anchor.diff:  <script type="text/javascript" src="${pageContext.request.contextPath}/scripts/feedback.js"></script>
   <script type="text/javascript" src="${pageContext.request.contextPath}/scripts/jquery.tablesorter.min.js"></script>
   <script type="text/javascript" src="${pageContext.request.contextPath}/scripts/common-query.js"></script>
  -<script language="javascript" type="text/javascript" src="${pageContext.request.contextPath}/scripts/jquery.flot.atlas.js"></script>
  -
  -<link rel="stylesheet" href="${pageContext.request.contextPath}/atlas.css" type="text/css" />
  -<link rel="stylesheet" href="${pageContext.request.contextPath}/geneView.css" type="text/css" />
  +<script language="javascript" type="text/javascript"
  +        src="${pageContext.request.contextPath}/scripts/jquery.flot.atlas.js"></script>
  +
  +<link rel="stylesheet" href="${pageContext.request.contextPath}/atlas.css" type="text/css"/>
  +<link rel="stylesheet" href="${pageContext.request.contextPath}/geneView.css" type="text/css"/>
   
   
   <script type="text/javascript">
   
  -    function showThumbTooltip(x, y, contents) {
  -        if(contents != 'Mean'){
  -            $('<div id="tooltip" />').text(contents).css( {
  -                position: 'absolute',
  -                display: 'none',
  -                top: (y+5)+'px',
  -                left: (x+5)+'px',
  -                border: '1px solid #005555',
  -                margin: '0px',
  -                backgroundColor: '#EEF5F5'
  -            }).appendTo("body").fadeIn('fast');
  -        }
  +function showThumbTooltip(x, y, contents) {
  +    if (contents != 'Mean') {
  +        $('<div id="tooltip" />').text(contents).css({
  +            position: 'absolute',
  +            display: 'none',
  +            top: (y + 5) + 'px',
  +            left: (x + 5) + 'px',
  +            border: '1px solid #005555',
  +            margin: '0px',
  +            backgroundColor: '#EEF5F5'
  +        }).appendTo("body").fadeIn('fast');
       }
  -
  -    function drawPlot(jsonObj, plot_id){
  -        if(jsonObj.series){
  -            var legend_id = plot_id.replace("_plot", "_legend");
  -            jsonObj.options.legend.container = '#' + legend_id;
  -            var plot = $.plot($('#'+plot_id), jsonObj.series, jsonObj.options);
  -
  -            var previousPoint = null;
  -            $('#'+plot_id).bind("plothover", function (event, pos, item) {
  -                if (item) {
  -                    if (previousPoint != item.datapoint) {
  -                        previousPoint = item.datapoint;
  -                        $("#tooltip").remove();
  -                        showThumbTooltip(item.pageX, item.pageY, item.series.label);
  -                    }
  -                }else {
  +}
  +
  +function drawPlot(jsonObj, plot_id) {
  +    if (jsonObj.series) {
  +        var legend_id = plot_id.replace("_plot", "_legend");
  +        jsonObj.options.legend.container = '#' + legend_id;
  +        var plot = $.plot($('#' + plot_id), jsonObj.series, jsonObj.options);
  +
  +        var previousPoint = null;
  +        $('#' + plot_id).bind("plothover", function (event, pos, item) {
  +            if (item) {
  +                if (previousPoint != item.datapoint) {
  +                    previousPoint = item.datapoint;
                       $("#tooltip").remove();
  -                    previousPoint = null;
  +                    showThumbTooltip(item.pageX, item.pageY, item.series.label);
                   }
  -            });
  -            return plot;
  -        }
  -        return null;
  -    }
  -
  -    function drawPlots(){
  -        $(".plot").each(function(){
  -            var plot_id = this.id;
  -            var tokens = plot_id.split('_');
  -            var eid = tokens[0];
  -            var gid = tokens[1];
  -            atlas.ajaxCall("plot", { gid: gid, eid: eid, plot: 'bar' }, function(o){
  -                drawPlot(o,plot_id);
  -            });
  -        });
  -    }
  -
  -    function redrawPlotForFactor(eid,gid,ef,mark,efv){
