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Changeset 0:89ad0a9cca52 (2011-11-21)

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/.classpath
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/.classpath Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="src"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+ <classpathentry kind="output" path="bin"/>
+</classpath>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/.project
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/.project Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>NGSrich_0.5.5</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/.settings/org.eclipse.jdt.core.prefs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/.settings/org.eclipse.jdt.core.prefs Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,12 @@
+#Tue Sep 13 11:09:23 CEST 2011
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.6

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/R/eval_details.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/R/eval_details.R Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,163 @@\n+#!/usr/bin/Rscript\n+\n+\n+##Input parameters########################################################################################################################\n+xml=as.character(commandArgs()[6])\n+bed=as.character(commandArgs()[7])\n+cov=as.character(commandArgs()[8])\n+chrinfo=as.character(commandArgs()[9])\n+outdir=as.character(commandArgs()[10])\n+genome=as.character(commandArgs()[11])\n+##########################################################################################################################################\n+\n+\n+\n+##Read data###############################################################################################################################\n+bedfile<-read.table(bed,header=FALSE,stringsAsFactors=FALSE)\n+wunknown<-which(bedfile$V4=="unknown")\n+bedfile$V4[wunknown]<-paste("unknown",seq(1,length(wunknown),1),sep="")\n+bedfile$V4<-gsub("/","-",bedfile$V4)\n+covdata<-readLines(cov,warn=FALSE)\n+\n+xmldata<-readLines(xml,warn=FALSE)\n+nbrline<-xmldata[grep("<NumberReads>",xmldata)]\n+rlenline<-xmldata[grep("<ReadLength>",xmldata)]\n+nbreads<-as.numeric(strsplit(strsplit(nbrline,">")[[1]][2],"<")[[1]][1])\n+rlength<-as.numeric(strsplit(strsplit(rlenline,">")[[1]][2],"<")[[1]][1])\n+\n+expect<-0\n+allchr<-levels(as.factor(bedfile$V1))\n+if(chrinfo!="none"){\n+ cinfo<-read.table(chrinfo,header=FALSE,stringsAsFactors=FALSE)\n+ gsize<-sum(as.numeric(cinfo[,2]))\n+ expect=(rlength*nbreads)/gsize\n+}\n+\n+dir.create(paste(outdir,"/chromosomes",sep=""),showWarnings=FALSE)\n+for(chr in allchr){dir.create(paste(outdir,"/chromosomes/",chr,sep=""),showWarnings=FALSE)}\n+\n+tcov<-list()\n+tstarts<-numeric(0)\n+tcov0<-character(0)\n+firstt=1\n+for(i in 1:length(covdata)){\n+ if(i%%10000==0){cat(i,"/",length(covdata),"\\n")}\n+ if(nchar(covdata[i])>10){\n+ if(firstt==0){\n+ tcov[[tname]]<-as.numeric(tcov0)\n+ tcov0<-character(0)\n+ }\n+ firstt=0\n+ nameel<-strsplit(covdata[i],"\\t")\n+ tname<-paste(nameel[[1]][1],":",nameel[[1]][2],"-",nameel[[1]][3],sep="")\n+ }\n+ else{tcov0<-c(tcov0,covdata[i])}\n+}\n+##########################################################################################################################################\n+\n+\n+sortchr<-function(x){\n+ if(sum(substr(x,1,3)=="chr")==length(x)){\n+ x0<-strsplit(x,"chr")\n+ xspl<-character(0)\n+ for(i in 1:length(x0)){xspl<-c(xspl,x0[[i]][2])}\n+ xnum<-xspl[!is.na(as.numeric(xspl))]\n+ xchar<-setdiff(xspl,xnum)\n+ xsorted<-paste("chr",c(sort(as.numeric(xnum)),sort(xchar)),sep="")\n+ return(xsorted)\n+ }\n+ else{return(x)}\n+}\n+\n+\n+##Create gene index#######################################################################################################################\n+allchr<-sortchr(levels(as.factor(bedfile$V1)))\n+outfile=paste(outdir,"/chromosomes/chromosomes.html",sep="")\n+cat(file=outfile,paste(\n+ "<html>\\n<head>\\n<title>Index of Target Regions</title>\\n",\n+ "<style type=\\"text/css\\">\\n body{font-family:sans-serif;}\\n h2,h3{color: darkblue;}\\n a{color:darkblue;}\\n table.output td{ padding: 4px; background-color: lightskyblue; border: 1px solid #000; border-color: darkblue; }\\n</style>\\n",\n+ "</head>\\n\\n",\n+ "<script language=\\"JavaScript\\">\\n var questionClass=\\"ChrList\\";\\n function collapseAll(){\\n var allSections=document.getElementsByTagName(\\"div\\");\\n for(i=0;i<allSections.length;i++){\\n if(allSections[i].className==questionClass){\\n allSections[i].style.display = \\"none\\";\\n }}}\\n function expand(name){\\n collapseAll();\\n var newStyle=\\"\\";\\n if(document.getElementById(name).style.display!=\\"block\\"){newStyle=\\"block\\";}\\n else{newStyle=\\"none\\";}\\n document.getElementById(name).style.display=newStyle;\\n }\\n</script>\\n\\n",\n+ "<body onload=\\"expand(\'",allchr[1],"\')\\">\\n<h2>Show Details on Genewise Coverage</h2>",sep=""))\n+\n+for(chr in allchr){\n+ cat(file=outfile,paste("<a href=\\"javascript:expand(\'",chr,"\')\\">",chr,"</a>\\n",sep=""),append=TRUE)\n+}\n+cat'..b'own"){genelab="unknown"}\n+ else{genelab=gene}\n+ cat(file=outfile,paste("<tr><td>",genelab,"</td><td>",tname,"</td><td><a href=\\"",chr,"/",gene,"/index.html\\">Show Details</a></td></tr>\\n",sep=""),append=TRUE)\n+ }\n+ cat(file=outfile,"</table>\\n</div>\\n",append=TRUE)\n+\n+}\n+cat(file=outfile,"</body></html>\\n",append=TRUE) \n+##########################################################################################################################################\n+\n+\n+\n+##Create genewise reports#################################################################################################################\n+firstgene=1\n+partest<-cv<-goftest<-numeric(0)\n+genebed<-split(bedfile,bedfile$V4)\n+\n+for(gene in names(genebed)){\n+\n+ thisbed<-genebed[[gene]]\n+ chr=thisbed$V1[1]\n+ \n+ if(substr(gene,1,7)=="unknown"){genelab="unknown"}\n+ else{genelab=gene}\n+\n+ ##Write HTML header\n+ outfile=paste(outdir,"/chromosomes/",chr,"/",gene,"/index.html",sep="")\n+ dir.create(paste(outdir,"/chromosomes/",chr,"/",gene,sep=""),showWarnings=FALSE)\n+ cat(file=outfile,paste("<html>\\n<head>\\n<title>Enrichment Details</title>\\n<style type=\\"text/css\\">\\n body{font-family:sans-serif;}\\n h2,h3{color: darkblue;}\\n a{color:darkblue;}\\n table.output td{ padding: 4px; background-color: lightskyblue; border: 1px solid #000; border-color: darkblue; } table.noborder td{padding: 0px; border: 0px solid #000; border-color: lightskyblue}\\n</style>\\n</head>\\n\\n<body>\\n<h2>Enrichment Details for ",genelab,"</h2>\\n<table class=\\"output\\">\\n<tr><td>Target Region</td><td>Coverage</td><td>Percentage</td><td>Enrichment Factor</td><td>Target Histogram</td><td>External Link</td></tr>\\n",sep=""))\n+ \n+ for(i in 1:nrow(thisbed)){\n+\n+ start=thisbed$V2[i]\n+ end=thisbed$V3[i]\n+ region=seq(start,end,1)\n+ tname=paste(chr,":",start,"-",end,sep="")\n+ \n+ if(is.element(tname,names(tcov))){\n+ basecov=tcov[[tname]]\n+ if(expect!=0){enrratio<-round(mean(basecov)/expect,1)}\n+ else{enrratio<-"unknown"}\n+ stddev=round(sd(basecov),2)\n+\n+ ##Create plots\n+ png(file=paste(outdir,"/chromosomes/",chr,"/",gene,"/h_",tname,".png",sep=""))\n+ plot(region,basecov,pch=".",xlab=paste("Physical Position [",chr,"]",sep=""),ylab="Coverage",col="tomato3")\n+ edgesx<-c(region,end,start)\n+ edgesy<-c(basecov,0,0)\n+ polygon(edgesx,edgesy,col="tomato3",border=NA)\n+ lines(c(start,start),c(-1000,1000000))\n+ lines(c(end,end),c(-1000,1000000))\n+ lines(c(start,end),c(mean(basecov),mean(basecov)),col="darkblue")\n+ lines(c(start,end),c(mean(basecov)-stddev,mean(basecov)-stddev),lty="dashed",col="darkblue")\n+ lines(c(start,end),c(mean(basecov)+stddev,mean(basecov)+stddev),lty="dashed",col="darkblue")\n+ dev.off()\n+\n+ ##Write HTML table\n+ ucsclink<-paste("http://www.genome.ucsc.edu/cgi-bin/hgTracks?&db=",genome,"&position=",chr,"%3A",start,"-",end,"&hgt.suggest=&pix=800&Submit=submit&hgsid=183341879",sep="")\n+ cat(file=outfile,paste("<tr><td>",tname," (",end-start+1," bp)</td><td><table class=\\"noborder\\"><tr><td>Mean:</td><td>",thisbed[i,5],"</td></tr><tr><td>Std Dev:</td><td>",stddev,"</td></tr></table></td><td><table class=\\"noborder\\"><tr><td>1x:</td><td>",thisbed[i,6],"%</td></tr><tr><td>5x:</td><td>",thisbed[i,7],"%</td></tr><tr><td>10x:</td><td>",thisbed[i,8],"%</td></tr><tr><td>20x:</td><td>",thisbed[i,9],"%</td></tr><tr><td>30x:</td><td>",thisbed[i,10],"%</td></tr></table></td><td>",enrratio,"</td><td><a href=\\"h_",tname,".png\\"><img src=\\"h_",tname,".png\\" width=160></img></a></td><td><a href=\\"",ucsclink,"\\">Show in Genome Browser</td></tr>\\n",sep=""),append=TRUE)\n+ }\n+ }\n+ cat(file=outfile,"</table>\\n</body>\\n</html>",append=TRUE)\n+\n+}\n+##########################################################################################################################################\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/R/eval_enrichment.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/R/eval_enrichment.R Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,401 @@\n+#!/usr/bin/Rscript\n+\n+xmlfile=as.character(commandArgs()[6])\n+bedfile=as.character(commandArgs()[7])\n+outdir=as.character(commandArgs()[8])\n+genome=as.character(commandArgs()[9])\n+poor=as.numeric(commandArgs()[10])\n+high=as.numeric(commandArgs()[11])\n+samplename=as.character(commandArgs()[12])\n+targetfile=as.character(commandArgs()[13])\n+details=as.numeric(commandArgs()[14])\n+cutoff=0\n+sdetails=""\n+#samplename0=strsplit(strsplit(xmlfile,"_")[[1]][1],"/")[[1]]\n+#samplename<-samplename0[length(samplename0)]\n+outfile=paste(outdir,"/",samplename,"_enrichment.html",sep="")\n+\n+##Read XML summary\n+cat("Reading XML file ... ")\n+xmltag<-function(line){\n+\treturn(strsplit(strsplit(line,">")[[1]][2],"</")[[1]][1])\n+}\n+xml<-readLines(xmlfile)\n+numreads<-numeric(0)\n+nextfold=0\n+for(line in xml){\n+ if(length(grep("ReadLength",line)>0)){\n+ readlength<-as.numeric(xmltag(line))\n+ }\n+ if(length(grep("NumberReads",line)>0)){\n+ numreads<-c(numreads,as.numeric(xmltag(line)))\n+ }\n+ if(length(grep("AvTargetCoverage",line)>0)){\n+ averagecov=as.numeric(xmltag(line))\n+ }\n+ if(details==1){\n+\tsdetails="<a href=\\"chromosomes/chromosomes.html\\">[Show Details]</a> "\n+ }\n+ if(length(grep("SDTargetCoverage",line)>0)){\n+ stddevcov=as.numeric(xmltag(line))\n+ }\n+ if(length(grep("TargetSize",line)>0)){\n+ targetsize=as.numeric(xmltag(line))\n+ }\n+ if(length(grep("<from1x>",line)>0)){nextfold=1}\n+ else{\n+ if((nextfold==1) && length(grep("PercBases",line))>0){\n+ sample1<-as.numeric(xmltag(line))\n+ nextfold=0\n+ }\n+ }\n+ if(length(grep("<from5x>",line)>0)){nextfold=5}\n+ else{\n+ if((nextfold==5) && length(grep("PercBases",line))>0){\n+ sample5<-as.numeric(xmltag(line))\n+ nextfold=0\n+ }\n+ }\n+ if(length(grep("<from10x>",line)>0)){nextfold=10}\t\n+ else{\n+ if((nextfold==10) && length(grep("PercBases",line))>0){\n+ sample10<-as.numeric(xmltag(line))\n+ nextfold=0\n+ }\n+ }\n+ if(length(grep("<from20x>",line)>0)){nextfold=20}\n+ else{\n+ if((nextfold==20) && length(grep("PercBases",line))>0){\n+ sample20<-as.numeric(xmltag(line))\n+ nextfold=0\n+ }\n+ }\n+ if(length(grep("<from30x>",line)>0)){nextfold=30}\n+ else{\n+ if((nextfold==30) && length(grep("PercBases",line))>0){\n+ \n+ sample30<-as.numeric(xmltag(line))\n+ nextfold=0\n+ }\n+ }\n+}\n+\n+numreads_total<-numreads[1]\n+numreads_target<-numreads[3]\n+tpkm=round(numreads_target/((targetsize/1000)*(numreads_total/1000000)),2)\n+\n+cat("ready.\\n")\n+\n+\n+##Read BED enrichment file and summarize output\n+cat("Reading BED file ... ")\n+bed<-read.table(bedfile,stringsAsFactors=FALSE)\n+area0_2<-sum(bed$V5<2)\n+area2_10<-sum((bed$V5>=2) & (bed$V5<10))\n+area10_20<-sum((bed$V5>=10) & (bed$V5<20))\n+area20_30<-sum((bed$V5>=20) & (bed$V5<30))\n+area30_50<-sum((bed$V5>=30) & (bed$V5<50))\n+area50_100<-sum((bed$V5>=50) & (bed$V5<100))\n+areagr100<-sum(bed$V5>100)\n+cat("ready.\\n")\n+\n+\n+##Create pieplot\n+cat("Creating coverage pieplot ... ")\n+png(file=paste(outdir,"/plots/",samplename,"_pieplot.png",sep=""),width=580)\n+par(mar=c(1,7,1,7))\n+pie(c(area0_2,area2_10,area10_20,area20_30,area30_50,area50_100,areagr100),\n+ labels=c(paste("0x to 2x (",area0_2,")",sep=""),\n+ paste("2x to 10x (",area2_10,")",sep=""),\n+ paste("10x to 20x (",area10_20,")",sep=""),\n+ paste("20x to 30x (",area20_30,")",sep=""),\n+ paste("30x to 50x (",area30_50,")",sep=""),\n+ paste("50x to 100x (",area50_100,")",sep=""),\n+ paste("above 100x (",areagr100,")",sep="")),\n+ col=c("gray30","gray40","gray50","gray60","gray70","gray80","gray90"),main="") ##Mean Coverage of Target Regions")\n+garbage<-dev.off()\n+cat("ready.\\n")\n+\n+\n+cat("Preparing coverage barplots ... ")\n+maxgenemean=0\n+genes<-levels(as.factor(bed$V4))\n+genes<-genes[genes!="unknown"]\n+ngenes<-length(genes)\n+\n+for(i in 1:ngenes){\n+ genemean<-mean(bed[bed$V4==genes[i],5])\n+ if(maxgenemean<genemean){maxgenemean=genemean}\n+}\n+\n+maxgenemean=maxgenemean-(maxgenemean%%1'..b'></td><td>",sample10,"</td></tr>\\n",\n+ " <tr><td>Covered 20x</td><td>",sample20,"</td></tr>\\n",\n+ " <tr><td>Covered 30x</td><td>",sample30,"</td></tr>\\n",\n+ " <tr><td>TPKM</td><td>",tpkm,"</td></tr>\\n",\n+ "</table>\\n",\n+ "</td>\\n",\n+ "<td width=\\"10%\\"></td>",\n+ "<td>\\n",\n+ "<img src=\\"plots/",samplename,"_pieplot.png\\"></img>\\n",\n+ "</td>\\n",\n+ "</tr>\\n",\n+ "</table>\\n",\n+ " \\n",\n+ "<h2>Genewise Target Coverage</h2>",sdetails," \\n",sep=""))\n+ \n+\n+if(ngenes>=2000){\n+for(chromosome in chromosomes){\n+ cat(file=outfile,paste("<a href=\\"javascript:expand(\'",chromosome,"\')\\">",chromosome,"</a>\\n",sep=""),append=TRUE)\n+}\n+for(chromosome in chromosomes){\n+ cat(file=outfile,paste("<div style=\\"height:480px; overflow:auto;\\" class=\\"chrView\\" id=\\"",chromosome,"\\"><img src=\\"plots/",samplename,"_target_coverage_",chromosome,".png\\"></img></div>\\n",sep=""),append=TRUE)\n+}\n+} else{\n+ cat(file=outfile,paste("<div style=\\"height:480px; overflow:auto;\\"><img src=\\"plots/",samplename,"_target_coverage.png\\"></img></div>\\n",sep=""),append=TRUE)\n+}\n+\n+cat(file=outfile,paste(" \\n",\n+ "<h2>Poorly Covered Genes (Cutoff: ",poor,"x)</h2>\\n",sep=""),append=TRUE)\n+if(nrow(poorly_covered)==0){\n+\tcat(file=outfile,"Nothing found for this cutoff.",append=TRUE)\n+} else{\n+cat(file=outfile,paste(\n+ "<table class=\\"output\\">\\n",\n+ " <tr>\\n",\n+ " <td>Region</td><td>Gene</td>\\n",\n+ " <td>Coverage Mean</td>\\n",\n+ " <td>Covered 1x</td><td>Covered 5x</td>\\n",\n+ " <td>Covered 10x</td><td>Covered 20x</td>\\n",\n+ " <td>Covered 30x</td><td>External Link</td>\\n",\n+ " </tr>\\n",sep=""),append=TRUE)\n+\n+for(i in 1:nrow(poorly_covered)){\n+cat(file=outfile,paste(\n+ " <tr>\\n",\n+ " <td>",poorly_covered[i,1],":",poorly_covered[i,2],"-",poorly_covered[i,3],"</td>\\n",\n+ " <td>",poorly_covered[i,4],"</td>\\n",\n+ " <td>",poorly_covered[i,5],"</td>\\n",\n+ " <td>",poorly_covered[i,7],"</td>\\n",\n+ " <td>",poorly_covered[i,8],"</td>\\n",\n+ " <td>",poorly_covered[i,9],"</td>\\n",\n+ " <td>",poorly_covered[i,10],"</td>\\n",\n+ " <td>",poorly_covered[i,11],"</td>\\n",\n+ " <td><a href=\\"",linkpoor[i],"\\">Show in Genome Browser</a></td>\\n",\n+ " </tr>\\n",sep=""),append=TRUE)\n+}\n+\n+cat(file=outfile,"</table> \\n",append=TRUE)\n+}\n+\n+cat(file=outfile,paste("<h2>Highly Covered Genes (Cutoff: ",high,"x)</h2>\\n",sep=""),append=TRUE)\n+if(nrow(highly_covered)==0){\n+ cat(file=outfile,"Nothing found for this cutoff.",append=TRUE)\n+} else{\n+cat(file=outfile,paste(\n+ "<table class=\\"output\\">\\n",\n+ " <tr>\\n",\n+ " <td>Target</td><td>Gene</td><td>Coverage Mean</td>",\n+ " <td>Covered 1x</td><td>Covered 5x</td><td>Covered 10x</td>",\n+ " <td>Covered 20x</td><td>Covered 30x</td><td>External Link</td>\\n",\n+ " </tr>\\n",sep=""),append=TRUE)\n+for(i in 1:nrow(highly_covered)){\n+cat(file=outfile,paste(" <tr>\\n",\n+ " <td>",highly_covered[i,1],":",highly_covered[i,2],"-",highly_covered[i,3],"</td>\\n",\n+ " <td>",highly_covered[i,4],"</td>\\n",\n+ " <td>",highly_covered[i,5],"</td>\\n",\n+ " <td>",highly_covered[i,7],"</td>\\n",\n+ " <td>",highly_covered[i,8],"</td>\\n",\n+ " <td>",highly_covered[i,9],"</td>\\n",\n+ " <td>",highly_covered[i,10],"</td>\\n",\n+ " <td>",highly_covered[i,11],"</td>\\n",\n+ " <td><a href=\\"",linkhigh[i],"\\">Show in Genome Browser</a></td>\\n",\n+ " </tr>",sep=""),append=TRUE)\n+}\n+\n+cat(file=outfile,"</table>\\n",append=TRUE)\n+}\n+cat(file=outfile," BED file used for specification of target regions: ",targetfile,append=TRUE)\n+cat(file=outfile,"</body>\\n</html>\\n",append=TRUE)\n+\n+cat("ready.\\n")\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/R/summarize_enrichment.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/R/summarize_enrichment.R Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,223 @@\n+#!/usr/bin/Rscript\n+\n+infile=as.character(commandArgs()[6])\n+outdir=as.character(commandArgs()[7])\n+poor=as.numeric(commandArgs()[8])\n+high=as.numeric(commandArgs()[9])\n+\n+\n+outfile=paste(outdir,"/summary.html",sep="")\n+cutoff=c(poor,high)\n+\n+xmlfiles<-bedfiles<-character(0)\n+indirs<-as.character(readLines(infile))\n+for(thisdir in indirs){\n+ thisdir=paste(thisdir,"/data",sep="")\n+ xmlfiles=c(xmlfiles,list.files(thisdir,pattern=".xml",full.names=TRUE))\n+ bedfiles=c(bedfiles,list.files(thisdir,pattern=".bed",full.names=TRUE))\n+}\n+nsamples<-length(indirs)\n+\n+samplenames<-character(0)\n+diffs<-matrix(nrow=5,ncol=nsamples)\n+averagecov<-stddevcov<-targetsize<-numreads_total<-numreads_target<-numeric(0)\n+sample1<-sample5<-sample10<-sample20<-sample30<-numeric(0)\n+\n+\n+##Read XML input files\n+xmltag<-function(line){\n+ return(strsplit(strsplit(line,">")[[1]][2],"</")[[1]][1])\n+}\n+i=1\n+nextfold=0\n+for(file in xmlfiles){\n+ numreads<-numeric(0)\n+ inlines<-readLines(file)\n+ for(line in inlines){\n+ if(length(grep("SampleName",line)>0)){samplenames<-c(samplenames,xmltag(line))}\n+ if(length(grep("NumberReads",line)>0)){numreads<-c(numreads,as.numeric(xmltag(line)))}\n+ if(length(grep("AvTargetCoverage",line)>0)){averagecov=c(averagecov,as.numeric(xmltag(line)))}\n+ if(length(grep("SDTargetCoverage",line)>0)){stddevcov=c(stddevcov,as.numeric(xmltag(line)))}\n+ if(length(grep("TargetSize",line)>0)){targetsize=as.numeric(xmltag(line))}\n+ if(length(grep("<from1x>",line)>0)){nextfold=1}\n+ else{\n+ if((nextfold==1) && length(grep("PercBases",line))>0){\n+ sample1<-c(sample1,as.numeric(xmltag(line)))\n+ nextfold=0\n+ }\n+ }\n+ if(length(grep("<from5x>",line)>0)){nextfold=5}\n+ else{\n+ if((nextfold==5) && length(grep("PercBases",line))>0){\n+ sample5<-c(sample5,as.numeric(xmltag(line)))\n+ nextfold=0\n+ }\n+ }\n+ if(length(grep("<from10x>",line)>0)){nextfold=10}\t\n+ else{\n+ if((nextfold==10) && length(grep("PercBases",line))>0){\n+ sample10<-c(sample10,as.numeric(xmltag(line)))\n+ nextfold=0\n+ }\n+ }\n+ if(length(grep("<from20x>",line)>0)){nextfold=20}\n+ else{\n+ if((nextfold==20) && length(grep("PercBases",line))>0){\n+ sample20<-c(sample20,as.numeric(xmltag(line)))\n+ nextfold=0\n+ }\n+ }\n+ if(length(grep("<from30x>",line)>0)){nextfold=30}\n+ else{\n+ if((nextfold==30) && length(grep("PercBases",line))>0){\n+ sample30<-c(sample30,as.numeric(xmltag(line)))\n+ nextfold=0\n+ }\n+ }\n+ }\n+ numreads_total<-c(numreads_total,numreads[1])\n+ numreads_target<-c(numreads_target,numreads[2])\n+ diffs[,i]<-c(sample30[i],sample20[i]-sample30[i],sample10[i]-sample20[i],sample5[i]-sample10[i],sample1[i]-sample5[i])\n+ i=i+1\n+}\n+\n+\n+##Create barplot\n+rownames(diffs)<-c("Covered 30x","Covered 20x","Covered 10x","Covered 5x","Covered 1x")\n+plot_samplenames<-samplenames\n+s=0\n+for(sname in plot_samplenames){\n+ s=s+1\n+ if(nchar(sname)>10){plot_samplenames[s]<-paste("Sample ",s,"\\n(table above)",sep="")}\n+}\n+colnames(diffs)<-plot_samplenames\n+png(file=paste(outdir,"/summary_plot.png",sep=""),width=66*(4+nsamples),height=400)\n+par(oma=c(1,0,0,1))\n+barplot(diffs,\n+ \tlegend=TRUE,\n+ col=c("darkblue","steelblue1","tomato1","tomato3","tomato4"),\n+ xlim=c(0,4+nsamples),ylim=c(0,100),\n+ ylab="Percentage",las=2 ) #,\n+# args.legend=list(x=nsamples+4,y=80))\n+dev.off()\n+\n+\n+\n+##Read BED files\n+sametarget=TRUE\n+thisbed<-read.table(bedfiles[1],stringsAsFactors=FALSE)\n+genes<-levels(as.factor(thisbed$V4))\n+meancov<-matrix(nrow=length(genes),ncol=length(bedfiles))\n+chr<-start<-end<-character(0)\n+\n+i=1\n+for(file in bedfiles){\n+ thisbed<-read.table(file,stringsAsFactors=FALSE)\n+ genes_thissample<-levels(as.factor(thisbed$V4))\n+ if(length(genes_thissample)!=length(genes)){sametarget=FALSE}\n+ for(j in 1:length(genes)){\n+ thisgene<-thisbed[thisbed$V4==genes[j],]\n+ chr[j]<-t'..b's)])),4)\n+ meancov$stddev[i]<-round(sd(as.numeric(meancov[i,4+(1:nsamples)])),4)\n+ meancov$mini[i]<-round(min(as.numeric(meancov[i,4+(1:nsamples)])),4)\n+ meancov$maxi[i]<-round(max(as.numeric(meancov[i,4+(1:nsamples)])),4)\n+}\n+meancov_sorted<-meancov[order(meancov$ave),]\n+poorly_all<-meancov_sorted[meancov_sorted$max<cutoff[1],]\n+\n+\n+##Write HTML output\n+cat(file=outfile,paste(\n+ "<html>\\n",\n+ "<head>\\n",\n+ "<title>Enrichment Performance</title>\\n",\n+ "<style type=\\"text/css\\">\\n",\n+ "body{font-family:sans-serif;}\\n",\n+ "h2,h3{color: darkblue;}\\n",\n+ "a{color: darkblue;}\\n",\n+ " table.output td{\\n",\n+ " padding: 4px; background-color: lightskyblue;\\n",\n+ " border: 1px solid #000; border-color: darkblue;\\n",\n+ "}\\n",\n+ "</Style>\\n",\n+ "</head>\\n",\n+ "<body>\\n",\n+ "<h2>Target Enrichment Performance</h2> \\n",\n+ "<table class=\\"output\\">\\n",\n+ " <tr>\\n",\n+ " <td>Sample</td><td># Reads</td><td># On Target</td><td>Coverage Mean</td><td>Coverage Std Dev</td><td>Covered 1x</td><td>Covered 5x</td><td>Covered 10x</td><td>Covered 20x</td><td>Covered 30x</td><td>Details</td>\\n",\n+ "</tr>\\n",sep=""))\n+for(i in 1:nsamples){\n+ cat(file=outfile,paste(\n+ "<tr><td>",samplenames[i],"</td><td>",numreads_total[i],"</td>",\n+ "<td>",numreads_target[i],"</td><td>",averagecov[i],"</td>",\n+ "<td>",stddevcov[i],"</td><td>",sample1[i],"</td><td>",sample5[i],"</td>",\n+ "<td>",sample10[i],"</td><td>",sample20[i],"</td><td>",sample30[i],"</td>",\n+ "<td><a href=\\"",rev(strsplit(indirs[i],"/")[[1]])[1],"/",samplenames[i],"_enrichment.html\\">Show</a></td></tr>\\n",\n+ sep=""),append=TRUE)\n+}\n+cat(file=outfile,paste(\n+ "</table>\\n",\n+ " \\n",\n+ "<h2>Target Base Percentage Covered</h2>\\n",\n+ "<img src=\\"summary_plot.png\\"></img>\\n",sep=""),append=TRUE)\n+if(!sametarget){\n+\twarning("Target regions are not the same for all samples.")\n+} else{\n+cat(file=outfile,paste(\n+ "<h2>Poorly Covered in All Samples (Cutoff: ",cutoff[1],"x)</h2>\\n",sep=""),append=TRUE)\n+if(nrow(poorly_all)==0){\n+cat(file=outfile,"Nothing found for this cutoff.",append=TRUE)\n+} else{\n+cat(file=outfile,paste(\n+ "<table class=\\"output\\">\\n",\n+ "<tr>\\n",\n+ "<td>Target Region</td><td>Gene</td><td>Mean Across Samples</td><td>Std Dev Across Samples</td>\\n",sep=""),append=TRUE)\n+for(i in 1:nrow(poorly_all)){\n+ cat(file=outfile,paste(\n+ "<tr>\\n",\n+ "<td>",poorly_all$chr[i],":",poorly_all$start[i],"-",poorly_all$end[i],"</td>\\n",\n+ "<td>",poorly_all$genes[i],"</td>\\n",\n+ "<td>",poorly_all$ave[i],"</td>\\n",\n+ "<td>",poorly_all$stddev[i],"</td>\\n",\n+ "<tr>\\n",sep=""),append=TRUE)\n+}\n+cat(file=outfile,"</table>\\n",append=TRUE)\n+}\n+\n+meancov_sorted<-meancov[order(meancov$ave,decreasing=TRUE),] ##Highly Covered\n+highly_all<-meancov_sorted[meancov_sorted$min>cutoff[2],]\n+cat(file=outfile,paste(\n+ "<h2>Highly Covered in All Samples (Cutoff: ",cutoff[2],"x)</h2>\\n",sep=""),append=TRUE)\n+if(nrow(highly_all)==0){\n+cat(file=outfile,"Nothing found for this cutoff.",append=TRUE)\n+} else{\n+\tcat(file=outfile,paste("<table class=\\"output\\">\\n",\n+ "<tr>\\n",\n+ "<td>Target Region</td><td>Gene</td><td>Mean Across Sample</td><td>Std Dev Across Samples</td>\\n",sep=""),append=TRUE)\n+for(i in 1:nrow(highly_all)){\n+ cat(file=outfile,paste(\n+ "<tr>\\n",\n+ "<td>",highly_all$chr[i],":",highly_all$start[i],"-",highly_all$end[i],"</td>\\n",\n+ "<td>",highly_all$genes[i],"</td>\\n",\n+ "<td>",highly_all$ave[i],"</td>\\n",\n+ "<td>",highly_all$stddev[i],"</td>\\n",\n+ "<tr>\\n",sep=""),append=TRUE)\n+}\n+cat(file=outfile,"</table>\\n",append=TRUE)\n+}\n+\n+}\n+\n+cat(file=outfile,"</body>\\n</html>\\n",append=TRUE)\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/README Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,89 @@
+NGSrich - Version 0.5.4
+Target enrichment performance for next-generation sequencing.
+
+
+Description:
+NGSrich is a tool for researchers concerned with target enrichment issues in next-generation sequencing.
+It evaluates the target enrichment performance of target regions given in BED format and outputs
+summary statistics, visualizations, and some additional files giving details on the analysis.
+
+
+---------------------------------------------------------------------------------------------------------
+
+
+Usage:
+java NGSrich evaluate -r <readsFile> -u <genomeName> -t <target>
+ [(-a|-g) <annotation>] [ -s <sName> ] [-T <tmpDir>] [ -o <outDir>] [-p <poor> -h <high>][--no-details]
+
+
+The program should be started from the bin directory of the software.
+Required arguments:
+ <readsFile>: Path to the read alignment file in SAM or BAM alignment format
+ (http://samtools.sourceforge.net/SAM-1.3.pdf)
+ <genomeName>: UCSC genome version name (e.g. 'hg19').
+ <target>: Path to the target file in BED annotation format
+ (http://genome.ucsc.edu/FAQ/FAQformat.html#format1, 3 columns required)
+Optional arguments:
+ <annotation>: the local path of the annotation of the genome
+ [default: genome annotation is downloaded from the site of the ucsc genome
+ browser and placed into the temporary directory of the sample.]
+ <sName>: Name of the sample being processed - defaults to prefix of <readsFile>.
+ <tmpDir>: Temporary directory - defaults to '/tmp'.
+ <outDir>: Output directory - defaults to '<pathToReadsFile>/enrichment'.
+ <poor>: Coverage cutoff to define poorly covered genes - defaults to 2.
+ <high>: Coverage cutoff to define highly covered genes - defaults to 200.
+ --no-details: Represses the computation of the evaluation details.
+
+
+Output:
+1. The HTML file contains a report of the target enrichment results including
+ tables of poorly and highly covered genes (defined by cutoffs <poor> and <high>.
+ For vizualisation, plots are embedded in this document. The contents of this report
+ are actually based on an evaluation of the XML and BED files.
+2. The XML file contains the summary statistics for the enrichment performance.
+3. The BED file contains detailed coverage information for each single region specified in
+ the input target file.
+4. The WIG files (http://genome.ucsc.edu/goldenPath/help/wiggle.html) contain a per-base
+ description of the coverage on the target regions, one for the target regions specified in
+ the input target file and one for the whole genome (gaps are skipped). These files can be
+ used for visualization in a Genome Browser, e.g. at http://genome.ucsc.edu/cgi-bin/hgGateway.
+
+
+---------------------------------------------------------------------------------------------------------
+
+
+Several enrichment performance reports can be summarized by the command NGSrich-summarize.
+This should also be started from the bin directory of the software.
+
+Usage: java NGSrich summarize -r <inputIndexFile> -o <outDir> [ -p <poor> -h <high> ]
+
+Required arguments:
+ <inputIndexFile>: Text file with each line containing the output directory of
+ the report for one of the samples to be summarized.
+ <outDir>: Output directory.
+
+Optional arguments:
+ <poor>: Coverage cutoff to define poorly covered genes - defaults to 2.
+ <high>: Coverage cutoff to define highly covered genes - defaults to 200.
+
+
+Output:
+The HTML file contains a summary report and summarizing performance statistics for several
+target enrichment experiments. For each sample, the detailed performance report can be
+accessed by a hyperlink.
+
+
+---------------------------------------------------------------------------------------------------------
+
+
+Requirements:
+The NGSrich software runs only on 64-bit Linux. It requires an installation of R and the Java
+Runtime Environment (JRE), which are preinstalled on most Linux distributions. If not,
+please visit the official sites for detailed installation instructions.
+
+
+Contact:
+You can send an e-mail to the NGSrich mailing list at <NGSrich-users@lists.sourceforge.net>.
+Please tell us your experiences with the software itself and the documentation. We particularly welcome new
+bug reports and suggestions for new or enhanced features.
+

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/DEFAULT.properties
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/DEFAULT.properties Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,10 @@
+! Path of the temporary directory.
+tmpDir: /tmp
+! Path of the father directory of the output directory. When empty the output directory is placed in the directory containing the reads alignment file.
+outDirPath:
+! Name of the output directory (not the path).
+outDir: enrichment
+! Define poorly covered genes.
+poor: 2
+! Defines highly covered genes.
+high: 200

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/adapters/OracleV1DOMAdapter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/adapters/OracleV2DOMAdapter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/adapters/XML4JDOMAdapter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/adapters/XercesDOMAdapter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/adapters/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/org/jdom/adapters/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,7 @@
+<body>
+
+Classes to interface with various DOM implementations. Not generally
+needed except in truly advanced situations. JAXPDOMAdapter is most commonly
+used.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/AbstractFilter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/Filter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/NegateFilter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/OrFilter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/filter/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/org/jdom/filter/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,9 @@
+<body>
+
+Classes to programmatically filter nodes of a document based on type, name,
+value, or other aspects and to boolean and/or/negate these rules. Filters can
+be used in methods like getContent(Filter) and getDescendants(Filter). A
+sampling of generally useful filters are provided here. Alternate filters can
+be user defined.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/BuilderErrorHandler.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/JAXPParserFactory.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/JDOMParseException.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/SAXBuilder.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/SAXHandler.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/TextBuffer.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/input/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/org/jdom/input/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,10 @@
+<body>
+
+Classes to build JDOM documents from various sources. The most common builder
+class is SAXBuilder which constructs a JDOM document using a SAX parser and
+can pull content from files, streams, sockets, readers, and so on. It can use
+any underlying SAX parser to handle the parsing chores. SAXHandler provides
+support for SAXBuilder. DOMBuilder lets you build from a pre-existing DOM
+tree.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/DOMOutputter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/EscapeStrategy.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/Format$DefaultEscapeStrategy.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/Format$TextMode.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/JDOMLocator.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/NamespaceStack.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/SAXOutputter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/XMLOutputter$NamespaceStack.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/XMLOutputter.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/output/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/org/jdom/output/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,15 @@
+<body>
+
+Classes to output JDOM documents to various destinations. The most common
+outputter class is XMLOutputter which outputs a document (or part of a
+document) as a stream of bytes. Format and EscapeStrategy support the
+XMLOutputter in letting you choose how the output should be formatted and how
+special characters should be escaped.
+
+SAXOutputter lets you output as a stream of SAX events (handy especially in
+transformations). JDOMLocator supports SAXOutputter and helps you observe the
+SAX output process.
+
+DOMOutputter lets you output a JDOM document as a DOM tree.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/org/jdom/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,13 @@
+<body>
+
+Classes to represent the components of an XML document. The Verifier is a
+special class useful in ensuring well-formedness of documents. The Parent
+interface is implemented by Document and Element exposing their commonality.
+The Content abstract class is extended by all the node types of a document
+except Document itself.
+
+The JDOMFactory interface and DefaultJDOMFactory standard implementation
+provide advanced users with the ability to create subtypes of the org.jdom
+classes.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/JDOMResult$DocumentBuilder.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/XSLTransformException.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/XSLTransformer.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/transform/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/org/jdom/transform/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,8 @@
+<body>
+
+Classes to help with transformations, based on the JAXP TrAX classes.
+JDOMTransformer supports simple transformations with one line of code.
+Advanced features are available with the JDOMSource and JDOMResult classes
+that interface with TrAX.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/xpath/XPath$XPathString.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/xpath/XPath.class

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/org/jdom/xpath/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/org/jdom/xpath/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,6 @@
+<body>
+
+Support for XPath from within JDOM. XPath provides a common interface with a
+pluggable back-end. The default back end is Jaxen.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/bin/xmlFilePattern.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/bin/xmlFilePattern.xml Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,62 @@
+<?xml version="1.0" ?>
+<SampleSet>
+ <NumberSamples>1</NumberSamples>
+ <Sample>
+ <SampleName>name</SampleName>
+ <ReadLength>0</ReadLength>
+ <NumberReads>0</NumberReads>
+ <TargetSize>0</TargetSize>
+ <AvTargetCoverage>0</AvTargetCoverage>
+ <SDTargetCoverage>0</SDTargetCoverage>
+ <ReadsOnTarget>
+ <OnTarget>
+ <NumberReads>0</NumberReads>
+ <PercReads>0</PercReads>
+ </OnTarget>
+ <Plus100>
+ <NumberReads>0</NumberReads>
+ <PercReads>0</PercReads>
+ </Plus100>
+ <Plus200>
+ <NumberReads>0</NumberReads>
+ <PercReads>0</PercReads>
+ </Plus200>
+ </ReadsOnTarget>
+ <ReadsOverlappingTarget>
+ <OnTarget>
+ <NumberReads>0</NumberReads>
+ <PercReads>0</PercReads>
+ </OnTarget>
+ <Plus100>
+ <NumberReads>0</NumberReads>
+ <PercReads>0</PercReads>
+ </Plus100>
+ <Plus200>
+ <NumberReads>0</NumberReads>
+ <PercReads>0</PercReads>
+ </Plus200>
+ </ReadsOverlappingTarget>
+ <TargetCovered>
+ <from1x>
+ <NumberBases>0</NumberBases>
+ <PercBases>0</PercBases>
+ </from1x>
+ <from5x>
+ <NumberBases>0</NumberBases>
+ <PercBases>0</PercBases>
+ </from5x>
+ <from10x>
+ <NumberBases>0</NumberBases>
+ <PercBases>0</PercBases>
+ </from10x>
+ <from20x>
+ <NumberBases>0</NumberBases>
+ <PercBases>0</PercBases>
+ </from20x>
+ <from30x>
+ <NumberBases>0</NumberBases>
+ <PercBases>0</PercBases>
+ </from30x>
+ </TargetCovered>
+ </Sample>
+</SampleSet>
\ No newline at end of file

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/DEFAULT.properties
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/DEFAULT.properties Mon Nov 21 08:12:19 2011 -0500

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/NGSrich.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/NGSrich.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,58 @@
+import java.io.IOException;
+
+import _main.NGSrichEvaluate;
+import _main.NGSrichSummarize;
+import exceptions.FileFormatException;
+
+/**
+ * This is the main class.
+ *
+ * @author Peter Frommolt
+ * @author Ali Abdallah
+ */
+
+public class NGSrich {
+
+ /**
+ * Self Explanatory.
+ *
+ * @param args an Array of argument. The first argument is command and the
+ * other arguments are its options.
+ *
+ * @throws FileFormatException if the used files have formally a bad format.
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ public static void main(String[] args) throws FileFormatException,
+ IOException, InterruptedException {
+
+ String usagestr =
+ "\nThis is NGSrich, version 0.5.4.\n\n"
+ + "Usage: java NGSrich [command] [options]\n\n"
+ + "\tCommands:\n"
+ + "\tevaluate"
+ + "\tEvaluate target enrichment for a single sample.\n"
+ + "\tsummarize"
+ + "\tCreate a summary report for several evaluations.\n";
+
+ int alen = args.length;
+ if (alen == 0) {
+ System.out.println(usagestr);
+ System.exit(0);
+ } else {
+ String[] cparams = new String[alen - 1];
+ for (int i = 0; i < alen - 1; i = i + 1) {
+ cparams[i] = args[i + 1];
+ }
+ String eval = "evaluate", summ = "summarize";
+ if (eval.equals(args[0])) {
+ // Geändert von AA 27.07.2011.
+ new NGSrichEvaluate(cparams).evaluate();
+ }
+ if (summ.equals(args[0])) {
+ // Geändert von AA 27.07.2011.
+ new NGSrichSummarize(cparams).summarize();
+ }
+ }
+ }
+}
\ No newline at end of file

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/_main/Enrichment.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/_main/Enrichment.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,490 @@\n+package _main;\n+\n+import java.io.File;\n+import java.io.FileWriter;\n+import java.io.IOException;\n+import java.sql.Time;\n+import java.util.Scanner;\n+\n+import middlewares.Misc;\n+import converters.Read2Wig;\n+import converters.ReadOnTarget2Wig;\n+import exceptions.ChromosomeFormatException;\n+import exceptions.ChromosomeMismatchException;\n+import exceptions.ChromosomeNotFoundException;\n+import exceptions.FileFormatException;\n+import exceptions.GenomeAnnotationException;\n+import exceptions.NullOrNegativeRangeException;\n+import exceptions.RangeFormatException;\n+import exceptions.RangeLimitNotFoundException;\n+import filters.Filter;\n+import filters.GenomeFilter;\n+import filters.ReadFilter;\n+import filters.TargetFilter;\n+\n+/**\n+ * This is a scheduler for the phases of the evaluation.\n+ * \n+ * @author Ali Abdallah\n+ * @version 19.03.2011\n+ * @since jdk 1.6\n+ */\n+\n+public class Enrichment {\n+\t\n+\tString \n+\t/**\n+\t * The name of the read alignment file.\n+\t */\n+\treadFileName, \n+\t/**\n+\t * the name of the genome annotation file.\n+\t */\n+\tgenomeFName, \n+\t/**\n+\t * the ucsc-name of the genome (e.g. hg19).\n+\t */\n+\tgenomeName, \n+\t/**\n+\t * the name of the file of the targeted regions.\n+\t */\n+\ttargetFName, \n+\t/**\n+\t * the temporary directory.\n+\t */\n+\ttmpDir,\n+\t/**\n+\t * the output directory.\n+\t */\n+\toutDir,\n+\t/**\n+\t * the xml summary file containing various overall statistics.\n+\t */\n+\txmlSummaryFile, \n+\t/**\n+\t * the name of the detailed coverage data file.\n+\t */\n+\tdetailsFileName, \n+\t/**\n+\t * the .bed file containing target-level coverage statistics data. \n+\t */\n+\tbeddetailsFileName,\n+\t/**\n+\t * the process number used for unique naming.\n+\t */\n+\tproc, \n+\t/**\n+\t * the name of the read alignment file without extension.\n+\t */\n+\tprefix, \n+\t/**\n+\t * the extension of the read alignment file.\n+\t */\n+\tsuffix,\n+\t/**\n+\t * The name of the read alignment file after the reduction.\n+\t */\n+\tareadFileName, \n+\t/**\n+\t * The name of the genome annotation file after the reduction.\n+\t */\n+\taGenomeFName, \n+\t/**\n+\t * the name of the file of the targeted regions after the reduction.\n+\t */\n+\taTargetFName;\n+\tint \n+\t/**\n+\t * Cutoff for poor coverage [default: 2].\n+\t * \n+\t */\n+\tpoor, \n+\t/**\n+\t * Cutoff for high coverage [default: 200].\n+\t */\n+\thigh,\n+\tdetails;\n+\n+\t/**\n+\t * Construcs an enrichment object and initializes the evaluation parameters.\n+\t * @param args the list of all evaluation parameters.\n+\t */\n+\tpublic Enrichment(String... args) {\n+\t\treadFileName = args[0];\n+\t\tgenomeName = args[8];\n+\t\ttargetFName = args[2];\n+\t\tif (!targetFName.endsWith("bed")) {\n+\t\t\tSystem.out.println("WARNING: Target file: " + targetFName + " must be in the bed format.");\n+\t\t}\n+\t\tif (args.length > 3) {\n+\t\t\tTime time = new Time(System.currentTimeMillis());\n+\t\t\tString nano = ""+System.nanoTime();\n+\t\t\t\n+\t\t\ttmpDir = args[3] + Misc.slash(args[3]) +"Sample_From_"+\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\ttime.getHours()+"_"+\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\ttime.getMinutes()+"_"+\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\ttime.getSeconds()+"_"+nano+ "/";\n+\t\t\tnew File(tmpDir).mkdir();\n+\t\t\tnew File(tmpDir).setReadable(true);\n+\t\t\tnew File(tmpDir).setWritable(true);\n+\t\t\toutDir = args[4] + Misc.slash(args[4]);\n+\n+\t\t\tif (!(new File(tmpDir).isDirectory()) && new File(tmpDir).exists()) {\n+\t\t\t\tSystem.out.println("File " + tmpDir\n+\t\t\t\t\t\t+ " is not a directory.\\nProgram stopped.");\n+\t\t\t\tSystem.exit(0);\n+\t\t\t} else if (!(new File(tmpDir).exists())) {\n+\t\t\t\tSystem.out.println("File " + tmpDir\n+\t\t\t\t\t\t+ " not found.\\nProgram stopped.");\n+\t\t\t\tSystem.exit(0);\n+\t\t\t}\n+\t\t}\n+\t\tif (args.length > 5) {\n+\t\t\ttry {\n+\t\t\t\tpoor = Integer.parseInt(args[5]);\n+\t\t\t\thigh = Integer.parseInt(args[6]);\n+\t\t\t} catch (NumberFormatException nfe) {\n+\t\t\t\tSystem.out\n+\t\t\t\t\t\t.println("Warning: poor or high must be integers.\\n<poor> and <high> are set to the standard values.");\n+\t\t\t\tpoor = 2;\n+\t\t\t\thigh = 200;\n+\t\t\t}\n+\t\t} else {\n+\t\t\tpoor = 2;\n+\t\t\thigh = 200;\n+\t\t}\n+\t\t\n+\t\tgenomeFName = (args[1].equals("none"))?downloadGenomeAnnotation():args[1];\n+\t\t\n+\t\tprefix = Misc.prefix(readFileName);\n+\t\tif (args[7] != "'..b'hrInfoPath);\n+\t\t\t\tscript = Misc.scriptDir() + Misc.slash(Misc.scriptDir())+"R/eval_details.R";\n+ outDirR = (lastSlash == outDir.length() - 1) ? outDir.substring(0, lastSlash) : outDir;\n+ \n+ String call2 = \t"Rscript "+ script + " " + xmlSummaryFile + " " + beddetailsFileName \n+\t\t\t\t\t\t\t+ " " + detailsFileName + " " + chrInfoPath + " " + outDirR + " " \n+\t\t\t\t\t\t\t+ genomeName;\n+ Process p2 = rt.exec(call2);\n+ stdout=new Scanner(p2.getInputStream());\n+ stderr=new Scanner(p2.getErrorStream());\n+ \n+ while(stdout.hasNextLine()){System.out.println(stdout.nextLine());}\n+ while(stderr.hasNextLine()){System.out.println(stderr.nextLine());}\n+ stdout.close(); stderr.close();\n+\t\t\t}\n+ \n+\t\t\tString path = outDir+prefix+"_enrichment.html";\n+\t\t\tSystem.out.println("Created plots and HTML summary report");\n+\t\t\tif (new File(path).exists()) {\n+\t\t\t System.out.println("\\nSTEP 3 successfully completed");\n+\t\t\t} else {\n+\t\t\t System.out.println("HTML FILE " + path + " not found");\n+\t\t\t System.out.println("\\nSTEP 3 unsuccessful");\n+\t\t\t}\n+\t\t}\n+\t\tcatch (IOException e) {\n+\t\t\te.printStackTrace();\n+\t\t}\n+\t}\n+\n+\t/**\n+\t * This is the fourth phase. In this phase the detailed datta from phase 2\n+\t * are converted to the wiggle format. The method uses a ReadOnTarget2Wig\n+\t * object to accomplish this task.\n+\t * \n+\t */\n+\tpublic void computeWiggleFile() {\n+\t\ttry {\n+\t\t\tSystem.out.println("Computing wiggle file for on-target reads");\n+\t\t\tif (!new File(detailsFileName).exists())\n+\t\t\t\tdetailsFileName = tmpDir + new File(detailsFileName).getName();\n+\t\t\t\n+\t\t\tnew ReadOnTarget2Wig(detailsFileName, prefix, outDir + "data", \n+\t\t\t\t\tMisc.prefix(readFileName)+ "\\nonTarget");\n+\t\t\tSystem.out.println("Wiggle file for on-target reads created");\n+\t\t\tSystem.out.println("Output written to " + outDir + "data/" + prefix + "_onTarget.wig");\n+\t\t\tFile[] outputFiles = new File(outDir + "data/")\n+\t\t\t\t\t.listFiles();\n+\t\t\tfor (int i = 0; i < outputFiles.length; i++) {\n+\t\t\t\tif (outputFiles[i].getName().endsWith("wig")\n+\t\t\t\t\t\t&& outputFiles[i].getName().startsWith(\n+\t\t\t\t\t\t\t\tdetailsFileName.substring(\n+\t\t\t\t\t\t\t\t\tdetailsFileName.lastIndexOf("/") + 1,\n+\t\t\t\t\t\t\t\t\t\tdetailsFileName.lastIndexOf(".")))) {\n+\t\t\t\t\tFile f = new File(outDir + "data"\n+\t\t\t\t\t\t\t+ "/" + Misc.prefix(readFileName) + "_onTarget.wig");\n+\t\t\t\t\toutputFiles[i].renameTo(f);\n+\t\t\t\t\tbreak;\n+\t\t\t\t}\n+\t\t\t}\n+\t\t\tif (new File(outDir+"data/"+prefix+"_onTarget.wig").exists()){\n+\t\t\t\tSystem.out.println("\\nSTEP 4 successfully completed.");\n+\t\t\t} else {\n+\t\t\t\tSystem.out.println(outDir+"data/"+ prefix\n+\t\t\t\t\t\t+ "_onTarget.wig not found!\\n\\nSTEP 4 unsuccessful");\n+\t\t\t}\n+\t\t} catch (IOException e) {\n+\t\t\tSystem.err.println("Target conversion in Wig unsuccessful");\n+\t\t\te.printStackTrace();\n+\t\t}\n+\t}\n+\n+\t/**\n+\t * This is the fifth and last phase of the evaluation process. In contrast\n+\t * to the fourth phase, this method uses a Read2Wig object to convert the\n+\t * detailed data for all reads (and not only for reads on targets) to the\n+\t * wiggle format.\n+\t * \n+\t */\n+\tvoid computeOverallWiggleFile() {\n+\t\ttry {\n+\t\t\tSystem.out.println("Computing wiggle file for all reads");\n+\t\t\tnew Read2Wig(areadFileName, prefix, outDir + "data", \n+\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenomeFName, tmpDir);\n+\t\t\tString overallWiggleFileName = prefix + ".wig";\n+\t\t\tSystem.out.println("Wiggle file for all reads created");\n+\t\t\tSystem.out.println("Output written to " + outDir + "data/" + \n+\t\t\t\t\t\t\t\t\t\t\t\t\t\toverallWiggleFileName);\n+\t\t\tif (new File(outDir + "data/" + overallWiggleFileName).exists()) {\n+\t\t\t\tSystem.out.println("\\nSTEP 5 successfully completed.");\n+\t\t\t} else {\n+\t\t\t\tSystem.out.println(outDir + "data/" + overallWiggleFileName\n+\t\t\t\t\t\t+ "not found\\n\\nSTEP 5 unsuccessful");\n+\t\t\t}\n+\t\t} catch (IOException e) {\n+\t\t\tSystem.err\n+\t\t\t\t\t.println("Creating wiggle file for all reads was unsuccessful");\n+\t\t\te.printStackTrace();\n+\t\t}\n+\t}\n+}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/_main/EnrichmentStatsComputer.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/_main/EnrichmentStatsComputer.java Mon Nov 21 08:12:19 2011 -0500

