From 9bffd3ba9c8a8fafb7b568fbc9e59b819e0fe70b Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 20:56:35 -0500
Subject: [PATCH 01/49] start calling the tracklist a config

---
 index.html    |  2 +-
 js/Browser.js | 42 ++++++++++++++++++++++++------------------
 2 files changed, 25 insertions(+), 19 deletions(-)

diff --git a/index.html b/index.html
index e396d5eb6f..eac3e69dc1 100644
--- a/index.html
+++ b/index.html
@@ -47,7 +47,7 @@
            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: {url: dataRoot + "/seq/refSeqs.json"},
-                                   tracklists: [
+                                   config: [
                                        {url: dataRoot + "/trackList.json"}
                                    ],
                                    nameUrl: dataRoot + "/names/root.json",
diff --git a/js/Browser.js b/js/Browser.js
index 36859741e6..2e8a99bfee 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -4,9 +4,9 @@
  * @constructor
  * @param params an object with the following properties:<br>
  * <ul>
+ * <li><code>config</code> - list of objects with "url" property that points to a config JSON file</li>
  * <li><code>containerID</code> - ID of the HTML element that contains the browser</li>
  * <li><code>refSeqs</code> - object with "url" property that is the URL to list of reference sequence information items</li>
- * <li><code>tracklists</code> - list of objects with "url" property that points to a track list JSON file</li>
  * <li><code>browserRoot</code> - (optional) URL prefix for the browser code</li>
  * <li><code>tracks</code> - (optional) comma-delimited string containing initial list of tracks to view</li>
  * <li><code>location</code> - (optional) string describing the initial location</li>
@@ -94,17 +94,21 @@ Browser.prototype.initialize = function() {
                        brwsr.addRefseqs(o);
                    });
 
-    for (var i = 0; i < this.params.tracklists.length; i++) {
-        (function(tracklist) {
-             Util.maybeLoad(tracklist.url,
-                            tracklist,
-                            function(o) {
-                                brwsr.addDeferred(
-                                    function() {
-                                        brwsr.addTracklist(tracklist.url, o);
-                                    });
-                            });
-         })(this.params.tracklists[i]);
+    if( typeof this.params.config != 'object' || !this.params.config.length )
+        this.params.config = [ this.params.config ];
+
+    for (var i = 0; i < this.params.config.length; i++) {
+        (function(config) {
+             Util.maybeLoad(
+                 config.url,
+                 config,
+                 function(o) {
+                     brwsr.addDeferred(
+                         function() {
+                             brwsr.addConfig(config.url, o);
+                         });
+                 });
+         })(this.params.config[i]);
     }
 };
 
@@ -119,12 +123,14 @@ Browser.prototype.addDeferred = function(f) {
         this.deferredFunctions.push(f);
 };
 
-Browser.prototype.addTracklist = function(url, trackList) {
-    if (1 == trackList.formatVersion) {
-        for (var i = 0; i < trackList.tracks.length; i++)
-            trackList.tracks[i].sourceUrl = url;
-        this.trackListWidget.insertNodes(false, trackList.tracks);
-        this.showTracks(this.origTracklist);
+Browser.prototype.addConfig = function( url, config ) {
+    if (1 == config.formatVersion) {
+        if( config.tracks ) {
+            for (var i = 0; i < config.tracks.length; i++)
+                config.tracks[i].sourceUrl = url;
+            this.trackListWidget.insertNodes(false, config.tracks);
+            this.showTracks(this.origTracklist);
+        }
     } else {
         throw "track list format " + trackList.formatVersion + " not supported";
     }

From 8fb03cb69f3451929f8748749aa5ddc9f28a76e9 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 21:53:07 -0500
Subject: [PATCH 02/49] make config-loading method take a hashref of additional
 data to merge in

---
 js/Browser.js | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index 2e8a99bfee..31d6be6976 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -88,12 +88,14 @@ Browser.prototype.initialize = function() {
         this.origTracklist = this.params.defaultTracks;
     }
 
+    // load our ref seqs
     var brwsr = this;
     Util.maybeLoad(this.params.refSeqs.url, this.params.refSeqs,
                    function(o) {
                        brwsr.addRefseqs(o);
                    });
 
+    // load any configuration files we've been passed
     if( typeof this.params.config != 'object' || !this.params.config.length )
         this.params.config = [ this.params.config ];
 
@@ -105,7 +107,7 @@ Browser.prototype.initialize = function() {
                  function(o) {
                      brwsr.addDeferred(
                          function() {
-                             brwsr.addConfig(config.url, o);
+                             brwsr.addConfig( o, { sourceUrl: config.url });
                          });
                  });
          })(this.params.config[i]);
@@ -123,11 +125,20 @@ Browser.prototype.addDeferred = function(f) {
         this.deferredFunctions.push(f);
 };
 
-Browser.prototype.addConfig = function( url, config ) {
+Browser.prototype.addConfig = function( config, additional ) {
+
+    // add any additional data to the config hash
+    for( p in additional ) {
+        if( additional.hasOwnProperty(p) )
+            config[p] = additional[p];
+    }
+
     if (1 == config.formatVersion) {
         if( config.tracks ) {
-            for (var i = 0; i < config.tracks.length; i++)
-                config.tracks[i].sourceUrl = url;
+            if( additional.sourceUrl ) {
+                for (var i = 0; i < config.tracks.length; i++)
+                    config.tracks[i].sourceUrl = additional.sourceUrl;
+            }
             this.trackListWidget.insertNodes(false, config.tracks);
             this.showTracks(this.origTracklist);
         }

From b8a4b6066c973eea8a3b65febb53748262841882 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 22:05:33 -0500
Subject: [PATCH 03/49] factor config-file loading into a separate method, and
 call it first during initialization

---
 js/Browser.js | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/js/Browser.js b/js/Browser.js
index 31d6be6976..8f0287f5ac 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -40,6 +40,9 @@ var Browser = function(params) {
 };
 
 Browser.prototype.initialize = function() {
+
+    this.loadConfig();
+
     //set up top nav/overview pane and main GenomeView pane
     dojo.addClass(document.body, "tundra");
     this.container = dojo.byId(this.params.containerID);
@@ -94,6 +97,12 @@ Browser.prototype.initialize = function() {
                    function(o) {
                        brwsr.addRefseqs(o);
                    });
+};
+
+// load our configuration files based on the parameters the
+// constructor was passed
+Browser.prototype.loadConfig = function () {
+    var brwsr = this;
 
     // load any configuration files we've been passed
     if( typeof this.params.config != 'object' || !this.params.config.length )

From bb2ac706f6eab7960523d4f6fef1c2555d9899b9 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 22:06:00 -0500
Subject: [PATCH 04/49] simplify code that calculates which tracks to display
 at startup

---
 js/Browser.js | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index 8f0287f5ac..227df26637 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -82,14 +82,15 @@ Browser.prototype.initialize = function() {
     topPane.appendChild(this.locationTrap);
     topPane.style.overflow="hidden";
 
-    var cookieTracks = dojo.cookie(this.container.id + "-tracks");
-    if (this.params.tracks) {
-        this.origTracklist = this.params.tracks;
-    } else if (cookieTracks) {
-        this.origTracklist = cookieTracks;
-    } else if (this.params.defaultTracks) {
-        this.origTracklist = this.params.defaultTracks;
-    }
+    // figure out what initial track list we will use:
+    //    from a param passed to our instance, or from a cookie, or
+    //    the passed defaults, or the last-resort default of "DNA"?
+    this.origTracklist =
+           this.params.tracks
+        || dojo.cookie( this.container.id + "-tracks" )
+        || this.params.defaultTracks
+        || "DNA";
+
 
     // load our ref seqs
     var brwsr = this;

From 6742f36dcb6c970f15dac43790a12e224faecd8a Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 22:16:18 -0500
Subject: [PATCH 05/49] correct small doc typo

---
 js/Util.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/Util.js b/js/Util.js
index cd286a98f3..d2b7d04f75 100644
--- a/js/Util.js
+++ b/js/Util.js
@@ -94,7 +94,7 @@ Util.fillTemplate = function(template, fillWith) {
  * function to load a specified resource only once
  * @param url URL to get
  * @param stateObj object that stores the state of the load
- * @param successCalback function to call on a successful load
+ * @param successCallback function to call on a successful load
  * @param errorCallback function to call on an unsuccessful load
  */
 Util.maybeLoad = function (url, stateObj, successCallback, errorCallback) {

From ecfa9b962abb936c6928b70862b0c948c00ddeca Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 22:21:12 -0500
Subject: [PATCH 06/49] make Browser constructor interpret bare strings passed
 as refSeqs or config params as URLs

---
 index.html    | 4 ++--
 js/Browser.js | 5 +++++
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/index.html b/index.html
index eac3e69dc1..828004a014 100644
--- a/index.html
+++ b/index.html
@@ -46,9 +46,9 @@
            var dataRoot = queryParams.data || 'data';
            var b = new Browser({
                                    containerID: "GenomeBrowser",
-                                   refSeqs: {url: dataRoot + "/seq/refSeqs.json"},
+                                   refSeqs: dataRoot + "/seq/refSeqs.json",
                                    config: [
-                                       {url: dataRoot + "/trackList.json"}
+                                     dataRoot + "/trackList.json",
                                    ],
                                    nameUrl: dataRoot + "/names/root.json",
                                    defaultTracks: "DNA,gene,mRNA,noncodingRNA",
diff --git a/js/Browser.js b/js/Browser.js
index 227df26637..4c6daaf1f2 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -94,6 +94,8 @@ Browser.prototype.initialize = function() {
 
     // load our ref seqs
     var brwsr = this;
+    if( typeof this.params.refSeqs == 'string' )
+        this.params.refSeqs = { url: this.params.refSeqs };
     Util.maybeLoad(this.params.refSeqs.url, this.params.refSeqs,
                    function(o) {
                        brwsr.addRefseqs(o);
@@ -110,6 +112,9 @@ Browser.prototype.loadConfig = function () {
         this.params.config = [ this.params.config ];
 
     for (var i = 0; i < this.params.config.length; i++) {
+        if( typeof this.params.config[i] == 'string' )
+            this.params.config[i] = { url: this.params.config[i] };
+
         (function(config) {
              Util.maybeLoad(
                  config.url,

From 1c8162f1ae84ed4bfaa1ac68a8698a396af82411 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 22:38:03 -0500
Subject: [PATCH 07/49] rename some "track" variables to "trackConfig" to be
 clearer that this is a object of track configuration data

---
 js/Browser.js | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index 4c6daaf1f2..c0acdf61c0 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -301,10 +301,10 @@ Browser.prototype.createTrackList = function(parent, params) {
        brwsr.view.showVisibleBlocks(true);
     };
 
-    var trackListCreate = function(track, hint) {
+    var trackListCreate = function( trackConfig, hint ) {
         var node = document.createElement("div");
         node.className = "tracklist-label";
-        node.innerHTML = track.key;
+        node.innerHTML = trackConfig.key;
         //in the list, wrap the list item in a container for
         //border drag-insertion-point monkeying
         if ("avatar" != hint) {
@@ -314,20 +314,20 @@ Browser.prototype.createTrackList = function(parent, params) {
             node = container;
         }
         node.id = dojo.dnd.getUniqueId();
-        return {node: node, data: track, type: ["track"]};
+        return {node: node, data: trackConfig, type: ["track"]};
     };
     this.trackListWidget = new dojo.dnd.Source(trackListDiv,
                                                {creator: trackListCreate,
                                                 accept: ["track"], // accepts tracks into left div
                                                 withHandles: false});
 
-    var trackCreate = function(track, hint) {
+    var trackCreate = function( trackConfig, hint) {
         var node;
         if ("avatar" == hint) {
-            return trackListCreate(track, hint);
+            return trackListCreate( trackConfig, hint);
         } else {
-            var klass = eval(track.type);
-            var newTrack = new klass(track, brwsr.refSeq,
+            var klass = eval( trackConfig.type);
+            var newTrack = new klass( trackConfig, brwsr.refSeq,
                                      {
                                          changeCallback: changeCallback,
                                          trackPadding: brwsr.view.trackPadding,
@@ -336,7 +336,7 @@ Browser.prototype.createTrackList = function(parent, params) {
                                      });
             node = brwsr.view.addTrack(newTrack);
         }
-        return {node: node, data: track, type: ["track"]};
+        return {node: node, data: trackConfig, type: ["track"]};
     };
 
 
@@ -363,7 +363,7 @@ Browser.prototype.createTrackList = function(parent, params) {
 Browser.prototype.onVisibleTracksChanged = function() {
     this.view.updateTrackList();
     var trackLabels = dojo.map(this.view.tracks,
-                               function(track) { return track.name; });
+                               function( trackConfig ) { return trackConfig.name; });
     dojo.cookie(this.container.id + "-tracks",
                 trackLabels.join(","),
                 {expires: 60});
@@ -566,8 +566,8 @@ Browser.prototype.visibleRegion = function() {
  */
 
 Browser.prototype.visibleTracks = function() {
-    var trackLabels = dojo.map(this.view.tracks,
-                               function(track) { return track.name; });
+    var trackLabels = dojo.map( this.view.tracks,
+                                function( trackConfig ) { return trackConfig.name; });
     return trackLabels.join(",");
 };
 

From ae6c183a5705e661018b971887fbaeb5e1392219 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 23:06:53 -0500
Subject: [PATCH 08/49] introduce a baseUrl in the track configurations that is
 conceptually separate from the sourceUrl, but defaults to the sourceUrl

---
 js/Browser.js       | 7 +++++--
 js/FeatureTrack.js  | 5 +++--
 js/ImageTrack.js    | 2 +-
 js/SequenceTrack.js | 2 +-
 4 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index c0acdf61c0..1217f4fdb2 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -148,11 +148,14 @@ Browser.prototype.addConfig = function( config, additional ) {
             config[p] = additional[p];
     }
 
