From 0fe2dea83d2ecafa497746d3ce42596ba0271cc5 Mon Sep 17 00:00:00 2001
From: corywang <cory.wang@uconn.edu>
Date: Wed, 22 Apr 2015 17:47:26 -0400
Subject: [PATCH] minor changes

---
 VQI_GenomeBrowser.js | 47 +++++++++++++++++++++++++++++---------------
 1 file changed, 31 insertions(+), 16 deletions(-)

diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js
index 88f35d3..7aa6ac4 100755
--- a/VQI_GenomeBrowser.js
+++ b/VQI_GenomeBrowser.js
@@ -54,17 +54,23 @@ function VQI_GenomeBrowser(id) {
     var navigateToRegion = function () {
         var navigate = $("#" + divId + " #navigate").val();
         navigate = navigate.split(/[:-]/);
-        var chrom = navigate[0].trim();
-        var chrom_start = Number(navigate[1].trim());
-        var chrom_end = Number(navigate[2].trim());
-        //Only need to set bounds if current chromosome is already graphed
-        if (chrom == chrom_curr)
-        {
-            setBounds(chrom_start, chrom_end);
+        if (navigate.length == 3){
+            var chrom = navigate[0].trim();
+            var chrom_start = Number(navigate[1].trim());
+            var chrom_end = Number(navigate[2].trim());
+            //Only need to set bounds if current chromosome is already graphed
+            if (chrom == chrom_curr)
+            {
+                setBounds(chrom_start, chrom_end);
+            }
+            else
+            {
+                graph(chrom, chrom_start, chrom_end);
+            }
         }
         else
         {
-            graph(chrom, chrom_start, chrom_end);
+            browseToGene();
         }
     };
     /*this.makeNavigationForm = function () {
@@ -77,7 +83,7 @@ function VQI_GenomeBrowser(id) {
      this.makeNavigationForm();*/
 
     var browseToGene = function () {
-        var geneName = $("#" + divId + " #geneName").val();
+        var geneName = $("#" + divId + " #navigate").val();
 
         var genes = [geneName];
         dataToPost = JSON.stringify(genes);
@@ -106,11 +112,11 @@ function VQI_GenomeBrowser(id) {
     this.makeNavigationForm = function () {
         var navigateBox = "<input type='text' name='navigate' id='navigate' size='30'>";
         var navigateButton = "<input type='button' id='navigatebutton' value='Go To'>";
-        var geneText = "Gene: <input type='text' name='geneName' id='geneName'>";
-        var geneSearchButton = "<input type='button' id='genesearchbutton' value='Search'>";
-        var form = "<form id='navigation_form'>" + navigateBox + navigateButton + geneText + geneSearchButton + "</form>";
+        //var geneText = "Gene: <input type='text' name='geneName' id='geneName'>";
+        //var geneSearchButton = "<input type='button' id='genesearchbutton' value='Search'>";
+        var form = "<form id='navigation_form'>" + navigateBox + navigateButton + "</form>";
         $("#" + divId).append(form);
-        $("#" + divId + " #genesearchbutton").on("click", browseToGene.bind(this));
+        //$("#" + divId + " #genesearchbutton").on("click", browseToGene.bind(this));
         $("#" + divId + " #navigatebutton").on("click", navigateToRegion.bind(this));
     };
     this.makeNavigationForm();
@@ -280,7 +286,7 @@ function VQI_GenomeBrowser(id) {
      };
      this.makeFormForRemoveTrack();*/
     
-    this.getSelectedTracks = function(){
+    this.getSelectedTrackNames = function(){
         var tracknames = []
         for (var i in trackList) {
             if (graphRegion.selectAll("g").data([trackList[i]['name']], function (d) {
@@ -293,6 +299,15 @@ function VQI_GenomeBrowser(id) {
         return tracknames;
     }
 
+    this.getSelectedTrackNames = function(){
+        tracknames = thisObj.getSelectedTrackNames();
+        tracks = [];
+        for (var i in tracknames) {
+            tracks.push(thisObj.getTrackByName(tracknames[i]));
+        }
+        return tracks;
+    }
+
     var exportSelectedTracks = function () {
         var tracknames = []
         for (var i in trackList) {
@@ -676,9 +691,9 @@ function VQI_GenomeBrowser(id) {
                     .attr("x", width)
                     .attr("y", -10)
                     .attr("class", "checkbox")
-                    .append("xhtml:body")
+                    .append("xhtml:div")
                     .html("<form><input type=checkbox id='check'/></form>")
-                    .on("click", function (d, i) {
+                    .on("click", function () {
 //                        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