From 722d894892242c4269c187c1f823890efad20be5 Mon Sep 17 00:00:00 2001
From: Andrew Duncan <andrew.duncan@oicr.on.ca>
Date: Mon, 28 Oct 2019 14:27:27 -0400
Subject: [PATCH] change to html features

---
 README.md                              | 4 ++--
 data/tracks.conf                       | 4 ++--
 gdc-viewer/js/View/GDCDialog.js        | 2 +-
 gdc-viewer/js/View/GDCProjectDialog.js | 2 +-
 gdc-viewer/js/View/Track/GeneTrack.js  | 8 ++++----
 gdc-viewer/js/View/Track/SSMTrack.js   | 8 ++++----
 6 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index 65678a4..4111301 100644
--- a/README.md
+++ b/README.md
@@ -92,7 +92,7 @@ Example Track:
 ```
 [tracks.GDC_Genes]
 storeClass=gdc-viewer/Store/SeqFeature/Genes
-type=JBrowse/View/Track/CanvasVariants
+type=JBrowse/View/Track/GeneTrack
 key=GDC Genes
 metadata.datatype=Gene
 unsafePopup=true
@@ -114,7 +114,7 @@ Example Track:
 ```
 [tracks.GDC_SSM]
 storeClass=gdc-viewer/Store/SeqFeature/SimpleSomaticMutations
-type=gdc-viewer/View/Track/CanvasVariants
+type=gdc-viewer/View/Track/SSMVariants
 key=GDC SSM
 metadata.datatype=SSM
 unsafePopup=true
diff --git a/data/tracks.conf b/data/tracks.conf
index d3cc37c..fd1c2f3 100644
--- a/data/tracks.conf
+++ b/data/tracks.conf
@@ -1,13 +1,13 @@
 [tracks.GDC_SSM]
 storeClass=gdc-viewer/Store/SeqFeature/SimpleSomaticMutations
-type=gdc-viewer/View/Track/CanvasVariants
+type=gdc-viewer/View/Track/SSMTrack
 key=GDC SSM
 metadata.datatype=SSM
 unsafePopup=true
 
 [tracks.GDC_Genes]
 storeClass=gdc-viewer/Store/SeqFeature/Genes
-type=gdc-viewer/View/Track/CanvasVariants
+type=gdc-viewer/View/Track/GeneTrack
 key=GDC Genes
 metadata.datatype=Gene
 unsafePopup=true
diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index 0efc2a6..1818e58 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -1055,7 +1055,7 @@ function (
         },
 
         /**
-         * Creates pagination buttons for search results in the given 'holder' using the 'pagination' object from the ICGC response
+         * Creates pagination buttons for search results in the given 'holder' using the 'pagination' object from the GDC response
          * @param {object} holder DOM location to place pagination buttons
          * @param {number} totalPages the total number of pages for the given query results
          * @param {string} type the type of results to create pagination button for
diff --git a/gdc-viewer/js/View/GDCProjectDialog.js b/gdc-viewer/js/View/GDCProjectDialog.js
index 2db74a8..3599331 100644
--- a/gdc-viewer/js/View/GDCProjectDialog.js
+++ b/gdc-viewer/js/View/GDCProjectDialog.js
@@ -308,7 +308,7 @@ function (
         },
 
         /**
-         * Creates pagination buttons for search results in the given 'holder' using the 'pagination' object from the ICGC response
+         * Creates pagination buttons for search results in the given 'holder' using the 'pagination' object from the GDC response
          * @param {number} totalPages total number of pages
          */
         createPaginationButtons: function(totalPages) {
diff --git a/gdc-viewer/js/View/Track/GeneTrack.js b/gdc-viewer/js/View/Track/GeneTrack.js
index 4780ecb..b7fe7cf 100644
--- a/gdc-viewer/js/View/Track/GeneTrack.js
+++ b/gdc-viewer/js/View/Track/GeneTrack.js
@@ -1,23 +1,23 @@
 define(
     [
         "dojo/_base/declare",
-        "JBrowse/View/Track/CanvasFeatures",
+        "JBrowse/View/Track/HTMLFeatures",
         'JBrowse/View/Track/_ExportMixin',
         'dojo/dom-construct'
     ],
    function(
        declare,
-       CanvasFeatures,
+       HTMLFeatures,
        ExportMixin,
        domConstruct) {
-   return declare([ CanvasFeatures, ExportMixin ], {
+   return declare([ HTMLFeatures, ExportMixin ], {
 
         _exportFormats: function() {
             return [
                 {name: 'gdc-viewer/View/Export/GFF3', label: 'GFF3', fileExt: 'gff3'},
                 {name: 'gdc-viewer/View/Export/BED', label: 'BED', fileExt: 'bed'},
                 {name: 'gdc-viewer/View/Export/CSV', label: 'CSV', fileExt: 'csv'},
-                {name: 'icgc-viewer/View/Export/SequinTable', label: 'Sequin Table', fileExt: 'sqn'},
+                {name: 'gdc-viewer/View/Export/SequinTable', label: 'Sequin Table', fileExt: 'sqn'},
                 {name: 'gdc-viewer/View/Export/TrackConfig', label: 'Track Config', fileExt: 'conf'},
                 {name: 'gdc-viewer/View/Export/TrackConfigJson', label: 'Track Config JSON', fileExt: 'json'}
             ];
diff --git a/gdc-viewer/js/View/Track/SSMTrack.js b/gdc-viewer/js/View/Track/SSMTrack.js
index de6d290..451726c 100644
--- a/gdc-viewer/js/View/Track/SSMTrack.js
+++ b/gdc-viewer/js/View/Track/SSMTrack.js
@@ -1,23 +1,23 @@
 define(
     [
         "dojo/_base/declare",
-        "JBrowse/View/Track/CanvasFeatures",
+        "JBrowse/View/Track/HTMLFeatures",
         'JBrowse/View/Track/_ExportMixin',
         'dojo/dom-construct'
     ],
    function(
        declare,
-       CanvasFeatures,
+       HTMLFeatures,
        ExportMixin,
        domConstruct) {
-   return declare([ CanvasFeatures, ExportMixin ], {
+   return declare([ HTMLFeatures, ExportMixin ], {
 
         _exportFormats: function() {
             return [
                 {name: 'gdc-viewer/View/Export/GFF3', label: 'GFF3', fileExt: 'gff3'},
                 {name: 'gdc-viewer/View/Export/BED', label: 'BED', fileExt: 'bed'},
                 {name: 'gdc-viewer/View/Export/CSV', label: 'CSV', fileExt: 'csv'},
-                {name: 'icgc-viewer/View/Export/SequinTable', label: 'Sequin Table', fileExt: 'sqn'},
+                {name: 'gdc-viewer/View/Export/SequinTable', label: 'Sequin Table', fileExt: 'sqn'},
                 {name: 'gdc-viewer/View/Export/TrackConfig', label: 'Track Config', fileExt: 'conf'},
                 {name: 'gdc-viewer/View/Export/TrackConfigJson', label: 'Track Config JSON', fileExt: 'json'}];
         },