Merge branch 'gh-pages'

DECIPHER-genomics · Oct 23, 2019 · 82125ce · 82125ce
2 parents b46d566 + cc3140f
commit 82125ce
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diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,3 @@
 /data*
 *.DS_Store
-
+node_modules/*
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,22 @@
+language: node_js
+node_js:
+  - "6"
+branches:
+  only:
+  - gh-pages
+  - /.*/
+
+# The following is needed for canvas to compile (taken from https://github.com/Automattic/node-canvas/blob/master/.travis.yml)
+addons:
+  apt:
+    sources:
+      - ubuntu-toolchain-r-test
+    packages:
+      - libcairo2-dev
+      - libjpeg8-dev
+      - libpango1.0-dev
+      - libgif-dev
+      - g++-4.9
+env:
+  - CXX=g++-4.9
+sudo: false
diff --git a/README → README.md b/README → README.md
@@ -1,9 +1,11 @@
+# Genoverse [![Build Status](https://travis-ci.org/wtsi-web/Genoverse.svg?branch=gh-pages)](https://travis-ci.org/wtsi-web/Genoverse)
+
 Genoverse is a portable, customizable, back-end independent JavaScript and HTML5 based genome browser which allows the user to explore data in a dynamic and interactive manner.
 
 Data is visualized in the browser, meaning Genoverse can be installed on any website and show data from a wide range of online or local sources.
 
 Genoverse works with a variety of formats, such as XML, JSON, BED, VCF, GFF, GFF3 or delimited text files, and can be customized to parse and display any data source as required.
 
-More information coming soon. If you have any questions, please contact [email protected]
+If you have any questions, please contact [email protected]
 
 Example: http://genoverse.org
diff --git a/css/genoverse.css b/css/genoverse.css
@@ -52,6 +52,16 @@
   height: 100%;
 }
 
+.gv-canvas-container .gv-track-container .gv-scroll-container-offset {
+  height: 100%;
+  overflow: hidden;
+  position: absolute;
+  /*
+    margin-left to be set in the track, with the gv-scroll-container being given a margin-left of -(this element's margin-left) to hide the first n pixels of the scroll container.
+    Used to stop a track with a vertical scalebar at its left edge from displaying features on top of the scalebar
+  */
+}
+
 .gv-canvas-container .gv-message-container {
   position: absolute;
   top: 0;
@@ -72,8 +82,7 @@
 
 .gv-canvas-container .gv-message-container .gv-messages {
   float: right;
-  padding-right: 10px;
-  padding-left: 15px;
+  padding: 0 5px;
   margin-bottom: -6px;
 }
 
@@ -86,18 +95,11 @@
   text-decoration: underline;
 }
 
-.gv-canvas-container .gv-message-container .gv-control {
-  position: absolute;
-  height: 14px;
-  cursor: pointer;
-}
-
 .gv-canvas-container .gv-message-container .gv-control:hover { text-decoration: underline; }
 .gv-canvas-container .gv-message-container .gv-expand,
 .gv-canvas-container .gv-message-container.gv-collapsed .gv-messages,
 .gv-canvas-container .gv-message-container.gv-collapsed .gv-collapse { display: none; }
-.gv-canvas-container .gv-message-container .gv-collapse              { display: inline; }
-.gv-canvas-container .gv-message-container.gv-collapsed .gv-expand   { display: inline; position: relative; }
+.gv-canvas-container .gv-message-container.gv-collapsed .gv-expand   { display: inline; }
 
 .gv-canvas-container .gv-image-container {
   height: 100%;
@@ -115,11 +117,12 @@
   background: rgba(204,204,204,0.4);
 }
 
-.gv-canvas-container .gv-image-container.gv-flip {
+.gv-canvas-container .gv-image-container.gv-invert {
   transform: scaleY(-1);
   -moz-transform: scaleY(-1);
   -webkit-transform: scaleY(-1);
   -o-transform: scaleY(-1);
+  z-index: 1;
 }
 
 .gv-canvas-container .gv-image-container img {
@@ -177,8 +180,9 @@
 }
 
 .gv-label-container li .gv-handle {
+  float: left;
   position: relative;
-  background-image: url(../i/Grabbar.png);
+  background-image: url(../i/sort_handle.png);
   cursor: move;
   display: inline-block;
   height: calc(100% - 20px);
@@ -196,13 +200,11 @@
 }
 
