changeset 39:c3e2db435a83 draft

Deleted selected files

Binary file ._datatypes_conf.xml has changed

Binary file ._fasta_to_bwa_index_converter.xml has changed

Binary file ._fasta_to_star_index_converter.xml has changed

Binary file ._jqBarGraph.1.1.min.js has changed

Binary file ._jqBarGraph.2.1.js has changed

Binary file ._jqBarGraph.2.1.min.js has changed

Binary file ._jquery-1.10.2.min.js has changed

Binary file ._tool_dependencies.xml has changed

Binary file ._vhom.py has changed

Binary file ._vhom_region.xml has changed

Binary file ._vhom_regionplot.py has changed

Binary file ._vhom_regions.py has changed

Binary file ._vmap.py has changed

Binary file ._vmap_dnaindex.py has changed

Binary file ._vmap_dnamap.xml has changed

Binary file ._vmap_rnaindex.py has changed

Binary file ._vmap_rnamap.xml has changed

Binary file ._vref.py has changed

Binary file ._vref_blast.xml has changed

Binary file ._vref_fasta.xml has changed

--- a/jqBarGraph.1.1.min.js	Wed Sep 25 08:55:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-/**
- * jqBarGraph - jQuery plugin
- * @version: 1.1 (2011/04/03)
- * @requires jQuery v1.2.2 or later 
- * @author Ivan Lazarevic
- * Examples and documentation at: http://www.workshop.rs/jqbargraph/
- * 
- * Dual licensed under the MIT and GPL licenses:
- *   http://www.opensource.org/licenses/mit-license.php
- *   http://www.gnu.org/licenses/gpl.html
- * 
- */
-
-(function($){var opts=new Array;var level=new Array;$.fn.jqBarGraph=$.fn.jqbargraph=function(options){init=function(el){opts[el.id]=$.extend({},$.fn.jqBarGraph.defaults,options);$(el).css({'width':opts[el.id].width,'height':opts[el.id].height,'position':'relative','text-align':'center'});doGraph(el);};sum=function(ar){total=0;for(val in ar){total+=ar[val];}
-return total.toFixed(2);};max=function(ar){maxvalue=0;for(var val in ar){value=ar[val][0];if(value instanceof Array)value=sum(value);if(parseFloat(value)>parseFloat(maxvalue))maxvalue=value;}
-return maxvalue;};maxMulti=function(ar){maxvalue=0;maxvalue2=0;for(var val in ar){ar2=ar[val][0];for(var val2 in ar2){if(ar2[val2]>maxvalue2)maxvalue2=ar2[val2];}
-if(maxvalue2>maxvalue)maxvalue=maxvalue2;}
-return maxvalue;};doGraph=function(el){arr=opts[el.id];data=arr.data;if(data==undefined){$(el).html('There is not enought data for graph');return;}
-if(arr.sort=='asc')data.sort(sortNumberAsc);if(arr.sort=='desc')data.sort(sortNumberDesc);legend='';prefix=arr.prefix;postfix=arr.postfix;space=arr.barSpace;legendWidth=arr.legend?arr.legendWidth:0;fieldWidth=($(el).width()-legendWidth)/data.length;totalHeight=$(el).height();var leg=new Array();max=max(data);colPosition=0;for(var val in data){valueData=data[val][0];if(valueData instanceof Array)
-value=sum(valueData);else
-value=valueData;lbl=data[val][1];color=data[val][2];unique=val+el.id;if(color==undefined&&arr.colors==false)
-color=arr.color;if(arr.colors&&!color){colorsCounter=arr.colors.length;if(colorsCounter==colPosition)colPosition=0;color=arr.colors[colPosition];colPosition++;}
-if(arr.type=='multi')color='none';if(lbl==undefined)lbl=arr.lbl;out="<div class='graphField"+el.id+"' id='graphField"+unique+"' style='position: absolute'>";out+="<div class='graphValue"+el.id+"' id='graphValue"+unique+"'>"+prefix+value+postfix+"</div>";out+="<div class='graphBar"+el.id+"' id='graphFieldBar"+unique+"' style='background-color:"+color+";position: relative; overflow: hidden;'></div>";if(!arr.legend||arr.legends)
-out+="<div class='graphLabel"+el.id+"' id='graphLabel"+unique+"'>"+lbl+"</div>";out+="</div>";$(el).append(out);totalHeightBar=totalHeight-$('.graphLabel'+el.id).height()-$('.graphValue'+el.id).height();fieldHeight=(totalHeightBar*value)/max;$('#graphField'+unique).css({'left':(fieldWidth)*val,'width':fieldWidth-space,'margin-left':space});if(valueData instanceof Array){if(arr.type=="multi"){maxe=maxMulti(data);totalHeightBar=fieldHeight=totalHeight-$('.graphLabel'+el.id).height();$('.graphValue'+el.id).remove();}else{maxe=max;}
-for(i in valueData){heig=totalHeightBar*valueData[i]/maxe;wid=parseInt((fieldWidth-space)/valueData.length);sv='';fs=0;if(arr.showValues){sv=arr.prefix+valueData[i]+arr.postfix;fs=12;}
-o="<div class='subBars"+el.id+"' style='height:"+heig+"px; background-color: "+arr.colors[i]+"; left:"+wid*i+"px; color:"+arr.showValuesColor+"; font-size:"+fs+"px' >"+sv+"</div>";$('#graphFieldBar'+unique).prepend(o);}}
-if(arr.type=='multi')
-$('.subBars'+el.id).css({'width':wid,'position':'absolute','bottom':0});if(arr.position=='bottom')$('.graphField'+el.id).css('bottom',0);if(!arr.legends)
-leg.push([color,lbl,el.id,unique]);if(arr.animate){$('#graphFieldBar'+unique).css({'height':0});$('#graphFieldBar'+unique).animate({'height':fieldHeight},arr.speed*1000);}else{$('#graphFieldBar'+unique).css({'height':fieldHeight});}}
-for(var l in arr.legends){leg.push([arr.colors[l],arr.legends[l],el.id,l]);}
-createLegend(leg);if(arr.legend){$(el).append("<div id='legendHolder"+unique+"'></div>");$('#legendHolder'+unique).css({'width':legendWidth,'float':'right','text-align':'left'});$('#legendHolder'+unique).append(legend);$('.legendBar'+el.id).css({'float':'left','margin':3,'height':12,'width':20,'font-size':0});}
-if(arr.title){$(el).wrap("<div id='graphHolder"+unique+"'></div>");$('#graphHolder'+unique).prepend(arr.title).css({'width':arr.width+'px','text-align':'center'});}};createLegend=function(legendArr){legend='';for(var val in legendArr){legend+="<div id='legend"+legendArr[val][3]+"' style='overflow: hidden; zoom: 1;'>";legend+="<div class='legendBar"+legendArr[val][2]+"' id='legendColor"+legendArr[val][3]+"' style='background-color:"+legendArr[val][0]+"'></div>";legend+="<div class='legendLabel"+legendArr[val][2]+"' id='graphLabel"+unique+"'>"+legendArr[val][1]+"</div>";legend+="</div>";}};this.each(function()
-{init(this);})};$.fn.jqBarGraph.defaults={barSpace:10,width:400,height:300,color:'#000000',colors:false,lbl:'',sort:false,position:'bottom',prefix:'',postfix:'',animate:true,speed:1.5,legendWidth:100,legend:false,legends:false,type:false,showValues:true,showValuesColor:'#fff',title:false};function sortNumberAsc(a,b){if(a[0]<b[0])return-1;if(a[0]>b[0])return 1;return 0;}
-function sortNumberDesc(a,b){if(a[0]>b[0])return-1;if(a[0]<b[0])return 1;return 0;}})(jQuery);
\ No newline at end of file

