if ( file.info("$bgP")\$size !=0 ) - { - bgP = read.table("$bgP") - } else { bgP = data.frame(factor(),integer()) } - - if ( file.info("$bgM")\$size !=0 ) - { - bgM = read.table("$bgM") - } else { bgM = data.frame(factor(),integer()) } - - f_both = function(chr,end) { - jpeg( paste0("$dir",as.character(chr),".png"), quality=100) - par(mfrow=c(2,1),mar=c(1,10,1,3)) - plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1]) - axis(side=2,las=2,tcl=.2) - mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2) - plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2]) - labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) - axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)])) - mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2) - dev.off() - } - - f_plus = function(chr,end) { - jpeg( paste0("$dir",as.character(chr),".png"), quality=100) - plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1]) - labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) - axis(side=2,las=2,tcl=.2) - mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2) - dev.off() - } - - f_minus = function(chr,end) { - jpeg( paste0("$dir",as.character(chr),".png"), quality=100) - plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2]) - labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) - axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)])) - mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2) - dev.off() - } - - fai_b = fai[fai\$V1 %in% intersect(bgM\$V1,bgP\$V1), ] - mapply( f_both, fai_b\$V1, fai_b\$V2) - - fai_p = fai[fai\$V1 %in% setdiff(bgP\$V1,bgM\$V1), ] - mapply( f_plus, fai_p\$V1, fai_p\$V2) - - fai_m = fai[fai\$V1 %in% setdiff(bgM\$V1,bgP\$V1), ] - mapply( f_minus, fai_m\$V1, fai_m\$V2) `); - - $R->stopR(); -} - -sub pie_chart -{ - my $dir = shift; - my $in = $dir.'repartition.txt'; - my $out = $dir.'pie_chart.png'; - - my $R = Statistics::R->new(); - $R->startR; - $R->send( - qq` - library(plotrix) - library(RColorBrewer) - R =read.table("$in",header=T) - values = round(R\$percentage) - keys = R\$type - lab = paste(values, "%", sep="") - png("$out") - colors <- brewer.pal(7,"Paired") - pie(values, col=colors, labels=lab, clockwise=TRUE) - legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3) - par(mai = c(0,0,0,0)) - layout(c(1,2),heights=c(0.3,1)) - plot.new() - legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3) - pie(values, col=colors, labels=lab, clockwise=TRUE) - dev.off()` - ); - $R->stopR(); -} - -1; diff -r 11708af40030 -r 967512924317 bin/align.pm --- a/bin/align.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,551 +0,0 @@ -package align; - -use strict; -use warnings; -use File::Basename; -use String::Random; - -use FindBin; -use lib $FindBin::Bin; -use Rcall qw ( histogram ); - -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT = qw( &rpms_rpkm_te &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam ); - -sub to_build -{ - my ( $toBuildTabP, $log, $newdir ) = @_; - - foreach my $pairs ( @{ $toBuildTabP } ) - { - if ( $pairs->[0] == 1 ) - { - my $sym = $newdir.basename(${$pairs->[1]}).'_symlink.fa'; - symlink( ${$pairs->[1]}, $sym ); - ${$pairs->[1]} = $sym; - build_index ( ${$pairs->[1]}, $log ); - } - } -} - -sub build_index -{ - my $to_index = shift; - my $log = shift; - my $index_log = $to_index.'_index.err'; - `bwa index '$to_index' 2> '$index_log'`; - print $log "Creating index for $to_index\n"; -} - -sub get_unique -{ - my ( $sam, $s_uni, $out_prefix, $col_prefix, $details, $report ) = @_; - - my $fout = $col_prefix.'_all_mappers.fastq'; - my $funi = $col_prefix.'_unique_mappers.fastq'; - my $frej = $col_prefix.'_unmapped.fastq'; - - my $repartition = $out_prefix.'distribution.txt'; - my $png_rep = $out_prefix.'distribution.png'; - my ( %duplicates, %genome_hits) ; - - #alignement to the first reference - my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \%duplicates, \%genome_hits, $report ); - my $ref_fai = $return[4]; - my $mappers = $return[5]; - my $mappers_uni = $return[6]; - my $size_mappedHashR = $return[7]; - - if ( $details == 1 ) - { - #print number of duplicates and hits number - my ($pourcentage, $total) =(0,0); - - $total += $_ foreach values %{$size_mappedHashR}; - open (my $rep, '>'.$repartition) || die "cannot create $repartition $!\n"; - print $rep "size\tnumber\tpercentage\n"; - foreach my $k (sort{$a cmp $b} keys (%{$size_mappedHashR})) - { - $pourcentage = 0; - $pourcentage = $size_mappedHashR->{$k} / $total * 100 unless $total ==0; - - print $rep "$k\t$size_mappedHashR->{$k}\t"; - printf $rep "%.2f\n",$pourcentage; - } - - histogram($size_mappedHashR, $png_rep, $total); - - - my $dup = $out_prefix.'dup_mapnum.txt'; - my $dup_u = $out_prefix .'dup_unique.txt'; - my $dup_r = $out_prefix .'dup_nonmapp.txt'; - open(my $tab,">".$dup) || die "cannot open output txt file\n"; - open(my $tab_r,">".$dup_r) || die "cannot open output txt file\n"; - open(my $tab_u,">".$dup_u) || die "cannot open output txt file\n"; - print $tab "sequence\tcount\tmapnum\n"; - print $tab_u "sequence\tcount\n"; - print $tab_r "sequence\tcount\n"; - foreach my $k (sort {$duplicates{$b} <=> $duplicates{$a}}keys %duplicates) - { - $duplicates{$k} = 0 unless exists($duplicates{$k}); - $genome_hits{$k} = 0 unless exists($genome_hits{$k}); - if ($genome_hits{$k} != 0) { print $tab $k."\t".$duplicates{$k}."\t".$genome_hits{$k}."\n"; } - else {print $tab_r $k."\t".$duplicates{$k}."\n";} - if ($genome_hits{$k} == 1) { print $tab_u $k."\t".$duplicates{$k}."\n"; } - } - close $dup; close $dup_r; close $dup_u; - } - return ( $ref_fai, $mappers, $mappers_uni ); -} - -sub sam_parse -{ - my ( $sam, $fastq_accepted, $fastq_accepted_unique, $fastq_rejected, $sam_unique, $duplicate_hashR, $best_hit_number_hashR, $report ) = @_ ; - my ($reads, $mappers, $mappersUnique, @garbage, %size_num, %size_num_spe, %number, %numberSens, %numberReverse, %unique_number, %numberNM, %numberM, %size); - $mappers = $mappersUnique = $reads = 0; - - open my $fic, '<', $sam || die "cannot open $sam $!\n"; - open my $accepted, '>', $fastq_accepted || die "cannot create $fastq_accepted $! \n"; - open my $unique, '>', $fastq_accepted_unique || die "cannot create $fastq_accepted_unique $! \n"; - open my $rejected, '>', $fastq_rejected || die "cannot create $fastq_rejected $! \n"; - open my $sam_uni, '>', $sam_unique || die "cannot create $sam_unique $! \n"; - my $sequence = ''; - while(<$fic>) - { - chomp $_; - if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) - { - if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/) - { - $size{$1} = $2; - $unique_number{$1} = 0; - $number{$1} = 0; - $numberNM{$1} = 0; - $numberM{$1} = 0; - } - print $sam_uni $_."\n"; - next; - } - $reads++; - my @line = split (/\t/,$_); - $sequence = $line[9]; - if ($line[1] & 16) - { - $sequence =reverse($sequence); - $sequence =~ tr/atgcuATGCU/tacgaTACGA/; - } - if ($line[1] == 16 || $line[1] == 0) - { - my $len = length($sequence); - $size_num{$len} ++; - $size_num_spe{$line[2]}{$len}++; - $mappers ++; - - ${$best_hit_number_hashR}{$sequence} = $1 if ($line[13] =~ /X0:i:(\d*)/ || $line[14] =~/X0:i:(\d*)/ ); - ${$duplicate_hashR}{$sequence}++; - $number{$line[2]}++; - $numberSens{$line[2]}++ if $line[1] == 0 ; - $numberReverse{$line[2]}++ if $line[1] == 16 ; - print $accepted "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; - - if ($line[11] eq "XT:A:U") - { - $unique_number{$line[2]}++; - $mappersUnique++; - print $unique "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; - print $sam_uni $_."\n"; - } - if ($_ =~ /.*XM:i:(\d+).*/) - { - if ($1 == 0){$numberNM{$line[2]}++;}else{$numberM{$line[2]}++;} - } - } - else - { - ${$best_hit_number_hashR}{$sequence} = 0; - ${$duplicate_hashR}{$sequence}++; - print $rejected "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; - } - } - close $fic; close $accepted; close $unique; close $rejected; close $sam_uni; - - print $report "Parsing $sam file\n"; - print $report "\treads: $reads\n"; - print $report "\tmappers: $mappers\n"; - print $report "\tunique mappers: $mappersUnique\n"; - print $report "-----------------------------\n"; - return (\%number, \%unique_number, \%numberSens, \%numberReverse, \%size, $mappers, $mappersUnique, \%size_num, \%size_num_spe, \%numberNM, \%numberM ); -} - -sub get_hash_alignment -{ - my ($index, $mismatches, $accept, $reject, $outA, $outR, $fastq, $number_of_cpus, $name, $sam, $report, $fai_f) = @_ ; - my ($reads, $mappers, $unmapped) = (0,0,0); - my $accep_unique; - BWA_call ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report ); - - open my $fic, '<', $sam || die "cannot open $sam $!\n"; - open my $accepted, '>', $outA || die "cannot open $outA\n" if $accept == 1; - open my $rejected, '>', $outR || die "cannot open $outR\n" if $reject == 1; - open my $fai, '>', $fai_f || die "cannot open $fai_f\n" if $fai_f; - #if ($name eq "snRNAs") { - # open ( $accep_unique, ">".$1."-unique.fastq") if $outR =~ /(.*)\.fastq/; - #} - my $sequence = ''; - while(<$fic>) - { - chomp $_; - if( $_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) - { - if ($fai_f && $_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/) - { - print $fai $1."\t".$2."\n"; - } - next; - } - $reads++; - my @line = split (/\t/,$_); - $sequence = $line[9]; - if ($line[1] & 16) - { - $sequence =reverse($sequence); - $sequence =~ tr/atgcuATGCU/tacgaTACGA/; - } - if ($line[1] & 16 || $line[1] == 0) - { - $mappers ++; - if ($accept == 1 ) - { - print $accepted "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; - # print $accep_unique "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n" if ($name eq "snRNAs" && $line[11] eq "XT:A:U"); - } - } - else - { - print $rejected "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n" if $reject == 1; - $unmapped++; - } - } - # close $accep_unique if ($name eq "bonafide_reads"); - close $fic; - close $accepted if $accept == 1; - close $rejected if $reject ==1; - close $fai if $fai_f; - print $report "\treads: $reads\n"; - print $report "\tmappers: $mappers\n"; - print $report "\tunmapped: $unmapped\n"; - print $report "-----------------------------\n"; - return ($mappers, $unmapped); -} - -sub sam_count -{ - my $sam = shift; - my ( %number, %size ); - - open my $fic, '<', $sam || die "cannot open $sam file $!\n"; - while(<$fic>) - { - chomp $_; - if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) - { - if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/) - { - $size{$1} = $2; - $number{$1} = 0; - } - } - else - { - my @line = split (/\t/,$_); - if ( $line[1] & 16 || $line[1] == 0 ) - { - $number{$line[2]}++; - } - } - } - close $fic; - return ( \%number, \%size ); -} - -sub sam_count_mis -{ - - my $sam = shift; - my ( %number, %numberNM, %numberM, %size); - - open my $fic, '<', $sam || die "cannot open $sam file $!\n"; - while(<$fic>) - { - chomp $_; - if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) - { - if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/) - { - $size{$1} = $2; - $number{$1} = [0,0,0,0,0,0,0]; - $numberNM{$1} = [0,0,0,0,0,0,0]; - $numberM{$1} = [0,0,0,0,0,0,0]; - } - } - else - { - my @line = split (/\t/,$_); - my @seq = split //, $line[9]; - if ( $line[1] == 16 || $line[1] == 0 ) - { - $number{ $line[2] }->[0]++; - if ($line[1] == 0) - { - $number{$line[2]}->[1]++; - $number{$line[2]}->[3]++ if $seq[0] eq 'T'; - $number{$line[2]}->[5]++ if $seq[9] eq 'A'; - } - else - { - $number{$line[2]}->[2]++; - $number{$line[2]}->[4]++ if $seq[9] eq 'A'; - $number{$line[2]}->[6]++ if $seq[0] eq 'T'; - } - if ($_ =~ /.*XM:i:(\d+).*/) - { - if ( $1 == 0 ) - { - $numberNM{$line[2]}->[0]++; - if ($line[1] == 0) - { - $numberNM{$line[2]}->[1]++; - $numberNM{$line[2]}->[3]++ if $seq[0] eq 'T'; - $numberNM{$line[2]}->[5]++ if $seq[9] eq 'A'; - } - else - { - $numberNM{$line[2]}->[2]++; - $numberNM{$line[2]}->[4]++ if $seq[9] eq 'A'; - $numberNM{$line[2]}->[6]++ if $seq[0] eq 'T'; - } - } - else - { - $numberM{$line[2]}->[0]++; - if ($line[1] == 0) - { - $numberM{$line[2]}->[1]++; - $numberM{$line[2]}->[3]++ if $seq[0] eq 'T'; - $numberM{$line[2]}->[5]++ if $seq[9] eq 'A'; - } - else - { - $numberM{$line[2]}->[2]++; - $numberM{$line[2]}->[4]++ if $seq[9] eq 'A'; - $numberM{$line[2]}->[6]++ if $seq[0] eq 'T'; - } - } - } - } - } - } - return (\%number, \%size, \%numberNM, \%numberM ); -} - -sub rpms_rpkm_te -{ - my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_; - open(my $out, ">".$out_file) || die "cannot open normalized file $! \n"; - print $out "ID\treads counts\tRPKM"; - print $out "\tper million of piRNAs" if ($piRNA_number != 0); - print $out "\tper million of miRNAs" if ($miRNA_number != 0); - print $out "\tper million of bonafide reads" if ($bonafide_number != 0); - print $out "\tsense reads counts\treverse reads counts"; - print $out "\t% of sense 1U\t% of sense 10A\t% of reverse 1U\t% of reverse 10A\n"; - foreach my $k ( sort keys %{$counthashR} ) - { - my ($rpkm, $pirna, $mirna, $bonafide) = (0,0,0,0); - - $rpkm = ( $counthashR->{$k}->[0] * 1000000000) / ( $sizehashR->{$k} * $mapped) if ( $sizehashR->{$k} * $mapped) != 0 ; - print $out $k."\t".$counthashR->{$k}->[0]."\t"; printf $out "%.2f",$rpkm; - - if ($piRNA_number != 0 ) - { - $pirna = ( $counthashR->{$k}->[0] * 1000000) / $piRNA_number; - printf $out "\t%.2f",$pirna; - } - if ($miRNA_number != 0 ) - { - $mirna = ( $counthashR->{$k}->[0] * 1000000) / $miRNA_number; - printf $out "\t%.2f",$mirna; - } - if ($bonafide_number != 0 ) - { - $bonafide = ( $counthashR->{$k}->[0] * 1000000) / $bonafide_number; - printf $out "\t%.2f",$bonafide; - } - - print $out "\t".$counthashR->{$k}->[1]."\t".$counthashR->{$k}->[2] ; - my $S1U = 0; - $S1U = $counthashR->{$k}->[3] / $counthashR->{$k}->[1] * 100 if $counthashR->{$k}->[1] != 0; - my $R1U = 0; - $R1U = $counthashR->{$k}->[6] / $counthashR->{$k}->[2] * 100 if $counthashR->{$k}->[2] != 0; - my $S10A = 0; - $S10A = $counthashR->{$k}->[5] / $counthashR->{$k}->[1] * 100 if $counthashR->{$k}->[1] != 0; - my $R10A = 0; - $R10A = $counthashR->{$k}->[4] / $counthashR->{$k}->[2] * 100 if $counthashR->{$k}->[2] != 0; - print $out "\t".$S1U."\t".$S10A."\t".$R1U."\t".$R10A; - - print $out "\n"; - } - close $out; -} - - -sub sam_to_bam_bg -{ - my ( $sam, $scale, $number_of_cpus ) = @_; - my ( $bam_sorted, $bedgraphM, $bedgraphP, $view_err, $sort_err ) = ( '', '', '', '', '' ); - if ( $sam =~ /(.*?).sam$/ ) - { - $bam_sorted = $1.'_sorted.bam'; - $bedgraphP= $1.'_plus.bedgraph'; - $bedgraphM = $1.'_minus.bedgraph'; - $view_err = $1.'_view.err'; - $sort_err = $1.'_sort.err'; - } - `samtools view -Shb --threads $number_of_cpus '$sam' 2> '$view_err' | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> '$sort_err' > '$bam_sorted'`; - `bedtools genomecov -scale $scale -strand + -bga -ibam '$bam_sorted' > '$bedgraphP'`; - `bedtools genomecov -scale $scale -strand - -bga -ibam '$bam_sorted' > '$bedgraphM'`; -} - -sub sam_sorted_bam -{ - my ( $sam, $number_of_cpus ) = @_; - my ( $bam_sorted, $view_err, $sort_err ) = ( '', '', '' ); - if ( $sam =~ /(.*?).sam$/ ) - { - $bam_sorted = $1.'_sorted.bam'; - $view_err = $1.'_view.err'; - $sort_err = $1.'_sort.err'; - - } - `samtools view -Shb --threads $number_of_cpus '$sam' 2> '$view_err' | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> '$sort_err' > '$bam_sorted'`; -} - -sub BWA_call -{ - my ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report ) = @_; - my ( $aln_err, $samse_err, $seq_num ) = ( $sam.'_aln.err', $sam.'_samse.err', 0 ); - print $report "-----------------------------\n"; - print $report "bwa aln -t $number_of_cpus -n $mismatches '$index' '$fastq' 2> '$aln_err' | bwa samse $index /dev/stdin '$fastq' 2> '$samse_err' > '$sam'\n"; - `bwa aln -t $number_of_cpus -n $mismatches '$index' '$fastq' 2> '$aln_err' | bwa samse $index /dev/stdin '$fastq' 2> '$samse_err' > '$sam' `; -} - -sub rpms_rpkm -{ - my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_; - open(my $out, ">".$out_file) || die "cannot open normalized file $! \n"; - print $out "ID\treads counts\tRPKM"; - print $out "\tper million of piRNAs" if ($piRNA_number != 0); - print $out "\tper million of miRNAs" if ($miRNA_number != 0); - print $out "\tper million of bonafide reads" if ($bonafide_number != 0); - print $out "\n"; - foreach my $k ( sort keys %{$counthashR} ) - { - my ($rpkm, $pirna, $mirna, $bonafide) = (0,0,0,0); - - $rpkm = ( $counthashR->{$k} * 1000000000) / ( $sizehashR->{$k} * $mapped) if ( $sizehashR->{$k} * $mapped) != 0 ; - print $out $k."\t".$counthashR->{$k}."\t"; printf $out "%.2f",$rpkm; - - if ($piRNA_number != 0 ) - { - $pirna = ( $counthashR->{$k} * 1000000) / $piRNA_number; - printf $out "\t%.2f",$pirna; - } - if ($miRNA_number != 0 ) - { - $mirna = ( $counthashR->{$k} * 1000000) / $miRNA_number; - printf $out "\t%.2f",$mirna; - } - if ($bonafide_number != 0 ) - { - $bonafide = ( $counthashR->{$k} * 1000000) / $bonafide_number; - printf $out "\t%.2f",$bonafide; - } - print $out "\n"; - } - close $out; -} - -sub extract_sam -{ - my ( $hashRef, $sam_in, $sam_out, $sam_uni_out, $fastq_out, $fastq_uni_out ) = @_; - - open my $s_in, '<', $sam_in || die "cannot open $sam_in file $!\n"; - - open my $f_out, '>', $fastq_out || die "cannot create $fastq_out $!\n"; - open my $f_uni_out, '>', $fastq_uni_out || die "cannot create $fastq_uni_out $!\n"; - - open my $s_out, '>', $sam_out || die "cannot create $sam_out file $!\n" if defined ($hashRef); - open my $s_uni_out, '>', $sam_uni_out || die "cannot create $sam_uni_out file $!\n"; - - my $sequence = ''; - while(<$s_in>) - { - if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) - { - print $s_out $_ if defined ($hashRef); - print $s_uni_out $_; - next; - } - my @line = split (/\t/,$_); - $sequence = $line[0]; - if ( (! defined ($hashRef) )|| ( exists $hashRef->{$sequence} && $hashRef->{$sequence} == 1 ) ) - { - my $arn = $line[9]; - if ($line[1] & 16) - { - $arn =reverse($arn); - $arn =~ tr/atgcuATGCU/tacgaTACGA/; - } - - if ( ( $line[1] == 16 || $line[1] == 0 ) ) - { - print $f_out "\@".$line[0]."\n".$arn."\n+\n".$line[10]."\n" ; - print $s_out $_ if defined ($hashRef); - if ( $line[11] eq "XT:A:U" ) - { - print $f_uni_out "\@".$line[0]."\n".$arn."\n+\n".$line[10]."\n" ; - print $s_uni_out $_ ; - } - } - } - } - close $s_in; close $s_out if defined ($hashRef); - close $s_uni_out; close $f_out; close $f_uni_out; -} - -sub get_fastq_seq -{ - my $fastq = shift; - my %hash; my $cmp = 0; - - open my $fic, '<', $fastq || die "cannot open input file $! \n"; - while(<$fic>) - { - chomp $_; - $cmp++; - if ($cmp % 4 == 1) - { - die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ ); - if ($_ =~ /^\@(.*)\s.*/) { $hash{$1} = 1;} - elsif ($_ =~ /^\@(.*)/) { $hash{$1} = 1;} - } - elsif ($cmp % 4 == 3 ) - { - die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/; - } - } - close $fic; - return \%hash; -} - -1; diff -r 11708af40030 -r 967512924317 bin/css/bootstrap-responsive.css --- a/bin/css/bootstrap-responsive.css Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1109 +0,0 @@ -/*! - * Bootstrap Responsive v2.3.2 - * - * Copyright 2012 Twitter, Inc - * Licensed under the Apache License v2.0 - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Designed and built with all the love in the world @twitter by @mdo and @fat. - */ - -.clearfix { - *zoom: 1; 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- } -} - -@media (max-width: 767px) { - .hidden-desktop { - display: inherit !important; - } - .visible-desktop { - display: none !important; - } - .visible-phone { - display: inherit !important; - } - .hidden-phone { - display: none !important; - } -} - -.visible-print { - display: none !important; -} - -@media print { - .visible-print { - display: inherit !important; - } - .hidden-print { - display: none !important; - } -} - -@media (min-width: 1200px) { - .row { - margin-left: -30px; - *zoom: 1; - } - .row:before, - .row:after { - display: table; - line-height: 0; - content: ""; - } - .row:after { - clear: both; - } - [class*="span"] { - float: left; - min-height: 1px; - margin-left: 30px; - } - .container, - .navbar-static-top .container, - .navbar-fixed-top .container, - .navbar-fixed-bottom .container { - width: 1170px; - } - .span12 { - width: 1170px; - } - .span11 { - width: 1070px; - } - .span10 { - width: 970px; - } - .span9 { - width: 870px; - } - .span8 { - width: 770px; - } - .span7 { - width: 670px; 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- *margin-left: 11.219583872105325%; - } - .row-fluid .offset1:first-child { - margin-left: 8.56353591160221%; - *margin-left: 8.457152932878806%; - } - input, - textarea, - .uneditable-input { - margin-left: 0; - } - .controls-row [class*="span"] + [class*="span"] { - margin-left: 20px; - } - input.span12, - textarea.span12, - .uneditable-input.span12 { - width: 710px; - } - input.span11, - textarea.span11, - .uneditable-input.span11 { - width: 648px; - } - input.span10, - textarea.span10, - .uneditable-input.span10 { - width: 586px; - } - input.span9, - textarea.span9, - .uneditable-input.span9 { - width: 524px; - } - input.span8, - textarea.span8, - .uneditable-input.span8 { - width: 462px; - } - input.span7, - textarea.span7, - .uneditable-input.span7 { - width: 400px; - } - input.span6, - textarea.span6, - .uneditable-input.span6 { - width: 338px; - } - input.span5, - textarea.span5, - .uneditable-input.span5 { - width: 276px; - } - input.span4, - textarea.span4, - .uneditable-input.span4 { - width: 214px; - } - input.span3, - textarea.span3, - .uneditable-input.span3 { - width: 152px; - } - input.span2, - textarea.span2, - .uneditable-input.span2 { - width: 90px; - } - input.span1, - textarea.span1, - .uneditable-input.span1 { - width: 28px; - } -} - -@media (max-width: 767px) { - body { - padding-right: 20px; - padding-left: 20px; - } - .navbar-fixed-top, - .navbar-fixed-bottom, - .navbar-static-top { - margin-right: -20px; - margin-left: -20px; - } - .container-fluid { - padding: 0; - } - .dl-horizontal dt { - float: none; - width: auto; - clear: none; - text-align: left; - } - .dl-horizontal dd { - margin-left: 0; - } - .container { - width: auto; - } - .row-fluid { - width: 100%; - } - .row, - .thumbnails { - margin-left: 0; - } - .thumbnails > li { - float: none; - margin-left: 0; - } - [class*="span"], - .uneditable-input[class*="span"], - .row-fluid [class*="span"] { - display: block; - float: none; - width: 100%; - margin-left: 0; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - box-sizing: border-box; - } - .span12, - .row-fluid .span12 { - width: 100%; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - box-sizing: border-box; - } - .row-fluid [class*="offset"]:first-child { - margin-left: 0; - } - .input-large, - .input-xlarge, - .input-xxlarge, - input[class*="span"], - select[class*="span"], - textarea[class*="span"], - .uneditable-input { - display: block; - width: 100%; - min-height: 30px; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - box-sizing: border-box; - } - .input-prepend input, - .input-append input, - .input-prepend input[class*="span"], - .input-append input[class*="span"] { - display: inline-block; - width: auto; - } - .controls-row [class*="span"] + [class*="span"] { - margin-left: 0; - } - .modal { - position: fixed; - top: 20px; - right: 20px; - left: 20px; - width: auto; - margin: 0; - } - .modal.fade { - top: -100px; - } - .modal.fade.in { - top: 20px; - } -} - -@media (max-width: 480px) { - .nav-collapse { - -webkit-transform: translate3d(0, 0, 0); - } - .page-header h1 small { - display: block; - line-height: 20px; - } - input[type="checkbox"], - input[type="radio"] { - border: 1px solid #ccc; - } - .form-horizontal .control-label { - float: none; - width: auto; - padding-top: 0; - text-align: left; - } - .form-horizontal .controls { - margin-left: 0; - } - .form-horizontal .control-list { - padding-top: 0; - } - .form-horizontal .form-actions { - padding-right: 10px; - padding-left: 10px; - } - .media .pull-left, - .media .pull-right { - display: block; - float: none; - margin-bottom: 10px; - } - .media-object { - margin-right: 0; - margin-left: 0; - } - .modal { - top: 10px; - right: 10px; - left: 10px; - } - .modal-header .close { - padding: 10px; - margin: -10px; - } - .carousel-caption { - position: static; - } -} - -@media (max-width: 979px) { - body { - padding-top: 0; - } - .navbar-fixed-top, - .navbar-fixed-bottom { - position: static; - } - .navbar-fixed-top { - margin-bottom: 20px; - } - .navbar-fixed-bottom { - margin-top: 20px; - } - .navbar-fixed-top .navbar-inner, - .navbar-fixed-bottom .navbar-inner { - padding: 5px; - } - .navbar .container { - width: auto; - padding: 0; - } - .navbar .brand { - padding-right: 