[

b"@@ -0,0 +1,595 @@\n+package _main;\n+\n+import java.io.File;\n+import java.io.FileNotFoundException;\n+import java.io.FileWriter;\n+import java.io.IOException;\n+import java.util.Scanner;\n+\n+import org.jdom.Element;\n+\n+import datastructures.ReducedReadLine;\n+import datastructures.TargetLine;\n+import exceptions.ChromosomeFormatException;\n+import exceptions.ChromosomeNotFoundException;\n+import exceptions.NullOrNegativeRangeException;\n+import exceptions.RangeFormatException;\n+import exceptions.RangeLimitNotFoundException;\n+\n+import middlewares.GeneExtractor;\n+import middlewares.HitsCounter;\n+import middlewares.Misc;\n+import middlewares.ReadCounter;\n+import middlewares.XMLSummaryFileBuilder;\n+\n+/**\n+ * This class is for computation of the coverage, BED coverage and statistics\n+ * output files.\n+ * \n+ * @author Ali Abdallah\n+ * @version 02.02.2011\n+ * @since jdk 1.6.0\n+ */\n+\n+public class EnrichmentStatsComputer {\n+\n+\t/* ***********************************************************************\n+\t * \t\t\t\t\t\t\tFIELDS OF THE CLASS\t\t\t\t\t\t\t\t\n+\t * ***********************************************************************/\n+\tprivate String \n+\t/** \n+\t * 4-column alignment file sorted by alignment subject and position.\n+\t */ \n+\talign, \n+\t/**\n+\t * 3-column target file sorted by subject and target starting position.\n+\t */\n+\ttarget, \n+\t/** \n+\t * Annotation file.\n+\t */\n+\tgenome, \n+\t/**\n+\t * Statistics file in the xml-format.\n+\t */\n+\tsummary, \n+\t/**\n+\t * Coverage file.\n+\t */\n+\tdetails, \n+\t/**\n+\t * Coverage BED file.\n+\t */\n+\ttargetCS,\n+\t/**\n+\t * The absolute name of the read alignment file without the extension.\n+\t */\n+\tprefix, \n+ \n+\t/**\n+\t * The directory under which temporary data are saved (temporary directory).\n+\t */\n+\ttmpDir, \n+\t/**\n+\t * The directory of the computed results (output directory).\n+\t */\n+\toutDir;\n+\t\n+\t\n+\tprivate Scanner \n+\t/**\n+\t * Scanner of the read alignment file (sam format).\n+\t */\n+\trScanner, \n+\t/**\n+\t * Scanner of the genome annotation file.\n+\t */\n+\tgScanner, \n+\t/**\n+\t * Scanner of the file of targets.\n+\t */\n+\ttScanner;\n+\t\n+\tprivate FileWriter \n+\t/**\n+\t * Writer used to write the computed statistics into the statistics file.\n+\t */\n+\tsummaryWriter, \n+\t/**\n+\t * Writer used to write coverage data at base-level into the coverage file. \n+\t */\n+\tdetailsWriter, \n+\t/**\n+\t * Writer used to write the summarized coverage data at target level into\n+\t * the coverage BED file.\n+\t */\n+\ttargetCSWriter;\n+\t\n+\t/**\n+\t * Counter used to counts the coverage frequencies at different levels. \n+\t */\n+\tprivate HitsCounter hc;\n+\t/**\n+\t * Counter used to count both: Reads exactly on the targets or overlapping\n+\t * the targets and Reads doing this in a scope of 100 resp. 200 bases from \n+\t * both end.\n+\t */\n+\tprivate ReadCounter rc;\n+\t\n+\t/**\n+\t * A Gene Extractor used to extract the genes overlapping the specified \n+\t * targets. \n+\t */\n+\tprivate GeneExtractor ge;\n+\t\n+\t/**\n+\t * Counter for the reads.\n+\t */\n+\tprivate int numReads = 0, \n+\t/**\n+\t * Counter for all target bases.\n+\t */\n+\ttargetBases = 0, \n+\t/**\n+\t * Counter for the bases in a specific target.\n+\t */\n+\tcurrTargetBases = 0;\n+\t\n+\t/**\n+\t * The average Coverage of the targets.\n+\t */\n+\tprivate double avCov = 0;\n+\t/**\n+\t * The average Coverage of the current observed target.\n+\t */\n+\tprivate double curAvCov = 0;\n+\t/**\n+\t * Flag indicating the end of the read file.\n+\t */\n+\tprivate boolean endReads = false;\n+\t/**\n+\t * Flag indicates if the coverage line was written or not. \n+\t */\n+\tprivate boolean covWritten = false;\n+\t\n+\t/**\n+\t * Contains always the current observers read line from the sam file.\n+\t */\n+\tprivate ReducedReadLine rLine;\n+\n+\n+\tprivate int rlength;\n+\t\n+\t/**\n+\t * ID's of the leaf-tags in the XML summary file. \n+\t */\n+\tprivate static final int \n+\tfrom30xPERC = 28, from30xBASES = 27,from20xPERC = 26, from20xBASES = 25, \n+\tfrom10xPERC = 24, from10xBASES = 23,from5xPERC = 22, from5xBASES = 21,\n+\tfrom1xPERC = 20, from1xBASES = 19, OV200P = 18, OV_200 = 17,\n+\tOV100P = 16, OV_100 = 15, OV_PERC = 14, OV = 13, "..b'ite(tLine + "\\t" + currTargetGene + "\\t"\n+\t\t\t\t+ dfloor((curAvCov / (double)currTargetBases), 2) + "\\t"\n+\t\t\t\t+ dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2)\n+\t\t\t\t+ "\\t"\n+\t\t\t\t+ dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2)\n+\t\t\t\t+ "\\t"\n+\t\t\t\t+ dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2)\n+\t\t\t\t+ "\\t"\n+\t\t\t\t+ dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2)\n+\t\t\t\t+ "\\t"\n+\t\t\t\t+ dfloor((hc.getNextLevelCurrentHits() / (double)currTargetBases)*100, 2)\n+\t\t\t\t+ "\\r\\n");\n+\t\tcovWritten = true;\n+\t\thc.resetCurrentHits();\n+\t}\n+\n+\t/**\n+\t * Cut decimal places greater than the specified one.\n+\t * @param number the number to be cut.\n+\t * @param decimalPlace the decimalPlace after which the cut-operation\n+\t * \t\t take place.\n+\t * @return the cut number.\n+\t */\n+\tpublic static double dfloor(double number, int decimalPlace) {\n+\t\treturn Math.floor(number * Math.pow(10, decimalPlace))\n+\t\t\t\t/ Math.pow(10, decimalPlace);\n+\t}\n+\n+\t/**\n+\t * Checks if the read exceeded the target.\n+\t * @param rl read line.\n+\t * @param tl target line.\n+\t * @return true if the read starts right to the end position of the target\n+\t * and false otherwise. \n+\t */\n+\tpublic static boolean readExceededTarget(ReducedReadLine rl, TargetLine tl) {\n+\t\treturn !(rl.start() <= tl.end() || rl.end() <= tl.end());\n+\t}\n+\n+\t/**\n+\t * <pre> \n+\t * 1. Increments the number of Reads, overlapping targets within a scope of \n+\t * \t 0, 100 and 200 bases from both ends, by one.\n+\t * 2. Increments the number of hits on the hitted bases by one. \n+\t * </pre>\n+\t * @param rl the read line.\n+\t * @param tl the target line.\n+\t * @param bases the base hits array of the target.\n+\t */\n+\tprivate void incOverlapsValues(ReducedReadLine rl, TargetLine tl, int[] bases) {\n+\t\t// Forward reads.\n+\t\tif (rl.isForwardRead()) {\n+\t\t\tif (rl.end() >= tl.start() && rl.start() <= tl.end()) {\n+\t\t\t\t// incrementing the number of his on the hitted bases by one.\n+\t\t\t\tint start = Math.max(0, rl.start() - tl.start());\n+\t\t\t\tint stop = Math.min(bases.length - 1, rl.end() - tl.start());\n+\t\t\t\tfor (int i = start; i <= stop; i++) \n+\t\t\t\t\tbases[i]++;\n+\t\t\t\t// incrementing the number of Reads overlapping targets by one.\n+\t\t\t\trc.incOver();\n+\t\t\t}\n+\t\t\tif (tl.start() - 100 <= rl.end() && rl.start() <= tl.end() + 100)\n+\t\t\t\t// incrementing the number of Reads overlapping targets(+/-100)\n+\t\t\t\t// by one.\n+\t\t\t\trc.incOver100();\n+\t\t\tif (tl.start() - 100 <= rl.end() && rl.start() <= tl.end() + 100)\n+\t\t\t\t// incrementing the number of Reads overlapping targets(+/-200)\n+\t\t\t\t// by one.\n+\t\t\t\trc.incOver200();\n+\t\t} \n+\t\t// Reverse reads.\n+\t\telse {\n+\t\t\tif (rl.start() >= tl.start() && rl.end() <= tl.end()) {\n+\t\t\t\tint start = Math.max(0, rl.end() - tl.start());\n+\t\t\t\tint stop = Math.min(bases.length - 1, rl.start() - tl.start());\n+\t\t\t\tfor (int i = start; i <= stop; i++) bases[i]++;\n+\t\t\t\trc.incOver();\n+\t\t\t}\n+\t\t\tif (rl.start() >= tl.start() - 100 && rl.end() <= tl.end() + 100)\n+\t\t\t\trc.incOver100();\n+\t\t\tif (rl.start() >= tl.start() - 100 && rl.end() <= tl.end() + 100)\n+\t\t\t\trc.incOver200();\n+\t\t}\n+\t}\n+\n+\t/**\n+\t * Increments the number of Reads on targets within a scope of 0, 100 and \n+\t * 200 bases from both ends, by one.\n+\t * @param rl the read line.\n+\t * @param tl the target line.\n+\t */\n+\tprivate void incOnTargetValues(ReducedReadLine rl, TargetLine tl) {\n+\t\t// Forward read.\n+\t\tif (rl.isForwardRead()) {\n+\t\t\tif ((tl.start() <= rl.start()) && (rl.end() <= tl.end()))\n+\t\t\t\trc.incOn();\n+\t\t\tif ((tl.start()-100 <= rl.start()) && (rl.end() <= tl.end()+100))\n+\t\t\t\trc.incOn100();\n+\t\t\tif ((tl.start()-200 <= rl.start()) && (rl.end() <= tl.end()+200))\n+\t\t\t\trc.incOn200();\n+\t\t} \n+\t\t// Reverse read.\n+\t\telse {\n+\t\t\tif (tl.start() <= rl.end() && rl.start() <= tl.end())\n+\t\t\t\trc.incOn();\n+\t\t\tif (tl.start()-100 <= rl.end() && rl.start()<= tl.end()+100)\n+\t\t\t\trc.incOn100();\n+\t\t\tif (tl.start()-200 <= rl.end() && rl.start() <= tl.end()+200)\n+\t\t\t\trc.incOn200();\n+\t\t}\n+\t}\n+\n+}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/_main/NGSrichEvaluate.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/_main/NGSrichEvaluate.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,227 @@\n+package _main;\n+\n+import java.io.BufferedInputStream;\n+import java.io.File;\n+import java.io.FileInputStream;\n+import java.io.FileWriter;\n+import java.io.IOException;\n+import java.sql.Time;\n+import java.util.Properties;\n+import middlewares.Misc;\n+import exceptions.ChromosomeMismatchException;\n+import exceptions.FileFormatException;\n+\n+/**\n+ * This is the Main-class of the evaluation part of the software. This class\n+ * uses the Enrichment-class to process the phases (the parts) of the pipeline.\n+ * \n+ * @author Ali Abdallah\n+ */\n+\n+public class NGSrichEvaluate {\n+\n+\t/**\n+\t * An array of arguments containing the following option elements in the \n+\t * following order:\n+\t * -r <readsFile> (-a|-g) <annotation> -t <target> [-s <sName>] \n+\t * [-T <tmpDir>][-o <outDir>][-p <poor> -h <high>][-no_details]\n+\t * \n+\t * Required:\n+\t * <readsFile> \tPath to read alignment file in SAM or BAM format.\n+\t * <annotation> UCSC genome version name.\n+\t * <target>\t\tPath to target file in BED format.\n+\t * \n+\t * Optional:\n+\t * <sName> \t\tSample name [default: prefix of <readsFile>].\n+\t * <tmpDir> \tTemporary directory [default: \'/tmp\'].\n+\t * <outDir> \tOutput directory [default: \'<pathToReadsFile>/enrichment\'].\n+\t * <poor> \t\tCutoff for poor coverage [default: 2].\n+\t * <high> \t\tCutoff for high coverage [default: 200].\n+\t */\n+\tString[] args;\n+\n+\tpublic NGSrichEvaluate(String[] args) {\n+\t\tthis.args = args;\n+\t}\n+\n+\tpublic void evaluate() throws IOException, FileFormatException,\n+\t\t\tInterruptedException {\n+\t\t/**\n+\t\t * Ordered List of Parameter (left/right): readFName genomeFName\n+\t\t * targetFName tmpDir outDir\n+\t\t * \n+\t\t */\n+\n+\t\tint alen = args.length;\n+\t\tString[] params = new String[10];\n+\n+\t\tString usagestr = \n+\t\t\t\t"\\nUsage: java NGSrich evaluate -r <readsFile> " \n+\t\t\t\t+ "-u <genome-name> -t <target> [(-a|-g) "\n+\t\t\t\t+ "<annotation>] [-s <sName>] [-T <tmpDir>] "\n+\t\t\t\t+ "[-o <outDir>] [-p <poor> -h <high>][--no-details>]\\n\\n\\tRequired:\\n\\t"\n+\t\t\t\t+ "<readsFile>\\tPath to read alignment file in SAM or BAM format."\n+\t\t\t\t+ "\\n\\t<genome-name>\\tUCSC genome version name.\\n\\t<target>\\tPath "\n+\t\t\t\t+ "to target file in BED format.\\n\\n\\tOptional:\\n\\t<sName>\\t\\t"\n+\t\t\t\t+ "Sample name [default: prefix of <readsFile>].\\n\\t<annotation>\\t\\t"\n+\t\t\t\t+ "path of the annotation file [default: the genome is " \n+\t\t\t\t+ "downloaded based on the genome version name].\\n\\t<tmpDir>\\t"\n+\t\t\t\t+ "Temporary directory [default: \'/tmp\'].\\n\\t<outDir>\\tOutput "\n+\t\t\t\t+ "directory [default: \'<pathToReadsFile>/enrichment\'].\\n\\t"\n+\t\t\t\t+ "<poor>\\t\\tCutoff for poor coverage [default: 2].\\n\\t<high>"\n+\t\t\t\t+ "\\t\\tCutoff for high coverage [default: 200]. \\n\\t--no-details\\tto repress the computation of the" +\n+\t\t\t\t\t\t" evaluation details\\n";\n+\t\t\n+\t\tif (alen == 0) {\n+\t\t\tSystem.out.println(usagestr);\n+\t\t\tSystem.exit(0);\n+\t\t}\n+\n+\t\tboolean t = false, o = false, h = false, po = false, sname = false, u = false, r = false, g = false,\n+\t\t\t\ta = false, T = false;\n+\t\tparams[9] = "1";\n+\t\tfor (int i = 0; i < alen; i = i + 2) {\n+\t\t\tif ((args[i].length() == 2 && args[i].charAt(0) == \'-\') || args[i].equals("--no-details")) {\n+\t\t\t\tchar flag = (args[i].length()==2)?args[i].charAt(1):args[i].charAt(2);\n+\t\t\t\tswitch (flag) {\n+\t\t\t\tcase \'r\': params[0] = args[i + 1];r = true;break;\n+\t\t\t\tcase \'g\': params[1] = args[i + 1];g = true;break;\n+\t\t\t\tcase \'a\': params[1] = args[i + 1];a = true;break;\n+\t\t\t\tcase \'t\': params[2] = args[i + 1];t = true;break;\n+\t\t\t\tcase \'T\': params[3] = args[i + 1];T = true;break;\n+\t\t\t\tcase \'o\': params[4] = args[i + 1];o = true;break;\n+\t\t\t\tcase \'p\': params[5] = args[i + 1];po = true;break;\n+\t\t\t\tcase \'h\': params[6] = args[i + 1];h = true;break;\n+\t\t\t\t// Added by PF 2011-07-12\n+\t\t\t\tcase \'s\': params[7] = args[i + 1];sname = true;break;\n+\t\t\t\tcase \'u\': params[8] = args[i+1]; u = true;break;\n+\t\t\t\tcase \'n\': params[9]="0";break;\n+\t\t\t\t}\n+\t\t\t} else {\n+\t\t\t\tSystem.out.println(usagestr);\n+\t\t\t\tSystem.exit(0);\n+\t\t\t}\n+\t\t}\n+\t\t\n+\t\tboolean required = r && t && u;\n+\t\t\n+\t\tif(!required){\n+\t\t\tSystem.out.println("Some requir'..b'params[0]);\n+\t\t\tparams[4] = oPath + Misc.slash(oPath) + p.getProperty("outDir");\n+\t\t\tnew File(params[4]).mkdir();\n+\t\t}\n+\t\tif (!po)params[5] = p.getProperty("poor");\n+\t\tif (!h)params[6] = p.getProperty("high");\n+\t\tif (!sname)params[7] = "none";\n+\t\tif (!(a||g))params[1] = "none";\n+\t\t\n+\t\tEnrichment ngs = new Enrichment(params);\n+\t\t// Convert BAM to SAM if necessary.\n+\t\tString infile = params[0];\n+\t\tif (infile.endsWith(".bam")) {\n+\t\t\tSystem.out.println("======================0======================");\n+\t\t\tSystem.out.println("\\n>>> Found BAM file: converting to SAM\\n");\n+\t\t\tinfile = ngs.bam2sam();\n+\t\t}\n+\t\tngs.readFileName = infile;\n+\n+\t\t//\t\tFile timeReport = \n+\t\t//\tnew File(params[3] + Misc.slash(params[3])+"TimeReport.txt");\n+\t\t//\t\tFileWriter trWriter = new FileWriter(timeReport);\n+\t\t\n+\t\t// Reduce the files.\n+\t\tSystem.out.println("======================1======================");\n+\t\tSystem.out.println(">>> STEP 1: reducing files\\n");\n+\t\ttry {\n+\t\t\tlong start = System.currentTimeMillis();\n+\t\t\tngs.reduceFiles();\n+\t\t\tlong rtime = System.currentTimeMillis() - start;\n+\t\t\tTime time = new Time(rtime);\n+\t\t\t//trWriter.write("Reducing files took: " + time + "\\n");\n+\n+\t\t} catch (ChromosomeMismatchException e) {\n+\t\t\te.printStackTrace();\n+\t\t}\n+\t\t\n+\t\t// Compute the target coverage files.\n+\t\tSystem.out.println("\\n======================2======================");\n+\t\tSystem.out.println(">>> STEP 2: computing target coverage data\\n");\n+\t\tlong start = System.currentTimeMillis();\n+\t\tngs.computeTargetCoverageFiles();\n+\t\tlong rtime = System.currentTimeMillis() - start;\n+\t\tTime time = new Time(rtime);\n+\t\t//\t\ttrWriter.write("Computing target coverage data took: " + time + "\\n");\n+\t\t\n+\t\t// Evaluate enrichment.\n+\t\tSystem.out.println("\\n======================3======================");\n+\t\tSystem.out.println(">>> STEP 3: evaluating enrichment files\\n");\n+\t\tstart = System.currentTimeMillis();\n+\t\tngs.evaluate();\n+\t\trtime = System.currentTimeMillis() - start;\n+\t\ttime = new Time(rtime);\n+\t\t//trWriter.write("Evaluating enrichment files took: " + time + "\\n");\n+\t\tThread.sleep(10000);\n+\t\t\n+\t\t// Compute the target wiggle files.\n+\t\tSystem.out.println("\\n======================4======================");\n+\t\tSystem.out.println(">>> STEP 4: computing targets wiggle data\\n");\n+\t\tstart = System.currentTimeMillis();\n+\t\tngs.computeWiggleFile();\n+\t\trtime = System.currentTimeMillis() - start;\n+\t\ttime = new Time(rtime);\n+\t\t//trWriter.write("Computing targets wiggle data took: " + time + "\\n");\n+\n+\t\t// Compute the overall wiggle files.\n+\t\tSystem.out.println("\\n======================5======================");\n+\t\tSystem.out.println(">>> STEP 5: computing overall wiggle data\\n");\n+\t\tngs.computeOverallWiggleFile();\n+\t\tstart = System.currentTimeMillis();\n+\t\tngs.computeOverallWiggleFile();\n+\t\trtime = System.currentTimeMillis() - start;\n+\t\ttime = new Time(rtime);\n+\t\t//trWriter.write("Computing targets wiggle data took: " + time + "\\n");\n+\t\tSystem.out.println("\\n=============================================");\n+\t\t//trWriter.close();\n+\t}\n+\n+\tprivate String createDefaultPropertiesFile() throws IOException {\n+\t\tString default_properties_file = \n+\t\t\tMisc.binDir()+Misc.slash(Misc.binDir())+"DEFAULT.properties";\n+\t\tif(!new File(default_properties_file).exists()){\n+\t\t\tString default_str = \n+\t\t\t\t"! Path of the temporary directory.\\n" +\n+\t\t\t\t"tmpDir: /tmp\\n" +\n+\t\t\t\t"! Path of the father directory of the output directory. " +\n+\t\t\t\t"When empty the output directory is placed in the directory " +\n+\t\t\t\t"containing the reads alignment file.\\n" +\n+\t\t\t\t"outDirPath:\\n" +\n+\t\t\t\t"! Name of the output directory (not the path).\\n" +\n+\t\t\t\t"outDir: enrichment\\n" +\n+\t\t\t\t"! Define poorly covered genes.\\n" +\n+\t\t\t\t"poor: 2\\n" +\n+\t\t\t\t"! Defines highly covered genes.\\n" +\n+\t\t\t\t"high: 200";\n+\t\t\tFileWriter properties_writer = \n+\t\t\t\t\t\t\t\t\tnew FileWriter(default_properties_file);\n+\t\t\tproperties_writer.write(default_str);\n+\t\t\tproperties_writer.close();\n+\t\t}\n+\t\treturn default_properties_file;\n+\t}\n+}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/_main/NGSrichSummarize.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/_main/NGSrichSummarize.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,106 @@
+package _main;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.Properties;
+import java.util.Scanner;
+
+import middlewares.Misc;
+import exceptions.FileFormatException;
+
+/**
+ * This is the Main-class of the summarization part of the software. This class
+ * is a wrapper class. It calls the r-script "summarize_enrichment.R" which
+ * summarizes the evaluations of multiple samples.
+ *
+ * @author Peter Frommolt
+ */
+
+public class NGSrichSummarize {
+
+ /**
+ * An array of arguments containing the following option elements in the
+ * very same order: -i <inputIndex> -o <outDir> [-p <poor> -h <high>]
+ *
+ * Required:
+ * <inputIndex> File with evaluation directories to be summarized, one per
+ * line.
+ * <outDir> Output directory.
+ *
+ * Optional:
+ * <poor> Cutoff for poorly covered genes [default: 2].
+ * <high> Cutoff for highly covered genes [default: 200].
+ *
+ */
+ String[] args;
+
+ public NGSrichSummarize(String[] args){
+ this.args = args;
+ }
+
+ public void summarize() throws FileFormatException,
+ IOException,
+ InterruptedException{
+ int alen = args.length;
+ String[] params = new String[4];
+
+ String usagestr="\nUsage: NGSrich summarize -i <inputIndex> -o <outDir> " +
+ "[-p <poor> -h <high>]\n\n\tRequired:\n\t<inputIndex>\tFile " +
+ "with evaluation directories to be summarized, one per line." +
+ "\n\t<outDir>\tOutput directory.\n\n\tOptional:\n\t<poor>\t\t" +
+ "Cutoff for poorly covered genes [default: 2].\n\t<high>\t\t" +
+ "Cutoff for highly covered genes [default: 200].\n";
+
+ if(alen==0){
+ System.out.println(usagestr);
+ System.exit(0);
+ }
+
+ boolean i=false, o=false, h=false, po=false;
+ for(int k = 0; k < alen; k=k+2){
+ if(args[k].length() == 2 && args[k].charAt(0)=='-'){
+ char flag = args[k].charAt(1);
+ switch(flag){
+ case 'i': params[0]=args[k+1]; i=true; break;
+ case 'o': params[1]=args[k+1]; o=true; break;
+ case 'p': params[2]=args[k+1]; po=true; break;
+ case 'h': params[3]=args[k+1]; h=true; break;
+ }
+ }
+ else{
+ System.out.println(usagestr);
+ System.exit(0);
+ }
+ }
+
+ Properties p = new Properties();
+ FileInputStream stream=new FileInputStream(Misc.binDir()+Misc.slash(Misc.binDir())+"DEFAULT.properties");
+ p.load(stream); stream.close();
+
+ String infile, outdir, poor, high;
+
+ if(!i){System.out.println("Error: Argument -i is mandatory"); System.exit(1);}
+ if(!o){System.out.println("Error: Argument -o is mandatory"); System.exit(1);}
+ infile=params[0]; outdir=params[1];
+
+ if(!po){poor=p.getProperty("poor");}
+ else{poor=params[2];}
+
+ if(!h){high=p.getProperty("high");}
+ else{high=params[3];}
+
+ Runtime rt=Runtime.getRuntime();
+ String rScriptAbsolutePathName=Misc.binDir()+Misc.slash(Misc.binDir())+"../R/summarize_enrichment.R";
+ Process proc = rt.exec(rScriptAbsolutePathName+" "+infile+" "+outdir+" "+poor+" "+high);
+
+ /*Scanner sc=new Scanner(proc.getInputStream()); String erg = "";
+ while(sc.hasNextLine()){erg += (sc.nextLine());}
+ sc.close();*/
+
+ Scanner stdout = new Scanner(proc.getInputStream());
+ Scanner stderr=new Scanner(proc.getErrorStream());
+ while (stdout.hasNextLine()){System.out.println(stdout.nextLine());}
+ while(stderr.hasNextLine()){System.out.println(stderr.nextLine());}
+ stdout.close(); stderr.close();
+
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/converters/Read2Wig.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/converters/Read2Wig.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,267 @@\n+package converters;\n+\n+import java.io.File;\n+import java.io.FileNotFoundException;\n+import java.io.FileWriter;\n+import java.io.IOException;\n+import java.util.Scanner;\n+\n+import datastructures.GenomeFrame;\n+import datastructures.ReadFrame;\n+import datastructures.ReducedReadLine;\n+import exceptions.ChromosomeFormatException;\n+import exceptions.ChromosomeNotFoundException;\n+import exceptions.RangeFormatException;\n+import exceptions.RangeLimitNotFoundException;\n+\n+import middlewares.Misc;\n+\n+/**\n+ * This is a converter class, wich convert a reduced alignment file with the \n+ * following format:\n+ * <TABLE>\n+ * \t<TR>\n+ * \t\t<TD width= "140">read-name</TD>\t\t\n+ * \t\t<TD width= "200">chromosom-name</TD>\t\t\n+ * \t\t<TD width= "150">start-position</TD>\t\t\n+ *\t\t<TD width= "200">end-position</TD>\n+ * </TR>\n+ * <TR height=""></TR>\n+ * </TABLE>\n+ * to the wiggle-format. The wiggle format (WIG) allows the display of continuous-\n+ * valued data in a track format and it is used to visualize the read enrichment\n+ * with the <a href="http://genome.ucsc.edu/cgi-bin/hgGateway" target="_new">ucsc genome browser</a>. Click on the following link: \n+ * <a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html" target="_new">\n+ * http://genome.ucsc.edu/goldenPath/help/wiggle.html</a> for more information.\n+ * \n+ * @author Ali Abdallah\n+ * @version 06.01.2011\n+ * @since jdk 1.6.0\n+ */\n+\n+public class Read2Wig {\n+\t\n+\tprivate static final int LENGTH = 1024;\n+\tprivate File alignFile;\n+\tprivate File outputFile;\n+\tprivate String outputDir;\n+\tprivate int gMin = Integer.MAX_VALUE;\n+\tprivate int gMax = Integer.MIN_VALUE;\n+\tprivate FileWriter tmpWigWriter;\n+\t\n+\t/**\n+\t * Constructs and initialzes a new Read2Wig object. \n+\t * Converts the read alignment file to a overall covrage wig file.\n+\t * \n+\t * @param alignFileName the name of the alignment file.\n+\t * @throws IOException\n+\t */\n+ public Read2Wig(String alignFileName,String outPrefix,String outputDir,String genome,String tmpDir) throws IOException{\n+\t\t// Das File-Objekt zur Behandlung der Alignment-Datei erzeugen.\n+\t\tthis.alignFile = new File(alignFileName);\n+\t\tthis.outputDir = outputDir+Misc.slash(outputDir);\n+\t\ttmpWigWriter = new FileWriter(tmpDir+Misc.slash(tmpDir)+"tmpWig.wig");\n+\t\tconvert(alignFileName,this.outputDir,outPrefix);\n+\t\ttry{\n+\t\t wigToBigWig("hg19",tmpDir);\n+\t\t}\n+\t\tcatch(Exception e){\n+\t\t\tSystem.err.println("Converting wig file to a bigwig file failed. " +\n+\t\t\t\t\t"Check whether you have a 64-bit linux system!");\n+\t\t}\n+\t}\n+ \n+ private void convert(String alignFileName, String outputDir,String outPrefix) throws FileNotFoundException, IOException {\n+\t\tScanner s = new Scanner(this.alignFile);\n+\t\tcomputeExtremas(s); s.close();\n+\t\tScanner readScanner = new Scanner(this.alignFile);\n+\t\talignFileName = Misc.prefix(alignFileName);\n+\t\tScanner as = new Scanner(alignFileName);\n+\t\tas.useDelimiter("_");\n+\t\tas.next();\n+\t\toutputFile = new File(outputDir+outPrefix+".wig");\n+\t\tFileWriter fw = new FileWriter(outputFile);\n+\t\t\n+\t\tannotationHeader(fw);\n+\n+\t\tReadFrame readF = computeNextRead(readScanner); //Current read frame\n+\t\tGenomeFrame frame = new GenomeFrame(readF.start(), LENGTH); //Current base frame\n+\t\tString chrom = readF.chrom(); //Current chromosome\n+\t\tif(frame.contains(readF)){frame.updateHits(readF);} //Sum up all hits of curr read\n+\t\twriteHeader(fw, frame, readF); //Write header line\n+\t\t\n+\t\twhile(true){\n+\t\t while(readScanner.hasNextLine() && chrom.equals(readF.chrom()) && frame.contains(readF)){\n+\t\t\tframe.updateHits(readF); readF = computeNextRead(readScanner);\n+\t\t }\n+\t\t while(readScanner.hasNextLine() && chrom.equals(readF.chrom()) && frame.overlaps(readF) && !frame.limitExceeded(readF)){\n+\t\t\tframe.updateFrameFromRightEnd(readF); frame.updateHits(readF); readF = computeNextRead(readScanner);\n+\t\t }\n+\t\t if(!readScanner.hasNextLine()){break;}\n+\t\t else if(!chrom.equals(readF.chrom())){\n+\t\t\tframe = new GenomeFrame(readF.st'..b'+".chrom.sizes");\n+\t\t\tScanner s = new Scanner(p.getInputStream());\n+\t\t\twhile(s.hasNextLine())\n+\t\t\t\tfw.write(s.nextLine()+"\\r\\n");\n+\t\t\tfw.close();\n+\t\t\t\n+\t\t\tRuntime.getRuntime().exec(wig2bw+" "+outputFile.getAbsolutePath()\n+\t\t\t\t\t+" "+outputDir+Misc.slash(outputDir)+genome+".chrom.sizes "+\n+\t\t\t\t\toutputDir+Misc.slash(outputDir)+\n+\t\t\t\t\tMisc.prefix(outputFile.getAbsolutePath())+".bw");\n+\t\t\tnew File(outputDir+Misc.slash(outputDir)+genome+".chrom.sizes").delete();\n+\t\t\tnew File(tmpDir+Misc.slash(tmpDir)+"tmpWig.wig").delete();\n+\t\t} catch (IOException e) {\n+\t\t\t// TODO Auto-generated catch block\n+\t\t\te.printStackTrace();\n+\t\t}\n+\t}\n+\n+\tprivate void computeExtremas(Scanner s){\n+\t\tString chrom = "Datei falsch formatiert.";\n+\t\tString oldChrom = null;\n+\t\tint start = -1;\n+\t\tint end = -1;\n+\t\tString line = s.nextLine();\n+\t\t\n+\t\toldChrom = chrom(line); start = start(line); end = end(line);\n+\t\t\n+\t\twhile(s.hasNextLine()){\n+\t\t\tline = s.nextLine();\n+\t\t\tif(isHeader(line)){\n+\t\t\t\tchrom = chrom(line); start = start(line); end = end(line);\n+\t\t\t\tif(gMin > start && chrom.equals(oldChrom))\n+\t\t\t\t\tgMin = start;\n+\n+\t\t\t\tif(gMax < end && chrom.equals(oldChrom))\n+\t\t\t\t\tgMax = end;\n+\t\t\t}\n+\t\t}\n+\t}\n+\t\n+\tprivate boolean isHeader(String line){\n+\t\treturn line.indexOf("chr")!=-1;\n+\t}\n+\t\n+\tprivate int start(String line){\n+\t\tScanner s = new Scanner(line);\n+\t\ts.next();s.next();\n+\t\treturn s.nextInt();\n+\t}\n+\t\n+\tprivate int end(String line){\n+\t\tScanner s = new Scanner(line);\n+\t\ts.next();s.next();s.next();\n+\t\treturn s.nextInt();\n+\t}\n+\t\n+\tprivate String chrom(String line){\n+\t\tScanner s = new Scanner(line);\n+\t\ts.next();\n+\t\treturn s.next();\n+\t}\n+\n+\tprivate void writeFramePortion(FileWriter fw, GenomeFrame frame, int start2) throws IOException {\t\t\n+\t\tfor(int base = frame.start(); base < start2; base++){\n+\t\t\tfw.write(frame.getHit(base)+"\\r\\n");\n+\t\t\ttmpWigWriter.write(frame.getHit(base)+"\\r\\n");\n+\t\t}\n+\t}\n+\n+\tprivate void writeFrameLeak(FileWriter fw, \n+\t\t\t\t\t\t\t\tGenomeFrame last, GenomeFrame frame, ReadFrame read) \n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tthrows IOException {\n+\t\tif(frame.start()-last.end() > 50){\n+\t\t\twriteHeader(fw, frame, read);\n+\t\t}\n+\t\telse{\n+\t\t\tfor(int i = 0; i < frame.start()-last.end()-1; i++){\n+\t\t\t\tfw.write(0+"\\r\\n");\n+\t\t\t\ttmpWigWriter.write(0+"\\r\\n");\n+\t\t\t}\n+\t\t}\n+\t}\n+\n+\tprivate void annotationHeader(FileWriter fw) throws IOException{\n+\t\tString browserLines = \t"browser position chr1:"+gMin+"-"+gMax+"\\r\\n"+\n+\t\t\t\t\t\t\t\t"browser hide all"+"\\r\\n"+\n+\t\t\t\t\t\t\t\t"browser pack refGene encodeRegions"+"\\r\\n"+\n+\t\t\t\t\t\t\t\t"browser full altGraph";\n+\t\tScanner as = new Scanner(alignFile.getName());\n+\t\tas.useDelimiter("_");as.next();\n+\t\tString trackLine = \t"track type=wiggle_0 name=\\""+as.next()+"\\" " +\n+\t\t\t\t\t\t\t"description=\\"Base read coverage\\" visibility=full " +\n+\t\t\t\t\t\t\t"color=0,0,0 altColor=255,0,0 priority=20 " +\n+\t\t\t\t\t\t\t"autoScale=on";\n+\t\tfw.write(browserLines+"\\r\\n"+trackLine+"\\r\\n");\n+\t}\n+\n+\tprivate void writeHeader(FileWriter fw, GenomeFrame frame, ReadFrame read)\n+\t\t\tthrows IOException {\n+\t\tfw.write("fixedStep chrom="+read.chrom()\n+\t\t\t\t\t\t\t\t\t+" start="+frame.start()\n+\t\t\t\t\t\t\t\t\t\t+ " step=1\\r\\n");\n+\t\ttmpWigWriter.write("fixedStep chrom="+read.chrom()\n+\t\t\t\t+" start="+frame.start()\n+\t\t\t\t\t+ " step=1\\r\\n");\n+\t}\n+\t\n+\tprivate void writeFrame(FileWriter fw, GenomeFrame frame) throws IOException {\n+\t\t// TODO Auto-generated method stub\n+\t\tfor(int base = frame.start(); base <= frame.end(); base++){\n+\t\t\tfw.write(frame.getHit(base)+"\\r\\n");\n+\t\t\ttmpWigWriter.write(frame.getHit(base)+"\\r\\n");\n+\t\t}\n+\t}\n+\n+\tprivate ReadFrame computeNextRead(Scanner afScanner) {\t\n+\t\tReducedReadLine rl = null;\n+\t\ttry {\n+\t\t\trl = new ReducedReadLine(afScanner.nextLine());\n+\t\t} catch (ChromosomeFormatException e) {\n+\t\t\te.printStackTrace();\n+\t\t} catch (ChromosomeNotFoundException e) {\n+\t\t\te.printStackTrace();\n+\t\t} catch (RangeFormatException e) {\n+\t\t\te.printStackTrace();\n+\t\t} catch (RangeLimitNotFoundException e) {\n+\t\t\te.printStackTrace();\n+\t\t}\t\t\t\t\n+\t\treturn new ReadFrame(rl.name(), rl.chrom(), rl.start(), rl.end());\n+\t}\n+\n+}\n+\n+\n+\n+\n+\n+\n+\n+\n+\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/converters/ReadOnTarget2Wig.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/converters/ReadOnTarget2Wig.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,187 @@
+package converters;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Scanner;
+import middlewares.Misc;
+
+/**
+ * Converts the detailed coverage data to the wig format. Used for the
+ * visualization of the coverage data in the ucsc-browser.
+ *
+ * @author Ali Abdallah
+ * @version 20.07.2011
+ * @since Java 1.6
+ */
+public class ReadOnTarget2Wig {
+
+ private int
+ /**
+ * The maximal number of hits on a base.
+ */
+ max,
+ /**
+ * The minimal number of hits on a base.
+ */
+ min,
+ /**
+ * The minimal position on chr1.
+ */
+ gMin,
+ /**
+ * the maximal position on chr1.
+ */
+ gMax;
+
+ private String
+ /**
+ * The name of the file of detailed coverage data.
+ */
+ filename,
+ /**
+ * The title of the track.
+ */
+ title;
+
+ /**
+ * Constructs an new ReadOnTarget2Wig object, initializes the parameters
+ * and call the conversion method.
+ *
+ * @param filename
+ * @param prefix
+ * @param outDir
+ * @param title
+ * @throws IOException
+ */
+ public ReadOnTarget2Wig(String filename, String prefix, String outDir, String title) throws IOException{
+ this.filename = filename;
+ max = Integer.MIN_VALUE; gMax = Integer.MIN_VALUE;
+ min = Integer.MAX_VALUE; gMin = Integer.MAX_VALUE;
+ this.title = title;
+ File f=new File(this.filename);
+ FileWriter fw=new FileWriter(outDir+Misc.slash(outDir)
+ +prefix+"_onTarget.wig");
+ Scanner scanForMinMax=new Scanner(f);
+ computeExtremas(scanForMinMax);
+ scanForMinMax.close();
+
+ Scanner s = new Scanner(f);
+ annotationHeader(fw);
+ toWiggleFormat(fw,s);
+ fw.close();
+ }
+
+ /**
+ * Writes the annotation header to the wig file.
+ *
+ * @param fw FileWriter
+ * @throws IOException if write operation is not possible.
+ */
+ private void annotationHeader(FileWriter fw) throws IOException{
+ String browserLines = "browser position chr1:"+gMin+"-"+gMax+"\r\n"+
+ "browser hide all"+"\r\n"+
+ "browser pack refGene encodeRegions"+"\r\n"+
+ "browser full altGraph";
+ String trackLine = "track type=wiggle_0 name=\""+title+"\" " +
+ "description=\"Base read coverage\" visibility=full "
+ +"color=0,0,0 altColor=255,0,0 priority=20 " +
+ "autoScale=off graphType=bar " +
+ "viewLimits="+min+":"+max;
+ fw.write(browserLines+"\r\n"+trackLine+"\r\n");
+ }
+
+ /**
+ * Computes the hit and position minimas and maxima.
+ *
+ * @param s the reader of the file of detailed coverage data.
+ */
+ private void computeExtremas(Scanner s){
+ String chrom = "Datei falsch formatiert.";
+ int start = -1; int end = -1;
+ while(s.hasNextLine()){
+ String line = s.nextLine();
+ if(isHeader(line)){
+ chrom = chrom(line); start = start(line); end = end(line);
+ if(gMin > start && chrom.equals("chr1")){gMin = start;}
+ if(gMax < end && chrom.equals("chr1")){gMax = end;}
+ }
+ else{
+ if(min > Integer.parseInt(line.trim())){
+ min = Integer.parseInt(line.trim());
+ }
+ if(max < Integer.parseInt(line.trim())){
+ max = Integer.parseInt(line.trim());
+ }
+ }
+ }
+ }
+
+ /**
+ * The main computation: conversion to wiggle format.
+ *
+ * @param fw FileWriter into the wig-file.
+ * @param s the reader of the file of detailed coverage data.
+ * @throws IOException if i/o fails.
+ */
+ private void toWiggleFormat(FileWriter fw, Scanner s) throws IOException {
+ String chrom = "Datei falsch formatiert.";
+ int start = -1;
+ while(s.hasNextLine()){
+ String line = s.nextLine();
+ if(isHeader(line)){
+ chrom = chrom(line); start = start(line);
+ fw.write(declarationLine(chrom, start));
+ }
+ else fw.write(line+"\r\n");
+ }
+ }
+
+ /**
+ * @param chrom
+ * @param start
+ * @return a String representing the declaration line corresponding to the
+ * specified parameters.
+ */
+ private String declarationLine(String chrom, int start) {
+ return "fixedStep chrom="+chrom+" start="+start+" step=1\r\n";
+ }
+
+ /**
+ * Check if the specified line is a header line.
+ *
+ * @param line the current observerd line in the file of detailed coverage
+ * data.
+ * @return true if line is a header and false otherwise.
+ */
+ private boolean isHeader(String line){
+ return line.indexOf("chr")!=-1;
+ }
+
+ /**
+ * @param line
+ * @return the start position of the current frame (header).
+ */
+ private int start(String line){
+ Scanner s = new Scanner(line);
+ s.next(); return s.nextInt();
+ }
+
+ /**
+ * @param line
+ * @return the end position of the current frame.
+ */
+ private int end(String line){
+ Scanner s = new Scanner(line);
+ s.next(); s.next();
+ return s.nextInt();
+ }
+
+ /**
+ * @param line
+ * @return the chromosome corresponding to the current frame.
+ */
+ private String chrom(String line){
+ Scanner s = new Scanner(line);
+ return s.next();
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/dataGenerators/AnnotationDataGenerator.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/dataGenerators/AnnotationDataGenerator.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,5 @@
+package dataGenerators;
+
+public class AnnotationDataGenerator {
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/dataGenerators/ReadAlginmentDataGenerator.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/dataGenerators/ReadAlginmentDataGenerator.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,30 @@
+package dataGenerators;
+
+import java.util.Random;
+
+public class ReadAlginmentDataGenerator {
+
+ String[] chrs = {"chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12",
+ "chr13","chr14", "chr15","chr16","chr17","chr18","chr19","chr20","chr21","chrX","chrY"};
+
+ String qname = "dummy";
+ String flag = "0";
+ String chr;
+ int start;
+ String mapq = "0";
+ String cigar = "dummy";
+ String mrnm = "*";
+ String mpos = "0";
+ String isize = "0";
+ String seq = "CAACCCTAACCCTAACCCAAACCCCAACCCTAACCCTACCCCTACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC";
+ String qua = "#################################################FCCGGGFGGD=GDDIHIGHIJIGHGDJJIHGIHHHGFIHHBHFFFFFFBCB";
+ String tvv = "dummy";
+
+ public String generateReadLine(int pos, int length){
+ Random r = new Random();
+ return null;
+
+
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/dataGenerators/TargetDataGenerator.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/dataGenerators/TargetDataGenerator.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,5 @@
+package dataGenerators;
+
+public class TargetDataGenerator {
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/dataGenerators/TestDataGenerator.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/dataGenerators/TestDataGenerator.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,7 @@
+package dataGenerators;
+
+public class TestDataGenerator {
+
+
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/AVLNode.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/AVLNode.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,32 @@
+package datastructures;
+
+
+// Basic node stored in AVL trees
+// Note that this class is not accessible outside
+// of package DataStructures
+
+class AVLNode
+{
+    // Constructors
+ @SuppressWarnings("unchecked")
+ AVLNode( Comparable theElement )
+    {
+        this( theElement, null, null );
+    }
+
+    @SuppressWarnings("unchecked")
+ AVLNode( Comparable theElement, AVLNode lt, AVLNode rt )
+    {
+        element  = theElement;
+        left     = lt;
+        right    = rt;
+        height   = 0;
+    }
+
+        // Friendly data; accessible by other package routines
+    @SuppressWarnings("unchecked")
+ Comparable element;      // The data in the node
+    AVLNode    left;         // Left child
+    AVLNode    right;        // Right child
+    int        height;       // Height
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/AVLTree.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/AVLTree.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,294 @@\n+package datastructures;\n+\n+// BinarySearchTree class\n+//\n+// CONSTRUCTION: with no initializer\n+//\n+// ******************PUBLIC OPERATIONS*********************\n+// void insert( x ) --> Insert x\n+// void remove( x ) --> Remove x (unimplemented)\n+// Comparable find( x ) --> Return item that matches x\n+// Comparable findMin( ) --> Return smallest item\n+// Comparable findMax( ) --> Return largest item\n+// boolean isEmpty( ) --> Return true if empty; else false\n+// void makeEmpty( ) --> Remove all items\n+// void printTree( ) --> Print tree in sorted order \n+\n+/**\n+ * Implements an AVL tree.\n+ * Note that all "matching" is based on the compareTo method.\n+ * @author Mark Allen Weiss\n+ */\n+public class AVLTree\n+{\n+ /**\n+ * Construct the tree.\n+ */\n+ public AVLTree( )\n+ {\n+ root = null;\n+ }\n+\n+ /**\n+ * Insert into the tree; duplicates are ignored.\n+ * @param x the item to insert.\n+ */\n+ @SuppressWarnings("unchecked")\n+\tpublic void insert(Comparable x )\n+ {\n+ root = insert( x, root );\n+ }\n+\n+ /**\n+ * Remove from the tree. Nothing is done if x is not found.\n+ * @param x the item to remove.\n+ */\n+ @SuppressWarnings("unchecked")\n+\tpublic void remove( Comparable x )\n+ {\n+ System.out.println( "Sorry, remove unimplemented" );\n+ }\n+\n+ /**\n+ * Find the smallest item in the tree.\n+ * @return smallest item or null if empty.\n+ */\n+ @SuppressWarnings("unchecked")\n+\tpublic Comparable findMin( )\n+ {\n+ return elementAt( findMin( root ) );\n+ }\n+\n+ /**\n+ * Find the largest item in the tree.\n+ * @return the largest item of null if empty.\n+ */\n+ @SuppressWarnings("unchecked")\n+\tpublic Comparable findMax( )\n+ {\n+ return elementAt( findMax( root ) );\n+ }\n+\n+ /**\n+ * Find an item in the tree.\n+ * @param x the item to search for.\n+ * @return the matching item or null if not found.\n+ */\n+ @SuppressWarnings("unchecked")\n+\tpublic Comparable find( Comparable x )\n+ {\n+ return elementAt( find( x, root ) );\n+ }\n+\n+ /**\n+ * Make the tree logically empty.\n+ */\n+ public void makeEmpty( )\n+ {\n+ root = null;\n+ }\n+\n+ /**\n+ * Test if the tree is logically empty.\n+ * @return true if empty, false otherwise.\n+ */\n+ public boolean isEmpty( )\n+ {\n+ return root == null;\n+ }\n+\n+ /**\n+ * Print the tree contents in sorted order.\n+ */\n+ public void printTree( )\n+ {\n+ if( isEmpty( ) )\n+ System.out.println( "Empty tree" );\n+ else\n+ printTree( root );\n+ }\n+\n+ /**\n+ * Internal method to get element field.\n+ * @param t the node.\n+ * @return the element field or null if t is null.\n+ */\n+ @SuppressWarnings("unchecked")\n+\tprivate Comparable elementAt( AVLNode t )\n+ {\n+ return t == null ? null : t.element;\n+ }\n+\n+ /**\n+ * Internal method to insert into a subtree.\n+ * @param x the item to insert.\n+ * @param t the node that roots the tree.\n+ * @return the new root.\n+ */\n+\t@SuppressWarnings("unchecked")\n+\tprivate AVLNode insert( Comparable x, AVLNode t )\n+ {\n+ if( t == null )\n+ t = new AVLNode( x, null, null );\n+ else if( x.compareTo( t.element ) < 0 )\n+ {\n+ t.left = insert( x, t.left );\n+ if( height( t.left ) - height( t.right ) == 2 )\n+ if( x.compareTo( t.left.element ) < 0 )\n+ t = rotateWithLeftChild( t );\n+ else\n+ t = doubleWithLeftChild( t );\n+ }\n+ else if( x.compareTo( t.element ) > 0 )\n+ {\n+ t.right = insert( x, t.right );\n+ if( height( t.right ) - height( t.left ) == 2 )\n+ if( x.compareTo( t.right.element ) > 0 )\n+ t = rotateWithRightChild( t );\n+ else\n+ '..b'cate; do nothing\n+ t.height = max( height( t.left ), height( t.right ) ) + 1;\n+ return t;\n+ }\n+\n+ /**\n+ * Internal method to find the smallest item in a subtree.\n+ * @param t the node that roots the tree.\n+ * @return node containing the smallest item.\n+ */\n+ private AVLNode findMin( AVLNode t )\n+ {\n+ if( t == null )\n+ return t;\n+\n+ while( t.left != null )\n+ t = t.left;\n+ return t;\n+ }\n+\n+ /**\n+ * Internal method to find the largest item in a subtree.\n+ * @param t the node that roots the tree.\n+ * @return node containing the largest item.\n+ */\n+ private AVLNode findMax( AVLNode t )\n+ {\n+ if( t == null )\n+ return t;\n+\n+ while( t.right != null )\n+ t = t.right;\n+ return t;\n+ }\n+\n+ /**\n+ * Internal method to find an item in a subtree.\n+ * @param x is item to search for.\n+ * @param t the node that roots the tree.\n+ * @return node containing the matched item.\n+ */\n+ @SuppressWarnings("unchecked")\n+\tprivate AVLNode find( Comparable x, AVLNode t )\n+ {\n+ while( t != null )\n+ if( x.compareTo( t.element ) < 0 )\n+ t = t.left;\n+ else if( x.compareTo( t.element ) > 0 )\n+ t = t.right;\n+ else\n+ return t; // Match\n+\n+ return null; // No match\n+ }\n+\n+ /**\n+ * Internal method to print a subtree in sorted order.\n+ * @param t the node that roots the tree.\n+ */\n+ private void printTree( AVLNode t )\n+ {\n+ if( t != null )\n+ {\n+ printTree( t.left );\n+ System.out.println( t.element );\n+ printTree( t.right );\n+ }\n+ }\n+\n+ /**\n+ * Return the height of node t, or -1, if null.\n+ */\n+ private static int height( AVLNode t )\n+ {\n+ return t == null ? -1 : t.height;\n+ }\n+\n+ /**\n+ * Return maximum of lhs and rhs.\n+ */\n+ private static int max( int lhs, int rhs )\n+ {\n+ return lhs > rhs ? lhs : rhs;\n+ }\n+\n+ /**\n+ * Rotate binary tree node with left child.\n+ * For AVL trees, this is a single rotation for case 1.\n+ * Update heights, then return new root.\n+ */\n+ private static AVLNode rotateWithLeftChild( AVLNode k2 )\n+ {\n+ AVLNode k1 = k2.left;\n+ k2.left = k1.right;\n+ k1.right = k2;\n+ k2.height = max( height( k2.left ), height( k2.right ) ) + 1;\n+ k1.height = max( height( k1.left ), k2.height ) + 1;\n+ return k1;\n+ }\n+\n+ /**\n+ * Rotate binary tree node with right child.\n+ * For AVL trees, this is a single rotation for case 4.\n+ * Update heights, then return new root.\n+ */\n+ private static AVLNode rotateWithRightChild( AVLNode k1 )\n+ {\n+ AVLNode k2 = k1.right;\n+ k1.right = k2.left;\n+ k2.left = k1;\n+ k1.height = max( height( k1.left ), height( k1.right ) ) + 1;\n+ k2.height = max( height( k2.right ), k1.height ) + 1;\n+ return k2;\n+ }\n+\n+ /**\n+ * Double rotate binary tree node: first left child\n+ * with its right child; then node k3 with new left child.\n+ * For AVL trees, this is a double rotation for case 2.\n+ * Update heights, then return new root.\n+ */\n+ private static AVLNode doubleWithLeftChild( AVLNode k3 )\n+ {\n+ k3.left = rotateWithRightChild( k3.left );\n+ return rotateWithLeftChild( k3 );\n+ }\n+\n+ /**\n+ * Double rotate binary tree node: first right child\n+ * with its left child; then node k1 with new right child.\n+ * For AVL trees, this is a double rotation for case 3.\n+ * Update heights, then return new root.\n+ */\n+ private static AVLNode doubleWithRightChild( AVLNode k1 )\n+ {\n+ k1.right = rotateWithLeftChild( k1.right );\n+ return rotateWithRightChild( k1 );\n+ }\n+\n+ /** The tree root. */\n+ private AVLNode root;\n+\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/AnnotationLine.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/AnnotationLine.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,99 @@
+package datastructures;
+
+import java.util.Scanner;
+
+public class AnnotationLine implements Comparable<Object>{
+
+ String seqName, chrom, gene;
+ int start, end;
+
+ public AnnotationLine(String seqName, String chrom, String gene,
+ int start, int end){
+ this.seqName = seqName;
+ this.chrom = chrom;
+ this.gene = gene;
+ this.start = start;
+ this.end = end;
+ }
+
+ public AnnotationLine(String line){
+ Scanner s = new Scanner(line);
+ seqName = s.next();
+ this.chrom = s.next();
+ this.start = s.nextInt();
+ this.end = s.nextInt();
+ this.gene = s.next();
+ }
+
+ public String seqName() {
+ return seqName;
+ }
+
+ public String chrom() {
+ return chrom;
+ }
+
+ public String gene() {
+ return gene;
+ }
+
+ public int start() {
+ return start;
+ }
+
+ public int end() {
+ return end;
+ }
+
+ public static AnnotationLine targetLine(String chrom, int tstart, int tend){
+ return new AnnotationLine("000\t"+chrom+"\t"+tstart+"\t"+tend+"\tdummy");
+ }
+
+ public int compareTo(Object otherLine) {
+ AnnotationLine other = (AnnotationLine)otherLine;
+
+ if(chrom.compareTo(other.chrom()) < 0
+ && !other.gene.equals("dummy"))
+ return -1;
+ else if(chrom.compareTo(other.chrom()) > 0
+ && !other.chrom().equals("dummy"))
+ return 1;
+ else{
+ /*
+ * 1. Eine Region überlappt mit einem Gen, wenn einer der folgenden
+ * 3 Fälle eintritt:
+ * a) Targetanfang kleiner als Genanfang und Targetende größer als
+ * Genende. (Gen ganz im Target enthalten)
+ * b) Targetanfang liegt zwischen Genanfang und Genende.
+ * c) Targetende liegt zwischen Genanfang und Genende.
+ */
+
+ // Für Targetsuche
+ if(this.gene().equals("dummy") &&
+ this.chrom().equals(other.chrom()) && (
+ (this.start() <= other.start() && this.end() >= other.end()) ||
+ (this.start() >= other.start() && this.start() <= other.end()) ||
+ (this.end() >= other.start() && this.end() <= other.end())
+ )
+ )
+ return 0;
+ // Für Gensuche zu Insertzwecken.
+ else if(start < other.start())
+ return -1;
+ else if(start > other.start())
+ return 1;
+ else{
+ if(end < other.end())
+ return -1;
+ else if(end > other.end())
+ return 1;
+ else return 0;
+ }
+ }
+ }
+
+ public String toString(){
+ return seqName +"\t" + chrom + "\t" + start + "\t" + end + "\t" + gene;
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/Format.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/Format.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,32 @@
+package datastructures;
+
+public enum Format{
+ type("type"),
+ sam("sam"),
+ maq("maq"),
+ megablast("megablast"),
+ eland("eland"),
+ roche("roche"),
+ genome("genome"),
+ target("target"),
+ invalid("invalid");
+
+ private String f;
+
+ Format(String format){
+ this.f = format;
+ }
+
+ public Format compile(String f){
+ this.f = f;
+ try{
+ return Format.valueOf(this.f);
+ }catch(IllegalArgumentException iae){
+ return invalid;
+ }
+ }
+
+ public boolean equals(Format other){
+ return this.f.equals(other.f);
+ }
+};

