Mercurial > repos > brasset_jensen > srnapipe
changeset 67:740884893563 draft
planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit fa75629bca78685de0106390758c0e85f1ca0836
| author | brasset_jensen |
|---|---|
| date | Thu, 31 Jan 2019 16:10:58 -0500 |
| parents | ff36e76d696a |
| children | a5a99218ef7a |
| files | README.rst bin/sRNAPipe.pl lib/sRNAPipe.pm lib/sRNAPipe/Rcall.pm lib/sRNAPipe/align.pm lib/sRNAPipe/css/bootstrap-responsive.css lib/sRNAPipe/css/bootstrap-table.css lib/sRNAPipe/css/bootstrap.css lib/sRNAPipe/html.pm lib/sRNAPipe/js/bootstrap-table.js lib/sRNAPipe/js/bootstrap.min.js lib/sRNAPipe/js/filter.js lib/sRNAPipe/js/jquery.galleriffic.js lib/sRNAPipe/js/jquery.js lib/sRNAPipe/js/jquery.opacityrollover.js lib/sRNAPipe/ppp.pm lib/sRNAPipe/resize.pm lib/sRNAPipe/subgroups.pm sRNAPipe.xml |
| diffstat | 19 files changed, 6 insertions(+), 14185 deletions(-) [+] |
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--- a/README.rst Wed Jan 30 06:26:32 2019 -0500 +++ b/README.rst Thu Jan 31 16:10:58 2019 -0500 @@ -7,13 +7,13 @@ A GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data Description -=========== +----------- The field of small RNA is one of the most investigated research areas since they were shown to regulate gene expression and play essential roles in fundamental biological processes. sRNAPipe a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: microRNAs, gene transcripts, small nuclear RNAs, ribosomal RNAs, transfer RNAs and transposable elements. It also provides individual mapping and counting for chromosomes, gene transcripts and transposable elements, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5’-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing numbers of overlaps and corresponding z-scores. Prerequisites -============= +------------- 1. Unix system with A Galaxy server (release 16.01 or later installed) @@ -29,7 +29,7 @@ 4. R project version higher than 3.1 is needed with libraries "plotrix", "bioconductor-sushi", "RColorBrewer" and "ggplot2" installed. You can find respectively these libraries here: https://cran.r-project.org/web/packages/plotrix/index.html and https://bioconductor.org/packages/release/bioc/html/Sushi.html and https://cran.r-project.org/web/packages/RColorBrewer/index.html and https://cran.r-project.org/web/packages/ggplot2/index.html Installation -============ +------------ The process has to be completed by an administrator of your Galaxy server to install sRNAPipe.
--- a/bin/sRNAPipe.pl Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,307 +0,0 @@ -#!/usr/bin/env perl -package main; -use strict; -use warnings; -use Getopt::Long; -use Parallel::ForkManager; -use File::Basename; -use File::Copy; -use POSIX; -use FindBin; -use lib "$FindBin::Bin/../lib"; -use sRNAPipe; -use sRNAPipe::resize qw ( size_distribution ); -use sRNAPipe::subgroups qw ( subgroups ); -use sRNAPipe::ppp qw ( ping_pong_partners ); -use sRNAPipe::Rcall qw (pie_chart bg_to_png ); -use sRNAPipe::align qw ( to_build get_unique sam_count sam_count_mis sam_sorted_bam rpms_rpkm rpms_rpkm_te BWA_call get_fastq_seq extract_sam sam_to_bam_bg ); -use sRNAPipe::html qw ( main_page details_pages menu_page ppp_page copy_css copy_js ); - -if(@ARGV) { - my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $mapnumf, $html_out); - my ( $ref, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE ); - my ( $si_min, $si_max, $pi_min, $pi_max ); - my ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_transcripts, $build_TE ); - my $max_procs = 8; - - ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_transcripts, $build_TE ) = (0,0,0,0,0,0,0); - ( $min, $max, $mis, $misTE, $si_min, $si_max, $pi_min, $pi_max, $dir ) = ( 18, 29, 0, 3, 21, 21, 23, 29 ); - $Pcheck ='true'; - - GetOptions ( - "fastq=s" => \@fastq, - "fastq_n=s" => \@fastq_n, - "dir=s" => \$dir, - "min:i" => \$min, - "max:i" => \$max, - "si_min:i" => \$si_min, - "si_max:i" => \$si_max, - "pi_min:i" => \$pi_min, - "pi_max:i" => \$pi_max, - "mis:i" => \$mis, - "misTE:i" => \$misTE, - "html:s" => \$html_out, - "PPPon:s" => \$Pcheck, - "help" => \$help, - "ref:s" => \$ref, - "tRNAs:s" => \$tRNAs, - "rRNAs:s" => \$rRNAs, - "snRNAs:s" => \$snRNAs, - "miRNAs:s" => \$miRNAs, - "transcripts:s" => \$transcripts, - "TE:s" => \$TE, - "build_index" => \$build_index, - "build_tRNAs" => \$build_tRNAs, - "build_snRNAs" => \$build_snRNAs, - "build_miRNAs" => \$build_miRNAs, - "build_transcripts" => \$build_transcripts, - "build_rRNAs" => \$build_rRNAs, - "build_TE" => \$build_TE - ); - - my $fq_collection = 'fastq_dir/'; - mkdir $dir; mkdir $fq_collection; - $dir = $dir.'/' unless $dir =~ /\/$/; - mkdir $dir.'/css';mkdir $dir.'/js'; - copy_css( $dir ); - copy_js( $dir ); - - my $file = $dir.'report.txt'; - open my $report, '>', $file or die "Cannot open $file $!\n"; - - my @toBuild = ( [$build_index, \$ref], [$build_tRNAs, \$tRNAs], [$build_rRNAs, \$rRNAs], [$build_snRNAs, \$snRNAs], [$build_miRNAs, \$miRNAs], [$build_transcripts, \$transcripts], [$build_TE, \$TE] ); - to_build ( \@toBuild, $report, $dir ); - - my $proc_child = ceil($max_procs / scalar(@fastq)); - my $proc_grand_child = ceil($proc_child/4); - my $pm = Parallel::ForkManager->new($max_procs); - my $pm2 = Parallel::ForkManager->new($proc_grand_child); - - $pm->run_on_finish( sub { - my ($pid, $exit_code, $ident) = @_; - print $report "Fastq fork $ident just finished ". - "with PID $pid and exit code: $exit_code\n"; - die "Something went wrong!\n" if $exit_code != 0; - }); - - - $pm->run_on_start( sub { - my ($pid,$ident)=@_; - print $report "Fastq fork : $ident started, pid: $pid\n"; - }); - - - $pm2->run_on_finish( sub { - my ($pid, $exit_code, $ident) = @_; - print $report "** Subgroup fork $ident just finished ". - "with PID $pid and exit code: $exit_code\n"; - die "Something went wrong!\n" if $exit_code != 0; - }); - - - $pm2->run_on_start( sub { - my ($pid,$ident)=@_; - print $report "** Subgroup fork $ident started, pid: $pid\n"; - }); - - foreach my $child ( 0 .. $#fastq ) - { - my @suffix = ('.fastq', '.fastq.gz,', '.fq', '.fq.gz', 'ref', '.dat', '.fa','.fas','.fasta', '.txt'); - my ( $name, $path, $suffix ) = fileparse( $fastq[$child], @suffix ); - my ( $ref_name, $ref_path, $ref_suffix ) = fileparse( $ref, @suffix ); - my ( $TE_name, $TE_path, $TE_suffix ) = fileparse( $TE, @suffix ); - my ( $ex_name, $ex_path, $ex_suffix ) = fileparse( $transcripts, @suffix ); - - $pm->start($fastq[$child]) and next; - - my $dir_fq = $dir.$fastq_n[$child].'/'; - mkdir $dir_fq; - - my $gen_dir = $dir_fq.'genome/'; - mkdir $gen_dir; - - my $size_dir = $dir_fq.'size/'; - mkdir $size_dir; - - my $fastq_resized = $dir_fq.$name.'_'.$min.'-'.$max.'.fastq'; - size_distribution ( $fastq[$child], $fastq_resized, $size_dir, $min, $max ); - - my $sam_genome = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'.sam'; - my $sam_genome_unique = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'_unique.sam'; - my $fastq_prefix = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max; - - BWA_call ( $ref, $fastq_resized, $sam_genome, $mis, $proc_child, $report ); - my ( $fai_ref_hashP, $ma, $ma_uni ) = get_unique ( $sam_genome, $sam_genome_unique, $gen_dir, $fq_collection.$fastq_n[$child], 1, $report ); - - die "No Reads mapped on the genome reference!\n" if $ma == 0; - my $scale = 1000000 / $ma; - sam_to_bam_bg ( $sam_genome_unique, $scale, $proc_child ); - sam_to_bam_bg ( $sam_genome, $scale, $proc_child ); - - my $Gviz_dir = $gen_dir.'Gviz/'; - my $fai_file = $gen_dir.'fai'; - mkdir $Gviz_dir; - my $Gviz_dir_rand = $Gviz_dir.'rand/'; - mkdir $Gviz_dir_rand; - my $Gviz_dir_uni = $Gviz_dir.'unique/'; - mkdir $Gviz_dir_uni; - - open my $gfai, '>', $fai_file; - foreach my $k ( sort keys %{$fai_ref_hashP} ) - { - print $gfai "$k\t$fai_ref_hashP->{$k}\n"; - } - close $gfai; - bg_to_png ( $fai_file, $fastq_prefix.'_unique_plus.bedgraph', $fastq_prefix.'_unique_minus.bedgraph', $Gviz_dir_uni, 'Mb' ); - bg_to_png ( $fai_file, $fastq_prefix.'_plus.bedgraph', $fastq_prefix.'_minus.bedgraph', $Gviz_dir_rand, 'Mb' ); - - my $group_dir = $dir_fq.'subgroups/'; - my $fastq_uni = $fq_collection.$fastq_n[$child].'_unique_mappers.fastq'; - my $fastq_all = $fq_collection.$fastq_n[$child].'_all_mappers.fastq'; - my ($bo, $mi, $pi) = subgroups ( $fastq_all, $group_dir, $mis, $misTE, $proc_child, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $si_min, $si_max, $pi_min, $pi_max, $report); - - pie_chart($group_dir); - - open (my $dupnum, $gen_dir.'dup_mapnum.txt') || die "cannot open dup_mapnum.txt $!"; - my %dupnum_genome; - my $header = <$dupnum>; - while (<$dupnum>) - { - chomp $_; - my @dupline = split /\t/, $_; - $dupnum_genome{$dupline[0]} = [$dupline[1], $dupline[2]]; - } - close $dupnum; - - my $mi_sam = $group_dir.'miRNAs.sam'; - mkdir $group_dir.'miRNAs/'; - my $mi_count_file = $group_dir.'miRNAs/miRNAs_reads_counts.txt'; - my ( $mi_count, $mi_ref_size ) = sam_count ( $mi_sam ); - - rpms_rpkm( $mi_count, $mi_ref_size, $ma, $mi_count_file, $pi, $mi, $bo ); - - my ( $sam_transcripts, $sam_TEs ) = ( $group_dir.'transcripts.sam', $group_dir.'TEs.sam' ); - my @types = ($group_dir.'bonafide_reads.fastq', $group_dir.'miRNAs.fastq', $group_dir.'siRNAs.fastq', $group_dir.'piRNAs.fastq' ); - my @types_names = ('bonafide_reads', 'miRNAs', 'siRNAs', 'piRNAs'); - foreach my $grand_child ( 0 .. $#types ) - { - my $type_dir = $group_dir.$types_names[$grand_child].'/'; - my $type_prefix = $types_names[$grand_child].'-'; - mkdir $type_dir; - $pm2->start($types[$grand_child]) and next; - my ( $type_sam_genome, $type_sam_TEs, $type_sam_transcripts ) = ( $type_dir.$type_prefix.'genome.sam', $type_dir.$type_prefix.'TEs.sam', $type_dir.$type_prefix.'transcripts.sam' ); - my ( $type_sam_uni_genome, $type_sam_uni_TEs, $type_sam_uni_transcripts ) = ( $type_dir.$type_prefix.'genome_unique.sam', $type_dir.$type_prefix.'TEs_unique.sam', $type_dir.$type_prefix.'transcripts_unique.sam' ); - my ( $type_uni_genome_fastq, $type_uni_TEs_fastq, $type_uni_transcripts_fastq ) = ( $fq_collection.$fastq_n[$child].'-'.$type_prefix.'genome_uni.fastq', $fq_collection.$fastq_n[$child].'-'.$type_prefix.'TEs_uni.fastq', $fq_collection.$fastq_n[$child].'-'.$type_prefix.'transcripts_uni.fastq'); - my ( $type_genome_fastq, $type_TEs_fastq, $type_transcripts_fastq ) = ( $fq_collection.$fastq_n[$child].'-'.$type_prefix.'genome.fastq', $fq_collection.$fastq_n[$child].'-'.$type_prefix.'TEs.fastq', $fq_collection.$fastq_n[$child].'-'.