+    config.baseUrl = config.baseUrl || config.sourceUrl;
+
     if (1 == config.formatVersion) {
         if( config.tracks ) {
-            if( additional.sourceUrl ) {
+            if( config.sourceUrl ) {
                 for (var i = 0; i < config.tracks.length; i++)
-                    config.tracks[i].sourceUrl = additional.sourceUrl;
+                    if( ! config.tracks[i].baseUrl )
+                        config.tracks[i].baseUrl = config.baseUrl;
             }
             this.trackListWidget.insertNodes(false, config.tracks);
             this.showTracks(this.origTracklist);
diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index d4c90c9a7c..c6e22ac1f2 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -2,7 +2,8 @@ function FeatureTrack(trackMeta, refSeq, browserParams) {
     //trackMeta: object with:
     //            key:   display text track name
     //            label: internal track name (no spaces, odd characters)
-    //            sourceUrl: URL of the tracklist containing this track entry
+    //            baseUrl: base URL to use for resolving relative URLs
+    //                     contained in the track's configuration
     //            config: configuration info for this track
     //refSeq: object with:
     //         name:  refseq name
@@ -18,7 +19,7 @@ function FeatureTrack(trackMeta, refSeq, browserParams) {
     this.fields = {};
     this.features = new NCList();
     this.refSeq = refSeq;
-    this.url = Util.resolveUrl(trackMeta.sourceUrl,
+    this.url = Util.resolveUrl(trackMeta.baseUrl,
                                Util.fillTemplate(trackMeta.config.urlTemplate,
                                                  {'refseq': refSeq.name}) );
     //number of histogram bins per block
diff --git a/js/ImageTrack.js b/js/ImageTrack.js
index eeb8c8980d..a9c819b7ac 100644
--- a/js/ImageTrack.js
+++ b/js/ImageTrack.js
@@ -5,7 +5,7 @@ function ImageTrack(trackMeta, refSeq, browserParams) {
     this.trackPadding = browserParams.trackPadding;
     this.tileToImage = {};
     this.zoomCache = {};
-    this.url = Util.resolveUrl(trackMeta.sourceUrl,
+    this.url = Util.resolveUrl(trackMeta.baseUrl,
                                Util.fillTemplate(trackMeta.config.urlTemplate,
                                                  {'refseq': refSeq.name}) );
     this.load(this.url);
diff --git a/js/SequenceTrack.js b/js/SequenceTrack.js
index e9586f9c6d..96bbb903ef 100644
--- a/js/SequenceTrack.js
+++ b/js/SequenceTrack.js
@@ -21,7 +21,7 @@ function SequenceTrack(trackMeta, refSeq, browserParams) {
     this.setLoaded();
     this.chunks = [];
     this.chunkSize = trackMeta.config.chunkSize;
-    this.url = Util.resolveUrl(trackMeta.sourceUrl,
+    this.url = Util.resolveUrl(trackMeta.baseUrl,
                                Util.fillTemplate(trackMeta.config.urlTemplate,
                                                  {'refseq': refSeq.name}) );
 }

From 962cb996843dc5f693796921227aaf54590bb719 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 5 Mar 2012 23:22:36 -0500
Subject: [PATCH 09/49] make sure the baseUrl config has a trailing slash

---
 js/Browser.js | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/js/Browser.js b/js/Browser.js
index 1217f4fdb2..9fb1f59068 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -149,6 +149,8 @@ Browser.prototype.addConfig = function( config, additional ) {
     }
 
     config.baseUrl = config.baseUrl || config.sourceUrl;
+    if( ! /\/$/.test(config.baseUrl) ) // make sure the baseUrl has a trailing slash
+        config.baseUrl += "/";
 
     if (1 == config.formatVersion) {
         if( config.tracks ) {

From ceeb09d81350b55b86968f213a2a899eaa53675f Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Thu, 8 Mar 2012 16:43:35 -0500
Subject: [PATCH 10/49] added test data consisting of volvox formatted with the
 1.2.1 release

---
 tests/data/volvox_formatted_1_2_1/refSeqs.js  | 11 +++
 .../volvox_formatted_1_2_1/seq/ctgA/0.txt     |  1 +
 .../volvox_formatted_1_2_1/seq/ctgA/1.txt     |  1 +
 .../volvox_formatted_1_2_1/seq/ctgA/2.txt     |  1 +
 .../data/volvox_formatted_1_2_1/trackInfo.js  | 78 +++++++++++++++++
 .../tracks/ctgA/Alignments/hist-10000-0.json  |  1 +
 .../tracks/ctgA/Alignments/names.json         |  1 +
 .../tracks/ctgA/Alignments/trackData.json     |  1 +
 .../tracks/ctgA/CDS/hist-50000-0.json         |  1 +
 .../tracks/ctgA/CDS/names.json                |  1 +
 .../tracks/ctgA/CDS/trackData.json            |  1 +
 .../tracks/ctgA/Clones/hist-200000-0.json     |  1 +
 .../tracks/ctgA/Clones/names.json             |  1 +
 .../tracks/ctgA/Clones/trackData.json         |  1 +
 .../tracks/ctgA/EST/hist-50000-0.json         |  1 +
 .../tracks/ctgA/EST/names.json                |  1 +
 .../tracks/ctgA/EST/trackData.json            |  1 +
 .../ctgA/ExampleFeatures/hist-10000-0.json    |  1 +
 .../tracks/ctgA/ExampleFeatures/names.json    |  1 +
 .../ctgA/ExampleFeatures/trackData.json       |  1 +
 .../tracks/ctgA/Genes/hist-200000-0.json      |  1 +
 .../tracks/ctgA/Genes/names.json              |  1 +
 .../tracks/ctgA/Genes/trackData.json          |  1 +
 .../tracks/ctgA/Motifs/hist-10000-0.json      |  1 +
 .../tracks/ctgA/Motifs/names.json             |  1 +
 .../tracks/ctgA/Motifs/trackData.json         |  1 +
 .../tracks/ctgA/NameTest/hist-50000-0.json    |  1 +
 .../tracks/ctgA/NameTest/names.json           |  1 +
 .../tracks/ctgA/NameTest/trackData.json       |  1 +
 .../ctgA/ReadingFrame/hist-50000-0.json       |  1 +
 .../tracks/ctgA/ReadingFrame/names.json       |  1 +
 .../tracks/ctgA/ReadingFrame/trackData.json   |  1 +
 .../tracks/ctgA/Transcript/hist-200000-0.json |  1 +
 .../tracks/ctgA/Transcript/names.json         |  1 +
 .../tracks/ctgA/Transcript/trackData.json     |  1 +
 .../tracks/ctgA/volvox_microarray.wig.json    | 85 +++++++++++++++++++
 36 files changed, 207 insertions(+)
 create mode 100644 tests/data/volvox_formatted_1_2_1/refSeqs.js
 create mode 100644 tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt
 create mode 100644 tests/data/volvox_formatted_1_2_1/seq/ctgA/1.txt
 create mode 100644 tests/data/volvox_formatted_1_2_1/seq/ctgA/2.txt
 create mode 100644 tests/data/volvox_formatted_1_2_1/trackInfo.js
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/hist-10000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/hist-50000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/hist-200000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/hist-50000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/hist-10000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/hist-200000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/hist-10000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/hist-50000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/hist-50000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/hist-200000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/names.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/trackData.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/volvox_microarray.wig.json