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/Frame.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/Frame.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,94 @@
+package datastructures;
+
+/**
+ * Used for various purposes.
+ *
+ * @author Ali Abdallah
+ * @version 01.2011
+ * @since jdk 1.6.0
+ */
+public class Frame {
+
+ // Self explanatory.
+ protected int start;
+ protected int end;
+ protected int length;
+
+ /**
+ * Constructs a frame with start position "start", length "length" and
+ * end position "start+length-1".
+ * @param start the start position of the frame.
+ * @param length the length of the frame.
+ */
+ public Frame(int start, int length) {
+ this.start = start; end = start+length-1;
+ this.length = length;
+ }
+
+ /**
+ * Verify if this frame overlaps the frame specified in the parameter.
+ * @param f the frame which potentially overlaps the calling frame.
+ * @return true if the two frames overlap each other and false otherwise.
+ */
+ public boolean overlaps(Frame f){
+ return (end >= f.start() && start < f.end());
+ }
+
+ /**
+ * Computes the size of the overlap area.
+ * @param f the frame overlapping the calling frame.
+ * @return the size of the overlap if an overlap exists and -1 otherwise.
+ */
+ public int overlapSize(Frame f){
+ if(this.overlaps(f)){
+ int s = Math.max(start, f.start());
+ int e = Math.min(end, f.end());
+ return e-s+1;
+ }
+ return -1;
+ }
+
+ /**
+ * Unify the calling frame with the frame specified in the parameter.
+ * @param f the frame to be unified with the calling frame.
+ * @return the union of the calling frame and f.
+ */
+ public Frame unify(Frame f){
+ return
+ new Frame(Math.min(this.start, f.start),
+ Math.max(this.end,f.end)-Math.min(this.start, f.start)+1);
+ }
+
+ /**
+ * self explanatory
+ * @return start of the frame.
+ */
+ public int start(){
+ return start;
+ }
+
+ /**
+ * self explanatory
+ * @return end of the frame.
+ */
+ public int end(){
+ return end;
+ }
+
+ /**
+ * self explanatory
+ * @return length of the frame.
+ */
+ public int length(){
+ return length;
+ }
+
+ /**
+ * Make a string representation of the frame.
+ * @return a string representation of the string.
+ */
+ public String toString(){
+ return start+":"+end;
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/GenomeFrame.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/GenomeFrame.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,87 @@
+package datastructures;
+
+import java.util.Vector;
+
+/**
+ * @author Ali Abdallah
+ * @version 01.2011
+ * @since jdk 1.6.0
+ */
+
+public class GenomeFrame extends Frame{
+
+ int limit;
+ Vector<Integer> hits;
+
+ public GenomeFrame(int start, int length) {
+ super(start, length);
+ limit = end;
+ hits = new Vector<Integer>(length);
+ hits.setSize(length);
+ for(int i = 0; i < length; i++){
+ hits.set(i, 0);
+ }
+ }
+
+ public int getHit(int base){
+ if(base-start < hits.size())
+ return hits.get(base-start);
+ else
+ return -1;
+ }
+
+ public void setHit(int base, int bhits){
+ if(base-start < hits.size()){
+ hits.set(base-start, bhits);
+ }
+ }
+
+ public boolean contains(ReadFrame r){
+ return (start <= r.start() && end >= r.end());
+ }
+
+ public boolean overlaps(ReadFrame r){
+ return (end >= r.start() && end < r.end());
+ }
+
+
+
+ public void addBases(int nr){
+ for(int i = 0; i < nr; i++){
+ hits.add(1);
+ }
+ }
+
+ public String toString(){
+ return start+":"+end+" ("+limit+")";
+ }
+
+
+ public void updateHits(ReadFrame read) {
+ for(int base = read.start(); base <= read.end(); base++){
+ setHit(base, getHit(base)+1);
+ }
+ }
+
+ public void updateFrameFromRightEnd(ReadFrame readF) {
+ // TODO Auto-generated method stub
+ for(int i = end+1; i <= readF.end(); i++)
+ hits.add(0);
+ end = readF.end();
+ }
+
+ public boolean limitExceeded(ReadFrame readF) {
+ return readF.start() > limit;
+ }
+
+ public void updateFrameFromBothEnds(ReadFrame readF, int length) {
+ for(int i = end-readF.start()+1; i < length; i++ )
+ hits.add(0);
+ for(int i = 0; i < readF.start()-start; i++)
+ hits.remove(0);
+ start = readF.start();
+ end = start+length-1;
+ limit = end;
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/GenomeLine.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/GenomeLine.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,57 @@
+package datastructures;
+
+import java.util.Scanner;
+
+public class GenomeLine implements Line {
+
+ boolean misformat = false;
+ String seqName, chrom, gene;
+ int start, end;
+
+ //fw.write(field(1)+"\t"+field(3)+"\t"
+ // +field(5)+"\t"+field(6)+"\t"+field(13)+"\r\n");
+
+ public GenomeLine(String line){
+ Scanner s = new Scanner(line);
+ if(line.startsWith("#")) misformat = true;
+ else
+ try{
+ seqName = s.next();s.next();
+ chrom = s.next();s.next();
+ start = s.nextInt();
+ end = s.nextInt();s.next();s.next();s.next();s.next();s.next();s.next();
+ gene = s.next();}
+ catch(Exception e){
+ misformat = true;
+ }
+ }
+
+ public boolean valid(){
+ return misformat == false;
+ }
+
+ public String chrom() {
+ return chrom;
+ }
+
+ public int end() {
+ return end;
+ }
+
+ public int start() {
+ return start;
+ }
+
+ public String gene(){
+ return gene;
+ }
+
+ public String seqName(){
+ return seqName;
+ }
+
+ public String toString(){
+ return seqName + "\t" + chrom + "\t" + start + "\t" + end + "\t" + gene;
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/Line.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/Line.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,9 @@
+package datastructures;
+
+public interface Line {
+
+ public String chrom();
+ public int start();
+ public int end();
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/Read.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/Read.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,96 @@
+package datastructures;
+
+import java.io.File;
+import java.io.IOException;
+import java.lang.InterruptedException;
+import java.util.Scanner;
+import java.util.Vector;
+
+public class Read implements Comparable<Object> {
+
+ String query;
+ int flag;
+ String rname;
+ int pos;
+ int mapq;
+ String cigar;
+ String rnext;
+ int pnext;
+ int tlen;
+ String seq;
+ String qual;
+ Vector<String> optional;
+
+ public Read(String line) {
+ Scanner s = new Scanner(line);
+ query = s.next();
+ flag = s.nextInt();
+ rname = s.next();
+ pos = s.nextInt();
+ mapq = s.nextInt();
+ cigar = s.next();
+ rnext = s.next();
+ pnext = s.nextInt();
+ tlen = s.nextInt();
+ seq = s.next();
+ qual = s.next();
+ if (s.hasNext()) {
+ optional = new Vector<String>();
+ while (s.hasNext()) {
+ optional.add(s.next());
+ }
+ }
+ }
+
+ public String getRname() {
+ return rname;
+ }
+
+ public int getPos() {
+ return pos;
+ }
+
+ @Override
+ public int compareTo(Object o) {
+ return 0;
+ }
+
+ public static void sort(File input) {
+ Runtime rt = Runtime.getRuntime();
+ try {
+ String rawOutput = input.getAbsolutePath(),
+ tmpD = input.getParentFile().getAbsolutePath(),
+ outputName = input.getName(),
+ pathname = input.getParentFile().getAbsolutePath() + "/" +
+ outputName + "Sorted";
+
+ input = new File(pathname);
+
+ if (!input.exists())
+ input.createNewFile();
+
+ String command = "sort -k3,3 -k4n,4 -T " + tmpD + " " + rawOutput+" > "+pathname;
+ Process p = rt.exec(command);
+ try{p.waitFor();}
+ catch(InterruptedException e){e.printStackTrace();}
+ System.out.println("Fertig");
+ /* Scanner ps = new Scanner(p.getInputStream());
+ FileWriter fw = new FileWriter(input);
+
+ while (ps.hasNextLine()) {
+ String nextLine = ps.nextLine();
+ fw.write(nextLine + "\r\n");
+ }
+
+ fw.close(); */
+
+ new File(rawOutput).delete();
+ new File(pathname).renameTo(new File(rawOutput));
+ System.out.println("File " + new File(rawOutput).getAbsolutePath()
+ + " sorted\n");
+
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/ReadFrame.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/ReadFrame.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,23 @@
+package datastructures;
+
+public class ReadFrame extends Frame{
+
+ private String chrom, name;
+
+ public ReadFrame(String name,String chrom, int start, int end) {
+ super(start, end-start+1);
+ this.chrom = chrom; this.name = name;
+ }
+
+ public String chrom(){
+ return chrom;
+ }
+
+ public String name(){
+ return name;
+ }
+
+ public int size(){
+ return end-start+1;
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/ReadLine.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/ReadLine.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,73 @@
+package datastructures;
+
+import java.util.Scanner;
+
+/**
+ * Represents a read line from the read alignment file.
+ *
+ * @author Ali Abdallah
+ * @version 03.08.2011
+ * @since Java 1.6
+ */
+
+public class ReadLine implements Line {
+
+ String
+ /**
+ * Query (pair) name.
+ */
+ name,
+ /**
+ * Reference sequence name.
+ */
+ chrom;
+ /**
+ * Start position of the read.
+ */
+ int start,
+ /**
+ * End Position of the read.
+ */
+ end,
+ /**
+ * Length of the read.
+ */
+ length;
+
+ public ReadLine(String line){
+ // line format:
+ // qname flag rname pos mapq cigar mrnm mpos isize seq qual tag
+ Scanner s = new Scanner(line);
+ name = s.next();
+ s.next();
+ chrom = s.next();
+ start = s.nextInt();
+ s.next(); s.next();s.next();s.next();s.next();
+ length = s.next().length();
+ end = start+length-1;
+ }
+
+ public String name(){
+ return name;
+ }
+
+ public String chrom() {
+ return chrom;
+ }
+
+ public int end() {
+ return end;
+ }
+
+ public int start() {
+ return start;
+ }
+
+ public int length(){
+ return length;
+ }
+
+ public String toString(){
+ return name+"\t"+chrom+"\t"+start+"\t"+end;
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/ReducedReadLine.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/ReducedReadLine.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,89 @@
+package datastructures;
+
+import java.util.Scanner;
+import exceptions.ChromosomeFormatException;
+import exceptions.ChromosomeNotFoundException;
+import exceptions.RangeFormatException;
+import exceptions.RangeLimitNotFoundException;
+
+/**
+ * Represents a read Line from the read alignment file.
+ *
+ * @author Ali Abdallah
+ * @version 22.07.2011
+ * @since Java 1.6
+ */
+public class ReducedReadLine implements Line{
+
+ String line;
+ String rName;
+ String chrom;
+ int start, end;
+
+ public ReducedReadLine(String line) throws ChromosomeFormatException,
+ ChromosomeNotFoundException,
+ RangeFormatException,
+ RangeLimitNotFoundException{
+ this.line = line;
+ Scanner s = new Scanner(line);
+ if(s.hasNext())
+ rName = s.next();
+ if(s.hasNext()){
+ chrom = s.next();
+ if(!(chrom.toLowerCase().startsWith("chr") || chrom.equals("*")))
+ throw new ChromosomeFormatException(chrom);
+ }
+ else
+ throw new ChromosomeNotFoundException();
+
+ if(s.hasNextInt()){
+ start = s.nextInt();
+ if(start < 0){
+ throw new RangeFormatException("Start position must be a positive integer.");
+ }
+ }
+ else if(!s.hasNext())
+ throw new RangeLimitNotFoundException("No range start found!");
+ else
+ throw new RangeFormatException("Found: "+start+". Start position ist not an integer. " +
+ "It must be a positive integer.");
+
+ if(s.hasNextInt()){
+ end = s.nextInt();
+ if(end < 0){
+ throw new RangeFormatException("End position must be a positive integer.");
+ }
+ }
+ else if(!s.hasNext())
+ throw new RangeLimitNotFoundException("No range end found!");
+ else
+ throw new RangeFormatException("Found: "+end+". End position ist not an integer. " +
+ "It must be a positive integer.");
+ }
+
+ public String chrom(){
+ return chrom;
+ }
+
+ public int start(){
+ return start;
+ }
+
+ public int end(){
+ return end;
+ }
+
+ public String toString(){
+ return line;
+ }
+
+ public boolean isForwardRead(){
+ return start <= end;
+ }
+
+ public String name() {
+ // TODO Auto-generated method stub
+ return rName;
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/datastructures/TargetLine.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/TargetLine.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,87 @@
+package datastructures;
+
+import java.util.Scanner;
+
+import exceptions.ChromosomeFormatException;
+import exceptions.ChromosomeNotFoundException;
+import exceptions.NullOrNegativeRangeException;
+import exceptions.RangeFormatException;
+import exceptions.RangeLimitNotFoundException;
+
+/**
+ * Represents a target Line from the target file.
+ *
+ * @author Ali Abdallah
+ * @version 19.07.2011
+ * @since Java 1.6
+ */
+
+public class TargetLine {
+
+ String line;
+ String chrom;
+ int start, end;
+
+ public TargetLine(String line) throws RangeFormatException,
+ ChromosomeFormatException,
+ ChromosomeNotFoundException,
+ RangeLimitNotFoundException,
+ NullOrNegativeRangeException {
+ this.line = line;
+ Scanner s = new Scanner(line);
+ if(s.hasNext()){
+ chrom = s.next();
+ if(!(chrom.toLowerCase().startsWith("chr") || chrom.equals("*")))
+ throw new ChromosomeFormatException(chrom);
+ }
+ else
+ throw new ChromosomeNotFoundException();
+
+ if(s.hasNextInt()){
+ start = s.nextInt();
+ if(start < 0){
+ throw new RangeFormatException("Start position of the target must be a " +
+ "positive integer.");
+ }
+ }
+ else if(!s.hasNext())
+ throw new RangeLimitNotFoundException("No target range start found!");
+ else
+ throw new RangeFormatException("Target start position" +
+ " is not an integer. It must be a positive" +
+ " integer."+ " Found: "+start);
+
+ if(s.hasNextInt()){
+ end = s.nextInt();
+ if(end < 0){
+ throw new RangeFormatException("Target end position must be a positive " +
+ "integer."+ " Found: "+end);
+ }
+ }
+ else if(!s.hasNext())
+ throw new RangeLimitNotFoundException("No range end found!");
+ else
+ throw new RangeFormatException("Found: "+end+". End position ist not an integer. " +
+ "It must be a positive integer.");
+
+ if(start >= end)
+ throw new NullOrNegativeRangeException("Target line \""+line+"\"");
+ }
+
+ public String chrom(){
+ return chrom;
+ }
+
+ public int start(){
+ return start;
+ }
+
+ public int end(){
+ return end;
+ }
+
+ public String toString(){
+ return line;
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/ChromosomeException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/ChromosomeException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,16 @@
+package exceptions;
+
+public class ChromosomeException extends Exception {
+
+ private static final long serialVersionUID = -2075266777182180011L;
+
+ public ChromosomeException(String curr){
+ super(curr);
+ }
+
+ public ChromosomeException(){
+ super();
+ System.out.println(this.getMessage());
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/ChromosomeFormatException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/ChromosomeFormatException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,12 @@
+package exceptions;
+
+public class ChromosomeFormatException extends ChromosomeException {
+
+ private static final long serialVersionUID = 2920204775834301041L;
+
+ public ChromosomeFormatException(String curr){
+ super("The format of the chromosome name is invalid\n" +
+ "Found chromosome name is: "+curr);
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/ChromosomeMismatchException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/ChromosomeMismatchException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,12 @@
+package exceptions;
+
+public class ChromosomeMismatchException extends ChromosomeException {
+
+ private static final long serialVersionUID = -2902763382812748929L;
+
+ public ChromosomeMismatchException(){
+ super("The chromosome names in target and alignment are different. " +
+ "The naming must be consistent.");
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/ChromosomeNotFoundException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/ChromosomeNotFoundException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,11 @@
+package exceptions;
+
+public class ChromosomeNotFoundException extends ChromosomeException {
+
+ private static final long serialVersionUID = 1L;
+
+ public ChromosomeNotFoundException(){
+ super("No chromosomes found.");
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/FileFormatException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/FileFormatException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,11 @@
+package exceptions;
+
+public class FileFormatException extends Exception {
+
+ private static final long serialVersionUID = -9091546054856311514L;
+
+ public FileFormatException(String s) {
+ super("Datei Format \""+s+"\" wird nicht unterstützt");
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/GenomeAnnotationException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/GenomeAnnotationException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,11 @@
+package exceptions;
+
+public class GenomeAnnotationException extends Throwable {
+
+ private static final long serialVersionUID = -9050133395128460361L;
+
+ public GenomeAnnotationException(){
+ super("The specified genome annotation is invalid\n");
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/NullOrNegativeRangeException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/NullOrNegativeRangeException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,16 @@
+package exceptions;
+
+public class NullOrNegativeRangeException extends RangeException {
+
+ private static final long serialVersionUID = 1L;
+
+ public NullOrNegativeRangeException(){
+ super("The start position is bigger than or equal to the end position.");
+ }
+
+ public NullOrNegativeRangeException(String message){
+ super( message + "\n" +
+ "The start position is bigger than or equal to the end position.");
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/RangeException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/RangeException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,15 @@
+package exceptions;
+
+public class RangeException extends Exception {
+
+ private static final long serialVersionUID = -8250851930700369771L;
+
+ public RangeException(){
+ super();
+ }
+
+ public RangeException(String s){
+ super(s);
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/RangeFormatException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/RangeFormatException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,15 @@
+package exceptions;
+
+public class RangeFormatException extends RangeException {
+
+ private static final long serialVersionUID = -7603714654119196278L;
+
+ public RangeFormatException(){
+ super("The range limits are misformatted.");
+ }
+
+ public RangeFormatException(String message){
+ super( message + "\n" +
+ "The range limits are misformatted.");
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/exceptions/RangeLimitNotFoundException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/exceptions/RangeLimitNotFoundException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,12 @@
+package exceptions;
+
+
+public class RangeLimitNotFoundException extends RangeException {
+
+ private static final long serialVersionUID = -4135602280097231477L;
+
+ public RangeLimitNotFoundException(String string) {
+ super(string);
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/filters/Filter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/filters/Filter.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,45 @@
+package filters;
+
+/**
+ * This abstract class is a framework for classes. It filters versatile formats
+ * into a single reduced format compatible with converter classes, such as the
+ * Read2Wig class.
+ *
+ * @author Ali Abdallah
+ * @version 01.08.2011
+ * @since jdk 1.6
+ */
+public abstract class Filter {
+
+ private String
+ /**
+ * The path of the input file.
+ */
+ input,
+ /**
+ * The path of the output file.
+ */
+ output;
+
+ public Filter(String input, String output){
+ this.input = input;
+ this.output = output;
+ }
+
+ public abstract void filter();
+
+ public abstract void sort();
+
+
+ public String getInputPath() {
+ return input;
+ }
+
+ public String getOutputPath() {
+ return output;
+ }
+
+ public void setInputPath(String input){
+ this.input = input;
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/filters/GenomeFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/filters/GenomeFilter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,91 @@
+package filters;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Scanner;
+import datastructures.GenomeLine;
+
+public class GenomeFilter extends Filter{
+
+ private File input, output;
+
+
+ public GenomeFilter(String inputFileName, String outputFileName) {
+ super(inputFileName, outputFileName);
+ input = new File(getInputPath());
+ output = new File(getOutputPath());
+ }
+
+ public void filter() {
+
+ Scanner s = null;
+ try {
+ s = new Scanner(input);
+
+ FileWriter fw = null;
+ fw = new FileWriter(getOutputPath());
+
+ while(s.hasNextLine()){
+ try {
+ GenomeLine gl = new GenomeLine(s.nextLine());
+// if(gl.chrom().equals("chr10")) System.out.println(gl);
+ if(gl.valid()) fw.write(gl+"\n");
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ fw.close();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ System.out.println("GENOME ANNOTATION FILE:");
+ System.out.println(getInputPath() + " reduced to " + getOutputPath());
+ sort();
+ }
+
+ public static void main(String[] args){
+ GenomeFilter gf =
+ new GenomeFilter("/home/abdallah/Desktop/input/refGene.txt",
+ "/home/abdallah/Desktop/output/refGeneReduced.txt");
+ gf.filter();
+ }
+
+ public void sort() {
+ Runtime rt = Runtime.getRuntime();
+ try {
+ String rawOutput = getOutputPath();
+ String outputName = output.getName();
+ String tmpD= output.getParentFile().getAbsolutePath();
+ String pathname = output.getParentFile().getAbsolutePath()+"/"+outputName+"Sorted";
+ output = new File(pathname);
+ if(!output.exists()) output.createNewFile();
+ String command = "sort -k2,2 -k3n,3 -k5,5 -T "+tmpD+" "+rawOutput;
+ Process p = rt.exec(command);
+ Scanner ps = new Scanner(p.getInputStream());
+ FileWriter fw = new FileWriter(output);
+ while(ps.hasNextLine()){
+ String nextLine = ps.nextLine();
+ fw.write(nextLine+"\n");
+ }
+ fw.close();
+
+ new File(rawOutput).delete();
+ new File(pathname).renameTo(new File(rawOutput));
+ System.out.println("Reduced file "+new File(rawOutput).getAbsolutePath()+" sorted\n");
+
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ }
+ }
+
+ public String toString(){
+ return "GenomeFilter";
+ }
+
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/filters/ReadFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/filters/ReadFilter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,177 @@
+package filters;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Scanner;
+import datastructures.ReadLine;
+
+public class ReadFilter extends Filter{
+
+ File input, output;
+
+ /**
+ * Constructs a SamAdapter object. The output of an adaption is written to the
+ * given file outputFileName.
+ *
+ * @param inputFileName the name of the read alignment input file.
+ * @param outputFileName the name of the output file containing the reduced
+ * format of the read alignment file. It must ends with ".red".
+ */
+ public ReadFilter(String inputFileName, String outputFileName) {
+ super(inputFileName, outputFileName);
+ input = new File(inputFileName);
+ output = new File(outputFileName);
+ }
+
+ /**
+ * 
+ * Uses ReadLine zu reduce each line of the read alignment file to following format: 
+ * <name> <chrom> <start> <end> (tab delimited).
+ * 
+ * In the following we list the 12 fields of the sam-alignment-file. We mark the fields we are
+ * interessted in with (!!):
+ * <PRE>
+ * 1. <QNAME> : Query pair NAME if paired; or Query NAME if unpaired (Ex: 6:105:18438:14421) (!!)
+ * 2. <FLAG> : bitwise FLAG a₀a₁a₂a₃a₄a₅a₆a₇a₈a₉a₁₀ (Ex: 0 forward, 16 reverse strand)
+ * a₀ : the read is paired in sequencing, (no matter whether it is mapped in a pair)
+ * a₁ : the read is mapped in a proper pair
+ * a₂ : the query sequence itself is unmapped
+ * a₃ : the mate is unmapped
+ * a₄ : strand of the query (0 for forward; 1 for reverse strand)
+ * a₅ : strand of the mate
+ * a₆ : the read is the first read in a pair
+ * a₇ : the read is the second read in a pair
+ * a₈ : the alignment is not primary
+ * a₉ : the read fails platform/vendor quality checks
+ * a₁₀: the read is either a PCR duplicate or an optical duplicate
+ * 3. <RNAME> : Reference sequence NAME (Ex: chr10) (!!)
+ * 4. <POS> : 1-based leftmost POSition/coordinate of the clipped sequence (Ex: 60041) (!!)
+ * 5. <MAPQ> : MAPping Quality (Ex: 0)
+ * (phred-scaled posterior probability that the mapping position of this read is incorrect)
+ * 6. <CIGAR> : extended CIGAR string (Ex: 150M)
+ * 7. <MRNM> : Mate Reference sequence NaMe; “=” if the same as <RNAME> (Ex:*)
+ * 8. <MPOS> : 1-based leftmost Mate POSition of the clipped sequence (Ex: 0)
+ * 9. <ISIZE> : inferred Insert SIZE (Ex: 0)
+ * 10. <SEQ> : query SEQuence; “=” for a match to the reference; n/N/. for ambiguity; cases are not maintained (!!)
+ * (Ex: TGTTGTTGTTATTTCTGAATGACATTTACTTTGCTGCTCTTTATTTTGCG
+ * TATTTAAAACTATTAGATCGTGTGATTATATTTGACAGGTCTTAATTGAC
+ * GCGCTGTTCAGCCCTTTGAGTTCGGTTGAGTTTTGTGTTGGAGAATTTTC)
+ * 11. <QUAL> : query QUALity; ASCII-33 gives the Phred base quality
+ * (Ex: /.8349-7:95@=8999;1:=;===AABD:=@A;>AD:E:9@==69<;@B3CBC@B8B;B89=8=3;@@@.:->>B?
+ * C4CBB8EDGDD8GDEEDEEE8EBA9B???=B;,8:+5;;A??>?#############################)
+ * 12. [<TAG>:<VTYPE>:<VALUE> [...]]: TAG/Value TYPE/match <VTYPE> (space allowed)
+ * (Ex: XT:A:R NM:i:2 X0:i:2 X1:i:0)
+ * </PRE>
+ */
+ public void filter() {
+ FileWriter fw = null;
+ Scanner s = null;
+
+ try {
+ s= new Scanner(input);
+ } catch (FileNotFoundException e) {
+ System.err.println("sam file not found");
+ e.printStackTrace();
+ }
+
+ try {
+ if(output == null){
+ output = new File(input.getName().
+ substring(0,input.getName().lastIndexOf("."))+".rsam");
+ }
+
+ fw = new FileWriter(output);
+
+ } catch (IOException e) {
+ System.err.println("Error generating rsam file");
+ e.printStackTrace();
+ }
+
+ String rawline;
+ ReadLine line = null;
+
+ do{
+ rawline = s.nextLine();
+ }while(rawline.startsWith("@"));
+
+ do{
+ try {
+ line = new ReadLine(rawline);
+ fw.write(line+"\r\n");
+ } catch (IOException e) {
+ System.err.println("Error writing reduced form of:\n"+rawline);
+ e.printStackTrace();
+ }
+ if(s.hasNextLine())
+ rawline = s.nextLine();
+ }while(s.hasNextLine());
+
+
+ try {
+ fw.write(line +"\r\n");
+ } catch (IOException e) {
+ System.err.println("Error writing reduced form of:\n"+line);
+ e.printStackTrace();
+ }
+
+ try {
+ fw.close();
+ } catch (IOException e) {
+ System.err.println("Error closing file");
+ e.printStackTrace();
+ }
+ s.close();
+
+ System.out.println("READS FILE:");
+ System.out.println(input.getAbsolutePath()+" reduced to "+
+ output.getAbsolutePath());
+ sort();
+ }
+
+
+ public void sort() {
+ Runtime rt = Runtime.getRuntime();
+ try {
+ String rawOutput = output.getAbsolutePath();
+ String outputName = output.getName();
+ String pathname = output.getParentFile().getAbsolutePath()+"/"+outputName+"Sorted";
+
+ output = new File(pathname);
+ String tmpD=output.getParentFile().getAbsolutePath();
+
+ if(!output.exists())output.createNewFile();
+ String command = "sort -k2,2 -k3n,3 -T "+tmpD+" "+rawOutput;
+ Process p = rt.exec(command);
+ Scanner ps = new Scanner(p.getInputStream());
+
+ FileWriter fw = new FileWriter(output);
+ while(ps.hasNextLine()){
+ String nextLine = ps.nextLine();
+ fw.write(nextLine+"\n");
+ }
+ fw.close();
+
+ Scanner psStdErr=new Scanner(p.getErrorStream());
+ while(psStdErr.hasNextLine()){
+ String errLine=psStdErr.nextLine();
+ System.out.println(errLine);
+ }
+
+ new File(rawOutput).delete();
+ new File(pathname).renameTo(new File(rawOutput));
+ System.out.println("Reduced file "+new File(rawOutput).getAbsolutePath()+" sorted\n");
+
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ }
+ }
+
+
+ public String toString(){
+ return "ReadFilter";
+ }
+
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/filters/TargetFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/filters/TargetFilter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,195 @@
+package filters;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Scanner;
+import middlewares.Misc;
+import datastructures.Frame;
+import datastructures.TargetLine;
+import exceptions.ChromosomeFormatException;
+import exceptions.ChromosomeNotFoundException;
+import exceptions.NullOrNegativeRangeException;
+import exceptions.RangeFormatException;
+import exceptions.RangeLimitNotFoundException;
+
+public class TargetFilter extends Filter {
+
+ // variables used for test purposes.
+ public int target_size, target_regions;
+
+ public TargetFilter(String input, String output) {
+ super(input, output);
+ target_size = 0;
+ target_regions = 0;
+ }
+
+ public void filter() {
+ try {
+
+ Scanner s = new Scanner(new File(getInputPath()));
+ FileWriter fw;
+ System.out.println("TARGET REGIONS FILE:");
+ /*
+ * 1. STEP:
+ * a. Remove all but the first track.
+ * b. Remove browser and track header lines of the first track
+ * c. Save the output in the output directory and return the path of the output file.
+ */
+ String finput = filterTracks(s);
+ setInputPath(finput);
+
+ /*
+ * 2. STEP:
+ * a. Sort the target region file lexicographically by chromomose-name.
+ * b. If chr-names are identical then numerically by the start position.
+ * c. If start positions are identical then numerically by the end position.
+ */
+ sort();
+
+ /*
+ * 3. STEP:
+ * Unify all overlapping target regions.
+ */
+ s = new Scanner(new File(getInputPath()));
+ fw = new FileWriter(getOutputPath());
+ // for all target regions do the following:
+ if (s.hasNextLine()) {
+ try {
+ // parse the current target region.
+ TargetLine tl = new TargetLine(s.nextLine());
+ // create a new frame representing the current target region.
+ Frame union = new Frame(tl.start(), tl.end() - tl.start() + 1);
+ String chrom = tl.chrom();
+ while (s.hasNextLine()) {
+ // parse the next target region.
+ tl = new TargetLine(s.nextLine());
+ // create the corresponding frame.
+ Frame nextTarget = new Frame(tl.start(), tl.end() - tl.start() + 1);
+ String nextChrom = tl.chrom();
+ // if current and next overlap each other.
+ if (union.overlaps(nextTarget) && chrom.equals(nextChrom)) {
+ // unify regions.
+ union = union.unify(nextTarget);
+ // go to the next iteration.
+ continue;
+ }
+ // else
+ // write the computed overlap-free target region.
+ target_size += union.end()-union.start()+1;
+ target_regions++;
+ fw.write(chrom +"\t"+ union.start() +"\t"+ union.end() +"\n");
+ // refresh the union and chrom variables for the next computation.
+ union = nextTarget;
+ chrom = nextChrom;
+ }
+
+ try {
+ target_size += union.end()-union.start()+1;
+ target_regions++;
+ fw.write(chrom+"\t"+union.start()+"\t"+union.end()+"\n");
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ fw.close();
+ } catch (RangeFormatException e) {
+ e.printStackTrace();
+ } catch (ChromosomeFormatException e) {
+ e.printStackTrace();
+ } catch (ChromosomeNotFoundException e) {
+ e.printStackTrace();
+ } catch (RangeLimitNotFoundException e) {
+ e.printStackTrace();
+ } catch (NullOrNegativeRangeException e) {
+ e.printStackTrace();
+ }
+ }
+ } catch (FileNotFoundException fnfe) {
+ fnfe.printStackTrace();
+ } catch (IOException ioe) {
+ ioe.printStackTrace();
+ }
+ System.out.println(getInputPath()+" reduced to "+getOutputPath());
+ }
+
+ /**
+ * 1. Removes all but the first track.
+ * 2. Removes browser and track header lines of the first track
+ * 3. Saves the output in the output directory and return the path of the output file.
+ *
+ * @param s the scanner reading the raw file.
+ * @return the path of the output file.
+ * @throws IOException if writing fails.
+ */
+ private String filterTracks(Scanner s) throws IOException {
+
+ String finput = Misc.path(getOutputPath())+ Misc.prefix(getInputPath()) + ".bed";
+ FileWriter fw = new FileWriter(finput);
+ // Counters for browser header lines and track header lines.
+ int browserRead = 0;
+ int trackRead = 0;
+ while (s.hasNextLine()) {
+ String line = s.nextLine();
+ // Count browser lines.
+ if (line.startsWith("browser")) {
+ browserRead++;
+ // Count header lines.
+ } else if (line.startsWith("track")) {
+ trackRead++;
+ } else {
+ // Write lines as long as they corresponds to the first track.
+ if (trackRead <= 1 && browserRead <= 1)
+ fw.write(line + "\n");
+ else
+ // Otherwise cancel the computation.
+ break;
+ }
+ }
+ fw.close();
+ return finput;
+ }
+
+ /**
+ * 1. Sort the target region file lexicographically by chromomose-name.
+ * 2. If chr-names are identical then numerically by the start position.
+ * 3. If start positions are identical then numerically by the end position.
+ */
+ public void sort() {
+ Runtime rt = Runtime.getRuntime();
+ try {
+ String unsorted = getInputPath();
+ String tmpD = new File(getOutputPath()).getParentFile().getAbsolutePath();
+ String sorted = tmpD+Misc.slash(tmpD)+Misc.prefix(unsorted)+"Sorted";
+ setInputPath(sorted);
+
+ if(!new File(getInputPath()).exists())
+ new File(getInputPath()).createNewFile();
+
+ String command = "sort -k1,1 -k2n,2 -k3n,3 -T "+tmpD+" "+unsorted;
+ Process p = rt.exec(command);
+ Scanner ps = new Scanner(p.getInputStream());
+ FileWriter fw = new FileWriter(getInputPath());
+ while(ps.hasNextLine()){
+ String nextLine = ps.nextLine();
+ fw.write(nextLine+"\n");
+ }
+ fw.close();
+ new File(sorted).renameTo(new File(unsorted));
+ setInputPath(unsorted);
+ System.out.println("Target file "+new File(unsorted).getAbsolutePath()+" sorted");
+
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ }
+ }
+
+ public static void main(String[] args){
+ new TargetFilter("/home/abdallah/Desktop/input/Agilent_SureSelect_50Mb.bed",
+ "/home/abdallah/Desktop/output/Agilent_SureSelect_50Mb_Output.bed")
+ .filter();
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/GeneExtractor.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/middlewares/GeneExtractor.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,68 @@
+package middlewares;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.Scanner;
+
+import datastructures.AVLTree;
+import datastructures.AnnotationLine;
+import datastructures.TargetLine;
+
+/**
+ *
+ * Generate a AVL-Tree for fast extraction of genes (logarithmic time).
+ *
+ * @author Ali Abdallah
+ * @version 0.4.5, 14.07.2011
+ * @since jdk 1.6.0
+ *
+ */
+
+public class GeneExtractor {
+
+ /**
+ * The path of the genome annotation file.
+ */
+ String genomeAnnotation;
+
+ /**
+ * The avl tree representing the genome annotation file.
+ */
+ AVLTree genesTree;
+
+ /**
+ * The scanner scanning the genome file.
+ */
+ Scanner s;
+
+ /**
+ * Constructs the avl-tree based on the genome annotation file.
+ * @param genomeAnnotation the genome annotation file.
+ */
+ public GeneExtractor(String genomeAnnotation) {
+ genesTree = new AVLTree();
+ this.genomeAnnotation = genomeAnnotation;
+ try {
+ s = new Scanner(new File(genomeAnnotation));
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ while (s.hasNextLine()) {
+ genesTree.insert(new AnnotationLine(s.nextLine()));
+ }
+ s.close();
+ }
+
+ /**
+ * Search the tree for a gene overlapping the specified target.
+ *
+ * @param tl the target line of the current target.
+ * @return the gene overlapping the specified target, if it exists and
+ * "unknown" otherwise.
+ */
+ public String extractGene(TargetLine tl) {
+ AnnotationLine a =
+ (AnnotationLine) genesTree.find(new AnnotationLine
+ ("*", tl.chrom(), "dummy", tl.start(), tl.end()));
+ return ((a != null) ? a.gene() : "unknown");
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/HitsCounter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/middlewares/HitsCounter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,105 @@
+package middlewares;
+import java.util.Vector;
+
+/**
+ * Counts the number of bases hit at least 1, 5, 10, 20 or 30 times.
+ *
+ * @author Ali Abdallah
+ * @version 22.07.2011
+ * @since Java 1.6
+ */
+public class HitsCounter {
+
+ /**
+ * The hits vector with the number of bases hit at different levels.
+ */
+ private Vector<Integer> hits;
+
+ /**
+ * The number of bases hit at the five different levels for a specific
+ * target.
+ */
+ private Vector<Integer> currentHits;
+
+ /**
+ * The levels at which the number of bases is counted.
+ */
+ private int[] levels = { 1, 5, 10, 20, 30 };
+
+ /**
+ * Creates and initializes a hit counter.
+ */
+ public HitsCounter() {
+ hits = new Vector<Integer>();
+ currentHits = new Vector<Integer>();
+ for (int i = 0; i < levels.length; i++) {
+ hits.add(0);
+ currentHits.add(0);
+ }
+ }
+
+ /**
+ * Update the number of bases hit at the specified different levels.
+ */
+ public void updateHits() {
+ for (int i = 0; i < hits.size(); i++) {
+ hits.set(i, hits.get(i) + currentHits.get(i));
+ }
+ }
+
+ /**
+ * Reset the number of bases hit at the specified different leverls for
+ * a specific target for user for the next target.
+ */
+ public void resetCurrentHits() {
+ currentHits = new Vector<Integer>();
+ for (int i = 0; i < levels.length; i++) {
+ currentHits.add(0);
+ }
+ }
+
+ /**
+ * Increments the number of bases hit at some levels by one, if the number
+ * of hits on this base reach or exceed this level.
+ *
+ * @param hitsOnBase
+ */
+ public void updateCurrentHits(int hitsOnBase) {
+ for (int i = 0; i < currentHits.size(); i++) {
+ if (hitsOnBase >= levels[i]) {
+ currentHits.set(i, currentHits.get(i) + 1);
+ }
+ }
+ }
+
+ // Index of the bases level of the current target.
+ int currHit = 0;
+
+ /**
+ * @return the number of bases hit at the next higher level in the current
+ * target.
+ */
+ public int getNextLevelCurrentHits() {
+ if (currHit < currentHits.size())
+ return currentHits.get(currHit++);
+ else {
+ currHit = 1;
+ return currentHits.get(0);
+ }
+ }
+
+ // Index of the bases level of the target.
+ int hit = -1;
+
+ /**
+ * @return the number of bases hit at the next higher level.
+ */
+ public int getNextLevelHits() {
+ if (++hit < hits.size()) {
+ return hits.get(hit);
+ } else {
+ return (hit = -1);
+ }
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/Misc.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/middlewares/Misc.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,206 @@
+package middlewares;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Scanner;
+
+import datastructures.ReducedReadLine;
+import datastructures.TargetLine;
+import exceptions.ChromosomeFormatException;
+import exceptions.ChromosomeNotFoundException;
+import exceptions.NullOrNegativeRangeException;
+import exceptions.RangeFormatException;
+import exceptions.RangeLimitNotFoundException;
+
+/**
+ * Miscellaneous methods for different uses.
+ *
+ * @author Ali Abdallah
+ * @version 01.2011
+ * @since jdk 1.6.0
+ */
+public class Misc {
+
+ /**
+ * Make the first letter big, if possible. nGSrich -> NGSrich.
+ *
+ * @param s the string
+ * @return the same string with the first letter big.
+ */
+ public static String bigFirst(String s) {
+ return s.substring(0, 1).toUpperCase() + s.substring(1);
+ }
+
+ /**
+ * Creates a shortcut for the file with a different file extension.
+ *
+ * @param fName the original file name.
+ * @param newExt the new extension of the file.
+ * @param dir the directory of the mad link.
+ * @return a link to the file fName with a different extension.
+ */
+ public static File rename(String fName, String newExt, String dir) {
+
+ String inDirShortCut = dir + Misc.slash(dir);
+ String fShortcutName = inDirShortCut + Misc.prefix(fName) + "."
+ + newExt;
+ Runtime r = Runtime.getRuntime();
+ try {
+ r.exec("ln -s " + fName + " " + fShortcutName);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ try {
+ Thread.sleep(100);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+ return new File(fShortcutName);
+ }
+
+ /**
+ * @return the path of the bin directory of this software.
+ */
+ public static String binDir() {
+ URL url = new Misc().getClass().getResource("Misc.class");
+ String path = url.toString().substring(url.toString().indexOf(":") + 1);
+ path = path.substring(0, path.lastIndexOf("/"));
+
+ return path.substring(0, path.lastIndexOf("/"));
+
+ }
+
+ /**
+ * @return the path of this software.
+ */
+ public static String scriptDir() {
+ URL url = new Misc().getClass().getResource("../NGSrich.class");
+ String path = url.toString().substring(url.toString().indexOf(":") + 1);
+ path = path.substring(0, path.lastIndexOf("/"));
+ return path.substring(0, path.lastIndexOf("/")+1);
+
+ }
+
+ public static void main(String[] args) {
+ System.out.println(scriptDir());
+ }
+
+ /**
+ * @param path
+ * @return extends the path by a slash at the end, in the case it don't
+ * exists.
+ */
+ public static String slash(String path) {
+ return (path.endsWith("/") ? "" : "/");
+ }
+
+ /**
+ * @return the name of the host.
+ */
+ public static String getHostName() {
+ Runtime rt = Runtime.getRuntime();
+ String erg = "";
+ try {
+ File f = new File("hostname.sh");
+ FileWriter fw = new FileWriter(f);
+
+ fw.write("#!/bin/bash\r\nproc=$(hostname -s).$$\r\necho $proc");
+ fw.close();
+ Process p = rt.exec("chmod 700 " + f.getAbsolutePath());
+ p = rt.exec("sh " + f.getAbsolutePath());
+
+ Scanner s = new Scanner(p.getInputStream());
+
+ while (s.hasNextLine()) {
+ erg += (s.nextLine());
+ }
+ s.close();
+
+ f.delete();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ return erg;
+ }
+
+ /**
+ * @param fileName
+ * @return the extension of the file.
+ */
+ public static String suffix(String fileName) {
+ return fileName.substring(fileName.lastIndexOf(".") + 1);
+ }
+
+ /**
+ * @param fileName
+ * @return the name of the file without the extension.
+ */
+ public static String prefix(String fileName) {
+ return fileName.substring(fileName.lastIndexOf("/") + 1,
+ fileName.lastIndexOf("."));
+ }
+
+ /**
+ * @param fileName
+ * @return the directory of the specified file.
+ */
+ public static String path(String fileName) {
+ String absolutePath =
+ new File(fileName).getParentFile().getAbsolutePath();
+ return absolutePath+slash(absolutePath);
+ }
+
+ /**
+ * Check if the chromosome names in the target file are a subset of the
+ * chromosome name in the alignment file.
+ *
+ * @param alignment the alignment file.
+ * @param target the target file.
+ * @return true if target chromosomes are a subset of alignment chromosome
+ * and false otherwise.
+ */
+ public static boolean areChromosomeCompatible(File alignment, File target){
+ Scanner aScan = null, tScan = null;
+ try {
+ aScan = new Scanner(alignment);
+ tScan = new Scanner(target);
+
+ ArrayList<String> alist = new ArrayList<String>();
+ ArrayList<String> tlist = new ArrayList<String>();
+ while(aScan.hasNextLine()){
+ ReducedReadLine rl = new ReducedReadLine(aScan.nextLine());
+ if(alist.indexOf(rl.chrom())==-1)
+ alist.add(rl.chrom());
+ }
+ while(tScan.hasNextLine()){
+ TargetLine tl = new TargetLine(tScan.nextLine());
+ if(tlist.indexOf(tl.chrom())==-1)
+ tlist.add(tl.chrom());
+ }
+ for(int i = 0; i < tlist.size(); i++){
+ if(alist.indexOf(tlist.get(i))!=-1)
+ return true;
+ }
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (ChromosomeFormatException e) {
+ e.printStackTrace();
+ } catch (ChromosomeNotFoundException e) {
+ e.printStackTrace();
+ } catch (RangeFormatException e) {
+ e.printStackTrace();
+ } catch (RangeLimitNotFoundException e) {
+ e.printStackTrace();
+ } catch (NullOrNegativeRangeException e) {
+ e.printStackTrace();
+ }
+
+
+ return false;
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/ReadCounter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/middlewares/ReadCounter.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,33 @@
+package middlewares;
+/**
+ * Counter for the reads on targets (+/- 0/100/200) and the reads overlapping
+ * targets (+/- 0/100/200).
+ *
+ * @author Ali Abdallah
+ * @version 14.07.2011
+ * @since jdk 1.6.0
+ */
+public class ReadCounter {
+
+ // Self explanatory.
+ private int on, on100, on200, over, over100, over200;
+
+ public ReadCounter(){on=0; on100=0; on200=0; over=0; over100=0; over200=0;}
+
+ public void incOn(){on++;}
+ public void incOn100(){on100++;}
+ public void incOn200(){on200++;}
+
+ public void incOver(){over++;}
+ public void incOver100(){over100++;}
+ public void incOver200(){over200++;}
+
+ public int on(){return on;}
+ public int on100(){return on100;}
+ public int on200(){return on200;}
+
+ public int over(){return over;}
+ public int over100(){return over100;}
+ public int over200(){return over200;}
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/middlewares/XMLSummaryFileBuilder.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/middlewares/XMLSummaryFileBuilder.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,136 @@
+package middlewares;
+
+import java.util.*;
+import java.io.*;
+import org.jdom.*;
+import org.jdom.input.*;
+import org.jdom.output.*;
+
+/**
+ * Used to construct the summary file based on the computation of an
+ * EnrichmentStatsComputer object. It uses a file pattern to generate this file
+ * dynamically.
+ *
+ * @author Ali Abdallah
+ * @version 20.07.2011
+ * @since Java 1.6
+ */
+
+public class XMLSummaryFileBuilder {
+
+ /**
+ * The pattern file containing the structure of the summary without real
+ * data.
+ */
+ static String xmlPatternFile;
+
+ /**
+ * The summary file containing the computed data.
+ */
+ static String xmlOutputFile;
+
+ /**
+ * An object with an abstract representation on an xml-file.
+ */
+ static Document doc;
+
+ /**
+ * The leaf-tags containing data as text.
+ */
+ List<Element> leafs;
+
+ /**
+ * The name of the current sample.
+ */
+ static String currSample;
+
+ /**
+ * Creates and initializes a XMLSummaryFileBuilder object.
+ *
+ * @param xmlPatternFile the pattern file.
+ * @param xmlOutputFile the output file.
+ * @param currSample the current read alignment sample name without
+ * the extension.
+ */
+ public XMLSummaryFileBuilder(String xmlPatternFile, String xmlOutputFile,
+ String currSample) {
+
+ leafs = new ArrayList<Element>();
+ XMLSummaryFileBuilder.xmlPatternFile = xmlPatternFile;
+ XMLSummaryFileBuilder.xmlOutputFile = xmlOutputFile;
+ XMLSummaryFileBuilder.currSample = currSample;
+ SAXBuilder builder = new SAXBuilder();
+ try {
+ doc = builder.build(xmlPatternFile);
+ } catch (JDOMException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Same as the constructor above but the pattern file is internally
+ * specified.
+ *
+ * @param xmlOutputFile the output file.
+ * @param currSample the current read alignment sample name without
+ * the extension.
+ */
+ public XMLSummaryFileBuilder(String xmlOutputFile,
+ String currSample) {
+ this(Misc.binDir()+"/xmlFilePattern.xml", xmlOutputFile, currSample);
+ }
+
+ /**
+ * Computes all the leafs of the subtree with root e.
+ *
+ * @param e an Element.
+ * @return all the leafs of the subtree with root e.
+ */
+ public Element[] getLeafs(Element e){
+ @SuppressWarnings("unchecked")
+ List<Element> children = e.getChildren();
+ for(int i = 0; i < children.size(); i++){
+ Element child = children.get(i);
+ if(child.getChildren().size() == 0)
+ leafs.add(child);
+ else
+ getLeafs(child);
+ }
+
+ Object[] oleafs = leafs.toArray();
+ Element[] eleafs = new Element[oleafs.length];
+ for(int i = 0; i < eleafs.length; i++)
+ eleafs[i] = (Element)oleafs[i];
+
+ return eleafs;
+ }
+
+ /**
+ * Same as the above method but the element is internally specified as the
+ * root of the document.
+ *
+ * @return an array with all leaf elements of the document.
+ */
+ public Element[] getLeafs(){
+ return getLeafs(doc.getRootElement());
+ }
+
+ /**
+ * Write the summary file created.
+ * @param name the name of the file.
+ */
+ public void writeXMLFile(String name) {
+ XMLOutputter outp = new XMLOutputter();
+ outp.setFormat(Format.getPrettyFormat());
+ try {
+ outp.output(doc, new FileOutputStream(name));
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Attribute.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Attribute.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,717 @@\n+/*--\n+\n+ $Id: Attribute.java,v 1.56 2007/11/10 05:28:58 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+import java.io.*;\n+\n+/**\n+ * An XML attribute. Methods allow the user to obtain the value of the attribute\n+ * as well as namespace and type information.\n+ *\n+ * @version $Revision: 1.56 $, $Date: 2007/11/10 05:28:58 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Elliotte Rusty Harold\n+ * @author Wesley Biggs\n+ * @author Victor Toni\n+ */\n+public class Attribute implements Serializable, Cloneable {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: Attribute.java,v $ $Revision: 1.56 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * Attribute type: the attribute has not been declared or type\n+ * is unknown.\n+ *\n+ * @see #getAttributeType\n+ */\n+ public final static int UNDECLARED_TYPE = 0;\n+\n+ /**\n+ * Attribute type: the attribute value is a string.\n+ *\n+ * @see #getAttributeType\n+ */\n+ public final static int CDATA_TYPE = 1;\n+\n+ /**\n+ * Attribute type: the attribute value is a unique identifier.\n+ *\n+ * @see #getAttributeType\n+ */\n+ public final static int ID_TYPE = 2;\n+\n+ /**\n+ * Attribute type: the attribute value is a reference to a\n+ * unique identifier.\n+ *\n+ * @see #getAttributeType\n+ */\n+ public final static int IDREF_TYPE = 3;\n+\n+ /**\n+ * Attribute type: the attribu'..b'sionException when conversion fails.\n+ */\n+ public long getLongValue() throws DataConversionException {\n+ try {\n+ return Long.parseLong(value.trim());\n+ } catch (final NumberFormatException e) {\n+ throw new DataConversionException(name, "long");\n+ }\n+ }\n+\n+ /**\n+ * This gets the value of the attribute, in\n+ * <code>float</code> form, and if no conversion\n+ * can occur, throws a\n+ * <code>{@link DataConversionException}</code>\n+ *\n+ * @return <code>float</code> value of attribute.\n+ * @throws DataConversionException when conversion fails.\n+ */\n+ public float getFloatValue() throws DataConversionException {\n+ try {\n+ // Avoid Float.parseFloat() to support JDK 1.1\n+ return Float.valueOf(value.trim()).floatValue();\n+ } catch (final NumberFormatException e) {\n+ throw new DataConversionException(name, "float");\n+ }\n+ }\n+\n+ /**\n+ * This gets the value of the attribute, in\n+ * <code>double</code> form, and if no conversion\n+ * can occur, throws a\n+ * <code>{@link DataConversionException}</code>\n+ *\n+ * @return <code>double</code> value of attribute.\n+ * @throws DataConversionException when conversion fails.\n+ */\n+ public double getDoubleValue() throws DataConversionException {\n+ try {\n+ // Avoid Double.parseDouble() to support JDK 1.1\n+ return Double.valueOf(value.trim()).doubleValue();\n+ } catch (final NumberFormatException e) {\n+ // Specially handle INF and -INF that Double.valueOf doesn\'t do\n+ String v = value.trim();\n+ if ("INF".equals(v)) {\n+ return Double.POSITIVE_INFINITY;\n+ }\n+ if ("-INF".equals(v)) {\n+ return Double.NEGATIVE_INFINITY;\n+ }\n+ throw new DataConversionException(name, "double");\n+ }\n+ }\n+\n+ /**\n+ * This gets the effective boolean value of the attribute, or throws a\n+ * <code>{@link DataConversionException}</code> if a conversion can\'t be\n+ * performed. True values are: "true", "on", "1", and "yes". False\n+ * values are: "false", "off", "0", and "no". Values are trimmed before\n+ * comparison. Values other than those listed here throw the exception.\n+ *\n+ * @return <code>boolean</code> value of attribute.\n+ * @throws DataConversionException when conversion fails.\n+ */\n+ public boolean getBooleanValue() throws DataConversionException {\n+ final String valueTrim = value.trim();\n+ if (\n+ (valueTrim.equalsIgnoreCase("true")) ||\n+ (valueTrim.equalsIgnoreCase("on")) ||\n+ (valueTrim.equalsIgnoreCase("1")) ||\n+ (valueTrim.equalsIgnoreCase("yes"))) {\n+ return true;\n+ } else if (\n+ (valueTrim.equalsIgnoreCase("false")) ||\n+ (valueTrim.equalsIgnoreCase("off")) ||\n+ (valueTrim.equalsIgnoreCase("0")) ||\n+ (valueTrim.equalsIgnoreCase("no"))\n+ ) {\n+ return false;\n+ } else {\n+ throw new DataConversionException(name, "boolean");\n+ }\n+ }\n+\n+ // Support a custom Namespace serialization so no two namespace\n+ // object instances may exist for the same prefix/uri pair\n+ private void writeObject(final ObjectOutputStream out) throws IOException {\n+\n+ out.defaultWriteObject();\n+\n+ // We use writeObject() and not writeUTF() to minimize space\n+ // This allows for writing pointers to already written strings\n+ out.writeObject(namespace.getPrefix());\n+ out.writeObject(namespace.getURI());\n+ }\n+\n+ private void readObject(final ObjectInputStream in)\n+ throws IOException, ClassNotFoundException {\n+\n+ in.defaultReadObject();\n+\n+ namespace = Namespace.getNamespace(\n+ (String) in.readObject(), (String) in.readObject());\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/AttributeList.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/AttributeList.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,518 @@\n+/*--\n+\n+ $Id: AttributeList.java,v 1.24 2007/11/10 05:28:58 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+import java.util.*;\n+\n+/**\n+ * <code>AttributeList</code> represents legal JDOM <code>Attribute</code>\n+ * content. This class is NOT PUBLIC; users should see it as a simple List\n+ * implementation.\n+ *\n+ * @author Alex Rosen\n+ * @author Philippe Riand\n+ * @author Bradley S. Huffman\n+ * @version $Revision: 1.24 $, $Date: 2007/11/10 05:28:58 $\n+ * @see CDATA\n+ * @see Comment\n+ * @see Element\n+ * @see EntityRef\n+ * @see ProcessingInstruction\n+ * @see Text\n+ */\n+class AttributeList extends AbstractList\n+ implements List, java.io.Serializable {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: AttributeList.java,v $ $Revision: 1.24 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";\n+\n+ private static final int INITIAL_ARRAY_SIZE = 5;\n+\n+ /** The backing list */\n+ private Attribute elementData[];\n+ private int size;\n+\n+ /** The parent Element */\n+ private Element parent;\n+\n+ /** Force an Element parent */\n+ private AttributeList() {}\n+\n+ /**\n+ * Create a new instance of the AttributeList representing\n+ * Element content\n+ *\n+ * @param parent element whose attributes are to be held\n+ */\n+ AttributeList(Element parent) {\n+ this.parent = parent;\n+ }\n+\n+ /**\n+ * Package internal method to support building from sources that are\n+ '..b'x: " + index +\n+ " Size: " + size());\n+\n+ Attribute old = elementData[index];\n+ old.setParent(null);\n+ int numMoved = size - index - 1;\n+ if (numMoved > 0)\n+ System.arraycopy(elementData, index+1, elementData, index,numMoved);\n+ elementData[--size] = null; // Let gc do its work\n+ modCount++;\n+ return old;\n+ }\n+\n+ /**\n+ * Remove the <code>Attribute</code> with the\n+ * given name and <code>Namespace</code>.\n+ *\n+ * @param namespace <code>Namespace</code> to match\n+ * @return the <code>true</code> if attribute was removed,\n+ * <code>false</code> otherwise\n+ */\n+ boolean remove(String name, Namespace namespace) {\n+ int index = indexOf(name, namespace);\n+ if (index < 0) {\n+ return false;\n+ }\n+ remove(index);\n+ return true;\n+ }\n+\n+ /**\n+ * Set the object at the specified location to the supplied\n+ * object.\n+ *\n+ * @param index The location to set the value to.\n+ * @param obj The location to set the value to.\n+ * @return The object which was replaced.\n+ * throws IndexOutOfBoundsException if index < 0 || index >= size()\n+ */\n+ public Object set(int index, Object obj) {\n+ if (obj instanceof Attribute) {\n+ Attribute attribute = (Attribute) obj;\n+ int duplicate = indexOfDuplicate(attribute);\n+ if ((duplicate >= 0) && (duplicate != index)) {\n+ throw new IllegalAddException("Cannot set duplicate attribute");\n+ }\n+ return set(index, attribute);\n+ }\n+ else if (obj == null) {\n+ throw new IllegalAddException("Cannot add null attribute");\n+ }\n+ else {\n+ throw new IllegalAddException("Class " +\n+ obj.getClass().getName() +\n+ " is not an attribute");\n+ }\n+ }\n+\n+ /**\n+ * Set the object at the specified location to the supplied\n+ * object. Note: does not check for duplicate attributes.\n+ *\n+ * @param index The location to set the value to.\n+ * @param attribute The attribute to set.\n+ * @return The object which was replaced.\n+ * throws IndexOutOfBoundsException if index < 0 || index >= size()\n+ */\n+ Object set(int index, Attribute attribute) {\n+ if (index < 0 || index >= size)\n+ throw new IndexOutOfBoundsException("Index: " + index +\n+ " Size: " + size());\n+\n+ if (attribute.getParent() != null) {\n+ throw new IllegalAddException(\n+ "The attribute already has an existing parent \\"" +\n+ attribute.getParent().getQualifiedName() + "\\"");\n+ }\n+\n+ String reason = Verifier.checkNamespaceCollision(attribute, parent);\n+ if (reason != null) {\n+ throw new IllegalAddException(parent, attribute, reason);\n+ }\n+\n+ Attribute old = (Attribute) elementData[index];\n+ old.setParent(null);\n+\n+ elementData[index] = attribute;\n+ attribute.setParent(parent);\n+ return old;\n+ }\n+\n+ /**\n+ * Return index of attribute with same name and Namespace, or\n+ * -1 if one doesn\'t exist\n+ */\n+ private int indexOfDuplicate(Attribute attribute) {\n+ int duplicate = -1;\n+ String name = attribute.getName();\n+ Namespace namespace = attribute.getNamespace();\n+ duplicate = indexOf(name, namespace);\n+ return duplicate;\n+ }\n+\n+ /**\n+ * Return the number of items in this list\n+ *\n+ * @return The number of items in this list.\n+ */\n+ public int size() {\n+ return size;\n+ }\n+\n+ /**\n+ * Return this list as a <code>String</code>\n+ */\n+ public String toString() {\n+ return super.toString();\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/CDATA.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/CDATA.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,205 @@\n+/*--\n+\n+ $Id: CDATA.java,v 1.32 2007/11/10 05:28:58 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+/**\n+ * An XML CDATA section. Represents character-based content within an XML\n+ * document that should be output within special CDATA tags. Semantically it\'s\n+ * identical to a simple {@link Text} object, but output behavior is different.\n+ * CDATA makes no guarantees about the underlying textual representation of\n+ * character data, but does expose that data as a Java String.\n+ *\n+ * @version $Revision: 1.32 $, $Date: 2007/11/10 05:28:58 $\n+ * @author Dan Schaffer\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Bradley S. Huffman\n+ * @author Victor Toni\n+ */\n+public class CDATA extends Text {\n+\n+ private static final String CVS_ID = \n+ "@(#) $RCSfile: CDATA.java,v $ $Revision: 1.32 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * This is the protected, no-args constructor standard in all JDOM\n+ * classes. It allows subclassers to get a raw instance with no\n+ * initialization.\n+ */\n+ protected CDATA() { }\n+\n+ /**\n+ * This constructor creates a new <code>CDATA</code> node, with the\n+ * supplied string value as it\'s character content.\n+ *\n+ * @param string the node\'s character content.\n+ * @throws IllegalDataException if <code>str</code> contains an \n+ * illegal character such as a vertical tab (as determined\n+ * by {@'..b'limiter <code>]]></code>.\n+ */\n+ public CDATA(final String string) {\n+ setText(string);\n+ }\n+\n+ /**\n+ * This will set the value of this <code>CDATA</code> node.\n+ *\n+ * @param str value for node\'s content.\n+ * @return the object on which the method was invoked\n+ * @throws IllegalDataException if <code>str</code> contains an \n+ * illegal character such as a vertical tab (as determined\n+ * by {@link org.jdom.Verifier#checkCharacterData})\n+ * or the CDATA end delimiter <code>]]></code>.\n+ */\n+ public Text setText(final String str) {\n+ // Overrides Text.setText() because this needs to check that CDATA rules\n+ // are enforced. We could have a separate Verifier check for CDATA\n+ // beyond Text and call that alone before super.setText().\n+\n+ if (str == null || "".equals(str)) {\n+ value = EMPTY_STRING;\n+ return this;\n+ }\n+\n+ final String reason = Verifier.checkCDATASection(str);\n+ if (reason != null) {\n+ throw new IllegalDataException(str, "CDATA section", reason);\n+ }\n+\n+ value = str;\n+\n+ return this;\n+ }\n+\n+ /**\n+ * This will append character content to whatever content already\n+ * exists within this <code>CDATA</code> node.\n+ *\n+ * @param str character content to append.\n+ * @throws IllegalDataException if <code>str</code> contains an \n+ * illegal character such as a vertical tab (as determined\n+ * by {@link org.jdom.Verifier#checkCharacterData})\n+ * or the CDATA end delimiter <code>]]></code>.\n+ */\n+ public void append(final String str) {\n+ // Overrides Text.append(String) because this needs to check that CDATA\n+ // rules are enforced. We could have a separate Verifier check for CDATA\n+ // beyond Text and call that alone before super.setText().\n+ \n+ if (str == null || "".equals(str)) {\n+ return;\n+ }\n+ \n+ // we need a temp value to ensure that the value is changed _after_\n+ // validation\n+ final String tmpValue;\n+ if (value == EMPTY_STRING) {\n+ tmpValue = str;\n+ } else {\n+ tmpValue = value + str;\n+ }\n+ \n+ // we have to do late checking since the end of a CDATA section could \n+ // have been created by concating both strings:\n+ // "]" + "]>" \n+ // or \n+ // "]]" + ">"\n+ // TODO: maybe this could be optimized for this two cases\n+ final String reason = Verifier.checkCDATASection(tmpValue);\n+ if (reason != null) {\n+ throw new IllegalDataException(str, "CDATA section", reason);\n+ }\n+ \n+ value = tmpValue;\n+ }\n+ \n+ /**\n+ * This will append the content of another <code>Text</code> node\n+ * to this node.\n+ *\n+ * @param text Text node to append.\n+ */\n+ public void append(final Text text) {\n+ // Overrides Text.append(Text) because this needs to check that CDATA\n+ // rules are enforced. We could have a separate Verifier check for CDATA\n+ // beyond Text and call that alone before super.setText().\n+ \n+ if (text == null) {\n+ return;\n+ }\n+ append(text.getText());\n+ }\n+\n+ /**\n+ * This returns a <code>String</code> representation of the\n+ * <code>CDATA</code> node, suitable for debugging. If the XML\n+ * representation of the <code>CDATA</code> node is desired,\n+ * either <code>{@link #getText}</code> or\n+ * {@link org.jdom.output.XMLOutputter#output(CDATA, java.io.Writer)}</code>\n+ * should be used.\n+ *\n+ * @return <code>String</code> - information about this node.\n+ */\n+ public String toString() {\n+ return new StringBuffer(64)\n+ .append("[CDATA: ")\n+ .append(getText())\n+ .append("]")\n+ .toString();\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Comment.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Comment.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,145 @@
+/*--
+
+ $Id: Comment.java,v 1.33 2007/11/10 05:28:58 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+/**
+ * An XML comment. Methods allow the user to get and set the text of the
+ * comment.
+ *
+ * @version $Revision: 1.33 $, $Date: 2007/11/10 05:28:58 $
+ * @author Brett McLaughlin
+ * @author Jason Hunter
+ */
+public class Comment extends Content {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: Comment.java,v $ $Revision: 1.33 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";
+
+ /** Text of the <code>Comment</code> */
+ protected String text;
+
+ /**
+ * Default, no-args constructor for implementations to use if needed.
+ */
+ protected Comment() {}
+
+ /**
+ * This creates the comment with the supplied text.
+ *
+ * @param text <code>String</code> content of comment.
+ */
+ public Comment(String text) {
+ setText(text);
+ }
+
+
+ /**
+ * Returns the XPath 1.0 string value of this element, which is the
+ * text of this comment.
+ *
+ * @return the text of this comment
+ */
+ public String getValue() {
+ return text;
+ }
+
+ /**
+ * This returns the textual data within the <code>Comment</code>.
+ *
+ * @return <code>String</code> - text of comment.
+ */
+ public String getText() {
+ return text;
+ }
+
+ /**
+ * This will set the value of the <code>Comment</code>.
+ *
+ * @param text <code>String</code> text for comment.
+ * @return <code>Comment</code> - this Comment modified.
+ * @throws IllegalDataException if the given text is illegal for a
+ * Comment.
+ */
+ public Comment setText(String text) {
+ String reason;
+ if ((reason = Verifier.checkCommentData(text)) != null) {
+ throw new IllegalDataException(text, "comment", reason);
+ }
+
+ this.text = text;
+ return this;
+ }
+
+ /**
+ * This returns a <code>String</code> representation of the
+ * <code>Comment</code>, suitable for debugging. If the XML
+ * representation of the <code>Comment</code> is desired,
+ * {@link org.jdom.output.XMLOutputter#outputString(Comment)}
+ * should be used.
+ *
+ * @return <code>String</code> - information about the
+ * <code>Attribute</code>
+ */
+ public String toString() {
+ return new StringBuffer()
+ .append("[Comment: ")
+ .append(new org.jdom.output.XMLOutputter().outputString(this))
+ .append("]")
+ .toString();
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Content.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Content.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,192 @@
+/*--
+
+ $Id: Content.java,v 1.6 2007/11/10 05:28:58 jhunter Exp $
+
+ Copyright (C) 2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+import java.io.*;
+
+/**
+ * Superclass for JDOM objects which can be legal child content
+ * of {@link org.jdom.Parent} nodes.
+ *
+ * @see org.jdom.Comment
+ * @see org.jdom.DocType
+ * @see org.jdom.Element
+ * @see org.jdom.EntityRef
+ * @see org.jdom.Parent
+ * @see org.jdom.ProcessingInstruction
+ * @see org.jdom.Text
+ *
+ * @author Bradley S. Huffman
+ * @author Jason Hunter
+ * @version $Revision: 1.6 $, $Date: 2007/11/10 05:28:58 $
+ */
+public abstract class Content implements Cloneable, Serializable {
+
+ protected Parent parent = null;
+
+ protected Content() {}
+
+ /**
+ * Detaches this child from its parent or does nothing if the child
+ * has no parent.
+ *
+ * @return this child detached
+ */
+ public Content detach() {
+ if (parent != null) {
+ parent.removeContent(this);
+ }
+ return this;
+ }
+
+ /**
+ * Return this child's parent, or null if this child is currently
+ * not attached. The parent can be either an {@link Element}
+ * or a {@link Document}.
+ *
+ * @return this child's parent or null if none
+ */
+ public Parent getParent() {
+ return parent;
+ }
+
+ /**
+ * A convenience method that returns any parent element for this element,
+ * or null if the element is unattached or is a root element. This was the
+ * original behavior of getParent() in JDOM Beta 9 which began returning
+ * Parent in Beta 10. This method provides a convenient upgrade path for
+ * JDOM Beta 10 and 1.0 users.
+ *
+ * @return the containing Element or null if unattached or a root element
+ */
+ public Element getParentElement() {
+ Parent parent = getParent();
+ return (Element) ((parent instanceof Element) ? parent : null);
+ }
+
+ /**
+ * Sets the parent of this Content. The caller is responsible for removing
+ * any pre-existing parentage.
+ *
+ * @param parent new parent element
+ * @return the target element
+ */
+ protected Content setParent(Parent parent) {
+ this.parent = parent;
+ return this;
+ }
+
+ /**
+ * Return this child's owning document or null if the branch containing
+ * this child is currently not attached to a document.
+ *
+ * @return this child's owning document or null if none
+ */
+ public Document getDocument() {
+ if (parent == null) return null;
+ return parent.getDocument();
+ }
+
+
+ /**
+ * Returns the XPath 1.0 string value of this child.
+ *
+ * @return xpath string value of this child.
+ */
+ public abstract String getValue();
+
+ /**
+ * Returns a deep, unattached copy of this child and its descendants
+ * detached from any parent or document.
+ *
+ * @return a detached deep copy of this child and descendants
+ */
+ public Object clone() {
+ try {
+ Content c = (Content)super.clone();
+ c.parent = null;
+ return c;
+ } catch (CloneNotSupportedException e) {
+ //Can not happen ....
+ //e.printStackTrace();
+ return null;
+ }
+ }
+
+ /**
+ * This tests for equality of this Content object to the supplied object.
+ * Content items are considered equal only if they are referentially equal
+ * (i.e. the same object). User code may choose to compare objects
+ * based on their properties instead.
+ *
+ * @param ob <code>Object</code> to compare to.
+ * @return <code>boolean</code> - whether the <code>Content</code> is
+ * equal to the supplied <code>Object</code>.
+ */
+ public final boolean equals(Object ob) {
+ return (ob == this);
+ }
+
+ /**
+ * This returns the hash code for this <code>Content</code> item.
+ *
+ * @return <code>int</code> - hash code.
+ */
+ public final int hashCode() {
+ return super.hashCode();
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/ContentList.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/ContentList.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,944 @@\n+/*--\n+\n+ $Id: ContentList.java,v 1.42 2007/11/10 05:28:58 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org).\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+import java.util.*;\n+\n+import org.jdom.filter.*;\n+\n+/**\n+ * A non-public list implementation holding only legal JDOM content, including\n+ * content for Document or Element nodes. Users see this class as a simple List\n+ * implementation.\n+ *\n+ * @see CDATA\n+ * @see Comment\n+ * @see Element\n+ * @see EntityRef\n+ * @see ProcessingInstruction\n+ * @see Text\n+ *\n+ * @version $Revision: 1.42 $, $Date: 2007/11/10 05:28:58 $\n+ * @author Alex Rosen\n+ * @author Philippe Riand\n+ * @author Bradley S. Huffman\n+ */\n+final class ContentList extends AbstractList implements java.io.Serializable {\n+\n+\tprivate static final String CVS_ID =\n+ "@(#) $RCSfile: ContentList.java,v $ $Revision: 1.42 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";\n+\n+\tprivate static final long serialVersionUID = 1L;\n+\n+\tprivate static final int INITIAL_ARRAY_SIZE = 5;\n+\n+ /** Our backing list */\n+ private Content elementData[];\n+ private int size;\n+\n+ /** Document or Element this list belongs to */\n+ private Parent parent;\n+\n+ /** Force either a Document or Element parent */\n+ ContentList(Parent parent) {\n+ this.parent = parent;\n+ }\n+\n+ /**\n+ * Package internal method to support building from sources that are\n+ * 100% trusted.\n+ *\n+ * @param c content to add without any checks\n+ */\n'..b'ow new NoSuchElementException("previous() is before the start of the Iterator");\n+\t\t\tindex = previousIndex();\n+\t\t\tcursor = tmpcursor;\n+\t\t\tforward = false;\n+\t\t\tcanremove = true;\n+\t\t\tcanset = true;\n+\t\t\treturn ContentList.this.get(cursor);\n+\t\t}\n+\n+ /**\n+\t\t * Returns the index of the element that would be returned by a\n+\t\t * subsequent call to <code>next</code>.\n+\t\t */\n+ public int nextIndex() {\n+ checkConcurrentModification();\n+ \tif (forward) {\n+ \t\t// Starting with next possibility ....\n+ \t\tfor (int i = cursor + 1; i < ContentList.this.size(); i++) {\n+ \t\t\tif (filter.matches(ContentList.this.get(i))) {\n+ \t\t\t\ttmpcursor = i;\n+ \t\t\t\treturn index + 1;\n+ \t\t\t}\n+ \t\t}\n+ \t\t\t// Never found another match.... put the insertion point at\n+ \t\t\t// the end of the list....\n+ \t\t\ttmpcursor = ContentList.this.size();\n+ \t\t\treturn index + 1;\n+ \t\t}\n+\n+ \t\t// We\'ve been going back... so nextIndex() returns the same\n+\t\t\t// element.\n+ \t\ttmpcursor = cursor;\n+ \t\treturn index;\n+ }\n+\n+ /**\n+ * Returns the index of the element that would be returned by a\n+ * subsequent call to <code>previous</code>. (Returns -1 if the\n+ * list iterator is at the beginning of the list.)\n+ */\n+ public int previousIndex() {\n+\t\t\tcheckConcurrentModification();\n+\t\t\tif (!forward) {\n+\t\t\t\t// starting with next possibility ....\n+\t\t\t\tfor (int i = cursor - 1; i >= 0; i--) {\n+\t\t\t\t\tif (filter.matches(ContentList.this.get(i))) {\n+\t\t\t\t\t\ttmpcursor = i;\n+\t\t\t\t\t\treturn index - 1;\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t\t// Never found another match.... put the insertion point at\n+\t\t\t\t// the start of the list....\n+\t\t\t\ttmpcursor = -1;\n+\t\t\t\treturn index - 1;\n+\t\t\t}\n+\n+\t\t\t// We\'ve been going forwards... so previousIndex() returns same\n+\t\t\t// element.\n+\t\t\ttmpcursor = cursor;\n+\t\t\treturn index;\n+\t\t}\n+\n+ /**\n+\t\t * Inserts the specified element into the list.\n+\t\t */\n+ public void add(Object obj) {\n+\t\t\t// Call to nextIndex() will check concurrent.\n+\t\t\tnextIndex();\n+\t\t\t// tmpcursor is the backing cursor of the next element\n+\t\t\t// Remember that List.add(index,obj) is really an insert....\n+\t\t\tContentList.this.add(tmpcursor, obj);\n+\t\t\tforward = true;\n+\t\t\texpected = ContentList.this.getModCount();\n+\t\t\tcanremove = canset = false;\n+\t\t\tindex = nextIndex();\n+\t\t\tcursor = tmpcursor;\n+\t\t\tfsize++;\n+\t\t}\n+\n+ /**\n+\t\t * Removes from the list the last element that was returned by\n+\t\t * the last call to <code>next</code> or <code>previous</code>.\n+\t\t */\n+ public void remove() {\n+\t\t\tif (!canremove)\n+\t\t\t\tthrow new IllegalStateException("Can not remove an "\n+\t\t\t\t\t\t+ "element unless either next() or previous() has been called "\n+\t\t\t\t\t\t+ "since the last remove()");\n+\t\t\tnextIndex(); // to get out cursor ...\n+\t\t\tContentList.this.remove(cursor);\n+\t\t\tcursor = tmpcursor - 1;\n+\t\t\texpected = ContentList.this.getModCount();\n+\n+\t\t\tforward = false;\n+\t\t\tcanremove = false;\n+\t\t\tcanset = false;\n+\t\t\tfsize--;\n+\t\t}\n+\n+ /**\n+\t\t * Replaces the last element returned by <code>next</code> or\n+\t\t * <code>previous</code> with the specified element.\n+\t\t */\n+ public void set(Object obj) {\n+\t\t\tif (!canset)\n+\t\t\t\tthrow new IllegalStateException("Can not set an element "\n+\t\t\t\t\t\t+ "unless either next() or previous() has been called since the " \n+\t\t\t\t\t\t+ "last remove() or set()");\n+\t\t\tcheckConcurrentModification();\n+\n+\t\t\tif (!filter.matches(obj)) {\n+\t\t\t\tthrow new IllegalAddException("Filter won\'t allow index " + index + " to be set to "\n+\t\t\t\t\t\t+ (obj.getClass()).getName());\n+\t\t\t}\n+\t\t\t\n+\t\t\tContentList.this.set(cursor, obj);\n+\t\t\texpected = ContentList.this.getModCount();\n+\t\t\t\n+\t\t}\n+\n+ /**\n+ * Check if are backing list is being modified by someone else.\n+ */\n+ private void checkConcurrentModification() {\n+ if (expected != ContentList.this.getModCount()) {\n+ throw new ConcurrentModificationException();\n+ }\n+ }\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/DataConversionException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/DataConversionException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,87 @@
+/*--
+
+ $Id: DataConversionException.java,v 1.14 2007/11/10 05:28:58 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+/**
+ * Thrown when a data conversion from a string to value type fails, such as
+ * can happen with the {@link Attribute} convenience getter functions.
+ *
+ * @version $Revision: 1.14 $, $Date: 2007/11/10 05:28:58 $
+ * @author Brett McLaughlin
+ * @author Jason Hunter
+ */
+public class DataConversionException extends JDOMException {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: DataConversionException.java,v $ $Revision: 1.14 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * Constructs an exception where the named construct couldn't be converted
+ * to the named data type.
+ *
+ * @param name name of the construct whose value failed conversion
+ * @param dataType type the conversion was attempting to create
+ */
+ public DataConversionException(String name, String dataType) {
+ super(new StringBuffer()
+ .append("The XML construct ")
+ .append(name)
+ .append(" could not be converted to a ")
+ .append(dataType)
+ .toString());
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/DefaultJDOMFactory.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/DefaultJDOMFactory.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,191 @@
+/*--
+
+ $Id: DefaultJDOMFactory.java,v 1.7 2007/11/10 05:28:58 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+import java.util.*;
+
+/**
+ * Creates the standard top-level JDOM classes (Element, Document, Comment,
+ * etc). A subclass of this factory might construct custom classes.
+ *
+ * @version $Revision: 1.7 $, $Date: 2007/11/10 05:28:58 $
+ * @author Ken Rune Holland
+ * @author Phil Nelson
+ * @author Bradley S. Huffman
+ */
+public class DefaultJDOMFactory implements JDOMFactory {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: DefaultJDOMFactory.java,v $ $Revision: 1.7 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";
+
+ public DefaultJDOMFactory() { }
+
+ // Allow Javadocs to inherit from JDOMFactory
+
+ public Attribute attribute(String name, String value, Namespace namespace) {
+ return new Attribute(name, value, namespace);
+ }
+
+ public Attribute attribute(String name, String value,
+ int type, Namespace namespace) {
+ return new Attribute(name, value, type, namespace);
+ }
+
+ public Attribute attribute(String name, String value) {
+ return new Attribute(name, value);
+ }
+
+ public Attribute attribute(String name, String value, int type) {
+ return new Attribute(name, value, type);
+ }
+
+ public CDATA cdata(String text) {
+ return new CDATA(text);
+ }
+
+ public Text text(String text) {
+ return new Text(text);
+ }
+
+ public Comment comment(String text) {
+ return new Comment(text);
+ }
+
+ public DocType docType(String elementName,
+ String publicID, String systemID) {
+ return new DocType(elementName, publicID, systemID);
+ }
+
+ public DocType docType(String elementName, String systemID) {
+ return new DocType(elementName, systemID);
+ }
+
+ public DocType docType(String elementName) {
+ return new DocType(elementName);
+ }
+
+ public Document document(Element rootElement, DocType docType) {
+ return new Document(rootElement, docType);
+ }
+
+ public Document document(Element rootElement, DocType docType, String baseURI) {
+ return new Document(rootElement, docType, baseURI);
+ }
+
+ public Document document(Element rootElement) {
+ return new Document(rootElement);
+ }
+
+ public Element element(String name, Namespace namespace) {
+ return new Element(name, namespace);
+ }
+
+ public Element element(String name) {
+ return new Element(name);
+ }
+
+ public Element element(String name, String uri) {
+ return new Element(name, uri);
+ }
+
+ public Element element(String name, String prefix, String uri) {
+ return new Element(name, prefix, uri);
+ }
+
+ public ProcessingInstruction processingInstruction(String target,
+ Map data) {
+ return new ProcessingInstruction(target, data);
+ }
+
+ public ProcessingInstruction processingInstruction(String target,
+ String data) {
+ return new ProcessingInstruction(target, data);
+ }
+
+ public EntityRef entityRef(String name) {
+ return new EntityRef(name);
+ }
+
+ public EntityRef entityRef(String name, String publicID, String systemID) {
+ return new EntityRef(name, publicID, systemID);
+ }
+
+ public EntityRef entityRef(String name, String systemID) {
+ return new EntityRef(name, systemID);
+ }
+
+ // =====================================================================
+ // List manipulation
+ // =====================================================================
+
+ public void addContent(Parent parent, Content child) {
+ if (parent instanceof Document) {
+ ((Document) parent).addContent(child);
+ }
+ else {
+ ((Element) parent).addContent(child);
+ }
+ }
+
+ public void setAttribute(Element parent, Attribute a) {
+ parent.setAttribute(a);
+ }
+
+ public void addNamespaceDeclaration(Element parent, Namespace additional) {
+ parent.addNamespaceDeclaration(additional);
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/DescendantIterator.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/DescendantIterator.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,173 @@
+/*--
+
+ $Id: DescendantIterator.java,v 1.6 2007/11/10 05:28:58 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+import java.util.*;
+import org.jdom.Content;
+import org.jdom.Element;
+import org.jdom.Parent;
+
+/**
+ * Traverse all a parent's descendants (all children at any level below
+ * the parent).
+ *
+ * @author Bradley S. Huffman
+ * @author Jason Hunter
+ * @version $Revision: 1.6 $, $Date: 2007/11/10 05:28:58 $
+ */
+class DescendantIterator implements Iterator {
+
+ private Iterator iterator;
+ private Iterator nextIterator;
+ private List stack = new ArrayList();
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: DescendantIterator.java,v $ $Revision: 1.6 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * Iterator for the descendants of the supplied object.
+ *
+ * @param parent document or element whose descendants will be iterated
+ */
+ DescendantIterator(Parent parent) {
+ if (parent == null) {
+ throw new IllegalArgumentException("parent parameter was null");
+ }
+ this.iterator = parent.getContent().iterator();
+ }
+
+ /**
+ * Returns true> if the iteration has more {@link Content} descendants.
+ *
+ * @return true is the iterator has more descendants
+ */
+ public boolean hasNext() {
+ if (iterator != null && iterator.hasNext()) return true;
+ if (nextIterator != null && nextIterator.hasNext()) return true;
+ if (stackHasAnyNext()) return true;
+ return false;
+ }
+
+ /**
+ * Returns the next {@link Content} descendant.
+ *
+ * @return the next descendant
+ */
+ public Object next() {
+ if (!hasNext()) {
+ throw new NoSuchElementException();
+ }
+
+ // If we need to descend, go for it and record where we are.
+ // We do the shuffle here on the next next() call so remove() is easy
+ // to code up.
+ if (nextIterator != null) {
+ push(iterator);
+ iterator = nextIterator;
+ nextIterator = null;
+ }
+
+ // If this iterator is finished, try moving up the stack
+ while (!iterator.hasNext()) {
+ if (stack.size() > 0) {
+ iterator = pop();
+ }
+ else {
+ throw new NoSuchElementException("Somehow we lost our iterator");
+ }
+ }
+
+ Content child = (Content) iterator.next();
+ if (child instanceof Element) {
+ nextIterator = ((Element)child).getContent().iterator();
+ }
+ return child;
+ }
+
+ /**
+ * Detaches the last {@link org.jdom.Content} returned by the last call to
+ * next from it's parent. Note: this does not affect
+ * iteration and all children, siblings, and any node following the
+ * removed node (in document order) will be visited.
+ */
+ public void remove() {
+ iterator.remove();
+ }
+
+ private Iterator pop() {
+ int stackSize = stack.size();
+ if (stackSize == 0) {
+ throw new NoSuchElementException("empty stack");
+ }
+ return (Iterator) stack.remove(stackSize - 1);
+ }
+
+ private void push(Iterator itr) {
+ stack.add(itr);
+ }
+
+ private boolean stackHasAnyNext() {
+ int size = stack.size();
+ for (int i = 0; i < size; i++) {
+ Iterator itr = (Iterator) stack.get(i);
+ if (itr.hasNext()) {
+ return true;
+ }
+ }
+ return false;
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/DocType.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/DocType.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,280 @@\n+/*--\n+\n+ $Id: DocType.java,v 1.32 2007/11/10 05:28:58 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+/**\n+ * An XML DOCTYPE declaration. Method allow the user to get and set the\n+ * root element name, public id, and system id.\n+ *\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @version $Revision: 1.32 $, $Date: 2007/11/10 05:28:58 $\n+ */\n+public class DocType extends Content {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: DocType.java,v $ $Revision: 1.32 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";\n+\n+ /** The element being constrained */\n+ protected String elementName;\n+\n+ /** The public ID of the DOCTYPE */\n+ protected String publicID;\n+\n+ /** The system ID of the DOCTYPE */\n+ protected String systemID;\n+\n+ /** The internal subset of the DOCTYPE */\n+ protected String internalSubset;\n+\n+ /**\n+ * Default, no-args constructor for implementations to use if needed.\n+ */\n+ protected DocType() {}\n+\n+ /*\n+ * XXX:\n+ * We need to take care of entities and notations here.\n+ */\n+\n+ /**\n+ * This will create the <code>DocType</code> with\n+ * the specified element name and a reference to an\n+ * external DTD.\n+ *\n+ * @param elementName <code>String</code> name of\n+ * element being constrained.\n+ * @param publicID <code>String</code> public ID of\n+ * referenced DTD\n+ * @param systemID <code>String<'..b'ent name for DOCTYPE\n+ */\n+ public String getElementName() {\n+ return elementName;\n+ }\n+\n+ /**\n+ * This will set the root element name declared by this\n+ * DOCTYPE declaration.\n+ *\n+ * @return DocType <code>DocType</code> this DocType object\n+ * @param elementName <code>String</code> name of\n+ * root element being constrained.\n+ * @throws IllegalNameException if the given root element name is not a\n+ * legal XML element name.\n+ */\n+ public DocType setElementName(String elementName) {\n+ // This can contain a colon so we use checkXMLName()\n+ // instead of checkElementName()\n+ String reason = Verifier.checkXMLName(elementName);\n+ if (reason != null) {\n+ throw new IllegalNameException(elementName, "DocType", reason);\n+ }\n+ this.elementName = elementName;\n+ return this;\n+ }\n+\n+ /**\n+ * This will retrieve the public ID of an externally\n+ * referenced DTD, or an empty <code>String</code> if\n+ * none is referenced.\n+ *\n+ * @return <code>String</code> - public ID of referenced DTD.\n+ */\n+ public String getPublicID() {\n+ return publicID;\n+ }\n+\n+ /**\n+ * This will set the public ID of an externally\n+ * referenced DTD.\n+ *\n+ * @param publicID id to set\n+ * @return DocType <code>DocType</code> this DocType object\n+ * @throws IllegalDataException if the given public ID is not a legal\n+ * public ID.\n+ */\n+ public DocType setPublicID(String publicID) {\n+ String reason = Verifier.checkPublicID(publicID);\n+ if (reason != null) {\n+ throw new IllegalDataException(publicID, "DocType", reason);\n+ }\n+ this.publicID = publicID;\n+\n+ return this;\n+ }\n+\n+ /**\n+ * This will retrieve the system ID of an externally\n+ * referenced DTD, or an empty <code>String</code> if\n+ * none is referenced.\n+ *\n+ * @return <code>String</code> - system ID of referenced DTD.\n+ */\n+ public String getSystemID() {\n+ return systemID;\n+ }\n+\n+ /**\n+ * This will set the system ID of an externally\n+ * referenced DTD.\n+ *\n+ * @param systemID id to set\n+ * @return systemID <code>String</code> system ID of\n+ * referenced DTD.\n+ * @throws IllegalDataException if the given system ID is not a legal\n+ * system literal.\n+ */\n+ public DocType setSystemID(String systemID) {\n+ String reason = Verifier.checkSystemLiteral(systemID);\n+ if (reason != null) {\n+ throw new IllegalDataException(systemID, "DocType", reason);\n+ }\n+ this.systemID = systemID;\n+\n+ return this;\n+ }\n+\n+ /**\n+ * Returns the empty string since doctypes don\'t have an XPath\n+ * 1.0 string value.\n+ * @return the empty string\n+ */\n+ public String getValue() {\n+ return ""; // doctypes don\'t have an XPath string value\n+ }\n+\n+ /**\n+ * This sets the data for the internal subset.\n+ *\n+ * @param newData data for the internal subset, as a\n+ * <code>String</code>.\n+ */\n+ public void setInternalSubset(String newData) {\n+ internalSubset = newData;\n+ }\n+\n+ /**\n+ * This returns the data for the internal subset.\n+ *\n+ * @return <code>String</code> - the internal subset\n+ */\n+ public String getInternalSubset() {\n+ return internalSubset;\n+ }\n+\n+ /**\n+ * This returns a <code>String</code> representation of the\n+ * <code>DocType</code>, suitable for debugging.\n+ *\n+ * @return <code>String</code> - information about the\n+ * <code>DocType</code>\n+ */\n+ public String toString() {\n+ return new StringBuffer()\n+ .append("[DocType: ")\n+ .append(new org.jdom.output.XMLOutputter().outputString(this))\n+ .append("]")\n+ .toString();\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Document.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Document.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,767 @@\n+/*--\n+\n+ $Id: Document.java,v 1.85 2007/11/10 05:28:58 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+import java.util.*;\n+import org.jdom.filter.*;\n+\n+/**\n+ * An XML document. Methods allow access to the root element as well as the\n+ * {@link DocType} and other document-level information.\n+ *\n+ * @version $Revision: 1.85 $, $Date: 2007/11/10 05:28:58 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Jools Enticknap\n+ * @author Bradley S. Huffman\n+ */\n+public class Document implements Parent {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: Document.java,v $ $Revision: 1.85 $ $Date: 2007/11/10 05:28:58 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * This document\'s content including comments, PIs, a possible\n+ * DocType, and a root element.\n+ * Subclassers have to track content using their own\n+ * mechanism.\n+ */\n+ ContentList content = new ContentList(this);\n+\n+ /**\n+ * See http://www.w3.org/TR/2003/WD-DOM-Level-3-Core-20030226/core.html#baseURIs-Considerations\n+ */\n+ protected String baseURI = null;\n+\n+ // Supports the setProperty/getProperty calls\n+ private HashMap propertyMap = null;\n+\n+ /**\n+ * Creates a new empty document. A document must have a root element,\n+ * so this document will not be well-formed and accessor methods will\n+ * throw an IllegalStateException if this document is accessed before a\n+ * root element is added. T'..b'pare to\n+ * @return <code>boolean</code> whether the <code>Document</code> is\n+ * equal to the supplied <code>Object</code>\n+ */\n+ public final boolean equals(Object ob) {\n+ return (ob == this);\n+ }\n+\n+ /**\n+ * This returns the hash code for this <code>Document</code>.\n+ *\n+ * @return <code>int</code> hash code\n+ */\n+ public final int hashCode() {\n+ return super.hashCode();\n+ }\n+\n+ /**\n+ * This will return a deep clone of this <code>Document</code>.\n+ *\n+ * @return <code>Object</code> clone of this <code>Document</code>\n+ */\n+ public Object clone() {\n+ Document doc = null;\n+\n+ try {\n+ doc = (Document) super.clone();\n+ } catch (CloneNotSupportedException ce) {\n+ // Can\'t happen\n+ }\n+\n+ // The clone has a reference to this object\'s content list, so\n+ // owerwrite with a empty list\n+ doc.content = new ContentList(doc);\n+\n+ // Add the cloned content to clone\n+\n+ for (int i = 0; i < content.size(); i++) {\n+ Object obj = content.get(i);\n+ if (obj instanceof Element) {\n+ Element element = (Element)((Element)obj).clone();\n+ doc.content.add(element);\n+ }\n+ else if (obj instanceof Comment) {\n+ Comment comment = (Comment)((Comment)obj).clone();\n+ doc.content.add(comment);\n+ }\n+ else if (obj instanceof ProcessingInstruction) {\n+ ProcessingInstruction pi = (ProcessingInstruction)\n+ ((ProcessingInstruction)obj).clone();\n+ doc.content.add(pi);\n+ }\n+ else if (obj instanceof DocType) {\n+ DocType dt = (DocType) ((DocType)obj).clone();\n+ doc.content.add(dt);\n+ }\n+ }\n+\n+ return doc;\n+ }\n+\n+ /**\n+ * Returns an iterator that walks over all descendants in document order.\n+ *\n+ * @return an iterator to walk descendants\n+ */\n+ public Iterator getDescendants() {\n+ return new DescendantIterator(this);\n+ }\n+\n+ /**\n+ * Returns an iterator that walks over all descendants in document order\n+ * applying the Filter to return only elements that match the filter rule.\n+ * With filters you can match only Elements, only Comments, Elements or\n+ * Comments, only Elements with a given name and/or prefix, and so on.\n+ *\n+ * @param filter filter to select which descendants to see\n+ * @return an iterator to walk descendants within a filter\n+ */\n+ public Iterator getDescendants(Filter filter) {\n+ return new FilterIterator(new DescendantIterator(this), filter);\n+ }\n+\n+ public Parent getParent() {\n+ return null; // documents never have parents\n+ }\n+\n+\n+\n+ /**\n+ * @see org.jdom.Parent#getDocument()\n+ */\n+ public Document getDocument() {\n+ return this;\n+ }\n+\n+ /**\n+ * Assigns an arbitrary object to be associated with this document under\n+ * the given "id" string. Null values are permitted. Strings beginning\n+ * with "http://www.jdom.org/ are reserved for JDOM use.\n+ *\n+ * @param id the id of the stored object\n+ * @param value the object to store\n+ */\n+ public void setProperty(String id, Object value) {\n+ if (propertyMap == null) {\n+ propertyMap = new HashMap();\n+ }\n+ propertyMap.put(id, value);\n+ }\n+\n+ /**\n+ * Returns the object associated with this document under the given "id"\n+ * string, or null if there is no binding or if the binding explicitly\n+ * stored a null value.\n+ *\n+ * @param id the id of the stored object to return\n+ * @return the object associated with the given id\n+ */\n+ public Object getProperty(String id) {\n+ if (propertyMap == null) return null;\n+ return propertyMap.get(id);\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Element.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Element.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,1564 @@\n+/*--\n+\n+ $Id: Element.java,v 1.159 2007/11/14 05:02:08 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+import java.io.*;\n+import java.util.*;\n+\n+import org.jdom.filter.*;\n+\n+/**\n+ * An XML element. Methods allow the user to get and manipulate its child\n+ * elements and content, directly access the element\'s textual content,\n+ * manipulate its attributes, and manage namespaces.\n+ *\n+ * @version $Revision: 1.159 $, $Date: 2007/11/14 05:02:08 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Lucas Gonze\n+ * @author Kevin Regan\n+ * @author Dan Schaffer\n+ * @author Yusuf Goolamabbas\n+ * @author Kent C. Johnson\n+ * @author Jools Enticknap\n+ * @author Alex Rosen\n+ * @author Bradley S. Huffman\n+ * @author Victor Toni\n+ */\n+public class Element extends Content implements Parent {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: Element.java,v $ $Revision: 1.159 $ $Date: 2007/11/14 05:02:08 $ $Name: jdom_1_1_1 $";\n+\n+ private static final int INITIAL_ARRAY_SIZE = 5;\n+\n+ /** The local name of the element */\n+ protected String name;\n+\n+ /** The namespace of the element */\n+ protected transient Namespace namespace;\n+\n+ /** Additional namespace declarations to store on this element; useful\n+ * during output */\n+ protected transient List additionalNamespaces;\n+\n+ // See http://lists.denveronline.net/lists/jdom-interest/2000-September/003030.html\n+ // for a possible memo'..b'ren to match\n+ * @param ns <code>Namespace</code> to search within\n+ * @return all matching child elements\n+ */\n+ public List getChildren(final String name, final Namespace ns) {\n+ return content.getView(new ElementFilter(name, ns));\n+ }\n+\n+ /**\n+ * This returns the first child element within this element with the\n+ * given local name and belonging to the given namespace.\n+ * If no elements exist for the specified name and namespace, null is\n+ * returned.\n+ *\n+ * @param name local name of child element to match\n+ * @param ns <code>Namespace</code> to search within\n+ * @return the first matching child element, or null if not found\n+ */\n+ public Element getChild(final String name, final Namespace ns) {\n+ final List elements = content.getView(new ElementFilter(name, ns));\n+ final Iterator iter = elements.iterator();\n+ if (iter.hasNext()) {\n+ return (Element) iter.next();\n+ }\n+ return null;\n+ }\n+\n+ /**\n+ * This returns the first child element within this element with the\n+ * given local name and belonging to no namespace.\n+ * If no elements exist for the specified name and namespace, null is\n+ * returned.\n+ *\n+ * @param name local name of child element to match\n+ * @return the first matching child element, or null if not found\n+ */\n+ public Element getChild(final String name) {\n+ return getChild(name, Namespace.NO_NAMESPACE);\n+ }\n+\n+ /**\n+ * \n+ * This removes the first child element (one level deep) with the\n+ * given local name and belonging to no namespace.\n+ * Returns true if a child was removed.\n+ * \n+ *\n+ * @param name the name of child elements to remove\n+ * @return whether deletion occurred\n+ */\n+ public boolean removeChild(final String name) {\n+ return removeChild(name, Namespace.NO_NAMESPACE);\n+ }\n+\n+ /**\n+ * \n+ * This removes the first child element (one level deep) with the\n+ * given local name and belonging to the given namespace.\n+ * Returns true if a child was removed.\n+ * \n+ *\n+ * @param name the name of child element to remove\n+ * @param ns <code>Namespace</code> to search within\n+ * @return whether deletion occurred\n+ */\n+ public boolean removeChild(final String name, final Namespace ns) {\n+ final Filter filter = new ElementFilter(name, ns);\n+ final List old = content.getView(filter);\n+ final Iterator iter = old.iterator();\n+ if (iter.hasNext()) {\n+ iter.next();\n+ iter.remove();\n+ return true;\n+ }\n+\n+ return false;\n+ }\n+\n+ /**\n+ * \n+ * This removes all child elements (one level deep) with the\n+ * given local name and belonging to no namespace.\n+ * Returns true if any were removed.\n+ * \n+ *\n+ * @param name the name of child elements to remove\n+ * @return whether deletion occurred\n+ */\n+ public boolean removeChildren(final String name) {\n+ return removeChildren(name, Namespace.NO_NAMESPACE);\n+ }\n+\n+ /**\n+ * \n+ * This removes all child elements (one level deep) with the\n+ * given local name and belonging to the given namespace.\n+ * Returns true if any were removed.\n+ * \n+ *\n+ * @param name the name of child elements to remove\n+ * @param ns <code>Namespace</code> to search within\n+ * @return whether deletion occurred\n+ */\n+ public boolean removeChildren(final String name, final Namespace ns) {\n+ boolean deletedSome = false;\n+\n+ final Filter filter = new ElementFilter(name, ns);\n+ final List old = content.getView(filter);\n+ final Iterator iter = old.iterator();\n+ while (iter.hasNext()) {\n+ iter.next();\n+ iter.remove();\n+ deletedSome = true;\n+ }\n+\n+ return deletedSome;\n+ }\n+\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/EntityRef.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/EntityRef.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,239 @@\n+/*--\n+\n+ $Id: EntityRef.java,v 1.22 2007/11/10 05:28:59 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+/**\n+ * An XML entity reference. Methods allow the user to manage its name, public\n+ * id, and system id.\n+ *\n+ * @version $Revision: 1.22 $, $Date: 2007/11/10 05:28:59 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Philip Nelson\n+ */\n+public class EntityRef extends Content {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: EntityRef.java,v $ $Revision: 1.22 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";\n+\n+ /** The name of the <code>EntityRef</code> */\n+ protected String name;\n+\n+ /** The PublicID of the <code>EntityRef</code> */\n+ protected String publicID;\n+\n+ /** The SystemID of the <code>EntityRef</code> */\n+ protected String systemID;\n+\n+ /**\n+ * Default, no-args constructor for implementations to use if needed.\n+ */\n+ protected EntityRef() {}\n+\n+ /**\n+ * This will create a new <code>EntityRef</code> with the supplied name.\n+ *\n+ * @param name <code>String</code> name of element.\n+ * @throws IllegalNameException if the given name is not a legal\n+ * XML name.\n+ */\n+ public EntityRef(String name) {\n+ this(name, null, null);\n+ }\n+\n+ /**\n+ * This will create a new <code>EntityRef</code>\n+ * with the supplied name and system id.\n+ *\n+ * @param name <code>String</code> name of element'..b'ame of element.\n+ * @param publicID public id of the entity reference being constructed\n+ * @param systemID system id of the entity reference being constructed\n+ * @throws IllegalDataException if the given system ID is not a legal\n+ * system literal or the the given public ID is not a\n+ * legal public ID\n+ * @throws IllegalNameException if the given name is not a legal\n+ * XML name.\n+ */\n+ public EntityRef(String name, String publicID, String systemID) {\n+ setName(name);\n+ setPublicID(publicID);\n+ setSystemID(systemID);\n+ }\n+\n+ /**\n+ * This returns the name of the <code>EntityRef</code>.\n+ *\n+ * @return <code>String</code> - entity name.\n+ */\n+ public String getName() {\n+ return name;\n+ }\n+\n+ /**\n+ * Returns the empty string since entity references don\'t have an XPath\n+ * 1.0 string value.\n+ * @return the empty string\n+ */\n+ public String getValue() {\n+ return ""; // entity references don\'t have XPath string values\n+ }\n+\n+ /**\n+ * This will return the publid ID of this <code>EntityRef</code>.\n+ * If there is no public ID, then this returns <code>null</code>.\n+ *\n+ * @return public ID of this <code>EntityRef</code>\n+ */\n+ public String getPublicID() {\n+ return publicID;\n+ }\n+\n+ /**\n+ * This will return the system ID of this <code>EntityRef</code>.\n+ * If there is no system ID, then this returns <code>null</code>.\n+ *\n+ * @return system ID of this <code>EntityRef</code>\n+ */\n+ public String getSystemID() {\n+ return systemID;\n+ }\n+\n+ /**\n+ * This will set the name of this <code>EntityRef</code>.\n+ *\n+ * @param name new name of the entity\n+ * @return this <code>EntityRef</code> modified.\n+ * @throws IllegalNameException if the given name is not a legal\n+ * XML name.\n+ */\n+ public EntityRef setName(String name) {\n+ // This can contain a colon so we use checkXMLName()\n+ // instead of checkElementName()\n+ String reason = Verifier.checkXMLName(name);\n+ if (reason != null) {\n+ throw new IllegalNameException(name, "EntityRef", reason);\n+ }\n+ this.name = name;\n+ return this;\n+ }\n+\n+ /**\n+ * This will set the public ID of this <code>EntityRef</code>.\n+ *\n+ * @param publicID new public id\n+ * @return this <code>EntityRef</code> modified.\n+ * @throws IllegalDataException if the given public ID is not a legal\n+ * public ID.\n+ */\n+ public EntityRef setPublicID(String publicID) {\n+ String reason = Verifier.checkPublicID(publicID);\n+ if (reason != null) {\n+ throw new IllegalDataException(publicID, "EntityRef", reason);\n+ }\n+ this.publicID = publicID;\n+ return this;\n+ }\n+\n+ /**\n+ * This will set the system ID of this <code>EntityRef</code>.\n+ *\n+ * @param systemID new system id\n+ * @throws IllegalDataException if the given system ID is not a legal\n+ * system literal.\n+ * @return this <code>EntityRef</code> modified.\n+ */\n+ public EntityRef setSystemID(String systemID) {\n+ String reason = Verifier.checkSystemLiteral(systemID);\n+ if (reason != null) {\n+ throw new IllegalDataException(systemID, "EntityRef", reason);\n+ }\n+ this.systemID = systemID;\n+ return this;\n+ }\n+\n+ /**\n+ * This returns a <code>String</code> representation of the\n+ * <code>EntityRef</code>, suitable for debugging.\n+ *\n+ * @return <code>String</code> - information about the\n+ * <code>EntityRef</code>\n+ */\n+ public String toString() {\n+ return new StringBuffer()\n+ .append("[EntityRef: ")\n+ .append("&")\n+ .append(name)\n+ .append(";")\n+ .append("]")\n+ .toString();\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/FilterIterator.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/FilterIterator.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,115 @@
+/*--
+
+ $Id: FilterIterator.java,v 1.6 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+import java.util.*;
+import org.jdom.filter.*;
+
+/**
+ * Traverse a parent's children that match the supplied filter.
+ *
+ * @author Bradley S. Huffman
+ * @version $Revision: 1.6 $, $Date: 2007/11/10 05:28:59 $
+ */
+class FilterIterator implements Iterator {
+
+ private Iterator iterator;
+ private Filter filter;
+ private Object nextObject;
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: FilterIterator.java,v $ $Revision: 1.6 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ public FilterIterator(Iterator iterator, Filter filter) {
+ if ((iterator == null) || (filter == null)) {
+ throw new IllegalArgumentException("null parameter");
+ }
+ this.iterator = iterator;
+ this.filter = filter;
+ }
+
+ public boolean hasNext() {
+ if (nextObject != null) {
+ return true;
+ }
+
+ while (iterator.hasNext()) {
+ Object obj = iterator.next();
+ if (filter.matches(obj)) {
+ nextObject = obj;
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public Object next() {
+ if (!hasNext()) {
+ throw new NoSuchElementException();
+ }
+
+ Object obj = nextObject;
+ nextObject = null;
+ return obj;
+ }
+
+ public void remove() {
+ // XXX Could cause probs for sure if hasNext() is
+ // called before the remove(), although that's unlikely.
+ iterator.remove();
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/IllegalAddException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/IllegalAddException.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,323 @@\n+/*-- \n+\n+ $Id: IllegalAddException.java,v 1.26 2007/11/10 05:28:59 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+package org.jdom;\n+\n+/**\n+ * Thrown when trying to add a illegal object to a JDOM construct.\n+ *\n+ * @version $Revision: 1.26 $, $Date: 2007/11/10 05:28:59 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ */\n+public class IllegalAddException extends IllegalArgumentException {\n+\n+ private static final String CVS_ID = \n+ "@(#) $RCSfile: IllegalAddException.java,v $ $Revision: 1.26 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * This will create an <code>Exception</code> indicating\n+ * that the addition of the <code>{@link Attribute}</code>\n+ * to the <code>{@link Element}</code> is illegal.\n+ *\n+ * @param base <code>Element</code> that <code>Attribute</code>\n+ * couldn\'t be added to\n+ * @param added <code>Attribute</code> that could not be added\n+ * @param reason cause of the problem\n+ */\n+ IllegalAddException(Element base, Attribute added, String reason) {\n+ super(new StringBuffer()\n+ .append("The attribute \\"")\n+ .append(added.getQualifiedName())\n+ .append("\\" could not be added to the element \\"")\n+ .append(base.getQualifiedName())\n+ .append("\\": ")\n+ .append(reason)\n+ .toString());\n+ }\n+\n+ /**\n+ * This will create an <code>Exception</'..b't</code> that the <code>Comment</code>\n+ * couldn\'t be added to\n+ * @param added <code>Text</code> that could not be added\n+ * @param reason cause of the problem\n+ */\n+ IllegalAddException(Element base, Text added, String reason) {\n+ super(new StringBuffer()\n+ .append("The Text \\"")\n+ .append(added.getText())\n+ .append("\\" could not be added as content to \\"")\n+ .append(base.getQualifiedName())\n+ .append("\\": ")\n+ .append(reason)\n+ .toString());\n+ }\n+\n+ /**\n+ * This will create an <code>Exception</code> indicating\n+ * that the addition of the <code>{@link Comment}</code>\n+ * to the <code>{@link Document}</code> is illegal.\n+ *\n+ * @param added <code>Comment</code> that could not be added\n+ * @param reason cause of the problem\n+ */\n+ IllegalAddException(Comment added, String reason) {\n+ super(new StringBuffer()\n+ .append("The comment \\"")\n+ .append(added.getText())\n+ .append("\\" could not be added to the top level of the document: ")\n+ .append(reason)\n+ .toString());\n+ }\n+\n+ /**\n+ * This will create an <code>Exception</code> indicating\n+ * that the addition of the <code>{@link EntityRef}</code>\n+ * to the <code>{@link Element}</code> is illegal.\n+ *\n+ * @param base <code>Element</code> that the <code>EntityRef</code>\n+ * couldn\'t be added to\n+ * @param added <code>EntityRef</code> reference that could not be added\n+ * @param reason cause of the problem\n+ */\n+ IllegalAddException(Element base, EntityRef added, String reason) {\n+ super(new StringBuffer()\n+ .append("The entity reference\\"")\n+ .append(added.getName())\n+ .append("\\" could not be added as content to \\"")\n+ .append(base.getQualifiedName())\n+ .append("\\": ")\n+ .append(reason)\n+ .toString());\n+ }\n+\n+ /**\n+ * This will create an <code>Exception</code> indicating\n+ * that the addition of the <code>{@link Namespace}</code>\n+ * to the <code>{@link Element}</code> is illegal.\n+ *\n+ * @param base <code>Element</code> that the <code>Namespace</code>\n+ * couldn\'t be added to\n+ * @param added <code>Namespace</code> that could not be added\n+ * @param reason cause of the problem\n+ */\n+ IllegalAddException(Element base, Namespace added, String reason) {\n+ super(new StringBuffer()\n+ .append("The namespace xmlns")\n+ .append((added.getPrefix() == null ||\n+ added.getPrefix().equals("")) ? "=" \n+ : ":" + added.getPrefix() + "=")\n+ .append("\\"")\n+ .append(added.getURI())\n+ .append("\\" could not be added as a namespace to \\"")\n+ .append(base.getQualifiedName())\n+ .append("\\": ")\n+ .append(reason)\n+ .toString());\n+ }\n+\n+ /**\n+ * This will create an <code>Exception</code> indicating\n+ * that the addition of the <code>{@link DocType}</code>\n+ * to the <code>{@link Document}</code> is illegal.\n+ *\n+ * @param added <code>DocType</code> that could not be added\n+ * @param reason cause of the problem\n+ */\n+ IllegalAddException(DocType added, String reason) {\n+ super(new StringBuffer()\n+ .append("The DOCTYPE ")\n+ .append(added.toString())\n+ .append(" could not be added to the document: ")\n+ .append(reason)\n+ .toString());\n+ }\n+\n+ /**\n+ * This will create an <code>Exception</code> with the specified\n+ * error message.\n+ *\n+ * @param reason cause of the problem\n+ */\n+ public IllegalAddException(String reason) {\n+ super(reason);\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/IllegalDataException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/IllegalDataException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,118 @@
+/*--
+
+ $Id: IllegalDataException.java,v 1.14 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+/**
+ * Thrown when illegal text is supplied to a JDOM construct.
+ *
+ * @version $Revision: 1.14 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ * @author Elliotte Rusty Harold
+ */
+public class IllegalDataException extends IllegalArgumentException {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: IllegalDataException.java,v $ $Revision: 1.14 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This will create an <code>Exception</code> indicating
+ * that the specified data is illegal for the construct
+ * it was supplied to.
+ *
+ * @param data <code>String</code> data that breaks rules.
+ * @param construct <code>String</code> construct that data is illegal for.
+ * @param reason <code>String</code> message or reason data is illegal.
+ */
+ IllegalDataException(String data, String construct, String reason) {
+ super(new StringBuffer()
+ .append("The data \"")
+ .append(data)
+ .append("\" is not legal for a JDOM ")
+ .append(construct)
+ .append(": ")
+ .append(reason)
+ .append(".")
+ .toString());
+ }
+
+ /**
+ * This will create an <code>Exception</code> indicating
+ * that the specified data is illegal for the construct
+ * it was supplied to.
+ *
+ * @param data <code>String</code> data that breaks rules.
+ * @param construct <code>String</code> construct that data is illegal for.
+ */
+ IllegalDataException(String data, String construct) {
+ super(new StringBuffer()
+ .append("The data \"")
+ .append(data)
+ .append("\" is not legal for a JDOM ")
+ .append(construct)
+ .append(".")
+ .toString());
+ }
+
+ /**
+ * This will create an exceptoin with the specified error message.
+ *
+ * @param reason cause of the problem
+ */
+ public IllegalDataException(String reason) {
+ super(reason);
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/IllegalNameException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/IllegalNameException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,121 @@
+/*--
+
+ $Id: IllegalNameException.java,v 1.14 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+/**
+ * Thrown when a name is supplied in construction of a JDOM construct whose
+ * where the name breaks XML naming conventions.
+ *
+ * @version $Revision: 1.14 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ * @author Elliotte Rusty Harold
+ */
+public class IllegalNameException extends IllegalArgumentException {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: IllegalNameException.java,v $ $Revision: 1.14 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This will create an <code>Exception</code> indicating
+ * that the specified name is illegal for the construct
+ * it was supplied to.
+ *
+ * @param name <code>String</code> name that breaks rules.
+ * @param construct <code>String</code> name of JDOM construct
+ * that <code>name</code> was supplied to.
+ * @param reason <code>String</code> message or reason name is illegal.
+ */
+ IllegalNameException(String name, String construct, String reason) {
+ super(new StringBuffer()
+ .append("The name \"")
+ .append(name)
+ .append("\" is not legal for JDOM/XML ")
+ .append(construct)
+ .append("s: ")
+ .append(reason)
+ .append(".")
+ .toString());
+ }
+
+ /**
+ * This will create an <code>Exception</code> indicating
+ * that the specified name is illegal for the construct
+ * it was supplied to.
+ *
+ * @param name <code>String</code> name that breaks rules.
+ * @param construct <code>String</code> name of JDOM construct
+ * that <code>name</code> was supplied to.
+ */
+ IllegalNameException(String name, String construct) {
+ super(new StringBuffer()
+ .append("The name \"")
+ .append(name)
+ .append("\" is not legal for JDOM/XML ")
+ .append(construct)
+ .append("s.")
+ .toString());
+ }
+
+ /**
+ * Creates an exception with the specified error message.
+ *
+ * @param reason cause of the problem
+ */
+ public IllegalNameException(String reason) {
+ super(reason);
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/IllegalTargetException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/IllegalTargetException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,97 @@
+/*--
+
+ $Id: IllegalTargetException.java,v 1.15 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+/**
+ * Thrown when a target is supplied in construction of a JDOM {@link
+ * ProcessingInstruction}, and that name breaks XML naming conventions.
+ *
+ * @version $Revision: 1.15 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ */
+public class IllegalTargetException extends IllegalArgumentException {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: IllegalTargetException.java,v $ $Revision: 1.15 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This will create an <code>Exception</code> indicating
+ * that the specified target is illegal for the
+ * <code>{@link ProcessingInstruction}</code> it was supplied to.
+ *
+ * @param target <code>String</code> target that breaks rules.
+ * @param reason <code>String</code> message or reason target is illegal.
+ */
+ IllegalTargetException(String target, String reason) {
+ super(new StringBuffer()
+ .append("The target \"")
+ .append(target)
+ .append("\" is not legal for JDOM/XML Processing Instructions: ")
+ .append(reason)
+ .append(".")
+ .toString());
+ }
+
+ /**
+ * Creates an exception with the specified error message.
+ *
+ * @param reason cause of the problem
+ */
+ public IllegalTargetException(String reason) {
+ super(reason);
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/JDOMException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/JDOMException.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,367 @@\n+/*-- \n+\n+ $Id: JDOMException.java,v 1.26 2008/12/10 00:59:51 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+package org.jdom;\n+\n+import java.io.*;\n+import java.lang.reflect.*;\n+import java.sql.*;\n+\n+import org.xml.sax.*;\n+\n+/**\n+ * The top level exception that JDOM classes can throw. Its subclasses add\n+ * specificity to the problems that can occur using JDOM. This single exception\n+ * can be caught to handle all JDOM specific problems (some methods may throw\n+ * {@link java.io.IOException} and such).\n+ *\n+ * @version $Revision: 1.26 $, $Date: 2008/12/10 00:59:51 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ */\n+public class JDOMException extends Exception {\n+\n+ private static final String CVS_ID = \n+ "@(#) $RCSfile: JDOMException.java,v $ $Revision: 1.26 $ $Date: 2008/12/10 00:59:51 $ $Name: jdom_1_1_1 $";\n+\n+ /** A wrapped <code>Throwable</code> */\n+ private Throwable cause;\n+\n+ /**\n+ * This will create an <code>Exception</code>.\n+ */\n+ public JDOMException() {\n+ super("Error occurred in JDOM application.");\n+ }\n+\n+ /**\n+ * This will create an <code>Exception</code> with the given message.\n+ *\n+ * @param message <code>String</code> message indicating\n+ * the problem that occurred.\n+ */ \n+ public JDOMException(String message) {\n+ super(message);\n+ }\n+\n+ /**\n+ * This will create an <code>Exception</code> with the given messag'..b' }\n+ \n+ if (parent instanceof SQLException) {\n+ return ((SQLException)parent).getNextException();\n+ }\n+ \n+ if (parent instanceof InvocationTargetException) {\n+ return ((InvocationTargetException)parent).getTargetException();\n+ }\n+ \n+ if (parent instanceof ExceptionInInitializerError) {\n+ return ((ExceptionInInitializerError)parent).getException();\n+ }\n+ \n+ // The RMI classes are not present in Android\'s Dalvik VM, so we use reflection to access them.\n+\n+ Throwable nestedException = getNestedExceptionFromField(parent, "java.rmi.RemoteException", "detail");\n+ if (nestedException != null) {\n+ return nestedException;\n+ }\n+ \n+ // These classes are not part of standard JDK 1.1 or 1.2, so again we use reflection to access them.\n+\n+ nestedException = getNestedException(parent, "javax.naming.NamingException", "getRootCause");\n+ if (nestedException != null) {\n+ return nestedException;\n+ }\n+ \n+ nestedException = getNestedException(parent, "javax.servlet.ServletException", "getRootCause");\n+ if (nestedException != null) {\n+ return nestedException;\n+ }\n+\n+ return null;\n+ }\n+\n+ // This method uses reflection to obtain the nest exception of a Throwable. We use reflection\n+ // because the desired class may not exist in the currently-running VM.\n+ private static Throwable getNestedException(\n+ Throwable parent, String className, String methodName) {\n+ try {\n+ // See if this Throwable is of the desired type, by using isAssignableFrom().\n+ Class testClass = Class.forName(className);\n+ Class objectClass = parent.getClass();\n+ if (testClass.isAssignableFrom(objectClass)) {\n+ // Use reflection to call the specified method.\n+ Class[] argClasses = new Class[0];\n+ Method method = testClass.getMethod(methodName, argClasses);\n+ Object[] args = new Object[0];\n+ return (Throwable)method.invoke(parent, args);\n+ }\n+ }\n+ catch(Exception ex) {\n+ // Most likely, the desired class is not available in this VM. That\'s fine.\n+ // Even if it\'s caused by something else, we don\'t want to display an error\n+ // here, since we\'re already in the process of trying to display the original\n+ // error - another error here will just confuse things.\n+ }\n+\n+ return null;\n+ }\n+\n+ // This method is similar to getNestedException() except it looks for a field instead\n+ // of a method.\n+ private static Throwable getNestedExceptionFromField(\n+ Throwable parent, String className, String fieldName) {\n+ try {\n+ // See if this Throwable is of the desired type, by using isAssignableFrom().\n+ Class testClass = Class.forName(className);\n+ Class objectClass = parent.getClass();\n+ if (testClass.isAssignableFrom(objectClass)) {\n+ // Use reflection to call the specified method.\n+ Class[] argClasses = new Class[0];\n+ Field field = testClass.getField(fieldName);\n+ return (Throwable)field.get(parent);\n+ }\n+ }\n+ catch(Exception ex) {\n+ // Most likely, the desired class is not available in this VM. That\'s fine.\n+ // Could be that the named field isn\'t of type Throwable, but that should happen\n+ // with proper call usage.\n+ // Even if it\'s caused by something else, we don\'t want to display an error\n+ // here, since we\'re already in the process of trying to display the original\n+ // error - another error here will just confuse things.\n+ }\n+\n+ return null;\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/JDOMFactory.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/JDOMFactory.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,338 @@\n+/*--\n+\n+ $Id: JDOMFactory.java,v 1.9 2007/11/10 05:28:59 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+import java.util.*;\n+\n+/**\n+ * An interface to be used by builders when constructing JDOM objects. The\n+ * <code>DefaultJDOMFactory</code> creates the standard top-level JDOM classes\n+ * (Element, Document, Comment, etc). Another implementation of this factory\n+ * could be used to create custom classes.\n+ *\n+ * @version $Revision: 1.9 $, $Date: 2007/11/10 05:28:59 $\n+ * @author Ken Rune Holland\n+ * @author Phil Nelson\n+ * @author Bradley S. Huffman\n+ */\n+public interface JDOMFactory {\n+\n+ // **** constructing Attributes ****\n+\n+ /**\n+ * \n+ * This will create a new <code>Attribute</code> with the\n+ * specified (local) name and value, and in the provided\n+ * <code>{@link org.jdom.Namespace}</code>.\n+ * \n+ *\n+ * @param name <code>String</code> name of <code>Attribute</code>.\n+ * @param value <code>String</code> value for new attribute.\n+ */\n+ public Attribute attribute(String name, String value, Namespace namespace);\n+\n+ /**\n+ * This will create a new <code>Attribute</code> with the\n+ * specified (local) name, value, and type, and in the provided\n+ * <code>{@link org.jdom.Namespace}</code>.\n+ *\n+ * @param name <code>String</code> name of <code>Attribute</code>.\n+ * @param value <code>String</code> value for new attribute.\n+ * @param type <cod'..b' for document root\n+ */\n+ public Document document(Element rootElement);\n+\n+ // **** constructing Elements ****\n+\n+ /**\n+ * This will create a new <code>Element</code>\n+ * with the supplied (local) name, and define\n+ * the <code>{@link org.jdom.Namespace}</code> to be used.\n+ *\n+ * @param name <code>String</code> name of element.\n+ * @param namespace <code>Namespace</code> to put element in.\n+ */\n+ public Element element(String name, Namespace namespace);\n+\n+ /**\n+ * This will create an <code>Element</code> in no\n+ * <code>{@link org.jdom.Namespace}</code>.\n+ *\n+ * @param name <code>String</code> name of element.\n+ */\n+ public Element element(String name);\n+\n+ /**\n+ * This will create a new <code>Element</code> with\n+ * the supplied (local) name, and specifies the URI\n+ * of the <code>{@link org.jdom.Namespace}</code> the <code>Element</code>\n+ * should be in, resulting it being unprefixed (in the default\n+ * namespace).\n+ *\n+ * @param name <code>String</code> name of element.\n+ * @param uri <code>String</code> URI for <code>Namespace</code> element\n+ * should be in.\n+ */\n+ public Element element(String name, String uri);\n+\n+ /**\n+ * This will create a new <code>Element</code> with\n+ * the supplied (local) name, and specifies the prefix and URI\n+ * of the <code>{@link org.jdom.Namespace}</code> the <code>Element</code>\n+ * should be in.\n+ *\n+ * @param name <code>String</code> name of element.\n+ * @param uri <code>String</code> URI for <code>Namespace</code> element\n+ * should be in.\n+ */\n+ public Element element(String name, String prefix, String uri);\n+\n+ // **** constructing ProcessingInstruction ****\n+\n+ /**\n+ * This will create a new <code>ProcessingInstruction</code>\n+ * with the specified target and data.\n+ *\n+ * @param target <code>String</code> target of PI.\n+ * @param data <code>Map</code> data for PI, in\n+ * name/value pairs\n+ */\n+ public ProcessingInstruction processingInstruction(String target,\n+ Map data);\n+\n+ /**\n+ * This will create a new <code>ProcessingInstruction</code>\n+ * with the specified target and data.\n+ *\n+ * @param target <code>String</code> target of PI.\n+ * @param data <code>String</code> data for PI.\n+ */\n+ public ProcessingInstruction processingInstruction(String target,\n+ String data);\n+\n+ // **** constructing EntityRef ****\n+\n+ /**\n+ * This will create a new <code>EntityRef</code>\n+ * with the supplied name.\n+ *\n+ * @param name <code>String</code> name of element.\n+ */\n+ public EntityRef entityRef(String name);\n+\n+ /**\n+ * This will create a new <code>EntityRef</code>\n+ * with the supplied name, public ID, and system ID.\n+ *\n+ * @param name <code>String</code> name of element.\n+ * @param publicID <code>String</code> public ID of element.\n+ * @param systemID <code>String</code> system ID of element.\n+ */\n+ public EntityRef entityRef(String name, String publicID, String systemID);\n+\n+ /**\n+ * This will create a new <code>EntityRef</code>\n+ * with the supplied name and system ID.\n+ *\n+ * @param name <code>String</code> name of element.\n+ * @param systemID <code>String</code> system ID of element.\n+ */\n+ public EntityRef entityRef(String name, String systemID);\n+\n+ // =====================================================================\n+ // List manipulation\n+ // =====================================================================\n+\n+ public void addContent(Parent parent, Content content);\n+\n+ public void setAttribute(Element element, Attribute a);\n+\n+ public void addNamespaceDeclaration(Element element, Namespace additional);\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Namespace.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Namespace.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,276 @@\n+/*-- \n+\n+ $Id: Namespace.java,v 1.44 2008/12/17 23:22:48 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+package org.jdom;\n+\n+import java.util.*;\n+\n+/**\n+ * An XML namespace representation, as well as a factory for creating XML\n+ * namespace objects. Namespaces are not Serializable, however objects that use\n+ * namespaces have special logic to handle serialization manually. These classes\n+ * call the getNamespace() method on deserialization to ensure there is one\n+ * unique Namespace object for any unique prefix/uri pair.\n+ *\n+ * @version $Revision: 1.44 $, $Date: 2008/12/17 23:22:48 $\n+ * @author Brett McLaughlin\n+ * @author Elliotte Rusty Harold\n+ * @author Jason Hunter\n+ * @author Wesley Biggs\n+ */\n+public final class Namespace {\n+\n+ // XXX May want to use weak references to keep the maps from growing \n+ // large with extended use\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: Namespace.java,v $ $Revision: 1.44 $ $Date: 2008/12/17 23:22:48 $ $Name: jdom_1_1_1 $";\n+\n+ /** \n+ * Factory list of namespaces. \n+ * Keys are prefix&URI. \n+ * Values are Namespace objects \n+ */\n+ private static HashMap namespaces;\n+\n+ /** Define a <code>Namespace</code> for when not in a namespace */\n+ public static final Namespace NO_NAMESPACE = new Namespace("", "");\n+\n+ /** Define a <code>Namespace</code> for the standard xml prefix. */\n+ public static final Namespace XML'..b'ect\n+ // namespace and prefix -- xml, http://www.w3.org/XML/1998/namespace\n+ // -- then it was already returned from the preexisting namespaces.\n+ // Thus any use of the xml prefix or the\n+ // http://www.w3.org/XML/1998/namespace URI at this point must be\n+ // incorrect. \n+ if (prefix.equals("xml")) {\n+ throw new IllegalNameException(prefix, "Namespace prefix",\n+ "The xml prefix can only be bound to " +\n+ "http://www.w3.org/XML/1998/namespace"); \n+ }\n+\n+ // The erratum to Namespaces in XML 1.0 that suggests this \n+ // next check is controversial. Not everyone accepts it. \n+ if (uri.equals("http://www.w3.org/XML/1998/namespace")) {\n+ throw new IllegalNameException(uri, "Namespace URI",\n+ "The http://www.w3.org/XML/1998/namespace must be bound to " +\n+ "the xml prefix."); \n+ }\n+\n+ // Finally, store and return\n+ Namespace ns = new Namespace(prefix, uri);\n+ synchronized (namespaces) {\n+ namespaces.put(lookup, ns);\n+ }\n+ return ns;\n+ }\n+\n+ /**\n+ * This will retrieve (if in existence) or create (if not) a \n+ * <code>Namespace</code> for the supplied URI, and make it usable \n+ * as a default namespace, as no prefix is supplied.\n+ *\n+ * @param uri <code>String</code> URI of new <code>Namespace</code>.\n+ * @return <code>Namespace</code> - ready to use namespace.\n+ */\n+ public static Namespace getNamespace(String uri) {\n+ return getNamespace("", uri);\n+ }\n+\n+ /**\n+ * This constructor handles creation of a <code>Namespace</code> object\n+ * with a prefix and URI; it is intentionally left <code>private</code>\n+ * so that it cannot be invoked by external programs/code.\n+ *\n+ * @param prefix <code>String</code> prefix to map to this namespace.\n+ * @param uri <code>String</code> URI for namespace.\n+ */\n+ private Namespace(String prefix, String uri) {\n+ this.prefix = prefix;\n+ this.uri = uri;\n+ }\n+\n+ /**\n+ * This returns the prefix mapped to this <code>Namespace</code>.\n+ *\n+ * @return <code>String</code> - prefix for this <code>Namespace</code>.\n+ */\n+ public String getPrefix() {\n+ return prefix;\n+ }\n+\n+ /**\n+ * This returns the namespace URI for this <code>Namespace</code>.\n+ *\n+ * @return <code>String</code> - URI for this <code>Namespace</code>.\n+ */\n+ public String getURI() {\n+ return uri;\n+ }\n+\n+ /**\n+ * This tests for equality - Two <code>Namespaces</code>\n+ * are equal if and only if their URIs are byte-for-byte equals.\n+ *\n+ * @param ob <code>Object</code> to compare to this <code>Namespace</code>.\n+ * @return <code>boolean</code> - whether the supplied object is equal to\n+ * this <code>Namespace</code>.\n+ */\n+ public boolean equals(Object ob) {\n+ if (this == ob) {\n+ return true;\n+ }\n+ if (ob instanceof Namespace) { // instanceof returns false if null\n+ return uri.equals(((Namespace)ob).uri);\n+ }\n+ return false;\n+ }\n+\n+ /**\n+ * This returns a <code>String</code> representation of this \n+ * <code>Namespace</code>, suitable for use in debugging.\n+ *\n+ * @return <code>String</code> - information about this instance.\n+ */\n+ public String toString() {\n+ return "[Namespace: prefix \\"" + prefix + "\\" is mapped to URI \\"" + \n+ uri + "\\"]";\n+ }\n+\n+ /**\n+ * This returns a probably unique hash code for the <code>Namespace</code>.\n+ * If two namespaces have the same URI, they are equal and have the same\n+ * hash code, even if they have different prefixes.\n+ *\n+ * @return <code>int</code> - hash code for this <code>Namespace</code>.\n+ */\n+ public int hashCode() {\n+ return uri.hashCode();\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/NamespaceKey.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/NamespaceKey.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,108 @@
+/*--
+
+ $Id: NamespaceKey.java,v 1.2 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom;
+
+import java.util.*;
+
+/**
+ * Key for storing a namespace representation in a map.
+ *
+ * @version $Revision: 1.2 $, $Date: 2007/11/10 05:28:59 $
+ * @author Tatu Saloranta
+ * @author Bradley S. Huffman
+ */
+final class NamespaceKey {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: NamespaceKey.java,v $ $Revision: 1.2 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ private String prefix;
+ private String uri;
+ private int hash;
+
+ public NamespaceKey(String prefix, String uri) {
+ this.prefix = prefix;
+ this.uri = uri;
+ this.hash = prefix.hashCode();
+ }
+
+ public NamespaceKey(Namespace namespace) {
+ this(namespace.getPrefix(), namespace.getURI());
+ }
+
+ public boolean equals(Object ob) {
+ if (this == ob) {
+ return true;
+ }
+ else if (ob instanceof NamespaceKey) {
+ NamespaceKey other = (NamespaceKey) ob;
+ return prefix.equals(other.prefix) && uri.equals(other.uri);
+ }
+ else {
+ return false;
+ }
+ }
+
+ public int hashCode() {
+ return hash;
+ }
+
+ public String toString() {
+ return "[NamespaceKey: prefix \"" + prefix +
+ "\" is mapped to URI \"" + uri + "\"]";
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Parent.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Parent.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,239 @@\n+/*--\n+\n+ $Id: Parent.java,v 1.13 2007/11/10 05:28:59 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+import java.io.Serializable;\n+import java.util.*;\n+import org.jdom.filter.Filter;\n+\n+/**\n+ * Superclass for JDOM objects which are allowed to contain\n+ * {@link Content} content.\n+ *\n+ * @see org.jdom.Content\n+ * @see org.jdom.Document\n+ * @see org.jdom.Element\n+ *\n+ * @author Bradley S. Huffman\n+ * @author Jason Hunter\n+ * @version $Revision: 1.13 $, $Date: 2007/11/10 05:28:59 $\n+ */\n+public interface Parent extends Cloneable, Serializable {\n+\n+ /**\n+ * Returns the number of children in this parent\'s content list.\n+ * Children may be any {@link Content} type.\n+ *\n+ * @return number of children\n+ */\n+ int getContentSize();\n+\n+ /**\n+ * Returns the index of the supplied child in the content list,\n+ * or -1 if not a child of this parent.\n+ *\n+ * @param child child to search for\n+ * @return index of child, or -1 if not found\n+ */\n+ int indexOf(Content child);\n+\n+// /**\n+// * Starting at the given index (inclusive), returns the index of\n+// * the first child matching the supplied filter, or -1\n+// * if none is found.\n+// *\n+// * @return index of child, or -1 if none found\n+// */\n+// int indexOf(int index, Filter filter);\n+\n+ /**\n+ * Returns a list containing detached clones of this parent\'s content list.\n+ *\n+ * @return list of cl'..b'al traversal through the List is best done with an Iterator\n+ * since the underlying implement of {@link java.util.List#size} may\n+ * require walking the entire list and indexed lookups may require\n+ * starting at the beginning each time.\n+ *\n+ * @return a list of the content of the parent\n+ * @throws IllegalStateException if parent is a Document\n+ * and the root element is not set\n+ */\n+ List getContent();\n+\n+ /**\n+ * Returns as a {@link java.util.List} the content of\n+ * this parent that matches the supplied filter. The returned list is\n+ * "live" and in document order. Any modifications to it affect\n+ * the element\'s actual contents. Modifications are checked for\n+ * conformance to XML 1.0 rules.\n+ * \n+ * Sequential traversal through the List is best done with an Iterator\n+ * since the underlying implement of {@link java.util.List#size} may\n+ * require walking the entire list and indexed lookups may require\n+ * starting at the beginning each time.\n+ *\n+ * @param filter filter to apply\n+ * @return a list of the content of the parent matching the filter\n+ * @throws IllegalStateException if parent is a Document\n+ * and the root element is not set\n+ */\n+ List getContent(Filter filter);\n+\n+ /**\n+ * Removes all content from this parent and returns the detached\n+ * children.\n+ *\n+ * @return list of the old content detached from this parent\n+ */\n+ List removeContent();\n+\n+ /**\n+ * Removes from this parent all child content matching the given filter\n+ * and returns a list of the detached children.\n+ *\n+ * @param filter filter to apply\n+ * @return list of the detached children matching the filter\n+ */\n+ List removeContent(Filter filter);\n+\n+ /**\n+ * Removes a single child node from the content list.\n+ *\n+ * @param child child to remove\n+ * @return whether the removal occurred\n+ */\n+ boolean removeContent(Content child);\n+\n+ /**\n+ * Removes and returns the child at the given\n+ * index, or returns null if there\'s no such child.\n+ *\n+ * @param index index of child to remove\n+ * @return detached child at given index or null if no\n+ * @throws IndexOutOfBoundsException if index is negative or beyond\n+ * the current number of children\n+ */\n+ Content removeContent(int index);\n+\n+ /**\n+ * Obtain a deep, unattached copy of this parent and it\'s children.\n+ *\n+ * @return a deep copy of this parent and it\'s children.\n+ */\n+ Object clone();\n+\n+ /**\n+ * Returns an {@link java.util.Iterator} that walks over all descendants\n+ * in document order.\n+ *\n+ * @return an iterator to walk descendants\n+ */\n+ Iterator getDescendants();\n+\n+ /**\n+ * Returns an {@link java.util.Iterator} that walks over all descendants\n+ * in document order applying the Filter to return only elements that\n+ * match the filter rule. With filters you can match only Elements,\n+ * only Comments, Elements or Comments, only Elements with a given name\n+ * and/or prefix, and so on.\n+ *\n+ * @param filter filter to select which descendants to see\n+ * @return an iterator to walk descendants that match a filter\n+ */\n+ Iterator getDescendants(Filter filter);\n+\n+ /**\n+ * Return this parent\'s parent, or null if this parent is currently\n+ * not attached to another parent. This is the same method as in Content but\n+ * also added to Parent to allow more easy up-the-tree walking.\n+ *\n+ * @return this parent\'s parent or null if none\n+ */\n+ Parent getParent();\n+\n+ /**\n+ * Return this parent\'s owning document or null if the branch containing\n+ * this parent is currently not attached to a document.\n+ *\n+ * @return this child\'s owning document or null if none\n+ */\n+ Document getDocument();\n+\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/ProcessingInstruction.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/ProcessingInstruction.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,473 @@\n+/*--\n+\n+ $Id: ProcessingInstruction.java,v 1.47 2007/11/10 05:28:59 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+import java.util.*;\n+\n+/**\n+ * An XML processing instruction. Methods allow the user to obtain the target of\n+ * the PI as well as its data. The data can always be accessed as a String or,\n+ * if the data appears akin to an attribute list, can be retrieved as name/value\n+ * pairs.\n+ *\n+ * @version $Revision: 1.47 $, $Date: 2007/11/10 05:28:59 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Steven Gould\n+ */\n+\n+public class ProcessingInstruction extends Content {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: ProcessingInstruction.java,v $ $Revision: 1.47 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";\n+\n+ /** The target of the PI */\n+ protected String target;\n+\n+ /** The data for the PI as a String */\n+ protected String rawData;\n+\n+ /** The data for the PI in name/value pairs */\n+ protected Map mapData;\n+\n+ /**\n+ * Default, no-args constructor for implementations\n+ * to use if needed.\n+ */\n+ protected ProcessingInstruction() { }\n+\n+ /**\n+ * This will create a new <code>ProcessingInstruction</code>\n+ * with the specified target and data.\n+ *\n+ * @param target <code>String</code> target of PI.\n+ * @param data <code>Map</code> data for PI, in\n+ * name/value pairs\n+ * @throws IllegalTargetExcepti'..b' // System.out.println("Extracted (name, value) pair: ("\n+ // + name + ", \'" + value+"\')");\n+\n+ // If both a name and a value have been found, then add\n+ // them to the data Map\n+ if (name.length() > 0 && value != null) {\n+ //if (data.containsKey(name)) {\n+ // A repeat, that\'s a parse error, so return a null map\n+ //return new HashMap();\n+ //}\n+ //else {\n+ data.put(name, value);\n+ //}\n+ }\n+ }\n+\n+ return data;\n+ }\n+\n+ /**\n+ * This is a helper routine, only used by parseData, to extract a\n+ * quoted String from the input parameter, rawData. A quoted string\n+ * can use either single or double quotes, but they must match up.\n+ * A singly quoted string can contain an unbalanced amount of double\n+ * quotes, or vice versa. For example, the String "JDOM\'s the best"\n+ * is legal as is \'JDOM"s the best\'.\n+ *\n+ * @param rawData the input string from which a quoted string is to\n+ * be extracted.\n+ * @return the first quoted string encountered in the input data. If\n+ * no quoted string is found, then the empty string, "", is\n+ * returned.\n+ * @see #parseData\n+ */\n+ private static int[] extractQuotedString(String rawData) {\n+ // Remembers whether we\'re actually in a quoted string yet\n+ boolean inQuotes = false;\n+\n+ // Remembers which type of quoted string we\'re in\n+ char quoteChar = \'"\';\n+\n+ // Stores the position of the first character inside\n+ // the quoted string (i.e. the start of the return string)\n+ int start = 0;\n+\n+ // Iterate through the input string looking for the start\n+ // and end of the quoted string\n+ for (int pos=0; pos < rawData.length(); pos++) {\n+ char currentChar = rawData.charAt(pos);\n+ if (currentChar==\'"\' || currentChar==\'\\\'\') {\n+ if (!inQuotes) {\n+ // We\'re entering a quoted string\n+ quoteChar = currentChar;\n+ inQuotes = true;\n+ start = pos+1;\n+ }\n+ else if (quoteChar == currentChar) {\n+ // We\'re leaving a quoted string\n+ inQuotes = false;\n+ return new int[] { start, pos };\n+ }\n+ // Otherwise we\'ve encountered a quote\n+ // inside a quote, so just continue\n+ }\n+ }\n+\n+ return null;\n+ }\n+\n+ /**\n+ * This returns a <code>String</code> representation of the\n+ * <code>ProcessingInstruction</code>, suitable for debugging. If the XML\n+ * representation of the <code>ProcessingInstruction</code> is desired,\n+ * {@link org.jdom.output.XMLOutputter#outputString(ProcessingInstruction)}\n+ * should be used.\n+ *\n+ * @return <code>String</code> - information about the\n+ * <code>ProcessingInstruction</code>\n+ */\n+ public String toString() {\n+ return new StringBuffer()\n+ .append("[ProcessingInstruction: ")\n+ .append(new org.jdom.output.XMLOutputter().outputString(this))\n+ .append("]")\n+ .toString();\n+ }\n+\n+ /**\n+ * This will return a clone of this <code>ProcessingInstruction</code>.\n+ *\n+ * @return <code>Object</code> - clone of this\n+ * <code>ProcessingInstruction</code>.\n+ */\n+ public Object clone() {\n+ ProcessingInstruction pi = (ProcessingInstruction) super.clone();\n+\n+ // target and rawdata are immutable and references copied by\n+ // Object.clone()\n+\n+ // Create a new Map object for the clone (since Map isn\'t Cloneable)\n+ if (mapData != null) {\n+ pi.mapData = parseData(rawData);\n+ }\n+ return pi;\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Text.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Text.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,271 @@\n+/*--\n+\n+ $Id: Text.java,v 1.25 2007/11/10 05:28:59 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom;\n+\n+/**\n+ * Character-based XML content. Provides a modular, parentable method of\n+ * representing text. Text makes no guarantees about the underlying textual\n+ * representation of character data, but does expose that data as a Java String.\n+ *\n+ * @version $Revision: 1.25 $, $Date: 2007/11/10 05:28:59 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Bradley S. Huffman\n+ */\n+public class Text extends Content {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: Text.java,v $ $Revision: 1.25 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";\n+\n+ static final String EMPTY_STRING = "";\n+\n+ /** The actual character content */\n+ // XXX See http://www.servlets.com/archive/servlet/ReadMsg?msgId=8612\n+ // from elharo for a description of why Java characters may not suffice\n+ // long term\n+ protected String value;\n+\n+ /**\n+ * This is the protected, no-args constructor standard in all JDOM\n+ * classes. It allows subclassers to get a raw instance with no\n+ * initialization.\n+ */\n+ protected Text() { }\n+\n+ /**\n+ * This constructor creates a new <code>Text</code> node, with the\n+ * supplied string value as it\'s character content.\n+ *\n+ * @param str the node\'s character content.\n+ * @throws IllegalDataException if <code>str</code> contains an\n+ * '..b'nly whitespace exists, the empty string is returned.\n+ * \n+ * Per XML 1.0 Production 3 whitespace includes: #x20, #x9, #xD, #xA\n+ * \n+ *\n+ * @param str string to be normalized.\n+ * @return normalized string or empty string\n+ */\n+ public static String normalizeString(String str) {\n+ if (str == null)\n+ return EMPTY_STRING;\n+\n+ char[] c = str.toCharArray();\n+ char[] n = new char[c.length];\n+ boolean white = true;\n+ int pos = 0;\n+ for (int i = 0; i < c.length; i++) {\n+ if (" \\t\\n\\r".indexOf(c[i]) != -1) {\n+ if (!white) {\n+ n[pos++] = \' \';\n+ white = true;\n+ }\n+ }\n+ else {\n+ n[pos++] = c[i];\n+ white = false;\n+ }\n+ }\n+ if (white && pos > 0) {\n+ pos--;\n+ }\n+ return new String(n, 0, pos);\n+ }\n+\n+ /**\n+ * This will set the value of this <code>Text</code> node.\n+ *\n+ * @param str value for node\'s content.\n+ * @return the object on which the method was invoked\n+ * @throws IllegalDataException if <code>str</code> contains an\n+ * illegal character such as a vertical tab (as determined\n+ * by {@link org.jdom.Verifier#checkCharacterData})\n+ */\n+ public Text setText(String str) {\n+ String reason;\n+\n+ if (str == null) {\n+ value = EMPTY_STRING;\n+ return this;\n+ }\n+\n+ if ((reason = Verifier.checkCharacterData(str)) != null) {\n+ throw new IllegalDataException(str, "character content", reason);\n+ }\n+ value = str;\n+ return this;\n+ }\n+\n+ /**\n+ * This will append character content to whatever content already\n+ * exists within this <code>Text</code> node.\n+ *\n+ * @param str character content to append.\n+ * @throws IllegalDataException if <code>str</code> contains an\n+ * illegal character such as a vertical tab (as determined\n+ * by {@link org.jdom.Verifier#checkCharacterData})\n+ */\n+ public void append(String str) {\n+ String reason;\n+\n+ if (str == null) {\n+ return;\n+ }\n+ if ((reason = Verifier.checkCharacterData(str)) != null) {\n+ throw new IllegalDataException(str, "character content", reason);\n+ }\n+\n+ if (str == EMPTY_STRING)\n+ value = str;\n+ else value += str;\n+ }\n+\n+ /**\n+ * This will append the content of another <code>Text</code> node\n+ * to this node.\n+ *\n+ * @param text Text node to append.\n+ */\n+ public void append(Text text) {\n+ if (text == null) {\n+ return;\n+ }\n+ value += text.getText();\n+ }\n+\n+ /**\n+ * Returns the XPath 1.0 string value of this element, which is the\n+ * text itself.\n+ *\n+ * @return the text\n+ */\n+ public String getValue() {\n+ return value;\n+ }\n+\n+ /**\n+ * This returns a <code>String</code> representation of the\n+ * <code>Text</code> node, suitable for debugging. If the XML\n+ * representation of the <code>Text</code> node is desired,\n+ * either <code>{@link #getText}</code> or\n+ * {@link org.jdom.output.XMLOutputter#outputString(Text)}</code>\n+ * should be used.\n+ *\n+ * @return <code>String</code> - information about this node.\n+ */\n+ public String toString() {\n+ return new StringBuffer(64)\n+ .append("[Text: ")\n+ .append(getText())\n+ .append("]")\n+ .toString();\n+ }\n+\n+ /**\n+ * This will return a clone of this <code>Text</code> node, with the\n+ * same character content, but no parent.\n+ *\n+ * @return <code>Text</code> - cloned node.\n+ */\n+ public Object clone() {\n+ Text text = (Text)super.clone();\n+ text.value = value;\n+ return text;\n+ }\n+\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/UncheckedJDOMFactory.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/UncheckedJDOMFactory.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,287 @@\n+/*-- \n+\n+ $Id: UncheckedJDOMFactory.java,v 1.4 2007/11/10 05:28:59 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+package org.jdom;\n+\n+import java.util.*;\n+\n+/**\n+ * Special factory for building documents without any content or structure\n+ * checking. This should only be used when you are 100% positive that the\n+ * input is absolutely correct. This factory can speed builds, but any\n+ * problems in the input will be uncaught until later when they could cause\n+ * infinite loops, malformed XML, or worse. Use with extreme caution.\n+ */\n+public class UncheckedJDOMFactory implements JDOMFactory {\n+\n+ // =====================================================================\n+ // Element Factory\n+ // =====================================================================\n+\n+ public Element element(String name, Namespace namespace) {\n+ Element e = new Element();\n+ e.name = name;\n+ if (namespace == null) {\n+ namespace = Namespace.NO_NAMESPACE;\n+ }\n+ e.namespace = namespace;\n+ return e;\n+ }\n+\n+ public Element element(String name) {\n+ Element e = new Element();\n+ e.name = name;\n+ e.namespace = Namespace.NO_NAMESPACE;\n+ return e;\n+ }\n+\n+ public Element element(String name, String uri) {\n+ return element(name, Namespace.getNamespace("", uri));\n+ }\n+\n+ public Element element(String name, String prefix, String uri) {\n+ return elem'..b'==\n+\n+ public Comment comment(String str) {\n+ Comment c = new Comment();\n+ c.text = str;\n+ return c;\n+ }\n+\n+ // =====================================================================\n+ // Processing Instruction Factory\n+ // =====================================================================\n+\n+ public ProcessingInstruction processingInstruction(String target, Map data) {\n+ ProcessingInstruction p = new ProcessingInstruction();\n+ p.target = target;\n+ p.setData(data);\n+ return p;\n+ }\n+\n+ public ProcessingInstruction processingInstruction(String target, String data) {\n+ ProcessingInstruction p = new ProcessingInstruction();\n+ p.target = target;\n+ p.setData(data);\n+ return p;\n+ }\n+\n+ // =====================================================================\n+ // Entity Ref Factory\n+ // =====================================================================\n+\n+ public EntityRef entityRef(String name) {\n+ EntityRef e = new org.jdom.EntityRef();\n+ e.name = name;\n+ return e;\n+ }\n+\n+ public EntityRef entityRef(String name, String systemID) {\n+ EntityRef e = new EntityRef();\n+ e.name = name;\n+ e.systemID = systemID;\n+ return e;\n+ }\n+\n+ public EntityRef entityRef(String name, String publicID, String systemID) {\n+ EntityRef e = new EntityRef();\n+ e.name = name;\n+ e.publicID = publicID;\n+ e.systemID = systemID;\n+ return e;\n+ }\n+\n+ // =====================================================================\n+ // DocType Factory\n+ // =====================================================================\n+\n+ public DocType docType(String elementName, String publicID, String systemID) {\n+ DocType d = new DocType();\n+ d.elementName = elementName;\n+ d.publicID = publicID;\n+ d.systemID = systemID;\n+ return d;\n+ }\n+\n+ public DocType docType(String elementName, String systemID) {\n+ return docType(elementName, null, systemID);\n+ }\n+\n+ public DocType docType(String elementName) {\n+ return docType(elementName, null, null);\n+ }\n+\n+ // =====================================================================\n+ // Document Factory\n+ // =====================================================================\n+\n+ public Document document(Element rootElement, DocType docType, String baseURI) {\n+ Document d = new Document();\n+ if (docType != null) {\n+ addContent(d, docType);\n+ }\n+ if (rootElement != null) {\n+ addContent(d, rootElement);\n+ }\n+ if (baseURI != null) {\n+ d.baseURI = baseURI;\n+ }\n+ return d;\n+ }\n+\n+ public Document document(Element rootElement, DocType docType) {\n+ return document(rootElement, docType, null);\n+ }\n+\n+ public Document document(Element rootElement) {\n+ return document(rootElement, null, null);\n+ }\n+\n+ // =====================================================================\n+ // List manipulation\n+ // =====================================================================\n+\n+ public void addContent(Parent parent, Content child) {\n+ if (parent instanceof Element) {\n+ Element elt = (Element) parent;\n+ elt.content.uncheckedAddContent(child);\n+ }\n+ else {\n+ Document doc = (Document) parent;\n+ doc.content.uncheckedAddContent(child);\n+ }\n+ }\n+\n+ public void setAttribute(Element parent, Attribute a) {\n+ parent.attributes.uncheckedAddAttribute(a);\n+ }\n+\n+ public void addNamespaceDeclaration(Element parent, Namespace additional) {\n+ if (parent.additionalNamespaces == null) {\n+ parent.additionalNamespaces = new ArrayList(5); //Element.INITIAL_ARRAY_SIZE\n+ }\n+ parent.additionalNamespaces.add(additional);\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/Verifier.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/Verifier.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,1271 @@\n+/*-- \n+\n+ $Id: Verifier.java,v 1.57 2009/07/23 05:54:23 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+package org.jdom;\n+\n+import java.util.*;\n+\n+/**\n+ * A utility class to handle well-formedness checks on names, data, and other\n+ * verification tasks for JDOM. The class is final and may not be subclassed.\n+ *\n+ * @version $Revision: 1.57 $, $Date: 2009/07/23 05:54:23 $\n+ * @author Brett McLaughlin\n+ * @author Elliotte Rusty Harold\n+ * @author Jason Hunter\n+ * @author Bradley S. Huffman\n+ */\n+final public class Verifier {\n+\n+ private static final String CVS_ID = \n+ "@(#) $RCSfile: Verifier.java,v $ $Revision: 1.57 $ $Date: 2009/07/23 05:54:23 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * Ensure instantation cannot occur.\n+ */\n+ private Verifier() { }\n+\n+ /**\n+ * This will check the supplied name to see if it is legal for use as\n+ * a JDOM <code>{@link Element}</code> name.\n+ *\n+ * @param name <code>String</code> name to check.\n+ * @return <code>String</code> reason name is illegal, or\n+ * <code>null</code> if name is OK.\n+ */\n+ public static String checkElementName(String name) {\n+ // Check basic XML name rules first\n+ String reason;\n+ if ((reason = checkXMLName(name)) != null) {\n+ return reason;\n+ }\n+\n+ // No colons allowed, since elements handle this internally\n+ if (name.indexOf(":") != -1) {\n+ return "Element na'..b" if (c < 0x0F90) return false; if (c <= 0x0F95) return true;\n+ if (c == 0x0F97) return true;\n+ if (c < 0x0F99) return false; if (c <= 0x0FAD) return true;\n+ \n+ if (c < 0x0FB1) return false; if (c <= 0x0FB7) return true;\n+ if (c == 0x0FB9) return true;\n+ if (c < 0x20D0) return false; if (c <= 0x20DC) return true;\n+ if (c == 0x20E1) return true;\n+ \n+ if (c < 0x302A) return false; if (c <= 0x302F) return true;\n+ if (c == 0x3099) return true;\n+ if (c == 0x309A) return true; \n+ \n+ return false;\n+ \n+ }\n+ \n+ /**\n+ * This is a utility function for determining whether a specified \n+ * character is an extender according to production 88 of the XML 1.0\n+ * specification.\n+ *\n+ * @param c <code>char</code> to check.\n+ * @return <code>String</code> true if it's an extender, false otherwise.\n+ */\n+ public static boolean isXMLExtender(char c) {\n+\n+ if (c < 0x00B6) return false; // quick short circuit\n+\n+ // Extenders \n+ if (c == 0x00B7) return true;\n+ if (c == 0x02D0) return true;\n+ if (c == 0x02D1) return true;\n+ if (c == 0x0387) return true;\n+ if (c == 0x0640) return true;\n+ if (c == 0x0E46) return true;\n+ if (c == 0x0EC6) return true;\n+ if (c == 0x3005) return true;\n+ \n+ if (c < 0x3031) return false; if (c <= 0x3035) return true;\n+ if (c < 0x309D) return false; if (c <= 0x309E) return true;\n+ if (c < 0x30FC) return false; if (c <= 0x30FE) return true;\n+ \n+ return false;\n+ \n+ }\n+ \n+ /**\n+ * This is a utility function for determining whether a specified \n+ * Unicode character\n+ * is a digit according to production 88 of the XML 1.0 specification.\n+ *\n+ * @param c <code>char</code> to check for XML digit compliance\n+ * @return <code>boolean</code> true if it's a digit, false otherwise\n+ */\n+ public static boolean isXMLDigit(char c) {\n+ \n+ if (c < 0x0030) return false; if (c <= 0x0039) return true;\n+ if (c < 0x0660) return false; if (c <= 0x0669) return true;\n+ if (c < 0x06F0) return false; if (c <= 0x06F9) return true;\n+ if (c < 0x0966) return false; if (c <= 0x096F) return true;\n+ \n+ if (c < 0x09E6) return false; if (c <= 0x09EF) return true;\n+ if (c < 0x0A66) return false; if (c <= 0x0A6F) return true;\n+ if (c < 0x0AE6) return false; if (c <= 0x0AEF) return true;\n+ \n+ if (c < 0x0B66) return false; if (c <= 0x0B6F) return true;\n+ if (c < 0x0BE7) return false; if (c <= 0x0BEF) return true;\n+ if (c < 0x0C66) return false; if (c <= 0x0C6F) return true;\n+ \n+ if (c < 0x0CE6) return false; if (c <= 0x0CEF) return true;\n+ if (c < 0x0D66) return false; if (c <= 0x0D6F) return true;\n+ if (c < 0x0E50) return false; if (c <= 0x0E59) return true;\n+ \n+ if (c < 0x0ED0) return false; if (c <= 0x0ED9) return true;\n+ if (c < 0x0F20) return false; if (c <= 0x0F29) return true; \n+ \n+ return false;\n+ } \n+ \n+ /**\n+ * This is a utility function for determining whether a specified \n+ * Unicode character is a whitespace character according to production 3\n+ * of the XML 1.0 specification.\n+ *\n+ * @param c <code>char</code> to check for XML whitespace compliance\n+ * @return <code>boolean</code> true if it's a whitespace, false otherwise\n+ */\n+ public static boolean isXMLWhitespace(char c) {\n+ if (c==' ' || c=='\\n' || c=='\\t' || c=='\\r' ){\n+ return true;\n+ }\n+ return false;\n+ }\n+}\n"