  -        var plot_id = eid+"_"+gid+"_plot";
  -        atlas.ajaxCall("plot", { gid: gid, eid: eid, ef: ef, plot: 'bar' }, function(o){
  -                var plot = drawPlot(o,plot_id);
  -                if(mark){
  -                    markClicked(eid, gid, ef, efv, plot, o);
  -                }
  -        });
  -        drawEFpagination(eid,gid,ef);
  -    }
  -
  -    function drawEFpagination(eid,gid,currentEF,plotType) {
  -        var panelContent = [];
  -
  -        $("#"+eid+"_EFpagination *").each(function(){
  -            var ef = $(this).attr("id");
  -            var ef_txt = $(this).html();
  -            if(ef == currentEF){
  -                panelContent.push("<span id='"+ef+"' class='current'>"+ef_txt+"</span>")
  -            }
  -            else{
  -                panelContent.push('<a id="'+ef+'" onclick="redrawPlotForFactor( \''+eid+'\',\''+gid+'\',\''+ef+'\',\''+plotType+'\',false)">'+ef_txt+'</a>');
  +            } else {
  +                $("#tooltip").remove();
  +                previousPoint = null;
               }
           });
  -
  -        $("#"+eid+"_EFpagination").empty();
  -        $("#"+eid+"_EFpagination").html(panelContent.join(""));
  +        return plot;
       }
  -
  -
  -    function markClicked(eid,gid,ef,efv,plot,jsonObj) {
  -
  -        var plot_id = eid+'_'+gid+'_plot';
  -        var allSeries = plot.getData();
  -        var series;
  -        var markColor;
  -
  -        for (var i = 0; i < allSeries.length; ++i){
  -            if(allSeries[i].label){
  -                if(allSeries[i].label.toLowerCase()==efv.toLowerCase()){
  -                    series = allSeries[i];
  -                    markColor = series.color;
  -                    break;
  -                }
  -            }
  +    return null;
  +}
  +
  +function drawPlots() {
  +    $(".plot").each(function() {
  +        var plot_id = this.id;
  +        var tokens = plot_id.split('_');
  +        var eid = tokens[0];
  +        var gid = tokens[1];
  +        atlas.ajaxCall("plot", { gid: gid, eid: eid, plot: 'bar' }, function(o) {
  +            drawPlot(o, plot_id);
  +        });
  +    });
  +}
  +
  +function redrawPlotForFactor(eid, gid, ef, mark, efv) {
  +    var plot_id = eid + "_" + gid + "_plot";
  +    atlas.ajaxCall("plot", { gid: gid, eid: eid, ef: ef, plot: 'bar' }, function(o) {
  +        var plot = drawPlot(o, plot_id);
  +        if (mark) {
  +            markClicked(eid, gid, ef, efv, plot, o);
           }
  -
  -        if(series==null){
  -            return ;
  +    });
  +    drawEFpagination(eid, gid, ef);
  +}
  +
  +function drawEFpagination(eid, gid, currentEF, plotType) {
  +    var panelContent = [];
  +
  +    $("#" + eid + "_EFpagination *").each(function() {
  +        var ef = $(this).attr("id");
  +        var ef_txt = $(this).html();
  +        if (ef == currentEF) {
  +            panelContent.push("<span id='" + ef + "' class='current'>" + ef_txt + "</span>")
           }
  -
  -        var data = series.data;
  -        var xMin= data[0][0]
  -        var xMax= data[data.length-1][0]
  -
  -        var overviewDiv = $('#'+plot_id+'_thm');
  -        if(allSeries.length>10 && data.length<5){
  -            if(overviewDiv.height()!=0){
  -                var overview = $.plot($('#'+plot_id+'_thm'), jsonObj.series, jsonObj.options);
  -
  -                overview.setSelection({ xaxis: { from: xMin-10, to: xMax+10 }});
  -            }
  -            plot = $.plot($('#'+plot_id), jsonObj.series,$.extend(true, {}, jsonObj.options, {
  -                grid:{ backgroundColor: '#fafafa',	autoHighlight: true, hoverable: true, borderWidth: 1, markings: [{ xaxis: { from: xMin-1, to: xMax+1 }, color: '#FFFFCC' }]},
  -                xaxis: { min: xMin-10, max: xMax+10  }, yaxis: {labelWidth:40}
  -            }));
  +        else {
  +            panelContent.push('<a id="' + ef + '" onclick="redrawPlotForFactor( \'' + eid + '\',\'' + gid + '\',\'' + ef + '\',\'' + plotType + '\',false)">' + ef_txt + '</a>');