diff --git a/tests/data/volvox_formatted_1_2_1/refSeqs.js b/tests/data/volvox_formatted_1_2_1/refSeqs.js
new file mode 100644
index 0000000000..fbb225dc35
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/refSeqs.js
@@ -0,0 +1,11 @@
+refSeqs = 
+[
+   {
+      "length" : 50001,
+      "name" : "ctgA",
+      "seqDir" : "seq/ctgA",
+      "seqChunkSize" : 20000,
+      "end" : 50001,
+      "start" : 0
+   }
+]
diff --git a/tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt b/tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt
new file mode 100644
index 0000000000..5d5e213224
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt
@@ -0,0 +1 @@
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c
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/seq/ctgA/1.txt b/tests/data/volvox_formatted_1_2_1/seq/ctgA/1.txt
new file mode 100644
index 0000000000..5a5378a120
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/seq/ctgA/1.txt
@@ -0,0 +1 @@
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a
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/seq/ctgA/2.txt b/tests/data/volvox_formatted_1_2_1/seq/ctgA/2.txt
new file mode 100644
index 0000000000..cf63d97e83
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/seq/ctgA/2.txt
@@ -0,0 +1 @@
+ggcgtggaggcatagggccggagtgttcccgtaccaattacgagctaagaccgcctgtccagccctggtgattacgtagtaagctcggtacaagcctgtaattagcttccgggtggcggacattcgttcatattgccagtcacggcagaggccgcgctagctaggccagccccgatgaaacacgtgctagttttctatcgtgcctaaggatcgatggctatcgcggcattgttaacttatcaagcagccgaatcggcgatagtggacacaacatgaacacgctaagctctgagtgccagactctaccgcggcgaatcctaggccctgctggggctcccccacagagcagtaatggtcttctgcggccgcgtgcattcaatccgcgctggtcaatgcgttccatcgtgccttaagcggggcagtgtgataagacaattttgggggtttcatggagatatcttcagaaacctcgcgaggtgcgtttagataccacacgcgcggcggtcttttcacacaattcagtccgcggccggtaacctaactttgcttatcaatacataatcctcccaaatgtacggtttcgaaggagatacctctcccctgttagactctaggttttgcagtgctacctagagatcacaccagcattaaaccaaggtatcagcatcgtaacatggggaggcacgcgcttggcggtaagtacccgccacgattactctgtttcatagcgccaacgcccgtatagtgtgcttttaacgtcctcagaaatcaccgactgatcagtatggcgacatcggagggaggttggcgaaatgttgcttttatagatcgttaaaacctatcgttggcgcgtatcgcctccatagaacttcttactcacctagtctgatcccgggactggtcgaaatggagacgacgtagcttgagatctggatcgatcgactgatatcacacttaaatatgatcagattttactacggtcgatctccatatatctatcccagcacttgatacctcctgtccagccgactgcttggaccctagcacgcgatattagagggcgcgttgtagctcaaagtaaccagtgggacgacccgagtgaggttaccgctggcacgtaagggtgacatgactcccccagaaacactgaatttgtctagcagtacatcataatctgagaacatttagcgaagacgagaacaagctgtctcaatggacgtaggacgagaggaatgtgacggttataatacgcgacctctatgtgtctattaaatccctacgggccgtagcgagcaagctcgggatctttagtagcggatcgggtcttctacatggcgcaccaggtttgatatttcgagctagagttgctctaaagaaacgctcttgcttgggaaagtgacctggggtacgacgaagacacgggcctggttgcataccgtctcaccttcattcatcgagcgcgatagcgtagcattatccagcacgggaggcacctggcatgggcgtgaaatacaatccgaagagcagcatgaaaaaaaaatgagcggtcgtgacccgagggtgcgtccctccgaacgttgttcgttgccaaggtaagggacccacgccaagcatggttagggaagcgtgaccgacacaacatagaggacaatctcaatatgccttctgggtatcacctgggtgtgtagcagtgctactgttacaagtcgcgccatctgcgacgtcgttcgtccctattccctcctaaaggccccgactctgaaaaaacctacaatcctagacacgttgtggcccagcacaacgcgtctgctatacagcaagtcattcgtcgaatggggcaacacgtataagaaggccgtgattccaagggcacatggcgggtctctcaatgatctacgacgtgacgcaaacggggaaaggctggaccgttgtccggtaggcgatccatcataaaaggcgtctggttctgtggttattgtgtacacgtttgaaatatctgactgtagaacgatggaggtctctacgtagctctgcacgattccctcgggctcacgttcatggcaaggcgacatcacatgaacagggttgggtaacagccatctctgaagcattcccccagctcgcacggctcctttacccgctactacgtcatgcactggctagagacccaccaactattgtgcaagtaaagaccataaaattttggagctgtagcgaaagcgagttgctgcgatggttagaccaacattgggtcaaactattctaatccggctaggctcattaagcatcgcagattgccgatactaatgctaacgagcgatgaatgggcctcttcgagacgcgtccgtacctgcgaatatcaaccatgaaccctaatctggaaagtttgatgccgctgtgatagccactcctgtgtcgcgacggcaacgtaatgtacgtgcttggtttgagctctaaacataccttcgttagagttggtcagaggaggatattgtcatagcgctacaaccagcgccaaaggatagctccgtggctggtcggacgcgctagaatctaggcagaacacgtgcggcttcttgcactctgacgctcacgcattggactttggcggtcatctggttctcataagtccgaatcacagtagataaagatccgcgtgataagatatgcctacgtacttaagtagcaccctctgttcttggcgatcctatcattgcgggttctatacatatgttgatccaaccatcggccgccgggccgtcgtaggatctaatggccaacacatcaatcaaatcactcgcgaggacgcggaggtcccgtccataggtgtgtatgttggtacgcagcacctaatctggtctggtcaagcaactggcttgttccagtatataatctcagatagactgccctgaaagtagacaatgataaatatgtaagagcggggaaatcccatcgtcgactgtgttgcggacgattagcttgcaaagagaggtgtgagcggctgtcttaaattatggactcctcgcttccgtcgaacgtctgactagagaatctcttggaggtacacacgaacgtaggttcctcacagtatgtggcatggacaccggacaggtcacttgtatttatccattgaacgtgatatagtgtgtcgagtcgttatacaatacatactccaagcgtactccctttgggtaacgggtttgggtacatattaccatggtgtggaccgatttgtaaccctataagcgttccgggtactttaccatcgcggatgcgatcgcggatctacctatgtcagcgacatactgcccgtccaaaagtgattcagtatgtgttaatcagcgtattgcatcatcagtcattgagagtggaccgttctcgaagagcaagattcctgaccctttccactgggccatccagtacacccaattatatgcagacgaaaagctccatacatatataatacctcttcacaccgtgtgcagagaccaacttgatcgatattgtactcactcgtacggaataattagaagggcccgactgtcgagaccgttagcatttgcattatcgcggtgagcgtatagaaacaattataggctttgctgcgatcgcagtgtctgggacagagtctcctagacctagatcagcttaaaacaatgattgtaggtaatgtgcgttgccgtcgggccacacctttcagttcggttacaccgactcagaattatcttctatcgggaccctcaaactgataatggggtcaaatggtggtggtcccgtctttctgcagtgctttgtgagcagaatagctctcgagcgctccagtacgcctgagtatggctgcgcccaccaattggcgccgttaatgcgtggcgacacaagagaaccagtccacataagttatgcccttaagaagatcaccgggtttgcgccatcctgattcaggtaacggacgtccgtgtacacgaaccatactaatgagttctacatcgctccaacgcgtcttgaaccctatcgacaattacaaatgcaaagtattagttgggtcagtgcgtagcttatccaagggctgcagtaagtcgtccccatgacagacggacggcataagggccaaaaattccgccgcattagctgttaataatgccatccagaaccggacagtctcgatatataacttacggctgcgaactggcccttatgaattacatccacgtgctagttaacaggacggatcgcccggactaattgccgatcggccgtcccattctccgtacgatgtactgaacccaggcgtgtgaatgggtatgtcaacgtttacccatcgaccctgcctatagacctgagtttcattccagttgagcgtagaatgggatgagcagctttgcttgaggtgcgatattcgggagacctggtcagcaggattgatggttttatagtgctggattccctgctgaaattctctcttctgccgcatgtgaagaaggccttgcttcccttccacatgattgtaagatttcctaaggcctcccagctgcgtggaactgtgagtcaattaaacctctttcctttataaattacccagtctcaggtatttccttatcgtggtatgagaacggattaatacagttgtgtaagccagctccttataataaatctctctccctctctctgcctctcatctatgtatgtatgtatctgtcatctatctcctataagttgtttcttttgagaactctgactaacatagacattaaataaacaatttgtatactgaataattatataactactgcttgggggtgtggttgtgttgtgtggtgagggggtgtagaaatgtctaggggttgatctagcctaacaccttccagatgaccctaggttctggcctttccccaaagagtcctggtctactcagtcatctcccacaatttggccatcttcttgggtgctcaggacaataaatgacccagccagatcctctagagtcgacctgcaggcatgcaagcttggcgtaatcatggtcatagctgtttgctgtgtgaaattgttatgcgctcacattgcacacaacatacgagccggaagcatacagtgtagagcctggggtggcgtatgagtgagctaactcacattaatttgcgtttgcgctcactgccgcttttcagtcggggaaactgtcgtgacagctgcatttaatgatcggtcatcgcgcggggagatgcggttttgcgtattgtgccgcaggtggttatttctctcaacagtgagacgggcacagctgattgccctcaccggctgggctgagagagttgcagcaagcgtacacgcggggtttgcccagcagggcgaaattcctgttgtgatgtggattccgaatcgggcaaatgccctataaatcaaagcatagtccgagatagggtttgagtgtgttcagttttgggacagaggtcactataaagaacgttgactgcacgtcaagggcgagaaacgtcatcaggcgattgcactacgtgacatcaccaatcagttttttgggtcaggtgcgtgagacttatcggaactaaaggagcccgttttagcttcggggaaacgcgaagtgtcggaagaaggaaaacgaagagcgggtatcgcggaatgtacgtgctgagcgaaaccaacgcgcgttacggtcaagcgtgtatgtgttttggaggtaagtttccctgataaagcggaacaggggctatgtgtttacgggggtcgcatggagtacaagggggcaggacaagatttgcgcgacatggttttttttaaattgcgggagatggttggctgtcccgatgagattagaacctgcttttgttttagtttcggttcggtcagttcggactttggattggttttgttgggtatttaagaagggtgtttgtgggatgtttttttttgggtcgagcatcactggactatgtgtgtcctgcgtatcgtggcggggcctcgaacttagaggtaggacgattccgatgcaacaaccttatgctttactccaagcgatggtgaggcaaccttgtacagaagtgcaaccgccattgtggctgggtcggcccaaggaacggatattctcctgggtactgacaacccaggtctactgggttctatcgacggtacagtcaagcctcgagtttactgtctcccacttaagtccgctctgggcattaatgagtctgtggggtatcaagggtcacccaacgaagtagctagtcccgttgtacatttcgcgcgttacctagggagcacggtgagctacgagggtgtagctgcacacagcacggtatataggaacgcaaacatagtagtatgtccctatgcataacagggagaagtgactctccgacggtcatttatcccagactctcctcgctccctactaattgttctatatacaatcggagtaaattggtacctctctgacaacataggggggttgaagtttatgccacgcagtctgttacacttttgccggggaattgtgtagaccatgactcaaggtggtggtgcgagttactctactatctactgcttctcattacacatctcttggcttacaggccccagttatcagttacgaggctgccttaagagaaggccaacattcatgatcagatccccgcacacgggatgatagtctgagatctgccggacgctcgtctgctacaagtgtgggttgagcatagggtaagcctaagggctcgtaatggtacttcgcgatgtttattcgatatgagctacaaggtataacgttgccttcaccatttcggctcacgactcttacctcgcctcaccgctagacaccctgaccaaccgttagggtactgacaaccgatcaggcgactcctaaaggacctctcagcctcccagacatgaggtccgctcgcatgctgttcagcgagtccatatcaggaacagcaacgagacaaggcgagagcaacactagacttggagacataccaccacatctgtttactcttgattcaggaagacctgtggtaactgggcgacgcgtgcgtttatccgtcttccaatctccacagaatctgctccgtcagagggatgtatgactaacgcactgattttttgttcagtaaccgggcgcggattacggggcgtattccaggggtacattcaacgggaccccaaggaaaagttcggggtatttaaggaggcggtccaactctcggacttattgggcgacgtaatgataagcacacctctgctcatacagtgcacgaagaccggcattgttcaaacacagccgtccattccgcgactattgtcctgtgtacaggtgcctcgggtcccaaatccagcttatacccaaaactctcccggacttttttcgtccttgcaggaggaaaggacctgactccacgtttattaggggatcgttgggcccggacaatcgtgtattcaacataataaatgggttctagtttaaagccggaggtgacggtggattatggactagaggtaaacatttccggcgtaggtcagaaagaatatagaccctaaatttacgcaaaacgtgcacacgattgtaggtggagtcgtattaggaactcagggcgggtggaacgagtgtgttttaggcttaccatgaaccgtcgcgcggaaaatgatgacagaatggacggtgcttttttgcggggccaacaaaactcgcttatgttcgccattggatgtaagtaccgctatactacgcagcgaccccttacgacattgttgatttccaatgctttcatggaggtttgtgagcggtcgctaggaatcttcctccagcgagtagccagctggccactagttagcaaccagagttcatatgagctccagtaacacgaaggtacataaggaacgcaagcaagttcgggactacatagaacttggggtgcgtctaagccggggatcttaatagacaagaggccatcgtatgggtcaaatttcatgtttcgtcagatgccctatccgtggacacctaaatcaagcatcatatcctaatgctatttgctctcgctttggtatgattcatatgcagccctgtccgtaaaatgacgggccagaggatacctgtcactacctatttcagattaccactgttcgaaaccttgctctgaaatcgatcttcgtagagtgttcgttaatcgccgcgtgaattatataatcccccaaggagtacccttcgtcggtgcagtctacgtaactttcccaggttagcccccatctaatcgacgtacgtgagggggctacgggagatcgcacaagccgaagcatttctgctctgtttcgttacaactggaatcctcatcacgcagcgctaccggatgccatccctagtcatccccgcgagtttaaccagtcgagatggctcgaaccgtgtttcgaaggctggctattgaaccagttataaagcaggggcgactgtccgtcggacttcgatataaactatcacaaatttggcataagtatatacagccaagaaggctcagataggcacacgcacccaaatagtgaccgcctacgttcaggttgcccggcaacgaagcgcgcttgctccattaatccactatcagaggtaacgaccctctttcaccgtagctgcccccatgtcggggcaacagtttcccaccgataacgtgttctgtctagtacgtgaaacggattggctaacccctgtcagcctaattagatgacatcctcgtacctctagagaaggtgaggagaccgctggaacataagtaaacagtttaccaaacaatgatcatacatataacagaaaggagagatgcccggtggggtcgaagatacagctgtggttgatatctgcaacggccaggctgtcatgaagatcacgcgcacgaagctatttatgaaagatacccatgccggggcggcagcggtacctagtcctaaataccgacacgtagcaacgcgtcccctgaggcccaccctagtcaagggaacttaaaatatacgctgactttgtctaccaatcatcttcgattaacaccggcatactaagtctaccctggacccagcaatgagaaaaacttttccgaatgatcattgtgagtttacagagattaggaacaccaaaaaaatttacgtacgtccggttacccctgtgtgacccttggccacaaaccgtaaggtgcagcatgggcgttgagtccagggtttgtgacaccagacatgaataccctgtggcgggttgttagcatgttattcggatccgatttcagagggtccgttgataccgggcagtacaagacaccccacaccactgaggtggtacgtccgccagtctgctccctacgttatgcaaaattccttccccggcgttcttgcctgtactactcctaaagggccgtgaaatccgacgttgctgctccgtctcgggacacccacacaacagctacggaaaatcgtgaggatgcacaagggtcttgcattgttgatctatacagctcttcgcacggtgtgctactgttttccacaatgggcaaggggcgtgtaggtcttatgtaggagtaccccgtgatctggctataccttgctatctattccaccaaaatagccggggtcttatagttttattccggatctatcaagtgacaagtccatggggtaaacggtaagtttcgtacgctgggcggtgatccccgcttataaacgagcaaaccgccaaagcaaccattgccgggcttccagctagtaaatgttgggtgtcaatcgtgcatgtgactacttacccacaaagggacgcttgaagcgcctgaactcgtcacgtcatgcctagctcccggttgaaacacgaagacgcgtgaacctatctttgcttactattcgcctcctttaagaggcttcttgatgtggctctgcgacatggacagtagtagttgtacctgggtatgttagtgaaattacaagtacctcaaaaacgaattacgtgtatagagattatgtcactccgtcac
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/trackInfo.js b/tests/data/volvox_formatted_1_2_1/trackInfo.js
new file mode 100644
index 0000000000..e2f4d85762
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/trackInfo.js
@@ -0,0 +1,78 @@
+trackInfo = 
+[
+   {
+      "url" : "seq/{refseq}/",
+      "args" : {
+         "chunkSize" : 20000
+      },
+      "label" : "DNA",
+      "type" : "SequenceTrack",
+      "key" : "DNA"
+   },
+   {
+      "url" : "tracks/{refseq}/ExampleFeatures/trackData.json",
+      "type" : "FeatureTrack",
+      "label" : "ExampleFeatures",
+      "key" : "Example Features"
+   },
+   {
+      "url" : "tracks/{refseq}/NameTest/trackData.json",
+      "label" : "NameTest",
+      "type" : "FeatureTrack",
+      "key" : "Name test track"
+   },
+   {
+      "url" : "tracks/{refseq}/Motifs/trackData.json",
+      "type" : "FeatureTrack",
+      "label" : "Motifs",
+      "key" : "Example motifs"
+   },
+   {
+      "url" : "tracks/{refseq}/Alignments/trackData.json",
+      "label" : "Alignments",
+      "type" : "FeatureTrack",
+      "key" : "Example alignments"
+   },
+   {
+      "url" : "tracks/{refseq}/Genes/trackData.json",
+      "type" : "FeatureTrack",
+      "label" : "Genes",
+      "key" : "Protein-coding genes"
+   },
+   {
+      "url" : "tracks/{refseq}/ReadingFrame/trackData.json",
+      "label" : "ReadingFrame",
+      "type" : "FeatureTrack",
+      "key" : "Frame usage"
+   },
+   {
+      "url" : "tracks/{refseq}/CDS/trackData.json",
+      "type" : "FeatureTrack",
+      "label" : "CDS",
+      "key" : "Predicted genes"
+   },
+   {
+      "url" : "tracks/{refseq}/Transcript/trackData.json",
+      "label" : "Transcript",
+      "type" : "FeatureTrack",
+      "key" : "Exonerate predictions"
+   },
+   {
+      "url" : "tracks/{refseq}/Clones/trackData.json",
+      "type" : "FeatureTrack",
+      "label" : "Clones",
+      "key" : "Fingerprinted BACs"
+   },
+   {
+      "url" : "tracks/{refseq}/EST/trackData.json",
+      "label" : "EST",
+      "type" : "FeatureTrack",
+      "key" : "ESTs"
+   },
+   {
+      "url" : "tracks/{refseq}/volvox_microarray.wig.json",
+      "type" : "ImageTrack",
+      "label" : "volvox_microarray.wig",
+      "key" : "volvox_microarray.wig"
+   }
+]
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/hist-10000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/hist-10000-0.json
new file mode 100644
index 0000000000..10cb5fbaee
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/hist-10000-0.json
@@ -0,0 +1 @@
+[2,3,6,7,4,2]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/names.json
new file mode 100644
index 0000000000..7bb004d736
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/names.json
@@ -0,0 +1 @@
+[[["seg08"],"Alignments","seg08","ctgA",18508,25367,"44"],[["seg12"],"Alignments","seg12","ctgA",12530,15870,"48"],[["seg14"],"Alignments","seg14","ctgA",41136,47829,"50"],[["seg03"],"Alignments","seg03","ctgA",6884,8999,"39"],[["seg05"],"Alignments","seg05","ctgA",26502,35904,"41"],[["seg09"],"Alignments","seg09","ctgA",36615,37227,"45"],[["seg04"],"Alignments","seg04","ctgA",5232,9825,"40"],[["seg13"],"Alignments","seg13","ctgA",49405,50000,"49"],[["seg06"],"Alignments","seg06","ctgA",19248,23427,"42"],[["seg10"],"Alignments","seg10","ctgA",29770,32937,"46"],[["seg15"],"Alignments","seg15","ctgA",39264,48453,"51"],[["seg11"],"Alignments","seg11","ctgA",24227,30738,"47"],[["seg02"],"Alignments","seg02","ctgA",26121,34466,"38"],[["seg01"],"Alignments","seg01","ctgA",32328,32359,"37"],[["seg07"],"Alignments","seg07","ctgA",44190,50000,"43"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/trackData.json
new file mode 100644
index 0000000000..598d8e48ee
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"10000","arrayParams":{"length":6,"chunkSize":10000,"urlTemplate":"hist-10000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name"],"lazyIndex":2,"featureCount":15,"histStats":[{"bases":10000,"max":7,"mean":4}],"featureNCList":[[5232,9825,-1,"40","seg04",[[6884,8999,-1,"39","seg03"]]],[12530,15870,1,"48","seg12"],[18508,25367,1,"44","seg08",[[19248,23427,1,"42","seg06"]]],[24227,30738,1,"47","seg11"],[26121,34466,1,"38","seg02"],[26502,35904,-1,"41","seg05",[[29770,32937,1,"46","seg10",[[32328,32359,1,"37","seg01"]]]]],[36615,37227,-1,"45","seg09"],[39264,48453,-1,"51","seg15",[[41136,47829,-1,"50","seg14"]]],[44190,50000,-1,"43","seg07"],[49405,50000,1,"49","seg13"]],"key":"Example alignments","className":"feature4","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"Alignments","type":"FeatureTrack","sublistIndex":5,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/hist-50000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/hist-50000-0.json
new file mode 100644
index 0000000000..b9b82b1c98