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/AbstractDOMAdapter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/AbstractDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,172 @@
+/*--
+
+ $Id: AbstractDOMAdapter.java,v 1.21 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.adapters;
+
+import java.io.*;
+import java.lang.reflect.*;
+
+import org.jdom.*;
+import org.w3c.dom.*;
+import org.w3c.dom.Document;
+
+/**
+ * A DOMAdapter utility abstract base class.
+ *
+ * @version $Revision: 1.21 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ * @author Jason Hunter
+ */
+public abstract class AbstractDOMAdapter implements DOMAdapter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: AbstractDOMAdapter.java,v $ $Revision: 1.21 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This creates a new <code>{@link Document}</code> from an
+ * existing <code>InputStream</code> by letting a DOM
+ * parser handle parsing using the supplied stream.
+ *
+ * @param filename file to parse.
+ * @param validate <code>boolean</code> to indicate if validation should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public Document getDocument(File filename, boolean validate)
+ throws IOException, JDOMException {
+
+ return getDocument(new FileInputStream(filename), validate);
+ }
+
+ /**
+ * This creates a new <code>{@link Document}</code> from an
+ * existing <code>InputStream</code> by letting a DOM
+ * parser handle parsing using the supplied stream.
+ *
+ * @param in <code>InputStream</code> to parse.
+ * @param validate <code>boolean</code> to indicate if validation should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public abstract Document getDocument(InputStream in, boolean validate)
+ throws IOException, JDOMException;
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation.
+ *
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public abstract Document createDocument() throws JDOMException;
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation with the given DOCTYPE.
+ * If the doctype parameter is null, the behavior is the same as
+ * calling <code>createDocument()</code>.
+ *
+ * @param doctype Initial <code>DocType</code> of the document.
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public Document createDocument(DocType doctype) throws JDOMException {
+ if (doctype == null) {
+ return createDocument();
+ }
+
+ DOMImplementation domImpl = createDocument().getImplementation();
+ DocumentType domDocType = domImpl.createDocumentType(
+ doctype.getElementName(),
+ doctype.getPublicID(),
+ doctype.getSystemID());
+
+ // Set the internal subset if possible
+ setInternalSubset(domDocType, doctype.getInternalSubset());
+
+ return domImpl.createDocument("http://temporary",
+ doctype.getElementName(),
+ domDocType);
+ }
+
+ /**
+ * This attempts to change the DocumentType to have the given internal DTD
+ * subset value. This is not a standard ability in DOM, so it's only
+ * available with some parsers. Subclasses can alter the mechanism by
+ * which the attempt is made to set the value.
+ *
+ * @param dt DocumentType to be altered
+ * @param s String to use as the internal DTD subset
+ */
+ protected void setInternalSubset(DocumentType dt, String s) {
+ if (dt == null || s == null) return;
+
+ // Default behavior is to attempt a setInternalSubset() call using
+ // reflection. This method is not part of the DOM spec, but it's
+ // available on Xerces 1.4.4+. It's not currently in Crimson.
+ try {
+ Class dtclass = dt.getClass();
+ Method setInternalSubset = dtclass.getMethod(
+ "setInternalSubset", new Class[] {java.lang.String.class});
+ setInternalSubset.invoke(dt, new Object[] {s});
+ }
+ catch (Exception e) {
+ // ignore
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/CrimsonDOMAdapter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/CrimsonDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,146 @@
+/*--
+
+ $Id: CrimsonDOMAdapter.java,v 1.17 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.adapters;
+
+import java.io.*;
+import java.lang.reflect.*;
+
+import org.jdom.*;
+import org.w3c.dom.Document;
+import org.xml.sax.*;
+
+/**
+ * An adapter for the Apache Crimson DOM parser.
+ *
+ * @version $Revision: 1.17 $, $Date: 2007/11/10 05:28:59 $
+ * @author Jason Hunter
+ */
+public class CrimsonDOMAdapter extends AbstractDOMAdapter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: CrimsonDOMAdapter.java,v $ $Revision: 1.17 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This creates a new <code>{@link Document}</code> from an
+ * existing <code>InputStream</code> by letting a DOM
+ * parser handle parsing using the supplied stream.
+ *
+ * @param in <code>InputStream</code> to parse.
+ * @param validate <code>boolean</code> to indicate if validation should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public Document getDocument(InputStream in, boolean validate)
+ throws IOException, JDOMException {
+
+ try {
+ Class[] parameterTypes = new Class[2];
+ parameterTypes[0] = Class.forName("java.io.InputStream");
+ parameterTypes[1] = boolean.class;
+
+ Object[] args = new Object[2];
+ args[0] = in;
+ args[1] = new Boolean(false);
+
+ // Load the parser class and invoke the parse method
+ Class parserClass = Class.forName("org.apache.crimson.tree.XmlDocument");
+ Method createXmlDocument =
+ parserClass.getMethod("createXmlDocument", parameterTypes);
+ Document doc =
+ (Document)createXmlDocument.invoke(null, args);
+
+ return doc;
+
+ } catch (InvocationTargetException e) {
+ Throwable targetException = e.getTargetException();
+ if (targetException instanceof org.xml.sax.SAXParseException) {
+ SAXParseException parseException = (SAXParseException)targetException;
+ throw new JDOMException("Error on line " + parseException.getLineNumber() +
+ " of XML document: " + parseException.getMessage(), parseException);
+ } else if (targetException instanceof IOException) {
+ IOException ioException = (IOException) targetException;
+ throw ioException;
+ } else {
+ throw new JDOMException(targetException.getMessage(), targetException);
+ }
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage(), e);
+ }
+ }
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation.
+ *
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public Document createDocument() throws JDOMException {
+ try {
+ return
+ (Document)Class.forName(
+ "org.apache.crimson.tree.XmlDocument")
+ .newInstance();
+
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage() + " when creating document", e);
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/DOMAdapter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/DOMAdapter.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,123 @@
+/*--
+
+ $Id: DOMAdapter.java,v 1.22 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.adapters;
+
+import java.io.*;
+
+import org.jdom.*;
+import org.w3c.dom.Document;
+
+/**
+ * Defines a standard set of adapter methods for interfacing with a DOM parser
+ * and obtaining a DOM {@link org.w3c.dom.Document org.w3c.dom.Document} object.
+ * Implementing classes map these calls to DOM parser-specific calls, allowing
+ * any third-party parser to be used with JDOM.
+ *
+ * @version $Revision: 1.22 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ * @author Jason Hunter
+ */
+public interface DOMAdapter {
+
+ /**
+ * This creates a new <code>Document</code> from a
+ * given filename by letting a DOM parser handle parsing from the file.
+ *
+ * @param filename file to parse.
+ * @param validate <code>boolean</code> to indicate if validation
+ * should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public Document getDocument(File filename, boolean validate)
+ throws IOException, JDOMException;
+
+ /**
+ * This creates a new <code>Document</code> from an
+ * existing <code>InputStream</code> by letting a DOM
+ * parser handle parsing using the supplied stream.
+ *
+ * @param in <code>InputStream</code> to parse.
+ * @param validate <code>boolean</code> to indicate if validation
+ * should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public Document getDocument(InputStream in, boolean validate)
+ throws IOException, JDOMException;
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation.
+ *
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public Document createDocument() throws JDOMException;
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation with the given DOCTYPE.
+ *
+ * @param doctype Initial <code>DocType</code> of the document.
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public Document createDocument(DocType doctype) throws JDOMException;
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/JAXPDOMAdapter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/JAXPDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,195 @@\n+/*-- \n+\n+ $Id: JAXPDOMAdapter.java,v 1.13 2007/11/10 05:28:59 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+package org.jdom.adapters;\n+\n+import java.io.*;\n+import java.lang.reflect.*;\n+\n+import org.jdom.*;\n+import org.jdom.input.*;\n+import org.w3c.dom.Document;\n+\n+/**\n+ * An adapter for any parser supporting the Sun JAXP APIs.\n+ * \n+ * @version $Revision: 1.13 $, $Date: 2007/11/10 05:28:59 $\n+ * @author Jason Hunter\n+ */\n+public class JAXPDOMAdapter extends AbstractDOMAdapter {\n+\n+ private static final String CVS_ID = \n+ "@(#) $RCSfile: JAXPDOMAdapter.java,v $ $Revision: 1.13 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * This creates a new <code>{@link Document}</code> from an\n+ * existing <code>InputStream</code> by letting a JAXP\n+ * parser handle parsing using the supplied stream.\n+ *\n+ * @param in <code>InputStream</code> to parse.\n+ * @param validate <code>boolean</code> to indicate if validation \n+ * should occur.\n+ * @return <code>Document</code> - instance ready for use.\n+ * @throws IOException when I/O error occurs.\n+ * @throws JDOMException when errors occur in parsing.\n+ */\n+ public Document getDocument(InputStream in, boolean validate)\n+ throws IOException, JDOMException {\n+\n+ try {\n+ // Try using JAXP...\n+ // Note we need DOM Level 2 and thus JAXP 1.1.\n+ Class.forName("javax.xml.transform.Tra'..b' Method newParserInstance =\n+ factoryClass.getMethod("newInstance", null);\n+ Object factory = newParserInstance.invoke(null, null);\n+\n+ // factory.setValidating(validate);\n+ Method setValidating =\n+ factoryClass.getMethod("setValidating",\n+ new Class[]{boolean.class});\n+ setValidating.invoke(factory,\n+ new Object[]{new Boolean(validate)});\n+\n+ // factory.setNamespaceAware(true);\n+ Method setNamespaceAware =\n+ factoryClass.getMethod("setNamespaceAware",\n+ new Class[]{boolean.class});\n+ setNamespaceAware.invoke(factory,\n+ new Object[]{Boolean.TRUE});\n+ \n+ // jaxpParser = factory.newDocumentBuilder();\n+ Method newDocBuilder =\n+ factoryClass.getMethod("newDocumentBuilder", null);\n+ Object jaxpParser = newDocBuilder.invoke(factory, null);\n+\n+ // jaxpParser.setErrorHandler(null);\n+ Class parserClass = jaxpParser.getClass();\n+ Method setErrorHandler =\n+ parserClass.getMethod("setErrorHandler",\n+ new Class[]{org.xml.sax.ErrorHandler.class});\n+ setErrorHandler.invoke(jaxpParser,\n+ new Object[]{new BuilderErrorHandler()});\n+\n+ // domDoc = jaxpParser.parse(in);\n+ Method parse = parserClass.getMethod(\n+ "parse", new Class[]{InputStream.class});\n+ org.w3c.dom.Document domDoc = (org.w3c.dom.Document)\n+ parse.invoke(jaxpParser, new Object[]{in});\n+\n+ return domDoc;\n+ } catch (InvocationTargetException e) {\n+ Throwable targetException = e.getTargetException();\n+ if (targetException instanceof IOException) {\n+ throw (IOException) targetException;\n+ } else {\n+ throw new JDOMException(targetException.getMessage(), targetException);\n+ }\n+ } catch (Exception e) {\n+ throw new JDOMException("Reflection failed while parsing a document with JAXP", e); \n+ }\n+\n+ // Allow all exceptions to pass through\n+ }\n+\n+ /**\n+ * This creates an empty <code>Document</code> object based\n+ * on a specific parser implementation.\n+ *\n+ * @return <code>Document</code> - created DOM Document.\n+ * @throws JDOMException when errors occur in parsing.\n+ */\n+ public Document createDocument() \n+ throws JDOMException {\n+\n+ try {\n+ // We need DOM Level 2 and thus JAXP 1.1.\n+ // If JAXP 1.0 is all that\'s available then we error out.\n+ Class.forName("javax.xml.transform.Transformer");\n+\n+ // Try JAXP 1.1 calls to build the document\n+ Class factoryClass =\n+ Class.forName("javax.xml.parsers.DocumentBuilderFactory");\n+\n+ // factory = DocumentBuilderFactory.newInstance();\n+ Method newParserInstance =\n+ factoryClass.getMethod("newInstance", null);\n+ Object factory = newParserInstance.invoke(null, null);\n+\n+ // jaxpParser = factory.newDocumentBuilder();\n+ Method newDocBuilder =\n+ factoryClass.getMethod("newDocumentBuilder", null);\n+ Object jaxpParser = newDocBuilder.invoke(factory, null);\n+\n+ // domDoc = jaxpParser.newDocument();\n+ Class parserClass = jaxpParser.getClass();\n+ Method newDoc = parserClass.getMethod("newDocument", null);\n+ org.w3c.dom.Document domDoc =\n+ (org.w3c.dom.Document) newDoc.invoke(jaxpParser, null);\n+\n+ return domDoc;\n+ } catch (Exception e) {\n+ throw new JDOMException("Reflection failed while creating new JAXP document", e); \n+ }\n+\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/OracleV1DOMAdapter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/OracleV1DOMAdapter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,145 @@
+/*--
+
+ $Id: OracleV1DOMAdapter.java,v 1.20 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.adapters;
+
+import java.io.*;
+import java.lang.reflect.*;
+
+import org.jdom.*;
+import org.w3c.dom.Document;
+import org.xml.sax.*;
+
+/**
+ * An adapter for the Oracle Version 1 DOM parser.
+ *
+ * @version $Revision: 1.20 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ * @author Jason Hunter
+ */
+public class OracleV1DOMAdapter extends AbstractDOMAdapter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: OracleV1DOMAdapter.java,v $ $Revision: 1.20 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This creates a new <code>{@link Document}</code> from an
+ * existing <code>InputStream</code> by letting a DOM
+ * parser handle parsing using the supplied stream.
+ *
+ * @param in <code>InputStream</code> to parse.
+ * @param validate <code>boolean</code> to indicate if validation should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public Document getDocument(InputStream in, boolean validate)
+ throws IOException, JDOMException {
+
+ try {
+ // Load the parser class
+ Class parserClass = Class.forName("oracle.xml.parser.XMLParser");
+ Object parser = parserClass.newInstance();
+
+ // Parse the document
+ Method parse =
+ parserClass.getMethod("parse",
+ new Class[] {org.xml.sax.InputSource.class});
+ parse.invoke(parser, new Object[] {new InputSource(in)});
+
+ // Get the Document object
+ Method getDocument = parserClass.getMethod("getDocument", null);
+ Document doc = (Document)getDocument.invoke(parser, null);
+
+ return doc;
+ } catch (InvocationTargetException e) {
+ Throwable targetException = e.getTargetException();
+ if (targetException instanceof org.xml.sax.SAXParseException) {
+ SAXParseException parseException = (SAXParseException) targetException;
+ throw new JDOMException("Error on line " + parseException.getLineNumber() +
+ " of XML document: " + parseException.getMessage(), parseException);
+ } else if (targetException instanceof IOException) {
+ IOException ioException = (IOException) targetException;
+ throw ioException;
+ } else {
+ throw new JDOMException(targetException.getMessage(), targetException);
+ }
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage(), e);
+ }
+ }
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation.
+ *
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public Document createDocument() throws JDOMException {
+ try {
+ return
+ (Document)Class.forName(
+ "oracle.xml.parser.XMLDocument")
+ .newInstance();
+
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage() + " when creating document", e);
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/OracleV2DOMAdapter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/OracleV2DOMAdapter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,145 @@
+/*--
+
+ $Id: OracleV2DOMAdapter.java,v 1.19 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.adapters;
+
+import java.io.*;
+import java.lang.reflect.*;
+
+import org.jdom.*;
+import org.w3c.dom.Document;
+import org.xml.sax.*;
+
+/**
+ * An adapter for the Oracle Version 2 DOM parser.
+ *
+ * @version $Revision: 1.19 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ * @author Jason Hunter
+ */
+public class OracleV2DOMAdapter extends AbstractDOMAdapter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: OracleV2DOMAdapter.java,v $ $Revision: 1.19 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This creates a new <code>{@link Document}</code> from an
+ * existing <code>InputStream</code> by letting a DOM
+ * parser handle parsing using the supplied stream.
+ *
+ * @param in <code>InputStream</code> to parse.
+ * @param validate <code>boolean</code> to indicate if validation should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public Document getDocument(InputStream in, boolean validate)
+ throws IOException, JDOMException {
+
+ try {
+ // Load the parser class
+ Class parserClass = Class.forName("oracle.xml.parser.v2.DOMParser");
+ Object parser = parserClass.newInstance();
+
+ // Parse the document
+ Method parse =
+ parserClass.getMethod("parse",
+ new Class[] {org.xml.sax.InputSource.class});
+ parse.invoke(parser, new Object[] {new InputSource(in)});
+
+ // Get the Document object
+ Method getDocument = parserClass.getMethod("getDocument", null);
+ Document doc = (Document)getDocument.invoke(parser, null);
+
+ return doc;
+ } catch (InvocationTargetException e) {
+ Throwable targetException = e.getTargetException();
+ if (targetException instanceof org.xml.sax.SAXParseException) {
+ SAXParseException parseException = (SAXParseException)targetException;
+ throw new JDOMException("Error on line " + parseException.getLineNumber() +
+ " of XML document: " + parseException.getMessage(), parseException);
+ } else if (targetException instanceof IOException) {
+ IOException ioException = (IOException) targetException;
+ throw ioException;
+ } else {
+ throw new JDOMException(targetException.getMessage(), targetException);
+ }
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage(), e);
+ }
+ }
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation.
+ *
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public Document createDocument() throws JDOMException {
+ try {
+ return
+ (Document)Class.forName(
+ "oracle.xml.parser.v2.XMLDocument")
+ .newInstance();
+
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage() + " when creating document", e);
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/XML4JDOMAdapter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/XML4JDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,171 @@
+/*--
+
+ $Id: XML4JDOMAdapter.java,v 1.18 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.adapters;
+
+import java.io.*;
+import java.lang.reflect.*;
+
+import org.jdom.*;
+import org.jdom.input.*;
+import org.w3c.dom.Document;
+import org.xml.sax.*;
+
+/**
+ * An adapter for the IBM XML4J DOM parser.
+ *
+ * @version $Revision: 1.18 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ * @author Jason Hunter
+ */
+public class XML4JDOMAdapter extends AbstractDOMAdapter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: XML4JDOMAdapter.java,v $ $Revision: 1.18 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This creates a new <code>{@link Document}</code> from an
+ * existing <code>InputStream</code> by letting a DOM
+ * parser handle parsing using the supplied stream.
+ *
+ * @param in <code>InputStream</code> to parse.
+ * @param validate <code>boolean</code> to indicate if validation should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public Document getDocument(InputStream in, boolean validate)
+ throws IOException, JDOMException {
+
+ try {
+ /*
+ * IBM XML4J actually uses the Xerces parser, so this is
+ * all Xerces specific code.
+ */
+
+ // Load the parser class
+ Class parserClass = Class.forName("org.apache.xerces.parsers.DOMParser");
+ Object parser = parserClass.newInstance();
+
+ // Set validation
+ Method setFeature =
+ parserClass.getMethod("setFeature",
+ new Class[] {java.lang.String.class,
+ boolean.class});
+ setFeature.invoke(parser, new Object[] {"http://xml.org/sax/features/validation",
+ new Boolean(validate)});
+
+ // Set namespaces
+ setFeature.invoke(parser, new Object[] {"http://xml.org/sax/features/namespaces",
+ new Boolean(false)});
+
+ // Set the error handler
+ if (validate) {
+ Method setErrorHandler =
+ parserClass.getMethod("setErrorHandler",
+ new Class[] {ErrorHandler.class});
+ setErrorHandler.invoke(parser, new Object[] {new BuilderErrorHandler()});
+ }
+
+ // Parse the document
+ Method parse =
+ parserClass.getMethod("parse",
+ new Class[] {org.xml.sax.InputSource.class});
+ parse.invoke(parser, new Object[]{new InputSource(in)});
+
+ // Get the Document object
+ Method getDocument = parserClass.getMethod("getDocument", null);
+ Document doc = (Document)getDocument.invoke(parser, null);
+
+ return doc;
+ } catch (InvocationTargetException e) {
+ Throwable targetException = e.getTargetException();
+ if (targetException instanceof org.xml.sax.SAXParseException) {
+ SAXParseException parseException = (SAXParseException)targetException;
+ throw new JDOMException("Error on line " + parseException.getLineNumber() +
+ " of XML document: " + parseException.getMessage(), parseException);
+ } else if (targetException instanceof IOException) {
+ IOException ioException = (IOException) targetException;
+ throw ioException;
+ } else {
+ throw new JDOMException(targetException.getMessage(), targetException);
+ }
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage(), e);
+ }
+ }
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation.
+ *
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public Document createDocument() throws JDOMException {
+ try {
+ return
+ (Document)Class.forName(
+ "org.apache.xerces.dom.DocumentImpl")
+ .newInstance();
+
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage() + " while creating document", e);
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/XercesDOMAdapter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/XercesDOMAdapter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,170 @@
+/*--
+
+ $Id: XercesDOMAdapter.java,v 1.19 2007/11/10 05:28:59 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.adapters;
+
+import java.io.*;
+import java.lang.reflect.*;
+
+import org.jdom.*;
+import org.jdom.input.*;
+import org.w3c.dom.Document;
+import org.xml.sax.*;
+
+/**
+ * An adapter for the Apache Xerces DOM parser.
+ *
+ * @version $Revision: 1.19 $, $Date: 2007/11/10 05:28:59 $
+ * @author Brett McLaughlin
+ * @author Jason Hunter
+ */
+public class XercesDOMAdapter extends AbstractDOMAdapter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: XercesDOMAdapter.java,v $ $Revision: 1.19 $ $Date: 2007/11/10 05:28:59 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This creates a new <code>{@link Document}</code> from an
+ * existing <code>InputStream</code> by letting a DOM
+ * parser handle parsing using the supplied stream.
+ *
+ * @param in <code>InputStream</code> to parse.
+ * @param validate <code>boolean</code> to indicate if validation
+ * should occur.
+ * @return <code>Document</code> - instance ready for use.
+ * @throws IOException when I/O error occurs.
+ * @throws JDOMException when errors occur in parsing.
+ */
+ public Document getDocument(InputStream in, boolean validate)
+ throws IOException, JDOMException {
+
+ try {
+ // Load the parser class
+ Class parserClass =
+ Class.forName("org.apache.xerces.parsers.DOMParser");
+ Object parser = parserClass.newInstance();
+
+ // Set validation
+ Method setFeature = parserClass.getMethod(
+ "setFeature",
+ new Class[] {java.lang.String.class, boolean.class});
+ setFeature.invoke(parser,
+ new Object[] {"http://xml.org/sax/features/validation",
+ new Boolean(validate)});
+
+ // Set namespaces true
+ setFeature.invoke(parser,
+ new Object[] {"http://xml.org/sax/features/namespaces",
+ new Boolean(true)});
+
+ // Set the error handler
+ if (validate) {
+ Method setErrorHandler = parserClass.getMethod(
+ "setErrorHandler",
+ new Class[] {ErrorHandler.class});
+ setErrorHandler.invoke(parser,
+ new Object[] {new BuilderErrorHandler()});
+ }
+
+ // Parse the document
+ Method parse = parserClass.getMethod(
+ "parse",
+ new Class[] {org.xml.sax.InputSource.class});
+ parse.invoke(parser, new Object[]{new InputSource(in)});
+
+ // Get the Document object
+ Method getDocument = parserClass.getMethod("getDocument", null);
+ Document doc = (Document)getDocument.invoke(parser, null);
+
+ return doc;
+ } catch (InvocationTargetException e) {
+ Throwable targetException = e.getTargetException();
+ if (targetException instanceof org.xml.sax.SAXParseException) {
+ SAXParseException parseException =
+ (SAXParseException)targetException;
+ throw new JDOMException("Error on line " +
+ parseException.getLineNumber() +
+ " of XML document: " +
+ parseException.getMessage(), e);
+ } else if (targetException instanceof IOException) {
+ IOException ioException = (IOException) targetException;
+ throw ioException;
+ } else {
+ throw new JDOMException(targetException.getMessage(), e);
+ }
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage(), e);
+ }
+ }
+
+ /**
+ * This creates an empty <code>Document</code> object based
+ * on a specific parser implementation.
+ *
+ * @return <code>Document</code> - created DOM Document.
+ * @throws JDOMException when errors occur.
+ */
+ public Document createDocument() throws JDOMException {
+ try {
+ return (Document)Class.forName(
+ "org.apache.xerces.dom.DocumentImpl").newInstance();
+ } catch (Exception e) {
+ throw new JDOMException(e.getClass().getName() + ": " +
+ e.getMessage() + " when creating document", e);
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/adapters/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/adapters/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,7 @@
+<body>
+
+Classes to interface with various DOM implementations. Not generally
+needed except in truly advanced situations. JAXPDOMAdapter is most commonly
+used.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/AbstractFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/filter/AbstractFilter.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,82 @@
+/*--
+
+ $Id: AbstractFilter.java,v 1.6 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.filter;
+
+/**
+ * Partial implementation of {@link Filter}.
+ *
+ * @author Bradley S. Huffman
+ * @version $Revision: 1.6 $, $Date: 2007/11/10 05:29:00 $
+ */
+public abstract class AbstractFilter implements Filter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: AbstractFilter.java,v $ $Revision: 1.6 $ $Date: 2007/11/10 05:29:00 $";
+
+ public Filter negate() {
+ return new NegateFilter(this);
+ }
+
+ public Filter or(Filter filter) {
+ return new OrFilter(this, filter);
+ }
+
+ public Filter and(Filter filter) {
+ return new AndFilter(this, filter);
+ }
+
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/AndFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/filter/AndFilter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,125 @@
+/*--
+
+ $Id: AndFilter.java,v 1.4 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.filter;
+
+/**
+ * Allow two filters to be chained together with a logical
+ * and operation.
+ *
+ * @author Bradley S. Huffman
+ * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:00 $
+ */
+final class AndFilter extends AbstractFilter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: AndFilter.java,v $ $Revision: 1.4 $ $Date: 2007/11/10 05:29:00 $";
+
+ // Filter for left side of logical and.
+ private Filter left;
+
+ // Filter for right side of logical and.
+ private Filter right;
+
+ /**
+ * Match if only both supplied filters match.
+ *
+ * @param left left side of logical and
+ * @param right right side of logical and
+ * @throws IllegalArgumentException if either supplied filter is null
+ */
+ public AndFilter(Filter left, Filter right) {
+ if ((left == null) || (right == null)) {
+ throw new IllegalArgumentException("null filter not allowed");
+ }
+ this.left = left;
+ this.right = right;
+ }
+
+ public boolean matches(Object obj) {
+ return left.matches(obj) && right.matches(obj);
+ }
+
+ public boolean equals(Object obj) {
+ if (this == obj) {
+ return true;
+ }
+
+ if (obj instanceof AndFilter) {
+ AndFilter filter = (AndFilter) obj;
+ if ((left.equals(filter.left) && right.equals(filter.right)) ||
+ (left.equals(filter.right) && right.equals(filter.left))) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public int hashCode() {
+ return (31 * left.hashCode()) + right.hashCode();
+ }
+
+ public String toString() {
+ return new StringBuffer(64)
+ .append("[AndFilter: ")
+ .append(left.toString())
+ .append(",\n")
+ .append(" ")
+ .append(right.toString())
+ .append("]")
+ .toString();
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/ContentFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/filter/ContentFilter.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,356 @@\n+/*--\n+\n+ $Id: ContentFilter.java,v 1.15 2007/11/10 05:29:00 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.filter;\n+\n+import org.jdom.*;\n+\n+/**\n+ * A general purpose Filter able to represent all legal JDOM objects or a\n+ * specific subset. Filtering is accomplished by way of a filtering mask in\n+ * which each bit represents whether a JDOM object is visible or not.\n+ * For example to view all Text and CDATA nodes in the content of element x.\n+ * <pre><code>\n+ * Filter filter = new ContentFilter(ContentFilter.TEXT |\n+ * ContentFilter.CDATA);\n+ * List content = x.getContent(filter);\n+ * </code></pre>\n+ * \n+ * For those who don\'t like bit-masking, set methods are provided as an\n+ * alternative. For example to allow everything except Comment nodes.\n+ * <pre><code>\n+ * Filter filter = new ContentFilter();\n+ * filter.setCommentVisible(false);\n+ * List content = x.getContent(filter);\n+ * </code></pre>\n+ * \n+ * The default is to allow all valid JDOM objects.\n+ *\n+ * @version $Revision: 1.15 $, $Date: 2007/11/10 05:29:00 $\n+ * @author Bradley S. Huffman\n+ */\n+public class ContentFilter extends AbstractFilter {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: ContentFilter.java,v $ $Revision: 1.15 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $";\n+\n+ /** Mask for JDOM {@link Element} objects */\n+ public static final int ELEMENT = 1;\n+\n+ /** M'..b'ask |= CDATA;\n+ }\n+ else {\n+ filterMask &= ~CDATA;\n+ }\n+ }\n+\n+ /**\n+ * Set visiblity of <code>Text</code> objects.\n+ *\n+ * @param visible whether Text nodes are visible, <code>true</code>\n+ * if yes, <code>false</code> if not\n+ */\n+ public void setTextVisible(boolean visible) {\n+ if (visible) {\n+ filterMask |= TEXT;\n+ }\n+ else {\n+ filterMask &= ~TEXT;\n+ }\n+ }\n+\n+ /**\n+ * Set visiblity of <code>Comment</code> objects.\n+ *\n+ * @param visible whether Comments are visible, <code>true</code>\n+ * if yes, <code>false</code> if not\n+ */\n+ public void setCommentVisible(boolean visible) {\n+ if (visible) {\n+ filterMask |= COMMENT;\n+ }\n+ else {\n+ filterMask &= ~COMMENT;\n+ }\n+ }\n+\n+ /**\n+ * Set visiblity of <code>ProcessingInstruction</code> objects.\n+ *\n+ * @param visible whether ProcessingInstructions are visible,\n+ * <code>true</code> if yes, <code>false</code> if not\n+ */\n+ public void setPIVisible(boolean visible) {\n+ if (visible) {\n+ filterMask |= PI;\n+ }\n+ else {\n+ filterMask &= ~PI;\n+ }\n+ }\n+\n+ /**\n+ * Set visiblity of <code>EntityRef</code> objects.\n+ *\n+ * @param visible whether EntityRefs are visible, <code>true</code>\n+ * if yes, <code>false</code> if not\n+ */\n+ public void setEntityRefVisible(boolean visible) {\n+ if (visible) {\n+ filterMask |= ENTITYREF;\n+ }\n+ else {\n+ filterMask &= ~ENTITYREF;\n+ }\n+ }\n+\n+ /**\n+ * Set visiblity of <code>DocType</code> objects.\n+ *\n+ * @param visible whether the DocType is visible, <code>true</code>\n+ * if yes, <code>false</code> if not\n+ */\n+ public void setDocTypeVisible(boolean visible) {\n+ if (visible) {\n+ filterMask |= DOCTYPE;\n+ }\n+ else {\n+ filterMask &= ~DOCTYPE;\n+ }\n+ }\n+\n+ /**\n+ * Check to see if the object matches according to the filter mask.\n+ *\n+ * @param obj The object to verify.\n+ * @return <code>true</code> if the objected matched a predfined\n+ * set of rules.\n+ */\n+ public boolean matches(Object obj) {\n+ if (obj instanceof Element) {\n+ return (filterMask & ELEMENT) != 0;\n+ }\n+ else if (obj instanceof CDATA) { // must come before Text check\n+ return (filterMask & CDATA) != 0;\n+ }\n+ else if (obj instanceof Text) {\n+ return (filterMask & TEXT) != 0;\n+ }\n+ else if (obj instanceof Comment) {\n+ return (filterMask & COMMENT) != 0;\n+ }\n+ else if (obj instanceof ProcessingInstruction) {\n+ return (filterMask & PI) != 0;\n+ }\n+ else if (obj instanceof EntityRef) {\n+ return (filterMask & ENTITYREF) != 0;\n+ }\n+ else if (obj instanceof Document) {\n+ return (filterMask & DOCUMENT) != 0;\n+ }\n+ else if (obj instanceof DocType) {\n+ return (filterMask & DOCTYPE) != 0;\n+ }\n+\n+ return false;\n+ }\n+\n+ /**\n+ * Returns whether the two filters are equivalent (i.e. the\n+ * matching mask values are identical).\n+ *\n+ * @param obj the object to compare against\n+ * @return whether the two filters are equal\n+ */\n+ public boolean equals(Object obj) {\n+ // Generated by IntelliJ\n+ if (this == obj) return true;\n+ if (!(obj instanceof ContentFilter)) return false;\n+\n+ final ContentFilter filter = (ContentFilter) obj;\n+\n+ if (filterMask != filter.filterMask) return false;\n+\n+ return true;\n+ }\n+\n+ public int hashCode() {\n+ // Generated by IntelliJ\n+ return filterMask;\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/ElementFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/filter/ElementFilter.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,189 @@
+/*--
+
+ $Id: ElementFilter.java,v 1.20 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.filter;
+
+import java.io.*;
+import org.jdom.*;
+
+/**
+ * A Filter that only matches {@link org.jdom.Element} objects.
+ *
+ * @version $Revision: 1.20 $, $Date: 2007/11/10 05:29:00 $
+ * @author Jools Enticknap
+ * @author Bradley S. Huffman
+ */
+public class ElementFilter extends AbstractFilter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: ElementFilter.java,v $ $Revision: 1.20 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $";
+
+ /** The element name */
+ private String name;
+
+ /** The element namespace */
+ private transient Namespace namespace;
+
+ /**
+ * Select only the Elements.
+ */
+ public ElementFilter() {}
+
+ /**
+ * Select only the Elements with the supplied name in any Namespace.
+ *
+ * @param name The name of the Element.
+ */
+ public ElementFilter(String name) {
+ this.name = name;
+ }
+
+ /**
+ * Select only the Elements with the supplied Namespace.
+ *
+ * @param namespace The namespace the Element lives in.
+ */
+ public ElementFilter(Namespace namespace) {
+ this.namespace = namespace;
+ }
+
+ /**
+ * Select only the Elements with the supplied name and Namespace.
+ *
+ * @param name The name of the Element.
+ * @param namespace The namespace the Element lives in.
+ */
+ public ElementFilter(String name, Namespace namespace) {
+ this.name = name;
+ this.namespace = namespace;
+ }
+
+ /**
+ * Check to see if the object matches a predefined set of rules.
+ *
+ * @param obj The object to verify.
+ * @return <code>true</code> if the objected matched a predfined
+ * set of rules.
+ */
+ public boolean matches(Object obj) {
+ if (obj instanceof Element) {
+ Element el = (Element) obj;
+ return
+ (this.name == null || this.name.equals(el.getName())) &&
+ (this.namespace == null || this.namespace.equals(el.getNamespace()));
+ }
+ return false;
+ }
+
+ /**
+ * Returns whether the two filters are equivalent (i.e. the
+ * matching names and namespace are equivalent).
+ *
+ * @param obj the object to compare against
+ * @return whether the two filters are equal
+ */
+ public boolean equals(Object obj) {
+ // Generated by IntelliJ
+ if (this == obj) return true;
+ if (!(obj instanceof ElementFilter)) return false;
+
+ final ElementFilter filter = (ElementFilter) obj;
+
+ if (name != null ? !name.equals(filter.name) : filter.name != null) return false;
+ if (namespace != null ? !namespace.equals(filter.namespace) : filter.namespace != null) return false;
+
+ return true;
+ }
+
+ public int hashCode() {
+ // Generated by IntelliJ
+ int result;
+ result = (name != null ? name.hashCode() : 0);
+ result = 29 * result + (namespace != null ? namespace.hashCode() : 0);
+ return result;
+ }
+
+ // Support a custom Namespace serialization so no two namespace
+ // object instances may exist for the same prefix/uri pair
+ private void writeObject(ObjectOutputStream out) throws IOException {
+
+ out.defaultWriteObject();
+
+ // We use writeObject() and not writeUTF() to minimize space
+ // This allows for writing pointers to already written strings
+ if (namespace != null) {
+ out.writeObject(namespace.getPrefix());
+ out.writeObject(namespace.getURI());
+ }
+ else {
+ out.writeObject(null);
+ out.writeObject(null);
+ }
+ }
+
+ private void readObject(ObjectInputStream in)
+ throws IOException, ClassNotFoundException {
+
+ in.defaultReadObject();
+
+ Object prefix = in.readObject();
+ Object uri = in.readObject();
+
+ if (prefix != null) { // else leave namespace null here
+ namespace = Namespace.getNamespace((String) prefix, (String) uri);
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/Filter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/filter/Filter.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,76 @@
+/*--
+
+ $Id: Filter.java,v 1.10 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.filter;
+
+
+/**
+ * A generalized filter to restrict visibility or mutability on a list.
+ *
+ * @version $Revision: 1.10 $, $Date: 2007/11/10 05:29:00 $
+ * @author Jools Enticknap
+ * @author Bradley S. Huffman
+ */
+public interface Filter extends java.io.Serializable {
+ /**
+ * Check to see if the object matches a predefined set of rules.
+ *
+ * @param obj The object to verify.
+ * @return <code>true</code> if the object matches a predfined
+ * set of rules.
+ */
+ public boolean matches(Object obj);
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/NegateFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/filter/NegateFilter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,113 @@
+/*--
+
+ $Id: NegateFilter.java,v 1.4 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.filter;
+
+/**
+ * Filter that is the logical negation operation of another filter.
+ *
+ *
+ * @author Bradley S. Huffman
+ * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:00 $
+ */
+final class NegateFilter extends AbstractFilter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: NegateFilter.java,v $ $Revision: 1.4 $ $Date: 2007/11/10 05:29:00 $";
+
+ // Underlying filter.
+ private Filter filter;
+
+ /**
+ * Match if the supplied filter does not match.
+ *
+ * @param filter filter to use.
+ */
+ public NegateFilter(Filter filter) {
+ this.filter = filter;
+ }
+
+ public boolean matches(Object obj) {
+ return !filter.matches(obj);
+ }
+
+ public Filter negate() {
+ return filter;
+ }
+
+ public boolean equals(Object obj) {
+ if (this == obj) {
+ return true;
+ }
+
+ if (obj instanceof NegateFilter) {
+ return filter.equals(((NegateFilter) obj).filter);
+ }
+ return false;
+ }
+
+ public int hashCode() {
+ return ~filter.hashCode();
+ }
+
+ public String toString() {
+ return new StringBuffer(64)
+ .append("[NegateFilter: ")
+ .append(filter.toString())
+ .append("]")
+ .toString();
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/OrFilter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/filter/OrFilter.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,125 @@
+/*--
+
+ $Id: OrFilter.java,v 1.5 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.filter;
+
+/**
+ * Allow two filters to be chained together with a logical
+ * or operation.
+ *
+ * @author Bradley S. Huffman
+ * @version $Revision: 1.5 $, $Date: 2007/11/10 05:29:00 $
+ */
+final class OrFilter extends AbstractFilter {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: OrFilter.java,v $ $Revision: 1.5 $ $Date: 2007/11/10 05:29:00 $";
+
+ /** Filter for left side of logical or */
+ private Filter left;
+
+ /** Filter for right side of logical or */
+ private Filter right;
+
+ /**
+ * Match if either of the supplied filters.
+ *
+ * @param left left side of logical or
+ * @param right right side of logical or
+ * @throws IllegalArgumentException if either supplied filter is null
+ */
+ public OrFilter(Filter left, Filter right) {
+ if ((left == null) || (right == null)) {
+ throw new IllegalArgumentException("null filter not allowed");
+ }
+ this.left = left;
+ this.right = right;
+ }
+
+ public boolean matches(Object obj) {
+ return left.matches(obj) || right.matches(obj);
+ }
+
+ public boolean equals(Object obj) {
+ if (this == obj) {
+ return true;
+ }
+
+ if (obj instanceof OrFilter) {
+ OrFilter filter = (OrFilter) obj;
+ if ((left.equals(filter.left) && right.equals(filter.right)) ||
+ (left.equals(filter.right) && right.equals(filter.left))) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public int hashCode() {
+ return (31 * left.hashCode()) + right.hashCode();
+ }
+
+ public String toString() {
+ return new StringBuffer(64)
+ .append("[OrFilter: ")
+ .append(left.toString())
+ .append(",\n")
+ .append(" ")
+ .append(right.toString())
+ .append("]")
+ .toString();
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/filter/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/filter/package.html Mon Nov 21 08:12:19 2011 -0500

