| Previous changeset 11:866d22e60e60 (2014-11-13) Next changeset 13:50260274967c (2014-11-13) |
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Commit message:
Uploaded |
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modified:
r_wrapper.sh style.css |
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removed:
asc.gif bg.gif desc.gif jquery.tablesorter.min.js |
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| diff -r 866d22e60e60 -r 24a80d4eff0c asc.gif |
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| Binary file asc.gif has changed |
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| diff -r 866d22e60e60 -r 24a80d4eff0c bg.gif |
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| Binary file bg.gif has changed |
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| diff -r 866d22e60e60 -r 24a80d4eff0c desc.gif |
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| Binary file desc.gif has changed |
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| diff -r 866d22e60e60 -r 24a80d4eff0c jquery.tablesorter.min.js --- a/jquery.tablesorter.min.js Thu Nov 13 10:33:04 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,4 +0,0 @@\n-\n-(function($){$.extend({tablesorter:new\n-function(){var parsers=[],widgets=[];this.defaults={cssHeader:"header",cssAsc:"headerSortUp",cssDesc:"headerSortDown",cssChildRow:"expand-child",sortInitialOrder:"asc",sortMultiSortKey:"shiftKey",sortForce:null,sortAppend:null,sortLocaleCompare:true,textExtraction:"simple",parsers:{},widgets:[],widgetZebra:{css:["even","odd"]},headers:{},widthFixed:false,cancelSelection:true,sortList:[],headerList:[],dateFormat:"us",decimal:\'/\\.|\\,/g\',onRenderHeader:null,selectorHeaders:\'thead th\',debug:false};function benchmark(s,d){log(s+","+(new Date().getTime()-d.getTime())+"ms");}this.benchmark=benchmark;function log(s){if(typeof console!="undefined"&&typeof console.debug!="undefined"){console.log(s);}else{alert(s);}}function buildParserCache(table,$headers){if(table.config.debug){var parsersDebug="";}if(table.tBodies.length==0)return;var rows=table.tBodies[0].rows;if(rows[0]){var list=[],cells=rows[0].cells,l=cells.length;for(var i=0;i<l;i++){var p=false;if($.metadata&&($($headers[i]).metadata()&&$($headers[i]).metadata().sorter)){p=getParserById($($headers[i]).metadata().sorter);}else if((table.config.headers[i]&&table.config.headers[i].sorter)){p=getParserById(table.config.headers[i].sorter);}if(!p){p=detectParserForColumn(table,rows,-1,i);}if(table.config.debug){parsersDebug+="column:"+i+" parser:"+p.id+"\\n";}list.push(p);}}if(table.config.debug){log(parsersDebug);}return list;};function detectParserForColumn(table,rows,rowIndex,cellIndex){var l=parsers.length,node=false,nodeValue=false,keepLooking=true;while(nodeValue==\'\'&&keepLooking){rowIndex++;if(rows[rowIndex]){node=getNodeFromRowAndCellIndex(rows,rowIndex,cellIndex);nodeValue=trimAndGetNodeText(table.config,node);if(table.config.debug){log(\'Checking if value was empty on row:\'+rowIndex);}}else{keepLooking=false;}}for(var i=1;i<l;i++){if(parsers[i].is(nodeValue,table,node)){return parsers[i];}}return parsers[0];}function getNodeFromRowAndCellIndex(rows,rowIndex,cellIndex){return rows[rowIndex].cells[cellIndex];}function trimAndGetNodeText(config,node){return $.trim(getElementText(config,node));}function getParserById(name){var l=parsers.length;for(var i=0;i<l;i++){if(parsers[i].id.toLowerCase()==name.toLowerCase()){return parsers[i];}}return false;}function buildCache(table){if(table.config.debug){var cacheTime=new Date();}var totalRows=(table.tBodies[0]&&table.tBodies[0].rows.length)||0,totalCells=(table.tBodies[0].rows[0]&&table.tBodies[0].rows[0].cells.length)||0,parsers=table.config.parsers,cache={row:[],normalized:[]};for(var i=0;i<totalRows;++i){var c=$(table.tBodies[0].rows[i]),cols=[];if(c.hasClass(table.config.cssChildRow)){cache.row[cache.row.length-1]=cache.row[cache.row.length-1].add(c);continue;}cache.row.push(c);for(var