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/hist-50000-0.json
@@ -0,0 +1 @@
+[3,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/names.json
new file mode 100644
index 0000000000..28c3c9bf85
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/names.json
@@ -0,0 +1 @@
+[[["Apple1"],"CDS","Apple1","ctgA",9999,11500,"52"],[["Apple3"],"CDS","Apple3","ctgA",17399,23000,"54"],[["Apple2"],"CDS","Apple2","ctgA",12999,17200,"53"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/trackData.json
new file mode 100644
index 0000000000..fda9faa244
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"50000","arrayParams":{"length":2,"chunkSize":10000,"urlTemplate":"hist-50000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name","phase"],"lazyIndex":2,"featureCount":3,"histStats":[{"bases":50000,"max":3,"mean":1.5}],"featureNCList":[[9999,11500,1,"52","Apple1","0"],[12999,17200,1,"53","Apple2","0"],[17399,23000,1,"54","Apple3",null]],"key":"Predicted genes","className":"cds","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"CDS","type":"FeatureTrack","sublistIndex":6,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/hist-200000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/hist-200000-0.json
new file mode 100644
index 0000000000..bace2a0be1
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/hist-200000-0.json
@@ -0,0 +1 @@
+[1]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/names.json
new file mode 100644
index 0000000000..4722a2ec61
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/names.json
@@ -0,0 +1 @@
+[[["b101.2"],"Clones","b101.2","ctgA",999,20000,"81"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/trackData.json
new file mode 100644
index 0000000000..e39237d1a6
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"200000","arrayParams":{"length":1,"chunkSize":10000,"urlTemplate":"hist-200000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name"],"lazyIndex":2,"featureCount":1,"histStats":[{"bases":200000,"max":1,"mean":1}],"featureNCList":[[999,20000,0,"81","b101.2"]],"key":"Fingerprinted BACs","className":"exon","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"Clones","type":"FeatureTrack","sublistIndex":5,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/hist-50000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/hist-50000-0.json
new file mode 100644
index 0000000000..c94180ee8a
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/hist-50000-0.json
@@ -0,0 +1 @@
+[6,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/names.json
new file mode 100644
index 0000000000..a5f2ad4916
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/names.json
@@ -0,0 +1 @@
+[[["agt830.5"],"EST","agt830.5","ctgA",1049,3202,"84"],[["agt767.3"],"EST","agt767.3","ctgA",7999,9000,"89"],[["agt221.3"],"EST","agt221.3","ctgA",7499,8000,"87"],[["agt221.5"],"EST","agt221.5","ctgA",1049,7300,"86"],[["agt767.5"],"EST","agt767.5","ctgA",1149,7200,"88"],[["agt830.3"],"EST","agt830.3","ctgA",5409,7503,"85"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/trackData.json
new file mode 100644
index 0000000000..28bd233734
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"50000","arrayParams":{"length":2,"chunkSize":10000,"urlTemplate":"hist-50000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name"],"lazyIndex":2,"featureCount":6,"histStats":[{"bases":50000,"max":6,"mean":3}],"featureNCList":[[1049,7300,1,"86","agt221.5",[[1049,3202,1,"84","agt830.5"],[1149,7200,1,"88","agt767.5"]]],[5409,7503,-1,"85","agt830.3"],[7499,8000,-1,"87","agt221.3"],[7999,9000,-1,"89","agt767.3"]],"key":"ESTs","className":"est","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"EST","type":"FeatureTrack","sublistIndex":5,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/hist-10000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/hist-10000-0.json
new file mode 100644
index 0000000000..ccce2da2bc
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/hist-10000-0.json
@@ -0,0 +1 @@
+[4,3,4,3,4,1]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/names.json
new file mode 100644
index 0000000000..e4ee658948
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/names.json
@@ -0,0 +1 @@
+[[["f13"],"ExampleFeatures","f13","ctgA",19156,22915,"7"],[["f12"],"ExampleFeatures","f12","ctgA",49757,50000,"16"],[["f02"],"ExampleFeatures","f02","ctgA",24561,28338,"10"],[["f09"],"ExampleFeatures","f09","ctgA",36033,38167,"11"],[["f03"],"ExampleFeatures","f03","ctgA",36648,40440,"12"],[["f11"],"ExampleFeatures","f11","ctgA",46989,48410,"15"],[["f07"],"ExampleFeatures","f07","ctgA",1658,1984,"2"],[["Remark:hga","hga"],"ExampleFeatures","Remark:hga","ctgA",999,2000,"17"],[["f01"],"ExampleFeatures","f01","ctgA",44704,47713,"14"],[["f04"],"ExampleFeatures","f04","ctgA",37241,38653,"13"],[["f10"],"ExampleFeatures","f10","ctgA",15328,15533,"6"],[["f06"],"ExampleFeatures","f06","ctgA",3013,6130,"3"],[["f14"],"ExampleFeatures","f14","ctgA",23071,23185,"9"],[["f15"],"ExampleFeatures","f15","ctgA",22131,24633,"8"],[["f05"],"ExampleFeatures","f05","ctgA",4714,5968,"4"],[["f08"],"ExampleFeatures","f08","ctgA",13279,16394,"5"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/trackData.json
new file mode 100644
index 0000000000..8a9b2eda70
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"10000","arrayParams":{"length":6,"chunkSize":10000,"urlTemplate":"hist-10000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name"],"lazyIndex":2,"featureCount":16,"histStats":[{"bases":10000,"max":4,"mean":3.16666666666667}],"featureNCList":[[999,2000,0,"17","Remark:hga",[[1658,1984,1,"2","f07"]]],[3013,6130,1,"3","f06",[[4714,5968,-1,"4","f05"]]],[13279,16394,1,"5","f08",[[15328,15533,1,"6","f10"]]],[19156,22915,-1,"7","f13"],[22131,24633,1,"8","f15",[[23071,23185,1,"9","f14"]]],[24561,28338,1,"10","f02"],[36033,38167,1,"11","f09"],[36648,40440,-1,"12","f03",[[37241,38653,1,"13","f04"]]],[44704,47713,-1,"14","f01"],[46989,48410,-1,"15","f11"],[49757,50000,-1,"16","f12"]],"key":"Example Features","className":"feature2","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"ExampleFeatures","type":"FeatureTrack","sublistIndex":5,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/hist-200000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/hist-200000-0.json
new file mode 100644
index 0000000000..bace2a0be1
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/hist-200000-0.json
@@ -0,0 +1 @@
+[1]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/names.json
new file mode 100644
index 0000000000..1704902c44
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/names.json
@@ -0,0 +1 @@
+[[["EDEN"],"Genes","EDEN","ctgA",1049,9000,"60"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/trackData.json
new file mode 100644
index 0000000000..889fa282b7
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"200000","arrayParams":{"length":1,"chunkSize":10000,"urlTemplate":"hist-200000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name"],"lazyIndex":2,"featureCount":1,"histStats":[{"bases":200000,"max":1,"mean":1}],"featureNCList":[[1049,9000,1,"60","EDEN"]],"key":"Protein-coding genes","className":"feature5","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"Genes","type":"FeatureTrack","sublistIndex":5,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/hist-10000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/hist-10000-0.json
new file mode 100644
index 0000000000..4881867869
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/hist-10000-0.json
@@ -0,0 +1 @@
+[0,7,3,4,3,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/names.json
new file mode 100644
index 0000000000..5e3290579a
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/names.json
@@ -0,0 +1 @@
+[[["m06"],"Motifs","m06","ctgA",30577,31748,"32"],[["m04"],"Motifs","m04","ctgA",33324,35791,"33"],[["m08"],"Motifs","m08","ctgA",17022,17675,"26"],[["m13"],"Motifs","m13","ctgA",17666,17690,"27"],[["m10"],"Motifs","m10","ctgA",28341,28447,"31"],[["m09"],"Motifs","m09","ctgA",46011,48851,"35"],[["m12"],"Motifs","m12","ctgA",21747,25612,"29"],[["m02"],"Motifs","m02","ctgA",28331,30033,"30"],[["m03"],"Motifs","m03","ctgA",15395,16159,"25"],[["m07"],"Motifs","m07","ctgA",18047,18552,"28"],[["m14"],"Motifs","m14","ctgA",14730,17239,"24"],[["m11"],"Motifs","m11","ctgA",11910,15561,"22"],[["m05"],"Motifs","m05","ctgA",13800,14007,"23"],[["m01"],"Motifs","m01","ctgA",48252,48366,"36"],[["m15"],"Motifs","m15","ctgA",37496,40559,"34"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/trackData.json
new file mode 100644
index 0000000000..36903d0499
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"10000","arrayParams":{"length":6,"chunkSize":10000,"urlTemplate":"hist-10000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name"],"lazyIndex":2,"featureCount":15,"histStats":[{"bases":10000,"max":7,"mean":2.83333333333333}],"featureNCList":[[11910,15561,1,"22","m11",[[13800,14007,-1,"23","m05"]]],[14730,17239,-1,"24","m14",[[15395,16159,1,"25","m03"]]],[17022,17675,1,"26","m08"],[17666,17690,1,"27","m13"],[18047,18552,-1,"28","m07"],[21747,25612,1,"29","m12"],[28331,30033,-1,"30","m02",[[28341,28447,-1,"31","m10"]]],[30577,31748,1,"32","m06"],[33324,35791,1,"33","m04"],[37496,40559,-1,"34","m15"],[46011,48851,1,"35","m09",[[48252,48366,1,"36","m01"]]]],"key":"Example motifs","className":"feature3","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"Motifs","type":"FeatureTrack","sublistIndex":5,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/hist-50000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/hist-50000-0.json
new file mode 100644
index 0000000000..27380f446e
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/hist-50000-0.json
@@ -0,0 +1 @@
+[4,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/names.json
new file mode 100644
index 0000000000..3068382880
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/names.json
@@ -0,0 +1 @@
+[[["Protein:HGB","hgb"],"NameTest","Protein:HGB","ctgA",1799,2900,"21"],[["Gene:hga","hga"],"NameTest","Gene:hga","ctgA",1099,2000,"18"],[["Gene:hgb","hgb"],"NameTest","Gene:hgb","ctgA",1599,3000,"20"],[["Protein:HGA","hga"],"NameTest","Protein:HGA","ctgA",1199,1900,"19"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/trackData.json
new file mode 100644
index 0000000000..e8726f229b
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"50000","arrayParams":{"length":2,"chunkSize":10000,"urlTemplate":"hist-50000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name"],"lazyIndex":2,"featureCount":4,"histStats":[{"bases":50000,"max":4,"mean":2}],"featureNCList":[[1099,2000,1,"18","Gene:hga",[[1199,1900,1,"19","Protein:HGA"]]],[1599,3000,-1,"20","Gene:hgb",[[1799,2900,-1,"21","Protein:HGB"]]]],"key":"Name test track","className":"feature2","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"NameTest","type":"FeatureTrack","sublistIndex":5,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/hist-50000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/hist-50000-0.json
new file mode 100644
index 0000000000..27380f446e
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/hist-50000-0.json
@@ -0,0 +1 @@
+[4,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/names.json
new file mode 100644
index 0000000000..b24354d43d
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/names.json
@@ -0,0 +1 @@
+[[["EDEN.3"],"ReadingFrame","EDEN.3","ctgA",1299,9000,"74"],[["EDEN.1"],"ReadingFrame","EDEN.1","ctgA",1049,9000,"61"],[["Apple3"],"ReadingFrame","Apple3","ctgA",17399,23000,"54"],[["EDEN.2"],"ReadingFrame","EDEN.2","ctgA",1049,9000,"68"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/trackData.json
new file mode 100644
index 0000000000..39ebb54c55
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"50000","arrayParams":{"length":2,"chunkSize":10000,"urlTemplate":"hist-50000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand","id","name"],"lazyIndex":2,"featureCount":4,"histStats":[{"bases":50000,"max":4,"mean":2}],"featureNCList":[[1049,9000,1,"61","EDEN.1"],[1049,9000,1,"68","EDEN.2"],[1299,9000,1,"74","EDEN.3"],[17399,23000,1,"54","Apple3"]],"key":"Frame usage","className":"dblhelix","clientConfig":null,"arrowheadClass":null,"subfeatureHeaders":["start","end","strand","type"],"label":"ReadingFrame","type":"FeatureTrack","sublistIndex":5,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/hist-200000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/hist-200000-0.json
new file mode 100644
index 0000000000..bace2a0be1
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/hist-200000-0.json
@@ -0,0 +1 @@
+[1]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/names.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/names.json
new file mode 100644
index 0000000000..f4b392da12
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/names.json
@@ -0,0 +1 @@
+[[["Apple3"],"Transcript","Apple3","ctgA",17399,23000,"54"]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/trackData.json
new file mode 100644
index 0000000000..370e1c312a
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"200000","arrayParams":{"length":1,"chunkSize":10000,"urlTemplate":"hist-200000-{chunk}.json"}}],"subfeatureClasses":{"CDS":"transcript-CDS","UTR":"transcript-UTR"},"headers":["start","end","strand","id","name","subfeatures"],"lazyIndex":2,"featureCount":1,"histStats":[{"bases":200000,"max":1,"mean":1}],"featureNCList":[[17399,23000,1,"54","Apple3",[[21200,23000,1,"UTR"],[18999,19500,1,"CDS"],[17999,18800,1,"CDS"],[20999,21200,1,"CDS"],[17399,17999,1,"UTR"]]]],"key":"Exonerate predictions","className":"transcript","clientConfig":null,"arrowheadClass":"transcript-arrowhead","subfeatureHeaders":["start","end","strand","type"],"label":"Transcript","type":"FeatureTrack","sublistIndex":6,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/volvox_microarray.wig.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/volvox_microarray.wig.json
new file mode 100644
index 0000000000..eb1b60b258
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/volvox_microarray.wig.json
@@ -0,0 +1,85 @@
+{
+   "zoomLevels" : [
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/1/",
+         "height" : 100,
+         "basesPerTile" : 2000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/2/",
+         "height" : 100,
+         "basesPerTile" : 4000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/5/",
+         "height" : 100,
+         "basesPerTile" : 10000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/10/",
+         "height" : 100,
+         "basesPerTile" : 20000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/20/",
+         "height" : 100,
+         "basesPerTile" : 40000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/50/",
+         "height" : 100,
+         "basesPerTile" : 100000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/100/",
+         "height" : 100,
+         "basesPerTile" : 200000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/200/",
+         "height" : 100,
+         "basesPerTile" : 400000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/500/",
+         "height" : 100,
+         "basesPerTile" : 1000000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/1000/",
+         "height" : 100,
+         "basesPerTile" : 2000000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/2000/",
+         "height" : 100,
+         "basesPerTile" : 4000000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/5000/",
+         "height" : 100,
+         "basesPerTile" : 10000000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/10000/",
+         "height" : 100,
+         "basesPerTile" : 20000000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/20000/",
+         "height" : 100,
+         "basesPerTile" : 40000000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/50000/",
+         "height" : 100,
+         "basesPerTile" : 100000000
+      },
+      {
+         "urlPrefix" : "tiles/volvox_microarray.wig/ctgA/100000/",
+         "height" : 100,
+         "basesPerTile" : 200000000
+      }
+   ],
+   "tileWidth" : 2000
+}