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/BuilderErrorHandler.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/input/BuilderErrorHandler.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,111 @@
+/*--
+
+ $Id: BuilderErrorHandler.java,v 1.13 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.input;
+
+import org.xml.sax.*;
+
+/**
+ * The standard JDOM error handler implementation.
+ *
+ * @author Jason Hunter
+ * @version $Revision: 1.13 $, $Date: 2007/11/10 05:29:00 $
+ */
+
+public class BuilderErrorHandler implements ErrorHandler {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: BuilderErrorHandler.java,v $ $Revision: 1.13 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * This method is called when a warning has occurred; this indicates
+ * that while no XML rules were broken, something appears to be
+ * incorrect or missing.
+ * The implementation of this method here is a "no op".
+ *
+ * @param exception <code>SAXParseException</code> that occurred.
+ * @throws SAXException when things go wrong
+ */
+ public void warning(SAXParseException exception) throws SAXException {
+ // nothing
+ }
+
+ /**
+ * This method is called in response to an error that has occurred;
+ * this indicates that a rule was broken, typically in validation, but
+ * that parsing could reasonably continue.
+ * The implementation of this method here is to rethrow the exception.
+ *
+ * @param exception <code>SAXParseException</code> that occurred.
+ * @throws SAXException when things go wrong
+ */
+ public void error(SAXParseException exception) throws SAXException {
+ throw exception;
+ }
+
+ /**
+ * This method is called in response to a fatal error; this indicates that
+ * a rule has been broken that makes continued parsing either impossible
+ * or an almost certain waste of time.
+ * The implementation of this method here is to rethrow the exception.
+ *
+ * @param exception <code>SAXParseException</code> that occurred.
+ * @throws SAXException when things go wrong
+ */
+ public void fatalError(SAXParseException exception) throws SAXException {
+ throw exception;
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/DOMBuilder.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/input/DOMBuilder.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,341 @@\n+/*--\n+\n+ $Id: DOMBuilder.java,v 1.60 2007/11/10 05:29:00 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.input;\n+\n+import org.jdom.*;\n+import org.jdom.Document;\n+import org.jdom.Element;\n+import org.w3c.dom.*;\n+\n+/**\n+ * Builds a JDOM {@link org.jdom.Document org.jdom.Document} from a pre-existing\n+ * DOM {@link org.w3c.dom.Document org.w3c.dom.Document}. Also handy for testing\n+ * builds from files to sanity check {@link SAXBuilder}.\n+ *\n+ * @version $Revision: 1.60 $, $Date: 2007/11/10 05:29:00 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Philip Nelson\n+ * @author Kevin Regan\n+ * @author Yusuf Goolamabbas\n+ * @author Dan Schaffer\n+ * @author Bradley S. Huffman\n+ */\n+public class DOMBuilder {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: DOMBuilder.java,v $ $Revision: 1.60 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $";\n+\n+ /** Adapter class to use */\n+ private String adapterClass;\n+\n+ /** The factory for creating new JDOM objects */\n+ private JDOMFactory factory = new DefaultJDOMFactory();\n+\n+ /**\n+ * This creates a new DOMBuilder which will attempt to first locate\n+ * a parser via JAXP, then will try to use a set of default parsers.\n+ * The underlying parser will not validate.\n+ */\n+ public DOMBuilder() {\n+ }\n+\n+ /**\n+ * This creates a new DOMBuilder using the specified DOMAdapter\n+ * implementation as a way to choose the underly'..b'r att = (Attr) attributeList.item(i);\n+\n+ String attname = att.getName();\n+\n+ if ( !attname.startsWith("xmlns")) {\n+ String attPrefix = "";\n+ String attLocalName = attname;\n+ colon = attname.indexOf(\':\');\n+ if (colon >= 0) {\n+ attPrefix = attname.substring(0, colon);\n+ attLocalName = attname.substring(colon + 1);\n+ }\n+\n+ String attvalue = att.getValue();\n+\n+ // Get attribute\'s namespace\n+ Namespace attns = null;\n+ if ("".equals(attPrefix)) {\n+ attns = Namespace.NO_NAMESPACE;\n+ }\n+ else {\n+ attns = element.getNamespace(attPrefix);\n+ }\n+\n+ Attribute attribute =\n+ factory.attribute(attLocalName, attvalue, attns);\n+ factory.setAttribute(element, attribute);\n+ }\n+ }\n+\n+ // Recurse on child nodes\n+ // The list should never be null nor should it ever contain\n+ // null nodes, but some DOM impls are broken\n+ NodeList children = node.getChildNodes();\n+ if (children != null) {\n+ int size = children.getLength();\n+ for (int i = 0; i < size; i++) {\n+ Node item = children.item(i);\n+ if (item != null) {\n+ buildTree(item, doc, element, false);\n+ }\n+ }\n+ }\n+ break;\n+\n+ case Node.TEXT_NODE:\n+ String data = node.getNodeValue();\n+ factory.addContent(current, factory.text(data));\n+ break;\n+\n+ case Node.CDATA_SECTION_NODE:\n+ String cdata = node.getNodeValue();\n+ factory.addContent(current, factory.cdata(cdata));\n+ break;\n+\n+\n+ case Node.PROCESSING_INSTRUCTION_NODE:\n+ if (atRoot) {\n+ factory.addContent(doc,\n+ factory.processingInstruction(node.getNodeName(),\n+ node.getNodeValue()));\n+ } else {\n+ factory.addContent(current,\n+ factory.processingInstruction(node.getNodeName(),\n+ node.getNodeValue()));\n+ }\n+ break;\n+\n+ case Node.COMMENT_NODE:\n+ if (atRoot) {\n+ factory.addContent(doc, factory.comment(node.getNodeValue()));\n+ } else {\n+ factory.addContent(current, factory.comment(node.getNodeValue()));\n+ }\n+ break;\n+\n+ case Node.ENTITY_REFERENCE_NODE:\n+ EntityRef entity = factory.entityRef(node.getNodeName());\n+ factory.addContent(current, entity);\n+ break;\n+\n+ case Node.ENTITY_NODE:\n+ // ??\n+ break;\n+\n+ case Node.DOCUMENT_TYPE_NODE:\n+ DocumentType domDocType = (DocumentType)node;\n+ String publicID = domDocType.getPublicId();\n+ String systemID = domDocType.getSystemId();\n+ String internalDTD = domDocType.getInternalSubset();\n+\n+ DocType docType = factory.docType(domDocType.getName());\n+ docType.setPublicID(publicID);\n+ docType.setSystemID(systemID);\n+ docType.setInternalSubset(internalDTD);\n+\n+ factory.addContent(doc, docType);\n+ break;\n+ }\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/JAXPParserFactory.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/input/JAXPParserFactory.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,179 @@
+/*--
+
+ $Id: JAXPParserFactory.java,v 1.6 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.input;
+
+import java.util.*;
+
+import javax.xml.parsers.*;
+
+import org.jdom.*;
+import org.xml.sax.*;
+
+/**
+ * A non-public utility class to allocate JAXP SAX parsers.
+ *
+ * @version $Revision: 1.6 $, $Date: 2007/11/10 05:29:00 $
+ * @author Laurent Bihanic
+ */
+class JAXPParserFactory { // package protected
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: JAXPParserFactory.java,v $ $Revision: 1.6 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $";
+
+ /** JAXP 1.2 schema language property id. */
+ private static final String JAXP_SCHEMA_LANGUAGE_PROPERTY =
+ "http://java.sun.com/xml/jaxp/properties/schemaLanguage";
+
+ /** JAXP 1.2 schema location property id. */
+ private static final String JAXP_SCHEMA_LOCATION_PROPERTY =
+ "http://java.sun.com/xml/jaxp/properties/schemaSource";
+
+ /**
+ * Private constructor to forbid allocating instances of this utility
+ * class.
+ */
+ private JAXPParserFactory() {
+ // Never called.
+ }
+
+ /* Implementor's note regarding createParser() design: The features and
+ properties are normally set in SAXBuilder, but we take them in
+ createParser() as well because some features or properties may need to be
+ applied during the JAXP parser construction. Today, for example, properties
+ is used as it's the only way to configure schema validation: JAXP defines
+ schema validation properties but SAX does not. This reflects in the Apache
+ Xerces implementation where the SAXParser implementation supports the JAXP
+ properties but the XMLReader does not. Hence, configuring schema validation
+ must be done on the SAXParser object which is only visible in
+ JAXParserFactory. Features is also passed in case some future JAXP release
+ defines JAXP-specific features.
+ */
+
+ /**
+ * Creates a SAX parser allocated through the configured JAXP SAX
+ * parser factory.
+ *
+ * @param validating whether a validating parser is requested.
+ * @param features the user-defined SAX features.
+ * @param properties the user-defined SAX properties.
+ *
+ * @return a configured XMLReader.
+ *
+ * @throws JDOMException if any error occurred when allocating or
+ * configuring the JAXP SAX parser.
+ */
+ public static XMLReader createParser(boolean validating,
+ Map features, Map properties) throws JDOMException {
+ try {
+ SAXParser parser = null;
+
+ // Allocate and configure JAXP SAX parser factory.
+ SAXParserFactory factory = SAXParserFactory.newInstance();
+ factory.setValidating(validating);
+ factory.setNamespaceAware(true);
+
+ try {
+ // Allocate parser.
+ parser = factory.newSAXParser();
+ }
+ catch (ParserConfigurationException e) {
+ throw new JDOMException("Could not allocate JAXP SAX Parser", e);
+ }
+
+ // Set user-defined JAXP properties (if any)
+ setProperty(parser, properties, JAXP_SCHEMA_LANGUAGE_PROPERTY);
+ setProperty(parser, properties, JAXP_SCHEMA_LOCATION_PROPERTY);
+
+ // Return configured SAX XMLReader.
+ return parser.getXMLReader();
+ }
+ catch (SAXException e) {
+ throw new JDOMException("Could not allocate JAXP SAX Parser", e);
+ }
+ }
+
+ /**
+ * Sets a property on a JAXP SAX parser object if and only if it
+ * is declared in the user-defined properties.
+ *
+ * @param parser the JAXP SAX parser to configure.
+ * @param properties the user-defined SAX properties.
+ * @param name the name of the property to set.
+ *
+ * @throws JDOMException if any error occurred while configuring
+ * the property.
+ */
+ private static void setProperty(SAXParser parser,
+ Map properties, String name) throws JDOMException {
+ try {
+ if (properties.containsKey(name)) {
+ parser.setProperty(name, properties.get(name));
+ }
+ }
+ catch (SAXNotSupportedException e) {
+ throw new JDOMException(
+ name + " property not supported for JAXP parser " +
+ parser.getClass().getName());
+ }
+ catch (SAXNotRecognizedException e) {
+ throw new JDOMException(
+ name + " property not recognized for JAXP parser " +
+ parser.getClass().getName());
+ }
+ }
+}
+