10px; - padding-left: 10px; - margin: 0 0 0 -5px; - } - .nav-collapse { - clear: both; - } - .nav-collapse .nav { - float: none; - margin: 0 0 10px; - } - .nav-collapse .nav > li { - float: none; - } - .nav-collapse .nav > li > a { - margin-bottom: 2px; - } - .nav-collapse .nav > .divider-vertical { - display: none; - } - .nav-collapse .nav .nav-header { - color: #777777; - text-shadow: none; - } - .nav-collapse .nav > li > a, - .nav-collapse .dropdown-menu a { - padding: 9px 15px; - font-weight: bold; - color: #777777; - -webkit-border-radius: 3px; - -moz-border-radius: 3px; - border-radius: 3px; - } - .nav-collapse .btn { - padding: 4px 10px 4px; - font-weight: normal; - -webkit-border-radius: 4px; - -moz-border-radius: 4px; - border-radius: 4px; - } - .nav-collapse .dropdown-menu li + li a { - margin-bottom: 2px; - } - .nav-collapse .nav > li > a:hover, - .nav-collapse .nav > li > a:focus, - .nav-collapse .dropdown-menu a:hover, - .nav-collapse .dropdown-menu a:focus { - background-color: #f2f2f2; - } - .navbar-inverse .nav-collapse .nav > li > a, - .navbar-inverse .nav-collapse .dropdown-menu a { - color: #999999; - } - .navbar-inverse .nav-collapse .nav > li > a:hover, - .navbar-inverse .nav-collapse .nav > li > a:focus, - .navbar-inverse .nav-collapse .dropdown-menu a:hover, - .navbar-inverse .nav-collapse .dropdown-menu a:focus { - background-color: #111111; - } - .nav-collapse.in .btn-group { - padding: 0; - margin-top: 5px; - } - .nav-collapse .dropdown-menu { - position: static; - top: auto; - left: auto; - display: none; - float: none; - max-width: none; - padding: 0; - margin: 0 15px; - background-color: transparent; - border: none; - -webkit-border-radius: 0; - -moz-border-radius: 0; - border-radius: 0; - -webkit-box-shadow: none; - -moz-box-shadow: none; - box-shadow: none; - } - .nav-collapse .open > .dropdown-menu { - display: block; - } - .nav-collapse .dropdown-menu:before, - .nav-collapse .dropdown-menu:after { - display: none; - } - .nav-collapse .dropdown-menu .divider { - display: none; - } - .nav-collapse .nav > li > .dropdown-menu:before, - .nav-collapse .nav > li > .dropdown-menu:after { - display: none; - } - .nav-collapse .navbar-form, - .nav-collapse .navbar-search { - float: none; - padding: 10px 15px; - margin: 10px 0; - border-top: 1px solid #f2f2f2; - border-bottom: 1px solid #f2f2f2; - -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); - -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); - box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); - } - .navbar-inverse .nav-collapse .navbar-form, - .navbar-inverse .nav-collapse .navbar-search { - border-top-color: #111111; - border-bottom-color: #111111; - } - .navbar .nav-collapse .nav.pull-right { - float: none; - margin-left: 0; - } - .nav-collapse, - .nav-collapse.collapse { - height: 0; - overflow: hidden; - } - .navbar .btn-navbar { - display: block; - } - .navbar-static .navbar-inner { - padding-right: 10px; - padding-left: 10px; - } -} - -@media (min-width: 980px) { - .nav-collapse.collapse { - height: auto !important; - overflow: visible !important; - } -} diff -r 11708af40030 -r 967512924317 bin/css/bootstrap-table.css --- a/bin/css/bootstrap-table.css Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,313 +0,0 @@ -/** - * @author zhixin wen - * version: 1.11.1 - * https://github.com/wenzhixin/bootstrap-table/ - */ - -.bootstrap-table .table { - margin-bottom: 0 !important; - border-bottom: 1px solid #dddddd; - border-collapse: collapse !important; - border-radius: 1px; -} - -.bootstrap-table .table:not(.table-condensed), -.bootstrap-table .table:not(.table-condensed) > tbody > tr > th, -.bootstrap-table .table:not(.table-condensed) > tfoot > tr > th, -.bootstrap-table .table:not(.table-condensed) > thead > tr > td, -.bootstrap-table .table:not(.table-condensed) > tbody > tr > td, -.bootstrap-table .table:not(.table-condensed) > tfoot > tr > td { - padding: 8px; -} - -.bootstrap-table .table.table-no-bordered > thead > tr > th, -.bootstrap-table .table.table-no-bordered > tbody > tr > td { - border-right: 2px solid transparent; -} - -.bootstrap-table .table.table-no-bordered > tbody > tr > td:last-child { - border-right: none; -} - -.fixed-table-container { - position: relative; - clear: both; - border: 1px solid #dddddd; - border-radius: 4px; - -webkit-border-radius: 4px; - -moz-border-radius: 4px; -} - -.fixed-table-container.table-no-bordered { - border: 1px solid transparent; -} - -.fixed-table-footer, -.fixed-table-header { - overflow: hidden; -} - -.fixed-table-footer { - border-top: 1px solid #dddddd; -} - -.fixed-table-body { - overflow-x: auto; - overflow-y: auto; - height: 100%; -} - -.fixed-table-container table { - width: 100%; -} - -.fixed-table-container thead th { - height: 0; - padding: 0; - margin: 0; - border-left: 1px solid #dddddd; -} - -.fixed-table-container thead th:focus { - outline: 0 solid transparent; -} - -.fixed-table-container thead th:first-child { - border-left: none; - border-top-left-radius: 4px; - -webkit-border-top-left-radius: 4px; - -moz-border-radius-topleft: 4px; -} - -.fixed-table-container thead th .th-inner, -.fixed-table-container tbody td .th-inner { - padding: 8px; - line-height: 24px; - vertical-align: top; - overflow: hidden; - text-overflow: ellipsis; - white-space: nowrap; -} - -.fixed-table-container thead th .sortable { - cursor: pointer; - background-position: right; - background-repeat: no-repeat; - padding-right: 30px; -} - -.fixed-table-container thead th .both { - background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAQAAADYWf5HAAAAkElEQVQoz7X QMQ5AQBCF4dWQSJxC5wwax1Cq1e7BAdxD5SL+Tq/QCM1oNiJidwox0355mXnG/DrEtIQ6azioNZQxI0ykPhTQIwhCR+BmBYtlK7kLJYwWCcJA9M4qdrZrd8pPjZWPtOqdRQy320YSV17OatFC4euts6z39GYMKRPCTKY9UnPQ6P+GtMRfGtPnBCiqhAeJPmkqAAAAAElFTkSuQmCC'); -} - -.fixed-table-container thead th .asc { - background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZ0lEQVQ4y2NgGLKgquEuFxBPAGI2ahhWCsS/gDibUoO0gPgxEP8H4ttArEyuQYxAPBdqEAxPBImTY5gjEL9DM+wTENuQahAvEO9DMwiGdwAxOymGJQLxTyD+jgWDxCMZRsEoGAVoAADeemwtPcZI2wAAAABJRU5ErkJggg=='); -} - -.fixed-table-container thead th .desc { - background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZUlEQVQ4y2NgGAWjYBSggaqGu5FA/BOIv2PBIPFEUgxjB+IdQPwfC94HxLykus4GiD+hGfQOiB3J8SojEE9EM2wuSJzcsFMG4ttQgx4DsRalkZENxL+AuJQaMcsGxBOAmGvopk8AVz1sLZgg0bsAAAAASUVORK5CYII= '); -} - -.fixed-table-container th.detail { - width: 30px; -} - -.fixed-table-container tbody td { - border-left: 1px solid #dddddd; -} - -.fixed-table-container tbody tr:first-child td { - border-top: none; -} - -.fixed-table-container tbody td:first-child { - border-left: none; -} - -/* the same color with .active */ -.fixed-table-container tbody .selected td { - background-color: #f5f5f5; -} - -.fixed-table-container .bs-checkbox { - text-align: center; -} - -.fixed-table-container .bs-checkbox .th-inner { - padding: 8px 0; -} - -.fixed-table-container input[type="radio"], -.fixed-table-container input[type="checkbox"] { - margin: 0 auto !important; -} - -.fixed-table-container .no-records-found { - text-align: center; -} - -.fixed-table-pagination div.pagination, -.fixed-table-pagination .pagination-detail { - margin-top: 10px; - margin-bottom: 10px; -} - -.fixed-table-pagination div.pagination .pagination { - margin: 0; -} - -.fixed-table-pagination .pagination a { - padding: 6px 12px; - line-height: 1.428571429; -} - -.fixed-table-pagination .pagination-info { - line-height: 34px; - margin-right: 5px; -} - -.fixed-table-pagination .btn-group { - position: relative; - display: inline-block; - vertical-align: middle; -} - -.fixed-table-pagination .dropup .dropdown-menu { - margin-bottom: 0; -} - -.fixed-table-pagination .page-list { - display: inline-block; -} - -.fixed-table-toolbar .columns-left { - margin-right: 5px; -} - -.fixed-table-toolbar .columns-right { - margin-left: 5px; -} - -.fixed-table-toolbar .columns label { - display: block; - padding: 3px 20px; - clear: both; - font-weight: normal; - line-height: 1.428571429; -} - -.fixed-table-toolbar .bs-bars, -.fixed-table-toolbar .search, -.fixed-table-toolbar .columns { - position: relative; - margin-top: 10px; - margin-bottom: 10px; - line-height: 34px; -} - -.fixed-table-pagination li.disabled a { - pointer-events: none; - cursor: default; -} - -.fixed-table-loading { - display: none; - position: absolute; - top: 42px; - right: 0; - bottom: 0; - left: 0; - z-index: 99; - background-color: #fff; - text-align: center; -} - -.fixed-table-body .card-view .title { - font-weight: bold; - display: inline-block; - min-width: 30%; - text-align: left !important; -} - -/* support bootstrap 2 */ -.fixed-table-body thead th .th-inner { - box-sizing: border-box; -} - -.table th, .table td { - vertical-align: middle; - box-sizing: border-box; -} - -.fixed-table-toolbar .dropdown-menu { - text-align: left; - max-height: 300px; - overflow: auto; -} - -.fixed-table-toolbar .btn-group > .btn-group { - display: inline-block; - margin-left: -1px !important; -} - -.fixed-table-toolbar .btn-group > .btn-group > .btn { - border-radius: 0; -} - -.fixed-table-toolbar .btn-group > .btn-group:first-child > .btn { - border-top-left-radius: 4px; - border-bottom-left-radius: 4px; -} - -.fixed-table-toolbar .btn-group > .btn-group:last-child > .btn { - border-top-right-radius: 4px; - border-bottom-right-radius: 4px; -} - -.bootstrap-table .table > thead > tr > th { - vertical-align: bottom; - border-bottom: 1px solid #ddd; -} - -/* support bootstrap 3 */ -.bootstrap-table .table thead > tr > th { - padding: 0; - margin: 0; -} - -.bootstrap-table .fixed-table-footer tbody > tr > td { - padding: 0 !important; -} - -.bootstrap-table .fixed-table-footer .table { - border-bottom: none; - border-radius: 0; - padding: 0 !important; -} - -.bootstrap-table .pull-right .dropdown-menu { - right: 0; - left: auto; -} - -/* calculate scrollbar width */ -p.fixed-table-scroll-inner { - width: 100%; - height: 200px; -} - -div.fixed-table-scroll-outer { - top: 0; - left: 0; - visibility: hidden; - width: 200px; - height: 150px; - overflow: hidden; -} - -/* for get correct heights */ -.fixed-table-toolbar:after, .fixed-table-pagination:after { - content: ""; - display: block; - clear: both; -} diff -r 11708af40030 -r 967512924317 bin/css/bootstrap.css --- a/bin/css/bootstrap.css Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6167 +0,0 @@ -/*! - * Bootstrap v2.3.2 - * - * Copyright 2012 Twitter, Inc - * Licensed under the Apache License v2.0 - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Designed and built with all the love in the world @twitter by @mdo and @fat. - */ - -.clearfix { - *zoom: 1; -} - -.clearfix:before, -.clearfix:after { - display: table; - line-height: 0; - content: ""; -} - -.clearfix:after { - clear: both; -} - -.hide-text { - font: 0/0 a; - color: transparent; - text-shadow: none; - background-color: transparent; - border: 0; -} - -.input-block-level { - display: block; - width: 100%; - min-height: 30px; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - box-sizing: border-box; -} - -article, -aside, -details, -figcaption, -figure, -footer, -header, -hgroup, -nav, -section { - display: block; -} - -audio, -canvas, -video { - display: inline-block; - *display: inline; - *zoom: 1; -} - -audio:not([controls]) { - display: none; -} - -html { - font-size: 100%; - -webkit-text-size-adjust: 100%; - -ms-text-size-adjust: 100%; -} - -a:focus { - outline: thin dotted #333; - outline: 5px auto -webkit-focus-ring-color; - outline-offset: -2px; -} - -a:hover, -a:active { - outline: 0; -} - -sub, -sup { - position: relative; - font-size: 75%; - line-height: 0; - vertical-align: baseline; -} - -sup { - top: -0.5em; -} - -sub { - bottom: -0.25em; -} - -img { - width: auto\9; - height: auto; - max-width: 100%; - vertical-align: middle; - border: 0; - -ms-interpolation-mode: bicubic; -} - -#map_canvas img, -.google-maps img { - max-width: none; -} - -button, -input, -select, -textarea { - margin: 0; - font-size: 100%; - vertical-align: middle; -} - -button, -input { - *overflow: visible; - line-height: normal; -} - -button::-moz-focus-inner, -input::-moz-focus-inner { - padding: 0; - border: 0; -} - -button, -html input[type="button"], -input[type="reset"], -input[type="submit"] { - cursor: pointer; - -webkit-appearance: button; -} - -label, -select, -button, -input[type="button"], -input[type="reset"], -input[type="submit"], -input[type="radio"], -input[type="checkbox"] { - cursor: pointer; -} - -input[type="search"] { - -webkit-box-sizing: content-box; - -moz-box-sizing: content-box; - box-sizing: content-box; - -webkit-appearance: textfield; -} - -input[type="search"]::-webkit-search-decoration, -input[type="search"]::-webkit-search-cancel-button { - -webkit-appearance: none; -} - -textarea { - overflow: auto; - vertical-align: top; -} - -@media print { - * { - color: #000 !important; - text-shadow: none !important; - background: transparent !important; - box-shadow: none !important; - } - a, - a:visited { - text-decoration: underline; - } - a[href]:after { - content: " (" attr(href) ")"; - } - abbr[title]:after { - content: " (" attr(title) ")"; - } - .ir a:after, - a[href^="javascript:"]:after, - a[href^="#"]:after { - content: ""; - } - pre, - blockquote { - border: 1px solid #999; - page-break-inside: avoid; - } - thead { - display: table-header-group; - } - tr, - img { - page-break-inside: avoid; - } - img { - max-width: 100% !important; - } - @page { - margin: 0.5cm; - } - p, - h2, - h3 { - orphans: 3; - widows: 3; - } - h2, - h3 { - page-break-after: avoid; - } -} - -body { - margin: 0; - font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; - font-size: 14px; - line-height: 20px; - color: #333333; - background-color: #ffffff; -} - -a { - color: #0088cc; - text-decoration: none; -} - -a:hover, -a:focus { - color: #005580; - text-decoration: underline; -} - -.img-rounded { - -webkit-border-radius: 6px; - -moz-border-radius: 6px; - border-radius: 6px; -} - -.img-polaroid { - padding: 4px; - background-color: #fff; - border: 1px solid #ccc; - border: 1px solid rgba(0, 0, 0, 0.2); - -webkit-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1); - -moz-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1); - box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1); 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- *background-color: #151515; -} - -.btn-inverse:active, -.btn-inverse.active { - background-color: #080808 \9; -} - -button.btn, -input[type="submit"].btn { - *padding-top: 3px; - *padding-bottom: 3px; -} - -button.btn::-moz-focus-inner, -input[type="submit"].btn::-moz-focus-inner { - padding: 0; - border: 0; -} - -button.btn.btn-large, -input[type="submit"].btn.btn-large { - *padding-top: 7px; - *padding-bottom: 7px; -} - -button.btn.btn-small, -input[type="submit"].btn.btn-small { - *padding-top: 3px; - *padding-bottom: 3px; -} - -button.btn.btn-mini, -input[type="submit"].btn.btn-mini { - *padding-top: 1px; - *padding-bottom: 1px; -} - -.btn-link, -.btn-link:active, -.btn-link[disabled] { - background-color: transparent; - background-image: none; - -webkit-box-shadow: none; - -moz-box-shadow: none; - box-shadow: none; -} - -.btn-link { - color: #0088cc; - cursor: pointer; - border-color: transparent; - -webkit-border-radius: 0; - -moz-border-radius: 0; - border-radius: 0; -} - -.btn-link:hover, -.btn-link:focus { - color: #005580; - text-decoration: underline; - background-color: transparent; -} - -.btn-link[disabled]:hover, -.btn-link[disabled]:focus { - color: #333333; - text-decoration: none; -} - -.btn-group { - position: relative; - display: inline-block; - *display: inline; - *margin-left: .3em; - font-size: 0; - white-space: nowrap; - vertical-align: middle; - *zoom: 1; -} - -.btn-group:first-child { - *margin-left: 0; -} - -.btn-group + .btn-group { - margin-left: 5px; -} - -.btn-toolbar { - margin-top: 10px; - margin-bottom: 10px; - font-size: 0; -} - -.btn-toolbar > .btn + .btn, -.btn-toolbar > .btn-group + .btn, -.btn-toolbar > .btn + .btn-group { - margin-left: 5px; -} - -.btn-group > .btn { - position: relative; - -webkit-border-radius: 0; - -moz-border-radius: 0; - border-radius: 0; -} - -.btn-group > .btn + .btn { - margin-left: -1px; -} - -.btn-group > .btn, -.btn-group > .dropdown-menu, -.btn-group > .popover { - font-size: 14px; -} - -.btn-group > .btn-mini { - font-size: 10.5px; -} - -.btn-group > .btn-small { - font-size: 11.9px; 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- padding-right: 5px; - *padding-bottom: 2px; - padding-left: 5px; -} - -.btn-group > .btn-small + .dropdown-toggle { - *padding-top: 5px; - *padding-bottom: 4px; -} - -.btn-group > .btn-large + .dropdown-toggle { - *padding-top: 7px; - padding-right: 12px; - *padding-bottom: 7px; - padding-left: 12px; -} - -.btn-group.open .dropdown-toggle { - background-image: none; - -webkit-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); - -moz-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); - box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); -} - -.btn-group.open .btn.dropdown-toggle { - background-color: #e6e6e6; -} - -.btn-group.open .btn-primary.dropdown-toggle { - background-color: #0044cc; -} - -.btn-group.open .btn-warning.dropdown-toggle { - background-color: #f89406; -} - -.btn-group.open .btn-danger.dropdown-toggle { - background-color: #bd362f; -} - -.btn-group.open .btn-success.dropdown-toggle { - background-color: #51a351; 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-} - -.nav-pills > li > a { - padding-top: 8px; - padding-bottom: 8px; - margin-top: 2px; - margin-bottom: 2px; - -webkit-border-radius: 5px; - -moz-border-radius: 5px; - border-radius: 5px; -} - -.nav-pills > .active > a, -.nav-pills > .active > a:hover, -.nav-pills > .active > a:focus { - color: #ffffff; - background-color: #0088cc; -} - -.nav-stacked > li { - float: none; -} - -.nav-stacked > li > a { - margin-right: 0; -} - -.nav-tabs.nav-stacked { - border-bottom: 0; -} - -.nav-tabs.nav-stacked > li > a { - border: 1px solid #ddd; - -webkit-border-radius: 0; - -moz-border-radius: 0; - border-radius: 0; -} - -.nav-tabs.nav-stacked > li:first-child > a { - -webkit-border-top-right-radius: 4px; - border-top-right-radius: 4px; - -webkit-border-top-left-radius: 4px; - border-top-left-radius: 4px; - -moz-border-radius-topright: 4px; - -moz-border-radius-topleft: 4px; -} - -.nav-tabs.nav-stacked > li:last-child > a { - -webkit-border-bottom-right-radius: 4px; - border-bottom-right-radius: 4px; 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- background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); -} - -.progress-info .bar, -.progress .bar-info { - background-color: #4bb1cf; - background-image: -moz-linear-gradient(top, #5bc0de, #339bb9); - background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9)); - background-image: -webkit-linear-gradient(top, #5bc0de, #339bb9); - background-image: -o-linear-gradient(top, #5bc0de, #339bb9); - background-image: linear-gradient(to bottom, #5bc0de, #339bb9); - background-repeat: repeat-x; - filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff339bb9', GradientType=0); -} - -.progress-info.progress-striped .bar, -.progress-striped .bar-info { - background-color: #5bc0de; - background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); - background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); - background-image: -moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); - background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); - background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); -} - -.progress-warning .bar, -.progress .bar-warning { - background-color: #faa732; - background-image: -moz-linear-gradient(top, #fbb450, #f89406); - background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406)); - background-image: -webkit-linear-gradient(top, #fbb450, #f89406); - background-image: -o-linear-gradient(top, #fbb450, #f89406); - background-image: linear-gradient(to bottom, #fbb450, #f89406); - background-repeat: repeat-x; - filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffbb450', endColorstr='#fff89406', GradientType=0); -} - -.progress-warning.progress-striped .bar, -.progress-striped .bar-warning { - background-color: #fbb450; - background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); - background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); - background-image: -moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); - background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); - background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); -} - -.accordion { - margin-bottom: 20px; -} - -.accordion-group { - margin-bottom: 2px; - border: 1px solid #e5e5e5; - -webkit-border-radius: 4px; - -moz-border-radius: 4px; - border-radius: 4px; -} - -.accordion-heading { - border-bottom: 0; -} - -.accordion-heading .accordion-toggle { - display: block; - padding: 8px 15px; -} - -.accordion-toggle { - cursor: pointer; -} - -.accordion-inner { - padding: 9px 15px; - border-top: 1px solid #e5e5e5; -} - -.carousel { - position: relative; - margin-bottom: 20px; - line-height: 1; -} - -.carousel-inner { - position: relative; - width: 100%; - overflow: hidden; -} - -.carousel-inner > .item { - position: relative; - display: none; - -webkit-transition: 0.6s ease-in-out left; - -moz-transition: 0.6s ease-in-out left; - -o-transition: 0.6s ease-in-out left; - transition: 0.6s ease-in-out left; -} - -.carousel-inner > .item > img, -.carousel-inner > .item > a > img { - display: block; - line-height: 1; -} - -.carousel-inner > .active, -.carousel-inner > .next, -.carousel-inner > .prev { - display: block; -} - -.carousel-inner > .active { - left: 0; -} - -.carousel-inner > .next, -.carousel-inner > .prev { - position: absolute; - top: 0; - width: 100%; -} - -.carousel-inner > .next { - left: 100%; -} - -.carousel-inner > .prev { - left: -100%; -} - -.carousel-inner > .next.left, -.carousel-inner > .prev.right { - left: 0; -} - -.carousel-inner > .active.left { - left: -100%; -} - -.carousel-inner > .active.right { - left: 100%; -} - -.carousel-control { - position: absolute; - top: 40%; - left: 15px; - width: 40px; - height: 40px; - margin-top: -20px; - font-size: 60px; - font-weight: 100; - line-height: 30px; - color: #ffffff; - text-align: center; - background: #222222; - border: 3px solid #ffffff; - -webkit-border-radius: 23px; - -moz-border-radius: 23px; - border-radius: 23px; - opacity: 0.5; - filter: alpha(opacity=50); -} - -.carousel-control.right { - right: 15px; - left: auto; -} - -.carousel-control:hover, -.carousel-control:focus { - color: #ffffff; - text-decoration: none; - opacity: 0.9; - filter: alpha(opacity=90); -} - -.carousel-indicators { - position: absolute; - top: 15px; - right: 15px; - z-index: 5; - margin: 0; - list-style: none; -} - -.carousel-indicators li { - display: block; - float: left; - width: 10px; - height: 10px; - margin-left: 5px; - text-indent: -999px; - background-color: #ccc; - background-color: rgba(255, 255, 255, 0.25); - border-radius: 5px; -} - -.carousel-indicators .active { - background-color: #fff; -} - -.carousel-caption { - position: absolute; - right: 0; - bottom: 0; - left: 0; - padding: 15px; - background: #333333; - background: rgba(0, 0, 0, 0.75); -} - -.carousel-caption h4, -.carousel-caption p { - line-height: 20px; - color: #ffffff; -} - -.carousel-caption h4 { - margin: 0 0 5px; -} - -.carousel-caption p { - margin-bottom: 0; -} - -.hero-unit { - padding: 60px; - margin-bottom: 30px; - font-size: 18px; - font-weight: 200; - line-height: 30px; - color: inherit; - background-color: #eeeeee; - -webkit-border-radius: 6px; - -moz-border-radius: 6px; - border-radius: 6px; -} - -.hero-unit h1 { - margin-bottom: 0; - font-size: 60px; - line-height: 1; - letter-spacing: -1px; - color: inherit; -} - -.hero-unit li { - line-height: 30px; -} - -.pull-right { - float: right; -} - -.pull-left { - float: left; -} - -.hide { - display: none; -} - -.show { - display: block; -} - -.invisible { - visibility: hidden; -} - -.affix { - position: fixed; -} diff -r 11708af40030 -r 967512924317 bin/html.pm --- a/bin/html.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,910 +0,0 @@ -package html; - -use strict; -use warnings; -use File::Basename; - -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page ); - -sub main_page -{ - my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_; - my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root ); - - open my $h, '>', $file || die "cannot create $file $!\n"; - header ( $h ); - navbar ( $h, $list_mainTabP, $current ); - print $h "