$type_prefix.'transcripts.fastq'); - my $type_sequence_hashP = get_fastq_seq ( $types[$grand_child] ); - - if ( $grand_child == 1 ) - { - BWA_call ( $TE, $types[$grand_child], $type_sam_TEs, $misTE, $proc_child, $report ); - BWA_call ( $transcripts, $types[$grand_child], $type_sam_transcripts, $mis, $proc_child, $report ); - BWA_call ( $ref, $types[$grand_child], $type_sam_genome, $mis, $proc_child, $report ); - extract_sam ( undef, $type_sam_TEs, $type_sam_TEs, $type_sam_uni_TEs, $type_uni_TEs_fastq, $type_uni_TEs_fastq ); - extract_sam ( undef, $type_sam_transcripts, $type_sam_transcripts, $type_sam_uni_transcripts, $type_transcripts_fastq, $type_uni_transcripts_fastq ); - extract_sam ( undef, $type_sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq ); - } - else - { - extract_sam ( $type_sequence_hashP, $sam_TEs, $type_sam_TEs, $type_sam_uni_TEs, $type_TEs_fastq, $type_uni_TEs_fastq ); - extract_sam ( $type_sequence_hashP, $sam_transcripts, $type_sam_transcripts, $type_sam_uni_transcripts, $type_transcripts_fastq, $type_uni_transcripts_fastq ); - extract_sam ( $type_sequence_hashP, $sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq ); - } - - my $ex_count_file = $type_dir.$type_prefix.'transcripts_reads_counts.txt'; - my ( $ex_count, $ex_ref_size ) = sam_count_mis ( $type_sam_transcripts ); - rpms_rpkm_te( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo ); - - my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs ); - my $TEs_count_file = $type_dir.$type_prefix.'TEs_reads_counts.txt'; - my $TEs_count_file_M = $type_dir.$type_prefix.'TEs_reads_counts_mismatches.txt'; - my $TEs_count_file_noM = $type_dir.$type_prefix.'TEs_reads_counts_nomismatches.txt'; - rpms_rpkm_te( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo ); - rpms_rpkm_te( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo ); - rpms_rpkm_te( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo ); - - sam_to_bam_bg ( $type_sam_TEs, $scale, $grand_child ); - sam_sorted_bam ( $type_sam_transcripts, $grand_child ); sam_sorted_bam ( $type_sam_uni_transcripts, $grand_child ); - sam_sorted_bam ( $type_sam_uni_TEs, $grand_child ); - - my $Gviz_TEs = $type_dir.'Gviz_TEs/'; - mkdir $Gviz_TEs; - bg_to_png ( $group_dir.'TEs.fai', $type_dir.$type_prefix.'TEs_plus.bedgraph', $type_dir.$type_prefix.'TEs_minus.bedgraph', $Gviz_TEs, 'Kb' ); - - my $Gviz_genome= $type_dir.'Gviz_genome/'; - my $Gviz_genome_rand = $Gviz_genome.'rand/'; - my $Gviz_genome_uni = $Gviz_genome.'unique/'; - mkdir $Gviz_genome; mkdir $Gviz_genome_uni; mkdir $Gviz_genome_rand; - - sam_to_bam_bg ( $type_sam_genome, $scale, $grand_child ); - sam_to_bam_bg ( $type_sam_uni_genome, $scale, $grand_child ); - - bg_to_png ( $fai_file, $type_dir.$type_prefix.'genome_unique_plus.bedgraph', $type_dir.$type_prefix.'genome_unique_minus.bedgraph', $Gviz_genome_uni, 'Mb' ); - bg_to_png ( $fai_file, $type_dir.$type_prefix.'genome_plus.bedgraph', $type_dir.$type_prefix.'genome_minus.bedgraph', $Gviz_genome_rand, 'Mb' ); - - #HTML Details - my $prefix_details_pages = $dir.$fastq_n[$child].'-'.$types_names[$grand_child]; - details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir, $Pcheck ); - - $pm2->finish(); - } - $pm2->wait_all_children; - - if ( $Pcheck eq 'true' ) - { - my $ppp = $group_dir.'PPPartners/'; mkdir $ppp; - print $report "ping_pong_partners $group_dir/piRNAs/TEs.sam $ppp\n"; - ping_pong_partners ( $group_dir.'TEs.fai', $group_dir.'piRNAs/piRNAs-TEs_sorted.bam', $ppp, $pi_min ); - my $ppp_page = $dir.$fastq_n[$child].'-piRNAs-PPP.html'; - ppp_page ( $group_dir, $ppp_page, \@fastq_n, $fastq_n[$child], $ppp, $dir ); - } - - #HTML Main Webpage - my $index_page = $dir.$fastq_n[$child].'.html'; - main_page ( $gen_dir, $index_page, \@fastq_n, $fastq_n[$child], $ma, $ma_uni, $dir ); - copy ($index_page, $html_out) if $child == 0; - #HTML Menu - my $menu_page = $dir.$fastq_n[$child].'-sub.html'; - menu_page ( $group_dir, $menu_page, \@fastq_n, $fastq_n[$child], $min, $max, $si_min, $si_max, $pi_min, $pi_max, $dir ); - unlink glob "'$group_dir'*.sam"; unlink glob "'$group_dir'*.fastq"; - $pm->finish(); # pass an exit code to finish - } - $pm->wait_all_children; - unlink glob "'$dir'"."dataset_*symlink.fa*"; - print $report "Job done!\n"; - close $report; -} else { - print "sRNAPipe version $sRNAPipe::VERSION - -Usage: - -sRNAPipe.pl --fastq <fastq file 1> --fastq_n <name 1> [--fastq <fastq file 2> --fastq_n <name 2> --fastq <fastq file 3> -- fastq_n <name 3> ...] --ref <reference genome> [--build_index] --transcripts <transcripts> [--build_transcripts] --TE <transposable elements> [--build_TE] --miRNAs <miRNAs> [--build_miRNAs] --snRNAs <snRNAs> [--build_snRNAs] --rRNAs <rRNAs> [--build_rRNAs] --tRNAs <tRNAs> [--buid_tRNAs] [options] - -Arguments: ---fastq <fastq file>\t\tFastq file to process ---fastq_n <name>\t\tName of the content to process ---ref <reference>\t\tFasta file containing the reference genome ---transcripts <transcripts>\tFasta file containing the transcripts ---TE <TE>\t\t\tFasta file containing the transposable elements ---miRNAs <miRNAs>\t\tFasta file containing the miRNAs ---snRNAs <snRNAs>\t\tFasta file containing the snRNAs ---rRNAs <rRNAs>\t\t\tFasta file containing the rRNAs ---tRNAs <tRNAS>\t\t\tFasta file containing the tRNAs - -For any fasta file, if a bwa index is not provided, you should build it through the corresponding '--build_[element]' argument - -Options: ---min <INT>\t\t\tMinimum read size (default: 18) ---max <INT>\t\t\tMaximum read size (default: 29) ---si_min <INT>\t\t\tLower bound of siRNA range (default: 21) ---si_max <INT>\t\t\tHigher bound of siRNA range (default: 21) ---pi_min <INT>\t\t\tLower bound of piRNA range (default: 23) ---pi_max <INT>\t\t\tHigher bound of piRNA range (default: 29) ---mis <INT>\t\t\tMaximal genome mismatches (default: 0) ---misTE <INT>\t\t\tMaximal TE mismatches (default: 3) ---PPPon <true|false>\t\tPing-pong partners (default: true) -"; -}
--- a/lib/sRNAPipe.pm Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -package sRNAPipe; - -our $VERSION = '1.1'; - -1;
--- a/lib/sRNAPipe/Rcall.pm Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,136 +0,0 @@ -package sRNAPipe::Rcall; - -use strict; -use warnings; -use Statistics::R; - -use Exporter; -our @ISA = qw(Exporter); -our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png ); - -sub histogram -{ - my ($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()` - ); - $R->stopR(); -} - -1;
--- a/lib/sRNAPipe/align.pm Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,551 +0,0 @@ -package sRNAPipe::align; - -use strict; -use warnings; -use File::Basename; -use String::Random; - -use FindBin; -use lib "$FindBin::Bin/../lib"; -use sRNAPipe::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;
--- a/lib/sRNAPipe/css/bootstrap-responsive.css Wed Jan 30 06:26:32 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; -} - -.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; -} - -@-ms-viewport { - width: device-width; -} - -.hidden { - display: none; - visibility: hidden; -} - -.visible-phone { - display: none !important; 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- } - 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; - } -}
--- a/lib/sRNAPipe/css/bootstrap-table.css Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,313 +0,0 @@ -/** - * @author zhixin wen <wenzhixin2010@gmail.com> - * 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; -}
--- a/lib/sRNAPipe/css/bootstrap.css Wed Jan 30 06:26:32 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; 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-} - -.icon-trash { - background-position: -456px 0; -} - -.icon-home { - background-position: 0 -24px; -} - -.icon-file { - background-position: -24px -24px; -} - -.icon-time { - background-position: -48px -24px; -} - -.icon-road { - background-position: -72px -24px; -} - -.icon-download-alt { - background-position: -96px -24px; -} - -.icon-download { - background-position: -120px -24px; -} - -.icon-upload { - background-position: -144px -24px; -} - -.icon-inbox { - background-position: -168px -24px; -} - -.icon-play-circle { - background-position: -192px -24px; -} - -.icon-repeat { - background-position: -216px -24px; -} - -.icon-refresh { - background-position: -240px -24px; -} - -.icon-list-alt { - background-position: -264px -24px; -} - -.icon-lock { - background-position: -287px -24px; -} - -.icon-flag { - background-position: -312px -24px; -} - -.icon-headphones { - background-position: -336px -24px; -} - -.icon-volume-off { - background-position: -360px -24px; -} - -.icon-volume-down { - background-position: -384px -24px; 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- -moz-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); - box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); - -webkit-background-clip: padding-box; - -moz-background-clip: padding; - background-clip: padding-box; -} - -.dropdown-menu.pull-right { - right: 0; - left: auto; -} - -.dropdown-menu .divider { - *width: 100%; - height: 1px; - margin: 9px 1px; - *margin: -5px 0 5px; - overflow: hidden; - background-color: #e5e5e5; - border-bottom: 1px solid #ffffff; -} - -.dropdown-menu > li > a { - display: block; - padding: 3px 20px; - clear: both; - font-weight: normal; - line-height: 20px; - color: #333333; - white-space: nowrap; -} - -.dropdown-menu > li > a:hover, -.dropdown-menu > li > a:focus, -.dropdown-submenu:hover > a, -.dropdown-submenu:focus > a { - color: #ffffff; - text-decoration: none; - background-color: #0081c2; - background-image: -moz-linear-gradient(top, #0088cc, #0077b3); - background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0077b3)); - background-image: -webkit-linear-gradient(top, #0088cc, #0077b3); - background-image: -o-linear-gradient(top, #0088cc, #0077b3); - background-image: linear-gradient(to bottom, #0088cc, #0077b3); - background-repeat: repeat-x; - filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff0088cc', endColorstr='#ff0077b3', GradientType=0); -} - -.dropdown-menu > .active > a, -.dropdown-menu > .active > a:hover, -.dropdown-menu > .active > a:focus { - color: #ffffff; - text-decoration: none; - background-color: #0081c2; - background-image: -moz-linear-gradient(top, #0088cc, #0077b3); - background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0077b3)); - background-image: -webkit-linear-gradient(top, #0088cc, #0077b3); - background-image: -o-linear-gradient(top, #0088cc, #0077b3); - background-image: linear-gradient(to bottom, #0088cc, #0077b3); - background-repeat: repeat-x; - outline: 0; - filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff0088cc', endColorstr='#ff0077b3', GradientType=0); -} - -.dropdown-menu > .disabled > a, -.dropdown-menu > .disabled > a:hover, -.dropdown-menu > .disabled > a:focus { - color: #999999; -} - -.dropdown-menu > .disabled > a:hover, -.dropdown-menu > .disabled > a:focus { - text-decoration: none; - cursor: default; - background-color: transparent; - background-image: none; - filter: progid:DXImageTransform.Microsoft.gradient(enabled=false); -} - -.open { - *z-index: 1000; -} - -.open > .dropdown-menu { - display: block; -} - -.dropdown-backdrop { - position: fixed; - top: 0; - right: 0; - bottom: 0; - left: 0; - z-index: 990; -} - -.pull-right > .dropdown-menu { - right: 0; - left: auto; -} - -.dropup .caret, -.navbar-fixed-bottom .dropdown .caret { - border-top: 0; - border-bottom: 4px solid #000000; - content: ""; -} - -.dropup .dropdown-menu, -.navbar-fixed-bottom .dropdown .dropdown-menu { - top: auto; - bottom: 100%; - margin-bottom: 1px; -} - -.dropdown-submenu { - position: relative; -} - -.dropdown-submenu > .dropdown-menu { - top: 0; - left: 100%; - margin-top: -6px; - margin-left: -1px; - -webkit-border-radius: 0 6px 6px 6px; - -moz-border-radius: 0 6px 6px 6px; - border-radius: 0 6px 6px 6px; -} - -.dropdown-submenu:hover > .dropdown-menu { - display: block; -} - -.dropup .dropdown-submenu > .dropdown-menu { - top: auto; - bottom: 0; - margin-top: 0; - margin-bottom: -2px; - -webkit-border-radius: 5px 5px 5px 0; - -moz-border-radius: 5px 5px 5px 0; - border-radius: 5px 5px 5px 0; -} - -.dropdown-submenu > a:after { - display: block; - float: right; - width: 0; - height: 0; - margin-top: 5px; - margin-right: -10px; - border-color: transparent; - border-left-color: #cccccc; - border-style: solid; - border-width: 5px 0 5px 5px; - content: " "; -} - -.dropdown-submenu:hover > a:after { - border-left-color: #ffffff; -} - -.dropdown-submenu.pull-left { - float: none; -} - -.dropdown-submenu.pull-left > .dropdown-menu { - left: -100%; - margin-left: 10px; - -webkit-border-radius: 6px 0 6px 6px; - -moz-border-radius: 6px 0 6px 6px; - border-radius: 6px 0 6px 6px; -} - -.dropdown .dropdown-menu .nav-header { - padding-right: 20px; - padding-left: 20px; 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-} - -.fade.in { - opacity: 1; -} - -.collapse { - position: relative; - height: 0; - overflow: hidden; - -webkit-transition: height 0.35s ease; - -moz-transition: height 0.35s ease; - -o-transition: height 0.35s ease; - transition: height 0.35s ease; -} - -.collapse.in { - height: auto; -} - -.close { - float: right; - font-size: 20px; - font-weight: bold; - line-height: 20px; - color: #000000; - text-shadow: 0 1px 0 #ffffff; - opacity: 0.2; - filter: alpha(opacity=20); -} - -.close:hover, -.close:focus { - color: #000000; - text-decoration: none; - cursor: pointer; - opacity: 0.4; - filter: alpha(opacity=40); -} - -button.close { - padding: 0; - cursor: pointer; - background: transparent; - border: 0; - -webkit-appearance: none; -} - -.btn { - display: inline-block; - *display: inline; - padding: 4px 12px; - margin-bottom: 0; - *margin-left: .3em; - font-size: 14px; - line-height: 20px; - color: #333333; - text-align: center; - text-shadow: 0 1px 1px rgba(255, 255, 255, 0.75); - vertical-align: middle; - cursor: pointer; - background-color: #f5f5f5; - *background-color: #e6e6e6; - background-image: -moz-linear-gradient(top, #ffffff, #e6e6e6); - background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6)); - background-image: -webkit-linear-gradient(top, #ffffff, #e6e6e6); - background-image: -o-linear-gradient(top, #ffffff, #e6e6e6); - background-image: linear-gradient(to bottom, #ffffff, #e6e6e6); - background-repeat: repeat-x; - border: 1px solid #cccccc; - *border: 0; - border-color: #e6e6e6 #e6e6e6 #bfbfbf; - border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); - border-bottom-color: #b3b3b3; - -webkit-border-radius: 4px; - -moz-border-radius: 4px; - border-radius: 4px; - filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0); - filter: progid:DXImageTransform.Microsoft.gradient(enabled=false); - *zoom: 1; - -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); 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-} - -.btn-inverse { - color: #ffffff; - text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); - background-color: #363636; - *background-color: #222222; - background-image: -moz-linear-gradient(top, #444444, #222222); - background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#444444), to(#222222)); - background-image: -webkit-linear-gradient(top, #444444, #222222); - background-image: -o-linear-gradient(top, #444444, #222222); - background-image: linear-gradient(to bottom, #444444, #222222); - background-repeat: repeat-x; - border-color: #222222 #222222 #000000; - border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); - filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff444444', endColorstr='#ff222222', GradientType=0); - filter: progid:DXImageTransform.Microsoft.gradient(enabled=false); -} - -.btn-inverse:hover, -.btn-inverse:focus, -.btn-inverse:active, -.btn-inverse.active, -.btn-inverse.disabled, -.btn-inverse[disabled] { - color: #ffffff; - background-color: #222222; - *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; -} - -.btn-group > .btn-large { - font-size: 17.5px; -} - -.btn-group > .btn:first-child { - margin-left: 0; - -webkit-border-bottom-left-radius: 4px; - border-bottom-left-radius: 4px; - -webkit-border-top-left-radius: 4px; - border-top-left-radius: 4px; - -moz-border-radius-bottomleft: 4px; - -moz-border-radius-topleft: 4px; -} - -.btn-group > .btn:last-child, -.btn-group > .dropdown-toggle { - -webkit-border-top-right-radius: 4px; - border-top-right-radius: 4px; - -webkit-border-bottom-right-radius: 4px; - border-bottom-right-radius: 4px; - -moz-border-radius-topright: 4px; - -moz-border-radius-bottomright: 4px; -} - -.btn-group > .btn.large:first-child { - margin-left: 0; - -webkit-border-bottom-left-radius: 6px; - border-bottom-left-radius: 6px; - -webkit-border-top-left-radius: 6px; - border-top-left-radius: 6px; - -moz-border-radius-bottomleft: 6px; - -moz-border-radius-topleft: 6px; -} - -.btn-group > .btn.large:last-child, -.btn-group > .large.dropdown-toggle { - -webkit-border-top-right-radius: 6px; 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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; - -webkit-border-bottom-left-radius: 4px; - border-bottom-left-radius: 4px; - -moz-border-radius-bottomright: 4px; - -moz-border-radius-bottomleft: 4px; -} - -.nav-tabs.nav-stacked > li > a:hover, -.nav-tabs.nav-stacked > li > a:focus { - z-index: 2; - border-color: #ddd; -} - -.nav-pills.nav-stacked > li > a { - margin-bottom: 3px; -} - -.nav-pills.nav-stacked > li:last-child > a { - margin-bottom: 1px; -} - -.nav-tabs .dropdown-menu { - -webkit-border-radius: 0 0 6px 6px; - -moz-border-radius: 0 0 6px 6px; - border-radius: 0 0 6px 6px; -} - -.nav-pills .dropdown-menu { - -webkit-border-radius: 6px; - -moz-border-radius: 6px; - border-radius: 6px; -} - -.nav .dropdown-toggle .caret { - margin-top: 6px; - border-top-color: #0088cc; - border-bottom-color: #0088cc; -} - -.nav .dropdown-toggle:hover .caret, -.nav .dropdown-toggle:focus .caret { - border-top-color: #005580; - border-bottom-color: #005580; -} - -/* move down carets for tabs */ - -.nav-tabs .dropdown-toggle .caret { - margin-top: 8px; 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- 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; -}
--- a/lib/sRNAPipe/html.pm Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,926 +0,0 @@ -package sRNAPipe::html; - -use strict; -use warnings; -use File::Basename; -use File::Copy::Recursive qw( dircopy ); - -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page ©_css ©_js ); - -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 $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details »</a></p></div>\n"; - futurette( $h, $current, $pngTabP, $futHashP ); - print $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\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 $h " <div class=\"container\"> <div class=\"row text-center\"> <img src=\"$html_ref/pie_chart.png\"/><br />\n"; - print $h " <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>"; - 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 " <div class=\"container\">"; - print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n"; - print $h "</div>"; - } - fut($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 '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n"; - print $h '<thead> - <tr> - <th data-sortable="true">ID</th> - <th data-sortable="true">overlap sum</th> - <th data-sortable="true">ten overlap sum</th> - <th data-sortable="true">mean</th> - <th data-sortable="true">standard deviation</th> - <th data-sortable="true">z-score</th> - <th data-sortable="true">p-value</th> - </tr> - </thead> - <tbody>'; - - open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n"; - while ( <$f> ) - { - chomp; - print $h '<tr>'; - 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 $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>"; - - open my $sub, '>', $sub_html || die "cannot create $sub_html\n"; - { - header($sub); - print $sub " - <div align=\"center\"> - <h2>$id</h2> - <p> <img class=\"featurette-image\" src=\"$id/histogram.png\"/></p> - <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p> - <p><a href=\"$id/sensPPP.txt\">sense reads with PPP</a></p> - <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p> - <p><a href=\"$id/sens.txt\">sense reads without PPP</a></p> - <p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p> - </div>"; - footer($sub); - } - close $sub; - } - else { print $h "<td> $id </td>\n"; } - print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n"; - - print $h '</tr>'; - } - close $f; - print $h "</tbody></table></div>"; - footer($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 " -<div class=\"container text-center\"> - <div class=\"row-fluid\"> - <div class=\"span6\"> - <h2>Bonafide</h2> - reads of size between $min and $max<br>with no mi, sn, t and r RNAs - <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p> - <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p> - <p><a class=\"btn\" href=\"$name-bonafide_reads-transcripts.html\">Transcripts</a></p> - <div class=\"row-fluid\"> - <div class=\"span6\"> - <h2>siRNAs</h2> - bonafide reads of size between $simin and $simax - <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p> - <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p> - <p><a class=\"btn\" href=\"$name-siRNAs-transcripts.html\">Transcripts</a></p> - </div> - <div class=\"span6\"> - <h2>piRNAs</h2> - bonafide reads of size between $pimin and $pimax - <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p> - <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p> - <p><a class=\"btn\" href=\"$name-piRNAs-transcripts.html\">Transcripts</a></p> - </div> - </div> - </div> - <div class=\"span6\"> - <h2>miRNAs</h2> - <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p> - <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p> - <p><a class=\"btn\" href=\"$name-miRNAs-transcripts.html\">Transcripts</a></p> - </div> - </div> -</div> -"; -} - -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 " - <!DOCTYPE html> - <html lang=\"en\"> - <head> - <meta charset=\"utf-8\"> - <title>pipeline</title> - <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\"> - <meta name=\"description\" content=\"\"> - <meta name=\"author\" content=\"\"> - <!