 .gv-label-container li .gv-name {
-  display: inline-block;
-  position: relative;
+  float: left;
+  position: absolute;
   overflow: hidden;
-  vertical-align: top;
   margin: 8px 0;
-  padding-right: 2px;
-  left: 5px;
+  left: 15px;
   width: 85%;
   color: #F2F5F7;
   text-shadow: 0 1px 0 rgba(0, 0, 0, 0.75);
@@ -212,10 +214,6 @@
   white-space: pre-wrap;
 }
 
-.gv-label-container li.gv-unsortable .gv-name {
-  left: 15px;
-}
-
 .gv-label-container li.gv-line-break .gv-name {
   text-overflow: inherit;
   word-spacing: 1000px;
@@ -241,7 +239,8 @@
   border-color: #000;
 }
 
-.gv-canvas-container .gv-wrapper > :last-child.gv-track-container-legend .gv-track-border {
+.gv-canvas-container .gv-wrapper > :last-child.gv-track-container-legend .gv-track-border,
+.gv-canvas-container .gv-wrapper > :last-child.gv-track-super-container > :last-child.gv-track-container-legend .gv-track-border {
   display: none;
 }
 
@@ -359,6 +358,16 @@
   color: #000;
 }
 
+.gv-menu .gv-menu-content .gv-menu-scroll-wrapper {
+  max-height: 300px;
+  overflow-y: auto;
+  margin: 10px 10px 10px 0;
+}
+
+.gv-menu .gv-menu-content .gv-menu-scroll-wrapper table {
+  margin: 0 10px;
+}
+
 .gv-selector {
   position: absolute;
   display: none;
@@ -432,3 +441,15 @@
   font-size: 75%;
   line-height: 1em;
 }
+
+.gv-canvas-container .gv-track-container canvas.gv-barchart-axis,
+.gv-canvas-container .gv-track-container canvas.gv-barchart-guide {
+  display: block!important;
+  height: auto;
+  bottom: 0;
+  z-index: 1;
+}
+
+.gv-hide {
+  display: none!important;
+}
diff --git a/css/trackControls.css b/css/trackControls.css
@@ -18,7 +18,17 @@
   background: rgba(0, 0, 0, 0.7);
 }
 
-.gv-track-controls-plugin .gv-track-container div.gv-track-controls > * {
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls .gv-track-controls-container {
+  display: none;
+}
+
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls.gv-maximized .gv-track-controls-container {
+  display: inline-block;
+  border-right: 1px solid white;
+  padding-right: 5px;
+}
+
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls .gv-track-controls-container > * {
   display: inline-block;
   min-width: 20px;
   text-align: center;
@@ -32,20 +42,50 @@
   text-decoration: underline;
 }
 
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.fa:hover {
+  text-decoration: none;
+}
+
 .gv-track-controls-plugin .gv-track-container:hover > div.gv-track-controls {
   display: block;
 }
 
-.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-hidden {
-  display: none!important;
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-track-controls-toggle {
+  padding-left: 5px;
+}
+
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls.gv-maximized a.gv-track-controls-toggle {
+  padding: 0 5px 0 10px;
+}
+
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-track-controls-toggle .fa {
+  margin-right: 5px;
+}
+
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls:not(.gv-maximized) a.gv-track-controls-toggle > :last-child,
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls.gv-maximized       a.gv-track-controls-toggle > :first-child {
+  display: none;
 }
 
 .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle {
-  background: url(../i/auto_height.png) center 1px no-repeat;
+  position: relative;
+}
+
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle .fa-sort-asc,
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle .fa-sort-desc,
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height .fa-sort {
+  display: none;
 }
 
-.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height {
-  background-position: center -17px;
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height .fa-sort-asc,
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height .fa-sort-desc {
+  display: inline-block;
+  position: absolute;
+  left: 6px;
+  top: -4px;
+}
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height .fa-sort-desc {
+  top: -15px;
 }
 
 .gv-track-controls-plugin .gv-track-container div.gv-track-controls select,
@@ -58,4 +98,12 @@
 