View details »

\n"; - futurette( $h, $current, $pngTabP, $futHashP ); - print $h "

mappers #: $ma

unique mappers #: $ma_uni

\n"; - carousel2( $h, $uniqueTabP, $randTabP, $dir_root ); - footer($h); - close $h; -} - -sub menu_page -{ - my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_; - my $html_ref = $1 if $dir =~ /$dir_root(.*)/; - open my $h, '>', $file || die "cannot create $file $!\n"; - header($h); - navbar ( $h, $list_mainTabP, $current ); - span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax ); - print $h "

\n"; - print $h " text file
\n
"; - footer($h); - close $h; -} - -sub details_pages -{ - my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_; - my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root ); - - my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/; - open my $h, '>', $prefix.'-TEs.html' || die "cannot create $prefix-TEs.html $!\n"; - header($h); - navbar ( $h, $list_mainTabP, $current ); - if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' ) - { - print $h "
"; - print $h "

Ping Pong Partners

\n"; - print $h "
"; - } - fut($h,'Transposable elements',$HTE); - carousel($h,$NonUniTE,$dir_root); - footer($h); - close $h; - - open $h, '>', $prefix.'-genome.html' || die "cannot create $prefix-genome.html $!\n"; - header($h); - navbar ( $h, $list_mainTabP, $current ); - fut($h,'Genome',$HG); - carousel2($h,$UniG, $NonUniG,$dir_root); - footer($h); - close $h; - - open $h, '>', $prefix.'-transcripts.html' || die "cannot create $prefix-transcripts.html $!\n"; - header($h); - navbar ( $h, $list_mainTabP, $current ); - fut($h,'transcripts',$Hex); - footer($h); - close $h; -} - -sub ppp_page -{ - my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_; - - my $ppp_file = $ppp.'ppp.txt'; - open my $h, '>', $file || die "cannot create $file $!\n"; - header($h); - navbar ( $h, $list_mainTabP, $current ); - print $h '
'."\n"; - print $h ' - - - - - - - - - - - '; - - open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n"; - while ( <$f> ) - { - chomp; - print $h ''; - my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_; - if( -d "$ppp/$id" ) - { - my $sub_html = $ppp.$id.'.html'; - my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/; - print $h ""; - - open my $sub, '>', $sub_html || die "cannot create $sub_html\n"; - { - header($sub); - print $sub " -
-

$id

-

-

ping pong signature

-

sense reads with PPP

-

reverse reads with PPP

-

sense reads without PPP

-

reverse reads without PPP

-
"; - footer($sub); - } - close $sub; - } - else { print $h "\n"; } - print $h "\n"; - - print $h ''; - } - close $f; - print $h "
IDoverlap sumten overlap summeanstandard deviationz-scorep-value
$id $id $sum $ten $mean $sd $zscore $prob
"; - footer($h); - close $h; -} - -sub get_genome -{ - my ( $dir, $dir_root ) = @_; - my ( %hash, @group, @Unique, @NonUnique, @png ); - - my $fut = "'$dir'".'/*'; - my @fut = glob $fut; - - - foreach my $fr ( @fut ) - { - my $f = $1 if $fr =~ /$dir_root(.*)/; - if ( $fr =~ /.*Gviz/ ) - { - my $nu = "'$fr'".'/rand/*'; - @NonUnique = glob $nu; - my $u = "'$fr'".'/unique/*'; - @Unique = glob $u; - } - elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; } - elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; } - elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; } - elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; } - elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; } - elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; } - elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; } - elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; } - elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; } - elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; } - elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; } - elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; } - elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; } - elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; } - else { unlink $fr; } - } - return (\%hash, \@Unique, \@NonUnique, \@png); -} - -sub span -{ - my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_; - - print $file " -
-
-
-

Bonafide

- reads of size between $min and $max
with no mi, sn, t and r RNAs -

Genome

-

TE

-

Transcripts

-
-
-

siRNAs

- bonafide reads of size between $simin and $simax -

Genome

-

TE

-

Transcripts

-
-
-

piRNAs

- bonafide reads of size between $pimin and $pimax -

Genome

-

TE

-

Transcripts

-
-
-
-
-

miRNAs

-

Genome

-

TE

-

Transcripts

-
-
-
-"; -} - -sub get_subgroups -{ - my ( $dir, $name, $misTE, $dir_root ) = @_; - my (%Hex, %HTE, %HG, @group, @png, @pngTE, @NonUniTE, @UniG, @NonUniG ); - - my $fut = "'$dir'".'/*'; - my @fut = glob $fut; - my $f =''; - foreach my $fr ( @fut ) - { - $f = $1 if $fr =~ /$dir_root(.*)/; - - if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} = $f; } - elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; } - elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; } - elsif ( $f =~ /genome_unique_plus\.bedgraph$/) { $HG{'bedgraph unique plus strand'} = $f; } - elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; } - elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; } - elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; } - elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; } - elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; } - elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;} - elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;} - elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (txt)'} = $f;} - elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; } - elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; } - elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; } - elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; } - elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; } - elsif ( $fr =~ /.*Gviz_TEs/ ) - { - my $nu = "'$fr'".'/*'; - @NonUniTE = glob $nu; - } - elsif ( $fr =~ /.*Gviz_genome/ ) - { - my $nu = "'$fr'".'/rand/*'; - @NonUniG = glob $nu; - my $u = "'$fr'".'/unique/*'; - @UniG = glob $u; - } - else { unlink $fr; } - } - return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG); -} - -sub header -{ - my $file = shift; - print $file " - - - - - pipeline - - - - - - - - - - - "; -} - -sub navbar -{ - my ( $file, $fastq, $actif ) = @_; - - print $file " -
-
-
- - Report -
-
    - "; - for (my $i = 0 ; $i <= $#{$fastq}; $i++) - { - # my $fa = basename($fastq->[$i],'.dat'); - my $fa = $fastq->[$i]; - if ($actif eq $fa){ print $file "
  • [$i].html\">$fa
    • ";} - else {print $file "
  • [$i].html\">$fa
    • " ;} - } - print $file " -
-
-
-
-
"; -} - -sub footer -{ - my $file = shift; - print $file " - -
-
- -
-
- - - - - - - - - - - - - "; -} - -sub carousel -{ - my ($file, $non_unique, $dir_root) = @_; - my $ac = 0; - print $file " -
-
-
-
-
-
-
-
-
-
Reads randomly assigned
-
-
- -
    - "; - foreach my $u (@{$non_unique}) - { - my $name = basename($u,'.png'); - $u = $1 if $u =~ /$dir_root(.*)/; - print $file " -
  • - $name -
    • - "; - } - print $file " -
-
-
-
-
- "; -} - -sub carousel2 -{ - my ($file, $unique, $non_unique, $dir_root) = @_; - print $file " -
-
-
-
-
-
-
-
-
-
Uniquely mapped reads
-
-
- -
    - "; - - foreach my $u (@{$unique}) - { - my $name = basename($u,'.png'); - $u = $1 if $u =~ /$dir_root(.*)/; - print $file " -
  • - $name -
    • - "; - } - print $file " -
-
-
-
-
-
-
-
-
-
-
-
-
Reads randomly assigned
-
-
- -
    - "; - - foreach my $nu (@{$non_unique}) - { - my $name = basename($nu,'.png'); - $nu = $1 if $nu =~ /$dir_root(.*)/; - print $file " -
  • - $name -
    • - "; - } - print $file " -
-
-
-
-
- "; -} - -sub futurette -{ - my ($file, $name, $png, $hash) = @_; - print $file " -
-
-

$name

-

- "; - foreach my $k (sort keys %{$hash}) - { - print $file "$k
\n" ; - } - - print $file " -

"; - - foreach my $pn (@{$png}){print $file "
";} - - print $file " -
-
- "; -} - -sub fut -{ - my ($file, $name, $hash) = @_; - print $file " -
-
-

$name

-

- "; - - foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash}) - { - print $file "$k
\n" ; - } - - print $file " -