-- Le styles --> - <link href=\"css/bootstrap.css\" rel=\"stylesheet\"> - <link href=\"css/bootstrap-table.css\" rel=\"stylesheet\"> - <style type=\"text/css\"> - body { - padding-top: 60px; - padding-bottom: 40px; - } - div#page { - width: 940px; - background-color: #fff; - margin: 0 auto; - text-align: left; - border-color: #fff; - border-style: none solid solid; - border-width: medium 1px 1px; - } - - div.content { - display: none; - float: right; - width: 550px; - } - div.content a, div.navigation a { - text-decoration: none; - color: #777; - } - div.content a:focus, div.content a:hover, div.content a:active { - text-decoration: underline; - } - - div.controls { - margin-top: 5px; - height: 23px; - } - - div.controls a { - padding: 5px; - } - div.ss-controls { - float: left; - } - div.nav-controls { - float: right; - } - div.slideshow-container { - position: relative; - clear: both; - height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */ - } - div.loader { - position: absolute; - top: 0; - left: 0; - background-image: url('loader.gif'); - background-repeat: no-repeat; - background-position: center; - width: 550px; - height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */ - } - div.slideshow { - - } - - div.slideshow span.image-wrapper { - display: block; - position: absolute; - top: 0; - left: 0; - } - div.slideshow a.advance-link { - display: block; - width: 550px; - height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */ - line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */ - text-align: center; - } - div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited { - text-decoration: none; - } - div.slideshow img { - vertical-align: middle; - border: 1px solid #ccc; - } - - div.image-title { - font-weight: bold; - font-size: 1.4em; - } - - div.image-desc { - line-height: 1.3em; - padding-top: 12px; - } - div.navigation { - - } - ul.thumbs { - clear: both; - margin: 0; - padding: 0; - } - ul.thumbs li { - float: none; - padding: 0; - margin: 0; - list-style: none; - } - a.thumb { - padding: 0; - display: inline; - border: none; - } - ul.thumbs li.selected a.thumb { - color: #000; - font-weight: bold; - } - a.thumb:focus { - outline: none; - } - ul.thumbs img { - border: none; - display: block; - } - div.pagination { - clear: both; - } - div.navigation div.top { - margin-bottom: 12px; - height: 11px; - } - div.navigation div.bottom { - margin-top: 12px; - } - div.pagination a, div.pagination span.current, div.pagination span.ellipsis { - display: block; - float: left; - margin-right: 2px; - padding: 4px 7px 2px 7px; - border: 1px solid #ccc; - } - div.pagination a:hover { - background-color: #eee; - text-decoration: none; - } - div.pagination span.current { - font-weight: bold; - background-color: #000; - border-color: #000; - color: #fff; - } - div.pagination span.ellipsis { - border: none; - padding: 5px 0 3px 2px; - } - - div.download { - float: right; - } - - div.caption-container { - position: relative; - clear: left; - height: 75px; - } - span.image-caption { - display: block; - position: absolute; - width: 550px; - top: 0; - left: 0; - } - div.caption { - padding: 12px; - } - - /* Featurettes - ------------------------- */ - - .featurette { - padding-top: 20px; /* Vertically center images part 1: add padding above and below text. */ - overflow: hidden; /* Vertically center images part 2: clear their floats. */ - text-align: center; - } - - .featurette-p - { - text-align: left; - } - - .featurette-image { - margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */ - width: 450px; - height: auto; - } - - </style> - <link href=\"css/bootstrap-responsive.css\" rel=\"stylesheet\"> - </head> - <body> - "; -} - -sub navbar -{ - my ( $file, $fastq, $actif ) = @_; - - print $file " - <div class=\"navbar navbar-inverse navbar-fixed-top\"> - <div class=\"navbar-inner\"> - <div class=\"container\"> - <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\"> - <span class=\"icon-bar\"></span> - <span class=\"icon-bar\"></span> - <span class=\"icon-bar\"></span> - </button> - <a class=\"brand\" href=\"report.txt\">Report</a> - <div class=\"nav-collapse collapse\"> - <ul class=\"nav\"> - "; - for (my $i = 0 ; $i <= $#{$fastq}; $i++) - { - # my $fa = basename($fastq->[$i],'.dat'); - my $fa = $fastq->[$i]; - if ($actif eq $fa){ print $file "<li class=\"active\"><a href=\"$fastq->[$i].html\">$fa</a></li>";} - else {print $file "<li><a href=\"$fastq->[$i].html\">$fa</a></li>" ;} - } - print $file " - </ul> - </div><!--/.nav-collapse --> - </div> - </div> - </div>"; -} - -sub footer -{ - my $file = shift; - print $file " - <!-- FOOTER --> - <div class=\"container\"> - <footer> - - </footer> - </div> - <!-- Le javascript - ================================================== --> - <!-- Placed at the end of the document so the pages load faster --> - <script type=\"text/javascript\" src=\"js/filter.js\"></script> - <script type=\"text/javascript\" src=\"js/jquery.js\"></script> - <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script> - <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script> - <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script> - <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script> - <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script> - <script type=\"text/javascript\"> - jQuery(document).ready(function(\$) { - // We only want these styles applied when javascript is enabled - \$('div.navigation').css({'width' : '300px', 'float' : 'left'}); - \$('div.content').css('display', 'block'); - - \$(\".each-gallery\").each(function(i){ - // Initially set opacity on thumbs and add - // additional styling for hover effect on thumbs - var onMouseOutOpacity = 0.67; - \$('#thumbs + i + ul.thumbs li').opacityrollover({ - mouseOutOpacity: onMouseOutOpacity, - mouseOverOpacity: 1.0, - fadeSpeed: 'fast', - exemptionSelector: '.selected' - }); - - // Initialize Advanced Galleriffic Gallery - var gallery = \$('#thumbs'+i).galleriffic({ - delay: 2500, - numThumbs: 22, - preloadAhead: 10, - enableTopPager: true, - enableBottomPager: true, - maxPagesToShow: 7, - imageContainerSel: '#slideshow'+ i, - controlsContainerSel: '#controls' + i, - captionContainerSel: '#caption' + i, - loadingContainerSel: '#loading' + i, - renderSSControls: true, - renderNavControls: true, - playLinkText: 'Play', - pauseLinkText: 'Pause', - prevLinkText: '‹ Previous', - nextLinkText: 'Next ›', - nextPageLinkText: 'Next ›', - prevPageLinkText: '‹ Prev', - enableHistory: false, - autoStart: false, - syncTransitions: true, - defaultTransitionDuration: 900, - onSlideChange: function(prevIndex, nextIndex) { - // 'this' refers to the gallery, which is an extension of \$('#thumbs') - this.find('ul.thumbs').children() - .eq(prevIndex).fadeTo('fast', onMouseOutOpacity).end() - .eq(nextIndex).fadeTo('fast', 1.0); - }, - onPageTransitionOut: function(callback) { - this.fadeTo('fast', 0.0, callback); - }, - onPageTransitionIn: function() { - this.fadeTo('fast', 1.0); - } - }); - }); - }); - </script> - </body> - </html> - "; -} - -sub carousel -{ - my ($file, $non_unique, $dir_root) = @_; - my $ac = 0; - print $file " - <div id=\"page\"> - <div id=\"container\"> - <div class=\"each-gallery\"> - <div id=\"gallery\" class=\"content\"> - <div id=\"controls0\" class=\"controls\"></div> - <div class=\"slideshow-container\"> - <div id=\"loading0\" class=\"loader\"></div> - <div id=\"slideshow0\" class=\"slideshow\"></div> - </div> - <div id=\"caption0\" class=\"caption-container\">Reads randomly assigned</div> - </div> - <div id=\"thumbs0\" class=\"navigation\"> - <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> - <ul class=\"thumbs noscript\"> - "; - foreach my $u (@{$non_unique}) - { - my $name = basename($u,'.png'); - $u = $1 if $u =~ /$dir_root(.*)/; - print $file " - <li> - <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a> - </li> - "; - } - print $file " - </ul> - </div> - <div style=\"clear: both;\"></div></div> - </div> - </div> - "; -} - -sub carousel2 -{ - my ($file, $unique, $non_unique, $dir_root) = @_; - print $file " - <div id=\"page\"> - <div id=\"container\"> - <div class=\"each-gallery\"> - <div id=\"gallery\" class=\"content\"> - <div id=\"controls0\" class=\"controls\"></div> - <div class=\"slideshow-container\"> - <div id=\"loading0\" class=\"loader\"></div> - <div id=\"slideshow0\" class=\"slideshow\"></div> - </div> - <div id=\"caption0\" class=\"caption-container\">Uniquely mapped reads</div> - </div> - <div id=\"thumbs0\" class=\"navigation\"> - <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> - <ul class=\"thumbs noscript\"> - "; - - foreach my $u (@{$unique}) - { - my $name = basename($u,'.png'); - $u = $1 if $u =~ /$dir_root(.*)/; - print $file " - <li> - <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a> - </li> - "; - } - print $file " - </ul> - </div> - </div> - <div id=\"page\"> - <div id=\"container\"> - <div class=\"each-gallery\"> - <div id=\"gallery\" class=\"content\"> - <div id=\"controls1\" class=\"controls\"></div> - <div class=\"slideshow-container\"> - <div id=\"loading1\" class=\"loader\"></div> - <div id=\"slideshow1\" class=\"slideshow\"></div> - </div> - <div id=\"caption1\" class=\"caption-container\">Reads randomly assigned</div> - </div> - <div id=\"thumbs1\" class=\"navigation\"> - <input type=\"text\" id=\"myInput1\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> - <ul class=\"thumbs noscript\"> - "; - - foreach my $nu (@{$non_unique}) - { - my $name = basename($nu,'.png'); - $nu = $1 if $nu =~ /$dir_root(.