 .gv-track-controls-plugin .gv-track-container div.gv-track-controls select {
   margin: 0 5px;
-}
+}
+
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls label {
+  margin: 0 0 0 5px;
+}
+
+.gv-track-controls-plugin .gv-track-container div.gv-track-controls .gv-track-controls-container > :first-child:not(select):not(label) {
+  margin-left: 5px;
+}
diff --git a/expanded.html b/expanded.html
@@ -5,11 +5,13 @@
 
     <link rel="stylesheet" type="text/css" href="css/genoverse.css" />
     <link rel="stylesheet" type="text/css" href="css/controlPanel.css" />
+    <link rel="stylesheet" type="text/css" href="css/fileDrop.css" />
+    <link rel="stylesheet" type="text/css" href="css/font-awesome.css" />
+    <link rel="stylesheet" type="text/css" href="css/fullscreen.css" />
     <link rel="stylesheet" type="text/css" href="css/karyotype.css" />
-    <link rel="stylesheet" type="text/css" href="css/trackControls.css" />
     <link rel="stylesheet" type="text/css" href="css/resizer.css" />
-    <link rel="stylesheet" type="text/css" href="css/fullscreen.css" />
     <link rel="stylesheet" type="text/css" href="css/tooltips.css" />
+    <link rel="stylesheet" type="text/css" href="css/trackControls.css" />
   </head>
   <body>
     <div id="genoverse"></div>
@@ -19,66 +21,71 @@
     <script type="text/javascript" src="js/lib/jquery.mousewheel.js"></script>
     <script type="text/javascript" src="js/lib/jquery.mousehold.js"></script>
     <script type="text/javascript" src="js/lib/jquery.tipsy.js"></script>
-
     <script type="text/javascript" src="js/lib/Base.js"></script>
     <script type="text/javascript" src="js/lib/rtree.js"></script>
     <script type="text/javascript" src="js/lib/dalliance-lib.min.js"></script>
-
+    <script type="text/javascript" src="js/lib/jDataView.js"></script>
+    <script type="text/javascript" src="js/lib/jParser.js"></script>
+    <script type="text/javascript" src="js/lib/BWReader.js"></script>
+    <script type="text/javascript" src="js/lib/VCFReader.js"></script>
     <script type="text/javascript" src="js/Genoverse.js"></script>
     <script type="text/javascript" src="js/Track.js"></script>
-
     <script type="text/javascript" src="js/Track/Controller.js"></script>
     <script type="text/javascript" src="js/Track/Model.js"></script>
     <script type="text/javascript" src="js/Track/View.js"></script>
-
     <script type="text/javascript" src="js/Track/library/Static.js"></script>
-
     <script type="text/javascript" src="js/Track/Controller/Stranded.js"></script>
     <script type="text/javascript" src="js/Track/Model/Stranded.js"></script>
-
+    <script type="text/javascript" src="js/Track/library/Graph.js"></script>
+    <script type="text/javascript" src="js/Track/library/Graph/Line.js"></script>
+    <script type="text/javascript" src="js/Track/library/Graph/Bar.js"></script>
     <script type="text/javascript" src="js/Track/Controller/Sequence.js"></script>
     <script type="text/javascript" src="js/Track/Model/Sequence.js"></script>
     <script type="text/javascript" src="js/Track/Model/Sequence/Fasta.js"></script>
     <script type="text/javascript" src="js/Track/Model/Sequence/Ensembl.js"></script>
-    <script type="text/javascript" src="js/Track/Model/Sequence/DAS.js"></script>
     <script type="text/javascript" src="js/Track/View/Sequence.js"></script>
     <script type="text/javascript" src="js/Track/View/Sequence/Variation.js"></script>
-
     <script type="text/javascript" src="js/Track/Model/SequenceVariation.js"></script>
-
     <script type="text/javascript" src="js/Track/Model/Gene.js"></script>
     <script type="text/javascript" src="js/Track/Model/Gene/Ensembl.js"></script>
     <script type="text/javascript" src="js/Track/View/Gene.js"></script>
     <script type="text/javascript" src="js/Track/View/Gene/Ensembl.js"></script>
-
     <script type="text/javascript" src="js/Track/Model/Transcript.js"></script>
     <script type="text/javascript" src="js/Track/Model/Transcript/Ensembl.js"></script>
-    <script type="text/javascript" src="js/Track/Model/Transcript/GFF3.js"></script>
     <script type="text/javascript" src="js/Track/View/Transcript.js"></script>
     <script type="text/javascript" src="js/Track/View/Transcript/Ensembl.js"></script>
-
     <script type="text/javascript" src="js/Track/Model/File.js"></script>
     <script type="text/javascript" src="js/Track/Model/File/BAM.js"></script>
     <script type="text/javascript" src="js/Track/Model/File/BED.js"></script>
     <script type="text/javascript" src="js/Track/Model/File/GFF.js"></script>
     <script type="text/javascript" src="js/Track/Model/File/VCF.js"></script>
-
+    <script type="text/javascript" src="js/Track/Model/File/WIG.js"></script>
     <script type="text/javascript" src="js/Track/library/Chromosome.js"></script>
     <script type="text/javascript" src="js/Track/library/dbSNP.js"></script>
     <script type="text/javascript" src="js/Track/library/File.js"></script>
     <script type="text/javascript" src="js/Track/library/File/BAM.js"></script>
     <script type="text/javascript" src="js/Track/library/File/BED.js"></script>
+    <script type="text/javascript" src="js/Track/library/File/BIGBED.js"></script>
+    <script type="text/javascript" src="js/Track/library/File/BIGWIG.js"></script>
     <script type="text/javascript" src="js/Track/library/File/GFF.js"></script>
-    <script type="text/javascript" src="js/Track/library/File/GFF3.js"></script>
     <script type="text/javascript" src="js/Track/library/File/VCF.js"></script>
+    <script type="text/javascript" src="js/Track/library/File/WIG.js"></script>
     <script type="text/javascript" src="js/Track/library/Gene.js"></script>
     <script type="text/javascript" src="js/Track/library/HighlightRegion.js"></script>
     <script type="text/javascript" src="js/Track/library/Legend.js"></script>
     <script type="text/javascript" src="js/Track/library/Scaleline.js"></script>
     <script type="text/javascript" src="js/Track/library/Scalebar.js"></script>
+    <script type="text/javascript" src="js/plugins/controlPanel.js"></script>
+    <script type="text/javascript" src="js/plugins/fileDrop.js"></script>
+    <script type="text/javascript" src="js/plugins/focusRegion.js"></script>
+    <script type="text/javascript" src="js/plugins/fullscreen.js"></script>
+    <script type="text/javascript" src="js/plugins/karyotype.js"></script>
+    <script type="text/javascript" src="js/plugins/resizer.js"></script>
+    <script type="text/javascript" src="js/plugins/tooltips.js"></script>
+    <script type="text/javascript" src="js/plugins/trackControls.js"></script>
 