--- a/vhom_regions.py	Wed Sep 25 08:55:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-from argparse import ArgumentParser
-import os
-from vhom import RegionRunner
-
-
-def printDir(directory):
-    rval=["<ul>"]
-    flist = os.listdir(directory)
-    
-    for entry in flist:
-        if(os.path.isdir(os.path.join(directory,entry))):
-             rval.append('<li>%s</li>'%entry)
-             rval.extend(printDir(os.path.join(directory,entry)))
-        else:
-            rval.append( '<li><a href="%s">%s</a></li>' % ( os.path.join(directory,entry), entry) )     
-    rval.append("</ul>")
-    return rval
-
-
-
-if __name__ == "__main__":
-    
-    
-    parser = ArgumentParser()
-    
-    a = parser.add_argument
-    a("-o","--html_file",dest="html_file")
-    a("-d","--directory",dest="directory")
-      
-    (options,args)= parser.parse_known_args()
-    
-    args.insert(0,"dummy")
-    try:
-        RegionRunner.run(argv=args)
-    except SystemExit:
-        f = open(options.html_file,'w')
-        rval = ["<html><head><title>Homologous groups and regions derived from hit files </title></head><body><p/>\n"]
-        rval.append('<div>This composite dataset is composed of the following files:<p/>')
-        directory= options.directory
-        rval.extend(printDir(directory))
-        
-        rval.append( '</body></html>' )
-    
-        f.write("\n".join( rval ))
-        f.close()