-
-
- "; -} - -sub get_distri_exon -{ - my ($dir, $name) = @_; - my (@out,@group); - my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-transcripts-*distribution-*.png'; - @group = glob $group; - foreach (my $g =0; $g <= $#group; $g++) - { - if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ ) - { - my $tmp = $1; - push @out, $1; - } - } - return (\@out); -} - -sub get_distri_TE -{ - my ($dir, $name) = @_; - my (@out,@group); - my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-*distribution-*.png'; - @group = glob $group; - foreach (my $g =0; $g <= $#group; $g++) - { - if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ ) - { - my $tmp = $1; - push @out, $1; - } - } - return (\@out); -} - -sub get_PPP -{ - my ($dir,$name) = @_; - my (%distri,@group); - my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-PPPartners-*'; - @group = glob $group; - - foreach (my $g =0; $g <= $#group; $g++) - { - if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ ) - { - my $tmp = $1; - if ($tmp =~ /PPPartners-(.*?)-sens\.txt$/) - { - $distri{$1} = ['','','','','',''] unless exists $distri{$1}; - $distri{$1}->[0] = $tmp; - } - elsif ($tmp =~ /PPPartners-(.*?)-antisens\.txt$/) - { - $distri{$1} = ['','','','','',''] unless exists $distri{$1}; - $distri{$1}->[1] = $tmp; - } - elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\.txt$/) - { - $distri{$1} = ['','','','','',''] unless exists $distri{$1}; - $distri{$1}->[2] = $tmp; - } - elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\.txt$/) - { - $distri{$1} = ['','','','','',''] unless exists $distri{$1}; - $distri{$1}->[3] = $tmp; - } - elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\.txt$/) - { - $distri{$1} = ['','','','','',''] unless exists $distri{$1}; - $distri{$1}->[4] = $tmp; - } - elsif ($tmp =~ /PPPartners-(.*?)-histogram\.png$/) - { - $distri{$1} = ['','','','','',''] unless exists $distri{$1}; - $distri{$1}->[5] = $tmp; - } - } - } - return \%distri; -} - -sub PPPrint -{ - my ($h, $hash) = @_; - my $cmp = 0; - - print $h "
\n"; - print $h "
"; - while ( my ($k,$v) = each %{$hash} ) - { - print $h "
" if $cmp != 0 && $cmp % 2 == 0; - print $h " - -
-

$k

-

[5]\"/>

-

[4]\">ping pong signature

-

[2]\">sense reads with PPP

-

[3]\">reverse reads with PPP

-

[0]\">sense reads without PPP

-

[1]\">reverse reads without PPP

-
- "; - $cmp++; - } - - print $h "
"; -} - -sub printDistri -{ - my ($h, $tab) = @_; - my ($txt, $name); - my $cmp = 0; - print $h "
\n"; - print $h "
"; - foreach my $k (@{$tab}) - { - if ($k =~ /(.*)-(.*)\.png$/) - { - $txt = $1.'-'.$2.'.txt'; - $name = $2; - } - print $h "
" if $cmp != 0 && $cmp % 2 == 0; - print $h " - -
-

$name

-

-

text file

-
- "; - $cmp++; - } - - print $h "
"; -} - -sub mapnum -{ - my $dupmapnum = shift; - my $dupnum_genome = shift; - open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\n"; - my %dupnum_TE = (); - my $header = <$dupTE>; - while (<$dupTE>) - { - chomp $_; - my @dupline = split /\t/, $_; - $dupnum_TE{$dupline[0]} = $dupline[2]; - } - close $dupTE; - open (my $du_TE, '>'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\n"; - print $du_TE "sequence\tduplicate\tgenome map num\tmap num\n"; - while (my ($k, $v) = each %dupnum_TE ) - { - my $hashRef = ${$dupnum_genome}{$k}; - print $du_TE "$k\t$hashRef->[0]\t$hashRef->[1]\t$v\n"; - } - close $du_TE; -} - -1; diff -r 11708af40030 -r 967512924317 bin/js/bootstrap-table.js --- a/bin/js/bootstrap-table.js Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3094 +0,0 @@ -/** - * @author zhixin wen - * version: 1.11.1 - * https://github.com/wenzhixin/bootstrap-table/ - */ - -(function ($) { - 'use strict'; - - // TOOLS DEFINITION - // ====================== - - var cachedWidth = null; - - // it only does '%s', and return '' when arguments are undefined - var sprintf = function (str) { - var args = arguments, - flag = true, - i = 1; - - str = str.replace(/%s/g, function () { - var arg = args[i++]; - - if (typeof arg === 'undefined') { - flag = false; - return ''; - } - return arg; - }); - return flag ? str : ''; - }; - - var getPropertyFromOther = function (list, from, to, value) { - var result = ''; - $.each(list, function (i, item) { - if (item[from] === value) { - result = item[to]; - return false; - } - return true; - }); - return result; - }; - - var getFieldIndex = function (columns, field) { - var index = -1; - - $.each(columns, function (i, column) { - if (column.field === field) { - index = i; - return false; - } - return true; - }); - return index; - }; - - // http://jsfiddle.net/wenyi/47nz7ez9/3/ - var setFieldIndex = function (columns) { - var i, j, k, - totalCol = 0, - flag = []; - - for (i = 0; i < columns[0].length; i++) { - totalCol += columns[0][i].colspan || 1; - } - - for (i = 0; i < columns.length; i++) { - flag[i] = []; - for (j = 0; j < totalCol; j++) { - flag[i][j] = false; - } - } - - for (i = 0; i < columns.length; i++) { - for (j = 0; j < columns[i].length; j++) { - var r = columns[i][j], - rowspan = r.rowspan || 1, - colspan = r.colspan || 1, - index = $.inArray(false, flag[i]); - - if (colspan === 1) { - r.fieldIndex = index; - // when field is undefined, use index instead - if (typeof r.field === 'undefined') { - r.field = index; - } - } - - for (k = 0; k < rowspan; k++) { - flag[i + k][index] = true; - } - for (k = 0; k < colspan; k++) { - flag[i][index + k] = true; - } - } - } - }; - - var getScrollBarWidth = function () { - if (cachedWidth === null) { - var inner = $('

').addClass('fixed-table-scroll-inner'), - outer = $('