From fa7fdd77c2026f2b5cd998bd8e30dcd03c4ea735 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Thu, 8 Mar 2012 22:29:55 -0500
Subject: [PATCH 11/49] ugly refactor to make VolvoxBiodbTest able to be
 inherited from, add a VolvoxBiodbTest121 test that inherits from it, but will
 test on a 1.2.1-formatted data directory

---
 tests/selenium_tests/jbrowse_selenium.py      |  4 ++--
 tests/selenium_tests/volvox_biodb_121_test.py | 11 +++++++++++
 tests/selenium_tests/volvox_biodb_test.py     | 11 +++++++++--
 tests/selenium_tests/yeast_biodb_test.py      |  5 +++--
 4 files changed, 25 insertions(+), 6 deletions(-)
 create mode 100644 tests/selenium_tests/volvox_biodb_121_test.py

diff --git a/tests/selenium_tests/jbrowse_selenium.py b/tests/selenium_tests/jbrowse_selenium.py
index 36c2bc210a..220a1873dc 100644
--- a/tests/selenium_tests/jbrowse_selenium.py
+++ b/tests/selenium_tests/jbrowse_selenium.py
@@ -1,7 +1,7 @@
 import os
 import time
 
-from unittest import TestCase
+import unittest
 
 from selenium                       import webdriver
 from selenium.webdriver             import ActionChains
@@ -9,7 +9,7 @@
 from selenium.common.exceptions     import NoSuchElementException
 from selenium.webdriver.support.ui  import Select
 
-class JBrowseTest( TestCase ):
+class JBrowseTest (object):
 
     base_url = "file://%s/index.html" % os.getcwd()
     data_dir = None
diff --git a/tests/selenium_tests/volvox_biodb_121_test.py b/tests/selenium_tests/volvox_biodb_121_test.py
new file mode 100644
index 0000000000..2d613e9dd0
--- /dev/null
+++ b/tests/selenium_tests/volvox_biodb_121_test.py
@@ -0,0 +1,11 @@
+import unittest
+from volvox_biodb_test import AbstractVolvoxBiodbTest
+
+class VolvoxBiodbTest121 ( AbstractVolvoxBiodbTest, unittest.TestCase ):
+
+    data_dir = 'tests/data/volvox_formatted_1_2_1/'
+
+    def setUp( self ):
+        # skip calling VolvoxBiodbTest's setUp, cause we are not
+        # actually running any formatting
+        super( AbstractVolvoxBiodbTest, self ).setUp()
diff --git a/tests/selenium_tests/volvox_biodb_test.py b/tests/selenium_tests/volvox_biodb_test.py
index 505cd0d4b9..76a12e71ee 100644
--- a/tests/selenium_tests/volvox_biodb_test.py
+++ b/tests/selenium_tests/volvox_biodb_test.py
@@ -1,9 +1,10 @@
 import time
 from subprocess import check_call as call
+import unittest
 
 from jbrowse_selenium import JBrowseTest;
 
-class VolvoxBiodbTest( JBrowseTest ):
+class AbstractVolvoxBiodbTest( JBrowseTest ):
 
     data_dir = 'sample_data/json/volvox'
 
@@ -13,7 +14,7 @@ def setUp( self ):
         call( "bin/biodb-to-json.pl --conf sample_data/raw/volvox.json --out sample_data/json/volvox/", shell=True )
         call( "bin/wig-to-json.pl --out sample_data/json/volvox/ --wig sample_data/raw/volvox/volvox_microarray.wig", shell=True )
         call( "bin/generate-names.pl --dir sample_data/json/volvox/", shell=True )
-        super( VolvoxBiodbTest, self ).setUp()
+        super( AbstractVolvoxBiodbTest, self ).setUp()
 
     def test_volvox( self ):
         # select "ctgA from the dropdown
@@ -80,6 +81,12 @@ def search_f15( self ):
         label = self.assert_element( xpath )
         assert label.text == 'f15';
 
+
+class VolvoxBiodbTest( AbstractVolvoxBiodbTest, unittest.TestCase ):
+    pass
+
+
 if __name__ == '__main__':
     import unittest
     unittest.main()
+
diff --git a/tests/selenium_tests/yeast_biodb_test.py b/tests/selenium_tests/yeast_biodb_test.py
index f4e46ed72d..09c6c9c730 100644
--- a/tests/selenium_tests/yeast_biodb_test.py
+++ b/tests/selenium_tests/yeast_biodb_test.py
@@ -1,8 +1,9 @@
+import unittest
 from subprocess import check_call as call
 
-import jbrowse_selenium
+from jbrowse_selenium import JBrowseTest
 
-class YeastBiodbTest ( jbrowse_selenium.JBrowseTest ):
+class YeastBiodbTest ( JBrowseTest, unittest.TestCase ):
 
     data_dir = 'sample_data/json/yeast'
 

From d4c3bcfd4d806d8557478426ff7e8160d5eb75bb Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Fri, 9 Mar 2012 12:08:28 -0500
Subject: [PATCH 12/49] classify all files in js/ according to MVC, many of
 them still need work to be good expressions of the paradigm.

Will move them into subdirectories later.
---
 js/ArrayRepr.js     | 2 ++
 js/Browser.js       | 2 ++
 js/FeatureTrack.js  | 2 ++
 js/GenomeView.js    | 2 ++
 js/GridTrack.js     | 2 ++
 js/ImageTrack.js    | 2 ++
 js/Layout.js        | 2 ++
 js/LazyArray.js     | 2 ++
 js/LazyPatricia.js  | 2 ++
 js/NCList.js        | 2 ++
 js/SequenceTrack.js | 2 ++
 js/StaticTrack.js   | 2 ++
 js/Track.js         | 2 ++
 js/Util.js          | 2 ++
 js/touchJBrowse.js  | 3 +--
 15 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/js/ArrayRepr.js b/js/ArrayRepr.js
index e33351d747..f76990f1d9 100644
--- a/js/ArrayRepr.js
+++ b/js/ArrayRepr.js
@@ -1,3 +1,5 @@
+// MODEL
+
 /*
     class for operating on indexed representations of objects
 
diff --git a/js/Browser.js b/js/Browser.js
index 9fb1f59068..1bbe4b0089 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -1,3 +1,5 @@
+// CONTROLLER
+
 /**
  * Construct a new Browser object.
  * @class This class is the main interface between JBrowse and embedders
diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index 481f38f146..49c1e84a07 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -1,3 +1,5 @@
+// VIEW
+
 function FeatureTrack(trackMeta, refSeq, browserParams) {
     //trackMeta: object with:
     //            key:   display text track name
diff --git a/js/GenomeView.js b/js/GenomeView.js
index 32317d2227..e320b4d82f 100644
--- a/js/GenomeView.js
+++ b/js/GenomeView.js
@@ -1,3 +1,5 @@
+// VIEW
+
 function Animation(subject, callback, time) {
     //subject: what's being animated
     //callback: function to call at the end of the animation
diff --git a/js/GridTrack.js b/js/GridTrack.js
index 68a0dd8c82..05f900d5e7 100644
--- a/js/GridTrack.js
+++ b/js/GridTrack.js
@@ -1,3 +1,5 @@
+// VIEW
+
 // This track draws vertical gridlines, which are divs with height:
 // 100%, absolutely positioned at the very top of all the tracks
 function GridTrack(name) {
diff --git a/js/ImageTrack.js b/js/ImageTrack.js
index a9c819b7ac..076cd5cbd1 100644
--- a/js/ImageTrack.js
+++ b/js/ImageTrack.js
@@ -1,3 +1,5 @@
+// VIEW
+
 function ImageTrack(trackMeta, refSeq, browserParams) {
     Track.call(this, trackMeta.label, trackMeta.key,
                false, browserParams.changeCallback);
diff --git a/js/Layout.js b/js/Layout.js
index 43422979b8..3af7d93566 100644
--- a/js/Layout.js
+++ b/js/Layout.js
@@ -1,3 +1,5 @@
+// VIEW
+
 /*
  * Code for laying out rectangles, given that layout is also happening
  * in adjacent blocks at the same time
diff --git a/js/LazyArray.js b/js/LazyArray.js
index f295693ccb..363baec60f 100644
--- a/js/LazyArray.js
+++ b/js/LazyArray.js
@@ -1,3 +1,5 @@
+// MODEL
+
 /*
  * For a JSON array that gets too large to load in one go, this class
  * helps break it up into chunks and provides an
diff --git a/js/LazyPatricia.js b/js/LazyPatricia.js
index 71ea01bcae..6b8eb37450 100644
--- a/js/LazyPatricia.js
+++ b/js/LazyPatricia.js
@@ -1,3 +1,5 @@
+// MODEL
+
 /*
   Implements a lazy PATRICIA tree.
 
diff --git a/js/NCList.js b/js/NCList.js
index b040edd632..0f2db29df2 100644
--- a/js/NCList.js
+++ b/js/NCList.js
@@ -1,3 +1,5 @@
+// MODEL
+
 //After
 //Alekseyenko, A., and Lee, C. (2007).
 //Nested Containment List (NCList): A new algorithm for accelerating
diff --git a/js/SequenceTrack.js b/js/SequenceTrack.js
index 66a4cb9642..e4562ca396 100644
--- a/js/SequenceTrack.js
+++ b/js/SequenceTrack.js
@@ -1,3 +1,5 @@
+// VIEW
+
 function SequenceTrack(trackMeta, refSeq, browserParams) {
     //trackMeta: object with:
     //  key:   display text track name
diff --git a/js/StaticTrack.js b/js/StaticTrack.js
index a59d402350..885c0e103f 100644
--- a/js/StaticTrack.js
+++ b/js/StaticTrack.js
@@ -1,3 +1,5 @@
+// VIEW
+
 //This track is for (e.g.) position and sequence information that should
 //always stay visible at the top of the view
 
diff --git a/js/Track.js b/js/Track.js
index c07739faa1..d46763d472 100644
--- a/js/Track.js
+++ b/js/Track.js
@@ -1,3 +1,5 @@
+// VIEW
+
 function Track(name, key, loaded, changeCallback) {
     this.name = name;
     this.key = key;
diff --git a/js/Util.js b/js/Util.js
index d2b7d04f75..2a9d5cfd2b 100644
--- a/js/Util.js
+++ b/js/Util.js
@@ -1,3 +1,5 @@
+// MISC
+
 var Util = {};
 
 Util.is_ie = navigator.appVersion.indexOf('MSIE') >= 0;
diff --git a/js/touchJBrowse.js b/js/touchJBrowse.js
index b1894740f9..2688e74072 100644
--- a/js/touchJBrowse.js
+++ b/js/touchJBrowse.js
@@ -1,5 +1,4 @@
-
-
+// INTEGRATE ME INTO BROWSER.JS
 
 function CompareObjPos(nodes, touch) {
    var samePos = 0,

From 3f70744ac2b770161054d11a261d97be510f8b17 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 12 Mar 2012 15:30:13 -0400
Subject: [PATCH 13/49] split data-reading code out of FeatureTrack into
 SeqFeature.NCList

