Merge branch 'biodalliance' of github.com:chfi/genenetwork2 into gn_server

6 files changed, 41 insertions, 39 deletions

diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js
index 849c9f67..51ee8f39 100644
--- a/wqflask/wqflask/static/new/javascript/biodalliance.js
+++ b/wqflask/wqflask/static/new/javascript/biodalliance.js
@@ -1,13 +1,15 @@
 "use strict";
 
-var bd_browser = null;
-var bd_data = {};
+
+var BD = {};
+BD.browser = null;
+BD.data = {};
 
 var getChrLen = function(chr) {
     return js_data[chr * 1];
 };
 
-var createBDBrowser = function(chr, start, end, speciesName, sources) {
+BD.createBrowser = function(chr, start, end, speciesName, sources) {
     console.log("creating BD browser");
     var b = new Browser({
         chr: chr,
@@ -30,32 +32,27 @@ var createBDBrowser = function(chr, start, end, speciesName, sources) {
     return b;
 };
 
-var showBDButton = function() {
+BD.showButton = function() {
     $('#open_bd').show();
     $('#close_bd').hide();
 };
 
-var hideBDButton = function() {
+BD.hideButton = 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;
+BD.putData = function(data) {
+    for (var key in data) {
+        BD.data[key] = data[key];
+    }
 };
 
-
-var openBDBrowser = function() {
+BD.openBrowser = function() {
     console.log("opening browser");
-    if (!bd_browser) {
-        bd_browser = createBDBrowser(bd_data.chr, 0, bd_data.length * 1000000, bd_data.species,
+    if (!BD.browser) {
+        BD.browser = BD.createBrowser(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',
@@ -68,8 +65,8 @@ var openBDBrowser = function() {
                                       }]
                                     );
     } else {
-        bd_browser.setLocation(bd_data.chr, 0, bd_data.length * 1000000);
+        BD.browser.setLocation(BD.data.chr, 0, BD.data.length * 1000000);
     }
 
-    bd_browser.maxViewWidth = bd_data.length * 1000000;
+    BD.browser.maxViewWidth = BD.data.length * 1000000;
 };
diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
index d3c1ee7d..173f8186 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
@@ -273,7 +273,8 @@ class Chr_Lod_Chart
         $("#return_to_full_view").hide()

         $('#topchart').remove()

         $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')

-        hideBDButton()

+        BD.hideButton()

+        $('#bd_container').hide()

         create_lod_chart()

 

     show_marker_in_table: (marker_info) ->

diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
index 0032858f..01bb4601 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
@@ -260,7 +260,8 @@ Chr_Lod_Chart = (function() {
     $("#return_to_full_view").hide();
     $('#topchart').remove();
     $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
-    hideBDButton();
+    BD.hideButton();
+    $('#bd_container').hide();
     return create_lod_chart();
   };
 
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
index 2da2e5bb..a65df84f 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
@@ -123,8 +123,8 @@ lodchart = () ->
                    .on("click", (d) ->
                       console.log("d is:", d)
                       redraw_plot(d)
-                      setBDData(d[0], d[1])
-                      showBDButton()
+                      BD.putData({chr: d[0], length: d[1]});
+                      BD.showButton()
                     )   
   
         # x-axis labels
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index c6d1045c..f1df6bd8 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -118,8 +118,11 @@ lodchart = function() {
       }).attr("stroke", "none").on("click", function(d) {
         console.log("d is:", d);
         redraw_plot(d);
-        setBDData(d[0], d[1]);
-        return showBDButton();
+        BD.putData({
+          chr: d[0],
+          length: d[1]
+        });
+        return BD.showButton();
       });
       xaxis = g.append("g").attr("class", "x axis");
       xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) {
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index efb80494..8e2af3cb 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -161,17 +161,17 @@
             {% if mapping_method != "gemma" %}
             <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
                 <div id="chart_container">
-                    <div id="return_to_full_view" style="display:none">
-                        Return to full view
-                    </div>
-
-                    <div id="open_bd" style="display:none">
-                        Open BioDalliance view
-                    </div>
-
-                    <div id="close_bd" style="display:none">
-                        Return to vector map
-                    </div>
+                    <ul class="nav nav-tabs">
+                        <li id="return_to_full_view" class="btn btn-default buttons-html5" style="display:none">
+                            Return to full view
+                        </li>
+                        <li id="open_bd" class="btn btn-default buttons-html5" style="display:none">
+                            Open BioDalliance view
+                        </li>
+                        <li id="close_bd" class="btn btn-default buttons-html5" style="display:none">
+                            Return to vector map
+                        </li>
+                    </ul>
 
                     <div class="qtlcharts" id="topchart"></div>
 
@@ -285,13 +285,13 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
 
-    <script language="javascript" type="text/javascript" src="/dalliance/dalliance-all.js"></script>
+    <script language="javascript" type="text/javascript" src="/dalliance/build/dalliance-all.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/biodalliance.js"></script>
     {% endif %}
 
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
-            setBDSpecies("{{ dataset.group.species }}");
+            BD.putData({species: "{{ dataset.group.species }}" });
 
             console.time("Creating table");
             $('#qtl_results').dataTable( {
@@ -355,7 +355,7 @@
                 $('#topchart').hide();
                 $('#bd_container').show();
 
-                openBDBrowser();
+                BD.openBrowser();
             })
         });