').addClass('fixed-table-scroll-outer'), - w1, w2; - - outer.append(inner); - $('body').append(outer); - - w1 = inner[0].offsetWidth; - outer.css('overflow', 'scroll'); - w2 = inner[0].offsetWidth; - - if (w1 === w2) { - w2 = outer[0].clientWidth; - } - - outer.remove(); - cachedWidth = w1 - w2; - } - return cachedWidth; - }; - - var calculateObjectValue = function (self, name, args, defaultValue) { - var func = name; - - if (typeof name === 'string') { - // support obj.func1.func2 - var names = name.split('.'); - - if (names.length > 1) { - func = window; - $.each(names, function (i, f) { - func = func[f]; - }); - } else { - func = window[name]; - } - } - if (typeof func === 'object') { - return func; - } - if (typeof func === 'function') { - return func.apply(self, args || []); - } - if (!func && typeof name === 'string' && sprintf.apply(this, [name].concat(args))) { - return sprintf.apply(this, [name].concat(args)); - } - return defaultValue; - }; - - var compareObjects = function (objectA, objectB, compareLength) { - // Create arrays of property names - var objectAProperties = Object.getOwnPropertyNames(objectA), - objectBProperties = Object.getOwnPropertyNames(objectB), - propName = ''; - - if (compareLength) { - // If number of properties is different, objects are not equivalent - if (objectAProperties.length !== objectBProperties.length) { - return false; - } - } - - for (var i = 0; i < objectAProperties.length; i++) { - propName = objectAProperties[i]; - - // If the property is not in the object B properties, continue with the next property - if ($.inArray(propName, objectBProperties) > -1) { - // If values of same property are not equal, objects are not equivalent - if (objectA[propName] !== objectB[propName]) { - return false; - } - } - } - - // If we made it this far, objects are considered equivalent - return true; - }; - - var escapeHTML = function (text) { - if (typeof text === 'string') { - return text - .replace(/&/g, '&') - .replace(//g, '>') - .replace(/"/g, '"') - .replace(/'/g, ''') - .replace(/`/g, '`'); - } - return text; - }; - - var getRealDataAttr = function (dataAttr) { - for (var attr in dataAttr) { - var auxAttr = attr.split(/(?=[A-Z])/).join('-').toLowerCase(); - if (auxAttr !== attr) { - dataAttr[auxAttr] = dataAttr[attr]; - delete dataAttr[attr]; - } - } - - return dataAttr; - }; - - var getItemField = function (item, field, escape) { - var value = item; - - if (typeof field !== 'string' || item.hasOwnProperty(field)) { - return escape ? escapeHTML(item[field]) : item[field]; - } - var props = field.split('.'); - for (var p in props) { - if (props.hasOwnProperty(p)) { - value = value && value[props[p]]; - } - } - return escape ? escapeHTML(value) : value; - }; - - var isIEBrowser = function () { - return !!(navigator.userAgent.indexOf("MSIE ") > 0 || !!navigator.userAgent.match(/Trident.*rv\:11\./)); - }; - - var objectKeys = function () { - // From https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/keys - if (!Object.keys) { - Object.keys = (function() { - var hasOwnProperty = Object.prototype.hasOwnProperty, - hasDontEnumBug = !({ toString: null }).propertyIsEnumerable('toString'), - dontEnums = [ - 'toString', - 'toLocaleString', - 'valueOf', - 'hasOwnProperty', - 'isPrototypeOf', - 'propertyIsEnumerable', - 'constructor' - ], - dontEnumsLength = dontEnums.length; - - return function(obj) { - if (typeof obj !== 'object' && (typeof obj !== 'function' || obj === null)) { - throw new TypeError('Object.keys called on non-object'); - } - - var result = [], prop, i; - - for (prop in obj) { - if (hasOwnProperty.call(obj, prop)) { - result.push(prop); - } - } - - if (hasDontEnumBug) { - for (i = 0; i < dontEnumsLength; i++) { - if (hasOwnProperty.call(obj, dontEnums[i])) { - result.push(dontEnums[i]); - } - } - } - return result; - }; - }()); - } - }; - - // BOOTSTRAP TABLE CLASS DEFINITION - // ====================== - - var BootstrapTable = function (el, options) { - this.options = options; - this.$el = $(el); - this.$el_ = this.$el.clone(); - this.timeoutId_ = 0; - this.timeoutFooter_ = 0; - - this.init(); - }; - - BootstrapTable.DEFAULTS = { - classes: 'table table-hover', - sortClass: undefined, - locale: undefined, - height: undefined, - undefinedText: '-', - sortName: undefined, - sortOrder: 'asc', - sortStable: false, - striped: false, - columns: [[]], - data: [], - totalField: 'total', - dataField: 'rows', - method: 'get', - url: undefined, - ajax: undefined, - cache: true, - contentType: 'application/json', - dataType: 'json', - ajaxOptions: {}, - queryParams: function (params) { - return params; - }, - queryParamsType: 'limit', // undefined - responseHandler: function (res) { - return res; - }, - pagination: false, - onlyInfoPagination: false, - paginationLoop: true, - sidePagination: 'client', // client or server - totalRows: 0, // server side need to set - pageNumber: 1, - pageSize: 10, - pageList: [10, 25, 50, 100], - paginationHAlign: 'right', //right, left - paginationVAlign: 'bottom', //bottom, top, both - paginationDetailHAlign: 'left', //right, left - paginationPreText: '‹', - paginationNextText: '›', - search: false, - searchOnEnterKey: false, - strictSearch: false, - searchAlign: 'right', - selectItemName: 'btSelectItem', - showHeader: true, - showFooter: false, - showColumns: false, - showPaginationSwitch: false, - showRefresh: false, - showToggle: false, - buttonsAlign: 'right', - smartDisplay: true, - escape: false, - minimumCountColumns: 1, - idField: undefined, - uniqueId: undefined, - cardView: false, - detailView: false, - detailFormatter: function (index, row) { - return ''; - }, - trimOnSearch: true, - clickToSelect: false, - singleSelect: false, - toolbar: undefined, - toolbarAlign: 'left', - checkboxHeader: true, - sortable: true, - silentSort: true, - maintainSelected: false, - searchTimeOut: 500, - searchText: '', - iconSize: undefined, - buttonsClass: 'default', - iconsPrefix: 'glyphicon', // glyphicon of fa (font awesome) - icons: { - paginationSwitchDown: 'glyphicon-collapse-down icon-chevron-down', - paginationSwitchUp: 'glyphicon-collapse-up icon-chevron-up', - refresh: 'glyphicon-refresh icon-refresh', - toggle: 'glyphicon-list-alt icon-list-alt', - columns: 'glyphicon-th icon-th', - detailOpen: 'glyphicon-plus icon-plus', - detailClose: 'glyphicon-minus icon-minus' - }, - - customSearch: $.noop, - - customSort: $.noop, - - rowStyle: function (row, index) { - return {}; - }, - - rowAttributes: function (row, index) { - return {}; - }, - - footerStyle: function (row, index) { - return {}; - }, - - onAll: function (name, args) { - return false; - }, - onClickCell: function (field, value, row, $element) { - return false; - }, - onDblClickCell: function (field, value, row, $element) { - return false; - }, - onClickRow: function (item, $element) { - return false; - }, - onDblClickRow: function (item, $element) { - return false; - }, - onSort: function (name, order) { - return false; - }, - onCheck: function (row) { - return false; - }, - onUncheck: function (row) { - return false; - }, - onCheckAll: function (rows) { - return false; - }, - onUncheckAll: function (rows) { - return false; - }, - onCheckSome: function (rows) { - return false; - }, - onUncheckSome: function (rows) { - return false; - }, - onLoadSuccess: function (data) { - return false; - }, - onLoadError: function (status) { - return false; - }, - onColumnSwitch: function (field, checked) { - return false; - }, - onPageChange: function (number, size) { - return false; - }, - onSearch: function (text) { - return false; - }, - onToggle: function (cardView) { - return false; - }, - onPreBody: function (data) { - return false; - }, - onPostBody: function () { - return false; - }, - onPostHeader: function () { - return false; - }, - onExpandRow: function (index, row, $detail) { - return false; - }, - onCollapseRow: function (index, row) { - return false; - }, - onRefreshOptions: function (options) { - return false; - }, - onRefresh: function (params) { - return false; - }, - onResetView: function () { - return false; - } - }; - - BootstrapTable.LOCALES = {}; - - BootstrapTable.LOCALES['en-US'] = BootstrapTable.LOCALES.en = { - formatLoadingMessage: function () { - return 'Loading, please wait...'; - }, - formatRecordsPerPage: function (pageNumber) { - return sprintf('%s rows per page', pageNumber); - }, - formatShowingRows: function (pageFrom, pageTo, totalRows) { - return sprintf('Showing %s to %s of %s rows', pageFrom, pageTo, totalRows); - }, - formatDetailPagination: function (totalRows) { - return sprintf('Showing %s rows', totalRows); - }, - formatSearch: function () { - return 'Search'; - }, - formatNoMatches: function () { - return 'No matching records found'; - }, - formatPaginationSwitch: function () { - return 'Hide/Show pagination'; - }, - formatRefresh: function () { - return 'Refresh'; - }, - formatToggle: function () { - return 'Toggle'; - }, - formatColumns: function () { - return 'Columns'; - }, - formatAllRows: function () { - return 'All'; - } - }; - - $.extend(BootstrapTable.DEFAULTS, BootstrapTable.LOCALES['en-US']); - - BootstrapTable.COLUMN_DEFAULTS = { - radio: false, - checkbox: false, - checkboxEnabled: true, - field: undefined, - title: undefined, - titleTooltip: undefined, - 'class': undefined, - align: undefined, // left, right, center - halign: undefined, // left, right, center - falign: undefined, // left, right, center - valign: undefined, // top, middle, bottom - width: undefined, - sortable: false, - order: 'asc', // asc, desc - visible: true, - switchable: true, - clickToSelect: true, - formatter: undefined, - footerFormatter: undefined, - events: undefined, - sorter: undefined, - sortName: undefined, - cellStyle: undefined, - searchable: true, - searchFormatter: true, - cardVisible: true, - escape : false - }; - - BootstrapTable.EVENTS = { - 'all.bs.table': 'onAll', - 'click-cell.bs.table': 'onClickCell', - 'dbl-click-cell.bs.table': 'onDblClickCell', - 'click-row.bs.table': 'onClickRow', - 'dbl-click-row.bs.table': 'onDblClickRow', - 'sort.bs.table': 'onSort', - 'check.bs.table': 'onCheck', - 'uncheck.bs.table': 'onUncheck', - 'check-all.bs.table': 'onCheckAll', - 'uncheck-all.bs.table': 'onUncheckAll', - 'check-some.bs.table': 'onCheckSome', - 'uncheck-some.bs.table': 'onUncheckSome', - 'load-success.bs.table': 'onLoadSuccess', - 'load-error.bs.table': 'onLoadError', - 'column-switch.bs.table': 'onColumnSwitch', - 'page-change.bs.table': 'onPageChange', - 'search.bs.table': 'onSearch', - 'toggle.bs.table': 'onToggle', - 'pre-body.bs.table': 'onPreBody', - 'post-body.bs.table': 'onPostBody', - 'post-header.bs.table': 'onPostHeader', - 'expand-row.bs.table': 'onExpandRow', - 'collapse-row.bs.table': 'onCollapseRow', - 'refresh-options.bs.table': 'onRefreshOptions', - 'reset-view.bs.table': 'onResetView', - 'refresh.bs.table': 'onRefresh' - }; - - BootstrapTable.prototype.init = function () { - this.initLocale(); - this.initContainer(); - this.initTable(); - this.initHeader(); - this.initData(); - this.initHiddenRows(); - this.initFooter(); - this.initToolbar(); - this.initPagination(); - this.initBody(); - this.initSearchText(); - this.initServer(); - }; - - BootstrapTable.prototype.initLocale = function () { - if (this.options.locale) { - var parts = this.options.locale.split(/-|_/); - parts[0].toLowerCase(); - if (parts[1]) parts[1].toUpperCase(); - if ($.fn.bootstrapTable.locales[this.options.locale]) { - // locale as requested - $.extend(this.options, $.fn.bootstrapTable.locales[this.options.locale]); - } else if ($.fn.bootstrapTable.locales[parts.join('-')]) { - // locale with sep set to - (in case original was specified with _) - $.extend(this.options, $.fn.bootstrapTable.locales[parts.join('-')]); - } else if ($.fn.bootstrapTable.locales[parts[0]]) { - // short locale language code (i.e. 'en') - $.extend(this.options, $.fn.bootstrapTable.locales[parts[0]]); - } - } - }; - - BootstrapTable.prototype.initContainer = function () { - this.$container = $([ - '
', - '
', - this.options.paginationVAlign === 'top' || this.options.paginationVAlign === 'both' ? - '
' : - '', - '
', - '
', - '
', - '
', - this.options.formatLoadingMessage(), - '
', - '
', - '
', - this.options.paginationVAlign === 'bottom' || this.options.paginationVAlign === 'both' ? - '
' : - '', - '
', - '
' - ].join('')); - - this.$container.insertAfter(this.$el); - this.$tableContainer = this.$container.find('.fixed-table-container'); - this.$tableHeader = this.$container.find('.fixed-table-header'); - this.$tableBody = this.$container.find('.fixed-table-body'); - this.$tableLoading = this.$container.find('.fixed-table-loading'); - this.$tableFooter = this.$container.find('.fixed-table-footer'); - this.$toolbar = this.$container.find('.fixed-table-toolbar'); - this.$pagination = this.$container.find('.fixed-table-pagination'); - - this.$tableBody.append(this.$el); - this.$container.after('
'); - - this.$el.addClass(this.options.classes); - if (this.options.striped) { - this.$el.addClass('table-striped'); - } - if ($.inArray('table-no-bordered', this.options.classes.split(' ')) !== -1) { - this.$tableContainer.addClass('table-no-bordered'); - } - }; - - BootstrapTable.prototype.initTable = function () { - var that = this, - columns = [], - data = []; - - this.$header = this.$el.find('>thead'); - if (!this.$header.length) { - this.$header = $('').appendTo(this.$el); - } - this.$header.find('tr').each(function () { - var column = []; - - $(this).find('th').each(function () { - // Fix #2014 - getFieldIndex and elsewhere assume this is string, causes issues if not - if (typeof $(this).data('field') !== 'undefined') { - $(this).data('field', $(this).data('field') + ''); - } - column.push($.extend({}, { - title: $(this).html(), - 'class': $(this).attr('class'), - titleTooltip: $(this).attr('title'), - rowspan: $(this).attr('rowspan') ? +$(this).attr('rowspan') : undefined, - colspan: $(this).attr('colspan') ? +$(this).attr('colspan') : undefined - }, $(this).data())); - }); - columns.push(column); - }); - if (!$.isArray(this.options.columns[0])) { - this.options.columns = [this.options.columns]; - } - this.options.columns = $.extend(true, [], columns, this.options.columns); - this.columns = []; - - setFieldIndex(this.options.columns); - $.each(this.options.columns, function (i, columns) { - $.each(columns, function (j, column) { - column = $.extend({}, BootstrapTable.COLUMN_DEFAULTS, column); - - if (typeof column.fieldIndex !== 'undefined') { - that.columns[column.fieldIndex] = column; - } - - that.options.columns[i][j] = column; - }); - }); - - // if options.data is setting, do not process tbody data - if (this.options.data.length) { - return; - } - - var m = []; - this.$el.find('>tbody>tr').each(function (y) { - var row = {}; - - // save tr's id, class and data-* attributes - row._id = $(this).attr('id'); - row._class = $(this).attr('class'); - row._data = getRealDataAttr($(this).data()); - - $(this).find('>td').each(function (x) { - var $this = $(this), - cspan = +$this.attr('colspan') || 1, - rspan = +$this.attr('rowspan') || 1, - tx, ty; - - for (; m[y] && m[y][x]; x++); //skip already occupied cells in current row - - for (tx = x; tx < x + cspan; tx++) { //mark matrix elements occupied by current cell with true - for (ty = y; ty < y + rspan; ty++) { - if (!m[ty]) { //fill missing rows - m[ty] = []; - } - m[ty][tx] = true; - } - } - - var field = that.columns[x].field; - - row[field] = $(this).html(); - // save td's id, class and data-* attributes - row['_' + field + '_id'] = $(this).attr('id'); - row['_' + field + '_class'] = $(this).attr('class'); - row['_' + field + '_rowspan'] = $(this).attr('rowspan'); - row['_' + field + '_colspan'] = $(this).attr('colspan'); - row['_' + field + '_title'] = $(this).attr('title'); - row['_' + field + '_data'] = getRealDataAttr($(this).data()); - }); - data.push(row); - }); - this.options.data = data; - if (data.length) this.fromHtml = true; - }; - - BootstrapTable.prototype.initHeader = function () { - var that = this, - visibleColumns = {}, - html = []; - - this.header = { - fields: [], - styles: [], - classes: [], - formatters: [], - events: [], - sorters: [], - sortNames: [], - cellStyles: [], - searchables: [] - }; - - $.each(this.options.columns, function (i, columns) { - html.push(''); - - if (i === 0 && !that.options.cardView && that.options.detailView) { - html.push(sprintf('
', - that.options.columns.length)); - } - - $.each(columns, function (j, column) { - var text = '', - halign = '', // header align style - align = '', // body align style - style = '', - class_ = sprintf(' class="%s"', column['class']), - order = that.options.sortOrder || column.order, - unitWidth = 'px', - width = column.width; - - if (column.width !== undefined && (!that.options.cardView)) { - if (typeof column.width === 'string') { - if (column.width.indexOf('%') !== -1) { - unitWidth = '%'; - } - } - } - if (column.width && typeof column.width === 'string') { - width = column.width.replace('%', '').replace('px', ''); - } - - halign = sprintf('text-align: %s; ', column.halign ? column.halign : column.align); - align = sprintf('text-align: %s; ', column.align); - style = sprintf('vertical-align: %s; ', column.valign); - style += sprintf('width: %s; ', (column.checkbox || column.radio) && !width ? - '36px' : (width ? width + unitWidth : undefined)); - - if (typeof column.fieldIndex !== 'undefined') { - that.header.fields[column.fieldIndex] = column.field; - that.header.styles[column.fieldIndex] = align + style; - that.header.classes[column.fieldIndex] = class_; - that.header.formatters[column.fieldIndex] = column.formatter; - that.header.events[column.fieldIndex] = column.events; - that.header.sorters[column.fieldIndex] = column.sorter; - that.header.sortNames[column.fieldIndex] = column.sortName; - that.header.cellStyles[column.fieldIndex] = column.cellStyle; - that.header.searchables[column.fieldIndex] = column.searchable; - - if (!column.visible) { - return; - } - - if (that.options.cardView && (!column.cardVisible)) { - return; - } - - visibleColumns[column.field] = column; - } - - html.push(''); - - html.push(sprintf('
', that.options.sortable && column.sortable ? - 'sortable both' : '')); - - text = that.options.escape ? escapeHTML(column.title) : column.title; - - if (column.checkbox) { - if (!that.options.singleSelect && that.options.checkboxHeader) { - text = ''; - } - that.header.stateField = column.field; - } - if (column.radio) { - text = ''; - that.header.stateField = column.field; - that.options.singleSelect = true; - } - - html.push(text); - html.push('
'); - html.push('
'); - html.push('
'); - html.push(''); - }); - html.push(''); - }); - - this.$header.html(html.join('')); - this.$header.find('th[data-field]').each(function (i) { - $(this).data(visibleColumns[$(this).data('field')]); - }); - this.$container.off('click', '.th-inner').on('click', '.th-inner', function (event) { - var target = $(this); - - if (that.options.detailView) { - if (target.closest('.bootstrap-table')[0] !== that.$container[0]) - return false; - } - - if (that.options.sortable && target.parent().data().sortable) { - that.onSort(event); - } - }); - - this.$header.children().children().off('keypress').on('keypress', function (event) { - if (that.options.sortable && $(this).data().sortable) { - var code = event.keyCode || event.which; - if (code == 13) { //Enter keycode - that.onSort(event); - } - } - }); - - $(window).off('resize.bootstrap-table'); - if (!this.options.showHeader || this.options.cardView) { - this.$header.hide(); - this.$tableHeader.hide(); - this.$tableLoading.css('top', 0); - } else { - this.$header.show(); - this.$tableHeader.show(); - this.$tableLoading.css('top', this.$header.outerHeight() + 1); - // Assign the correct sortable arrow - this.getCaret(); - $(window).on('resize.bootstrap-table', $.proxy(this.resetWidth, this)); - } - - this.$selectAll = this.$header.find('[name="btSelectAll"]'); - this.$selectAll.off('click').on('click', function () { - var checked = $(this).prop('checked'); - that[checked ? 'checkAll' : 'uncheckAll'](); - that.updateSelected(); - }); - }; - - BootstrapTable.prototype.initFooter = function () { - if (!this.options.showFooter || this.options.cardView) { - this.$tableFooter.hide(); - } else { - this.$tableFooter.show(); - } - }; - - /** - * @param data - * @param type: append / prepend - */ - BootstrapTable.prototype.initData = function (data, type) { - if (type === 'append') { - this.data = this.data.concat(data); - } else if (type === 'prepend') { - this.data = [].concat(data).concat(this.data); - } else { - this.data = data || this.options.data; - } - - // Fix #839 Records deleted when adding new row on filtered table - if (type === 'append') { - this.options.data = this.options.data.concat(data); - } else if (type === 'prepend') { - this.options.data = [].concat(data).concat(this.options.data); - } else { - this.options.data = this.data; - } - - if (this.options.sidePagination === 'server') { - return; - } - this.initSort(); - }; - - BootstrapTable.prototype.initSort = function () { - var that = this, - name = this.options.sortName, - order = this.options.sortOrder === 'desc' ? -1 : 1, - index = $.inArray(this.options.sortName, this.header.fields), - timeoutId = 0; - - if (this.options.customSort !== $.noop) { - this.options.customSort.apply(this, [this.options.sortName, this.options.sortOrder]); - return; - } - - if (index !== -1) { - if (this.options.sortStable) { - $.each(this.data, function (i, row) { - if (!row.hasOwnProperty('_position')) row._position = i; - }); - } - - this.data.sort(function (a, b) { - if (that.header.sortNames[index]) { - name = that.header.sortNames[index]; - } - var aa = getItemField(a, name, that.options.escape), - bb = getItemField(b, name, that.options.escape), - value = calculateObjectValue(that.header, that.header.sorters[index], [aa, bb]); - - if (value !== undefined) { - return order * value; - } - - // Fix #161: undefined or null string sort bug. - if (aa === undefined || aa === null) { - aa = ''; - } - if (bb === undefined || bb === null) { - bb = ''; - } - - if (that.options.sortStable && aa === bb) { - aa = a._position; - bb = b._position; - } - - // IF both values are numeric, do a numeric comparison - if ($.isNumeric(aa) && $.isNumeric(bb)) { - // Convert numerical values form string to float. - aa = parseFloat(aa); - bb = parseFloat(bb); - if (aa < bb) { - return order * -1; - } - return order; - } - - if (aa === bb) { - return 0; - } - - // If value is not a string, convert to string - if (typeof aa !== 'string') { - aa = aa.toString(); - } - - if (aa.localeCompare(bb) === -1) { - return order * -1; - } - - return order; - }); - - if (this.options.sortClass !== undefined) { - clearTimeout(timeoutId); - timeoutId = setTimeout(function () { - that.$el.removeClass(that.options.sortClass); - var index = that.$header.find(sprintf('[data-field="%s"]', - that.options.sortName).index() + 1); - that.$el.find(sprintf('tr td:nth-child(%s)', index)) - .addClass(that.options.sortClass); - }, 250); - } - } - }; - - BootstrapTable.prototype.onSort = function (event) { - var $this = event.type === "keypress" ? $(event.currentTarget) : $(event.currentTarget).parent(), - $this_ = this.$header.find('th').eq($this.index()); - - this.$header.add(this.$header_).find('span.order').remove(); - - if (this.options.sortName === $this.data('field')) { - this.options.sortOrder = this.options.sortOrder === 'asc' ? 'desc' : 'asc'; - } else { - this.options.sortName = $this.data('field'); - this.options.sortOrder = $this.data('order') === 'asc' ? 'desc' : 'asc'; - } - this.trigger('sort', this.options.sortName, this.options.sortOrder); - - $this.add($this_).data('order', this.options.sortOrder); - - // Assign the correct sortable arrow - this.getCaret(); - - if (this.options.sidePagination === 'server') { - this.initServer(this.options.silentSort); - return; - } - - this.initSort(); - this.initBody(); - }; - - BootstrapTable.prototype.initToolbar = function () { - var that = this, - html = [], - timeoutId = 0, - $keepOpen, - $search, - switchableCount = 0; - - if (this.$toolbar.find('.bs-bars').children().length) { - $('body').append($(this.options.toolbar)); - } - this.$toolbar.html(''); - - if (typeof this.options.toolbar === 'string' || typeof this.options.toolbar === 'object') { - $(sprintf('
', this.options.toolbarAlign)) - .appendTo(this.$toolbar) - .append($(this.options.toolbar)); - } - - // showColumns, showToggle, showRefresh - html = [sprintf('
', - this.options.buttonsAlign, this.options.buttonsAlign)]; - - if (typeof this.options.icons === 'string') { - this.options.icons = calculateObjectValue(null, this.options.icons); - } - - if (this.options.showPaginationSwitch) { - html.push(sprintf(''); - } - - if (this.options.showRefresh) { - html.push(sprintf(''); - } - - if (this.options.showToggle) { - html.push(sprintf(''); - } - - if (this.options.showColumns) { - html.push(sprintf('
', - this.options.formatColumns()), - '', - '', - '
'); - } - - html.push('
'); - - // Fix #188: this.showToolbar is for extensions - if (this.showToolbar || html.length > 2) { - this.$toolbar.append(html.join('')); - } - - if (this.options.showPaginationSwitch) { - this.$toolbar.find('button[name="paginationSwitch"]') - .off('click').on('click', $.proxy(this.togglePagination, this)); - } - - if (this.options.showRefresh) { - this.$toolbar.find('button[name="refresh"]') - .off('click').on('click', $.proxy(this.refresh, this)); - } - - if (this.options.showToggle) { - this.$toolbar.find('button[name="toggle"]') - .off('click').on('click', function () { - that.toggleView(); - }); - } - - if (this.options.showColumns) { - $keepOpen = this.$toolbar.find('.keep-open'); - - if (switchableCount <= this.options.minimumCountColumns) { - $keepOpen.find('input').prop('disabled', true); - } - - $keepOpen.find('li').off('click').on('click', function (event) { - event.stopImmediatePropagation(); - }); - $keepOpen.find('input').off('click').on('click', function () { - var $this = $(this); - - that.toggleColumn($(this).val(), $this.prop('checked'), false); - that.trigger('column-switch', $(this).data('field'), $this.prop('checked')); - }); - } - - if (this.options.search) { - html = []; - html.push( - '