j=0;j<totalCells;++j){cols.push(parsers[j].format(getElementText(table.config,c[0].cells[j]),table,c[0].cells[j]));}cols.push(cache.normalized.length);cache.normalized.push(cols);cols=null;};if(table.config.debug){benchmark("Building cache for "+totalRows+" rows:",cacheTime);}return cache;};function getElementText(config,node){var text="";if(!node)return"";if(!config.supportsTextContent)config.supportsTextContent=node.textContent||false;if(config.textExtraction=="simple"){if(config.supportsTextContent){text=node.textContent;}else{if(node.childNodes[0]&&node.childNodes[0].hasChildNodes()){text=node.childNodes[0].innerHTML;}else{text=node.innerHTML;}}}else{if(typeof(config.textExtraction)=="function"){text=config.textExtraction(node);}else{text=$(node).text();}}return text;}function appendToTable(table,cache){if(table.config.debug){var appendTime=new Date()}var c=cache,r=c.row,n=c.normalized,totalRows=n.length,checkCell=(n[0].length-1),tableBody=$(table.tBodies[0]),rows=[];for(var i=0;i<totalRows;i++){var pos=n[i][checkCell];rows.push(r[pos]);if(!table.config.appender){var l=r[pos].length;for(var j=0;j<l;j++){tableBody[0].appendChild(r[pos][j]);}}}if(table.config.appender){table.config.appende'..b'ta().sortlist)){config.sortList=$(this).metadata().sortlist;}if(config.sortList.length>0){$this.trigger("sorton",[config.sortList]);}applyWidget(this);});};this.addParser=function(parser){var l=parsers.length,a=true;for(var i=0;i<l;i++){if(parsers[i].id.toLowerCase()==parser.id.toLowerCase()){a=false;}}if(a){parsers.push(parser);};};this.addWidget=function(widget){widgets.push(widget);};this.formatFloat=function(s){var i=parseFloat(s);return(isNaN(i))?0:i;};this.formatInt=function(s){var i=parseInt(s);return(isNaN(i))?0:i;};this.isDigit=function(s,config){return/^[-+]?\\d*$/.test($.trim(s.replace(/[,.\']/g,\'\')));};this.clearTableBody=function(table){if($.browser.msie){function empty(){while(this.firstChild)this.removeChild(this.firstChild);}empty.apply(table.tBodies[0]);}else{table.tBodies[0].innerHTML="";}};}});$.fn.extend({tablesorter:$.tablesorter.construct});var ts=$.tablesorter;ts.addParser({id:"text",is:function(s){return true;},format:function(s){return $.trim(s.toLocaleLowerCase());},type:"text"});ts.addParser({id:"digit",is:function(s,table){var c=table.config;return $.tablesorter.isDigit(s,c);},format:function(s){return $.tablesorter.formatFloat(s);},type:"numeric"});ts.addParser({id:"currency",is:function(s){return/^[\xc2\xa3$\xe2\x82\xac?.]/.test(s);},format:function(s){return $.tablesorter.formatFloat(s.replace(new RegExp(/[\xc2\xa3$\xe2\x82\xac]/g),""));},type:"numeric"});ts.addParser({id:"ipAddress",is:function(s){return/^\\d{2,3}[\\.]\\d{2,3}[\\.]\\d{2,3}[\\.]\\d{2,3}$/.test(s);},format:function(s){var a=s.split("."),r="",l=a.length;for(var i=0;i<l;i++){var item=a[i];if(item.length==2){r+="0"+item;}else{r+=item;}}return $.tablesorter.formatFloat(r);},type:"numeric"});ts.addParser({id:"url",is:function(s){return/^(https?|ftp|file):\\/\\/$/.test(s);},format:function(s){return jQuery.trim(s.replace(new RegExp(/(https?|ftp|file):\\/\\//),\'\'));},type:"text"});ts.addParser({id:"isoDate",is:function(s){return/^\\d{4}[\\/-]\\d{1,2}[\\/-]\\d{1,2}$/.test(s);},format:function(s){return $.tablesorter.formatFloat((s!="")?new Date(s.replace(new RegExp(/-/g),"/")).getTime():"0");},type:"numeric"});ts.addParser({id:"percent",is:function(s){return/\\%$/.test($.trim(s));},format:function(s){return $.tablesorter.formatFloat(s.replace(new RegExp(/%/g),""));},type:"numeric"});ts.addParser({id:"usLongDate",is:function(s){return s.match(new RegExp(/^[A-Za-z]{3,10}\\.? [0-9]{1,2}, ([0-9]{4}|\'?[0-9]{2}) (([0-2]?[0-9]:[0-5][0-9])|([0-1]?