*)/; - print $file " - <li> - <a class=\"thumb\" href=\"$nu\" title=\"$name\">$name</a> - </li> - "; - } - print $file " - </ul> - </div> - <div style=\"clear: both;\"></div></div> - </div> - </div> - "; -} - -sub futurette -{ - my ($file, $name, $png, $hash) = @_; - print $file " - <div class=\"container\"> - <div class=\"featurette\"> - <h1>$name</h1> - <p class=\"featurette-p\"> - "; - foreach my $k (sort keys %{$hash}) - { - print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ; - } - - print $file " - </p>"; - - foreach my $pn (@{$png}){print $file "<img class=\"featurette-image\" src=\"$pn\"/><br />";} - - print $file " - </div> - </div> - "; -} - -sub fut -{ - my ($file, $name, $hash) = @_; - print $file " - <div class=\"container\"> - <div class=\"featurette\"> - <h1>$name</h1> - <p class=\"featurette-p\"> - "; - - foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash}) - { - print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ; - } - - print $file " - </p> - </div> - </div> - "; -} - -sub get_distri_exon -{ - my ($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 "<div class=\"container\">\n"; - print $h "<div class=\"row text-center\">"; - while ( my ($k,$v) = each %{$hash} ) - { - print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0; - print $h " - - <div class=\"span6\"> - <h2>$k</h2> - <p class=\"featurette-p\"> <img src=\"$v->[5]\"/></p> - <p class=\"featurette-p\"><a href=\"$v->[4]\">ping pong signature</a></p> - <p class=\"featurette-p\"><a href=\"$v->[2]\">sense reads with PPP</a></p> - <p class=\"featurette-p\"><a href=\"$v->[3]\">reverse reads with PPP</a></p> - <p class=\"featurette-p\"><a href=\"$v->[0]\">sense reads without PPP</a></p> - <p class=\"featurette-p\"><a href=\"$v->[1]\">reverse reads without PPP</a></p> - </div> - "; - $cmp++; - } - - print $h "</div></div>"; -} - -sub printDistri -{ - my ($h, $tab) = @_; - my ($txt, $name); - my $cmp = 0; - print $h "<div class=\"container\">\n"; - print $h "<div class=\"row text-center\">"; - foreach my $k (@{$tab}) - { - if ($k =~ /(.*)-(.*)\.png$/) - { - $txt = $1.'-'.$2.'.txt'; - $name = $2; - } - print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0; - print $h " - - <div class=\"span6\"> - <h2>$name</h2> - <p> <img src=\"$k\"/></p> - <p class=\"featurette-p\"><a href=\"$txt\">text file</a></p> - </div> - "; - $cmp++; - } - - print $h "</div></div>"; -} - -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; -} - -sub copy_css -{ - my $dir = shift; - my $path = dirname(__FILE__); - dircopy( $path.'/css', $dir.'/css' ); -} - - -sub copy_js -{ - my $dir = shift; - my $path = dirname(__FILE__); - dircopy( $path.'/js', $dir.'/js' ); -} - -1;
--- a/lib/sRNAPipe/js/bootstrap-table.js Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3094 +0,0 @@ -/** - * @author zhixin wen <wenzhixin2010@gmail.com> - * version: 1.11.1 - * https://github.com/wenzhixin/bootstrap-table/ - */ - -(function ($) { - '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 = $('<p/>').addClass('fixed-table-scroll-inner'), - outer = $('<div/>').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, ''') - .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 = $([ - '<div class="bootstrap-table">', - '<div class="fixed-table-toolbar"></div>', - this.options.paginationVAlign === 'top' || this.options.paginationVAlign === 'both' ? - '<div class="fixed-table-pagination" style="clear: both;"></div>' : - '', - '<div class="fixed-table-container">', - '<div class="fixed-table-header"><table></table></div>', - '<div class="fixed-table-body">', - '<div class="fixed-table-loading">', - this.options.formatLoadingMessage(), - '</div>', - '</div>', - '<div class="fixed-table-footer"><table><tr></tr></table></div>', - this.options.paginationVAlign === 'bottom' || this.options.paginationVAlign === 'both' ? - '<div class="fixed-table-pagination"></div>' : - '', - '</div>', - '</div>' - ].join('')); - - this.$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('<div class="clearfix"></div>'); - - 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 = $('<thead></thead>').appendTo(this.$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('<tr>'); - - if (i === 0 && !that.options.cardView && that.options.detailView) { - html.push(sprintf('<th class="detail" rowspan="%s"><div class="fht-cell"></div></th>', - 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('<th' + sprintf(' title="%s"', column.titleTooltip), - column.checkbox || column.radio ? - sprintf(' class="bs-checkbox %s"', column['class'] || '') : - class_, - sprintf(' style="%s"', halign + style), - sprintf(' rowspan="%s"', column.rowspan), - sprintf(' colspan="%s"', column.colspan), - sprintf(' data-field="%s"', column.field), - '>'); - - html.push(sprintf('<div class="th-inner %s">', 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 = '<input name="btSelectAll" type="checkbox" />'; - } - that.header.stateField = column.field; - } - if (column.radio) { - text = ''; - that.header.stateField = column.field; - that.options.singleSelect = true; - } - - html.push(text); - html.push('</div>'); - html.push('<div class="fht-cell"></div>'); - html.push('</div>'); - html.push('</th>'); - }); - html.push('</tr>'); - }); - - 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') { - $(sprintf('<div class="bs-bars pull-%s"></div>', this.options.toolbarAlign)) - .appendTo(this.$toolbar) - .append($(this.options.toolbar)); - } - - // showColumns, showToggle, showRefresh - html = [sprintf('<div class="columns columns-%s btn-group pull-%s">', - 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('<button class="btn' + - sprintf(' btn-%s', this.options.buttonsClass) + - sprintf(' btn-%s', this.options.iconSize) + - '" type="button" name="paginationSwitch" aria-label="pagination Switch" title="%s">', - this.options.formatPaginationSwitch()), - sprintf('<i class="%s %s"></i>', this.options.iconsPrefix, this.options.icons.paginationSwitchDown), - '</button>'); - } - - if (this.options.showRefresh) { - html.push(sprintf('<button class="btn' + - sprintf(' btn-%s', this.options.buttonsClass) + - sprintf(' btn-%s', this.options.iconSize) + - '" type="button" name="refresh" aria-label="refresh" title="%s">', - this.options.formatRefresh()), - sprintf('<i class="%s %s"></i>', this.options.iconsPrefix, this.options.icons.refresh), - '</button>'); - } - - if (this.options.showToggle) { - html.push(sprintf('<button class="btn' + - sprintf(' btn-%s', this.options.buttonsClass) + - sprintf(' btn-%s', this.options.iconSize) + - '" type="button" name="toggle" aria-label="toggle" title="%s">', - this.options.formatToggle()), - sprintf('<i class="%s %s"></i>', this.options.iconsPrefix, this.options.icons.toggle), - '</button>'); - } - - if (this.options.showColumns) { - html.push(sprintf('<div class="keep-open btn-group" title="%s">', - this.options.formatColumns()), - '<button type="button" aria-label="columns" class="btn' + - sprintf(' btn-%s', this.options.buttonsClass) + - sprintf(' btn-%s', this.options.iconSize) + - ' dropdown-toggle" data-toggle="dropdown">', - sprintf('<i class="%s %s"></i>', this.options.iconsPrefix, this.options.icons.columns), - ' <span class="caret"></span>', - '</button>', - '<ul class="dropdown-menu" role="menu">'); - - $.each(this.columns, function (i, column) { - if (column.radio || column.checkbox) { - return; - } - - if (that.options.cardView && !column.cardVisible) { - return; - } - - var checked = column.visible ? ' checked="checked"' : ''; - - if (column.switchable) { - html.push(sprintf('<li role="menuitem">' + - '<label><input type="checkbox" data-field="%s" value="%s"%s> %s</label>' + - '</li>', column.field, i, checked, column.title)); - switchableCount++; - } - }); - html.push('</ul>', - '</div>'); - } - - html.push('</div>'); - - // Fix #188: this.showToolbar is for extensions - if (this.showToolbar || html.length > 2) { - this.$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'), $this.prop('checked')); - }); - } - - if (this.options.search) { - html = []; - html.push( - '<div class="pull-' + this.options.searchAlign + ' search">', - sprintf('<input class="form-control' + - sprintf(' input-%s', this.options.iconSize) + - '" type="text" placeholder="%s">', - this.options.formatSearch()), - '</div>'); - - this.$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( - '<div class="pull-' + this.options.paginationDetailHAlign + ' pagination-detail">', - '<span class="pagination-info">', - this.options.onlyInfoPagination ? this.options.formatDetailPagination(this.options.totalRows) : - this.options.formatShowingRows(this.pageFrom, this.pageTo, this.options.totalRows), - '</span>'); - - if (!this.options.onlyInfoPagination) { - html.push('<span class="page-list">'); - - var pageNumber = [ - sprintf('<span class="btn-group %s">', - this.options.paginationVAlign === 'top' || this.options.paginationVAlign === 'both' ? - 'dropdown' : 'dropup'), - '<button type="button" class="btn' + - sprintf(' btn-%s', this.options.buttonsClass) + - sprintf(' btn-%s', this.options.iconSize) + - ' dropdown-toggle" data-toggle="dropdown">', - '<span class="page-size">', - $allSelected ? this.options.formatAllRows() : this.options.pageSize, - '</span>', - ' <span class="caret"></span>', - '</button>', - '<ul class="dropdown-menu" role="menu">' - ]; - - if (typeof this.options.pageList === 'string') { - var list = this.options.pageList.replace('[', '').replace(']', '') - .replace(/ /g, '').split(','); - - pageList = []; - $.each(list, function (i, value) { - pageList.push(value.toUpperCase() === that.options.formatAllRows().toUpperCase() ? - that.options.formatAllRows() : +value); - }); - } - - $.each(pageList, function (i, page) { - if (!that.options.smartDisplay || i === 0 || pageList[i - 1] < that.options.totalRows) { - var active; - if ($allSelected) { - active = page === that.options.formatAllRows() ? ' class="active"' : ''; - } else { - active = page === that.options.pageSize ? ' class="active"' : ''; - } - pageNumber.push(sprintf('<li role="menuitem"%s><a href="#">%s</a></li>', active, page)); - } - }); - pageNumber.push('</ul></span>'); - - html.push(this.options.formatRecordsPerPage(pageNumber.join(''))); - html.push('</span>'); - - html.push('</div>', - '<div class="pull-' + this.options.paginationHAlign + ' pagination">', - '<ul class="pagination' + sprintf(' pagination-%s', this.options.iconSize) + '">', - '<li class="page-pre"><a href="#">' + this.options.paginationPreText + '</a></li>'); - - if (this.totalPages < 5) { - from = 1; - to = this.totalPages; - } else { - from = this.options.pageNumber - 2; - to = from + 4; - if (from < 1) { - from = 1; - to = 5; - } - if (to > this.totalPages) { - to = this.totalPages; - from = to - 4; - } - } - - if (this.totalPages >= 6) { - if (this.options.pageNumber >= 3) { - html.push('<li class="page-first' + (1 === this.options.pageNumber ? ' active' : '') + '">', - '<a href="#">', 1, '</a>', - '</li>'); - - from++; - } - - if (this.options.pageNumber >= 4) { - if (this.options.pageNumber == 4 || this.totalPages == 6 || this.totalPages == 7) { - from--; - } else { - html.push('<li class="page-first-separator disabled">', - '<a href="#">...</a>', - '</li>'); - } - - to--; - } - } - - if (this.totalPages >= 7) { - if (this.options.pageNumber >= (this.totalPages - 2)) { - from--; - } - } - - if (this.totalPages == 6) { - if (this.options.pageNumber >= (this.totalPages - 2)) { - to++; - } - } else if (this.totalPages >= 7) { - if (this.totalPages == 7 || this.options.pageNumber >= (this.totalPages - 3)) { - to++; - } - } - - for (i = from; i <= to; i++) { - html.push('<li class="page-number' + (i === this.options.pageNumber ? ' active' : '') + '">', - '<a href="#">', i, '</a>', - '</li>'); - } - - if (this.totalPages >= 8) { - if (this.options.pageNumber <= (this.totalPages - 4)) { - html.push('<li class="page-last-separator disabled">', - '<a href="#">...