     <script>
-      var genoverseConfig = {
+      window.genoverse = new Genoverse({
         container : '#genoverse',
         width     : 800,
         genome    : 'grch38',
@@ -99,16 +106,14 @@
           Genoverse.Track.Gene,
           Genoverse.Track.extend({
             name            : 'Regulatory Features',
-            url             : 'http://rest.ensembl.org/overlap/region/human/__CHR__:__START__-__END__?feature=regulatory;content-type=application/json',
+            url             : '//rest.ensembl.org/overlap/region/human/__CHR__:__START__-__END__?feature=regulatory;content-type=application/json',
             resizable       : 'auto',
             model           : Genoverse.Track.Model.extend({ dataRequestLimit : 5000000 }),
             setFeatureColor : function (f) { f.color = '#AAA'; }
           }),
           Genoverse.Track.dbSNP
         ]
-      }
-
-      $(document).ready(function () { window.genoverse = new Genoverse(genoverseConfig); });
+      });
     </script>
   </body>
 </html>
diff --git a/i/auto_height.png b/i/auto_height.png
diff --git a/i/bg.jpg b/i/bg.jpg
diff --git a/i/bg.png b/i/bg.png
diff --git a/i/blue_line.jpg b/i/blue_line.jpg
diff --git a/i/greypx.png b/i/greypx.png
diff --git a/i/loadingBG.png b/i/loadingBG.png
diff --git a/i/Grabbar.png → i/sort_handle.png b/i/Grabbar.png → i/sort_handle.png