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/JDOMParseException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/input/JDOMParseException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,175 @@
+/*--
+
+ $Id: JDOMParseException.java,v 1.8 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.input;
+
+import org.jdom.*;
+import org.xml.sax.*;
+
+/**
+ * Thrown during parse errors, with information about where the parse error
+ * occurred as well as access to the partially built document.
+ *
+ * @version $Revision: 1.8 $, $Date: 2007/11/10 05:29:00 $
+ * @author Laurent Bihanic
+ */
+public class JDOMParseException extends JDOMException {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: JDOMParseException.java,v $ $Revision: 1.8 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $";
+
+ /**
+ * The portion of the document that was successfully built before
+ * the parse error occurred.
+ */
+ private final Document partialDocument;
+
+ /**
+ * This will create a parse <code>Exception</code> with the given
+ * message and wrap the <code>Exception</code> that cause a document
+ * parse to fail.
+ *
+ * @param message <code>String</code> message indicating
+ * the problem that occurred.
+ * @param cause <code>Throwable</code> that caused this
+ * to be thrown.
+ */
+ public JDOMParseException(String message, Throwable cause) {
+ this(message, cause, null);
+ }
+
+ /**
+ * This will create a parse <code>Exception</code> with the given
+ * message and the partial document and wrap the
+ * <code>Exception</code> that cause a document parse to fail.
+ *
+ * @param message <code>String</code> message indicating
+ * the problem that occurred.
+ * @param cause <code>Throwable</code> that caused this
+ * to be thrown.
+ * @param partialDocument <code>Document</code> the portion of
+ * the input XML document that was
+ * successfully built.
+ */
+ public JDOMParseException(String message, Throwable cause,
+ Document partialDocument) {
+ super(message, cause);
+ this.partialDocument = partialDocument;
+ }
+
+ /**
+ * Returns the partial document that was successfully built before
+ * the error occurred.
+ *
+ * @return the partial document or null if none.
+ */
+ public Document getPartialDocument() {
+ return partialDocument;
+ }
+
+ /**
+ * Returns the public identifier of the entity where the
+ * parse error occurred.
+ *
+ * @return a string containing the public identifier, or
+ * <code>null</code> if the information is not available.
+ */
+ public String getPublicId() {
+ return (getCause() instanceof SAXParseException)?
+ ((SAXParseException)getCause()).getPublicId(): null;
+ }
+
+ /**
+ * Returns the system identifier of the entity where the
+ * parse error occurred.
+ *
+ * @return a string containing the system identifier, or
+ * <code>null</code> if the information is not available.
+ */
+ public String getSystemId() {
+ return (getCause() instanceof SAXParseException)?
+ ((SAXParseException)getCause()).getSystemId(): null;
+ }
+
+ /**
+ * Returns the line number of the end of the text where the
+ * parse error occurred.
+ * 
+ * The first line in the document is line 1.
+ *
+ * @return an integer representing the line number, or -1
+ * if the information is not available.
+ */
+ public int getLineNumber() {
+ return (getCause() instanceof SAXParseException)?
+ ((SAXParseException)getCause()).getLineNumber(): -1;
+ }
+
+ /**
+ * Returns the column number of the end of the text where the
+ * parse error occurred.
+ * 
+ * The first column in a line is position 1.
+ *
+ * @return an integer representing the column number, or -1
+ * if the information is not available.
+ */
+ public int getColumnNumber() {
+ return (getCause() instanceof SAXParseException)?
+ ((SAXParseException)getCause()).getColumnNumber(): -1;
+ }
+}
+

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/SAXBuilder.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/input/SAXBuilder.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,1105 @@\n+/*--\n+\n+ $Id: SAXBuilder.java,v 1.93 2009/07/23 06:26:26 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.input;\n+\n+import java.io.*;\n+import java.lang.reflect.*;\n+import java.net.*;\n+import java.util.*;\n+\n+import org.jdom.*;\n+\n+import org.xml.sax.*;\n+import org.xml.sax.helpers.XMLReaderFactory;\n+\n+/**\n+ * Builds a JDOM document from files, streams, readers, URLs, or a SAX {@link\n+ * org.xml.sax.InputSource} instance using a SAX parser. The builder uses a\n+ * third-party SAX parser (chosen by JAXP by default, or you can choose\n+ * manually) to handle the parsing duties and simply listens to the SAX events\n+ * to construct a document. Details which SAX does not provide, such as\n+ * whitespace outside the root element, are not represented in the JDOM\n+ * document. Information about SAX can be found at <a\n+ * href="http://www.saxproject.org">http://www.saxproject.org</a>.\n+ * \n+ * Known issues: Relative paths for a {@link DocType} or {@link EntityRef} may\n+ * be converted by the SAX parser into absolute paths.\n+ *\n+ * @version $Revision: 1.93 $, $Date: 2009/07/23 06:26:26 $\n+ * @author Jason Hunter\n+ * @author Brett McLaughlin\n+ * @author Dan Schaffer\n+ * @author Philip Nelson\n+ * @author Alex Rosen\n+ */\n+public class SAXBuilder {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: SAXBuilder.java,v $ $Revision: 1.93 $ $Date: 2009/07/23 06:26:26 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * Default parser class to use'..b'1.2 method, reimplemented\n+// * here to work with JDK 1.1.\n+// *\n+// * @see java.io.File\n+// *\n+// * @param f the file to convert\n+// * @return the file path converted to a file: URL\n+// */\n+// protected URL fileToURL(File f) throws MalformedURLException {\n+// String path = f.getAbsolutePath();\n+// if (File.separatorChar != \'/\') {\n+// path = path.replace(File.separatorChar, \'/\');\n+// }\n+// if (!path.startsWith("/")) {\n+// path = "/" + path;\n+// }\n+// if (!path.endsWith("/") && f.isDirectory()) {\n+// path = path + "/";\n+// }\n+// return new URL("file", "", path);\n+// }\n+\n+ /** Custom File.toUrl() implementation to handle special chars in file names\n+ *\n+ * @param file file object whose path will be converted\n+ * @return URL form of the file, with special characters handled\n+ * @throws MalformedURLException if there\'s a problem constructing a URL\n+ */\n+ private static URL fileToURL(File file) throws MalformedURLException {\n+ StringBuffer buffer = new StringBuffer();\n+ String path = file.getAbsolutePath();\n+\n+ // Convert non-URL style file separators\n+ if (File.separatorChar != \'/\') {\n+ path = path.replace(File.separatorChar, \'/\');\n+ }\n+\n+ // Make sure it starts at root\n+ if (!path.startsWith("/")) {\n+ buffer.append(\'/\');\n+ }\n+\n+ // Copy, converting URL special characters as we go\n+ int len = path.length();\n+ for (int i = 0; i < len; i++) {\n+ char c = path.charAt(i);\n+ if (c == \' \')\n+ buffer.append("%20");\n+ else if (c == \'#\')\n+ buffer.append("%23");\n+ else if (c == \'%\')\n+ buffer.append("%25");\n+ else if (c == \'&\')\n+ buffer.append("%26");\n+ else if (c == \';\')\n+ buffer.append("%3B");\n+ else if (c == \'<\')\n+ buffer.append("%3C");\n+ else if (c == \'=\')\n+ buffer.append("%3D");\n+ else if (c == \'>\')\n+ buffer.append("%3E");\n+ else if (c == \'?\')\n+ buffer.append("%3F");\n+ else if (c == \'~\')\n+ buffer.append("%7E");\n+ else\n+ buffer.append(c);\n+ }\n+\n+ // Make sure directories end with slash\n+ if (!path.endsWith("/") && file.isDirectory()) {\n+ buffer.append(\'/\');\n+ }\n+\n+ // Return URL\n+ return new URL("file", "", buffer.toString());\n+ }\n+\n+ /**\n+ * Returns whether or not entities are being expanded into normal text\n+ * content.\n+ *\n+ * @return whether entities are being expanded\n+ */\n+ public boolean getExpandEntities() {\n+ return expand;\n+ }\n+\n+ /**\n+ * \n+ * This sets whether or not to expand entities for the builder.\n+ * A true means to expand entities as normal content. A false means to\n+ * leave entities unexpanded as <code>EntityRef</code> objects. The\n+ * default is true.\n+ * \n+ * \n+ * When this setting is false, the internal DTD subset is retained; when\n+ * this setting is true, the internal DTD subset is not retained.\n+ * \n+ * \n+ * Note that Xerces (at least up to 1.4.4) has a bug where entities\n+ * in attribute values will be misreported if this flag is turned off,\n+ * resulting in entities to appear within element content. When turning\n+ * entity expansion off either avoid entities in attribute values, or\n+ * use another parser like Crimson.\n+ * http://nagoya.apache.org/bugzilla/show_bug.cgi?id=6111\n+ * \n+ *\n+ * @param expand <code>boolean</code> indicating whether entity expansion\n+ * should occur.\n+ */\n+ public void setExpandEntities(boolean expand) {\n+ this.expand = expand;\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/SAXHandler.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/input/SAXHandler.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,1018 @@\n+/*--\n+\n+ $Id: SAXHandler.java,v 1.73 2007/11/10 05:29:00 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.input;\n+\n+import java.util.*;\n+\n+import org.jdom.*;\n+import org.xml.sax.*;\n+import org.xml.sax.ext.*;\n+import org.xml.sax.helpers.*;\n+\n+/**\n+ * A support class for {@link SAXBuilder}.\n+ *\n+ * @version $Revision: 1.73 $, $Date: 2007/11/10 05:29:00 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Philip Nelson\n+ * @author Bradley S. Huffman\n+ * @author phil@triloggroup.com\n+ */\n+public class SAXHandler extends DefaultHandler implements LexicalHandler,\n+ DeclHandler,\n+ DTDHandler {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: SAXHandler.java,v $ $Revision: 1.73 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $";\n+\n+ /** Hash table to map SAX attribute type names to JDOM attribute types. */\n+ private static final Map attrNameToTypeMap = new HashMap(13);\n+\n+ /** <code>Document</code> object being built */\n+ private Document document;\n+\n+ /** <code>Element</code> object being built */\n+ private Element currentElement;\n+\n+ /** Indicator of where in the document we are */\n+ private boolean atRoot;\n+\n+ /** Indicator of whether we are in the DocType. Note that the DTD consists\n+ * of both the internal subset (inside the <!DOCTYPE> tag) and the\n+ *'..b' Handler for unparsed entity declarations in the DTD\n+ *\n+ * @param name <code>String</code> of the unparsed entity decl\n+ * @param publicID <code>String</code> of the unparsed entity decl\n+ * @param systemID <code>String</code> of the unparsed entity decl\n+ * @param notationName <code>String</code> of the unparsed entity decl\n+ */\n+ public void unparsedEntityDecl(String name, String publicID,\n+ String systemID, String notationName)\n+ throws SAXException {\n+\n+ if (!inInternalSubset) return;\n+\n+ internalSubset.append(" <!ENTITY ")\n+ .append(name);\n+ appendExternalId(publicID, systemID);\n+ internalSubset.append(" NDATA ")\n+ .append(notationName);\n+ internalSubset.append(">\\n");\n+ }\n+\n+ /**\n+ * Appends an external ID to the internal subset buffer. Either publicID\n+ * or systemID may be null, but not both.\n+ *\n+ * @param publicID the public ID\n+ * @param systemID the system ID\n+ */\n+ private void appendExternalId(String publicID, String systemID) {\n+ if (publicID != null) {\n+ internalSubset.append(" PUBLIC \\"")\n+ .append(publicID)\n+ .append(\'\\"\');\n+ }\n+ if (systemID != null) {\n+ if (publicID == null) {\n+ internalSubset.append(" SYSTEM ");\n+ }\n+ else {\n+ internalSubset.append(\' \');\n+ }\n+ internalSubset.append(\'\\"\')\n+ .append(systemID)\n+ .append(\'\\"\');\n+ }\n+ }\n+\n+ /**\n+ * Returns the being-parsed element.\n+ *\n+ * @return <code>Element</code> - element being built.\n+ * @throws SAXException\n+ */\n+ public Element getCurrentElement() throws SAXException {\n+ if (currentElement == null) {\n+ throw new SAXException(\n+ "Ill-formed XML document (multiple root elements detected)");\n+ }\n+ return currentElement;\n+ }\n+\n+ /**\n+ * Returns the the JDOM Attribute type value from the SAX 2.0\n+ * attribute type string provided by the parser.\n+ *\n+ * @param typeName <code>String</code> the SAX 2.0 attribute\n+ * type string.\n+ *\n+ * @return <code>int</code> the JDOM attribute type.\n+ *\n+ * @see Attribute#setAttributeType\n+ * @see Attributes#getType\n+ */\n+ private static int getAttributeType(String typeName) {\n+ Integer type = (Integer)(attrNameToTypeMap.get(typeName));\n+ if (type == null) {\n+ if (typeName != null && typeName.length() > 0 &&\n+ typeName.charAt(0) == \'(\') {\n+ // Xerces 1.4.X reports attributes of enumerated type with\n+ // a type string equals to the enumeration definition, i.e.\n+ // starting with a parenthesis.\n+ return Attribute.ENUMERATED_TYPE;\n+ }\n+ else {\n+ return Attribute.UNDECLARED_TYPE;\n+ }\n+ } else {\n+ return type.intValue();\n+ }\n+ }\n+\n+ /**\n+ * Receives an object for locating the origin of SAX document\n+ * events. This method is invoked by the SAX parser.\n+ * \n+ * {@link org.jdom.JDOMFactory} implementations can use the\n+ * {@link #getDocumentLocator} method to get access to the\n+ * {@link Locator} during parse.\n+ * \n+ *\n+ * @param locator <code>Locator</code> an object that can return\n+ * the location of any SAX document event.\n+ */\n+ public void setDocumentLocator(Locator locator) {\n+ this.locator = locator;\n+ }\n+\n+ /**\n+ * Provides access to the {@link Locator} object provided by the\n+ * SAX parser.\n+ *\n+ * @return <code>Locator</code> an object that can return\n+ * the location of any SAX document event.\n+ */\n+ public Locator getDocumentLocator() {\n+ return locator;\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/TextBuffer.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/input/TextBuffer.java Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,186 @@
+/*--
+
+ $Id: TextBuffer.java,v 1.10 2007/11/10 05:29:00 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.input;
+
+import org.jdom.*;
+
+/**
+ * A non-public utility class similar to StringBuffer but optimized for XML
+ * parsing where the common case is that you get only one chunk of characters
+ * per text section. TextBuffer stores the first chunk of characters in a
+ * String, which can just be returned directly if no second chunk is received.
+ * Subsequent chunks are stored in a supplemental char array (like StringBuffer
+ * uses). In this case, the returned text will be the first String chunk,
+ * concatenated with the subsequent chunks stored in the char array. This
+ * provides optimal performance in the common case, while still providing very
+ * good performance in the uncommon case. Furthermore, avoiding StringBuffer
+ * means that no extra unused char array space will be kept around after parsing
+ * is through.
+ *
+ * @version $Revision: 1.10 $, $Date: 2007/11/10 05:29:00 $
+ * @author Bradley S. Huffman
+ * @author Alex Rosen
+ */
+class TextBuffer {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: TextBuffer.java,v $ $Revision: 1.10 $ $Date: 2007/11/10 05:29:00 $ $Name: jdom_1_1_1 $";
+
+ /** The first part of the text value (the "prefix"). If null, the
+ * text value is the empty string. */
+ private String prefixString;
+
+ /** The rest of the text value (the "suffix"). Only the first
+ * code>arraySize</code> characters are valid. */
+ private char[] array;
+
+ /** The size of the rest of the text value. If zero, then only
+ * code>prefixString</code> contains the text value. */
+ private int arraySize;
+
+ /** Constructor */
+ TextBuffer() {
+ array = new char[4096]; // initial capacity
+ arraySize = 0;
+ }
+
+ /** Append the specified text to the text value of this buffer. */
+ void append(char[] source, int start, int count) {
+ if (prefixString == null) {
+ // This is the first chunk, so we'll store it in the prefix string
+ prefixString = new String(source, start, count);
+ }
+ else {
+ // This is a subsequent chunk, so we'll add it to the char array
+ ensureCapacity(arraySize + count);
+ System.arraycopy(source, start, array, arraySize, count);
+ arraySize += count;
+ }
+ }
+
+ /** Returns the size of the text value. */
+ int size() {
+ if (prefixString == null) {
+ return 0;
+ }
+ else {
+ return prefixString.length() + arraySize;
+ }
+ }
+
+ /** Clears the text value and prepares the TextBuffer for reuse. */
+ void clear() {
+ arraySize = 0;
+ prefixString = null;
+ }
+
+ boolean isAllWhitespace() {
+ if ((prefixString == null) || (prefixString.length() == 0)) {
+ return true;
+ }
+
+ int size = prefixString.length();
+ for(int i = 0; i < size; i++) {
+ if ( !Verifier.isXMLWhitespace(prefixString.charAt(i))) {
+ return false;
+ }
+ }
+
+ for(int i = 0; i < arraySize; i++) {
+ if ( !Verifier.isXMLWhitespace(array[i])) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /** Returns the text value stored in the buffer. */
+ public String toString() {
+ if (prefixString == null) {
+ return "";
+ }
+
+ String str = "";
+ if (arraySize == 0) {
+ // Char array is empty, so the text value is just prefixString.
+ str = prefixString;
+ }
+ else {
+ // Char array is not empty, so the text value is prefixString
+ // plus the char array.
+ str = new StringBuffer(prefixString.length() + arraySize)
+ .append(prefixString)
+ .append(array, 0, arraySize)
+ .toString();
+ }
+ return str;
+ }
+
+ // Ensure that the char array has room for at least "csize" characters.
+ private void ensureCapacity(int csize) {
+ int capacity = array.length;
+ if (csize > capacity) {
+ char[] old = array;
+ int nsize = capacity;
+ while (csize > nsize) {
+ nsize += (capacity/2);
+ }
+ array = new char[nsize];
+ System.arraycopy(old, 0, array, 0, arraySize);
+ }
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/input/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/input/package.html Mon Nov 21 08:12:19 2011 -0500

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/DOMOutputter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/output/DOMOutputter.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,454 @@\n+/*-- \n+\n+ $Id: DOMOutputter.java,v 1.43 2007/11/10 05:29:01 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+\n+package org.jdom.output;\n+\n+import java.util.*;\n+\n+import org.jdom.*;\n+import org.jdom.adapters.*;\n+\n+\n+/**\n+ * Outputs a JDOM {@link org.jdom.Document org.jdom.Document} as a DOM {@link\n+ * org.w3c.dom.Document org.w3c.dom.Document}.\n+ *\n+ * @version $Revision: 1.43 $, $Date: 2007/11/10 05:29:01 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Matthew Merlo\n+ * @author Dan Schaffer\n+ * @author Yusuf Goolamabbas\n+ * @author Bradley S. Huffman\n+ */\n+public class DOMOutputter {\n+\n+ private static final String CVS_ID = \n+ "@(#) $RCSfile: DOMOutputter.java,v $ $Revision: 1.43 $ $Date: 2007/11/10 05:29:01 $ $Name: jdom_1_1_1 $";\n+\n+ /** Default adapter class */\n+ private static final String DEFAULT_ADAPTER_CLASS =\n+ "org.jdom.adapters.XercesDOMAdapter";\n+\n+ /** Adapter to use for interfacing with the DOM implementation */\n+ private String adapterClass;\n+\n+ /** Output a DOM with namespaces but just the empty namespace */\n+ private boolean forceNamespaceAware;\n+\n+ /**\n+ * This creates a new DOMOutputter which will attempt to first locate\n+ * a DOM implementation to use via JAXP, and if JAXP does not exist or\n+ * there\'s a problem, will fall back to the default parser.\n+ */\n+ public DOMOutputter() {\n+ // nothing\n+ }\n+\n+ /**\n+ * This creates a '..b' org.w3c.dom.Text domText = domDoc.createTextNode(str);\n+ domElement.appendChild(domText);\n+ }\n+ else if (node instanceof CDATA) {\n+ CDATA cdata = (CDATA) node;\n+ org.w3c.dom.CDATASection domCdata =\n+ domDoc.createCDATASection(cdata.getText());\n+ domElement.appendChild(domCdata);\n+ }\n+ else if (node instanceof Text) {\n+ Text text = (Text) node;\n+ org.w3c.dom.Text domText =\n+ domDoc.createTextNode(text.getText());\n+ domElement.appendChild(domText);\n+ }\n+ else if (node instanceof Comment) {\n+ Comment comment = (Comment) node;\n+ org.w3c.dom.Comment domComment =\n+ domDoc.createComment(comment.getText());\n+ domElement.appendChild(domComment);\n+ }\n+ else if (node instanceof ProcessingInstruction) {\n+ ProcessingInstruction pi = \n+ (ProcessingInstruction) node;\n+ org.w3c.dom.ProcessingInstruction domPI =\n+ domDoc.createProcessingInstruction(\n+ pi.getTarget(), pi.getData());\n+ domElement.appendChild(domPI);\n+ }\n+ else if (node instanceof EntityRef) {\n+ EntityRef entity = (EntityRef) node;\n+ org.w3c.dom.EntityReference domEntity =\n+ domDoc.createEntityReference(entity.getName());\n+ domElement.appendChild(domEntity);\n+ }\n+ else {\n+ throw new JDOMException(\n+ "Element contained content with type:" +\n+ node.getClass().getName());\n+ }\n+ }\n+ \n+ // Remove declared namespaces from stack\n+ while (namespaces.size() > previouslyDeclaredNamespaces) {\n+ namespaces.pop();\n+ }\n+\n+ return domElement;\n+ }\n+ catch (Exception e) {\n+ throw new JDOMException("Exception outputting Element " +\n+ element.getQualifiedName(), e);\n+ }\n+ }\n+\n+ private org.w3c.dom.Attr output(Attribute attribute,\n+ org.w3c.dom.Document domDoc)\n+ throws JDOMException {\n+ org.w3c.dom.Attr domAttr = null;\n+ try {\n+ if (attribute.getNamespace() == Namespace.NO_NAMESPACE) {\n+ // No namespace, use createAttribute\n+ if (forceNamespaceAware) {\n+ domAttr = domDoc.createAttributeNS(null, attribute.getQualifiedName());\n+ } else {\n+ domAttr = domDoc.createAttribute(attribute.getQualifiedName());\n+ }\n+ }\n+ else {\n+ domAttr = domDoc.createAttributeNS(attribute.getNamespaceURI(),\n+ attribute.getQualifiedName());\n+ }\n+ domAttr.setValue(attribute.getValue());\n+ } catch (Exception e) {\n+ throw new JDOMException("Exception outputting Attribute " +\n+ attribute.getQualifiedName(), e);\n+ }\n+ return domAttr;\n+ }\n+\n+ /**\n+ * This will handle adding any <code>{@link Namespace}</code>\n+ * attributes to the DOM tree.\n+ *\n+ * @param ns <code>Namespace</code> to add definition of\n+ */\n+ private static String getXmlnsTagFor(Namespace ns) {\n+ String attrName = "xmlns";\n+ if (!ns.getPrefix().equals("")) {\n+ attrName += ":";\n+ attrName += ns.getPrefix();\n+ }\n+ return attrName;\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/EscapeStrategy.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/output/EscapeStrategy.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,76 @@
+/*--
+
+ $Id: EscapeStrategy.java,v 1.4 2007/11/10 05:29:01 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.output;
+
+/**
+ * Logic to determine which characters should be formatted as character
+ * entities.
+ *
+ * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:01 $
+ * @author Alex Rosen
+ * @author Bradley S. Huffman
+ * @author Jason Hunter
+ */
+public interface EscapeStrategy {
+
+ /**
+ * Test whether the supplied character should be formatted literally
+ * or as a character entity.
+ */
+ public boolean shouldEscape(char ch);
+}
+

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/Format.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/output/Format.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,615 @@\n+/*--\n+\n+ $Id: Format.java,v 1.14 2009/07/23 05:54:23 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.output;\n+\n+import java.lang.reflect.Method;\n+import org.jdom.Verifier;\n+\n+/**\n+ * Class to encapsulate XMLOutputter format options.\n+ * Typical users can use the standard format configurations obtained by\n+ * {@link #getRawFormat} (no whitespace changes),\n+ * {@link #getPrettyFormat} (whitespace beautification), and\n+ * {@link #getCompactFormat} (whitespace normalization).\n+ * \n+ * Several modes are available to effect the way textual content is printed.\n+ * See the documentation for {@link TextMode} for details.\n+ *\n+ * @version $Revision: 1.14 $, $Date: 2009/07/23 05:54:23 $\n+ * @author Jason Hunter\n+ */\n+public class Format implements Cloneable {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: Format.java,v $ $Revision: 1.14 $ $Date: 2009/07/23 05:54:23 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * Returns a new Format object that performs no whitespace changes, uses\n+ * the UTF-8 encoding, doesn\'t expand empty elements, includes the\n+ * declaration and encoding, and uses the default entity escape strategy.\n+ * Tweaks can be made to the returned Format instance without affecting\n+ * other instances.\n+\n+ * @return a Format with no whitespace changes\n+ */\n+ public static Format getRawFormat() {\n+ return new Format();\n+ }\n+\n+ /**\n+ * Returns a new '..b'nvoke(encoder, new Object[]{new Character(ch)});\n+ return !val.booleanValue();\n+ }\n+ catch (Exception ignored) {\n+ }\n+ }\n+ // Return false if we don\'t know. This risks not escaping\n+ // things which should be escaped, but also means people won\'t\n+ // start getting loads of unnecessary escapes.\n+ return false;\n+ }\n+ }\n+ }\n+\n+\n+ /**\n+ * Class to signify how text should be handled on output. The following\n+ * table provides details.\n+ *\n+ * <table>\n+ * <tr>\n+ * <th align="left">\n+ * Text Mode\n+ * </th>\n+ * <th>\n+ * Resulting behavior.\n+ * </th>\n+ * </tr>\n+ *\n+ * <tr valign="top">\n+ * <td>\n+ * PRESERVE (Default)\n+ * </td>\n+ * <td>\n+ * All content is printed in the format it was created, no whitespace\n+ * or line separators are are added or removed.\n+ * </td>\n+ * </tr>\n+ *\n+ * <tr valign="top">\n+ * <td>\n+ * TRIM_FULL_WHITE\n+ * </td>\n+ * <td>\n+ * Content between tags consisting of all whitespace is not printed.\n+ * If the content contains even one non-whitespace character, it is\n+ * printed verbatim, whitespace and all.\n+ * </td>\n+ * </tr>\n+ *\n+ * <tr valign="top">\n+ * <td>\n+ * TRIM\n+ * </td>\n+ * <td>\n+ * Same as TrimAllWhite, plus leading/trailing whitespace are\n+ * trimmed.\n+ * </td>\n+ * </tr>\n+ *\n+ * <tr valign="top">\n+ * <td>\n+ * NORMALIZE\n+ * </td>\n+ * <td>\n+ * Same as TextTrim, plus addition interior whitespace is compressed\n+ * to a single space.\n+ * </td>\n+ * </tr>\n+ * </table>\n+ *\n+ * In most cases textual content is aligned with the surrounding tags\n+ * (after the appropriate text mode is applied). In the case where the only\n+ * content between the start and end tags is textual, the start tag, text,\n+ * and end tag are all printed on the same line. If the document being\n+ * output already has whitespace, it\'s wise to turn on TRIM mode so the\n+ * pre-existing whitespace can be trimmed before adding new whitespace.\n+ * \n+ * When a element has a xml:space attribute with the value of "preserve",\n+ * all formating is turned off and reverts back to the default until the\n+ * element and its contents have been printed. If a nested element contains\n+ * another xml:space with the value "default" formatting is turned back on\n+ * for the child element and then off for the remainder of the parent\n+ * element.\n+ */\n+ public static class TextMode {\n+ /**\n+ * Mode for literal text preservation.\n+ */\n+ public static final TextMode PRESERVE = new TextMode("PRESERVE");\n+\n+ /**\n+ * Mode for text trimming (left and right trim).\n+ */\n+ public static final TextMode TRIM = new TextMode("TRIM");\n+\n+ /**\n+ * Mode for text normalization (left and right trim plus internal\n+ * whitespace is normalized to a single space.\n+ * @see org.jdom.Element#getTextNormalize\n+ */\n+ public static final TextMode NORMALIZE = new TextMode("NORMALIZE");\n+\n+ /**\n+ * Mode for text trimming of content consisting of nothing but\n+ * whitespace but otherwise not changing output.\n+ */\n+ public static final TextMode TRIM_FULL_WHITE =\n+ new TextMode("TRIM_FULL_WHITE");\n+\n+ private final String name;\n+\n+ private TextMode(String name) {\n+ this.name = name;\n+ }\n+\n+ public String toString() {\n+ return name;\n+ }\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/JDOMLocator.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/output/JDOMLocator.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,118 @@
+/*--
+
+ $Id: JDOMLocator.java,v 1.4 2007/11/10 05:29:01 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.output;
+
+import org.xml.sax.*;
+import org.xml.sax.helpers.*;
+
+/**
+ * An implementation of the SAX {@link Locator} interface that
+ * exposes the JDOM node being processed by SAXOutputter.
+ *
+ * @author Laurent Bihanic
+ *
+ * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:01 $
+ */
+public class JDOMLocator extends LocatorImpl {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: JDOMLocator.java,v $ $Revision: 1.4 $ $Date: 2007/11/10 05:29:01 $ $Name: jdom_1_1_1 $";
+
+ /** The JDOM node being processed by SAXOutputter. */
+ private Object node;
+
+ /**
+ * Default no-arg constructor.
+ */
+ JDOMLocator() { // package protected
+ super();
+ }
+
+ /**
+ * Copy contructor.
+ *
+ * @param locator <code>Locator</code> to copy location
+ * information from.
+ */
+ JDOMLocator(Locator locator) { // package protected
+ super(locator);
+
+ if (locator instanceof JDOMLocator) {
+ this.setNode(((JDOMLocator)locator).getNode());
+ }
+ }
+
+ /**
+ * Returns the JDOM node being processed by SAXOutputter.
+ *
+ * @return the JDOM node being processed by SAXOutputter.
+ */
+ public Object getNode() {
+ return this.node;
+ }
+
+ /**
+ * Sets the being-processed node.
+ *
+ * @param node <code>Object</code> node currently processed
+ * by SAXOutputter.
+ */
+ void setNode(Object node) { // package protected
+ this.node = node;
+ }
+}
+