', - sprintf('', - this.options.formatSearch()), - '
'); - - this.$toolbar.append(html.join('')); - $search = this.$toolbar.find('.search input'); - $search.off('keyup drop blur').on('keyup drop blur', function (event) { - if (that.options.searchOnEnterKey && event.keyCode !== 13) { - return; - } - - if ($.inArray(event.keyCode, [37, 38, 39, 40]) > -1) { - return; - } - - clearTimeout(timeoutId); // doesn't matter if it's 0 - timeoutId = setTimeout(function () { - that.onSearch(event); - }, that.options.searchTimeOut); - }); - - if (isIEBrowser()) { - $search.off('mouseup').on('mouseup', function (event) { - clearTimeout(timeoutId); // doesn't matter if it's 0 - timeoutId = setTimeout(function () { - that.onSearch(event); - }, that.options.searchTimeOut); - }); - } - } - }; - - BootstrapTable.prototype.onSearch = function (event) { - var text = $.trim($(event.currentTarget).val()); - - // trim search input - if (this.options.trimOnSearch && $(event.currentTarget).val() !== text) { - $(event.currentTarget).val(text); - } - - if (text === this.searchText) { - return; - } - this.searchText = text; - this.options.searchText = text; - - this.options.pageNumber = 1; - this.initSearch(); - this.updatePagination(); - this.trigger('search', text); - }; - - BootstrapTable.prototype.initSearch = function () { - var that = this; - - if (this.options.sidePagination !== 'server') { - if (this.options.customSearch !== $.noop) { - this.options.customSearch.apply(this, [this.searchText]); - return; - } - - var s = this.searchText && (this.options.escape ? - escapeHTML(this.searchText) : this.searchText).toLowerCase(); - var f = $.isEmptyObject(this.filterColumns) ? null : this.filterColumns; - - // Check filter - this.data = f ? $.grep(this.options.data, function (item, i) { - for (var key in f) { - if ($.isArray(f[key]) && $.inArray(item[key], f[key]) === -1 || - !$.isArray(f[key]) && item[key] !== f[key]) { - return false; - } - } - return true; - }) : this.options.data; - - this.data = s ? $.grep(this.data, function (item, i) { - for (var j = 0; j < that.header.fields.length; j++) { - - if (!that.header.searchables[j]) { - continue; - } - - var key = $.isNumeric(that.header.fields[j]) ? parseInt(that.header.fields[j], 10) : that.header.fields[j]; - var column = that.columns[getFieldIndex(that.columns, key)]; - var value; - - if (typeof key === 'string') { - value = item; - var props = key.split('.'); - for (var prop_index = 0; prop_index < props.length; prop_index++) { - value = value[props[prop_index]]; - } - - // Fix #142: respect searchForamtter boolean - if (column && column.searchFormatter) { - value = calculateObjectValue(column, - that.header.formatters[j], [value, item, i], value); - } - } else { - value = item[key]; - } - - if (typeof value === 'string' || typeof value === 'number') { - if (that.options.strictSearch) { - if ((value + '').toLowerCase() === s) { - return true; - } - } else { - if ((value + '').toLowerCase().indexOf(s) !== -1) { - return true; - } - } - } - } - return false; - }) : this.data; - } - }; - - BootstrapTable.prototype.initPagination = function () { - if (!this.options.pagination) { - this.$pagination.hide(); - return; - } else { - this.$pagination.show(); - } - - var that = this, - html = [], - $allSelected = false, - i, from, to, - $pageList, - $first, $pre, - $next, $last, - $number, - data = this.getData(), - pageList = this.options.pageList; - - if (this.options.sidePagination !== 'server') { - this.options.totalRows = data.length; - } - - this.totalPages = 0; - if (this.options.totalRows) { - if (this.options.pageSize === this.options.formatAllRows()) { - this.options.pageSize = this.options.totalRows; - $allSelected = true; - } else if (this.options.pageSize === this.options.totalRows) { - // Fix #667 Table with pagination, - // multiple pages and a search that matches to one page throws exception - var pageLst = typeof this.options.pageList === 'string' ? - this.options.pageList.replace('[', '').replace(']', '') - .replace(/ /g, '').toLowerCase().split(',') : this.options.pageList; - if ($.inArray(this.options.formatAllRows().toLowerCase(), pageLst) > -1) { - $allSelected = true; - } - } - - this.totalPages = ~~((this.options.totalRows - 1) / this.options.pageSize) + 1; - - this.options.totalPages = this.totalPages; - } - if (this.totalPages > 0 && this.options.pageNumber > this.totalPages) { - this.options.pageNumber = this.totalPages; - } - - this.pageFrom = (this.options.pageNumber - 1) * this.options.pageSize + 1; - this.pageTo = this.options.pageNumber * this.options.pageSize; - if (this.pageTo > this.options.totalRows) { - this.pageTo = this.options.totalRows; - } - - html.push( - '
', - '', - this.options.onlyInfoPagination ? this.options.formatDetailPagination(this.options.totalRows) : - this.options.formatShowingRows(this.pageFrom, this.pageTo, this.options.totalRows), - ''); - - if (!this.options.onlyInfoPagination) { - html.push(''); - - var pageNumber = [ - sprintf('', - this.options.paginationVAlign === 'top' || this.options.paginationVAlign === 'both' ? - 'dropdown' : 'dropup'), - '', - ''); - - html.push(this.options.formatRecordsPerPage(pageNumber.join(''))); - html.push(''); - - html.push('
', - ''); - } - this.$pagination.html(html.join('')); - - if (!this.options.onlyInfoPagination) { - $pageList = this.$pagination.find('.page-list a'); - $first = this.$pagination.find('.page-first'); - $pre = this.$pagination.find('.page-pre'); - $next = this.$pagination.find('.page-next'); - $last = this.$pagination.find('.page-last'); - $number = this.$pagination.find('.page-number'); - - if (this.options.smartDisplay) { - if (this.totalPages <= 1) { - this.$pagination.find('div.pagination').hide(); - } - if (pageList.length < 2 || this.options.totalRows <= pageList[0]) { - this.$pagination.find('span.page-list').hide(); - } - - // when data is empty, hide the pagination - this.$pagination[this.getData().length ? 'show' : 'hide'](); - } - - if (!this.options.paginationLoop) { - if (this.options.pageNumber === 1) { - $pre.addClass('disabled'); - } - if (this.options.pageNumber === this.totalPages) { - $next.addClass('disabled'); - } - } - - if ($allSelected) { - this.options.pageSize = this.options.formatAllRows(); - } - $pageList.off('click').on('click', $.proxy(this.onPageListChange, this)); - $first.off('click').on('click', $.proxy(this.onPageFirst, this)); - $pre.off('click').on('click', $.proxy(this.onPagePre, this)); - $next.off('click').on('click', $.proxy(this.onPageNext, this)); - $last.off('click').on('click', $.proxy(this.onPageLast, this)); - $number.off('click').on('click', $.proxy(this.onPageNumber, this)); - } - }; - - BootstrapTable.prototype.updatePagination = function (event) { - // Fix #171: IE disabled button can be clicked bug. - if (event && $(event.currentTarget).hasClass('disabled')) { - return; - } - - if (!this.options.maintainSelected) { - this.resetRows(); - } - - this.initPagination(); - if (this.options.sidePagination === 'server') { - this.initServer(); - } else { - this.initBody(); - } - - this.trigger('page-change', this.options.pageNumber, this.options.pageSize); - }; - - BootstrapTable.prototype.onPageListChange = function (event) { - var $this = $(event.currentTarget); - - $this.parent().addClass('active').siblings().removeClass('active'); - this.options.pageSize = $this.text().toUpperCase() === this.options.formatAllRows().toUpperCase() ? - this.options.formatAllRows() : +$this.text(); - this.$toolbar.find('.page-size').text(this.options.pageSize); - - this.updatePagination(event); - return false; - }; - - BootstrapTable.prototype.onPageFirst = function (event) { - this.options.pageNumber = 1; - this.updatePagination(event); - return false; - }; - - BootstrapTable.prototype.onPagePre = function (event) { - if ((this.options.pageNumber - 1) === 0) { - this.options.pageNumber = this.options.totalPages; - } else { - this.options.pageNumber--; - } - this.updatePagination(event); - return false; - }; - - BootstrapTable.prototype.onPageNext = function (event) { - if ((this.options.pageNumber + 1) > this.options.totalPages) { - this.options.pageNumber = 1; - } else { - this.options.pageNumber++; - } - this.updatePagination(event); - return false; - }; - - BootstrapTable.prototype.onPageLast = function (event) { - this.options.pageNumber = this.totalPages; - this.updatePagination(event); - return false; - }; - - BootstrapTable.prototype.onPageNumber = function (event) { - if (this.options.pageNumber === +$(event.currentTarget).text()) { - return; - } - this.options.pageNumber = +$(event.currentTarget).text(); - this.updatePagination(event); - return false; - }; - - BootstrapTable.prototype.initRow = function(item, i, data, parentDom) { - var that=this, - key, - html = [], - style = {}, - csses = [], - data_ = '', - attributes = {}, - htmlAttributes = []; - - if ($.inArray(item, this.hiddenRows) > -1) { - return; - } - - style = calculateObjectValue(this.options, this.options.rowStyle, [item, i], style); - - if (style && style.css) { - for (key in style.css) { - csses.push(key + ': ' + style.css[key]); - } - } - - attributes = calculateObjectValue(this.options, - this.options.rowAttributes, [item, i], attributes); - - if (attributes) { - for (key in attributes) { - htmlAttributes.push(sprintf('%s="%s"', key, escapeHTML(attributes[key]))); - } - } - - if (item._data && !$.isEmptyObject(item._data)) { - $.each(item._data, function(k, v) { - // ignore data-index - if (k === 'index') { - return; - } - data_ += sprintf(' data-%s="%s"', k, v); - }); - } - - html.push('' - ); - - if (this.options.cardView) { - html.push(sprintf('
', this.header.fields.length)); - } - - if (!this.options.cardView && this.options.detailView) { - html.push('', - '', - sprintf('', this.options.iconsPrefix, this.options.icons.detailOpen), - '', - ''); - } - - $.each(this.header.fields, function(j, field) { - var text = '', - value_ = getItemField(item, field, that.options.escape), - value = '', - type = '', - cellStyle = {}, - id_ = '', - class_ = that.header.classes[j], - data_ = '', - rowspan_ = '', - colspan_ = '', - title_ = '', - column = that.columns[j]; - - if (that.fromHtml && typeof value_ === 'undefined') { - return; - } - - if (!column.visible) { - return; - } - - if (that.options.cardView && (!column.cardVisible)) { - return; - } - - if (column.escape) { - value_ = escapeHTML(value_); - } - - style = sprintf('style="%s"', csses.concat(that.header.styles[j]).join('; ')); - - // handle td's id and class - if (item['_' + field + '_id']) { - id_ = sprintf(' id="%s"', item['_' + field + '_id']); - } - if (item['_' + field + '_class']) { - class_ = sprintf(' class="%s"', item['_' + field + '_class']); - } - if (item['_' + field + '_rowspan']) { - rowspan_ = sprintf(' rowspan="%s"', item['_' + field + '_rowspan']); - } - if (item['_' + field + '_colspan']) { - colspan_ = sprintf(' colspan="%s"', item['_' + field + '_colspan']); - } - if (item['_' + field + '_title']) { - title_ = sprintf(' title="%s"', item['_' + field + '_title']); - } - cellStyle = calculateObjectValue(that.header, - that.header.cellStyles[j], [value_, item, i, field], cellStyle); - if (cellStyle.classes) { - class_ = sprintf(' class="%s"', cellStyle.classes); - } - if (cellStyle.css) { - var csses_ = []; - for (var key in cellStyle.css) { - csses_.push(key + ': ' + cellStyle.css[key]); - } - style = sprintf('style="%s"', csses_.concat(that.header.styles[j]).join('; ')); - } - - value = calculateObjectValue(column, - that.header.formatters[j], [value_, item, i], value_); - - if (item['_' + field + '_data'] && !$.isEmptyObject(item['_' + field + '_data'])) { - $.each(item['_' + field + '_data'], function(k, v) { - // ignore data-index - if (k === 'index') { - return; - } - data_ += sprintf(' data-%s="%s"', k, v); - }); - } - - if (column.checkbox || column.radio) { - type = column.checkbox ? 'checkbox' : type; - type = column.radio ? 'radio' : type; - - text = [sprintf(that.options.cardView ? - '
' : '', column['class'] || ''), - '', - that.header.formatters[j] && typeof value === 'string' ? value : '', - that.options.cardView ? '
' : '' - ].join(''); - - item[that.header.stateField] = value === true || (value && value.checked); - } else { - value = typeof value === 'undefined' || value === null ? - that.options.undefinedText : value; - - text = that.options.cardView ? ['
', - that.options.showHeader ? sprintf('%s', style, - getPropertyFromOther(that.columns, 'field', 'title', field)) : '', - sprintf('%s', value), - '
' - ].join('') : [sprintf('', - id_, class_, style, data_, rowspan_, colspan_, title_), - value, - '' - ].join(''); - - // Hide empty data on Card view when smartDisplay is set to true. - if (that.options.cardView && that.options.smartDisplay && value === '') { - // Should set a placeholder for event binding correct fieldIndex - text = '
'; - } - } - - html.push(text); - }); - - if (this.options.cardView) { - html.push('
'); - } - html.push(''); - - return html.join(' '); - }; - - BootstrapTable.prototype.initBody = function (fixedScroll) { - var that = this, - html = [], - data = this.getData(); - - this.trigger('pre-body', data); - - this.$body = this.$el.find('>tbody'); - if (!this.$body.length) { - this.$body = $('').appendTo(this.$el); - } - - //Fix #389 Bootstrap-table-flatJSON is not working - - if (!this.options.pagination || this.options.sidePagination === 'server') { - this.pageFrom = 1; - this.pageTo = data.length; - } - - var trFragments = $(document.createDocumentFragment()); - var hasTr; - - for (var i = this.pageFrom - 1; i < this.pageTo; i++) { - var item = data[i]; - var tr = this.initRow(item, i, data, trFragments); - hasTr = hasTr || !!tr; - if (tr&&tr!==true) { - trFragments.append(tr); - } - } - - // show no records - if (!hasTr) { - trFragments.append('' + - sprintf('%s', - this.$header.find('th').length, - this.options.formatNoMatches()) + - ''); - } - - this.$body.html(trFragments); - - if (!fixedScroll) { - this.scrollTo(0); - } - - // click to select by column - this.$body.find('> tr[data-index] > td').off('click dblclick').on('click dblclick', function (e) { - var $td = $(this), - $tr = $td.parent(), - item = that.data[$tr.data('index')], - index = $td[0].cellIndex, - fields = that.getVisibleFields(), - field = fields[that.options.detailView && !that.options.cardView ? index - 1 : index], - column = that.columns[getFieldIndex(that.columns, field)], - value = getItemField(item, field, that.options.escape); - - if ($td.find('.detail-icon').length) { - return; - } - - that.trigger(e.type === 'click' ? 'click-cell' : 'dbl-click-cell', field, value, item, $td); - that.trigger(e.type === 'click' ? 'click-row' : 'dbl-click-row', item, $tr, field); - - // if click to select - then trigger the checkbox/radio click - if (e.type === 'click' && that.options.clickToSelect && column.clickToSelect) { - var $selectItem = $tr.find(sprintf('[name="%s"]', that.options.selectItemName)); - if ($selectItem.length) { - $selectItem[0].click(); // #144: .trigger('click') bug - } - } - }); - - this.$body.find('> tr[data-index] > td > .detail-icon').off('click').on('click', function () { - var $this = $(this), - $tr = $this.parent().parent(), - index = $tr.data('index'), - row = data[index]; // Fix #980 Detail view, when searching, returns wrong row - - // remove and update - if ($tr.next().is('tr.detail-view')) { - $this.find('i').attr('class', sprintf('%s %s', that.options.iconsPrefix, that.options.icons.detailOpen)); - that.trigger('collapse-row', index, row); - $tr.next().remove(); - } else { - $this.find('i').attr('class', sprintf('%s %s', that.options.iconsPrefix, that.options.icons.detailClose)); - $tr.after(sprintf('', $tr.find('td').length)); - var $element = $tr.next().find('td'); - var content = calculateObjectValue(that.options, that.options.detailFormatter, [index, row, $element], ''); - if($element.length === 1) { - $element.append(content); - } - that.trigger('expand-row', index, row, $element); - } - that.resetView(); - return false; - }); - - this.$selectItem = this.$body.find(sprintf('[name="%s"]', this.options.selectItemName)); - this.$selectItem.off('click').on('click', function (event) { - event.stopImmediatePropagation(); - - var $this = $(this), - checked = $this.prop('checked'), - row = that.data[$this.data('index')]; - - if (that.options.maintainSelected && $(this).is(':radio')) { - $.each(that.options.data, function (i, row) { - row[that.header.stateField] = false; - }); - } - - row[that.header.stateField] = checked; - - if (that.options.singleSelect) { - that.$selectItem.not(this).each(function () { - that.data[$(this).data('index')][that.header.stateField] = false; - }); - that.$selectItem.filter(':checked').not(this).prop('checked', false); - } - - that.updateSelected(); - that.trigger(checked ? 'check' : 'uncheck', row, $this); - }); - - $.each(this.header.events, function (i, events) { - if (!events) { - return; - } - // fix bug, if events is defined with namespace - if (typeof events === 'string') { - events = calculateObjectValue(null, events); - } - - var field = that.header.fields[i], - fieldIndex = $.inArray(field, that.getVisibleFields()); - - if (that.options.detailView && !that.options.cardView) { - fieldIndex += 1; - } - - for (var key in events) { - that.$body.find('>tr:not(.no-records-found)').each(function () { - var $tr = $(this), - $td = $tr.find(that.options.cardView ? '.card-view' : 'td').eq(fieldIndex), - index = key.indexOf(' '), - name = key.substring(0, index), - el = key.substring(index + 1), - func = events[key]; - - $td.find(el).off(name).on(name, function (e) { - var index = $tr.data('index'), - row = that.data[index], - value = row[field]; - - func.apply(this, [e, value, row, index]); - }); - }); - } - }); - - this.updateSelected(); - this.resetView(); - - this.trigger('post-body', data); - }; - - BootstrapTable.prototype.initServer = function (silent, query, url) { - var that = this, - data = {}, - params = { - searchText: this.searchText, - sortName: this.options.sortName, - sortOrder: this.options.sortOrder - }, - request; - - if (this.options.pagination) { - params.pageSize = this.options.pageSize === this.options.formatAllRows() ? - this.options.totalRows : this.options.pageSize; - params.pageNumber = this.options.pageNumber; - } - - if (!(url || this.options.url) && !this.options.ajax) { - return; - } - - if (this.options.queryParamsType === 'limit') { - params = { - search: params.searchText, - sort: params.sortName, - order: params.sortOrder - }; - - if (this.options.pagination) { - params.offset = this.options.pageSize === this.options.formatAllRows() ? - 0 : this.options.pageSize * (this.options.pageNumber - 1); - params.limit = this.options.pageSize === this.options.formatAllRows() ? - this.options.totalRows : this.options.pageSize; - } - } - - if (!($.isEmptyObject(this.filterColumnsPartial))) { - params.filter = JSON.stringify(this.filterColumnsPartial, null); - } - - data = calculateObjectValue(this.options, this.options.queryParams, [params], data); - - $.extend(data, query || {}); - - // false to stop request - if (data === false) { - return; - } - - if (!silent) { - this.$tableLoading.show(); - } - request = $.extend({}, calculateObjectValue(null, this.options.ajaxOptions), { - type: this.options.method, - url: url || this.options.url, - data: this.options.contentType === 'application/json' && this.options.method === 'post' ? - JSON.stringify(data) : data, - cache: this.options.cache, - contentType: this.options.contentType, - dataType: this.options.dataType, - success: function (res) { - res = calculateObjectValue(that.options, that.options.responseHandler, [res], res); - - that.load(res); - that.trigger('load-success', res); - if (!silent) that.$tableLoading.hide(); - }, - error: function (res) { - that.trigger('load-error', res.status, res); - if (!silent) that.$tableLoading.hide(); - } - }); - - if (this.options.ajax) { - calculateObjectValue(this, this.options.ajax, [request], null); - } else { - if (this._xhr && this._xhr.readyState !== 4) { - this._xhr.abort(); - } - this._xhr = $.ajax(request); - } - }; - - BootstrapTable.prototype.initSearchText = function () { - if (this.options.search) { - if (this.options.searchText !== '') { - var $search = this.$toolbar.find('.search input'); - $search.val(this.options.searchText); - this.onSearch({currentTarget: $search}); - } - } - }; - - BootstrapTable.prototype.getCaret = function () { - var that = this; - - $.each(this.$header.find('th'), function (i, th) { - $(th).find('.sortable').removeClass('desc asc').addClass($(th).data('field') === that.options.sortName ? that.options.sortOrder : 'both'); - }); - }; - - BootstrapTable.prototype.updateSelected = function () { - var checkAll = this.$selectItem.filter(':enabled').length && - this.$selectItem.filter(':enabled').length === - this.$selectItem.filter(':enabled').filter(':checked').length; - - this.$selectAll.add(this.$selectAll_).prop('checked', checkAll); - - this.$selectItem.each(function () { - $(this).closest('tr')[$(this).prop('checked') ? 'addClass' : 'removeClass']('selected'); - }); - }; - - BootstrapTable.prototype.updateRows = function () { - var that = this; - - this.$selectItem.each(function () { - that.data[$(this).data('index')][that.header.stateField] = $(this).prop('checked'); - }); - }; - - BootstrapTable.prototype.resetRows = function () { - var that = this; - - $.each(this.data, function (i, row) { - that.$selectAll.prop('checked', false); - that.$selectItem.prop('checked', false); - if (that.header.stateField) { - row[that.header.stateField] = false; - } - }); - this.initHiddenRows(); - }; - - BootstrapTable.prototype.trigger = function (name) { - var args = Array.prototype.slice.call(arguments, 1); - - name += '.bs.table'; - this.options[BootstrapTable.EVENTS[name]].apply(this.options, args); - this.$el.trigger($.Event(name), args); - - this.options.onAll(name, args); - this.$el.trigger($.Event('all.bs.table'), [name, args]); - }; - - BootstrapTable.prototype.resetHeader = function () { - // fix #61: the hidden table reset header bug. - // fix bug: get $el.css('width') error sometime (height = 500) - clearTimeout(this.timeoutId_); - this.timeoutId_ = setTimeout($.proxy(this.fitHeader, this), this.$el.is(':hidden') ? 100 : 0); - }; - - BootstrapTable.prototype.fitHeader = function () { - var that = this, - fixedBody, - scrollWidth, - focused, - focusedTemp; - - if (that.$el.is(':hidden')) { - that.timeoutId_ = setTimeout($.proxy(that.fitHeader, that), 100); - return; - } - fixedBody = this.$tableBody.get(0); - - scrollWidth = fixedBody.scrollWidth > fixedBody.clientWidth && - fixedBody.scrollHeight > fixedBody.clientHeight + this.$header.outerHeight() ? - getScrollBarWidth() : 0; - - this.$el.css('margin-top', -this.$header.outerHeight()); - - focused = $(':focus'); - if (focused.length > 0) { - var $th = focused.parents('th'); - if ($th.length > 0) { - var dataField = $th.attr('data-field'); - if (dataField !== undefined) { - var $headerTh = this.$header.find("[data-field='" + dataField + "']"); - if ($headerTh.length > 0) { - $headerTh.find(":input").addClass("focus-temp"); - } - } - } - } - - this.$header_ = this.$header.clone(true, true); - this.$selectAll_ = this.$header_.find('[name="btSelectAll"]'); - this.$tableHeader.css({ - 'margin-right': scrollWidth - }).find('table').css('width', this.$el.outerWidth()) - .html('').attr('class', this.$el.attr('class')) - .append(this.$header_); - - - focusedTemp = $('.focus-temp:visible:eq(0)'); - if (focusedTemp.length > 0) { - focusedTemp.focus(); - this.$header.find('.focus-temp').removeClass('focus-temp'); - } - - // fix bug: $.data() is not working as expected after $.append() - this.$header.find('th[data-field]').each(function (i) { - that.$header_.find(sprintf('th[data-field="%s"]', $(this).data('field'))).data($(this).data()); - }); - - var visibleFields = this.getVisibleFields(), - $ths = this.$header_.find('th'); - - this.$body.find('>tr:first-child:not(.no-records-found) > *').each(function (i) { - var $this = $(this), - index = i; - - if (that.options.detailView && !that.options.cardView) { - if (i === 0) { - that.$header_.find('th.detail').find('.fht-cell').width($this.innerWidth()); - } - index = i - 1; - } - - var $th = that.$header_.find(sprintf('th[data-field="%s"]', visibleFields[index])); - if ($th.length > 1) { - $th = $($ths[$this[0].cellIndex]); - } - - $th.find('.fht-cell').width($this.innerWidth()); - }); - // horizontal scroll event - // TODO: it's probably better improving the layout than binding to scroll event - this.$tableBody.off('scroll').on('scroll', function () { - that.$tableHeader.scrollLeft($(this).scrollLeft()); - - if (that.options.showFooter && !that.options.cardView) { - that.$tableFooter.scrollLeft($(this).scrollLeft()); - } - }); - that.trigger('post-header'); - }; - - BootstrapTable.prototype.resetFooter = function () { - var that = this, - data = that.getData(), - html = []; - - if (!this.options.showFooter || this.options.cardView) { //do nothing - return; - } - - if (!this.options.cardView && this.options.detailView) { - html.push('
 
