minor changes.

VQI_GenomeBrowser.js

@@ -119,6 +119,11 @@ function VQI_GenomeBrowser(id) {
         var track1Name = $("#" + divId + " #track1").val();
         var track2Name = $("#" + divId + " #track2").val();
         var coloc_dist = $("#" + divId + " #coloc_dist").val();
+
+        if(track1Name === track2Name){
+            alert("Track1 and Track2 cannot be same for colocalization.");
+            return;
+        }
 
         var data1 = this.getTrackByName(track1Name);
         var data2 = this.getTrackByName(track2Name);
@@ -184,7 +189,8 @@ function VQI_GenomeBrowser(id) {
             async: true
         }).success(function (data) {
             console.log(data);
-            alert("pvalue = " + data);
+            $("#pvalue_div").empty().append("p-value = " + data);
+//            alert("pvalue = " + data);
 
 //            objVQIResult.parseSNPAndSNP(data, true);
         }).error(function (req, status, error) {
@@ -215,7 +221,8 @@ function VQI_GenomeBrowser(id) {
         var distanceTextBox = "<input type=text name='coloc_dist' id='coloc_dist' value='100'>";
 
         var colocalizeButton = "<input type='button' id='colocalize' value='colocalize'>";
-        var form = "<form id='colocalization_form'>" + track1Select + track2Select + distanceTextBox + colocalizeButton + "</form>";
+        var pValueDiv = "<div id='pvalue_div'></div>"
+        var form = "<form id='colocalization_form'>" + track1Select + track2Select + distanceTextBox + colocalizeButton + pValueDiv + "</form>";
         $("#" + divId).append(form);
         $("#" + divId + " #colocalize").on("click", colocalize.bind(this));
     };
@@ -272,6 +279,19 @@ function VQI_GenomeBrowser(id) {
      $("#" + divId + " #removetrackbutton").on("click", removeTrack.bind(this));
      };
      this.makeFormForRemoveTrack();*/
+
+    this.getSelectedTracks = function(){
+        var tracknames = []
+        for (var i in trackList) {
+            if (graphRegion.selectAll("g").data([trackList[i]['name']], function (d) {
+                return d;
+            }).select("#check").node().checked)
+            {
+                tracknames.push(trackList[i]['name']);
+            }
+        }
+        return tracknames;
+    }
 
     var exportSelectedTracks = function () {
         var tracknames = []
@@ -320,7 +340,8 @@ function VQI_GenomeBrowser(id) {
     this.makeSelectionForm = function () {
         var removeButton = "<input type='button' id='removetrackbutton' value='Remove Track'>";
         var exportButton = "<input type='button' id='exporttrackbutton' value='Export'>";
-        var form = "<form id='selectionForm'>" + removeButton + exportButton + "</form>";
+        var scoreButton = "<input type='button' id='scoreTracks' value='Score' onclick='VQI_ControlPanel.scoreButtonClicked()'>";
+        var form = "<form id='selectionForm'>" + removeButton + exportButton + scoreButton + "</form>";
         $("#" + divId).append(form);
         $("#" + divId + " #removetrackbutton").on("click", removeSelectedTracks.bind(this));
         $("#" + divId + " #exporttrackbutton").on("click", exportSelectedTracks.bind(this));
@@ -535,7 +556,7 @@ function VQI_GenomeBrowser(id) {
     }
 
     var addOneTrack = function (data, name, type, i) {
-
+//        console.log(data);
         i = Number(i);
         var trackIndex;
         if (!isNaN(i)) {
@@ -591,6 +612,8 @@ function VQI_GenomeBrowser(id) {
                     .attr("transform", "translate(" + 0 + "," + (margin + bufferSpace + i * (trackHeight + bufferSpace)) + ")");
         }
     }
+
+
 
     var initTrack = function (name) {
 
@@ -654,9 +677,10 @@ function VQI_GenomeBrowser(id) {
                     .attr("y", -10)
                     .attr("class", "checkbox")
                     .append("xhtml:body")
-                    .html("<form><input type=checkbox id=check class=" + name + "/></form>")
+                    .html("<form><input type=checkbox id='check'/></form>")
                     .on("click", function (d, i) {
-                        //console.log(trackGroup.select("#check").node().checked);
+//                        console.log("clicked " + d + " -- " + i);
+//                        console.log(trackGroup.select("#check").property('checked'));
                         xAxisSelection.call(xAxis);//I have no idea why it won't redraw the checkbox unless I call this
                     });
         }
@@ -1366,6 +1390,8 @@ function VQI_GenomeBrowser(id) {
         temp = [];
 
         //console.log(data[1].join("\t"));
+//        var header = ["CHROM", "CHROM_START", "CHROM_END", "NAME", "SCORE", "STRAND"];
+//        temp.push(header.join("\t"));
 
         for (i in data)
         {