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/NamespaceStack.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/output/NamespaceStack.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,154 @@
+/*--
+
+ $Id: NamespaceStack.java,v 1.14 2007/11/10 05:29:01 jhunter Exp $
+
+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+package org.jdom.output;
+
+import java.util.*;
+
+import org.jdom.Namespace;
+
+/**
+ * A non-public utility class used by both <code>{@link XMLOutputter}</code> and
+ * <code>{@link SAXOutputter}</code> to manage namespaces in a JDOM Document
+ * during output.
+ *
+ * @version $Revision: 1.14 $, $Date: 2007/11/10 05:29:01 $
+ * @author Elliotte Rusty Harolde
+ * @author Fred Trimble
+ * @author Brett McLaughlin
+ */
+class NamespaceStack {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: NamespaceStack.java,v $ $Revision: 1.14 $ $Date: 2007/11/10 05:29:01 $ $Name: jdom_1_1_1 $";
+
+ /** The prefixes available */
+ private Stack prefixes;
+
+ /** The URIs available */
+ private Stack uris;
+
+ /**
+ * This creates the needed storage.
+ */
+ NamespaceStack() {
+ prefixes = new Stack();
+ uris = new Stack();
+ }
+
+ /**
+ * This will add a new <code>{@link Namespace}</code>
+ * to those currently available.
+ *
+ * @param ns <code>Namespace</code> to add.
+ */
+ public void push(Namespace ns) {
+ prefixes.push(ns.getPrefix());
+ uris.push(ns.getURI());
+ }
+
+ /**
+ * This will remove the topmost (most recently added)
+ * <code>{@link Namespace}</code>, and return its prefix.
+ *
+ * @return <code>String</code> - the popped namespace prefix.
+ */
+ public String pop() {
+ String prefix = (String)prefixes.pop();
+ uris.pop();
+
+ return prefix;
+ }
+
+ /**
+ * This returns the number of available namespaces.
+ *
+ * @return <code>int</code> - size of the namespace stack.
+ */
+ public int size() {
+ return prefixes.size();
+ }
+
+ /**
+ * Given a prefix, this will return the namespace URI most
+ * rencently (topmost) associated with that prefix.
+ *
+ * @param prefix <code>String</code> namespace prefix.
+ * @return <code>String</code> - the namespace URI for that prefix.
+ */
+ public String getURI(String prefix) {
+ int index = prefixes.lastIndexOf(prefix);
+ if (index == -1) {
+ return null;
+ }
+ String uri = (String)uris.elementAt(index);
+ return uri;
+ }
+
+ /**
+ * This will print out the size and current stack, from the
+ * most recently added <code>{@link Namespace}</code> to
+ * the "oldest," all to <code>System.out</code>.
+ */
+ public String toString() {
+ StringBuffer buf = new StringBuffer();
+ String sep = System.getProperty("line.separator");
+ buf.append("Stack: " + prefixes.size() + sep);
+ for (int i = 0; i < prefixes.size(); i++) {
+ buf.append(prefixes.elementAt(i) + "&" + uris.elementAt(i) + sep);
+ }
+ return buf.toString();
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/SAXOutputter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/output/SAXOutputter.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,1439 @@\n+/*--\n+\n+ $Id: SAXOutputter.java,v 1.40 2007/11/10 05:29:01 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.output;\n+\n+import java.io.*;\n+import java.lang.reflect.*;\n+import java.util.*;\n+\n+import org.jdom.*;\n+import org.xml.sax.*;\n+import org.xml.sax.ext.*;\n+import org.xml.sax.helpers.*;\n+\n+/**\n+ * Outputs a JDOM document as a stream of SAX2 events.\n+ * \n+ * Most ContentHandler callbacks are supported. Both\n+ * <code>ignorableWhitespace()</code> and <code>skippedEntity()</code> have not\n+ * been implemented. The <code>{@link JDOMLocator}</code> class returned by\n+ * <code>{@link #getLocator}</code> exposes the current node being operated\n+ * upon.\n+ * \n+ * At this time, it is not possible to access notations and unparsed entity\n+ * references in a DTD from JDOM. Therefore, <code>DTDHandler</code> callbacks\n+ * have not been implemented yet.\n+ * \n+ * The <code>ErrorHandler</code> callbacks have not been implemented, since\n+ * these are supposed to be invoked when the document is parsed and at this\n+ * point the document exists in memory and is known to have no errors. \n+ *\n+ * @version $Revision: 1.40 $, $Date: 2007/11/10 05:29:01 $\n+ * @author Brett McLaughlin\n+ * @author Jason Hunter\n+ * @author Fred Trimble\n+ * @author Bradley S. Huffman\n+ */\n+public class SAXOutputter {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: SAXOutputter.java,v $ $Revision: 1.40 $ $Date: 2007/11/10 05:29:01 $ $Name: jdo'..b'r", null);\n+ parser = (XMLReader)getXMLReader.invoke(jaxpParser, null);\n+ } catch (ClassNotFoundException e) {\n+ //e.printStackTrace();\n+ } catch (InvocationTargetException e) {\n+ //e.printStackTrace();\n+ } catch (NoSuchMethodException e) {\n+ //e.printStackTrace();\n+ } catch (IllegalAccessException e) {\n+ //e.printStackTrace();\n+ }\n+\n+ // Check to see if we got a parser yet, if not, try to use a\n+ // hard coded default\n+ if (parser == null) {\n+ parser = XMLReaderFactory.createXMLReader(\n+ "org.apache.xerces.parsers.SAXParser");\n+ }\n+ return parser;\n+ }\n+\n+ /**\n+ * \n+ * This will create a SAX XMLReader capable of parsing a DTD and\n+ * configure it so that the DTD parsing events are routed to the\n+ * handlers registered onto this SAXOutputter.\n+ * \n+ *\n+ * @return <code>XMLReader</code> a SAX2 parser.\n+ *\n+ * @throws JDOMException if no parser can be created.\n+ */\n+ private XMLReader createDTDParser() throws JDOMException {\n+ XMLReader parser = null;\n+\n+ // Get a parser instance\n+ try\n+ {\n+ parser = createParser();\n+ }\n+ catch (Exception ex1) {\n+ throw new JDOMException("Error in SAX parser allocation", ex1);\n+ }\n+\n+ // Register handlers\n+ if (this.getDTDHandler() != null) {\n+ parser.setDTDHandler(this.getDTDHandler());\n+ }\n+ if (this.getEntityResolver() != null) {\n+ parser.setEntityResolver(this.getEntityResolver());\n+ }\n+ if (this.getLexicalHandler() != null) {\n+ try {\n+ parser.setProperty(LEXICAL_HANDLER_SAX_PROPERTY,\n+ this.getLexicalHandler());\n+ }\n+ catch (SAXException ex1) {\n+ try {\n+ parser.setProperty(LEXICAL_HANDLER_ALT_PROPERTY,\n+ this.getLexicalHandler());\n+ } catch (SAXException ex2) {\n+ // Forget it!\n+ }\n+ }\n+ }\n+ if (this.getDeclHandler() != null) {\n+ try {\n+ parser.setProperty(DECL_HANDLER_SAX_PROPERTY,\n+ this.getDeclHandler());\n+ }\n+ catch (SAXException ex1) {\n+ try {\n+ parser.setProperty(DECL_HANDLER_ALT_PROPERTY,\n+ this.getDeclHandler());\n+ } catch (SAXException ex2) {\n+ // Forget it!\n+ }\n+ }\n+ }\n+\n+ // Absorb errors as much as possible, per Laurent\n+ parser.setErrorHandler(new DefaultHandler());\n+\n+ return parser;\n+ }\n+\n+ /**\n+ * Returns a JDOMLocator object referencing the node currently\n+ * being processed by this outputter. The returned object is a\n+ * snapshot of the location information and can thus safely be\n+ * memorized for later use.\n+ * \n+ * This method allows direct access to the location information\n+ * maintained by SAXOutputter without requiring to implement\n+ * <code>XMLFilter</code>. (In SAX, locators are only available\n+ * though the <code>ContentHandler</code> interface).\n+ * \n+ * Note that location information is only available while\n+ * SAXOutputter is outputting nodes. Hence this method should\n+ * only be used by objects taking part in the output processing\n+ * such as <code>ErrorHandler</code>s.\n+ *\n+ * @return a JDOMLocator object referencing the node currently\n+ * being processed or <code>null</code> if no output\n+ * operation is being performed.\n+ */\n+ public JDOMLocator getLocator() {\n+ return (locator != null)? new JDOMLocator(locator): null;\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/XMLOutputter.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/output/XMLOutputter.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,1640 @@\n+/*--\n+\n+ $Id: XMLOutputter.java,v 1.117 2009/07/23 05:54:23 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.output;\n+\n+import java.io.*;\n+import java.util.*;\n+\n+import javax.xml.transform.Result;\n+\n+import org.jdom.*;\n+\n+/**\n+ * Outputs a JDOM document as a stream of bytes. The outputter can manage many\n+ * styles of document formatting, from untouched to pretty printed. The default\n+ * is to output the document content exactly as created, but this can be changed\n+ * by setting a new Format object. For pretty-print output, use\n+ * <code>{@link Format#getPrettyFormat()}</code>. For whitespace-normalized\n+ * output, use <code>{@link Format#getCompactFormat()}</code>.\n+ * \n+ * There are <code>{@link #output output(...)}</code> methods to print any of\n+ * the standard JDOM classes, including Document and Element, to either a Writer\n+ * or an OutputStream. Warning: When outputting to a Writer, make sure\n+ * the writer\'s encoding matches the encoding setting in the Format object. This\n+ * ensures the encoding in which the content is written (controlled by the\n+ * Writer configuration) matches the encoding placed in the document\'s XML\n+ * declaration (controlled by the XMLOutputter). Because a Writer cannot be\n+ * queried for its encoding, the information must be passed to the Format\n+ * manually in its constructor or via the\n+ * <code>{@link Format#setEncoding}</code> method. The default encoding is\n+ * UTF-8.\n+ * \n+ * The met'..b' return super.clone();\n+ }\n+ catch (java.lang.CloneNotSupportedException e) {\n+ // even though this should never ever happen, it\'s still\n+ // possible to fool Java into throwing a\n+ // CloneNotSupportedException. If that happens, we\n+ // shouldn\'t swallow it.\n+ throw new RuntimeException(e.toString());\n+ }\n+ }\n+\n+ /**\n+ * Return a string listing of the settings for this\n+ * XMLOutputter instance.\n+ *\n+ * @return a string listing the settings for this XMLOutputter instance\n+ */\n+ public String toString() {\n+ StringBuffer buffer = new StringBuffer();\n+ for (int i = 0; i < userFormat.lineSeparator.length(); i++) {\n+ char ch = userFormat.lineSeparator.charAt(i);\n+ switch (ch) {\n+ case \'\\r\': buffer.append("\\\\r");\n+ break;\n+ case \'\\n\': buffer.append("\\\\n");\n+ break;\n+ case \'\\t\': buffer.append("\\\\t");\n+ break;\n+ default: buffer.append("[" + ((int)ch) + "]");\n+ break;\n+ }\n+ }\n+\n+ return (\n+ "XMLOutputter[omitDeclaration = " + userFormat.omitDeclaration + ", " +\n+ "encoding = " + userFormat.encoding + ", " +\n+ "omitEncoding = " + userFormat.omitEncoding + ", " +\n+ "indent = \'" + userFormat.indent + "\'" + ", " +\n+ "expandEmptyElements = " + userFormat.expandEmptyElements + ", " +\n+ "lineSeparator = \'" + buffer.toString() + "\', " +\n+ "textMode = " + userFormat.mode + "]"\n+ );\n+ }\n+\n+ /**\n+ * Factory for making new NamespaceStack objects. The NamespaceStack\n+ * created is actually an inner class extending the package protected\n+ * NamespaceStack, as a way to make NamespaceStack "friendly" toward\n+ * subclassers.\n+ */\n+ private NamespaceStack createNamespaceStack() {\n+ // actually returns a XMLOutputter.NamespaceStack (see below)\n+ return new NamespaceStack();\n+ }\n+\n+ /**\n+ * Our own null subclass of NamespaceStack. This plays a little\n+ * trick with Java access protection. We want subclasses of\n+ * XMLOutputter to be able to override protected methods that\n+ * declare a NamespaceStack parameter, but we don\'t want to\n+ * declare the parent NamespaceStack class as public.\n+ */\n+ protected class NamespaceStack\n+ extends org.jdom.output.NamespaceStack\n+ {\n+ }\n+\n+ // Support method to print a name without using elt.getQualifiedName()\n+ // and thus avoiding a StringBuffer creation and memory churn\n+ private void printQualifiedName(Writer out, Element e) throws IOException {\n+ if (e.getNamespace().getPrefix().length() == 0) {\n+ out.write(e.getName());\n+ }\n+ else {\n+ out.write(e.getNamespace().getPrefix());\n+ out.write(\':\');\n+ out.write(e.getName());\n+ }\n+ }\n+\n+ // Support method to print a name without using att.getQualifiedName()\n+ // and thus avoiding a StringBuffer creation and memory churn\n+ private void printQualifiedName(Writer out, Attribute a) throws IOException {\n+ String prefix = a.getNamespace().getPrefix();\n+ if ((prefix != null) && (!prefix.equals(""))) {\n+ out.write(prefix);\n+ out.write(\':\');\n+ out.write(a.getName());\n+ }\n+ else {\n+ out.write(a.getName());\n+ }\n+ }\n+\n+ // * * * * * * * * * * Deprecated methods * * * * * * * * * *\n+\n+ /* The methods below here are deprecations of protected methods. We\n+ * don\'t usually deprecate protected methods, so they\'re commented out.\n+ * They\'re left here in case this mass deprecation causes people trouble.\n+ * Since we\'re getting close to 1.0 it\'s actually better for people to\n+ * raise issues early though.\n+ */\n+\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/output/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/output/package.html Mon Nov 21 08:12:19 2011 -0500

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/package.html Mon Nov 21 08:12:19 2011 -0500

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/JDOMResult.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/transform/JDOMResult.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,670 @@\n+/*-- \n+\n+ $Id: JDOMResult.java,v 1.24 2007/11/10 05:29:02 jhunter Exp $\n+\n+ Copyright (C) 2001-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+package org.jdom.transform;\n+\n+import java.util.*;\n+\n+import javax.xml.transform.sax.*;\n+\n+import org.jdom.*;\n+import org.jdom.input.*;\n+import org.xml.sax.*;\n+import org.xml.sax.ext.*;\n+import org.xml.sax.helpers.*;\n+\n+/**\n+ * A holder for an XSL Transformation result, generally a list of nodes\n+ * although it can be a JDOM Document also. As stated by the XSLT 1.0\n+ * specification, the result tree generated by an XSL transformation is not\n+ * required to be a well-formed XML document. The result tree may have "any\n+ * sequence of nodes as children that would be possible for an\n+ * element node".\n+ * \n+ * The following example shows how to apply an XSL Transformation\n+ * to a JDOM document and get the transformation result in the form\n+ * of a list of JDOM nodes:\n+ * <pre><code>\n+ * public static List transform(Document doc, String stylesheet)\n+ * throws JDOMException {\n+ * try {\n+ * Transformer transformer = TransformerFactory.newInstance()\n+ * .newTransformer(new StreamSource(stylesheet));\n+ * JDOMSource in = new JDOMSource(doc);\n+ * JDOMResult out = new JDOMResult();\n+ * transformer.transform(in, out);\n+ * return out.getResult();\n+ * }\n+ * catch (TransformerException e) {\n+ * throw new JDOMException("XSLT Transfo'..b' throws SAXException {\n+ this.ensureInitialization();\n+ super.processingInstruction(target, data);\n+ }\n+\n+ /**\n+ * [SAX ContentHandler interface support] Receives\n+ * notification of a skipped entity.\n+ */\n+ public void skippedEntity(String name) throws SAXException {\n+ this.ensureInitialization();\n+ super.skippedEntity(name);\n+ }\n+\n+ //-----------------------------------------------------------------------\n+ // LexicalHandler interface support\n+ //-----------------------------------------------------------------------\n+\n+ /**\n+ * [SAX LexicalHandler interface support] Reports the\n+ * start of DTD declarations, if any.\n+ *\n+ * @param name the document type name.\n+ * @param publicId the declared public identifier for the\n+ * external DTD subset, or <code>null</code>\n+ * if none was declared.\n+ * @param systemId the declared system identifier for the\n+ * external DTD subset, or <code>null</code>\n+ * if none was declared.\n+ *\n+ * @throws SAXException The application may raise an exception.\n+ */\n+ public void startDTD(String name, String publicId, String systemId)\n+ throws SAXException {\n+ this.ensureInitialization();\n+ this.saxHandler.startDTD(name, publicId, systemId);\n+ }\n+\n+ /**\n+ * [SAX LexicalHandler interface support] Reports the end\n+ * of DTD declarations.\n+ *\n+ * @throws SAXException The application may raise an exception.\n+ */\n+ public void endDTD() throws SAXException {\n+ this.saxHandler.endDTD();\n+ }\n+\n+ /**\n+ * [SAX LexicalHandler interface support] Reports the\n+ * beginning of some internal and external XML entities.\n+ *\n+ * @param name the name of the entity. If it is a parameter\n+ * entity, the name will begin with \'%\', and if it\n+ * is the external DTD subset, it will be "[dtd]".\n+ *\n+ * @throws SAXException The application may raise an exception.\n+ */\n+ public void startEntity(String name) throws SAXException {\n+ this.ensureInitialization();\n+ this.saxHandler.startEntity(name);\n+ }\n+\n+ /**\n+ * [SAX LexicalHandler interface support] Reports the end\n+ * of an entity.\n+ *\n+ * @param name the name of the entity that is ending.\n+ *\n+ * @throws SAXException The application may raise an exception.\n+ */\n+ public void endEntity(String name) throws SAXException {\n+ this.saxHandler.endEntity(name);\n+ }\n+\n+ /**\n+ * [SAX LexicalHandler interface support] Reports the\n+ * start of a CDATA section.\n+ *\n+ * @throws SAXException The application may raise an exception.\n+ */\n+ public void startCDATA() throws SAXException {\n+ this.ensureInitialization();\n+ this.saxHandler.startCDATA();\n+ }\n+\n+ /**\n+ * [SAX LexicalHandler interface support] Reports the end\n+ * of a CDATA section.\n+ *\n+ * @throws SAXException The application may raise an exception.\n+ */\n+ public void endCDATA() throws SAXException {\n+ this.saxHandler.endCDATA();\n+ }\n+\n+ /**\n+ * [SAX LexicalHandler interface support] Reports an XML\n+ * comment anywhere in the document.\n+ *\n+ * @param ch an array holding the characters in the comment.\n+ * @param start the starting position in the array.\n+ * @param length the number of characters to use from the array.\n+ *\n+ * @throws SAXException The application may raise an exception.\n+ */\n+ public void comment(char ch[], int start, int length)\n+ throws SAXException {\n+ this.ensureInitialization();\n+ this.saxHandler.comment(ch, start, length);\n+ }\n+ }\n+}\n+\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/JDOMSource.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/transform/JDOMSource.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,535 @@\n+/*-- \n+\n+ $Id: JDOMSource.java,v 1.20 2007/11/10 05:29:02 jhunter Exp $\n+\n+ Copyright (C) 2001-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+ \n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+ \n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+ \n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows \n+ these conditions in the documentation and/or other materials \n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+ \n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+ \n+ In addition, we request (but do not require) that you include in the \n+ end-user documentation provided with the redistribution and/or in the \n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos \n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many \n+ individuals on behalf of the JDOM Project and was originally \n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+ \n+ */\n+\n+package org.jdom.transform;\n+\n+import java.io.*;\n+import java.util.*;\n+\n+import javax.xml.transform.sax.*;\n+\n+import org.jdom.*;\n+import org.jdom.output.*;\n+import org.xml.sax.*;\n+\n+/**\n+ * A holder for an XML Transformation source: a Document, Element, or list of\n+ * nodes.\n+ * \n+ * The is provides input to a\n+ * {@link javax.xml.transform.Transformer JAXP TrAX Transformer}.\n+ * \n+ * The following example shows how to apply an XSL Transformation\n+ * to a JDOM document and get the transformation result in the form\n+ * of a list of JDOM nodes:\n+ * <pre><code>\n+ * public static List transform(Document doc, String stylesheet)\n+ * throws JDOMException {\n+ * try {\n+ * Transformer transformer = TransformerFactory.newInstance()\n+ * .newTransformer(new StreamSource(stylesheet));\n+ * JDOMSource in = new JDOMSource(doc);\n+ * JDOMResult out = new JDOMResult();\n+ * transformer.transform(in, out);\n+ * return out.getResult();\n+ * }\n+ * catch (TransformerException e) {\n+ * throw new JDOMException("XSLT Transformation failed", e);\n+ * }\n+ * }\n+ * </code></pre>\n+ *\n+ * @see org.jdom.transform.JDOMResult\n+ *\n+ * @version $Revision: 1.20 $, $Date: 2007/11/10 05:29:02 $\n+ * @author Laurent Bihanic\n+ * @author Jason Hunter\n+ */\n'..b'ow new UnsupportedOperationException();\n+ }\n+\n+ /**\n+ * Gets the character stream for this input source.\n+ * \n+ * Note that this method is only provided to make this\n+ * InputSource implementation acceptable by any XML\n+ * parser. As it generates an in-memory string representation\n+ * of the JDOM document, it is quite inefficient from both\n+ * speed and memory consumption points of view.\n+ * \n+ *\n+ * @return a Reader to a string representation of the\n+ * source JDOM document.\n+ */\n+ public Reader getCharacterStream() {\n+ Object src = this.getSource();\n+ Reader reader = null;\n+\n+ if (src instanceof Document) {\n+ // Get an in-memory string representation of the document\n+ // and return a reader on it.\n+ reader = new StringReader(\n+ new XMLOutputter().outputString((Document)src));\n+ }\n+ else {\n+ if (src instanceof List) {\n+ reader = new StringReader(\n+ new XMLOutputter().outputString((List)src));\n+ }\n+ // Else: No source, no reader!\n+ }\n+ return reader;\n+ }\n+ }\n+\n+ //=========================================================================\n+ // DocumentReader nested class\n+ //=========================================================================\n+\n+ /**\n+ * An implementation of the SAX2 XMLReader interface that presents\n+ * a SAX view of a JDOM Document. The actual generation of the\n+ * SAX events is delegated to JDOM\'s SAXOutputter.\n+ *\n+ * @see org.jdom.Document\n+ * @see org.jdom.output.SAXOutputter\n+ */\n+ private static class DocumentReader extends SAXOutputter\n+ implements XMLReader {\n+ /**\n+ * Public default constructor.\n+ */\n+ public DocumentReader() {\n+ super();\n+ }\n+\n+ //----------------------------------------------------------------------\n+ // SAX XMLReader interface support\n+ //----------------------------------------------------------------------\n+\n+ /**\n+ * Parses an XML document from a system identifier (URI).\n+ * \n+ * This implementation does not support reading XML data from\n+ * system identifiers, only from JDOM documents. Hence,\n+ * this method always throws a {@link SAXNotSupportedException}.\n+ * \n+ *\n+ * @param systemId the system identifier (URI).\n+ *\n+ * @throws SAXNotSupportedException always!\n+ */\n+ public void parse(String systemId) throws SAXNotSupportedException {\n+ throw new SAXNotSupportedException(\n+ "Only JDOM Documents are supported as input");\n+ }\n+\n+ /**\n+ * Parses an XML document.\n+ * \n+ * The methods accepts only <code>JDOMInputSource</code>s\n+ * instances as input sources.\n+ * \n+ *\n+ * @param input the input source for the top-level of the\n+ * XML document.\n+ *\n+ * @throws SAXException any SAX exception,\n+ * possibly wrapping\n+ * another exception.\n+ * @throws SAXNotSupportedException if the input source does\n+ * not wrap a JDOM document.\n+ */\n+ public void parse(InputSource input) throws SAXException {\n+ if (input instanceof JDOMInputSource) {\n+ try {\n+ Object source = ((JDOMInputSource)input).getSource();\n+ if (source instanceof Document) {\n+ this.output((Document)source);\n+ }\n+ else {\n+ this.output((List)source);\n+ }\n+ }\n+ catch (JDOMException e) {\n+ throw new SAXException(e.getMessage(), e);\n+ }\n+ }\n+ else {\n+ throw new SAXNotSupportedException(\n+ "Only JDOM Documents are supported as input");\n+ }\n+ }\n+ }\n+}\n+\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/XSLTransformException.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/transform/XSLTransformException.java Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,82 @@
+/*--
+
+ $Id: XSLTransformException.java,v 1.4 2007/11/10 05:29:02 jhunter Exp $
+
+ Copyright (C) 2003-2007 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <request_AT_jdom_DOT_org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <request_AT_jdom_DOT_org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information
+ on the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
+package org.jdom.transform;
+
+import org.jdom.JDOMException;
+
+/**
+ * Thrown when an XSL stylesheet fails to compile or an XSL transform fails
+ *
+ * @version $Revision: 1.4 $, $Date: 2007/11/10 05:29:02 $
+ * @author Jason Hunter
+ */
+public class XSLTransformException extends JDOMException {
+
+ private static final String CVS_ID =
+ "@(#) $RCSfile: XSLTransformException.java,v $ $Revision: 1.4 $ $Date: 2007/11/10 05:29:02 $ $Name: jdom_1_1_1 $";
+
+ public XSLTransformException() {
+ }
+
+ public XSLTransformException(String message) {
+ super(message);
+ }
+
+ public XSLTransformException(String message, Exception cause) {
+ super(message, cause);
+ }
+}

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/XSLTransformer.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/transform/XSLTransformer.java Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,291 @@\n+/*--\n+\n+ $Id: XSLTransformer.java,v 1.5 2007/11/14 04:36:54 jhunter Exp $\n+\n+ Copyright (C) 2001-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.transform;\n+\n+import java.util.*;\n+import java.io.*;\n+import javax.xml.transform.*;\n+import javax.xml.transform.stream.StreamSource;\n+import org.jdom.*;\n+import org.xml.sax.EntityResolver;\n+\n+/**\n+ * A convenience class to handle simple transformations. The JAXP TrAX classes\n+ * have more bells and whistles and can be used with {@link JDOMSource} and\n+ * {@link JDOMResult} for advanced uses. This class handles the common case and\n+ * presents a simple interface. XSLTransformer is thread safe and may be\n+ * used from multiple threads.\n+ *\n+ * <pre><code>\n+ * XSLTransformer transformer = new XSLTransformer("file.xsl");\n+ *\n+ * Document x2 = transformer.transform(x); // x is a Document\n+ * Document y2 = transformer.transform(y); // y is a Document\n+ * </code></pre>\n+ *\n+ * JDOM relies on TrAX to perform the transformation.\n+ * The <code>javax.xml.transform.TransformerFactory</code> Java system property\n+ * determines which XSLT engine TrAX uses. Its value should be\n+ * the fully qualified name of the implementation of the abstract\n+ * <code>javax.xml.transform.TransformerFactory</code> class.\n+ * Values of this property for popular XSLT processors include:\n+ * \n+ * <ul><li>Saxon 6.x: <code>com.icl.saxon.TransformerFactoryImpl</code></li>\n+ * <li>Saxon 7.x: <code>net.sf.saxon.TransformerFactoryImpl</code></li>\n+ * <'..b'specified\n+ * <code>File</code>.\n+ * \n+ *\n+ * @param stylesheet <code>File</code> from which the stylesheet is read.\n+ * @throws XSLTransformException when an IOException, format error, or\n+ * something else prevents the stylesheet from being compiled\n+ */\n+ public XSLTransformer(File stylesheet) throws XSLTransformException {\n+ this(new StreamSource(stylesheet));\n+ }\n+\n+ /**\n+ * \n+ * This will create a new <code>XSLTransformer</code> by\n+ * reading the stylesheet from the specified\n+ * <code>Document</code>.\n+ * \n+ *\n+ * @param stylesheet <code>Document</code> containing the stylesheet.\n+ * @throws XSLTransformException when the supplied <code>Document</code>\n+ * is not syntactically correct XSLT\n+ */\n+ public XSLTransformer(Document stylesheet) throws XSLTransformException {\n+ this(new JDOMSource(stylesheet));\n+ }\n+\n+ /**\n+ * Transforms the given input nodes to a list of output nodes.\n+ *\n+ * @param inputNodes input nodes\n+ * @return transformed output nodes\n+ * @throws XSLTransformException if there\'s a problem in the transformation\n+ */\n+ public List transform(List inputNodes) throws XSLTransformException {\n+ JDOMSource source = new JDOMSource(inputNodes);\n+ JDOMResult result = new JDOMResult();\n+ result.setFactory(factory); // null ok\n+ try {\n+ templates.newTransformer().transform(source, result);\n+ return result.getResult();\n+ }\n+ catch (TransformerException e) {\n+ throw new XSLTransformException("Could not perform transformation", e);\n+ }\n+ }\n+ \n+ /**\n+ * Transforms the given document to an output document.\n+ *\n+ * @param inputDoc input document\n+ * @return transformed output document\n+ * @throws XSLTransformException if there\'s a problem in the transformation\n+ */\n+ public Document transform(Document inputDoc) throws XSLTransformException {\n+ \treturn transform(inputDoc, null);\n+ }\n+\n+ /**\n+ * Transforms the given document to an output document.\n+ *\n+ * @param inputDoc input document\n+ * @param resolver\t\t\t entity resolver for the input document\n+ * @return transformed output document\n+ * @throws XSLTransformException if there\'s a problem in the transformation\n+ */\n+ public Document transform(Document inputDoc, EntityResolver resolver) throws XSLTransformException {\n+ JDOMSource source = new JDOMSource(inputDoc, resolver);\n+ JDOMResult result = new JDOMResult();\n+ result.setFactory(factory); // null ok\n+ try {\n+ templates.newTransformer().transform(source, result);\n+ return result.getDocument();\n+ }\n+ catch (TransformerException e) {\n+ throw new XSLTransformException("Could not perform transformation", e);\n+ }\n+ }\n+\n+ /**\n+ * Sets a custom JDOMFactory to use when building the\n+ * transformation result. Use a custom factory to build the tree\n+ * with your own subclasses of the JDOM classes.\n+ *\n+ * @param factory the custom <code>JDOMFactory</code> to use or\n+ * <code>null</code> to use the default JDOM\n+ * classes.\n+ *\n+ * @see #getFactory\n+ */\n+ public void setFactory(JDOMFactory factory) {\n+ this.factory = factory;\n+ }\n+\n+ /**\n+ * Returns the custom JDOMFactory used to build the transformation\n+ * result.\n+ *\n+ * @return the custom <code>JDOMFactory</code> used to build the\n+ * transformation result or <code>null</code> if the\n+ * default JDOM classes are being used.\n+ *\n+ * @see #setFactory\n+ */\n+ public JDOMFactory getFactory() {\n+ return this.factory;\n+ }\n+}\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/transform/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/transform/package.html Mon Nov 21 08:12:19 2011 -0500

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/xpath/JaxenXPath.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/xpath/JaxenXPath.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,356 @@\n+///*--\n+//\n+// $Id: JaxenXPath.java,v 1.20 2007/11/10 05:29:02 jhunter Exp $\n+//\n+// Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+// All rights reserved.\n+//\n+// Redistribution and use in source and binary forms, with or without\n+// modification, are permitted provided that the following conditions\n+// are met:\n+//\n+// 1. Redistributions of source code must retain the above copyright\n+// notice, this list of conditions, and the following disclaimer.\n+//\n+// 2. Redistributions in binary form must reproduce the above copyright\n+// notice, this list of conditions, and the disclaimer that follows\n+// these conditions in the documentation and/or other materials\n+// provided with the distribution.\n+//\n+// 3. The name "JDOM" must not be used to endorse or promote products\n+// derived from this software without prior written permission. For\n+// written permission, please contact <request_AT_jdom_DOT_org>.\n+//\n+// 4. Products derived from this software may not be called "JDOM", nor\n+// may "JDOM" appear in their name, without prior written permission\n+// from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+//\n+// In addition, we request (but do not require) that you include in the\n+// end-user documentation provided with the redistribution and/or in the\n+// software itself an acknowledgement equivalent to the following:\n+// "This product includes software developed by the\n+// JDOM Project (http://www.jdom.org/)."\n+// Alternatively, the acknowledgment may be graphical using the logos\n+// available at http://www.jdom.org/images/logos.\n+//\n+// THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+// DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+// SUCH DAMAGE.\n+//\n+// This software consists of voluntary contributions made by many\n+// individuals on behalf of the JDOM Project and was originally\n+// created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+// Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+// on the JDOM Project, please see <http://www.jdom.org/>.\n+//\n+// */\n+//\n+//package org.jdom.xpath;\n+//\n+//\n+//import java.util.*;\n+//\n+//import org.jaxen.*;\n+//import org.jaxen.jdom.*;\n+//import org.jdom.*;\n+//\n+//\n+///**\n+// * A non-public concrete XPath implementation for Jaxen.\n+// *\n+// * @version $Revision: 1.20 $, $Date: 2007/11/10 05:29:02 $\n+// * @author Laurent Bihanic\n+// */\n+//class JaxenXPath extends XPath { // package protected\n+//\n+// private static final String CVS_ID =\n+// "@(#) $RCSfile: JaxenXPath.java,v $ $Revision: 1.20 $ $Date: 2007/11/10 05:29:02 $ $Name: jdom_1_1_1 $";\n+//\n+// /**\n+// * The compiled XPath object to select nodes. This attribute can\n+// * not be made final as it needs to be set upon object\n+// * deserialization.\n+// */\n+// private transient JDOMXPath xPath;\n+//\n+// /**\n+// * The current context for XPath expression evaluation.\n+// */\n+// private Object currentContext;\n+//\n+// /**\n+// * Creates a new XPath wrapper object, compiling the specified\n+// * XPath expression.\n+// *\n+// * @param expr the XPath expression to wrap.\n+// *\n+// * @throws JDOMException if the XPath expression is invalid.\n+// */\n+// public JaxenXPath(String expr) throws JDOMException {\n+// setXPath(expr);\n+// '..b' supported by the underlying\n+// * implementation\n+// */\n+// public void setVariable(String name, Object value)\n+// throws IllegalArgumentException {\n+// Object o = xPath.getVariableContext();\n+// if (o instanceof SimpleVariableContext) {\n+// ((SimpleVariableContext)o).setVariableValue(null, name, value);\n+// }\n+// }\n+//\n+// /**\n+// * Adds a namespace definition to the list of namespaces known of\n+// * this XPath expression.\n+// * \n+// * Note: In XPath, there is no such thing as a\n+// * \'default namespace\'. The empty prefix always resolves\n+// * to the empty namespace URI.\n+// *\n+// * @param namespace the namespace.\n+// */\n+// public void addNamespace(Namespace namespace) {\n+// try {\n+// xPath.addNamespace(namespace.getPrefix(), namespace.getURI());\n+// }\n+// catch (JaxenException ex1) { /* Can\'t happen here. */ }\n+// }\n+//\n+// /**\n+// * Returns the wrapped XPath expression as a string.\n+// *\n+// * @return the wrapped XPath expression as a string.\n+// */\n+// public String getXPath() {\n+// return (xPath.toString());\n+// }\n+//\n+// /**\n+// * Compiles and sets the XPath expression wrapped by this object.\n+// *\n+// * @param expr the XPath expression to wrap.\n+// *\n+// * @throws JDOMException if the XPath expression is invalid.\n+// */\n+// private void setXPath(String expr) throws JDOMException {\n+// try {\n+// xPath = new JDOMXPath(expr);\n+// xPath.setNamespaceContext(new NSContext());\n+// }\n+// catch (Exception ex1) {\n+// throw new JDOMException(\n+// "Invalid XPath expression: \\"" + expr + "\\"", ex1);\n+// }\n+// }\n+//\n+// public String toString() {\n+// return (xPath.toString());\n+// }\n+//\n+// public boolean equals(Object o) {\n+// if (o instanceof JaxenXPath) {\n+// JaxenXPath x = (JaxenXPath)o;\n+//\n+// return (super.equals(o) &&\n+// xPath.toString().equals(x.xPath.toString()));\n+// }\n+// return false;\n+// }\n+//\n+// public int hashCode() {\n+// return xPath.hashCode();\n+// }\n+//\n+// private class NSContext extends SimpleNamespaceContext {\n+// public NSContext() {\n+// super();\n+// }\n+//\n+// /**\n+// * [Jaxen NamespaceContext interface support] Translates\n+// * the provided namespace prefix into the matching bound\n+// * namespace URI.\n+// *\n+// * @param prefix the namespace prefix to resolve.\n+// *\n+// * @return the namespace URI matching the prefix.\n+// */\n+// public String translateNamespacePrefixToUri(String prefix) {\n+// if ((prefix == null) || (prefix.length() == 0)) {\n+// return null;\n+// }\n+//\n+// String uri = super.translateNamespacePrefixToUri(prefix);\n+// if (uri == null) {\n+// Object ctx = currentContext;\n+// if (ctx != null) {\n+// Element elt = null;\n+//\n+// // Get closer element node\n+// if (ctx instanceof Element) {\n+// elt = (Element)ctx;\n+// } else if (ctx instanceof Attribute) {\n+// elt = ((Attribute)ctx).getParent();\n+// } else if (ctx instanceof Content) {\n+// elt = ((Content) ctx).getParentElement();\n+// } else if (ctx instanceof Document) {\n+// elt = ((Document)ctx).getRootElement();\n+// }\n+//\n+// if (elt != null) {\n+// Namespace ns = elt.getNamespace(prefix);\n+// if (ns != null) {\n+// uri = ns.getURI();\n+// }\n+// }\n+// }\n+// }\n+// return uri;\n+// }\n+// }\n+//}\n+\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/xpath/XPath.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/xpath/XPath.java Mon Nov 21 08:12:19 2011 -0500

[

b'@@ -0,0 +1,453 @@\n+/*--\n+\n+ $Id: XPath.java,v 1.17 2007/11/10 05:29:02 jhunter Exp $\n+\n+ Copyright (C) 2000-2007 Jason Hunter & Brett McLaughlin.\n+ All rights reserved.\n+\n+ Redistribution and use in source and binary forms, with or without\n+ modification, are permitted provided that the following conditions\n+ are met:\n+\n+ 1. Redistributions of source code must retain the above copyright\n+ notice, this list of conditions, and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright\n+ notice, this list of conditions, and the disclaimer that follows\n+ these conditions in the documentation and/or other materials\n+ provided with the distribution.\n+\n+ 3. The name "JDOM" must not be used to endorse or promote products\n+ derived from this software without prior written permission. For\n+ written permission, please contact <request_AT_jdom_DOT_org>.\n+\n+ 4. Products derived from this software may not be called "JDOM", nor\n+ may "JDOM" appear in their name, without prior written permission\n+ from the JDOM Project Management <request_AT_jdom_DOT_org>.\n+\n+ In addition, we request (but do not require) that you include in the\n+ end-user documentation provided with the redistribution and/or in the\n+ software itself an acknowledgement equivalent to the following:\n+ "This product includes software developed by the\n+ JDOM Project (http://www.jdom.org/)."\n+ Alternatively, the acknowledgment may be graphical using the logos\n+ available at http://www.jdom.org/images/logos.\n+\n+ THIS SOFTWARE IS PROVIDED ``AS IS\'\' AND ANY EXPRESSED OR IMPLIED\n+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT\n+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF\n+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\n+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT\n+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF\n+ SUCH DAMAGE.\n+\n+ This software consists of voluntary contributions made by many\n+ individuals on behalf of the JDOM Project and was originally\n+ created by Jason Hunter <jhunter_AT_jdom_DOT_org> and\n+ Brett McLaughlin <brett_AT_jdom_DOT_org>. For more information\n+ on the JDOM Project, please see <http://www.jdom.org/>.\n+\n+ */\n+\n+package org.jdom.xpath;\n+\n+\n+import java.io.*;\n+import java.lang.reflect.*;\n+import java.util.*;\n+\n+import org.jdom.*;\n+\n+\n+/**\n+ * A utility class for performing XPath calls on JDOM nodes, with a factory\n+ * interface for obtaining a first XPath instance. Users operate against this\n+ * class while XPath vendors can plug-in implementations underneath. Users\n+ * can choose an implementation using either {@link #setXPathClass} or\n+ * the system property "org.jdom.xpath.class".\n+ *\n+ * @version $Revision: 1.17 $, $Date: 2007/11/10 05:29:02 $\n+ * @author Laurent Bihanic\n+ */\n+public abstract class XPath implements Serializable {\n+\n+ private static final String CVS_ID =\n+ "@(#) $RCSfile: XPath.java,v $ $Revision: 1.17 $ $Date: 2007/11/10 05:29:02 $ $Name: jdom_1_1_1 $";\n+\n+ /**\n+ * The name of the system property from which to retrieve the\n+ * name of the implementation class to use.\n+ * \n+ * The property name is:\n+ * "<code>org.jdom.xpath.class</code>".\n+ */\n+ private final static String XPATH_CLASS_PROPERTY = "org.jdom.xpath.class";\n+\n+ /**\n+ * The default implementation class to use if none was configured.\n+ */\n+ private final static String DEFAULT_XPATH_CLASS =\n+ "org.jdom.xpath.JaxenXPath";\n+\n+ /**\n+ * The string passable to the JAXP 1.3 XPathFactory is'..b'first\n+ * entry in the list of selected nodes (or atomics).\n+ * \n+ * Note: This method should not be used when the\n+ * same XPath expression needs to be applied several times (on the\n+ * same or different contexts) as it requires the expression to be\n+ * compiled before being evaluated. In such cases,\n+ * {@link #newInstance allocating} an XPath wrapper instance and\n+ * {@link #selectSingleNode(java.lang.Object) evaluating} it\n+ * several times is way more efficient.\n+ * \n+ *\n+ * @param context the element to use as context for evaluating\n+ * the XPath expression.\n+ * @param path the XPath expression to evaluate.\n+ *\n+ * @return the first selected item, which may be of types: {@link Element},\n+ * {@link Attribute}, {@link Text}, {@link CDATA},\n+ * {@link Comment}, {@link ProcessingInstruction}, Boolean,\n+ * Double, String, or <code>null</code> if no item was selected.\n+ *\n+ * @throws JDOMException if the XPath expression is invalid or\n+ * its evaluation on the specified context\n+ * failed.\n+ */\n+ public static Object selectSingleNode(Object context, String path)\n+ throws JDOMException {\n+ return newInstance(path).selectSingleNode(context);\n+ }\n+\n+\n+ //-------------------------------------------------------------------------\n+ // Serialization support\n+ //-------------------------------------------------------------------------\n+\n+ /**\n+ * [Serialization support] Returns the alternative object\n+ * to write to the stream when serializing this object. This\n+ * method returns an instance of a dedicated nested class to\n+ * serialize XPath expressions independently of the concrete\n+ * implementation being used.\n+ * \n+ * Note: Subclasses are not allowed to override\n+ * this method to ensure valid serialization of all\n+ * implementations.\n+ *\n+ * @return an XPathString instance configured with the wrapped\n+ * XPath expression.\n+ *\n+ * @throws ObjectStreamException never.\n+ */\n+ protected final Object writeReplace() throws ObjectStreamException {\n+ return new XPathString(this.getXPath());\n+ }\n+\n+ /**\n+ * The XPathString is dedicated to serialize instances of\n+ * XPath subclasses in a implementation-independent manner.\n+ * \n+ * XPathString ensures that only string data are serialized. Upon\n+ * deserialization, XPathString relies on XPath factory method to\n+ * to create instances of the concrete XPath wrapper currently\n+ * configured.\n+ */\n+ private final static class XPathString implements Serializable {\n+ /**\n+ * The XPath expression as a string.\n+ */\n+ private String xPath = null;\n+\n+ /**\n+ * Creates a new XPathString instance from the specified\n+ * XPath expression.\n+ *\n+ * @param xpath the XPath expression.\n+ */\n+ public XPathString(String xpath) {\n+ super();\n+\n+ this.xPath = xpath;\n+ }\n+\n+ /**\n+ * [Serialization support] Resolves the read XPathString\n+ * objects into XPath implementations.\n+ *\n+ * @return an instance of a concrete implementation of\n+ * XPath.\n+ *\n+ * @throws ObjectStreamException if no XPath could be built\n+ * from the read object.\n+ */\n+ private Object readResolve() throws ObjectStreamException {\n+ try {\n+ return XPath.newInstance(this.xPath);\n+ }\n+ catch (JDOMException ex1) {\n+ throw new InvalidObjectException(\n+ "Can\'t create XPath object for expression \\"" +\n+ this.xPath + "\\": " + ex1.toString());\n+ }\n+ }\n+ }\n+}\n+\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/org/jdom/xpath/package.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/org/jdom/xpath/package.html Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,6 @@
+<body>
+
+Support for XPath from within JDOM. XPath provides a common interface with a
+pluggable back-end. The default back end is Jaxen.
+
+</body>

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/src/xmlFilePattern.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/xmlFilePattern.xml Mon Nov 21 08:12:19 2011 -0500

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/anoGam1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/anoGam1.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,7 @@
+chr2L 48795086 /gbdb/anoGam1/nib/chr2L.nib
+chr2R 62725911 /gbdb/anoGam1/nib/chr2R.nib
+chr3L 41284009 /gbdb/anoGam1/nib/chr3L.nib
+chr3R 53272125 /gbdb/anoGam1/nib/chr3R.nib
+chrM 15363 /gbdb/anoGam1/nib/chrM.nib
+chrU 59568033 /gbdb/anoGam1/nib/chrU.nib
+chrX 22145176 /gbdb/anoGam1/nib/chrX.nib

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/bosTau4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/bosTau4.txt Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,11900 @@\n+chr1\t161106243\t/gbdb/bosTau4/bosTau4.2bit\n+chr2\t140800416\t/gbdb/bosTau4/bosTau4.2bit\n+chr3\t127923604\t/gbdb/bosTau4/bosTau4.2bit\n+chr5\t125847759\t/gbdb/bosTau4/bosTau4.2bit\n+chr4\t124454208\t/gbdb/bosTau4/bosTau4.2bit\n+chr6\t122561022\t/gbdb/bosTau4/bosTau4.2bit\n+chr8\t116942821\t/gbdb/bosTau4/bosTau4.2bit\n+chr7\t112078216\t/gbdb/bosTau4/bosTau4.2bit\n+chr11\t110171769\t/gbdb/bosTau4/bosTau4.2bit\n+chr9\t108145351\t/gbdb/bosTau4/bosTau4.2bit\n+chr10\t106383598\t/gbdb/bosTau4/bosTau4.2bit\n+chrX\t88516663\t/gbdb/bosTau4/bosTau4.2bit\n+chr12\t85358539\t/gbdb/bosTau4/bosTau4.2bit\n+chr15\t84633453\t/gbdb/bosTau4/bosTau4.2bit\n+chr13\t84419198\t/gbdb/bosTau4/bosTau4.2bit\n+chr14\t81345643\t/gbdb/bosTau4/bosTau4.2bit\n+chr16\t77906053\t/gbdb/bosTau4/bosTau4.2bit\n+chr17\t76506943\t/gbdb/bosTau4/bosTau4.2bit\n+chr20\t75796353\t/gbdb/bosTau4/bosTau4.2bit\n+chr21\t69173390\t/gbdb/bosTau4/bosTau4.2bit\n+chr18\t66141439\t/gbdb/bosTau4/bosTau4.2bit\n+chr19\t65312493\t/gbdb/bosTau4/bosTau4.2bit\n+chr24\t65020233\t/gbdb/bosTau4/bosTau4.2bit\n+chr22\t61848140\t/gbdb/bosTau4/bosTau4.2bit\n+chr23\t53376148\t/gbdb/bosTau4/bosTau4.2bit\n+chr29\t51998940\t/gbdb/bosTau4/bosTau4.2bit\n+chr26\t51750746\t/gbdb/bosTau4/bosTau4.2bit\n+chr27\t48749334\t/gbdb/bosTau4/bosTau4.2bit\n+chr28\t46084206\t/gbdb/bosTau4/bosTau4.2bit\n+chr25\t44060403\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.1\t3546887\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.2\t2346095\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.3\t2196958\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.4\t1827879\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.5\t1667370\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.6\t1456232\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.7\t1284506\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.8\t1221492\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.9\t1190529\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.10\t1137730\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11\t1114776\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.12\t998484\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.13\t870761\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.14\t855941\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.15\t834570\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.16\t832387\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.17\t829265\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.18\t814724\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.19\t812995\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.20\t789248\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.21\t763971\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.22\t738377\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.23\t698114\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.24\t691804\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.25\t691051\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.26\t685649\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.27\t675210\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.28\t672366\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.29\t662952\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.30\t661155\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.31\t660698\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.32\t649628\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.33\t635995\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.34\t628163\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.35\t624422\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.36\t622436\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.37\t622408\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.38\t605721\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.39\t581943\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.40\t578006\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.41\t574489\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.42\t573429\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.43\t558548\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.44\t546915\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.45\t539620\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.46\t511300\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.47\t508129\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.48\t503446\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.49\t502438\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.50\t499685\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.51\t495720\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.52\t492991\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.53\t488077\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.54\t466057\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.55\t461126\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.56\t459452\t/gbdb/bosTau4/bosTau4.2bi'..b'49\t1028\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11750\t1028\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11751\t1027\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11752\t1027\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11753\t1026\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11754\t1026\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11755\t1026\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11756\t1026\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11757\t1026\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11758\t1026\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11759\t1025\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11760\t1024\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11761\t1024\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11762\t1023\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11763\t1023\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11764\t1023\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11765\t1023\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11766\t1023\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11767\t1023\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11768\t1023\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11769\t1022\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11770\t1021\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11771\t1021\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11772\t1021\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11773\t1021\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11774\t1021\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11775\t1021\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11776\t1020\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11777\t1019\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11778\t1018\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11779\t1017\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11780\t1017\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11781\t1016\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11782\t1016\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11783\t1016\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11784\t1016\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11785\t1015\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11786\t1015\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11787\t1014\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11788\t1013\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11789\t1013\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11790\t1013\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11791\t1013\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11792\t1012\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11793\t1012\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11794\t1012\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11795\t1012\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11796\t1011\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11797\t1011\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11798\t1011\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11799\t1010\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11800\t1009\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11801\t1009\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11802\t1009\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11803\t1009\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11804\t1008\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11805\t1008\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11806\t1006\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11807\t1006\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11808\t1006\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11809\t1006\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11810\t1006\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11811\t1005\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11812\t1005\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11813\t1005\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11814\t1004\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11815\t1004\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11816\t1003\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11817\t1003\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11818\t1003\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11819\t1002\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11820\t1002\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11821\t1001\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11822\t1001\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11823\t1000\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11824\t1000\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11825\t1000\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11826\t999\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11827\t999\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11828\t999\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11829\t999\t/gbdb/bosTau4/bosTau4.2bit\n+chrUn.004.11830\t999\t/gbdb/bosTau4/bosTau4.2bit\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/cb3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/cb3.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,13 @@
+chrI 11274843 /gbdb/cb3/cb3.2bit
+chrII 14512975 /gbdb/cb3/cb3.2bit
+chrIII 13544562 /gbdb/cb3/cb3.2bit
+chrIII_random 864856 /gbdb/cb3/cb3.2bit
+chrII_random 2252910 /gbdb/cb3/cb3.2bit
+chrIV 15290274 /gbdb/cb3/cb3.2bit
+chrIV_random 751081 /gbdb/cb3/cb3.2bit
+chrI_random 3509021 /gbdb/cb3/cb3.2bit
+chrUn 7311690 /gbdb/cb3/cb3.2bit
+chrV 16004101 /gbdb/cb3/cb3.2bit
+chrV_random 2554181 /gbdb/cb3/cb3.2bit
+chrX 20608032 /gbdb/cb3/cb3.2bit
+chrM 14420 /gbdb/cb3/cb3.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/ce4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/ce4.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,7 @@
+chrI 15072419 /gbdb/ce4/ce4.2bit
+chrII 15279316 /gbdb/ce4/ce4.2bit
+chrIII 13783681 /gbdb/ce4/ce4.2bit
+chrIV 17493784 /gbdb/ce4/ce4.2bit
+chrM 13794 /gbdb/ce4/ce4.2bit
+chrV 20919398 /gbdb/ce4/ce4.2bit
+chrX 17718852 /gbdb/ce4/ce4.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/ce6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/ce6.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,7 @@
+chrV 20919568 /gbdb/ce6/ce6.2bit
+chrX 17718854 /gbdb/ce6/ce6.2bit
+chrIV 17493785 /gbdb/ce6/ce6.2bit
+chrII 15279323 /gbdb/ce6/ce6.2bit
+chrI 15072421 /gbdb/ce6/ce6.2bit
+chrIII 13783681 /gbdb/ce6/ce6.2bit
+chrM 13794 /gbdb/ce6/ce6.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/danRer5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/danRer5.txt Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,5036 @@\n+chr5\t70371393\t/gbdb/danRer5/danRer5.2bit\n+chr7\t70262009\t/gbdb/danRer5/danRer5.2bit\n+chr3\t62931207\t/gbdb/danRer5/danRer5.2bit\n+chr6\t59200669\t/gbdb/danRer5/danRer5.2bit\n+chr20\t56528676\t/gbdb/danRer5/danRer5.2bit\n+chr14\t56522864\t/gbdb/danRer5/danRer5.2bit\n+chr8\t56456705\t/gbdb/danRer5/danRer5.2bit\n+chr1\t56204684\t/gbdb/danRer5/danRer5.2bit\n+chr2\t54366722\t/gbdb/danRer5/danRer5.2bit\n+chr13\t53547397\t/gbdb/danRer5/danRer5.2bit\n+chr16\t53070661\t/gbdb/danRer5/danRer5.2bit\n+chr17\t52310423\t/gbdb/danRer5/danRer5.2bit\n+chr9\t51490918\t/gbdb/danRer5/danRer5.2bit\n+chr18\t49281368\t/gbdb/danRer5/danRer5.2bit\n+chr12\t47523734\t/gbdb/danRer5/danRer5.2bit\n+chr15\t46629432\t/gbdb/danRer5/danRer5.2bit\n+chr23\t46388020\t/gbdb/danRer5/danRer5.2bit\n+chr19\t46181231\t/gbdb/danRer5/danRer5.2bit\n+chr21\t46057314\t/gbdb/danRer5/danRer5.2bit\n+chr11\t44616367\t/gbdb/danRer5/danRer5.2bit\n+chr4\t42602441\t/gbdb/danRer5/danRer5.2bit\n+chr10\t42379582\t/gbdb/danRer5/danRer5.2bit\n+chr24\t40293347\t/gbdb/danRer5/danRer5.2bit\n+chr22\t38981829\t/gbdb/danRer5/danRer5.2bit\n+chr25\t32876240\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2558\t2492985\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2487\t2490681\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2561\t1518658\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2559\t1317754\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2536\t854719\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2498\t818287\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2643\t682458\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2490\t634744\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2492\t601617\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2623\t562554\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2\t531032\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA240\t523564\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA465\t519282\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2551\t510381\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA65\t507785\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA538\t504980\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA72\t497427\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2593\t481448\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA53\t479688\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2532\t442274\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2543\t436318\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2570\t432419\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2631\t411754\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA470\t411571\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA291\t411167\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA746\t410814\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2619\t402087\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2632\t399669\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA289\t382333\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2524\t377760\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2547\t377245\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA592\t376255\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA58\t367219\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA924\t366698\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA743\t358713\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA737\t356673\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2628\t352938\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA395\t352853\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA724\t352180\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA725\t351949\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA122\t350329\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2553\t348507\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2586\t346401\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2640\t334594\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA6\t333456\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA74\t330246\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2529\t327850\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA354\t327159\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2648\t324104\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2602\t324053\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2597\t322408\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA643\t321130\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA259\t317389\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2512\t316215\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA695\t314564\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2596\t314031\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA681\t310961\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2645\t309079\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA8\t306107\t/gbdb/danRer5/danRer5.2bit\n+Zv7_scaffold2514\t302962\t/gbdb/danRer5/danRer5.2b'..b'7_NA6567\t2035\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA726\t2035\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7739\t2035\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1276\t2034\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1541\t2034\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2187\t2034\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4109\t2034\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2616\t2033\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4023\t2033\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4190\t2033\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4324\t2033\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7373\t2033\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2066\t2032\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA5301\t2032\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1246\t2030\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1934\t2029\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA6324\t2029\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA6332\t2029\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7616\t2029\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2974\t2028\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3912\t2028\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7004\t2028\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7618\t2028\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7711\t2027\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1325\t2026\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1917\t2026\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2804\t2026\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4160\t2026\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2883\t2025\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3495\t2024\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4173\t2023\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4327\t2023\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2278\t2022\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3542\t2022\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4271\t2022\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2517\t2021\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2534\t2021\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3427\t2021\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3457\t2021\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7389\t2021\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1851\t2020\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4683\t2020\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA6311\t2020\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3990\t2019\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3926\t2018\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4412\t2017\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA495\t2017\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7637\t2016\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3875\t2015\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3921\t2015\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA6205\t2015\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2840\t2014\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4961\t2014\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7447\t2014\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4396\t2013\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4929\t2013\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA6113\t2013\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4900\t2012\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7548\t2012\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2728\t2010\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4270\t2010\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2677\t2009\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA6733\t2009\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1544\t2008\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2731\t2008\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1937\t2007\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2440\t2007\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA5765\t2007\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA6991\t2007\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3686\t2006\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4025\t2006\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4956\t2006\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA5550\t2006\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7269\t2006\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7382\t2006\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA7682\t2006\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3720\t2005\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4776\t2005\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2705\t2004\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA3538\t2004\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1234\t2003\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2544\t2003\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2627\t2003\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2720\t2003\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA4748\t2003\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1523\t2002\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1533\t2002\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2719\t2002\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA2729\t2001\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA1247\t2000\t/gbdb/danRer5/danRer5.2bit\n+Zv7_NA5415\t2000\t/gbdb/danRer5/danRer5.2bit\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/danRer6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/danRer6.txt Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,11724 @@\n+chr7\t76918211\t/gbdb/danRer6/danRer6.2bit\n+chr5\t74451498\t/gbdb/danRer6/danRer6.2bit\n+chr4\t71658100\t/gbdb/danRer6/danRer6.2bit\n+chr6\t61647013\t/gbdb/danRer6/danRer6.2bit\n+chr3\t60907308\t/gbdb/danRer6/danRer6.2bit\n+chr1\t59305620\t/gbdb/danRer6/danRer6.2bit\n+chr2\t58009534\t/gbdb/danRer6/danRer6.2bit\n+chr8\t55568185\t/gbdb/danRer6/danRer6.2bit\n+chr9\t54736511\t/gbdb/danRer6/danRer6.2bit\n+chr14\t52930158\t/gbdb/danRer6/danRer6.2bit\n+chr16\t51890894\t/gbdb/danRer6/danRer6.2bit\n+chr20\t51884995\t/gbdb/danRer6/danRer6.2bit\n+chr13\t50748729\t/gbdb/danRer6/danRer6.2bit\n+chr17\t49469313\t/gbdb/danRer6/danRer6.2bit\n+chr18\t49271716\t/gbdb/danRer6/danRer6.2bit\n+chr19\t48708673\t/gbdb/danRer6/danRer6.2bit\n+chr21\t47572505\t/gbdb/danRer6/danRer6.2bit\n+chr15\t47237297\t/gbdb/danRer6/danRer6.2bit\n+chr12\t46853116\t/gbdb/danRer6/danRer6.2bit\n+chr23\t44714728\t/gbdb/danRer6/danRer6.2bit\n+chr11\t44116856\t/gbdb/danRer6/danRer6.2bit\n+chr10\t43467561\t/gbdb/danRer6/danRer6.2bit\n+chr22\t41415389\t/gbdb/danRer6/danRer6.2bit\n+chr24\t40403431\t/gbdb/danRer6/danRer6.2bit\n+chr25\t38768535\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold464\t2604789\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1585\t2015512\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold32\t1305644\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold477\t964789\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1242\t809594\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3025\t794780\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold803\t782640\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold2292\t779331\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3117\t777796\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1746\t689110\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1026\t657781\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1983\t613609\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold786\t597906\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold955\t593455\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold432\t556279\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold667\t549754\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1453\t547950\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3059\t537443\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3028\t519547\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3016\t483285\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3041\t471087\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3062\t462670\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold207\t457989\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA3584\t427969\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold2633\t413475\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6036\t409760\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3077\t407901\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1380\t400064\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3049\t396897\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3035\t389258\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3027\t384923\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3085\t383920\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold2198\t381172\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3123\t375588\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold2521\t373446\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold420\t371247\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold2578\t369303\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1149\t362163\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA4819\t360952\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold977\t354978\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3106\t351597\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1395\t350512\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold1261\t345956\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA3328\t341385\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold282\t340764\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3050\t338251\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3029\t335883\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA3748\t331185\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold2796\t323037\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3127\t321032\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold872\t319267\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3020\t316424\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3084\t314974\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1968\t314389\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold2917\t314369\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold3112\t314093\t/gbdb/danRer6/danRer6.2bit\n+Zv8_scaffold956\t313376\t/gbdb/danRer6/danRer6.2bit\n+Zv'..b'005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6874\t2005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6985\t2005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA7007\t2005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA7283\t2005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8126\t2005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8814\t2005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8882\t2005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9819\t2005\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA161\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1698\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA236\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA2795\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA2890\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA3204\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA38\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA4240\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA4405\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA5300\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6511\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6871\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA7592\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA815\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8376\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9708\t2004\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1070\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA11081\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA11096\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA11241\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1369\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1866\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA3372\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA4357\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA5152\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6938\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA7781\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA7792\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8597\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8860\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9882\t2003\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1050\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10535\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1155\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA1875\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA250\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA3362\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA3371\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8239\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8891\t2002\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10066\t2001\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA4760\t2001\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA5424\t2001\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6044\t2001\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6559\t2001\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6701\t2001\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA7162\t2001\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8411\t2001\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10004\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10497\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10518\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10533\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10667\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10923\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10970\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA10997\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA11020\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA11176\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA11393\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA2881\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA3180\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA341\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA398\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA4833\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA5235\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA5342\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6090\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA6924\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA7204\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA7870\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8173\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8183\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8193\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8225\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8301\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA8791\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9068\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9122\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9604\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9751\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9892\t2000\t/gbdb/danRer6/danRer6.2bit\n+Zv8_NA9916\t2000\t/gbdb/danRer6/danRer6.2bit\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/danRer7.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/danRer7.txt Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,1133 @@\n+chr7\t77276063\t/gbdb/danRer7/danRer7.2bit\n+chr5\t75682077\t/gbdb/danRer7/danRer7.2bit\n+chr3\t63268876\t/gbdb/danRer7/danRer7.2bit\n+chr4\t62094675\t/gbdb/danRer7/danRer7.2bit\n+chr1\t60348388\t/gbdb/danRer7/danRer7.2bit\n+chr2\t60300536\t/gbdb/danRer7/danRer7.2bit\n+chr6\t59938731\t/gbdb/danRer7/danRer7.2bit\n+chr16\t58780683\t/gbdb/danRer7/danRer7.2bit\n+chr9\t58232459\t/gbdb/danRer7/danRer7.2bit\n+chr8\t56184765\t/gbdb/danRer7/danRer7.2bit\n+chr20\t55952140\t/gbdb/danRer7/danRer7.2bit\n+chr13\t54093808\t/gbdb/danRer7/danRer7.2bit\n+chr17\t53984731\t/gbdb/danRer7/danRer7.2bit\n+chr14\t53733891\t/gbdb/danRer7/danRer7.2bit\n+chr12\t50697278\t/gbdb/danRer7/danRer7.2bit\n+chr19\t50254551\t/gbdb/danRer7/danRer7.2bit\n+chr18\t49877488\t/gbdb/danRer7/danRer7.2bit\n+chr15\t47442429\t/gbdb/danRer7/danRer7.2bit\n+chr11\t46661319\t/gbdb/danRer7/danRer7.2bit\n+chr10\t46591166\t/gbdb/danRer7/danRer7.2bit\n+chr23\t46386876\t/gbdb/danRer7/danRer7.2bit\n+chr21\t44544065\t/gbdb/danRer7/danRer7.2bit\n+chr24\t43947580\t/gbdb/danRer7/danRer7.2bit\n+chr22\t42261000\t/gbdb/danRer7/danRer7.2bit\n+chr25\t38499472\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3530\t1544009\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3503\t965101\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3463\t664565\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3471\t638129\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3455\t543129\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3518\t504410\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3465\t500345\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3520\t436282\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3470\t425063\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3459\t417943\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3480\t407754\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3536\t368818\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3473\t352305\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3545\t351865\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3498\t343018\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3485\t341688\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3554\t332968\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3535\t329156\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3495\t321770\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA675\t312116\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3551\t306644\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3461\t302948\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3548\t301592\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3563\t295849\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3477\t292984\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3491\t284732\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3482\t283152\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3540\t281342\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3510\t279262\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3539\t276747\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3515\t276154\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3500\t271256\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3509\t266362\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3547\t260465\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3538\t253640\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3456\t253302\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA672\t248473\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3550\t245711\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3533\t242772\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA849\t242593\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3492\t236140\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3494\t233193\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3487\t231704\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3517\t225600\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3514\t225481\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3462\t224830\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3458\t223119\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA722\t221151\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3488\t217805\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3483\t213343\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3529\t212462\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3506\t210931\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3534\t206488\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA372\t206081\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3561\t204746\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3453\t203829\t/gbdb/danRer7/danRer7.2bit\n+Zv9_scaffold3486\t202621\t/gbdb/danRe'..b'7.2bit\n+Zv9_NA478\t6919\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA886\t6767\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA862\t6736\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA931\t6731\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA985\t6726\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA967\t6697\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA180\t6675\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA50\t6674\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA890\t6597\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA288\t6556\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA684\t6489\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA6\t6378\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA371\t6328\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA925\t6296\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA119\t6288\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA750\t6274\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA411\t6273\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA861\t6161\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA939\t6107\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA260\t5952\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA705\t5946\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA108\t5702\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA843\t5690\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA188\t5676\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA347\t5663\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA666\t5580\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA7\t5401\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA539\t5114\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA884\t4454\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA18\t4371\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA987\t4206\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA978\t3784\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA157\t3679\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA334\t3679\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA891\t3607\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA902\t3484\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA920\t3455\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA877\t3381\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA796\t3298\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA945\t3228\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA946\t3086\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA949\t3033\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA933\t3012\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA951\t2975\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA957\t2866\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA971\t2865\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA960\t2671\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA954\t2620\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA912\t2460\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA712\t2434\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA961\t2357\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA988\t2311\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA977\t2246\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA932\t2185\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA993\t2100\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA943\t2065\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA462\t2052\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA919\t2001\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA165\t1990\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA955\t1989\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA956\t1989\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA989\t1920\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA982\t1919\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA983\t1919\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA909\t1916\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA980\t1872\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA969\t1853\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA981\t1813\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA901\t1786\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA950\t1755\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA984\t1745\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA962\t1732\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA935\t1714\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA976\t1692\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA986\t1639\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA953\t1633\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA941\t1591\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA929\t1577\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA936\t1530\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA975\t1452\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA958\t1428\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA212\t1347\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA979\t1346\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA952\t1326\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA934\t1266\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA944\t1251\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA745\t1198\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA968\t1173\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA959\t1142\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA937\t1137\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA802\t1126\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA1000\t942\t/gbdb/danRer7/danRer7.2bit\n+Zv9_NA997\t650\t/gbdb/danRer7/danRer7.2bit\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/dm2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/dm2.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,13 @@
+chr4 1281640 /gbdb/dm2/nib/chr4.nib
+chrM 19517 /gbdb/dm2/nib/chrM.nib
+chrU 8724946 /gbdb/dm2/nib/chrU.nib
+chrX 22224390 /gbdb/dm2/nib/chrX.nib
+chr2L 22407834 /gbdb/dm2/nib/chr2L.nib
+chr2R 20766785 /gbdb/dm2/nib/chr2R.nib
+chr2h 1694122 /gbdb/dm2/nib/chr2h.nib
+chr3L 23771897 /gbdb/dm2/nib/chr3L.nib
+chr3R 27905053 /gbdb/dm2/nib/chr3R.nib
+chr3h 2955737 /gbdb/dm2/nib/chr3h.nib
+chr4h 88110 /gbdb/dm2/nib/chr4h.nib
+chrXh 359526 /gbdb/dm2/nib/chrXh.nib
+chrYh 396896 /gbdb/dm2/nib/chrYh.nib