---
 index.html                   |   2 +
 js/ArrayRepr.js              |  59 +++++++++++++++++
 js/Browser.js                |   8 ++-
 js/FeatureTrack.js           | 123 +++++++++++++++--------------------
 js/SeqFeatureStore.js        |  30 +++++++++
 js/SeqFeatureStore/NCList.js |  91 ++++++++++++++++++++++++++
 6 files changed, 239 insertions(+), 74 deletions(-)
 create mode 100644 js/SeqFeatureStore.js
 create mode 100644 js/SeqFeatureStore/NCList.js

diff --git a/index.html b/index.html
index 828004a014..c7f5d6c1bd 100644
--- a/index.html
+++ b/index.html
@@ -25,6 +25,8 @@
     <script type="text/javascript" src="js/Track.js"></script>
     <script type="text/javascript" src="js/SequenceTrack.js"></script>
     <script type="text/javascript" src="js/Layout.js"></script>
+    <script type="text/javascript" src="js/SeqFeatureStore.js"></script>
+    <script type="text/javascript" src="js/SeqFeatureStore/NCList.js"></script>
     <script type="text/javascript" src="js/FeatureTrack.js"></script>
     <script type="text/javascript" src="js/StaticTrack.js"></script>
     <script type="text/javascript" src="js/GridTrack.js"></script>
diff --git a/js/ArrayRepr.js b/js/ArrayRepr.js
index f76990f1d9..e1ccd6db44 100644
--- a/js/ArrayRepr.js
+++ b/js/ArrayRepr.js
@@ -172,6 +172,65 @@ ArrayRepr.prototype.construct = function(self, obj, klass) {
     return result;
 };
 
+ArrayRepr.prototype.accessors = function () {
+    return this._accessors = this._accessors || this._makeAccessors();
+};
+
+// make an object like
+//     { get: { attrname: func() {}, ... },
+//       set: { attrname: func() {}. ... }
+//     }
+// prototype object that, when set as the prototype on a data
+// array, provides nicely-named, fast accessors to access the
+// attributes in that array
+ArrayRepr.prototype._makeAccessors = function() {
+    var that = this,
+        accessors = {
+            get: function(field) {
+                try { return this.get[field].call(this); }
+                catch (x) { return undefined; }
+            },
+            set: function(field,val) {
+                try { return this.set[field].call(this,val); }
+                catch (x) { return undefined; }
+            }
+        };
+
+    // make a data structure as: { attr_name: [offset,offset,offset], }
+    // that will be convenient for finding the location of the attr
+    // for a given class like: indexForAttr{attrname}[classnum]
+    var indices = {};
+    dojo.forEach( this.classes, function(cdef,classnum) {
+        dojo.forEach( cdef.attributes || [], function(attrname,offset) {
+            attrname = attrname.toLowerCase();
+            indices[attrname] = indices[attrname] || [];
+            indices[attrname][classnum] = offset + 1;
+        });
+    });
+
+    for( var attrname in indices ) {
+        if( ! indices.hasOwnProperty(attrname) ) continue;
+
+        // make a get accessor
+        accessors.get[ attrname ] = (function() {
+            var attr_indices = indices[attrname];
+            return !attr_indices ? function() { return undefined; } : function() {
+                return this[ attr_indices[ this[0] ] ];
+            };
+        })();
+
+        // make a set accessor
+        accessors.set[ attrname ] = (function() {
+            var attr_indices =  indices[attrname];
+            return !attr_indices ? function() { return undefined; } : function(v) {
+                return ( this[ attr_indices[ this[0] ] ] = v );
+            };
+        })();
+    }
+
+    return accessors;
+};
+
 /*
 
 Copyright (c) 2007-2010 The Evolutionary Software Foundation
diff --git a/js/Browser.js b/js/Browser.js
index 1bbe4b0089..ac74f5db27 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -150,10 +150,14 @@ Browser.prototype.addConfig = function( config, additional ) {
             config[p] = additional[p];
     }
 
-    config.baseUrl = config.baseUrl || config.sourceUrl;
-    if( ! /\/$/.test(config.baseUrl) ) // make sure the baseUrl has a trailing slash
+    // make a default baseUrl if one is not already set
+    if( !config.baseUrl ) {
+        config.baseUrl = Util.resolveUrl( config.sourceUrl, '.' );
+    }
+    if( ! /\/$/.test( config.baseUrl ) )
         config.baseUrl += "/";
 
+
     if (1 == config.formatVersion) {
         if( config.tracks ) {
             if( config.sourceUrl ) {
diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index 49c1e84a07..f6d0357698 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -1,6 +1,6 @@
 // VIEW
 
-function FeatureTrack(trackMeta, refSeq, browserParams) {
+function FeatureTrack( trackMeta, refSeq, browserParams ) {
     //trackMeta: object with:
     //            key:   display text track name
     //            label: internal track name (no spaces, odd characters)
@@ -19,11 +19,21 @@ function FeatureTrack(trackMeta, refSeq, browserParams) {
     Track.call(this, trackMeta.label, trackMeta.key,
                false, browserParams.changeCallback);
     this.fields = {};
-    this.features = new NCList();
     this.refSeq = refSeq;
-    this.url = Util.resolveUrl(trackMeta.baseUrl,
-                               Util.fillTemplate(trackMeta.config.urlTemplate,
-                                                 {'refseq': refSeq.name}) );
+
+    this.featureStore = new SeqFeatureStore.NCList({
+        urlTemplate: trackMeta.config.urlTemplate,
+        baseUrl: trackMeta.baseUrl,
+        refSeq: refSeq
+    });
+
+    // connect the store and track loadSuccess and loadFailed events
+    // to eachother
+    dojo.connect( this.featureStore, 'loadSuccess', this, 'loadSuccess' );
+    dojo.connect( this.featureStore, 'loadFail',    this, 'loadFail' );
+
+    this.featureStore.load();
+
     //number of histogram bins per block
     this.numBins = 25;
     this.histLabel = false;
@@ -32,23 +42,11 @@ function FeatureTrack(trackMeta, refSeq, browserParams) {
 
     this.trackMeta = trackMeta;
     this.config = trackMeta.config;
-    this.load(this.url);
 }
 
 FeatureTrack.prototype = new Track("");
 
 FeatureTrack.prototype.loadSuccess = function(trackInfo, url) {
-    var startTime = new Date().getTime();
-    this.count = trackInfo.featureCount;
-    // average feature density per base
-    this.density = trackInfo.featureCount / this.refSeq.length;
-    
-    this.attrs = new ArrayRepr(trackInfo.intervals.classes);
-    this.features.importExisting(trackInfo.intervals.nclist,
-                                 this.attrs,
-                                 url,
-                                 trackInfo.intervals.urlTemplate,
-                                 trackInfo.intervals.lazyClass);
 
     var defaultConfig = {
         style: {
@@ -60,7 +58,7 @@ FeatureTrack.prototype.loadSuccess = function(trackInfo, url) {
             subfeature: 80
         },
         hooks: {
-            create: function(track, feat, attrs) {
+            create: function(track, feat ) {
                 var featDiv;
                 var featUrl = track.featureUrl(feat);
                 if (featUrl) {
@@ -79,13 +77,13 @@ FeatureTrack.prototype.loadSuccess = function(trackInfo, url) {
 
     if (! this.config.linkTemplate) {
         defaultConfig.events.click =
-            function(track, elem, feat, attrs, event) {
-	        alert("clicked on feature\n" +
-                      "start: " + (Number(attrs.get(feat, "Start"))+1) +
-	              ", end: " + Number(attrs.get(feat, "End")) +
-	              ", strand: " + attrs.get(feat, "Strand") +
-	              ", label: " + attrs.get(feat, "Name") +
-	              ", ID: " + attrs.get(feat, "ID") );
+            function(track, elem, feat, event) {
+	        alert( "clicked on feature\n" +
+                       "start: " + (Number( feat.get('start') )+1) +
+	               ", end: " + Number( feat.get('end') ) +
+	               ", strand: " + feat.get('strand') +
+	               ", label: " + feat.get('name') +
+	               ", ID: " + feat.get('id') );
             };
     }
 
@@ -101,14 +99,6 @@ FeatureTrack.prototype.loadSuccess = function(trackInfo, url) {
             this.wrapHandler(this.evalHook(this.config.events[event]));
     }
 
-    if (trackInfo.histograms) {
-        this.histograms = trackInfo.histograms;
-        for (var i = 0; i < this.histograms.meta.length; i++) {
-            this.histograms.meta[i].lazyArray =
-                new LazyArray(this.histograms.meta[i].arrayParams, url);
-        }
-    }
-
     this.setLoaded();
 };
 
@@ -137,16 +127,14 @@ FeatureTrack.prototype.wrapHandler = function(handler) {
         //instead of the parent feature
         if (!elem.feature) elem = elem.parentElement;
         if (!elem.feature) return; //shouldn't happen; just bail if it does
-        handler(track, elem, elem.feature, track.attrs, event);
+        handler(track, elem, elem.feature, event);
     };
 };
 
 FeatureTrack.prototype.setViewInfo = function(genomeView, numBlocks,
                                               trackDiv, labelDiv,
                                               widthPct, widthPx, scale) {
-    Track.prototype.setViewInfo.apply(this, [genomeView, numBlocks,
-                                             trackDiv, labelDiv,
-                                             widthPct, widthPx, scale]);
+    Track.prototype.setViewInfo.apply(this, arguments );
     this.setLabel(this.key);
 };
 
@@ -157,7 +145,7 @@ FeatureTrack.prototype.fillHist = function(blockIndex, block,
     var bpPerBin = (rightBase - leftBase) / this.numBins;
     var pxPerCount = 2;
     var logScale = false;
-    var stats = this.histograms.stats;
+    var stats = this.featureStore.histograms.stats;
     for (var i = 0; i < stats.length; i++) {
         if (stats[i].bases >= bpPerBin) {
             //console.log("bpPerBin: " + bpPerBin + ", histStats bases: " + this.histStats[i].bases + ", mean/max: " + (this.histStats[i].mean / this.histStats[i].max));
@@ -209,10 +197,10 @@ FeatureTrack.prototype.fillHist = function(blockIndex, block,
     // is at 50,000 bases/bin, and we have server histograms at 20,000
     // and 2,000 bases/bin, then we should choose the 2,000 histogramMeta
     // rather than the 20,000)
-    var histogramMeta = this.histograms.meta[0];
-    for (var i = 0; i < this.histograms.meta.length; i++) {
-        if (bpPerBin >= this.histograms.meta[i].basesPerBin)
-            histogramMeta = this.histograms.meta[i];
+    var histogramMeta = this.featureStore.histograms.meta[0];
+    for (var i = 0; i < this.featureStore.histograms.meta.length; i++) {
+        if (bpPerBin >= this.featureStore.histograms.meta[i].basesPerBin)
+            histogramMeta = this.featureStore.histograms.meta[i];
     }
 
     // number of bins in the server-supplied histogram for each current bin
@@ -243,8 +231,8 @@ FeatureTrack.prototype.fillHist = function(blockIndex, block,
         );
     } else {
         // make our own counts
-        this.features.histogram(leftBase, rightBase,
-                                this.numBins, makeHistBlock);
+        this.featureStore.histogram( leftBase, rightBase,
+                                     this.numBins, makeHistBlock);
     }
 };
 
@@ -263,7 +251,7 @@ FeatureTrack.prototype.fillBlock = function(blockIndex, block,
                                             scale, stripeWidth,
                                             containerStart, containerEnd) {
     //console.log("scale: %d, histScale: %d", scale, this.histScale);
-    if (this.histograms &&
+    if (this.featureStore.histograms &&
         (scale < (this.density * this.config.scaleThresh.hist)) ) {
 	this.fillHist(blockIndex, block, leftBase, rightBase, stripeWidth,
                       containerStart, containerEnd);
@@ -305,7 +293,7 @@ FeatureTrack.prototype.transfer = function(sourceBlock, destBlock, scale,
 	}
 	if (sourceSlot && sourceSlot.feature) {
 	    if ( sourceSlot.layoutEnd > destLeft
-		 && this.attrs.get(sourceSlot.feature, "Start") < destRight ) {
+		 && sourceSlot.feature.get('start') < destRight ) {
 
                 sourceBlock.removeChild(sourceSlot);
                 delete sourceBlock.featureNodes[overlaps[i].id];
@@ -378,8 +366,7 @@ FeatureTrack.prototype.fillFeatures = function(blockIndex, block,
     var startBase = goLeft ? rightBase : leftBase;
     var endBase = goLeft ? leftBase : rightBase;
 
-
-    this.features.iterate(startBase, endBase, featCallback,
+    this.featureStore.iterate(startBase, endBase, featCallback,
                           function () {
                               block.style.backgroundColor = "";
                               curTrack.heightUpdate(layouter.totalHeight,
@@ -437,10 +424,10 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
     //featureStart and featureEnd indicate how far left or right
     //the feature extends in bp space, including labels
     //and arrowheads if applicable
-    var featureEnd = this.attrs.get(feature, "End");
-    var featureStart = this.attrs.get(feature, "Start");
+    var featureEnd = feature.get('end');
+    var featureStart = feature.get('start');
     if (this.arrowheadClass) {
-        switch (this.attrs.get(feature, "Strand")) {
+        switch ( feature.get('strand') ) {
         case 1:
         case '+':
             featureEnd   += (this.plusArrowWidth / scale); break;
@@ -454,7 +441,7 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
 
     // if the label extends beyond the feature, use the
     // label end position as the end position for layout
-    var name = this.attrs.get(feature, "Name");
+    var name = feature.get('name');
     var labelScale = this.density * this.config.scaleThresh.label;
     if (name && (scale > labelScale)) {
 	featureEnd = Math.max(featureEnd,
@@ -469,7 +456,7 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
                                           featureEnd,
                                           levelHeight);
 
