Add functions for creating, configuring BD browser

1 files changed, 53 insertions, 2 deletions

diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js
index 6b082fbb..2dde6365 100644
--- a/wqflask/wqflask/static/new/javascript/biodalliance.js
+++ b/wqflask/wqflask/static/new/javascript/biodalliance.js
@@ -1,6 +1,13 @@
 "use strict";
 
-var createBDBrowser = function(chr, start, end, sources) {
+var bd_browser = null;
+var bd_data = {};
+
+var getChrLen = function(chr) {
+    return js_data[chr * 1];
+};
+
+var createBDBrowser = function(chr, start, end, speciesName, sources) {
     console.log("creating BD browser");
     var b = new Browser({
         chr: chr,
@@ -8,7 +15,7 @@ var createBDBrowser = function(chr, start, end, sources) {
         viewEnd: end,
 
         coordSystem: {
-            speciesName: 'Mouse'
+            speciesName: speciesName
         },
 
         sources: sources,
@@ -22,3 +29,47 @@ var createBDBrowser = function(chr, start, end, sources) {
     console.log("created BD browser");
     return b;
 };
+
+var showBDButton = function() {
+    $('#open_bd').show();
+    $('#close_bd').hide();
+};
+
+var hideBDButton = function() {
+    $('#close_bd').show();
+    $('#open_bd').hide();
+};
+
+
+var setBDData = function(chr, length) {
+    // bd_data = { chr: chr, length: length };
+    bd_data.chr = chr;
+    bd_data.length = length;
+};
+
+var setBDSpecies = function(species) {
+    bd_data.species = species;
+};
+
+
+var openBDBrowser = function() {
+    console.log("opening browser");
+    if (!bd_browser) {
+        bd_browser = createBDBrowser(bd_data.chr, 0, bd_data.length * 1000000, bd_data.species,
+                                     [{name: 'Genome',
+                                       twoBitURI:  'http://www.biodalliance.org/datasets/GRCm38/mm10.2bit',
+                                       desc: 'Mouse reference genome build GRCm38',
+                                       tier_type: 'sequence',
+                                       provides_entrypoints: true},
+                                      {name: 'QTL',
+                                       tier_type: 'qtl',
+                                       uri: 'http://gsocbox:8880/static/qtl/lod2.csv',
+                                       stylesheet_uri: "http://gsocbox:8880/stylesheets/qtl-stylesheet.xml"
+                                      }]
+                                    );
+    } else {
+        bd_browser.setLocation(bd_data.chr, 0, bd_data.length * 1000000);
+    }
+
+    bd_browser.maxViewWidth = bd_data.length * 1000000;
+};