           }
  -        else{
  -
  -            plot = $.plot($('#'+plot_id), jsonObj.series, $.extend(true, {}, jsonObj.options, {
  -                grid:{ backgroundColor: '#fafafa',	autoHighlight: true, hoverable: true, borderWidth: 1, markings: [{ xaxis: { from: xMin-1, to: xMax+1 }, color: '#FFFFCC' }]},
  -                yaxis: {labelWidth:40}
  -            }));
  -            if(overviewDiv.height() != 0) {
  -                var overview = $.plot($('#'+plot_id+'_thm'), jsonObj.series,$.extend(true,{},jsonObj.options,{color:['#999999','#D3D3D3']}));
  -
  -                overview.setSelection({ xaxis: { from: xMin-10, to: xMax+10 }});
  +    });
  +
  +    $("#" + eid + "_EFpagination").empty();
  +    $("#" + eid + "_EFpagination").html(panelContent.join(""));
  +}
  +
  +
  +function markClicked(eid, gid, ef, efv, plot, jsonObj) {
  +
  +    var plot_id = eid + '_' + gid + '_plot';
  +    var allSeries = plot.getData();
  +    var series;
  +    var markColor;
  +
  +    for (var i = 0; i < allSeries.length; ++i) {
  +        if (allSeries[i].label) {
  +            if (allSeries[i].label.toLowerCase() == efv.toLowerCase()) {
  +                series = allSeries[i];
  +                markColor = series.color;
  +                break;
               }
           }
       }
   
  -
  -    function reloadExps(){
  -
  -        $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList",{gid:${atlasGene.geneId},from:"1", to:"5"},drawPlots);
  -        $('#pagingSummary').empty();
  -        $(".heatmap_over").removeClass("heatmap_over");
  -        paginateExperiments();
  -        countExperiments();
  -	}
  -
  -    function countExperiments(){
  -       $("#pagingSummary").text("${noAtlasExps} experiment${noAtlasExps>1?'s':''} showing differential expression");  
  +    if (series == null) {
  +        return;
       }
   
  -    function paginateExperiments(){
  -         // Create pagination element
  -         <c:if test="${noAtlasExps > 5}">
  -        	$("#Pagination").pagination(${noAtlasExps}, {
  -				num_edge_entries: 2,
  -				num_display_entries: 5,
  -				items_per_page:5,
  -                callback: pageselectCallback
  -         	});
  -         </c:if>
  +    var data = series.data;
  +    var xMin = data[0][0]
  +    var xMax = data[data.length - 1][0]
  +
  +    var overviewDiv = $('#' + plot_id + '_thm');
  +    if (allSeries.length > 10 && data.length < 5) {
  +        if (overviewDiv.height() != 0) {
  +            var overview = $.plot($('#' + plot_id + '_thm'), jsonObj.series, jsonObj.options);
  +
  +            overview.setSelection({ xaxis: { from: xMin - 10, to: xMax + 10 }});
  +        }
  +        plot = $.plot($('#' + plot_id), jsonObj.series, $.extend(true, {}, jsonObj.options, {
  +            grid:{ backgroundColor: '#fafafa',    autoHighlight: true, hoverable: true, borderWidth: 1, markings: [
  +                { xaxis: { from: xMin - 1, to: xMax + 1 }, color: '#FFFFCC' }
  +            ]},
  +            xaxis: { min: xMin - 10, max: xMax + 10  }, yaxis: {labelWidth:40}
  +        }));
       }
  -
  -	function pageselectCallback(page_id){
  -		var fromPage = (page_id*5) +1;
  -		var toPage = (page_id*5) + 5;
  -		$('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList",{gid:${atlasGene.geneId},from:fromPage, to: toPage},drawPlots);
  -	}
  -
  -
  -	function FilterExps(el,fv,ef){
  -
  -        $('#ExperimentResult').empty();                            
  -
  -		$('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList",{gid:${atlasGene.geneId}, efv: fv, factor:ef},
  -							function(){
  -								for (var i = 0; i < exps.length; ++i){
  -									var eid = jQuery.trim(exps[i].id);
  -									redrawPlotForFactor(eid,'${atlasGene.geneId}',ef,true,fv);
  -								}
  -								$('#pagingSummary').text(exps.length+" experiment"+(exps.length>1?"s":'')+" showing differential expression in \""+ fv + "\"");
  -								var lnk = $("<a>Show all studies</a>").bind("click", reloadExps);
  -								$("#Pagination").empty().append(lnk);