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/dm3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/dm3.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,15 @@
+chr2L 23011544 /gbdb/dm3/dm3.2bit
+chr2LHet 368872 /gbdb/dm3/dm3.2bit
+chr2R 21146708 /gbdb/dm3/dm3.2bit
+chr2RHet 3288761 /gbdb/dm3/dm3.2bit
+chr3L 24543557 /gbdb/dm3/dm3.2bit
+chr3LHet 2555491 /gbdb/dm3/dm3.2bit
+chr3R 27905053 /gbdb/dm3/dm3.2bit
+chr3RHet 2517507 /gbdb/dm3/dm3.2bit
+chr4 1351857 /gbdb/dm3/dm3.2bit
+chrU 10049037 /gbdb/dm3/dm3.2bit
+chrUextra 29004656 /gbdb/dm3/dm3.2bit
+chrX 22422827 /gbdb/dm3/dm3.2bit
+chrXHet 204112 /gbdb/dm3/dm3.2bit
+chrYHet 347038 /gbdb/dm3/dm3.2bit
+chrM 19517 /gbdb/dm3/dm3.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/galGal2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/galGal2.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,54 @@
+chr1 188239860 /gbdb/galGal2/nib/chr1.nib
+chr1_random 1356957 /gbdb/galGal2/nib/chr1_random.nib
+chr10 20909726 /gbdb/galGal2/nib/chr10.nib
+chr10_random 3871218 /gbdb/galGal2/nib/chr10_random.nib
+chr11 19020054 /gbdb/galGal2/nib/chr11.nib
+chr11_random 1153135 /gbdb/galGal2/nib/chr11_random.nib
+chr12 19821895 /gbdb/galGal2/nib/chr12.nib
+chr13 17279963 /gbdb/galGal2/nib/chr13.nib
+chr13_random 1219686 /gbdb/galGal2/nib/chr13_random.nib
+chr14 20603938 /gbdb/galGal2/nib/chr14.nib
+chr15 12438626 /gbdb/galGal2/nib/chr15.nib
+chr16 239457 /gbdb/galGal2/nib/chr16.nib
+chr16_random 1085578 /gbdb/galGal2/nib/chr16_random.nib
+chr17 10632206 /gbdb/galGal2/nib/chr17.nib
+chr18 8919268 /gbdb/galGal2/nib/chr18.nib
+chr19 9463882 /gbdb/galGal2/nib/chr19.nib
+chr2 147590765 /gbdb/galGal2/nib/chr2.nib
+chr2_random 125104 /gbdb/galGal2/nib/chr2_random.nib
+chr20 13506680 /gbdb/galGal2/nib/chr20.nib
+chr21 6202554 /gbdb/galGal2/nib/chr21.nib
+chr22 2228820 /gbdb/galGal2/nib/chr22.nib
+chr23 5666127 /gbdb/galGal2/nib/chr23.nib
+chr24 5910111 /gbdb/galGal2/nib/chr24.nib
+chr24_random 149561 /gbdb/galGal2/nib/chr24_random.nib
+chr26 4255270 /gbdb/galGal2/nib/chr26.nib
+chr27 2668888 /gbdb/galGal2/nib/chr27.nib
+chr27_random 721164 /gbdb/galGal2/nib/chr27_random.nib
+chr28 4731479 /gbdb/galGal2/nib/chr28.nib
+chr28_random 6240 /gbdb/galGal2/nib/chr28_random.nib
+chr3 108638738 /gbdb/galGal2/nib/chr3.nib
+chr3_random 1636275 /gbdb/galGal2/nib/chr3_random.nib
+chr32 1018878 /gbdb/galGal2/nib/chr32.nib
+chr32_random 61160 /gbdb/galGal2/nib/chr32_random.nib
+chr4 90634903 /gbdb/galGal2/nib/chr4.nib
+chr4_random 1174127 /gbdb/galGal2/nib/chr4_random.nib
+chr5 56310377 /gbdb/galGal2/nib/chr5.nib
+chr5_random 54865 /gbdb/galGal2/nib/chr5_random.nib
+chr6 33893787 /gbdb/galGal2/nib/chr6.nib
+chr6_random 3628 /gbdb/galGal2/nib/chr6_random.nib
+chr7 37338262 /gbdb/galGal2/nib/chr7.nib
+chr7_random 2315 /gbdb/galGal2/nib/chr7_random.nib
+chr8 30024636 /gbdb/galGal2/nib/chr8.nib
+chr8_random 15783 /gbdb/galGal2/nib/chr8_random.nib
+chr9 23409228 /gbdb/galGal2/nib/chr9.nib
+chrE22C19W28 70504 /gbdb/galGal2/nib/chrE22C19W28.nib
+chrE26C13 231937 /gbdb/galGal2/nib/chrE26C13.nib
+chrE50C23 21569 /gbdb/galGal2/nib/chrE50C23.nib
+chrE64 1525 /gbdb/galGal2/nib/chrE64.nib
+chrM 16775 /gbdb/galGal2/nib/chrM.nib
+chrUn 165033910 /gbdb/galGal2/nib/chrUn.nib
+chrW 4916845 /gbdb/galGal2/nib/chrW.nib
+chrW_random 455598 /gbdb/galGal2/nib/chrW_random.nib
+chrZ 33651169 /gbdb/galGal2/nib/chrZ.nib
+chrZ_random 14994570 /gbdb/galGal2/nib/chrZ_random.nib

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/galGal3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/galGal3.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,57 @@
+chr1 200994015 /gbdb/galGal3/galGal3.2bit
+chr1_random 222095 /gbdb/galGal3/galGal3.2bit
+chr10 22556432 /gbdb/galGal3/galGal3.2bit
+chr10_random 13679 /gbdb/galGal3/galGal3.2bit
+chr11 21928095 /gbdb/galGal3/galGal3.2bit
+chr11_random 72667 /gbdb/galGal3/galGal3.2bit
+chr12 20536687 /gbdb/galGal3/galGal3.2bit
+chr12_random 7060 /gbdb/galGal3/galGal3.2bit
+chr13 18911934 /gbdb/galGal3/galGal3.2bit
+chr13_random 35775 /gbdb/galGal3/galGal3.2bit
+chr14 15819469 /gbdb/galGal3/galGal3.2bit
+chr15 12968165 /gbdb/galGal3/galGal3.2bit
+chr16 432983 /gbdb/galGal3/galGal3.2bit
+chr16_random 246252 /gbdb/galGal3/galGal3.2bit
+chr17 11182526 /gbdb/galGal3/galGal3.2bit
+chr17_random 2911 /gbdb/galGal3/galGal3.2bit
+chr18 10925261 /gbdb/galGal3/galGal3.2bit
+chr18_random 11891 /gbdb/galGal3/galGal3.2bit
+chr19 9939723 /gbdb/galGal3/galGal3.2bit
+chr2 154873767 /gbdb/galGal3/galGal3.2bit
+chr2_random 142837 /gbdb/galGal3/galGal3.2bit
+chr20 13986235 /gbdb/galGal3/galGal3.2bit
+chr20_random 75095 /gbdb/galGal3/galGal3.2bit
+chr21 6959642 /gbdb/galGal3/galGal3.2bit
+chr22 3936574 /gbdb/galGal3/galGal3.2bit
+chr22_random 156216 /gbdb/galGal3/galGal3.2bit
+chr23 6042217 /gbdb/galGal3/galGal3.2bit
+chr24 6400109 /gbdb/galGal3/galGal3.2bit
+chr25 2031799 /gbdb/galGal3/galGal3.2bit
+chr25_random 80372 /gbdb/galGal3/galGal3.2bit
+chr26 5102438 /gbdb/galGal3/galGal3.2bit
+chr27 4841970 /gbdb/galGal3/galGal3.2bit
+chr28 4512026 /gbdb/galGal3/galGal3.2bit
+chr28_random 105415 /gbdb/galGal3/galGal3.2bit
+chr3 113657789 /gbdb/galGal3/galGal3.2bit
+chr32 1028 /gbdb/galGal3/galGal3.2bit
+chr4 94230402 /gbdb/galGal3/galGal3.2bit
+chr4_random 180706 /gbdb/galGal3/galGal3.2bit
+chr5 62238931 /gbdb/galGal3/galGal3.2bit
+chr5_random 27907 /gbdb/galGal3/galGal3.2bit
+chr6 37400442 /gbdb/galGal3/galGal3.2bit
+chr6_random 34212 /gbdb/galGal3/galGal3.2bit
+chr7 38384769 /gbdb/galGal3/galGal3.2bit
+chr7_random 104000 /gbdb/galGal3/galGal3.2bit
+chr8 30671729 /gbdb/galGal3/galGal3.2bit
+chr8_random 420759 /gbdb/galGal3/galGal3.2bit
+chr9 25554352 /gbdb/galGal3/galGal3.2bit
+chrE22C19W28_E50C23 895237 /gbdb/galGal3/galGal3.2bit
+chrE22C19W28_E50C23_random 191099 /gbdb/galGal3/galGal3.2bit
+chrE64 49846 /gbdb/galGal3/galGal3.2bit
+chrE64_random 557643 /gbdb/galGal3/galGal3.2bit
+chrM 16775 /gbdb/galGal3/galGal3.2bit
+chrUn_random 63870806 /gbdb/galGal3/galGal3.2bit
+chrW 259642 /gbdb/galGal3/galGal3.2bit
+chrW_random 729481 /gbdb/galGal3/galGal3.2bit
+chrZ 74602320 /gbdb/galGal3/galGal3.2bit
+chrZ_random 346234 /gbdb/galGal3/galGal3.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/hg18.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/hg18.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,49 @@
+chr1 247249719 /gbdb/hg18/nib/chr1.nib
+chr1_random 1663265 /gbdb/hg18/nib/chr1_random.nib
+chr10 135374737 /gbdb/hg18/nib/chr10.nib
+chr10_random 113275 /gbdb/hg18/nib/chr10_random.nib
+chr11 134452384 /gbdb/hg18/nib/chr11.nib
+chr11_random 215294 /gbdb/hg18/nib/chr11_random.nib
+chr12 132349534 /gbdb/hg18/nib/chr12.nib
+chr13 114142980 /gbdb/hg18/nib/chr13.nib
+chr13_random 186858 /gbdb/hg18/nib/chr13_random.nib
+chr14 106368585 /gbdb/hg18/nib/chr14.nib
+chr15 100338915 /gbdb/hg18/nib/chr15.nib
+chr15_random 784346 /gbdb/hg18/nib/chr15_random.nib
+chr16 88827254 /gbdb/hg18/nib/chr16.nib
+chr16_random 105485 /gbdb/hg18/nib/chr16_random.nib
+chr17 78774742 /gbdb/hg18/nib/chr17.nib
+chr17_random 2617613 /gbdb/hg18/nib/chr17_random.nib
+chr18 76117153 /gbdb/hg18/nib/chr18.nib
+chr18_random 4262 /gbdb/hg18/nib/chr18_random.nib
+chr19 63811651 /gbdb/hg18/nib/chr19.nib
+chr19_random 301858 /gbdb/hg18/nib/chr19_random.nib
+chr2 242951149 /gbdb/hg18/nib/chr2.nib
+chr2_random 185571 /gbdb/hg18/nib/chr2_random.nib
+chr20 62435964 /gbdb/hg18/nib/chr20.nib
+chr21 46944323 /gbdb/hg18/nib/chr21.nib
+chr21_random 1679693 /gbdb/hg18/nib/chr21_random.nib
+chr22 49691432 /gbdb/hg18/nib/chr22.nib
+chr22_random 257318 /gbdb/hg18/nib/chr22_random.nib
+chr22_h2_hap1 63661 /gbdb/hg18/nib/chr22_h2_hap1.nib
+chr3 199501827 /gbdb/hg18/nib/chr3.nib
+chr3_random 749256 /gbdb/hg18/nib/chr3_random.nib
+chr4 191273063 /gbdb/hg18/nib/chr4.nib
+chr4_random 842648 /gbdb/hg18/nib/chr4_random.nib
+chr5 180857866 /gbdb/hg18/nib/chr5.nib
+chr5_random 143687 /gbdb/hg18/nib/chr5_random.nib
+chr5_h2_hap1 1794870 /gbdb/hg18/nib/chr5_h2_hap1.nib
+chr6 170899992 /gbdb/hg18/nib/chr6.nib
+chr6_random 1875562 /gbdb/hg18/nib/chr6_random.nib
+chr6_cox_hap1 4731698 /gbdb/hg18/nib/chr6_cox_hap1.nib
+chr6_qbl_hap2 4565931 /gbdb/hg18/nib/chr6_qbl_hap2.nib
+chr7 158821424 /gbdb/hg18/nib/chr7.nib
+chr7_random 549659 /gbdb/hg18/nib/chr7_random.nib
+chr8 146274826 /gbdb/hg18/nib/chr8.nib
+chr8_random 943810 /gbdb/hg18/nib/chr8_random.nib
+chr9 140273252 /gbdb/hg18/nib/chr9.nib
+chr9_random 1146434 /gbdb/hg18/nib/chr9_random.nib
+chrM 16571 /gbdb/hg18/nib/chrM.nib
+chrX 154913754 /gbdb/hg18/nib/chrX.nib
+chrX_random 1719168 /gbdb/hg18/nib/chrX_random.nib
+chrY 57772954 /gbdb/hg18/nib/chrY.nib

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/hg19.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/hg19.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,93 @@
+chr1 249250621 /gbdb/hg19/hg19.2bit
+chr2 243199373 /gbdb/hg19/hg19.2bit
+chr3 198022430 /gbdb/hg19/hg19.2bit
+chr4 191154276 /gbdb/hg19/hg19.2bit
+chr5 180915260 /gbdb/hg19/hg19.2bit
+chr6 171115067 /gbdb/hg19/hg19.2bit
+chr7 159138663 /gbdb/hg19/hg19.2bit
+chrX 155270560 /gbdb/hg19/hg19.2bit
+chr8 146364022 /gbdb/hg19/hg19.2bit
+chr9 141213431 /gbdb/hg19/hg19.2bit
+chr10 135534747 /gbdb/hg19/hg19.2bit
+chr11 135006516 /gbdb/hg19/hg19.2bit
+chr12 133851895 /gbdb/hg19/hg19.2bit
+chr13 115169878 /gbdb/hg19/hg19.2bit
+chr14 107349540 /gbdb/hg19/hg19.2bit
+chr15 102531392 /gbdb/hg19/hg19.2bit
+chr16 90354753 /gbdb/hg19/hg19.2bit
+chr17 81195210 /gbdb/hg19/hg19.2bit
+chr18 78077248 /gbdb/hg19/hg19.2bit
+chr20 63025520 /gbdb/hg19/hg19.2bit
+chrY 59373566 /gbdb/hg19/hg19.2bit
+chr19 59128983 /gbdb/hg19/hg19.2bit
+chr22 51304566 /gbdb/hg19/hg19.2bit
+chr21 48129895 /gbdb/hg19/hg19.2bit
+chr6_ssto_hap7 4928567 /gbdb/hg19/hg19.2bit
+chr6_mcf_hap5 4833398 /gbdb/hg19/hg19.2bit
+chr6_cox_hap2 4795371 /gbdb/hg19/hg19.2bit
+chr6_mann_hap4 4683263 /gbdb/hg19/hg19.2bit
+chr6_apd_hap1 4622290 /gbdb/hg19/hg19.2bit
+chr6_qbl_hap6 4611984 /gbdb/hg19/hg19.2bit
+chr6_dbb_hap3 4610396 /gbdb/hg19/hg19.2bit
+chr17_ctg5_hap1 1680828 /gbdb/hg19/hg19.2bit
+chr4_ctg9_hap1 590426 /gbdb/hg19/hg19.2bit
+chr1_gl000192_random 547496 /gbdb/hg19/hg19.2bit
+chrUn_gl000225 211173 /gbdb/hg19/hg19.2bit
+chr4_gl000194_random 191469 /gbdb/hg19/hg19.2bit
+chr4_gl000193_random 189789 /gbdb/hg19/hg19.2bit
+chr9_gl000200_random 187035 /gbdb/hg19/hg19.2bit
+chrUn_gl000222 186861 /gbdb/hg19/hg19.2bit
+chrUn_gl000212 186858 /gbdb/hg19/hg19.2bit
+chr7_gl000195_random 182896 /gbdb/hg19/hg19.2bit
+chrUn_gl000223 180455 /gbdb/hg19/hg19.2bit
+chrUn_gl000224 179693 /gbdb/hg19/hg19.2bit
+chrUn_gl000219 179198 /gbdb/hg19/hg19.2bit
+chr17_gl000205_random 174588 /gbdb/hg19/hg19.2bit
+chrUn_gl000215 172545 /gbdb/hg19/hg19.2bit
+chrUn_gl000216 172294 /gbdb/hg19/hg19.2bit
+chrUn_gl000217 172149 /gbdb/hg19/hg19.2bit
+chr9_gl000199_random 169874 /gbdb/hg19/hg19.2bit
+chrUn_gl000211 166566 /gbdb/hg19/hg19.2bit
+chrUn_gl000213 164239 /gbdb/hg19/hg19.2bit
+chrUn_gl000220 161802 /gbdb/hg19/hg19.2bit
+chrUn_gl000218 161147 /gbdb/hg19/hg19.2bit
+chr19_gl000209_random 159169 /gbdb/hg19/hg19.2bit
+chrUn_gl000221 155397 /gbdb/hg19/hg19.2bit
+chrUn_gl000214 137718 /gbdb/hg19/hg19.2bit
+chrUn_gl000228 129120 /gbdb/hg19/hg19.2bit
+chrUn_gl000227 128374 /gbdb/hg19/hg19.2bit
+chr1_gl000191_random 106433 /gbdb/hg19/hg19.2bit
+chr19_gl000208_random 92689 /gbdb/hg19/hg19.2bit
+chr9_gl000198_random 90085 /gbdb/hg19/hg19.2bit
+chr17_gl000204_random 81310 /gbdb/hg19/hg19.2bit
+chrUn_gl000233 45941 /gbdb/hg19/hg19.2bit
+chrUn_gl000237 45867 /gbdb/hg19/hg19.2bit
+chrUn_gl000230 43691 /gbdb/hg19/hg19.2bit
+chrUn_gl000242 43523 /gbdb/hg19/hg19.2bit
+chrUn_gl000243 43341 /gbdb/hg19/hg19.2bit
+chrUn_gl000241 42152 /gbdb/hg19/hg19.2bit
+chrUn_gl000236 41934 /gbdb/hg19/hg19.2bit
+chrUn_gl000240 41933 /gbdb/hg19/hg19.2bit
+chr17_gl000206_random 41001 /gbdb/hg19/hg19.2bit
+chrUn_gl000232 40652 /gbdb/hg19/hg19.2bit
+chrUn_gl000234 40531 /gbdb/hg19/hg19.2bit
+chr11_gl000202_random 40103 /gbdb/hg19/hg19.2bit
+chrUn_gl000238 39939 /gbdb/hg19/hg19.2bit
+chrUn_gl000244 39929 /gbdb/hg19/hg19.2bit
+chrUn_gl000248 39786 /gbdb/hg19/hg19.2bit
+chr8_gl000196_random 38914 /gbdb/hg19/hg19.2bit
+chrUn_gl000249 38502 /gbdb/hg19/hg19.2bit
+chrUn_gl000246 38154 /gbdb/hg19/hg19.2bit
+chr17_gl000203_random 37498 /gbdb/hg19/hg19.2bit
+chr8_gl000197_random 37175 /gbdb/hg19/hg19.2bit
+chrUn_gl000245 36651 /gbdb/hg19/hg19.2bit
+chrUn_gl000247 36422 /gbdb/hg19/hg19.2bit
+chr9_gl000201_random 36148 /gbdb/hg19/hg19.2bit
+chrUn_gl000235 34474 /gbdb/hg19/hg19.2bit
+chrUn_gl000239 33824 /gbdb/hg19/hg19.2bit
+chr21_gl000210_random 27682 /gbdb/hg19/hg19.2bit
+chrUn_gl000231 27386 /gbdb/hg19/hg19.2bit
+chrUn_gl000229 19913 /gbdb/hg19/hg19.2bit
+chrM 16571 /gbdb/hg19/hg19.2bit
+chrUn_gl000226 15008 /gbdb/hg19/hg19.2bit
+chr18_gl000207_random 4262 /gbdb/hg19/hg19.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/mm8.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/mm8.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,34 @@
+chr1 197069962 /gbdb/mm8/mm8.2bit
+chr2 181976762 /gbdb/mm8/mm8.2bit
+chr3 159872112 /gbdb/mm8/mm8.2bit
+chr4 155029701 /gbdb/mm8/mm8.2bit
+chr5 152003063 /gbdb/mm8/mm8.2bit
+chr6 149525685 /gbdb/mm8/mm8.2bit
+chr7 145134094 /gbdb/mm8/mm8.2bit
+chr8 132085098 /gbdb/mm8/mm8.2bit
+chr9 124000669 /gbdb/mm8/mm8.2bit
+chrM 16299 /gbdb/mm8/mm8.2bit
+chrX 165556469 /gbdb/mm8/mm8.2bit
+chrY 16029404 /gbdb/mm8/mm8.2bit
+chr10 129959148 /gbdb/mm8/mm8.2bit
+chr11 121798632 /gbdb/mm8/mm8.2bit
+chr12 120463159 /gbdb/mm8/mm8.2bit
+chr13 120614378 /gbdb/mm8/mm8.2bit
+chr14 123978870 /gbdb/mm8/mm8.2bit
+chr15 103492577 /gbdb/mm8/mm8.2bit
+chr16 98252459 /gbdb/mm8/mm8.2bit
+chr17 95177420 /gbdb/mm8/mm8.2bit
+chr18 90736837 /gbdb/mm8/mm8.2bit
+chr19 61321190 /gbdb/mm8/mm8.2bit
+chr1_random 172274 /gbdb/mm8/mm8.2bit
+chr5_random 2921247 /gbdb/mm8/mm8.2bit
+chr7_random 243910 /gbdb/mm8/mm8.2bit
+chr8_random 206961 /gbdb/mm8/mm8.2bit
+chr9_random 17232 /gbdb/mm8/mm8.2bit
+chrX_random 39696 /gbdb/mm8/mm8.2bit
+chrY_random 14577732 /gbdb/mm8/mm8.2bit
+chr10_random 10781 /gbdb/mm8/mm8.2bit
+chr13_random 436191 /gbdb/mm8/mm8.2bit
+chr15_random 105932 /gbdb/mm8/mm8.2bit
+chr17_random 89091 /gbdb/mm8/mm8.2bit
+chrUn_random 1540053 /gbdb/mm8/mm8.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/mm9.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/mm9.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,35 @@
+chr1 197195432 /gbdb/mm9/mm9.2bit
+chr2 181748087 /gbdb/mm9/mm9.2bit
+chr3 159599783 /gbdb/mm9/mm9.2bit
+chr4 155630120 /gbdb/mm9/mm9.2bit
+chr5 152537259 /gbdb/mm9/mm9.2bit
+chr6 149517037 /gbdb/mm9/mm9.2bit
+chr7 152524553 /gbdb/mm9/mm9.2bit
+chr8 131738871 /gbdb/mm9/mm9.2bit
+chr9 124076172 /gbdb/mm9/mm9.2bit
+chr10 129993255 /gbdb/mm9/mm9.2bit
+chr11 121843856 /gbdb/mm9/mm9.2bit
+chr12 121257530 /gbdb/mm9/mm9.2bit
+chr13 120284312 /gbdb/mm9/mm9.2bit
+chr14 125194864 /gbdb/mm9/mm9.2bit
+chr15 103494974 /gbdb/mm9/mm9.2bit
+chr16 98319150 /gbdb/mm9/mm9.2bit
+chr17 95272651 /gbdb/mm9/mm9.2bit
+chr18 90772031 /gbdb/mm9/mm9.2bit
+chr19 61342430 /gbdb/mm9/mm9.2bit
+chrX 166650296 /gbdb/mm9/mm9.2bit
+chrY 15902555 /gbdb/mm9/mm9.2bit
+chrM 16299 /gbdb/mm9/mm9.2bit
+chr13_random 400311 /gbdb/mm9/mm9.2bit
+chr16_random 3994 /gbdb/mm9/mm9.2bit
+chr17_random 628739 /gbdb/mm9/mm9.2bit
+chr1_random 1231697 /gbdb/mm9/mm9.2bit
+chr3_random 41899 /gbdb/mm9/mm9.2bit
+chr4_random 160594 /gbdb/mm9/mm9.2bit
+chr5_random 357350 /gbdb/mm9/mm9.2bit
+chr7_random 362490 /gbdb/mm9/mm9.2bit
+chr8_random 849593 /gbdb/mm9/mm9.2bit
+chr9_random 449403 /gbdb/mm9/mm9.2bit
+chrUn_random 5900358 /gbdb/mm9/mm9.2bit
+chrX_random 1785075 /gbdb/mm9/mm9.2bit
+chrY_random 58682461 /gbdb/mm9/mm9.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/panTro3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/panTro3.txt Mon Nov 21 08:12:19 2011 -0500

b'@@ -0,0 +1,24132 @@\n+chr2B\t247518478\t/gbdb/panTro3/panTro3.2bit\n+chr1\t228333871\t/gbdb/panTro3/panTro3.2bit\n+chr3\t202329955\t/gbdb/panTro3/panTro3.2bit\n+chr4\t193495092\t/gbdb/panTro3/panTro3.2bit\n+chr5\t182651097\t/gbdb/panTro3/panTro3.2bit\n+chr6\t172623881\t/gbdb/panTro3/panTro3.2bit\n+chr7\t161824586\t/gbdb/panTro3/panTro3.2bit\n+chrX\t156848144\t/gbdb/panTro3/panTro3.2bit\n+chr8\t143986469\t/gbdb/panTro3/panTro3.2bit\n+chr9\t137840987\t/gbdb/panTro3/panTro3.2bit\n+chr12\t134246214\t/gbdb/panTro3/panTro3.2bit\n+chr10\t133524379\t/gbdb/panTro3/panTro3.2bit\n+chr11\t133121534\t/gbdb/panTro3/panTro3.2bit\n+chr13\t115123233\t/gbdb/panTro3/panTro3.2bit\n+chr2A\t113622374\t/gbdb/panTro3/panTro3.2bit\n+chr14\t106544938\t/gbdb/panTro3/panTro3.2bit\n+chr15\t99548318\t/gbdb/panTro3/panTro3.2bit\n+chr16\t89983829\t/gbdb/panTro3/panTro3.2bit\n+chr17\t82630442\t/gbdb/panTro3/panTro3.2bit\n+chr18\t76611499\t/gbdb/panTro3/panTro3.2bit\n+chr19\t63644993\t/gbdb/panTro3/panTro3.2bit\n+chr20\t61729293\t/gbdb/panTro3/panTro3.2bit\n+chr22\t49737984\t/gbdb/panTro3/panTro3.2bit\n+chr21\t32799110\t/gbdb/panTro3/panTro3.2bit\n+chrY\t23952694\t/gbdb/panTro3/panTro3.2bit\n+chr13_GL392075_random\t7510047\t/gbdb/panTro3/panTro3.2bit\n+chr11_GL391837_random\t5442033\t/gbdb/panTro3/panTro3.2bit\n+chr6_GL390389_random\t4046914\t/gbdb/panTro3/panTro3.2bit\n+chr8_GL390916_random\t3851136\t/gbdb/panTro3/panTro3.2bit\n+chr10_GL391668_random\t2614554\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393505\t1195001\t/gbdb/panTro3/panTro3.2bit\n+chr17_GL392652_random\t1012752\t/gbdb/panTro3/panTro3.2bit\n+chr19_GL392890_random\t922365\t/gbdb/panTro3/panTro3.2bit\n+chr4_GL389982_random\t806427\t/gbdb/panTro3/panTro3.2bit\n+chr9_GL391077_random\t720526\t/gbdb/panTro3/panTro3.2bit\n+chr15_GL392258_random\t711350\t/gbdb/panTro3/panTro3.2bit\n+chr17_GL392680_random\t691484\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393516\t597384\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393518\t573897\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393522\t458469\t/gbdb/panTro3/panTro3.2bit\n+chr20_GL393023_random\t436282\t/gbdb/panTro3/panTro3.2bit\n+chr2A_GL389368_random\t417915\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393519\t413329\t/gbdb/panTro3/panTro3.2bit\n+chr16_GL392457_random\t408961\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393523\t405060\t/gbdb/panTro3/panTro3.2bit\n+chr7_GL390650_random\t398731\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393524\t393793\t/gbdb/panTro3/panTro3.2bit\n+chr18_GL392798_random\t373489\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393525\t371432\t/gbdb/panTro3/panTro3.2bit\n+chr16_GL392524_random\t370847\t/gbdb/panTro3/panTro3.2bit\n+chrX_GL393313_random\t364597\t/gbdb/panTro3/panTro3.2bit\n+chr20_GL393019_random\t358895\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393530\t355541\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393527\t341619\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393542\t339612\t/gbdb/panTro3/panTro3.2bit\n+chrY_DP000056_random\t331329\t/gbdb/panTro3/panTro3.2bit\n+chr22_GL393078_random\t277661\t/gbdb/panTro3/panTro3.2bit\n+chrY_DP000055_random\t276070\t/gbdb/panTro3/panTro3.2bit\n+chr16_GL392506_random\t257012\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393533\t243864\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393535\t241809\t/gbdb/panTro3/panTro3.2bit\n+chr8_GL390880_random\t230064\t/gbdb/panTro3/panTro3.2bit\n+chr7_GL390654_random\t229574\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393532\t223908\t/gbdb/panTro3/panTro3.2bit\n+chr14_GL392151_random\t223111\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393534\t222311\t/gbdb/panTro3/panTro3.2bit\n+chr9_GL391203_random\t222250\t/gbdb/panTro3/panTro3.2bit\n+chr7_GL390752_random\t218097\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393539\t212451\t/gbdb/panTro3/panTro3.2bit\n+chr17_GL392651_random\t209936\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393541\t207381\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393537\t206612\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL396822\t202225\t/gbdb/panTro3/panTro3.2bit\n+chrX_GL393375_random\t197187\t/gbdb/panTro3/panTro3.2bit\n+chrUn_GL393540\t192064\t/gbdb/panTro3/panTro3.2bit\n+chr1_GL389174_random\t191010\t/gbdb/panTro3/panTro3.2bit\n+chr10_GL391667_random\t190155\t/gbdb/panTro3/panTro3.2bit\n+chr17_GL392675_random\t188176\t/gbdb/panTro3/panTro3.2bit\n+chr15_GL392289_random\t1'..b'it\n+chr6_AACZ03160190_random\t1178\t/gbdb/panTro3/panTro3.2bit\n+chr9_AACZ03165271_random\t1166\t/gbdb/panTro3/panTro3.2bit\n+chr18_AACZ03175668_random\t1158\t/gbdb/panTro3/panTro3.2bit\n+chr6_AACZ03160191_random\t1143\t/gbdb/panTro3/panTro3.2bit\n+chr19_AACZ03176425_random\t1126\t/gbdb/panTro3/panTro3.2bit\n+chr12_AACZ03170019_random\t1124\t/gbdb/panTro3/panTro3.2bit\n+chr11_AACZ03169134_random\t1121\t/gbdb/panTro3/panTro3.2bit\n+chrX_AACZ03178602_random\t1120\t/gbdb/panTro3/panTro3.2bit\n+chr20_AACZ03176904_random\t1117\t/gbdb/panTro3/panTro3.2bit\n+chr6_AACZ03159656_random\t1114\t/gbdb/panTro3/panTro3.2bit\n+chr2B_AACZ03153615_random\t1113\t/gbdb/panTro3/panTro3.2bit\n+chr19_AACZ03176437_random\t1104\t/gbdb/panTro3/panTro3.2bit\n+chr3_AACZ03155018_random\t1100\t/gbdb/panTro3/panTro3.2bit\n+chr9_AACZ03165347_random\t1090\t/gbdb/panTro3/panTro3.2bit\n+chr15_AACZ03172446_random\t1079\t/gbdb/panTro3/panTro3.2bit\n+chr1_AACZ03151783_random\t1075\t/gbdb/panTro3/panTro3.2bit\n+chr1_AACZ03151688_random\t1073\t/gbdb/panTro3/panTro3.2bit\n+chr8_AACZ03163611_random\t1073\t/gbdb/panTro3/panTro3.2bit\n+chr15_AACZ03172500_random\t1070\t/gbdb/panTro3/panTro3.2bit\n+chr11_AACZ03169120_random\t1065\t/gbdb/panTro3/panTro3.2bit\n+chr1_AACZ03151643_random\t1057\t/gbdb/panTro3/panTro3.2bit\n+chr12_AACZ03169983_random\t1038\t/gbdb/panTro3/panTro3.2bit\n+chr5_AACZ03158305_random\t1036\t/gbdb/panTro3/panTro3.2bit\n+chr5_AACZ03158221_random\t1035\t/gbdb/panTro3/panTro3.2bit\n+chr12_AACZ03170032_random\t1032\t/gbdb/panTro3/panTro3.2bit\n+chr18_AACZ03175672_random\t1016\t/gbdb/panTro3/panTro3.2bit\n+chr2B_AACZ03153607_random\t1015\t/gbdb/panTro3/panTro3.2bit\n+chr14_AACZ03171691_random\t1008\t/gbdb/panTro3/panTro3.2bit\n+chr8_AACZ03163602_random\t995\t/gbdb/panTro3/panTro3.2bit\n+chr7_AACZ03162167_random\t992\t/gbdb/panTro3/panTro3.2bit\n+chr11_AACZ03169132_random\t981\t/gbdb/panTro3/panTro3.2bit\n+chr14_AACZ03171726_random\t977\t/gbdb/panTro3/panTro3.2bit\n+chr1_AACZ03151510_random\t967\t/gbdb/panTro3/panTro3.2bit\n+chr16_AACZ03174069_random\t965\t/gbdb/panTro3/panTro3.2bit\n+chr18_AACZ03175682_random\t960\t/gbdb/panTro3/panTro3.2bit\n+chr14_AACZ03171712_random\t959\t/gbdb/panTro3/panTro3.2bit\n+chrX_AACZ03178598_random\t958\t/gbdb/panTro3/panTro3.2bit\n+chr8_AACZ03163637_random\t957\t/gbdb/panTro3/panTro3.2bit\n+chr9_AACZ03165403_random\t946\t/gbdb/panTro3/panTro3.2bit\n+chr11_AACZ03169131_random\t930\t/gbdb/panTro3/panTro3.2bit\n+chr14_AACZ03171718_random\t925\t/gbdb/panTro3/panTro3.2bit\n+chrX_AACZ03178599_random\t901\t/gbdb/panTro3/panTro3.2bit\n+chr3_AACZ03155017_random\t900\t/gbdb/panTro3/panTro3.2bit\n+chr3_AACZ03155010_random\t899\t/gbdb/panTro3/panTro3.2bit\n+chr8_AACZ03163641_random\t897\t/gbdb/panTro3/panTro3.2bit\n+chr8_AACZ03163613_random\t896\t/gbdb/panTro3/panTro3.2bit\n+chr2B_AACZ03153521_random\t885\t/gbdb/panTro3/panTro3.2bit\n+chr3_AACZ03155053_random\t882\t/gbdb/panTro3/panTro3.2bit\n+chr1_AACZ03151847_random\t873\t/gbdb/panTro3/panTro3.2bit\n+chr2A_AACZ03152669_random\t873\t/gbdb/panTro3/panTro3.2bit\n+chr1_AACZ03151840_random\t870\t/gbdb/panTro3/panTro3.2bit\n+chr2A_AACZ03152778_random\t851\t/gbdb/panTro3/panTro3.2bit\n+chr4_AACZ03156965_random\t850\t/gbdb/panTro3/panTro3.2bit\n+chr8_AACZ03163636_random\t829\t/gbdb/panTro3/panTro3.2bit\n+chr16_AACZ03174058_random\t822\t/gbdb/panTro3/panTro3.2bit\n+chr12_AACZ03170074_random\t821\t/gbdb/panTro3/panTro3.2bit\n+chr13_AACZ03171025_random\t814\t/gbdb/panTro3/panTro3.2bit\n+chr17_AACZ03175059_random\t801\t/gbdb/panTro3/panTro3.2bit\n+chr2A_AACZ03152776_random\t801\t/gbdb/panTro3/panTro3.2bit\n+chr4_AACZ03157024_random\t796\t/gbdb/panTro3/panTro3.2bit\n+chr11_AACZ03169133_random\t778\t/gbdb/panTro3/panTro3.2bit\n+chr4_AACZ03157023_random\t773\t/gbdb/panTro3/panTro3.2bit\n+chr7_AACZ03162166_random\t764\t/gbdb/panTro3/panTro3.2bit\n+chr11_AACZ03169135_random\t762\t/gbdb/panTro3/panTro3.2bit\n+chr18_AACZ03175702_random\t741\t/gbdb/panTro3/panTro3.2bit\n+chr6_AACZ03158310_random\t740\t/gbdb/panTro3/panTro3.2bit\n+chr2B_AACZ03153257_random\t661\t/gbdb/panTro3/panTro3.2bit\n+chr16_AACZ03174065_random\t659\t/gbdb/panTro3/panTro3.2bit\n+chr1_AACZ03151841_random\t373\t/gbdb/panTro3/panTro3.2bit\n'

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/rn3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/rn3.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,44 @@
+chr1 268121971 /gbdb/rn3/nib/chr1.nib
+chr2 258222147 /gbdb/rn3/nib/chr2.nib
+chr3 170969371 /gbdb/rn3/nib/chr3.nib
+chr4 187371129 /gbdb/rn3/nib/chr4.nib
+chr5 173106704 /gbdb/rn3/nib/chr5.nib
+chr6 147642806 /gbdb/rn3/nib/chr6.nib
+chr7 143082968 /gbdb/rn3/nib/chr7.nib
+chr8 129061546 /gbdb/rn3/nib/chr8.nib
+chr9 113649943 /gbdb/rn3/nib/chr9.nib
+chrX 160775580 /gbdb/rn3/nib/chrX.nib
+chr1_random 3887217 /gbdb/rn3/nib/chr1_random.nib
+chr2_random 4341851 /gbdb/rn3/nib/chr2_random.nib
+chr3_random 1724363 /gbdb/rn3/nib/chr3_random.nib
+chr4_random 2124656 /gbdb/rn3/nib/chr4_random.nib
+chr5_random 2145107 /gbdb/rn3/nib/chr5_random.nib
+chr6_random 1770534 /gbdb/rn3/nib/chr6_random.nib
+chr7_random 1175105 /gbdb/rn3/nib/chr7_random.nib
+chr8_random 887087 /gbdb/rn3/nib/chr8_random.nib
+chr9_random 1166303 /gbdb/rn3/nib/chr9_random.nib
+chrX_random 1977738 /gbdb/rn3/nib/chrX_random.nib
+chr10 110733352 /gbdb/rn3/nib/chr10.nib
+chr11 87800381 /gbdb/rn3/nib/chr11.nib
+chr12 46649226 /gbdb/rn3/nib/chr12.nib
+chr13 111348958 /gbdb/rn3/nib/chr13.nib
+chr14 112220682 /gbdb/rn3/nib/chr14.nib
+chr15 109774626 /gbdb/rn3/nib/chr15.nib
+chr16 90224819 /gbdb/rn3/nib/chr16.nib
+chr17 97307196 /gbdb/rn3/nib/chr17.nib
+chr18 87338544 /gbdb/rn3/nib/chr18.nib
+chr19 59223525 /gbdb/rn3/nib/chr19.nib
+chr20 55296979 /gbdb/rn3/nib/chr20.nib
+chrUn 75822765 /gbdb/rn3/nib/chrUn.nib
+chr10_random 870782 /gbdb/rn3/nib/chr10_random.nib
+chr11_random 1278614 /gbdb/rn3/nib/chr11_random.nib
+chr12_random 953141 /gbdb/rn3/nib/chr12_random.nib
+chr13_random 608348 /gbdb/rn3/nib/chr13_random.nib
+chr14_random 1825095 /gbdb/rn3/nib/chr14_random.nib
+chr15_random 1609635 /gbdb/rn3/nib/chr15_random.nib
+chr16_random 1400107 /gbdb/rn3/nib/chr16_random.nib
+chr17_random 615889 /gbdb/rn3/nib/chr17_random.nib
+chr18_random 594525 /gbdb/rn3/nib/chr18_random.nib
+chr19_random 984116 /gbdb/rn3/nib/chr19_random.nib
+chr20_random 604928 /gbdb/rn3/nib/chr20_random.nib
+chrUn_random 6862066 /gbdb/rn3/nib/chrUn_random.nib

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/rn4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/rn4.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,45 @@
+chr1 267910886 /gbdb/rn4/rn4.2bit
+chr1_random 3887217 /gbdb/rn4/rn4.2bit
+chr10 110718848 /gbdb/rn4/rn4.2bit
+chr10_random 870782 /gbdb/rn4/rn4.2bit
+chr11 87759784 /gbdb/rn4/rn4.2bit
+chr11_random 1278614 /gbdb/rn4/rn4.2bit
+chr12 46782294 /gbdb/rn4/rn4.2bit
+chr12_random 953141 /gbdb/rn4/rn4.2bit
+chr13 111154910 /gbdb/rn4/rn4.2bit
+chr13_random 608348 /gbdb/rn4/rn4.2bit
+chr14 112194335 /gbdb/rn4/rn4.2bit
+chr14_random 1825095 /gbdb/rn4/rn4.2bit
+chr15 109758846 /gbdb/rn4/rn4.2bit
+chr15_random 1609635 /gbdb/rn4/rn4.2bit
+chr16 90238779 /gbdb/rn4/rn4.2bit
+chr16_random 1400107 /gbdb/rn4/rn4.2bit
+chr17 97296363 /gbdb/rn4/rn4.2bit
+chr17_random 615889 /gbdb/rn4/rn4.2bit
+chr18 87265094 /gbdb/rn4/rn4.2bit
+chr18_random 594525 /gbdb/rn4/rn4.2bit
+chr19 59218465 /gbdb/rn4/rn4.2bit
+chr19_random 984116 /gbdb/rn4/rn4.2bit
+chr2 258207540 /gbdb/rn4/rn4.2bit
+chr2_random 4341851 /gbdb/rn4/rn4.2bit
+chr20 55268282 /gbdb/rn4/rn4.2bit
+chr20_random 604928 /gbdb/rn4/rn4.2bit
+chr3 171063335 /gbdb/rn4/rn4.2bit
+chr3_random 1724363 /gbdb/rn4/rn4.2bit
+chr4 187126005 /gbdb/rn4/rn4.2bit
+chr4_random 2124656 /gbdb/rn4/rn4.2bit
+chr5 173096209 /gbdb/rn4/rn4.2bit
+chr5_random 2145107 /gbdb/rn4/rn4.2bit
+chr6 147636619 /gbdb/rn4/rn4.2bit
+chr6_random 1770534 /gbdb/rn4/rn4.2bit
+chr7 143002779 /gbdb/rn4/rn4.2bit
+chr7_random 1175105 /gbdb/rn4/rn4.2bit
+chr8 129041809 /gbdb/rn4/rn4.2bit
+chr8_random 887087 /gbdb/rn4/rn4.2bit
+chr9 113440463 /gbdb/rn4/rn4.2bit
+chr9_random 1166303 /gbdb/rn4/rn4.2bit
+chrM 16300 /gbdb/rn4/rn4.2bit
+chrUn 75822765 /gbdb/rn4/rn4.2bit
+chrUn_random 6862066 /gbdb/rn4/rn4.2bit
+chrX 160699376 /gbdb/rn4/rn4.2bit
+chrX_random 1977738 /gbdb/rn4/rn4.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/chromInfo/susScr2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/chromInfo/susScr2.txt Mon Nov 21 08:12:19 2011 -0500

@@ -0,0 +1,20 @@
+chr1 295529705 /gbdb/susScr2/susScr2.2bit
+chr14 148510138 /gbdb/susScr2/susScr2.2bit
+chr13 145235301 /gbdb/susScr2/susScr2.2bit
+chr2 140133492 /gbdb/susScr2/susScr2.2bit
+chr7 136409062 /gbdb/susScr2/susScr2.2bit
+chr4 136254946 /gbdb/susScr2/susScr2.2bit
+chr15 134541103 /gbdb/susScr2/susScr2.2bit
+chr9 132468591 /gbdb/susScr2/susScr2.2bit
+chrX 125871292 /gbdb/susScr2/susScr2.2bit
+chr3 123599780 /gbdb/susScr2/susScr2.2bit
+chr6 123305171 /gbdb/susScr2/susScr2.2bit
+chr8 119985671 /gbdb/susScr2/susScr2.2bit
+chr5 100516970 /gbdb/susScr2/susScr2.2bit
+chr11 79814395 /gbdb/susScr2/susScr2.2bit
+chr16 77435658 /gbdb/susScr2/susScr2.2bit
+chr10 66736929 /gbdb/susScr2/susScr2.2bit
+chr17 64395339 /gbdb/susScr2/susScr2.2bit
+chr12 57431344 /gbdb/susScr2/susScr2.2bit
+chr18 54309914 /gbdb/susScr2/susScr2.2bit
+chrM 16770 /gbdb/susScr2/susScr2.2bit

diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/fetchChromSizes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/thirdparty/fetchChromSizes Mon Nov 21 08:12:19 2011 -0500

[

@@ -0,0 +1,94 @@
+#!/bin/sh
+
+# fetchChromSizes - script to grab chrom.sizes from UCSC via either of:
+# mysql, wget or ftp
+
+# "$Id: fetchChromSizes,v 1.2 2009/03/26 18:40:09 hiram Exp $"
+
+usage() {
+ echo "usage: fetchChromSizes <db> > <db>.chrom.sizes"
+ echo " used to fetch chrom.sizes information from UCSC for the given <db>"
+ echo "<db> - name of UCSC database, e.g.: hg18, mm9, etc ..."
+ echo ""
+ echo "This script expects to find one of the following commands:"
+ echo " wget, mysql, or ftp in order to fetch information from UCSC."
+ echo "Route the output to the file <db>.chrom.sizes as indicated above."
+ echo ""
+ echo "Example: fetchChromSizes hg18 > hg18.chrom.sizes"
+ exit 255
+}
+
+DB=$1
+export DB
+if [ -z "${DB}" ]; then
+ usage
+fi
+
+WGET=`type wget 2> /dev/null | sed -e "s/.* is //"`
+MYSQL=`type mysql 2> /dev/null | sed -e "s/.* is //"`
+FTP=`type ftp 2> /dev/null | sed -e "s/.* is //"`
+
+if [ -z "${WGET}" -a -z "${MYSQL}" -a -z "${FTP}" ]; then
+ echo "ERROR: can not find any of the commands: wget mysql or ftp"
+ usage
+fi
+
+DONE=0
+export DONE
+if [ -n "${MYSQL}" ]; then
+ echo "INFO: trying MySQL ${MYSQL} for database ${DB}" 1>&2
+ ${MYSQL} -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
+ "SELECT chrom,size FROM chromInfo ORDER BY size DESC;" ${DB}
+ if [ $? -ne 0 ]; then
+ echo "WARNING: mysql command failed" 1>&2
+ else
+ DONE=1
+ fi
+fi
+
+if [ "${DONE}" -eq 1 ]; then
+ exit 0
+fi
+
+if [ -n "${WGET}" ]; then
+ echo "INFO: trying WGET ${WGET} for database ${DB}" 1>&2
+ tmpResult=chromInfoTemp.$$.gz
+ ${WGET} \
+"ftp://hgdownload.cse.ucsc.edu/goldenPath/${DB}/database/chromInfo.txt.gz" \
+ -O ${tmpResult} 2> /dev/null
+ if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then
+ echo "WARNING: wget command failed" 1>&2
+ rm -f "${tmpResult}"
+ else
+ zcat ${tmpResult} 2> /dev/null | cut -f1,2 | sort -k2nr
+ rm -f "${tmpResult}"
+ DONE=1
+ fi
+fi
+
+if [ "${DONE}" -eq 1 ]; then
+ exit 0
+fi
+
+if [ -n "${FTP}" ]; then
+ echo "INFO: trying FTP ${FTP} for database ${DB}" 1>&2
+ tmpFtpRsp=fetchTemp.$$
+ echo "user anonymous fetchChromSizes@" > ${tmpFtpRsp}
+ echo "cd goldenPath/${DB}/database" >> ${tmpFtpRsp}
+ echo "get chromInfo.txt.gz ${tmpResult}" >> ${tmpFtpRsp}
+ echo "bye" >> ${tmpFtpRsp}
+ ${FTP} -u -n -i hgdownload.cse.ucsc.edu < ${tmpFtpRsp} > /dev/null 2>&1
+ if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then
+ echo "ERROR: ftp command failed" 1>&2
+ rm -f "${tmpFtpRsp}" "${tmpResult}"
+ else
+ zcat ${tmpResult} | cut -f1,2 | sort -k2nr
+ rm -f "${tmpFtpRsp}" "${tmpResult}"
+ DONE=1
+ fi
+fi
+
+if [ "${DONE}" -eq 0 ]; then
+ echo "ERROR: sorry, attempt to fetch chrom.sizes has failed ?" 1>&2
+ exit 255
+fi

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diff -r 000000000000 -r 89ad0a9cca52 NGSrich_0.5.5/thirdparty/wigToBigWig

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