From 28792f5e529af05b6cef96012cf703b3a9eeb3e3 Mon Sep 17 00:00:00 2001
From: Aysam Guerler <aysam.guerler@gmail.com>
Date: Wed, 10 Apr 2013 16:50:54 -0400
Subject: [PATCH 1/3] Enhance button for trackster visualization in data
 display viewer

---
 static/scripts/mvc/data.js | 26 ++++++++------------------
 1 file changed, 8 insertions(+), 18 deletions(-)

diff --git a/static/scripts/mvc/data.js b/static/scripts/mvc/data.js
index 34c7d20b0a3..7a3e62d0a2c 100644
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -112,7 +112,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
     initialize: function(options)
     {
         // load trackster button
-        (new TabularButtonTrackster(options)).render();
+        (new TabularButtonTracksterView(options)).render();
     },
 
     render: function()
@@ -226,13 +226,13 @@ var TabularDatasetChunkedView = Backbone.View.extend({
 });
 
 // button for trackster visualization
-var TabularButtonTrackster = Backbone.View.extend(
+var TabularButtonTracksterView = Backbone.View.extend(
 {
     // gene region columns
     col: {
         chrom   : null,
         start   : null,
-        end     : null,
+        end     : null
     },
 
     // url for trackster
@@ -251,8 +251,7 @@ var TabularButtonTrackster = Backbone.View.extend(
         var metadata = options.model.attributes.metadata.attributes;
         if (typeof metadata.chromCol === "undefined" || typeof metadata.startCol === "undefined" || typeof metadata.endCol === "undefined")
             console.log("TabularButtonTrackster : Metadata for column identification is missing.");
-        else
-        {
+        else {
             // read in columns
             this.col.chrom   = metadata.chromCol - 1;
             this.col.start   = metadata.startCol - 1;
@@ -260,7 +259,7 @@ var TabularButtonTrackster = Backbone.View.extend(
         }
         
         // check
-        if(this.col.chrom == null)
+        if(this.col.chrom)
             return;
      
         // get dataset id
@@ -291,7 +290,7 @@ var TabularButtonTrackster = Backbone.View.extend(
     btn_viz_show: function (e)
     {
         // check
-        if(this.col.chrom == null)
+        if(this.col.chrom)
             return;
             
         // get selected data line
@@ -301,7 +300,7 @@ var TabularButtonTrackster = Backbone.View.extend(
         var chrom = row.children().eq(this.col.chrom).html();
         var start = row.children().eq(this.col.start).html();
         var end   = row.children().eq(this.col.end).html();
-        if (chrom != "" && start != "" && end != "")
+        if (chrom !== "" && start !== "" && end !== "")
         {
             // get target gene region
             var btn_viz_pars = {
@@ -325,21 +324,12 @@ var TabularButtonTrackster = Backbone.View.extend(
     },
     
     // hide button
-    btn_viz_hide: function (e)
+    btn_viz_hide: function ()
     {
         // hide button from screen
         $('#btn_viz').hide();
     },
     
-    
-    // create action
-    create_trackster_action_new : function (vis_url, dataset_params, dbkey)
-    {
-        return function () {
-            window.parent.location.href = vis_url + "/trackster?" + $.param(dataset_params);
-        }
-    },
-    
     // create action
     create_trackster_action : function (vis_url, dataset_params, dbkey) {
         return function() {

From 959a335b67dc1f13ce1524eb0f87b56f7717702b Mon Sep 17 00:00:00 2001
From: Aysam Guerler <aysam.guerler@gmail.com>
Date: Wed, 10 Apr 2013 17:30:27 -0400
Subject: [PATCH 2/3] Enhance button for trackster visualization in data
 display viewer

---
 static/scripts/mvc/data.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/static/scripts/mvc/data.js b/static/scripts/mvc/data.js
index 7a3e62d0a2c..2735b75452b 100644
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -257,11 +257,11 @@ var TabularButtonTracksterView = Backbone.View.extend(
             this.col.start   = metadata.startCol - 1;
             this.col.end     = metadata.endCol - 1;
         }
-        
+
         // check
-        if(this.col.chrom)
+        if(this.col.chrom === null)
             return;
-     
+
         // get dataset id
         if (typeof options.model.attributes.id === "undefined")
             console.log("TabularButtonTrackster : Dataset identification is missing.");
@@ -290,7 +290,7 @@ var TabularButtonTracksterView = Backbone.View.extend(
     btn_viz_show: function (e)
     {
         // check
-        if(this.col.chrom)
+        if(this.col.chrom === null)
             return;
             
         // get selected data line

From 56ace3827090a3e9b715cb8b0623871b3930dd78 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 11 Apr 2013 08:44:42 -0400
Subject: [PATCH 3/3] Whitespace fixes for Vcf datatype.

---
 lib/galaxy/datatypes/tabular.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 316338a2a7c..9c710052000 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -546,12 +546,13 @@ class Vcf( Tabular ):
     def sniff( self, filename ):
         headers = get_headers( filename, '\n', count=1 )
         return headers[0][0].startswith("##fileformat=VCF")
+
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
         return Tabular.make_html_table( self, dataset, column_names=self.column_names )
 
     def get_track_type( self ):
-        return "VcfTrack", {"data": "tabix", "index": "summary_tree"}
+        return "VcfTrack", { "data": "tabix", "index": "summary_tree" }
 
 class Eland( Tabular ):
     """Support for the export.txt.gz file used by Illumina's ELANDv2e aligner"""