  -							});
  -
  -
  -        old = $(".heatmap_over");
  -		old.removeClass("heatmap_over");
  -        old.addClass ("heatmap_row");
  -		el.className = "heatmap_over";
  -		//window.scrollTo(0,0);
  -	}
  -
  -
  -    function FilterExpsEfo(el,efo){
  -        $('#ExperimentResult').empty();
  -        $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList",{gid:${atlasGene.geneId}, efo: efo},
  -                            function(){
  -                                for (var i = 0; i < exps.length; ++i){
  -                                    var eid = jQuery.trim(exps[i].id);
  -                                    redrawPlotForFactor(eid,'${atlasGene.geneId}','organismpart',true,'');
  -                                }
  -                                $('#pagingSummary').text(exps.length+" experiment"+(exps.length>1?"s":'')+" showing differential expression in \""+ efo + "\"");
  -                                var lnk = $("<a>Show all studies</a>").bind("click", reloadExps);
  -                                $("#Pagination").empty().append(lnk);
  -                            });
  -        old = $(".heatmap_over");
  -        old.removeClass("heatmap_over");
  -        old.addClass ("heatmap_row");
  -        el.className = "heatmap_over";
  -        //window.scrollTo(0,0);
  +    else {
  +
  +        plot = $.plot($('#' + plot_id), jsonObj.series, $.extend(true, {}, jsonObj.options, {
  +            grid:{ backgroundColor: '#fafafa',    autoHighlight: true, hoverable: true, borderWidth: 1, markings: [
  +                { xaxis: { from: xMin - 1, to: xMax + 1 }, color: '#FFFFCC' }
  +            ]},
  +            yaxis: {labelWidth:40}
  +        }));
  +        if (overviewDiv.height() != 0) {
  +            var overview = $.plot($('#' + plot_id + '_thm'), jsonObj.series, $.extend(true, {}, jsonObj.options, {color:['#999999','#D3D3D3']}));
  +
  +            overview.setSelection({ xaxis: { from: xMin - 10, to: xMax + 10 }});
  +        }
       }
  -
  -    jQuery(document).ready(function()
  -    {
  -        countExperiments();
  -        paginateExperiments();
  -        $("#heatmap_tbl").tablesorter({
  -            headers: {2: {sorter: false}}});
  -        drawPlots();
  +}
  +
  +
  +function reloadExps() {
  +
  +    $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList", {gid:${atlasGene.geneId},from:"1", to:"5"}, drawPlots);
  +    $('#pagingSummary').empty();
  +    $(".heatmap_over").removeClass("heatmap_over");
  +    paginateExperiments();
  +    countExperiments();
  +}
  +
  +function countExperiments() {
  +    $("#pagingSummary").text("${noAtlasExps} experiment${noAtlasExps>1?'s':''} showing differential expression");
  +}
  +
  +function paginateExperiments() {
  +    // Create pagination element
  +<c:if test="${noAtlasExps > 5}">
  +    $("#Pagination").pagination(${noAtlasExps}, {
  +        num_edge_entries: 2,
  +        num_display_entries: 5,
  +        items_per_page:5,
  +        callback: pageselectCallback
       });
  +</c:if>
  +}
  +
  +function pageselectCallback(page_id) {
  +    var fromPage = (page_id * 5) + 1;
  +    var toPage = (page_id * 5) + 5;
  +    $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList", {gid:${atlasGene.geneId},from:fromPage, to: toPage}, drawPlots);
  +}
  +
  +
  +function FilterExps(el, fv, ef) {
  +
  +    $('#ExperimentResult').empty();
  +
  +    $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList", {gid:${atlasGene.geneId}, efv: fv, factor:ef},
  +            function() {
  +                for (var i = 0; i < exps.length; ++i) {
  +                    var eid = jQuery.trim(exps[i].id);
  +                    redrawPlotForFactor(eid, '${atlasGene.geneId}', ef, true, fv);
  +                }
  +                $('#pagingSummary').text(exps.length + " experiment" + (exps.length > 1 ? "s" : '') + " showing differential expression in \"" + fv + "\"");
  +                var lnk = $("<a>Show all studies</a>").bind("click", reloadExps);