</a>', - '</li>'); - } - } - - if (this.totalPages >= 6) { - if (this.options.pageNumber <= (this.totalPages - 3)) { - html.push('<li class="page-last' + (this.totalPages === this.options.pageNumber ? ' active' : '') + '">', - '<a href="#">', this.totalPages, '</a>', - '</li>'); - } - } - - html.push( - '<li class="page-next"><a href="#">' + this.options.paginationNextText + '</a></li>', - '</ul>', - '</div>'); - } - 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('<tr', - sprintf(' %s', htmlAttributes.join(' ')), - sprintf(' id="%s"', $.isArray(item) ? undefined : item._id), - sprintf(' class="%s"', style.classes || ($.isArray(item) ? undefined : item._class)), - sprintf(' data-index="%s"', i), - sprintf(' data-uniqueid="%s"', item[this.options.uniqueId]), - sprintf('%s', data_), - '>' - ); - - if (this.options.cardView) { - html.push(sprintf('<td colspan="%s"><div class="card-views">', this.header.fields.length)); - } - - if (!this.options.cardView && this.options.detailView) { - html.push('<td>', - '<a class="detail-icon" href="#">', - sprintf('<i class="%s %s"></i>', this.options.iconsPrefix, this.options.icons.detailOpen), - '</a>', - '</td>'); - } - - $.each(this.header.fields, function(j, field) { - var text = '', - value_ = getItemField(item, field, that.options.escape), - value = '', - type = '', - cellStyle = {}, - id_ = '', - class_ = that.header.classes[j], - data_ = '', - rowspan_ = '', - colspan_ = '', - title_ = '', - column = that.columns[j]; - - if (that.fromHtml && typeof value_ === 'undefined') { - return; - } - - if (!column.visible) { - return; - } - - if (that.options.cardView && (!column.cardVisible)) { - return; - } - - if (column.escape) { - value_ = escapeHTML(value_); - } - - style = sprintf('style="%s"', csses.concat(that.header.styles[j]).join('; ')); - - // handle td's id and class - if (item['_' + field + '_id']) { - id_ = sprintf(' id="%s"', item['_' + field + '_id']); - } - if (item['_' + field + '_class']) { - class_ = sprintf(' class="%s"', item['_' + field + '_class']); - } - if (item['_' + field + '_rowspan']) { - rowspan_ = sprintf(' rowspan="%s"', item['_' + field + '_rowspan']); - } - if (item['_' + field + '_colspan']) { - colspan_ = sprintf(' colspan="%s"', item['_' + field + '_colspan']); - } - if (item['_' + field + '_title']) { - title_ = sprintf(' title="%s"', item['_' + field + '_title']); - } - cellStyle = calculateObjectValue(that.header, - that.header.cellStyles[j], [value_, item, i, field], cellStyle); - if (cellStyle.classes) { - class_ = sprintf(' class="%s"', cellStyle.classes); - } - if (cellStyle.css) { - var csses_ = []; - for (var key in cellStyle.css) { - csses_.push(key + ': ' + cellStyle.css[key]); - } - style = sprintf('style="%s"', csses_.concat(that.header.styles[j]).join('; ')); - } - - value = calculateObjectValue(column, - that.header.formatters[j], [value_, item, i], value_); - - if (item['_' + field + '_data'] && !$.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 ? - '<div class="card-view %s">' : '<td class="bs-checkbox %s">', column['class'] || ''), - '<input' + - sprintf(' data-index="%s"', i) + - sprintf(' name="%s"', that.options.selectItemName) + - sprintf(' type="%s"', type) + - sprintf(' value="%s"', item[that.options.idField]) + - sprintf(' checked="%s"', value === true || - (value_ || value && value.checked) ? 'checked' : undefined) + - sprintf(' disabled="%s"', !column.checkboxEnabled || - (value && value.disabled) ? 'disabled' : undefined) + - ' />', - that.header.formatters[j] && typeof value === 'string' ? value : '', - that.options.cardView ? '</div>' : '</td>' - ].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 ? ['<div class="card-view">', - that.options.showHeader ? sprintf('<span class="title" %s>%s</span>', style, - getPropertyFromOther(that.columns, 'field', 'title', field)) : '', - sprintf('<span class="value">%s</span>', value), - '</div>' - ].join('') : [sprintf('<td%s %s %s %s %s %s %s>', - id_, class_, style, data_, rowspan_, colspan_, title_), - value, - '</td>' - ].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 = '<div class="card-view"></div>'; - } - } - - html.push(text); - }); - - if (this.options.cardView) { - html.push('</div></td>'); - } - html.push('</tr>'); - - 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 = $('<tbody></tbody>').appendTo(this.$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 = $(document.createDocumentFragment()); - var hasTr; - - for (var i = this.pageFrom - 1; i < this.pageTo; i++) { - var item = data[i]; - var tr = this.initRow(item, i, data, trFragments); - hasTr = hasTr || !!tr; - if (tr&&tr!==true) { - trFragments.append(tr); - } - } - - // show no records - if (!hasTr) { - trFragments.append('<tr class="no-records-found">' + - sprintf('<td colspan="%s">%s</td>', - this.$header.find('th').length, - this.options.formatNoMatches()) + - '</tr>'); - } - - 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 class="detail-view"><td colspan="%s"></td></tr>', $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('<td><div class="th-inner"> </div><div class="fht-cell"></div></td>'); - } - - $.each(this.columns, function (i, column) { - var key, - falign = '', // footer align style - valign = '', - csses = [], - style = {}, - class_ = sprintf(' class="%s"', column['class']); - - if (!column.visible) { - return; - } - - if (that.options.cardView && (!column.cardVisible)) { - return; - } - - falign = sprintf('text-align: %s; ', column.falign ? column.falign : column.align); - valign = sprintf('vertical-align: %s; ', column.valign); - - style = calculateObjectValue(null, that.options.footerStyle); - - if (style && style.css) { - for (key in style.css) { - csses.push(key + ': ' + style.css[key]); - } - } - - html.push('<td', class_, sprintf(' style="%s"', falign + valign + csses.concat().join('; ')), '>'); - html.push('<div class="th-inner">'); - - html.push(calculateObjectValue(column, column.footerFormatter, [data], ' ') || ' '); - - html.push('</div>'); - html.push('<div class="fht-cell"></div>'); - html.push('</div>'); - html.push('</td>'); - }); - - this.$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 $.grep(this.columns, function (column) { - return !column.visible; - }); - }; - - BootstrapTable.prototype.getVisibleColumns = function () { - return $.grep(this.columns, function (column) { - return column.visible; - }); - }; - - BootstrapTable.prototype.toggleAllColumns = function (visible) { - $.each(this.columns, function (i, column) { - this.columns[i].visible = visible; - }); - - this.initHeader(); - this.initSearch(); - this.initPagination(); - this.initBody(); - if (this.options.showColumns) { - var $items = this.$toolbar.find('.keep-open input').prop('disabled', false); - - if ($items.filter(':checked').length <= this.options.minimumCountColumns) { - $items.filter(':checked').prop('disabled', true); - } - } - }; - - BootstrapTable.prototype.showAllColumns = function () { - this.toggleAllColumns(true); - }; - - BootstrapTable.prototype.hideAllColumns = function () { - this.toggleAllColumns(false); - }; - - BootstrapTable.prototype.filterBy = function (columns) { - this.filterColumns = $.isEmptyObject(columns) ? {} : columns; - this.options.pageNumber = 1; - this.initSearch(); - this.updatePagination(); - }; - - BootstrapTable.prototype.scrollTo = function (value) { - if (typeof value === 'string') { - value = value === 'bottom' ? this.$tableBody[0].scrollHeight : 0; - } - if (typeof value === 'number') { - this.$tableBody.scrollTop(value); - } - if (typeof value === 'undefined') { - return this.$tableBody.scrollTop(); - } - }; - - BootstrapTable.prototype.getScrollPosition = function () { - return this.scrollTo(); - }; - - BootstrapTable.prototype.selectPage = function (page) { - if (page > 0 && page <= this.options.totalPages) { - this.options.pageNumber = page; - this.updatePagination(); - } - }; - - BootstrapTable.prototype.prevPage = function () { - if (this.options.pageNumber > 1) { - this.options.pageNumber--; - this.updatePagination(); - } - }; - - BootstrapTable.prototype.nextPage = function () { - if (this.options.pageNumber < this.options.totalPages) { - this.options.pageNumber++; - this.updatePagination(); - } - }; - - BootstrapTable.prototype.toggleView = function () { - this.options.cardView = !this.options.cardView; - this.initHeader(); - // Fixed remove toolbar when click cardView button. - //that.initToolbar(); - this.initBody(); - this.trigger('toggle', this.options.cardView); - }; - - BootstrapTable.prototype.refreshOptions = function (options) { - //If the objects are equivalent then avoid the call of destroy / init methods - if (compareObjects(this.options, options, true)) { - return; - } - this.options = $.extend(this.options, options); - this.trigger('refresh-options', this.options); - this.destroy(); - this.init(); - }; - - BootstrapTable.prototype.resetSearch = function (text) { - var $search = this.$toolbar.find('.search input'); - $search.val(text || ''); - this.onSearch({currentTarget: $search}); - }; - - BootstrapTable.prototype.expandRow_ = function (expand, index) { - var $tr = this.$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(); - this.initPagination(); - this.initBody(); - }; - - // BOOTSTRAP TABLE PLUGIN DEFINITION - // ======================= - - var allowedMethods = [ - 'getOptions', - 'getSelections', 'getAllSelections', 'getData', - 'load', 'append', 'prepend', 'remove', 'removeAll', - 'insertRow', 'updateRow', 'updateCell', 'updateByUniqueId', 'removeByUniqueId', - 'getRowByUniqueId', 'showRow', 'hideRow', 'getHiddenRows', - 'mergeCells', - 'checkAll', 'uncheckAll', 'checkInvert', - 'check', 'uncheck', - 'checkBy', 'uncheckBy', - 'refresh', - 'resetView', - 'resetWidth', - 'destroy', - 'showLoading', 'hideLoading', - 'showColumn', 'hideColumn', 'getHiddenColumns', 'getVisibleColumns', - 'showAllColumns', 'hideAllColumns', - 'filterBy', - 'scrollTo', - 'getScrollPosition', - 'selectPage', 'prevPage', 'nextPage', - 'togglePagination', - 'toggleView', - 'refreshOptions', - 'resetSearch', - 'expandRow', 'collapseRow', 'expandAllRows', 'collapseAllRows', - 'updateFormatText' - ]; - - $.fn.bootstrapTable = function (option) { - var value, - args = Array.prototype.slice.call(arguments, 1); - - this.each(function () { - var $this = $(this), - data = $this.data('bootstrap.table'), - options = $.extend({}, BootstrapTable.DEFAULTS, $this.data(), - typeof option === 'object' && option); - - if (typeof option === 'string') { - if ($.inArray(option, allowedMethods) < 0) { - throw new Error("Unknown method: " + option); - } - - if (!data) { - return; - } - - value = data[option].apply(data, args); - - if (option === 'destroy') { - $this.removeData('bootstrap.table'); - } - } - - if (!data) { - $this.data('bootstrap.table', (data = new BootstrapTable(this, options))); - } - }); - - return typeof value === 'undefined' ? this : value; - }; - - $.fn.bootstrapTable.Constructor = BootstrapTable; - $.fn.bootstrapTable.defaults = BootstrapTable.DEFAULTS; - $.fn.bootstrapTable.columnDefaults = BootstrapTable.COLUMN_DEFAULTS; - $.fn.bootstrapTable.locales = BootstrapTable.LOCALES; - $.fn.bootstrapTable.methods = allowedMethods; - $.fn.bootstrapTable.utils = { - sprintf: sprintf, - getFieldIndex: getFieldIndex, - compareObjects: compareObjects, - calculateObjectValue: calculateObjectValue, - getItemField: getItemField, - objectKeys: objectKeys, - isIEBrowser: isIEBrowser - }; - - // BOOTSTRAP TABLE INIT - // ======================= - - $(function () { - $('[data-toggle="table"]').bootstrapTable(); - }); -})(jQuery);