-    var featDiv = this.config.hooks.create(this, feature, this.attrs);
+    var featDiv = this.config.hooks.create(this, feature );
     for (event in this.eventHandlers) {
         featDiv["on" + event] = this.eventHandlers[event];
     }
@@ -478,7 +465,7 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
 
     block.featureNodes[uniqueId] = featDiv;
 
-    var strand = this.attrs.get(feature, "Strand");
+    var strand = feature.get('strand');
     switch (strand) {
     case 1:
     case '+':
@@ -493,7 +480,7 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
         featDiv.className = "minus-" + this.config.style.className; break;
     }
 
-    var phase = this.attrs.get(feature, "Phase");
+    var phase = feature.get('phase');
     if ((phase !== null) && (phase !== undefined))
         featDiv.className = featDiv.className + " " + featDiv.className + "_phase" + phase;
 
@@ -503,10 +490,8 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
     // To make sure the truncated end of the feature never gets shown,
     // we'll destroy and re-create the feature (with updated truncated
     // boundaries) in the transfer method.
-    var displayStart = Math.max(this.attrs.get(feature, "Start"),
-                                containerStart);
-    var displayEnd = Math.min(this.attrs.get(feature, "End"),
-                              containerEnd);
+    var displayStart = Math.max( feature.get('start'), containerStart );
+    var displayEnd = Math.min( feature.get('end'), containerEnd );
     var blockWidth = block.endBase - block.startBase;
     featDiv.style.cssText =
         "left:" + (100 * (displayStart - block.startBase) / blockWidth) + "%;"
@@ -559,7 +544,7 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
         block.appendChild(labelDiv);
     }
 
-    var subfeatures = this.attrs.get(feature, "Subfeatures");
+    var subfeatures = feature.get('subfeatures');
     if( subfeatures ) {
         for (var i = 0; i < subfeatures.length; i++) {
             this.renderSubfeature(feature, featDiv,
@@ -569,7 +554,7 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
     }
 
     if (this.config.hooks.modify) {
-        this.config.hooks.modify(this, feature, this.attrs, featDiv);
+        this.config.hooks.modify(this, feature, featDiv);
     }
 
     //ie6 doesn't respect the height style if the div is empty
@@ -580,11 +565,10 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
 
 FeatureTrack.prototype.featureUrl = function(feature) {
     var urlValid = true;
-    var attrs = this.attrs;
     if (this.urlTemplate) {
         var href = this.urlTemplate.replace(/\{([^}]+)\}/g,
         function(match, group) {
-            var val = attrs.get(feature, group);
+            var val = feature.get( group.toLowerCase() );
             if (val !== undefined)
                 return val;
             else
@@ -598,24 +582,19 @@ FeatureTrack.prototype.featureUrl = function(feature) {
 
 FeatureTrack.prototype.renderSubfeature = function(feature, featDiv, subfeature,
                                                    displayStart, displayEnd) {
-    var subStart = this.attrs.get(subfeature, "Start");
-    var subEnd = this.attrs.get(subfeature, "End");
+    var subStart = subfeature.get('start');
+    var subEnd = subfeature.get('end');
     var featLength = displayEnd - displayStart;
 
     var subDiv = document.createElement("div");
 
     if( this.config.style.subfeatureClasses ) {
-        var type = this.attrs.get(subfeature, "Type");
+        var type = subfeature.get('type');
         subDiv.className = this.config.style.subfeatureClasses[type];
-        switch (this.attrs.get(subfeature, "Strand")) {
+        switch ( subfeature.get('strand') ) {
             case 1:
             case '+':
                 subDiv.className += " plus-" + subDiv.className; break;
-            case 0:
-            case '.':
-            case null:
-            case undefined:
-                subDiv.className = className; break;
             case -1:
             case '-':
                 subDiv.className += " minus-" + subDiv.className; break;
diff --git a/js/SeqFeatureStore.js b/js/SeqFeatureStore.js
new file mode 100644
index 0000000000..f93f81e0fd
--- /dev/null
+++ b/js/SeqFeatureStore.js
@@ -0,0 +1,30 @@
+//MODEL
+
+/**
+ * Base class for JBrowse data backends that hold sequences and
+ * features.  Some aspects reminiscent of Lincoln Stein's
+ * Bio::DB::SeqFeature::Store.
+  *
+ * @class
+ * @constructor
+ *
+ */
+
+function SeqFeatureStore(args) {
+    if( !args ) return;
+
+    this.loaded  = args.loaded;
+    this.changed = args.changeCallback;
+};
+
+
+
+/**
+ * Return a stored feature given its primary unique identifier.
+ */
+
+SeqFeatureStore.prototype.get_feature_by_id = function(id) {
+
+};
+
+
diff --git a/js/SeqFeatureStore/NCList.js b/js/SeqFeatureStore/NCList.js
new file mode 100644
index 0000000000..f3145fe899
--- /dev/null
+++ b/js/SeqFeatureStore/NCList.js
@@ -0,0 +1,91 @@
+/**
+ * Implementation of SeqFeatureStore using using nested containment
+ * lists held in static files that are lazily fetched from the web
+ * server.
+ *
+ * @class
+ * @augments SeqFeatureStore
+ */
+
+var SeqFeatureStore;
+
+SeqFeatureStore.NCList = function(args) {
+    SeqFeatureStore.call( this, args );
+
+    this.nclist = new NCList();
+
+    this.baseUrl = args.baseUrl;
+    this.urlTemplates = { tracklist: args.urlTemplate };
+    this.refSeq = args.refSeq;
+};
+
+SeqFeatureStore.NCList.prototype = new SeqFeatureStore();
+
+SeqFeatureStore.NCList.prototype.load = function() {
+    var that = this,
+         url = Util.resolveUrl(
+                   this.baseUrl,
+                   Util.fillTemplate( this.urlTemplates.tracklist,
+                                      {'refseq': this.refSeq.name}
+                                    )
+               );
+    // fetch the trackList
+    dojo.xhrGet({ url: url,
+                  handleAs: "json",
+                  load:  function(o) { that.loadSuccess(o, url); },
+                  error: function(o) { that.loadFail(o, url);    }
+	        });
+};
+
+SeqFeatureStore.NCList.prototype.loadSuccess = function( trackInfo, url ) {
+
+    this.count = trackInfo.featureCount;
+    // average feature density per base
+    this.density = trackInfo.featureCount / this.refSeq.length;
+
+    this.attrs = new ArrayRepr(trackInfo.intervals.classes);
+    this.nclist.importExisting( trackInfo.intervals.nclist,
+                                this.attrs,
+                                url,
+                                trackInfo.intervals.urlTemplate,
+                                trackInfo.intervals.lazyClass
+                              );
+
+    if (trackInfo.histograms) {
+        this.histograms = trackInfo.histograms;
+        for (var i = 0; i < this.histograms.meta.length; i++) {
+            this.histograms.meta[i].lazyArray =
+                new LazyArray(this.histograms.meta[i].arrayParams, url);
+        }
+    }
+};
+
+SeqFeatureStore.NCList.prototype.loadFail = function(trackInfo,url) {
+    this.empty = true;
+    this.setLoaded();
+};
+
+// just forward histogram() and iterate() to our encapsulate nclist
+SeqFeatureStore.NCList.prototype.histogram = function() {
+    return this.nclist.histogram.apply( this.nclist, arguments );
+};
+
+SeqFeatureStore.NCList.prototype.iterate = function( startBase, endBase, origFeatCallback, finishCallback ) {
+    var that = this;
+    var accessors    = this.attrs.accessors(),
+        featCallBack = function( feature, path ) {
+            that._add_getters( accessors.get, feature );
+            return origFeatCallback( feature, path );
+        };
+
+    return this.nclist.iterate.call( this.nclist, startBase, endBase, featCallBack, finishCallback );
+};
+
+// helper method to recursively add a .get method to a feature and its
+// subfeatures
+SeqFeatureStore.NCList.prototype._add_getters = function(getter,feature) {
+    var that = this;
+    feature.get = getter;
+    dojo.forEach( feature.get('subfeatures'), function(f) { that._add_getters( getter, f ); } );
+};
+

From ac393695bff0b19fe3fcd116a1c6cca82535e792 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 12 Mar 2012 15:59:38 -0400
Subject: [PATCH 14/49] remove unused fastSet and fastGet functions from
 ArrayRepr.js

---
 js/ArrayRepr.js | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/js/ArrayRepr.js b/js/ArrayRepr.js
index e1ccd6db44..c13b637175 100644
--- a/js/ArrayRepr.js
+++ b/js/ArrayRepr.js
@@ -109,12 +109,6 @@ ArrayRepr.prototype.get = function(obj, attr) {
     }
 };
 
-ArrayRepr.prototype.fastGet = function(obj, attr) {
-    // can be used only if attr is guaranteed to be in
-    // the "classes" array for this object
-    return obj[self.fields[obj[0]][attr]];
-};
-
 ArrayRepr.prototype.set = function(obj, attr, val) {
     if (attr in this.fields[obj[0]]) {
         obj[this.fields[obj[0]][attr]] = val;
@@ -126,12 +120,6 @@ ArrayRepr.prototype.set = function(obj, attr, val) {
     }
 };
 
-ArrayRepr.prototype.fastSet = function(obj, attr, val) {
-    // can be used only if attr is guaranteed to be in
-    // the "classes" array for this object
-    obj[this.fields[obj[0]][attr]] = val;
-};
-
 ArrayRepr.prototype.makeSetter = function(attr) {
     var self = this;
     return function(obj, val) { self.set(obj, attr, val); };

From 4046a19d7cdc1d145a623702fc7c70aad7c69e9f Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 12 Mar 2012 16:07:44 -0400
Subject: [PATCH 15/49] missing semicolon

---
 js/Browser.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/Browser.js b/js/Browser.js
index ac74f5db27..05bc5a5308 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -484,7 +484,7 @@ Browser.prototype.navigateToLocation = function( location ) {
 
     return;
     //this.view.centerAtBase( location.end );
-}
+};
 
 // given a string name, search for matching feature names and set the
 // view location to any that match

From 2f575541620f3d0cd4bb24ccfc7d3f1cfe0d0dc7 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 12 Mar 2012 16:52:00 -0400
Subject: [PATCH 16/49] improve ArrayRepr inline doc

---
 js/ArrayRepr.js | 67 ++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 55 insertions(+), 12 deletions(-)

diff --git a/js/ArrayRepr.js b/js/ArrayRepr.js
index c13b637175..e58ede0ce5 100644
--- a/js/ArrayRepr.js
+++ b/js/ArrayRepr.js
@@ -1,21 +1,34 @@
 // MODEL
 
-/*
-    class for operating on indexed representations of objects
+/**
+    @class
+    @constructor
+
+    @description
+
+    Class for operating on indexed array representations of objects.
 
-    For example, if we have a lot of objects with similar attributes, e.g.:
+    For example, if we have a lot of objects with similar attrbutes, e.g.:
+
+    <pre class="code">
         [
             {start: 1, end: 2, strand: -1},
             {start: 5, end: 6, strand: 1},
             ...
         ]
+    </pre>
+
+    @description
     we can represent them more compactly (e.g., in JSON) something like this:
+
+    <pre class="code">
         class = ["start", "end", "strand"]
         [
             [1, 2, -1],
             [5, 6, 1],
             ...
         ]
+    </pre>
 
     If we want to represent a few different kinds of objects in our big list,
     we can have multiple "class" arrays, and tag each object to identify
@@ -23,6 +36,8 @@
 
     For example, if we have a lot of instances of a few types of objects,
     like this:
+
+    <pre class="code">
         [
             {start: 1, end: 2, strand: 1, id: 1},
             {start: 5, end: 6, strand: 1, id: 2},
@@ -31,8 +46,12 @@
             {start: 30, end: 40, chunk: 2},
             ...
         ]
+    </pre>
+
     We could use the first array position to indicate the "class" for the
     object, like this:
+
+    <pre class="code">
         classes = [["start", "end", "strand", "id"], ["start", "end", "chunk"]]
         [
             [0, 1, 2, 1, 1],
@@ -41,13 +60,18 @@
             [1, 10, 20, 1],
             [1, 30, 40, 1]
         ]
+    </pre>
+
     Also, if we occasionally want to add an ad-hoc attribute, we could just
     stick an optional dictionary onto the end:
+
+    <pre class="code">
         classes = [["start", "end", "strand", "id"], ["start", "end", "chunk"]]
         [
             [0, 1, 2, 1, 1],
             [0, 5, 6, 1, 2, {foo: 1}]
         ]
+    </pre>
 
     Given that individual objects are being represented by arrays, generic
     code needs some way to differentiate arrays that are meant to be objects
@@ -61,15 +85,15 @@
 
     In the end, we get something like this:
 
+    <pre class="code">
         classes=[
             {'attributes': ['Start', 'End', 'Subfeatures'],
              'proto': {'Chrom': 'chr1'},
              'isArrayAttr': {Subfeatures: true}}
             ]
+    </pre>
 
     That's what this class facilitates.
-    """
-
 */
 function ArrayRepr (classes) {
     this.classes = classes;
@@ -86,6 +110,9 @@ function ArrayRepr (classes) {
     }
 }
 
+/**
+ * @private
+ */
 ArrayRepr.prototype.attrIndices = function(attr) {
     return this.classes.map(
         function(x) {
@@ -160,17 +187,33 @@ ArrayRepr.prototype.construct = function(self, obj, klass) {
     return result;
 };
 
+
+/**
+
+Returns fast pre-compiled getter and setter functions for use with
+Arrays that use this representation.
+
+When the returned <code>get</code> and <code>set</code> functions are
+added as methods to an Array that contains data in this
+representation, they provide fast access by name to the data.
+
+@returns {Object} <code>{ get: function() {...}, set: function(val) {...} }</code>
+
+@example
+var accessors = attrs.accessors();
+var feature = get_feature_from_someplace();
+feature.get = accessors.get;
+// print out the feature start and end
+console.log( feature.get('start') + ',' + feature.get('end') );
+
+*/
 ArrayRepr.prototype.accessors = function () {
     return this._accessors = this._accessors || this._makeAccessors();
 };
 