  +                $("#Pagination").empty().append(lnk);
  +            });
  +
  +
  +    old = $(".heatmap_over");
  +    old.removeClass("heatmap_over");
  +    old.addClass("heatmap_row");
  +    el.className = "heatmap_over";
  +    //window.scrollTo(0,0);
  +}
  +
  +
  +function FilterExpsEfo(el, efo) {
  +    $('#ExperimentResult').empty();
  +    $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList", {gid:${atlasGene.geneId}, efo: efo},
  +            function() {
  +                for (var i = 0; i < exps.length; ++i) {
  +                    var eid = jQuery.trim(exps[i].id);
  +                    redrawPlotForFactor(eid, '${atlasGene.geneId}', 'organismpart', true, '');
  +                }
  +                $('#pagingSummary').text(exps.length + " experiment" + (exps.length > 1 ? "s" : '') + " showing differential expression in \"" + efo + "\"");
  +                var lnk = $("<a>Show all studies</a>").bind("click", reloadExps);
  +                $("#Pagination").empty().append(lnk);
  +            });
  +    old = $(".heatmap_over");
  +    old.removeClass("heatmap_over");
  +    old.addClass("heatmap_row");
  +    el.className = "heatmap_over";
  +    //window.scrollTo(0,0);
  +}
  +
  +jQuery(document).ready(function()
  +{
  +    countExperiments();
  +    paginateExperiments();
  +    $("#heatmap_tbl").tablesorter({
  +        headers: {2: {sorter: false}}});
  +    drawPlots();
  +});
   </script>
   
   
  -<link rel="stylesheet" href="${pageContext.request.contextPath}/blue/style.css" type="text/css" media="print, projection, screen" />
  -<link rel="stylesheet" href="${pageContext.request.contextPath}/structured-query.css" type="text/css" />
  +<link rel="stylesheet" href="${pageContext.request.contextPath}/blue/style.css" type="text/css"
  +      media="print, projection, screen"/>
  +<link rel="stylesheet" href="${pageContext.request.contextPath}/structured-query.css" type="text/css"/>
   ${atlasProperties.htmlBodyStart}
   
   <div class="contents" id="contents">
  
positive.code: <%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
  <%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="f"%>
  <%@ taglib uri="http://ebi.ac.uk/ae3/functions" prefix="u"%>
  <%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
  <%--
    ~ Copyright 2008-2010 Microarray Informatics Team, EMBL-European Bioinformatics Institute
  
negative.code: <table style="border-bottom:1px solid #DEDEDE;margin:0 0 10px 0;width:100%;height:30px;">
      <tr>
          <td align="left" valign="bottom" width="55" style="padding-right:10px;">
              <a href="${pageContext.request.contextPath}/" title="Gene Expression Atlas Homepage"><img border="0"
                                                                                                        width="55"
                                                                                                        src="${pageContext.request.contextPath}/images/atlas-logo.png"
                                                                                                        alt="Gene Expression Atlas"/></a>
          </td>
          <td align="right" valign="bottom">
              <a href="${pageContext.request.contextPath}/">home</a> |
              <a href="${pageContext.request.contextPath}/help/AboutAtlas">about the project</a> |
              <a href="${pageContext.request.contextPath}/help/AtlasFaq">faq</a> |
              <a id="feedback_href" href="javascript:showFeedbackForm()">feedback</a> <span id="feedback_thanks"
                                                                                            style="font-weight:bold;display:none">thanks!</span>
              |
              <a target="_blank" href="http://arrayexpress-atlas.blogspot.com">blog</a> |
              <a href="${pageContext.request.contextPath}/help/AtlasDasSource">das</a> |
              <a href="${pageContext.request.contextPath}/help/AtlasApis">api</a> <b>new</b> |
              <a href="${pageContext.request.contextPath}/help">help</a>
          </td>
  