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--- a/lib/sRNAPipe/js/filter.js Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -function search(input) { - // Declare variables - var elt, filter, uls, li, a, i; - elt = input.parentElement; - filter = input.value.toUpperCase(); - uls = elt.getElementsByClassName('thumbs'); - - // Loop through all list items, and hide those who don't match the search query - for (j = 0; j < uls.length; j++) { - li = uls[j].getElementsByTagName('li'); - for (i = 0; i < li.length; i++) { - a = li[i].getElementsByTagName("a")[0]; - if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { - li[i].style.display = ""; - } else { - li[i].style.display = "none"; - } - } - } -}
--- a/lib/sRNAPipe/js/jquery.galleriffic.js Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,979 +0,0 @@ -/** - * jQuery Galleriffic plugin - * - * Copyright (c) 2008 Trent Foley (http://trentacular.com) - * Licensed under the MIT License: - * http://www.opensource.org/licenses/mit-license.php - * - * Much thanks to primary contributer Ponticlaro (http://www.ponticlaro.com) - */ -;(function($) { - // Globally keep track of all images by their unique hash. 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.$imageContainer - .append('<span class="image-wrapper current"><a class="advance-link" rel="history" href="#'+this.data[nextIndex].hash+'" title="'+imageData.title+'"> </a></span>') - .find('span.current').css('opacity', '0'); - - newSlide.find('a') - .append(imageData.image) - .click(function(e) { - gallery.clickHandler(e, this); - }); - - var newCaption = 0; - if (this.$captionContainer) { - // Construct new hidden caption for the image - newCaption = this.$captionContainer - .append('<span class="image-caption current"></span>') - .find('span.current').css('opacity', '0') - .append(imageData.caption); - } - - // Hide the loading conatiner - if (this.$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('<div class="top pagination"></div>').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('<div class="bottom pagination"></div>').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('<a rel="history" href="#'+this.data[prevPage].hash+'" title="'+this.prevPageLinkText+'">'+this.prevPageLinkText+'</a>'); - } - - // Create First Page link if needed - if (pageNum > 0) { - this.buildPageLink(pager, 0, numPages); - if (pageNum > 1) - pager.append('<span class="ellipsis">…</span>'); - - 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('<span class="ellipsis">…</span>'); - - this.buildPageLink(pager, lastPageNum, numPages); - } - - // Next Page Link - var nextPage = startIndex + this.numThumbs; - if (nextPage < this.data.length) { - pager.append('<a rel="history" href="#'+this.data[nextPage].hash+'" title="'+this.nextPageLinkText+'">'+this.nextPageLinkText+'</a>'); - } - - 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('<span class="current">'+pageLabel+'</span>'); - else if (pageNum < numPages) { - var imageIndex = pageNum*this.numThumbs; - pager.append('<a rel="history" href="#'+this.data[imageIndex].hash+'" title="'+pageLabel+'">'+pageLabel+'</a>'); - } - - 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('<div class="ss-controls"><a href="#pause" class="pause" title="'+this.pauseLinkText+'">'+this.pauseLinkText+'</a></div>'); - } else { - this.$controlsContainer - .append('<div class="ss-controls"><a href="#play" class="play" title="'+this.playLinkText+'">'+this.playLinkText+'</a></div>'); - } - - this.$controlsContainer.find('div.ss-controls a') - .click(function(e) { - gallery.toggleSlideshow(); - e.preventDefault(); - return false; - }); - } - - if (this.renderNavControls) { - this.$controlsContainer - .append('<div class="nav-controls"><a class="prev" rel="history" title="'+this.prevLinkText+'">'+this.prevLinkText+'</a><a class="next" rel="history" title="'+this.nextLinkText+'">'+this.nextLinkText+'</a></div>') - .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) { - $(document).keydown(function(e) { - var key = e.charCode ? e.charCode : e.keyCode ? e.keyCode : 0; - switch(key) { - case 32: // space - gallery.next(); - e.preventDefault(); - break; - case 33: // Page Up - gallery.previousPage(); - e.preventDefault(); - break; - case 34: // Page Down - gallery.nextPage(); - e.preventDefault(); - break; - case 35: // End - gallery.gotoIndex(gallery.data.length-1); - e.preventDefault(); - break; - case 36: // Home - gallery.gotoIndex(0); - e.preventDefault(); - break; - case 37: // left arrow - gallery.previous(); - e.preventDefault(); - break; - case 39: // right arrow - gallery.next(); - e.preventDefault(); - break; - } - }); - } - - // Auto start the slideshow - if (this.autoStart) - this.play(); - - // Kickoff Image Preloader after 1 second - setTimeout(function() { gallery.preloadInit(); }, 1000); - - return this; - }; -})(jQuery);
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--- a/lib/sRNAPipe/js/jquery.opacityrollover.js Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -/** - * jQuery Opacity Rollover plugin - * - * Copyright (c) 2009 Trent Foley (http://trentacular.com) - * Licensed under the MIT License: - * http://www.opensource.org/licenses/mit-license.php - */ -;(function($) { - var defaults = { - mouseOutOpacity: 0.67, - mouseOverOpacity: 1.0, - fadeSpeed: 'fast', - exemptionSelector: '.selected' - }; - - $.fn.opacityrollover = function(settings) { - // Initialize the effect - $.extend(this, defaults, settings); - - var config = this; - - function fadeTo(element, opacity) { - var $target = $(element); - - if (config.exemptionSelector) - $target = $target.not(config.exemptionSelector); - - $target.fadeTo(config.fadeSpeed, opacity); - } - - this.css('opacity', this.mouseOutOpacity) - .hover( - function () { - fadeTo(this, config.mouseOverOpacity); - }, - function () { - fadeTo(this, config.mouseOutOpacity); - }); - - return this; - }; -})(jQuery);
--- a/lib/sRNAPipe/ppp.pm Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,230 +0,0 @@ -package sRNAPipe::ppp; - -use strict; -use warnings; -use FindBin; -use lib "$FindBin::Bin/../lib"; -use sRNAPipe::Rcall qw ( histogram ); -use Math::CDF; - -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT_OK = qw( &ping_pong_partners ); - -sub ping_pong_partners -{ - my ( $TE_fai, $sam, $dir, $max ) = @_; - my ( $hashRef, $dupRef, $hasPpp ) = count_mapped ( $TE_fai, $sam ); - my ( %num_per_overlap_size, $overlap_number, $reverseR, $begRev, $endRev, $sensR, $begSens, $endSens, $snum, $rnum, $overlap ); - my ( $SP, $AP, $SN, $AN, $txt ); - my $flag = 0; - my @distri_overlap = (); my @overlaps_names = (); - - open my $ppp_f, '>', $dir."ppp.txt" || die "cannot create ppp.txt $!\n"; - foreach my $k ( sort keys %{$hashRef} ) - { - my $v = $hashRef->{$k}; - my $TE_dir = $dir.$k.'/'; - - %num_per_overlap_size = (); $overlap_number = 0; - $flag = 0; - for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ ) - { - $reverseR = ${$v->[1]}[$i] ; - $begRev = $reverseR->[0]; - $endRev = $begRev + length($reverseR->[1]) - 1; - - my $revR = reverse($reverseR->[1]); - $revR =~ tr/atgcuATGCU/tacgaTACGA/; - - for ( my $j = 0; $j <= $#{$v->[0]}; $j++ ) - { - $sensR = ${$v->[0]}[$j]; - $begSens = $sensR->[0]; - $endSens = $begSens + length($sensR->[1]) - 1; - - if ( $begSens <= $endRev && $endSens > $endRev ) - { - $flag = 1; - mkdir $TE_dir; - open $txt, '>', $TE_dir.'overlap_size.txt' || die "cannot open repartition\n"; - - $overlap = $endRev - $begSens + 1; - $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]}; - $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]}; - - if ( $overlap == 10 ) - { - $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } = 1; - $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } = 1; - } - next if $overlap > $max; - if ( $snum < $rnum ) - { - $num_per_overlap_size{$overlap} += $snum; - $overlap_number += $snum; - } - else - { - $num_per_overlap_size{$overlap} += $rnum ; - $overlap_number += $rnum ; - } - } - } - } - if ( $max != 0 ) - { - my @overlaps = (); - push @overlaps_names, $k; - for my $i (1..$max) - { - $num_per_overlap_size{$i} = 0 unless exists( $num_per_overlap_size{$i} ); - push @overlaps, $num_per_overlap_size{$i}; - } - push @distri_overlap, \@overlaps; - } - - if ( $flag == 1 ) - { - open $AP, '>', $TE_dir."antisensPPP.txt" || die "cannot create antisensPPP\n"; - open $AN, '>', $TE_dir."antisens.txt" || die "cannot create antisens\n"; - for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ ) - { - $reverseR = ${$v->[1]}[$i] ; - my $revR = reverse($reverseR->[1]); - $revR =~ tr/atgcuATGCU/tacgaTACGA/; - $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]}; - if ( $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } == 1 ) - { - print $AP ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$rnum\n$revR\n"; - } - else - { - print $AN ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$rnum\n$revR\n"; - } - } - close $AP; close $AN; - - open $SP, '>', $TE_dir."sensPPP.txt" || die "cannot create sensPPP\n"; - open $SN, '>', $TE_dir."sens.txt" || die "cannot create sens\n"; - for ( my $j = 0; $j <= $#{$v->[0]}; $j++ ) - { - $sensR = ${$v->[0]}[$j]; - $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]}; - if ( $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } == 1 ) - { - print $SP ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\n$sensR->[1]\n"; - } - else - { - print $SN ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\n$sensR->[1]\n"; - } - } - close $SP; close $SN; - - my $histo_png = $TE_dir.'histogram.png'; - histogram( \%num_per_overlap_size, $histo_png, $overlap_number ); - print $txt "size\tnumber\tpercentage of the total overlap number\n"; - foreach my $k ( sort {$a <=> $b} keys %num_per_overlap_size ) - { - my $percentage = 0; - $percentage = $num_per_overlap_size{$k} * 100 / $overlap_number unless $overlap_number == 0; - print $txt "$k\t$num_per_overlap_size{$k}\t"; printf $txt "%.2f\n",$percentage; - } - close $txt; - } - } - - foreach my $tabP ( @distri_overlap ) - { - my $sum = sum($tabP); - my $ten = $tabP->[9]; - my $mean = mean($tabP); - my $std = standard_deviation($tabP, $mean); - my $zsc = z_significance($ten, $mean, $std); - my $name = shift @overlaps_names; - my $prob = 'NA'; - $prob = 1 - &Math::CDF::pnorm( $zsc ) if $zsc ne 'NA'; - print $ppp_f (join ("\t", $name, $sum, $ten, $mean, $std, $zsc, $prob ),"\n" ); - } - close $ppp_f; -} - -sub count_mapped -{ - my ( $fai, $in_file ) = @_; - my ( %mapped, %dup, %has_ppp ); - - open my $f, '<', $fai || die "cannot open $fai $! \n"; - while(<$f>) - { - if ($_ =~ /(.