[0-9]:[0-5][0-9]\\s(AM|PM)))$/));},format:function(s){return $.tablesorter.formatFloat(new Date(s).getTime());},type:"numeric"});ts.addParser({id:"shortDate",is:function(s){return/\\d{1,2}[\\/\\-]\\d{1,2}[\\/\\-]\\d{2,4}/.test(s);},format:function(s,table){var c=table.config;s=s.replace(/\\-/g,"/");if(c.dateFormat=="us"){s=s.replace(/(\\d{1,2})[\\/\\-](\\d{1,2})[\\/\\-](\\d{4})/,"$3/$1/$2");}else if(c.dateFormat=="uk"){s=s.replace(/(\\d{1,2})[\\/\\-](\\d{1,2})[\\/\\-](\\d{4})/,"$3/$2/$1");}else if(c.dateFormat=="dd/mm/yy"||c.dateFormat=="dd-mm-yy"){s=s.replace(/(\\d{1,2})[\\/\\-](\\d{1,2})[\\/\\-](\\d{2})/,"$1/$2/$3");}return $.tablesorter.formatFloat(new Date(s).getTime());},type:"numeric"});ts.addParser({id:"time",is:function(s){return/^(([0-2]?[0-9]:[0-5][0-9])|([0-1]?[0-9]:[0-5][0-9]\\s(am|pm)))$/.test(s);},format:function(s){return $.tablesorter.formatFloat(new Date("2000/01/01 "+s).getTime());},type:"numeric"});ts.addParser({id:"metadata",is:function(s){return false;},format:function(s,table,cell){var c=table.config,p=(!c.parserMetadataName)?\'sortValue\':c.parserMetadataName;return $(cell).metadata()[p];},type:"numeric"});ts.addWidget({id:"zebra",format:function(table){if(table.config.debug){var time=new Date();}var $tr,row=-1,odd;$("tr:visible",table.tBodies[0]).each(function(i){$tr=$(this);if(!$tr.hasClass(table.config.cssChildRow))row++;odd=(row%2==0);$tr.removeClass(table.config.widgetZebra.css[odd?0:1]).addClass(table.config.widgetZebra.css[odd?1:0])});if(table.config.debug){$.tablesorter.benchmark("Applying Zebra widget",time);}}});})(jQuery);\n\\ No newline at end of file\n' |
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| diff -r 866d22e60e60 -r 24a80d4eff0c r_wrapper.sh --- a/r_wrapper.sh Thu Nov 13 10:33:04 2014 -0500 +++ b/r_wrapper.sh Thu Nov 13 10:36:33 2014 -0500 |
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| @@ -18,10 +18,6 @@ cp $dir/style.css $outputDir cp $dir/script.js $outputDir cp $dir/jquery-1.11.0.min.js $outputDir -cp $dir/jquery.tablesorter.min.js $outputDir -cp $dir/asc.gif $outputDir -cp $dir/desc.gif $outputDir -cp $dir/bg.gif $outputDir samples=`cat $outputDir/samples.txt` echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $2 echo "<html><head><title>Report on:" >> $outputFile @@ -31,7 +27,6 @@ echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile -echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile @@ -103,7 +98,7 @@ hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" if [[ "$hasJunctionData" == "Yes" ]] ; then - echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table' class='tablesorter'><thead><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile + echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'><thead><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP do echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile |
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| diff -r 866d22e60e60 -r 24a80d4eff0c style.css --- a/style.css Thu Nov 13 10:33:04 2014 -0500 +++ b/style.css Thu Nov 13 10:36:33 2014 -0500 |
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| @@ -107,44 +107,3 @@ height:200px; overflow:auto; } - -/* tables */ -table.tablesorter { - font-family:arial; - background-color: #CDCDCD; - margin:10px 0pt 15px; - font-size: 8pt; - width: 100%; - text-align: left; -} -table.tablesorter thead tr th, table.tablesorter tfoot tr th { - background-color: #e6EEEE; - border: 1px solid #FFF; - font-size: 8pt; - padding: 4px; -} -table.tablesorter thead tr .header { - background-image: url(bg.gif); - background-repeat: no-repeat; - background-position: center right; - cursor: pointer; -} -table.tablesorter tbody td { - color: #3D3D3D; - padding: 4px; - background-color: #FFF; - vertical-align: top; -} -table.tablesorter tbody tr.odd td { - background-color:#F0F0F6; -} -table.tablesorter thead tr .headerSortUp { - background-image: url(asc.gif); -} -table.tablesorter thead tr .headerSortDown { - background-image: url(desc.gif); -} -table.tablesorter thead tr .headerSortDown, table.tablesorter thead tr .headerSortUp { -background-color: #8dbdd8; -} - |