'); - } - - $.each(this.columns, function (i, column) { - var key, - falign = '', // footer align style - valign = '', - csses = [], - style = {}, - class_ = sprintf(' class="%s"', column['class']); - - if (!column.visible) { - return; - } - - if (that.options.cardView && (!column.cardVisible)) { - return; - } - - falign = sprintf('text-align: %s; ', column.falign ? column.falign : column.align); - valign = sprintf('vertical-align: %s; ', column.valign); - - style = calculateObjectValue(null, that.options.footerStyle); - - if (style && style.css) { - for (key in style.css) { - csses.push(key + ': ' + style.css[key]); - } - } - - html.push(''); - html.push('
'); - - html.push(calculateObjectValue(column, column.footerFormatter, [data], ' ') || ' '); - - html.push('
'); - html.push('
'); - html.push('
'); - html.push(''); - }); - - this.$tableFooter.find('tr').html(html.join('')); - this.$tableFooter.show(); - clearTimeout(this.timeoutFooter_); - this.timeoutFooter_ = setTimeout($.proxy(this.fitFooter, this), - this.$el.is(':hidden') ? 100 : 0); - }; - - BootstrapTable.prototype.fitFooter = function () { - var that = this, - $footerTd, - elWidth, - scrollWidth; - - clearTimeout(this.timeoutFooter_); - if (this.$el.is(':hidden')) { - this.timeoutFooter_ = setTimeout($.proxy(this.fitFooter, this), 100); - return; - } - - elWidth = this.$el.css('width'); - scrollWidth = elWidth > this.$tableBody.width() ? getScrollBarWidth() : 0; - - this.$tableFooter.css({ - 'margin-right': scrollWidth - }).find('table').css('width', elWidth) - .attr('class', this.$el.attr('class')); - - $footerTd = this.$tableFooter.find('td'); - - this.$body.find('>tr:first-child:not(.no-records-found) > *').each(function (i) { - var $this = $(this); - - $footerTd.eq(i).find('.fht-cell').width($this.innerWidth()); - }); - }; - - BootstrapTable.prototype.toggleColumn = function (index, checked, needUpdate) { - if (index === -1) { - return; - } - this.columns[index].visible = checked; - this.initHeader(); - this.initSearch(); - this.initPagination(); - this.initBody(); - - if (this.options.showColumns) { - var $items = this.$toolbar.find('.keep-open input').prop('disabled', false); - - if (needUpdate) { - $items.filter(sprintf('[value="%s"]', index)).prop('checked', checked); - } - - if ($items.filter(':checked').length <= this.options.minimumCountColumns) { - $items.filter(':checked').prop('disabled', true); - } - } - }; - - BootstrapTable.prototype.getVisibleFields = function () { - var that = this, - visibleFields = []; - - $.each(this.header.fields, function (j, field) { - var column = that.columns[getFieldIndex(that.columns, field)]; - - if (!column.visible) { - return; - } - visibleFields.push(field); - }); - return visibleFields; - }; - - // PUBLIC FUNCTION DEFINITION - // ======================= - - BootstrapTable.prototype.resetView = function (params) { - var padding = 0; - - if (params && params.height) { - this.options.height = params.height; - } - - this.$selectAll.prop('checked', this.$selectItem.length > 0 && - this.$selectItem.length === this.$selectItem.filter(':checked').length); - - if (this.options.height) { - var toolbarHeight = this.$toolbar.outerHeight(true), - paginationHeight = this.$pagination.outerHeight(true), - height = this.options.height - toolbarHeight - paginationHeight; - - this.$tableContainer.css('height', height + 'px'); - } - - if (this.options.cardView) { - // remove the element css - this.$el.css('margin-top', '0'); - this.$tableContainer.css('padding-bottom', '0'); - this.$tableFooter.hide(); - return; - } - - if (this.options.showHeader && this.options.height) { - this.$tableHeader.show(); - this.resetHeader(); - padding += this.$header.outerHeight(); - } else { - this.$tableHeader.hide(); - this.trigger('post-header'); - } - - if (this.options.showFooter) { - this.resetFooter(); - if (this.options.height) { - padding += this.$tableFooter.outerHeight() + 1; - } - } - - // Assign the correct sortable arrow - this.getCaret(); - this.$tableContainer.css('padding-bottom', padding + 'px'); - this.trigger('reset-view'); - }; - - BootstrapTable.prototype.getData = function (useCurrentPage) { - return (this.searchText || !$.isEmptyObject(this.filterColumns) || !$.isEmptyObject(this.filterColumnsPartial)) ? - (useCurrentPage ? this.data.slice(this.pageFrom - 1, this.pageTo) : this.data) : - (useCurrentPage ? this.options.data.slice(this.pageFrom - 1, this.pageTo) : this.options.data); - }; - - BootstrapTable.prototype.load = function (data) { - var fixedScroll = false; - - // #431: support pagination - if (this.options.sidePagination === 'server') { - this.options.totalRows = data[this.options.totalField]; - fixedScroll = data.fixedScroll; - data = data[this.options.dataField]; - } else if (!$.isArray(data)) { // support fixedScroll - fixedScroll = data.fixedScroll; - data = data.data; - } - - this.initData(data); - this.initSearch(); - this.initPagination(); - this.initBody(fixedScroll); - }; - - BootstrapTable.prototype.append = function (data) { - this.initData(data, 'append'); - this.initSearch(); - this.initPagination(); - this.initSort(); - this.initBody(true); - }; - - BootstrapTable.prototype.prepend = function (data) { - this.initData(data, 'prepend'); - this.initSearch(); - this.initPagination(); - this.initSort(); - this.initBody(true); - }; - - BootstrapTable.prototype.remove = function (params) { - var len = this.options.data.length, - i, row; - - if (!params.hasOwnProperty('field') || !params.hasOwnProperty('values')) { - return; - } - - for (i = len - 1; i >= 0; i--) { - row = this.options.data[i]; - - if (!row.hasOwnProperty(params.field)) { - continue; - } - if ($.inArray(row[params.field], params.values) !== -1) { - this.options.data.splice(i, 1); - if (this.options.sidePagination === 'server') { - this.options.totalRows -= 1; - } - } - } - - if (len === this.options.data.length) { - return; - } - - this.initSearch(); - this.initPagination(); - this.initSort(); - this.initBody(true); - }; - - BootstrapTable.prototype.removeAll = function () { - if (this.options.data.length > 0) { - this.options.data.splice(0, this.options.data.length); - this.initSearch(); - this.initPagination(); - this.initBody(true); - } - }; - - BootstrapTable.prototype.getRowByUniqueId = function (id) { - var uniqueId = this.options.uniqueId, - len = this.options.data.length, - dataRow = null, - i, row, rowUniqueId; - - for (i = len - 1; i >= 0; i--) { - row = this.options.data[i]; - - if (row.hasOwnProperty(uniqueId)) { // uniqueId is a column - rowUniqueId = row[uniqueId]; - } else if(row._data.hasOwnProperty(uniqueId)) { // uniqueId is a row data property - rowUniqueId = row._data[uniqueId]; - } else { - continue; - } - - if (typeof rowUniqueId === 'string') { - id = id.toString(); - } else if (typeof rowUniqueId === 'number') { - if ((Number(rowUniqueId) === rowUniqueId) && (rowUniqueId % 1 === 0)) { - id = parseInt(id); - } else if ((rowUniqueId === Number(rowUniqueId)) && (rowUniqueId !== 0)) { - id = parseFloat(id); - } - } - - if (rowUniqueId === id) { - dataRow = row; - break; - } - } - - return dataRow; - }; - - BootstrapTable.prototype.removeByUniqueId = function (id) { - var len = this.options.data.length, - row = this.getRowByUniqueId(id); - - if (row) { - this.options.data.splice(this.options.data.indexOf(row), 1); - } - - if (len === this.options.data.length) { - return; - } - - this.initSearch(); - this.initPagination(); - this.initBody(true); - }; - - BootstrapTable.prototype.updateByUniqueId = function (params) { - var that = this; - var allParams = $.isArray(params) ? params : [ params ]; - - $.each(allParams, function(i, params) { - var rowId; - - if (!params.hasOwnProperty('id') || !params.hasOwnProperty('row')) { - return; - } - - rowId = $.inArray(that.getRowByUniqueId(params.id), that.options.data); - - if (rowId === -1) { - return; - } - $.extend(that.options.data[rowId], params.row); - }); - - this.initSearch(); - this.initPagination(); - this.initSort(); - this.initBody(true); - }; - - BootstrapTable.prototype.insertRow = function (params) { - if (!params.hasOwnProperty('index') || !params.hasOwnProperty('row')) { - return; - } - this.data.splice(params.index, 0, params.row); - this.initSearch(); - this.initPagination(); - this.initSort(); - this.initBody(true); - }; - - BootstrapTable.prototype.updateRow = function (params) { - var that = this; - var allParams = $.isArray(params) ? params : [ params ]; - - $.each(allParams, function(i, params) { - if (!params.hasOwnProperty('index') || !params.hasOwnProperty('row')) { - return; - } - $.extend(that.options.data[params.index], params.row); - }); - - this.initSearch(); - this.initPagination(); - this.initSort(); - this.initBody(true); - }; - - BootstrapTable.prototype.initHiddenRows = function () { - this.hiddenRows = []; - }; - - BootstrapTable.prototype.showRow = function (params) { - this.toggleRow(params, true); - }; - - BootstrapTable.prototype.hideRow = function (params) { - this.toggleRow(params, false); - }; - - BootstrapTable.prototype.toggleRow = function (params, visible) { - var row, index; - - if (params.hasOwnProperty('index')) { - row = this.getData()[params.index]; - } else if (params.hasOwnProperty('uniqueId')) { - row = this.getRowByUniqueId(params.uniqueId); - } - - if (!row) { - return; - } - - index = $.inArray(row, this.hiddenRows); - - if (!visible && index === -1) { - this.hiddenRows.push(row); - } else if (visible && index > -1) { - this.hiddenRows.splice(index, 1); - } - this.initBody(true); - }; - - BootstrapTable.prototype.getHiddenRows = function (show) { - var that = this, - data = this.getData(), - rows = []; - - $.each(data, function (i, row) { - if ($.inArray(row, that.hiddenRows) > -1) { - rows.push(row); - } - }); - this.hiddenRows = rows; - return rows; - }; - - BootstrapTable.prototype.mergeCells = function (options) { - var row = options.index, - col = $.inArray(options.field, this.getVisibleFields()), - rowspan = options.rowspan || 1, - colspan = options.colspan || 1, - i, j, - $tr = this.$body.find('>tr'), - $td; - - if (this.options.detailView && !this.options.cardView) { - col += 1; - } - - $td = $tr.eq(row).find('>td').eq(col); - - if (row < 0 || col < 0 || row >= this.data.length) { - return; - } - - for (i = row; i < row + rowspan; i++) { - for (j = col; j < col + colspan; j++) { - $tr.eq(i).find('>td').eq(j).hide(); - } - } - - $td.attr('rowspan', rowspan).attr('colspan', colspan).show(); - }; - - BootstrapTable.prototype.updateCell = function (params) { - if (!params.hasOwnProperty('index') || - !params.hasOwnProperty('field') || - !params.hasOwnProperty('value')) { - return; - } - this.data[params.index][params.field] = params.value; - - if (params.reinit === false) { - return; - } - this.initSort(); - this.initBody(true); - }; - - BootstrapTable.prototype.getOptions = function () { - return this.options; - }; - - BootstrapTable.prototype.getSelections = function () { - var that = this; - - return $.grep(this.options.data, function (row) { - // fix #2424: from html with checkbox - return row[that.header.stateField] === true; - }); - }; - - BootstrapTable.prototype.getAllSelections = function () { - var that = this; - - return $.grep(this.options.data, function (row) { - return row[that.header.stateField]; - }); - }; - - BootstrapTable.prototype.checkAll = function () { - this.checkAll_(true); - }; - - BootstrapTable.prototype.uncheckAll = function () { - this.checkAll_(false); - }; - - BootstrapTable.prototype.checkInvert = function () { - var that = this; - var rows = that.$selectItem.filter(':enabled'); - var checked = rows.filter(':checked'); - rows.each(function() { - $(this).prop('checked', !$(this).prop('checked')); - }); - that.updateRows(); - that.updateSelected(); - that.trigger('uncheck-some', checked); - checked = that.getSelections(); - that.trigger('check-some', checked); - }; - - BootstrapTable.prototype.checkAll_ = function (checked) { - var rows; - if (!checked) { - rows = this.getSelections(); - } - this.$selectAll.add(this.$selectAll_).prop('checked', checked); - this.$selectItem.filter(':enabled').prop('checked', checked); - this.updateRows(); - if (checked) { - rows = this.getSelections(); - } - this.trigger(checked ? 'check-all' : 'uncheck-all', rows); - }; - - BootstrapTable.prototype.check = function (index) { - this.check_(true, index); - }; - - BootstrapTable.prototype.uncheck = function (index) { - this.check_(false, index); - }; - - BootstrapTable.prototype.check_ = function (checked, index) { - var $el = this.$selectItem.filter(sprintf('[data-index="%s"]', index)).prop('checked', checked); - this.data[index][this.header.stateField] = checked; - this.updateSelected(); - this.trigger(checked ? 'check' : 'uncheck', this.data[index], $el); - }; - - BootstrapTable.prototype.checkBy = function (obj) { - this.checkBy_(true, obj); - }; - - BootstrapTable.prototype.uncheckBy = function (obj) { - this.checkBy_(false, obj); - }; - - BootstrapTable.prototype.checkBy_ = function (checked, obj) { - if (!obj.hasOwnProperty('field') || !obj.hasOwnProperty('values')) { - return; - } - - var that = this, - rows = []; - $.each(this.options.data, function (index, row) { - if (!row.hasOwnProperty(obj.field)) { - return false; - } - if ($.inArray(row[obj.field], obj.values) !== -1) { - var $el = that.$selectItem.filter(':enabled') - .filter(sprintf('[data-index="%s"]', index)).prop('checked', checked); - row[that.header.stateField] = checked; - rows.push(row); - that.trigger(checked ? 'check' : 'uncheck', row, $el); - } - }); - this.updateSelected(); - this.trigger(checked ? 'check-some' : 'uncheck-some', rows); - }; - - BootstrapTable.prototype.destroy = function () { - this.$el.insertBefore(this.$container); - $(this.options.toolbar).insertBefore(this.$el); - this.$container.next().remove(); - this.$container.remove(); - this.$el.html(this.$el_.html()) - .css('margin-top', '0') - .attr('class', this.$el_.attr('class') || ''); // reset the class - }; - - BootstrapTable.prototype.showLoading = function () { - this.$tableLoading.show(); - }; - - BootstrapTable.prototype.hideLoading = function () { - this.$tableLoading.hide(); - }; - - BootstrapTable.prototype.togglePagination = function () { - this.options.pagination = !this.options.pagination; - var button = this.$toolbar.find('button[name="paginationSwitch"] i'); - if (this.options.pagination) { - button.attr("class", this.options.iconsPrefix + " " + this.options.icons.paginationSwitchDown); - } else { - button.attr("class", this.options.iconsPrefix + " " + this.options.icons.paginationSwitchUp); - } - this.updatePagination(); - }; - - BootstrapTable.prototype.refresh = function (params) { - if (params && params.url) { - this.options.url = params.url; - } - if (params && params.pageNumber) { - this.options.pageNumber = params.pageNumber; - } - if (params && params.pageSize) { - this.options.pageSize = params.pageSize; - } - this.initServer(params && params.silent, - params && params.query, params && params.url); - this.trigger('refresh', params); - }; - - BootstrapTable.prototype.resetWidth = function () { - if (this.options.showHeader && this.options.height) { - this.fitHeader(); - } - if (this.options.showFooter) { - this.fitFooter(); - } - }; - - BootstrapTable.prototype.showColumn = function (field) { - this.toggleColumn(getFieldIndex(this.columns, field), true, true); - }; - - BootstrapTable.prototype.hideColumn = function (field) { - this.toggleColumn(getFieldIndex(this.columns, field), false, true); - }; - - BootstrapTable.prototype.getHiddenColumns = function () { - return 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this.$body.find(sprintf('> tr[data-index="%s"]', index)); - if ($tr.next().is('tr.detail-view') === (expand ? false : true)) { - $tr.find('> td > .detail-icon').click(); - } - }; - - BootstrapTable.prototype.expandRow = function (index) { - this.expandRow_(true, index); - }; - - BootstrapTable.prototype.collapseRow = function (index) { - this.expandRow_(false, index); - }; - - BootstrapTable.prototype.expandAllRows = function (isSubTable) { - if (isSubTable) { - var $tr = this.$body.find(sprintf('> tr[data-index="%s"]', 0)), - that = this, - detailIcon = null, - executeInterval = false, - idInterval = -1; - - if (!$tr.next().is('tr.detail-view')) { - $tr.find('> td > .detail-icon').click(); - executeInterval = true; - } else if (!$tr.next().next().is('tr.detail-view')) { - $tr.next().find(".detail-icon").click(); - executeInterval = true; - } - - if (executeInterval) { - try { - idInterval = setInterval(function () { - detailIcon = that.$body.find("tr.detail-view").last().find(".detail-icon"); - if (detailIcon.length > 0) { - detailIcon.click(); - } else { - clearInterval(idInterval); - } - }, 1); - } catch (ex) { - clearInterval(idInterval); - } - } - } else { - var trs = this.$body.children(); - for (var i = 0; i < trs.length; i++) { - this.expandRow_(true, $(trs[i]).data("index")); - } - } - }; - - BootstrapTable.prototype.collapseAllRows = function (isSubTable) { - if (isSubTable) { - this.expandRow_(false, 0); - } else { - var trs = this.$body.children(); - for (var i = 0; i < trs.length; i++) { - this.expandRow_(false, $(trs[i]).data("index")); - } - } - }; - - BootstrapTable.prototype.updateFormatText = function (name, text) { - if (this.options[sprintf('format%s', name)]) { - if (typeof text === 'string') { - this.options[sprintf('format%s', name)] = function () { - return text; - }; - } else if (typeof text === 'function') { - this.options[sprintf('format%s', name)] = text; - } - } - this.initToolbar(); 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Each item is an image data object. - var allImages = {}; - var imageCounter = 0; - - // Galleriffic static class - $.galleriffic = { - version: '2.0.1', - - // Strips invalid characters and any leading # characters - normalizeHash: function(hash) { - return hash.replace(/^.*#/, '').replace(/\?.*$/, ''); - }, - - getImage: function(hash) { - if (!hash) - return undefined; - - hash = $.galleriffic.normalizeHash(hash); - return allImages[hash]; - }, - - // Global function that looks up an image by its hash and displays the image. - // Returns false when an image is not found for the specified hash. - // @param {String} hash This is the unique hash value assigned to an image. - gotoImage: function(hash) { - var imageData = $.galleriffic.getImage(hash); - if (!imageData) - return false; - - var gallery = imageData.gallery; - gallery.gotoImage(imageData); - - return true; - }, - - // Removes an image from its respective gallery by its hash. - // Returns false when an image is not found for the specified hash or the - // specified owner gallery does match the located images gallery. - // @param {String} hash This is the unique hash value assigned to an image. - // @param {Object} ownerGallery (Optional) When supplied, the located images - // gallery is verified to be the same as the specified owning gallery before - // performing the remove operation. - removeImageByHash: function(hash, ownerGallery) { - var imageData = $.galleriffic.getImage(hash); - if (!imageData) - return false; - - var gallery = imageData.gallery; - if (ownerGallery && ownerGallery != gallery) - return false; - - return gallery.removeImageByIndex(imageData.index); - } - }; - - var defaults = { - delay: 3000, - numThumbs: 20, - preloadAhead: 40, // Set to -1 to preload all images - enableTopPager: false, - enableBottomPager: true, - maxPagesToShow: 7, - imageContainerSel: '', - captionContainerSel: '', - controlsContainerSel: '', - loadingContainerSel: '', - renderSSControls: true, - renderNavControls: true, - playLinkText: 'Play', - pauseLinkText: 'Pause', - prevLinkText: 'Previous', - nextLinkText: 'Next', - nextPageLinkText: 'Next ›', - prevPageLinkText: '‹ Prev', - enableHistory: false, - enableKeyboardNavigation: true, - autoStart: false, - syncTransitions: false, - defaultTransitionDuration: 1000, - onSlideChange: undefined, // accepts a delegate like such: function(prevIndex, nextIndex) { ... } - onTransitionOut: undefined, // accepts a delegate like such: function(slide, caption, isSync, callback) { ... } - onTransitionIn: undefined, // accepts a delegate like such: function(slide, caption, isSync) { ... } - onPageTransitionOut: undefined, // accepts a delegate like such: function(callback) { ... } - onPageTransitionIn: undefined, // accepts a delegate like such: function() { ... } - onImageAdded: undefined, // accepts a delegate like such: function(imageData, $li) { ... } - onImageRemoved: undefined // accepts a delegate like such: function(imageData, $li) { ... } - }; - - // Primary Galleriffic initialization function that should be called on the thumbnail container. - $.fn.galleriffic = function(settings) { - // Extend Gallery Object - $.extend(this, { - // Returns the version of the script - version: $.galleriffic.version, - - // Current state of the slideshow - isSlideshowRunning: false, - slideshowTimeout: undefined, - - // This function is attached to the click event of generated hyperlinks within the gallery - clickHandler: function(e, link) { - this.pause(); - - if (!this.enableHistory) { - // The href attribute holds the unique hash for an image - var hash = $.galleriffic.normalizeHash($(link).attr('href')); - $.galleriffic.gotoImage(hash); - e.preventDefault(); - } - }, - - // Appends an image to the end of the set of images. Argument listItem can be either a jQuery DOM element or arbitrary html. - // @param listItem Either a jQuery object or a string of html of the list item that is to be added to the gallery. - appendImage: function(listItem) { - this.addImage(listItem, false, false); - return this; - }, - - // Inserts an image into the set of images. Argument listItem can be either a jQuery DOM element or arbitrary html. - // @param listItem Either a jQuery object or a string of html of the list item that is to be added to the gallery. - // @param {Integer} position The index within the gallery where the item shouold be added. - insertImage: function(listItem, position) { - this.addImage(listItem, false, true, position); - return this; - }, - - // Adds an image to the gallery and optionally inserts/appends it to the DOM (thumbExists) - // @param listItem Either a jQuery object or a string of html of the list item that is to be added to the gallery. - // @param {Boolean} thumbExists Specifies whether the thumbnail already exists in the DOM or if it needs to be added. - // @param {Boolean} insert Specifies whether the the image is appended to the end or inserted into the gallery. - // @param {Integer} position The index within the gallery where the item shouold be added. - addImage: function(listItem, thumbExists, insert, position) { - var $li = ( typeof listItem === "string" ) ? $(listItem) : listItem; - var $aThumb = $li.find('a.thumb'); - var slideUrl = $aThumb.attr('href'); - var title = $aThumb.attr('title'); - var $caption = $li.find('.caption').remove(); - var hash = $aThumb.attr('name'); - - // Increment the image counter - imageCounter++; - - // Autogenerate a hash value if none is present or if it is a duplicate - if (!hash || allImages[''+hash]) { - hash = imageCounter; - } - - // Set position to end when not specified - if (!insert) - position = this.data.length; - - var imageData = { - title:title, - slideUrl:slideUrl, - caption:$caption, - hash:hash, - gallery:this, - index:position - }; - - // Add the imageData to this gallery's array of images - if (insert) { - this.data.splice(position, 0, imageData); - - // Reset index value on all imageData objects - this.updateIndices(position); - } - else { - this.data.push(imageData); - } - - var gallery = this; - - // Add the element to the DOM - if (!thumbExists) { - // Update thumbs passing in addition post transition out handler - this.updateThumbs(function() { - var $thumbsUl = gallery.find('ul.thumbs'); - if (insert) - $thumbsUl.children(':eq('+position+')').before($li); - else - $thumbsUl.append($li); - - if (gallery.onImageAdded) - gallery.onImageAdded(imageData, $li); - }); - } - - // Register the image globally - allImages[''+hash] = imageData; - - // Setup attributes and click handler - $aThumb.attr('rel', 'history') - .attr('href', '#'+hash) - .removeAttr('name') - .click(function(e) { - gallery.clickHandler(e, this); - }); - - return this; - }, - - // Removes an image from the gallery based on its index. - // Returns false when the index is out of range. - removeImageByIndex: function(index) { - if (index < 0 || index >= this.data.length) - return false; - - var imageData = this.data[index]; - if (!imageData) - return false; - - this.removeImage(imageData); - - return true; - }, - - // Convenience method that simply calls the global removeImageByHash method. - removeImageByHash: function(hash) { - return $.galleriffic.removeImageByHash(hash, this); - }, - - // Removes an image from the gallery. - removeImage: function(imageData) { - var index = imageData.index; - - // Remove the image from the gallery data array - this.data.splice(index, 1); - - // Remove the global registration - delete allImages[''+imageData.hash]; - - // Remove the image's list item from the DOM - this.updateThumbs(function() { - var $li = gallery.find('ul.thumbs') - .children(':eq('+index+')') - .remove(); - - if (gallery.onImageRemoved) - gallery.onImageRemoved(imageData, $li); - }); - - // Update each image objects index value - this.updateIndices(index); - - return this; - }, - - // Updates the index values of the each of the images in the gallery after the specified index - updateIndices: function(startIndex) { - for (i = startIndex; i < this.data.length; i++) { - this.data[i].index = i; - } - - return this; - }, - - // Scraped the thumbnail container for thumbs and adds each to the gallery - initializeThumbs: function() { - this.data = []; - var gallery = this; - - this.find('ul.thumbs > li').each(function(i) { - gallery.addImage($(this), true, false); - }); - - return this; - }, - - isPreloadComplete: false, - - // Initalizes the image preloader - preloadInit: function() { - if (this.preloadAhead == 0) return this; - - this.preloadStartIndex = this.currentImage.index; - var nextIndex = this.getNextIndex(this.preloadStartIndex); - return this.preloadRecursive(this.preloadStartIndex, nextIndex); - }, - - // Changes the location in the gallery the preloader should work - // @param {Integer} index The index of the image where the preloader should restart at. - preloadRelocate: function(index) { - // By changing this startIndex, the current preload script will restart - this.preloadStartIndex = index; - return this; - }, - - // Recursive function that performs the image preloading - // @param {Integer} startIndex The index of the first image the current preloader started on. - // @param {Integer} currentIndex The index of the current image to preload. - preloadRecursive: function(startIndex, currentIndex) { - // Check if startIndex has been relocated - if (startIndex != this.preloadStartIndex) { - var nextIndex = this.getNextIndex(this.preloadStartIndex); - return this.preloadRecursive(this.preloadStartIndex, nextIndex); - } - - var gallery = this; - - // Now check for preloadAhead count - var preloadCount = currentIndex - startIndex; - if (preloadCount < 0) - preloadCount = this.data.length-1-startIndex+currentIndex; - if (this.preloadAhead >= 0 && preloadCount > this.preloadAhead) { - // Do this in order to keep checking for relocated start index - setTimeout(function() { gallery.preloadRecursive(startIndex, currentIndex); }, 500); - return this; - } - - var imageData = this.data[currentIndex]; - if (!imageData) - return this; - - // If already loaded, continue - if (imageData.image) - return this.preloadNext(startIndex, currentIndex); - - // Preload the image - var image = new Image(); - - image.onload = function() { - imageData.image = this; - gallery.preloadNext(startIndex, currentIndex); - }; - - image.alt = imageData.title; - image.src = imageData.slideUrl; - - return this; - }, - - // Called by preloadRecursive in order to preload the next image after the previous has loaded. - // @param {Integer} startIndex The index of the first image the current preloader started on. - // @param {Integer} currentIndex The index of the current image to preload. - preloadNext: function(startIndex, currentIndex) { - var nextIndex = this.getNextIndex(currentIndex); - if (nextIndex == startIndex) { - this.isPreloadComplete = true; - } else { - // Use setTimeout to free up thread - var gallery = this; - setTimeout(function() { gallery.preloadRecursive(startIndex, nextIndex); }, 100); - } - - return this; - }, - - // Safe way to get the next image index relative to the current image. - // If the current image is the last, returns 0 - getNextIndex: function(index) { - var nextIndex = index+1; - if (nextIndex >= this.data.length) - nextIndex = 0; - return nextIndex; - }, - - // Safe way to get the previous image index relative to the current image. - // If the current image is the first, return the index of the last image in the gallery. - getPrevIndex: function(index) { - var prevIndex = index-1; - if (prevIndex < 0) - prevIndex = this.data.length-1; - return prevIndex; - }, - - // Pauses the slideshow - pause: function() { - this.isSlideshowRunning = false; - if (this.slideshowTimeout) { - clearTimeout(this.slideshowTimeout); - this.slideshowTimeout = undefined; - } - - if (this.$controlsContainer) { - this.$controlsContainer - .find('div.ss-controls a').removeClass().addClass('play') - .attr('title', this.playLinkText) - .attr('href', '#play') - .html(this.playLinkText); - } - - return this; - }, - - // Plays the slideshow - play: function() { - this.isSlideshowRunning = true; - - if (this.$controlsContainer) { - this.$controlsContainer - .find('div.ss-controls a').removeClass().addClass('pause') - .attr('title', this.pauseLinkText) - .attr('href', '#pause') - .html(this.pauseLinkText); - } - - if (!this.slideshowTimeout) { - var gallery = this; - this.slideshowTimeout = setTimeout(function() { gallery.ssAdvance(); }, this.delay); - } - - return this; - }, - - // Toggles the state of the slideshow (playing/paused) - toggleSlideshow: function() { - if (this.isSlideshowRunning) - this.pause(); - else - this.play(); - - return this; - }, - - // Advances the slideshow to the next image and delegates navigation to the - // history plugin when history is enabled - // enableHistory is true - ssAdvance: function() { - if (this.isSlideshowRunning) - this.next(true); - - return this; - }, - - // Advances the gallery to the next image. - // @param {Boolean} dontPause Specifies whether to pause the slideshow. - // @param {Boolean} bypassHistory Specifies whether to delegate navigation to the history plugin when history is enabled. - next: function(dontPause, bypassHistory) { - this.gotoIndex(this.getNextIndex(this.currentImage.index), dontPause, bypassHistory); - return this; - }, - - // Navigates to the previous image in the gallery. - // @param {Boolean} dontPause Specifies whether to pause the slideshow. - // @param {Boolean} bypassHistory Specifies whether to delegate navigation to the history plugin when history is enabled. - previous: function(dontPause, bypassHistory) { - this.gotoIndex(this.getPrevIndex(this.currentImage.index), dontPause, bypassHistory); - return this; - }, - - // Navigates to the next page in the gallery. - // @param {Boolean} dontPause Specifies whether to pause the slideshow. - // @param {Boolean} bypassHistory Specifies whether to delegate navigation to the history plugin when history is enabled. - nextPage: function(dontPause, bypassHistory) { - var page = this.getCurrentPage(); - var lastPage = this.getNumPages() - 1; - if (page < lastPage) { - var startIndex = page * this.numThumbs; - var nextPage = startIndex + this.numThumbs; - this.gotoIndex(nextPage, dontPause, bypassHistory); - } - - return this; - }, - - // Navigates to the previous page in the gallery. - // @param {Boolean} dontPause Specifies whether to pause the slideshow. - // @param {Boolean} bypassHistory Specifies whether to delegate navigation to the history plugin when history is enabled. - previousPage: function(dontPause, bypassHistory) { - var page = this.getCurrentPage(); - if (page > 0) { - var startIndex = page * this.numThumbs; - var prevPage = startIndex - this.numThumbs; - this.gotoIndex(prevPage, dontPause, bypassHistory); - } - - return this; - }, - - // Navigates to the image at the specified index in the gallery - // @param {Integer} index The index of the image in the gallery to display. - // @param {Boolean} dontPause Specifies whether to pause the slideshow. - // @param {Boolean} bypassHistory Specifies whether to delegate navigation to the history plugin when history is enabled. - gotoIndex: function(index, dontPause, bypassHistory) { - if (!dontPause) - this.pause(); - - if (index < 0) index = 0; - else if (index >= this.data.length) index = this.data.length-1; - - var imageData = this.data[index]; - - if (!bypassHistory && this.enableHistory) - $.historyLoad(String(imageData.hash)); // At the moment, historyLoad only accepts string arguments - else - this.gotoImage(imageData); - - return this; - }, - - // This function is garaunteed to be called anytime a gallery slide changes. - // @param {Object} imageData An object holding the image metadata of the image to navigate to. - gotoImage: function(imageData) { - var index = imageData.index; - - if (this.onSlideChange) - this.onSlideChange(this.currentImage.index, index); - - this.currentImage = imageData; - this.preloadRelocate(index); - - this.refresh(); - - return this; - }, - - // Returns the default transition duration value. The value is halved when not - // performing a synchronized transition. - // @param {Boolean} isSync Specifies whether the transitions are synchronized. - getDefaultTransitionDuration: function(isSync) { - if (isSync) - return this.defaultTransitionDuration; - return this.defaultTransitionDuration / 2; - }, - - // Rebuilds the slideshow image and controls and performs transitions - refresh: function() { - var imageData = this.currentImage; - if (!imageData) - return this; - - var index = imageData.index; - - // Update Controls - if (this.$controlsContainer) { - this.$controlsContainer - .find('div.nav-controls a.prev').attr('href', '#'+this.data[this.getPrevIndex(index)].hash).end() - .find('div.nav-controls a.next').attr('href', '#'+this.data[this.getNextIndex(index)].hash); - } - - var previousSlide = this.$imageContainer.find('span.current').addClass('previous').removeClass('current'); - var previousCaption = 0; - - if (this.$captionContainer) { - previousCaption = this.$captionContainer.find('span.current').addClass('previous').removeClass('current'); - } - - // Perform transitions simultaneously if syncTransitions is true and the next image is already preloaded - var isSync = this.syncTransitions && imageData.image; - - // Flag we are transitioning - var isTransitioning = true; - var gallery = this; - - var transitionOutCallback = function() { - // Flag that the transition has completed - isTransitioning = false; - - // Remove the old slide - previousSlide.remove(); - - // Remove old caption - if (previousCaption) - previousCaption.remove(); - - if (!isSync) { - if (imageData.image && imageData.hash == gallery.data[gallery.currentImage.index].hash) { - gallery.buildImage(imageData, isSync); - } else { - // Show loading container - if (gallery.$loadingContainer) { - gallery.$loadingContainer.show(); - } - } - } - }; - - if (previousSlide.length == 0) { - // For the first slide, the previous slide will be empty, so we will call the callback immediately - transitionOutCallback(); - } else { - if (this.onTransitionOut) { - this.onTransitionOut(previousSlide, previousCaption, isSync, transitionOutCallback); - } else { - previousSlide.fadeTo(this.getDefaultTransitionDuration(isSync), 0.0, transitionOutCallback); - if (previousCaption) - previousCaption.fadeTo(this.getDefaultTransitionDuration(isSync), 0.0); - } - } - - // Go ahead and begin transitioning in of next image - if (isSync) - this.buildImage(imageData, isSync); - - if (!imageData.image) { - var image = new Image(); - - // Wire up mainImage onload event - image.onload = function() { - imageData.image = this; - - // Only build image if the out transition has completed and we are still on the same image hash - if (!isTransitioning && imageData.hash == gallery.data[gallery.currentImage.index].hash) { - gallery.buildImage(imageData, isSync); - } - }; - - // set alt and src - image.alt = imageData.title; - image.src = imageData.slideUrl; - } - - // This causes the preloader (if still running) to relocate out from the currentIndex - this.relocatePreload = true; - - return this.syncThumbs(); - }, - - // Called by the refresh method after the previous image has been transitioned out or at the same time - // as the out transition when performing a synchronous transition. - // @param {Object} imageData An object holding the image metadata of the image to build. - // @param {Boolean} isSync Specifies whether the transitions are synchronized. - buildImage: function(imageData, isSync) { - var gallery = this; - var nextIndex = this.getNextIndex(imageData.index); - - // Construct new hidden span for the image - var newSlide = this.$imageContainer - .append(' ') - .find('span.current').css('opacity', '0'); - - newSlide.find('a') - .append(imageData.image) - .click(function(e) { - gallery.clickHandler(e, this); - }); - - var newCaption = 0; - if (this.$captionContainer) { - // Construct new hidden caption for the image - newCaption = this.$captionContainer - .append('') - .find('span.current').css('opacity', '0') - .append(imageData.caption); - } - - // Hide the loading conatiner - if (this.$loadingContainer) { - this.$loadingContainer.hide(); - } - - // Transition in the new image - if (this.onTransitionIn) { - this.onTransitionIn(newSlide, newCaption, isSync); - } else { - newSlide.fadeTo(this.getDefaultTransitionDuration(isSync), 1.0); - if (newCaption) - newCaption.fadeTo(this.getDefaultTransitionDuration(isSync), 1.0); - } - - if (this.isSlideshowRunning) { - if (this.slideshowTimeout) - clearTimeout(this.slideshowTimeout); - - this.slideshowTimeout = setTimeout(function() { gallery.ssAdvance(); }, this.delay); - } - - return this; - }, - - // Returns the current page index that should be shown for the currentImage - getCurrentPage: function() { - return Math.floor(this.currentImage.index / this.numThumbs); - }, - - // Applies the selected class to the current image's corresponding thumbnail. - // Also checks if the current page has changed and updates the displayed page of thumbnails if necessary. - syncThumbs: function() { - var page = this.getCurrentPage(); - if (page != this.displayedPage) - this.updateThumbs(); - - // Remove existing selected class and add selected class to new thumb - var $thumbs = this.find('ul.thumbs').children(); - $thumbs.filter('.selected').removeClass('selected'); - $thumbs.eq(this.currentImage.index).addClass('selected'); - - return this; - }, - - // Performs transitions on the thumbnails container and updates the set of - // thumbnails that are to be displayed and the navigation controls. - // @param {Delegate} postTransitionOutHandler An optional delegate that is called after - // the thumbnails container has transitioned out and before the thumbnails are rebuilt. - updateThumbs: function(postTransitionOutHandler) { - var gallery = this; - var transitionOutCallback = function() { - // Call the Post-transition Out Handler - if (postTransitionOutHandler) - postTransitionOutHandler(); - - gallery.rebuildThumbs(); - - // Transition In the thumbsContainer - if (gallery.onPageTransitionIn) - gallery.onPageTransitionIn(); - else - gallery.show(); - }; - - // Transition Out the thumbsContainer - if (this.onPageTransitionOut) { - this.onPageTransitionOut(transitionOutCallback); - } else { - this.hide(); - transitionOutCallback(); - } - - return this; - }, - - // Updates the set of thumbnails that are to be displayed and the navigation controls. - rebuildThumbs: function() { - var needsPagination = this.data.length > this.numThumbs; - - // Rebuild top pager - if (this.enableTopPager) { - var $topPager = this.find('div.top'); - if ($topPager.length == 0) - $topPager = this.prepend('').find('div.top'); - else - $topPager.empty(); - - if (needsPagination) - this.buildPager($topPager); - } - - // Rebuild bottom pager - if (this.enableBottomPager) { - var $bottomPager = this.find('div.bottom'); - if ($bottomPager.length == 0) - $bottomPager = this.append('').find('div.bottom'); - else - $bottomPager.empty(); - - if (needsPagination) - this.buildPager($bottomPager); - } - - var page = this.getCurrentPage(); - var startIndex = page*this.numThumbs; - var stopIndex = startIndex+this.numThumbs-1; - if (stopIndex >= this.data.length) - stopIndex = this.data.length-1; - - // Show/Hide thumbs - var $thumbsUl = this.find('ul.thumbs'); - $thumbsUl.find('li').each(function(i) { - var $li = $(this); - if (i >= startIndex && i <= stopIndex) { - $li.show(); - } else { - $li.hide(); - } - }); - - this.displayedPage = page; - - // Remove the noscript class from the thumbs container ul - $thumbsUl.removeClass('noscript'); - - return this; - }, - - // Returns the total number of pages required to display all the thumbnails. - getNumPages: function() { - return Math.ceil(this.data.length/this.numThumbs); - }, - - // Rebuilds the pager control in the specified matched element. - // @param {jQuery} pager A jQuery element set matching the particular pager to be rebuilt. - buildPager: function(pager) { - var gallery = this; - var numPages = this.getNumPages(); - var page = this.getCurrentPage(); - var startIndex = page * this.numThumbs; - var pagesRemaining = this.maxPagesToShow - 1; - - var pageNum = page - Math.floor((this.maxPagesToShow - 1) / 2) + 1; - if (pageNum > 0) { - var remainingPageCount = numPages - pageNum; - if (remainingPageCount < pagesRemaining) { - pageNum = pageNum - (pagesRemaining - remainingPageCount); - } - } - - if (pageNum < 0) { - pageNum = 0; - } - - // Prev Page Link - if (page > 0) { - var prevPage = startIndex - this.numThumbs; - pager.append(''+this.prevPageLinkText+''); - } - - // Create First Page link if needed - if (pageNum > 0) { - this.buildPageLink(pager, 0, numPages); - if (pageNum > 1) - pager.append('…'); - - pagesRemaining--; - } - - // Page Index Links - while (pagesRemaining > 0) { - this.buildPageLink(pager, pageNum, numPages); - pagesRemaining--; - pageNum++; - } - - // Create Last Page link if needed - if (pageNum < numPages) { - var lastPageNum = numPages - 1; - if (pageNum < lastPageNum) - pager.append('…'); - - this.buildPageLink(pager, lastPageNum, numPages); - } - - // Next Page Link - var nextPage = startIndex + this.numThumbs; - if (nextPage < this.data.length) { - pager.append(''+this.nextPageLinkText+''); - } - - pager.find('a').click(function(e) { - gallery.clickHandler(e, this); - }); - - return this; - }, - - // Builds a single page link within a pager. This function is called by buildPager - // @param {jQuery} pager A jQuery element set matching the particular pager to be rebuilt. - // @param {Integer} pageNum The page number of the page link to build. - // @param {Integer} numPages The total number of pages required to display all thumbnails. - buildPageLink: function(pager, pageNum, numPages) { - var pageLabel = pageNum + 1; - var currentPage = this.getCurrentPage(); - if (pageNum == currentPage) - pager.append(''+pageLabel+''); - else if (pageNum < numPages) { - var imageIndex = pageNum*this.numThumbs; - pager.append(''+pageLabel+''); - } - - return this; - } - }); - - // Now initialize the gallery - $.extend(this, defaults, settings); - - // Verify the history plugin is available - if (this.enableHistory && !$.historyInit) - this.enableHistory = false; - - // Select containers - if (this.imageContainerSel) this.$imageContainer = $(this.imageContainerSel); - if (this.captionContainerSel) this.$captionContainer = $(this.captionContainerSel); - if (this.loadingContainerSel) this.$loadingContainer = $(this.loadingContainerSel); - - // Initialize the thumbails - this.initializeThumbs(); - - if (this.maxPagesToShow < 3) - this.maxPagesToShow = 3; - - this.displayedPage = -1; - this.currentImage = this.data[0]; - var gallery = this; - - // Hide the loadingContainer - if (this.$loadingContainer) - this.$loadingContainer.hide(); - - // Setup controls - if (this.controlsContainerSel) { - this.$controlsContainer = $(this.controlsContainerSel).empty(); - - if (this.renderSSControls) { - if (this.autoStart) { - this.$controlsContainer - .append('
    '+this.pauseLinkText+'
    '); - } else { - this.$controlsContainer - .append('
    '+this.playLinkText+'
    '); - } - - this.$controlsContainer.find('div.ss-controls a') - .click(function(e) { - gallery.toggleSlideshow(); - e.preventDefault(); - return false; - }); - } - - if (this.renderNavControls) { - this.$controlsContainer - .append('
    ') - .find('div.nav-controls a') - .click(function(e) { - gallery.clickHandler(e, this); - }); - } - } - - var initFirstImage = !this.enableHistory || !location.hash; - if (this.enableHistory && location.hash) { - var hash = $.galleriffic.normalizeHash(location.hash); - var imageData = allImages[hash]; - if (!imageData) - initFirstImage = true; - } - - // Setup gallery to show the first image - if (initFirstImage) - this.gotoIndex(0, false, true); - - // Setup Keyboard Navigation - if (this.enableKeyboardNavigation) { - $(document).keydown(function(e) { - var key = e.charCode ? e.charCode : e.keyCode ? e.keyCode : 0; - switch(key) { - case 32: // space - gallery.next(); - e.preventDefault(); - break; - case 33: // Page Up - gallery.previousPage(); - e.preventDefault(); - break; - case 34: // Page Down - gallery.nextPage(); - e.preventDefault(); - break; - case 35: // End - gallery.gotoIndex(gallery.data.length-1); - e.preventDefault(); - break; - case 36: // Home - gallery.gotoIndex(0); - e.preventDefault(); - break; - case 37: // left arrow - gallery.previous(); - e.preventDefault(); - break; - case 39: // right arrow - gallery.next(); - e.preventDefault(); - break; - } - }); - } - - // Auto start the slideshow - if (this.autoStart) - this.play(); - - // Kickoff Image Preloader after 1 second - setTimeout(function() { gallery.preloadInit(); }, 1000); - - return this; - }; -})(jQuery); diff -r 11708af40030 -r 967512924317 bin/js/jquery.js --- a/bin/js/jquery.js Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -/*! jQuery v1.9.1 | (c) 2005, 2012 jQuery Foundation, Inc. | jquery.org/license -//@ sourceMappingURL=jquery.min.map -*/(function(e,t){var n,r,i=typeof t,o=e.document,a=e.location,s=e.jQuery,u=e.$,l={},c=[],p="1.9.1",f=c.concat,d=c.push,h=c.slice,g=c.indexOf,m=l.toString,y=l.hasOwnProperty,v=p.trim,b=function(e,t){return new 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