*)\t(\d+)\n/) - { - $mapped{$1} = []; - $mapped{$1}->[0] = []; $mapped{$1}->[1] = []; - } - } - close $f; - - open my $infile, "samtools view '$in_file' |"|| die "cannot open input file $! \n"; - while(<$infile>) - { - unless ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) - { - my @line = split (/\t/,$_); - if ($line[1] == 0) - { - unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) ) - { - push @{$mapped{$line[2]}->[0]} , [$line[3], $line[9], $line[1], $line[2]]; - $has_ppp {$line[3].$line[9].$line[1].$line[2]} = 0; - } - $dup{$line[3].$line[9].$line[1].$line[2]}+=1; - } - elsif ($line[1] == 16) - { - unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) ) - { - push @{$mapped{$line[2]}->[1]} , [$line[3], $line[9], $line[1], $line[2]]; - $has_ppp{$line[3].$line[9].$line[1].$line[2]} = 0; - } - $dup{$line[3].$line[9].$line[1].$line[2]}+=1 - } - } - } - close $infile; - return (\%mapped, \%dup, \%has_ppp ); -} - -sub sum -{ - my $arrayref = shift; - my $result = 0; - foreach (@$arrayref) {$result += $_} - return $result; -} - -sub mean -{ - my $arrayref = shift; - my $result; - foreach (@$arrayref) {$result += $_} - return $result / scalar(@$arrayref); -} - -sub standard_deviation -{ - my ($arrayref, $mean) = @_; - return sqrt ( mean ( [map $_**2 , @$arrayref ]) - ($mean**2)); -} - -sub z_significance -{ - my ($ten, $mean, $std) = @_; - my $z = 'NA'; - $z = (($ten - $mean) / $std) if $std != 0; - return $z; -} - -1; -
--- a/lib/sRNAPipe/resize.pm Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ -package sRNAPipe::resize; - -use strict; -use warnings; - -use FindBin; -use lib "$FindBin::Bin/../lib"; -use sRNAPipe::Rcall qw ( histogram ); - -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT_OK = qw( &size_distribution ); - -sub size_distribution -{ - my ( $fastq, $fastq_out, $dir, $min, $max ) = @_; - - my ( %fragments_size, %duplicates ) ; - my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates); - - my $png = $dir.'histogram.png'; - histogram(\%fragments_size, $png, $num); - - my $size = $dir.'reads_size.txt'; - - - my $pourcentage; - open my $o, '>', $size || die "cannot open $size $!\n"; - print $o "size\tnumber\tpercentage\n"; - foreach my $k (sort { $a <=> $b } keys %fragments_size ) - { - $pourcentage = $fragments_size{$k} / $num * 100; - - print $o "$k\t$fragments_size{$k}\t"; - printf $o "%.2f\n",$pourcentage; - } - close $o; - - my $dup = $dir.'duplicates.txt' ; - open $o, '>', $dup || die "cannot open $size $!\n"; - print $o "size\tnumber\n"; - foreach my $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates ) - { - print $o "$k\t$duplicates{$k}\n"; - } - close $o; -} - -sub size -{ - my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_; - my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0); - my @fastq; - open (my $in, $in_file) || die "cannot open $in_file $!\n"; - open (my $out, ">".$out_file) || die "cannot create $out_file $!\n"; - while(<$in>) - { - chomp $_; - $cmp++; $line++; - if ($cmp == 1) - { - die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ ); - $ok = 0; @fastq = (); - push(@fastq,$_); - } - elsif ($cmp == 2) - { - #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ ); - push(@fastq,$_); - $size = length($_); - if ($size >= $min && $size <= $max) - { - $numreads++; - ${$sizeHashR}{$size}+=1; - ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR)); - $ok = 1; - } - } - elsif ($cmp == 3 ) - { - die "file do not contain a + at line $line\n" unless $_ =~ /^\+/; - push(@fastq,$_); - } - elsif ($cmp == 4 ) - { - push(@fastq,$_); - $cmp = 0; - if ($ok == 1) - { - foreach my $t (@fastq) - { - print $out $t."\n"; - } - } - } - } - close $in; close $out; - return $numreads; -} - -1;
--- a/lib/sRNAPipe/subgroups.pm Wed Jan 30 06:26:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,174 +0,0 @@ -package sRNAPipe::subgroups; - -use strict; -use warnings; -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT_OK = qw( &subgroups ); - -use POSIX; -use File::Copy; -use FindBin; -use lib "$FindBin::Bin/../lib"; -use sRNAPipe::align qw ( get_hash_alignment ); - -sub subgroups -{ - my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_; - my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref ); - - srand(); - print $report "----------------------------\n"; - print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n"; - - mkdir $dir; - $dir = $dir.'/' unless $dir =~ /(.*)\/$/; - - my $accept_miRNas = $dir.'miRNAs.fastq'; - my $reject_miRNAs = $dir.'miRNAs_rejected.fastq'; - my $sam_miRNAs = $dir.'miRNAs.sam'; - my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report); - my $mi = $tmp[0]; my $sam = ''; - $repartition{'miRNAs'} = $mi; - - - my $reject_rRNAs = $dir.'rRNAs_rejected.fastq'; - if ( $rRNAs eq 'None') - { - move($reject_miRNAs,$reject_rRNAs); - } - else - { - $sam = new String::Random; - $sam = $sam->randpattern("CCcccccc"); - @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report); - $repartition{'rRNAs'} = $tmp[0]; - unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - } - - my $reject_tRNAs = $dir.'rRNAs_rejected.fastq'; - if ( $rRNAs eq 'None') - { - move($reject_rRNAs,$reject_tRNAs); - } - else - { - $sam = new String::Random; - $sam = $sam->randpattern("CCcccccc"); - @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report); - $repartition{'tRNAs'} = $tmp[0]; - unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - } - - - my $bonafide = $dir.'bonafide_reads.fastq'; - if ( $rRNAs eq 'None') - { - move($reject_tRNAs,$bonafide); - } - else - { - $sam = new String::Random; - $sam = $sam->randpattern("CCcccccc"); - @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report); - $repartition{'snRNAs'} = $tmp[0]; - - unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - } - my $bo = $tmp[1]; - - my $sam_transcripts = $dir.'transcripts.sam'; - my $reject_transcripts = $dir.'rejected_transcripts.fastq'; - @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai'); - $repartition{'transcripts'} = $tmp[0]; - - - my $sam_TEs = $dir.'TEs.sam'; - my $reject_TEs = $dir.'rejected.fastq'; - @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' ); - $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1]; - unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - unlink $reject_transcripts; - unlink $reject_rRNAs; - unlink $reject_miRNAs; - unlink $reject_tRNAs; - - #create repartition - my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi ); - - open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n"; - print $re "type\tnumber\tpercentage\n"; - $sum += $_ foreach values %repartition; - foreach my $k ( sort keys %repartition ) - { - my $prct = 0; - $prct = $repartition{$k} / $sum * 100 if $sum != 0; - print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct; - } - return ( $bo, $mi, $pi); -} - -sub fastqSubgroups -{ - my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_; - my $fastq_siRNA = $output_directory."siRNAs.fastq"; - my $fastq_piRNA = $output_directory."piRNAs.fastq"; - - open my $fic, '<', $fastq || die "cannot open input file $! \n"; - open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n"; - open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n"; - - my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0); - my (@fastq) =(); my $seq_name; - my $out; - while(<$fic>) - { - chomp $_; - $cmp++; - if ($cmp == 1) - { - die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ ); - $type = 0; @fastq = (); - if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;} - elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;} - push(@fastq,$_); - } - elsif ($cmp == 2) - { - #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/; - push(@fastq,$_); - $length = length($_); - $type = 0; - if ( $length >= $min_si && $length <= $max_si ) - { - $type = 2; - $siRNA_number++; - } - if ($length >= $min_pi && $length <= $max_pi ) - { - $type += 4; - $piRNA_number++; - } - } - elsif ($cmp == 3 ) - { - die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/; - push(@fastq,$_); - } - elsif ($cmp == 4 ) - { - push(@fastq,$_); - $cmp = 0; - if ($type != 0) - { - if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} } - if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} } - } - } - } - close $fic; - close $si; close $pi; - return ($piRNA_number); -} - -1;
--- a/sRNAPipe.xml Wed Jan 30 06:26:32 2019 -0500 +++ b/sRNAPipe.xml Thu Jan 31 16:10:58 2019 -0500 @@ -22,25 +22,11 @@ </xml> </macros> <requirements> - <requirement type="package" version="1.9">samtools</requirement> - <requirement type="package">bwa</requirement> - <requirement type="package">bedtools</requirement> - <requirement type="package">perl</requirement> - <requirement type="package">perl-getopt-long</requirement> - <requirement type="package">perl-parallel-forkmanager</requirement> - <requirement type="package">perl-statistics-r</requirement> - <requirement type="package">perl-string-random</requirement> - <requirement type="package">perl-file-copy-recursive</requirement> - <requirement type="package">perl-math-cdf</requirement> - <requirement type="package">r-base</requirement> - <requirement type="package">r-plotrix</requirement> - <requirement type="package">r-rcolorbrewer</requirement> - <requirement type="package">r-ggplot2</requirement> - <requirement type="package" version="1.14.0">bioconductor-sushi</requirement> + <requirement type="package" version="1.1">srnapipe</requirement> </requirements> - <version_command>perl '$__tool_directory__/bin/sRNAPipe.pl' | grep 'version' | grep "version" | cut -d ' ' -f 3</version_command> + <version_command>srnapipe | grep 'version' | grep "version" | cut -d ' ' -f 3</version_command> <command detect_errors="aggressive"><![CDATA[ - perl '$__tool_directory__/bin/sRNAPipe.pl' + srnapipe --fastq '${first_input}' --fastq_n '${first_input.name}'