-// make an object like
-//     { get: { attrname: func() {}, ... },
-//       set: { attrname: func() {}. ... }
-//     }
-// prototype object that, when set as the prototype on a data
-// array, provides nicely-named, fast accessors to access the
-// attributes in that array
+/**
+ * @private
+ */
 ArrayRepr.prototype._makeAccessors = function() {
     var that = this,
         accessors = {

From a29762376d9d54401a59c9dfea59ca8619d20be2 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 12 Mar 2012 18:08:55 -0400
Subject: [PATCH 17/49] improvements to inline documentation

---
 js/FeatureTrack.js           |  3 +++
 js/GenomeView.js             | 12 ++++++++++++
 js/GridTrack.js              | 10 +++++++---
 js/ImageTrack.js             |  3 +++
 js/Layout.js                 |  6 +++++-
 js/LazyArray.js              | 10 +++++-----
 js/LazyPatricia.js           |  9 +++++++--
 js/NCList.js                 | 23 +++++++++++++++++------
 js/SeqFeatureStore/NCList.js |  1 +
 js/SequenceTrack.js          | 13 +++++++++----
 js/StaticTrack.js            |  9 +++++++--
 js/Track.js                  |  3 +++
 js/Util.js                   |  7 +++++++
 13 files changed, 86 insertions(+), 23 deletions(-)

diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index f6d0357698..355f23ed4d 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function FeatureTrack( trackMeta, refSeq, browserParams ) {
     //trackMeta: object with:
     //            key:   display text track name
diff --git a/js/GenomeView.js b/js/GenomeView.js
index e320b4d82f..c26171c2f3 100644
--- a/js/GenomeView.js
+++ b/js/GenomeView.js
@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function Animation(subject, callback, time) {
     //subject: what's being animated
     //callback: function to call at the end of the animation
@@ -59,6 +62,9 @@ Animation.prototype.stop = function() {
     this.callback(this);
 };
 
+/**
+ * @class
+ */
 function Slider(view, callback, time, distance) {
     Animation.call(this, view, callback, time);
     this.slideStart = view.getX();
@@ -78,6 +84,9 @@ Slider.prototype.step = function(pos) {
     this.subject.setX(newX);
 };
 
+/**
+ * @class
+ */
 function Zoomer(scale, toScroll, callback, time, zoomLoc) {
     Animation.call(this, toScroll, callback, time);
     this.toZoom = toScroll.zoomContainer;
@@ -115,6 +124,9 @@ Zoomer.prototype.step = function(pos) {
     this.subject.updateTrackLabels(this.initialX - newLeft);
 };
 
+/**
+ * @class
+ */
 function GenomeView(elem, stripeWidth, refseq, zoomLevel, browserRoot) {
     //all coordinates are interbase
 
diff --git a/js/GridTrack.js b/js/GridTrack.js
index 05f900d5e7..f06a3c9702 100644
--- a/js/GridTrack.js
+++ b/js/GridTrack.js
@@ -1,7 +1,12 @@
 // VIEW
 
-// This track draws vertical gridlines, which are divs with height:
-// 100%, absolutely positioned at the very top of all the tracks
+/**
+
+This track draws vertical gridlines, which are divs with height 100%,
+absolutely positioned at the very top of all the tracks.
+
+@class
+*/
 function GridTrack(name) {
     Track.call(this, name, name, true, function() {});
 }
@@ -46,4 +51,3 @@ GridTrack.prototype.renderGridlines = function(block,leftBase,rightBase) {
 
 };
 
-
diff --git a/js/ImageTrack.js b/js/ImageTrack.js
index 076cd5cbd1..5753494199 100644
--- a/js/ImageTrack.js
+++ b/js/ImageTrack.js
@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function ImageTrack(trackMeta, refSeq, browserParams) {
     Track.call(this, trackMeta.label, trackMeta.key,
                false, browserParams.changeCallback);
diff --git a/js/Layout.js b/js/Layout.js
index 3af7d93566..b5dce48f77 100644
--- a/js/Layout.js
+++ b/js/Layout.js
@@ -1,6 +1,6 @@
 // VIEW
 
-/*
+/**
  * Code for laying out rectangles, given that layout is also happening
  * in adjacent blocks at the same time
  *
@@ -10,6 +10,7 @@
  * contour spans and give up some packing closeness in exchange for speed
  * (the code already merges spans that have the same x-coord and are vertically
  * contiguous).
+ * @class
  */
 
 function Contour(top) {
@@ -183,6 +184,9 @@ Contour.prototype.getNextTop = function(fit) {
     return this.spans[fit.above].top + this.spans[fit.above].height;
 };
 
+/**
+ * @class
+ */
 function Layout(leftBound, rightBound) {
     this.leftBound = leftBound;
     this.rightBound = rightBound;
diff --git a/js/LazyArray.js b/js/LazyArray.js
index 363baec60f..0335a8a8fc 100644
--- a/js/LazyArray.js
+++ b/js/LazyArray.js
@@ -7,10 +7,10 @@
  */
 
 /**
- * Construct a new LazyArray
- * @class This class makes it easier to partially load a large JSON array
+ * Construct a new LazyArray, which partially loads large JSON arrays.
+ * @class
  * @constructor
- * @param lazyArrayParams object with:<br>
+ * @param lazyArrayParams {Object} as:
  * <ul>
  * <li><code>urlTemplate</code> - for each lazily-loaded array chunk, the chunk number will get substituted for {chunk} in this template, and the result will beused as the URL of the JSON for that array chunk</li>
  * <li><code>length</code> - length of the overall array</li>
@@ -56,7 +56,7 @@ LazyArray.prototype.range = function(start, end, callback, postFun, param) {
     var firstChunk = Math.floor(start / this.chunkSize);
     var lastChunk = Math.floor(end / this.chunkSize);
 
-    if (postFun === undefined) postFun = function() {};
+    if (postFun === undefined) /** @inner */ postFun = function() {};
     var finish = new Finisher(postFun);
 
     for (var chunk = firstChunk; chunk <= lastChunk; chunk++) {
@@ -124,4 +124,4 @@ LazyArray.prototype._processChunk = function(start, end, chunk,
     for (var i = chunkStart; i <= chunkEnd; i++) {
         callback(i + firstIndex, this.chunks[chunk][i], param);
     }
-};
\ No newline at end of file
+};
diff --git a/js/LazyPatricia.js b/js/LazyPatricia.js
index 6b8eb37450..8c5656e7bf 100644
--- a/js/LazyPatricia.js
+++ b/js/LazyPatricia.js
@@ -1,6 +1,7 @@
 // MODEL
 
-/*
+/**
+<pre>
   Implements a lazy PATRICIA tree.
 
   This class is a map where the keys are strings.  The map supports fast
@@ -49,7 +50,11 @@
   the wire (so, no type tags in the JSON to distinguish loaded nodes,
   lazy nodes, and leaves) while supporting lazy loading and reasonably
   fast lookups.
- */
+</pre>
+
+@class
+
+*/
 
 function LazyTrie(rootURL, chunkTempl) {
     this.rootURL = rootURL;
diff --git a/js/NCList.js b/js/NCList.js
index 0f2db29df2..184a21d291 100644
--- a/js/NCList.js
+++ b/js/NCList.js
@@ -1,11 +1,22 @@
 // MODEL
 
-//After
-//Alekseyenko, A., and Lee, C. (2007).
-//Nested Containment List (NCList): A new algorithm for accelerating
-//   interval query of genome alignment and interval databases.
-//Bioinformatics, doi:10.1093/bioinformatics/btl647
-//http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1
+/**
+
+Nested containment list.
+
+@class
+
+After
+<pre>
+  Alekseyenko, A., and Lee, C. (2007).
+  Nested Containment List (NCList): A new algorithm for accelerating
+     interval query of genome alignment and interval databases.
+  Bioinformatics, doi:10.1093/bioinformatics/btl647
+</pre>
+
+<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1">http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1</a>
+
+ */
 
 function NCList() {
 }
diff --git a/js/SeqFeatureStore/NCList.js b/js/SeqFeatureStore/NCList.js
index f3145fe899..1264c5948d 100644
--- a/js/SeqFeatureStore/NCList.js
+++ b/js/SeqFeatureStore/NCList.js
@@ -73,6 +73,7 @@ SeqFeatureStore.NCList.prototype.histogram = function() {
 SeqFeatureStore.NCList.prototype.iterate = function( startBase, endBase, origFeatCallback, finishCallback ) {
     var that = this;
     var accessors    = this.attrs.accessors(),
+        /** @inner */
         featCallBack = function( feature, path ) {
             that._add_getters( accessors.get, feature );
             return origFeatCallback( feature, path );
diff --git a/js/SequenceTrack.js b/js/SequenceTrack.js
index e4562ca396..ca59869403 100644
--- a/js/SequenceTrack.js
+++ b/js/SequenceTrack.js
@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function SequenceTrack(trackMeta, refSeq, browserParams) {
     //trackMeta: object with:
     //  key:   display text track name
@@ -124,10 +127,12 @@ SequenceTrack.prototype.renderSeqDiv = function ( start, end, seq ) {
     return container;
 };
 
-SequenceTrack.prototype.getRange = function(start, end, callback) {
-    //start: start coord, in interbase
-    //end: end coord, in interbase
-    //callback: function that takes (start, end, seq)
+/**
+ * @param start start coord, in interbase
+ * @param end end coord, in interbase
+ * @param callback function that takes ( start, end, seq )
+ */
+SequenceTrack.prototype.getRange = function( /**Number*/ start, /**Number*/ end, /**Function*/ callback) {
     var firstChunk = Math.floor( Math.max(0,start) / this.chunkSize);
     var lastChunk = Math.floor((end - 1) / this.chunkSize);
     var chunkSize = this.chunkSize;
diff --git a/js/StaticTrack.js b/js/StaticTrack.js
index 885c0e103f..8d0097ef54 100644
--- a/js/StaticTrack.js
+++ b/js/StaticTrack.js
@@ -1,7 +1,12 @@
 // VIEW
 
-//This track is for (e.g.) position and sequence information that should
-//always stay visible at the top of the view
+/**
+
+This track is for (e.g.) position and sequence information that should
+always stay visible at the top of the view.
+
+@class
+*/
 
 function StaticTrack(name, labelClass, posHeight) {
     Track.call(this, name, name, true, function() {});
diff --git a/js/Track.js b/js/Track.js
index d46763d472..5ae328f448 100644
--- a/js/Track.js
+++ b/js/Track.js
@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function Track(name, key, loaded, changeCallback) {
     this.name = name;
     this.key = key;
diff --git a/js/Util.js b/js/Util.js
index 2a9d5cfd2b..feed5e3384 100644
--- a/js/Util.js
+++ b/js/Util.js
@@ -1,5 +1,9 @@
 // MISC
 
+/**
+ * @namespace
+ */
+
 var Util = {};
 
 Util.is_ie = navigator.appVersion.indexOf('MSIE') >= 0;
@@ -364,6 +368,9 @@ if (!Array.prototype.indexOf)
   };
 }
 
+/**
+ * @class
+ */
 function Finisher(fun) {
     this.fun = fun;
     this.count = 0;

From 394a116322fd4be6276727ae59f9dea24c78dfe0 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Mon, 12 Mar 2012 19:59:43 -0400
Subject: [PATCH 18/49] fix FF 10 performance regression: firefox try/catch is
 apparently quite slow

---
 js/ArrayRepr.js | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/js/ArrayRepr.js b/js/ArrayRepr.js
index e58ede0ce5..147540936e 100644
--- a/js/ArrayRepr.js
+++ b/js/ArrayRepr.js
@@ -218,12 +218,18 @@ ArrayRepr.prototype._makeAccessors = function() {
     var that = this,
         accessors = {
             get: function(field) {
-                try { return this.get[field].call(this); }
-                catch (x) { return undefined; }
+                var f = this.get[field];
+                if( f )
+                    return f.call(this);
+                else
+                    return undefined;
             },
             set: function(field,val) {
-                try { return this.set[field].call(this,val); }
-                catch (x) { return undefined; }
+                var f = this.set[field];
+                if( f )
+                    return f.call(this,val);
+                else
+                    return undefined;
             }
         };
 
@@ -259,6 +265,7 @@ ArrayRepr.prototype._makeAccessors = function() {
         })();
     }
 
+
     return accessors;
 };
 

From 8ed5d2d1b0fc165686467193257a5c0294492ca0 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 10:20:03 -0400
Subject: [PATCH 19/49] change new "config" param name to "configFile"

---
 index.html    |  2 +-
 js/Browser.js | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/index.html b/index.html
index c7f5d6c1bd..a6c3847e0a 100644
--- a/index.html
+++ b/index.html
@@ -49,7 +49,7 @@
            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: dataRoot + "/seq/refSeqs.json",
-                                   config: [
+                                   configFile: [
                                      dataRoot + "/trackList.json",
                                    ],
                                    nameUrl: dataRoot + "/names/root.json",
diff --git a/js/Browser.js b/js/Browser.js
index 05bc5a5308..3ba96e4fab 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -110,12 +110,12 @@ Browser.prototype.loadConfig = function () {
     var brwsr = this;
 
     // load any configuration files we've been passed
-    if( typeof this.params.config != 'object' || !this.params.config.length )
-        this.params.config = [ this.params.config ];
+    if( typeof this.params.configFile != 'object' || !this.params.configFile.length )
+        this.params.configFile = [ this.params.configFile ];
 
-    for (var i = 0; i < this.params.config.length; i++) {
-        if( typeof this.params.config[i] == 'string' )
-            this.params.config[i] = { url: this.params.config[i] };
+    for (var i = 0; i < this.params.configFile.length; i++) {
+        if( typeof this.params.configFile[i] == 'string' )
+            this.params.configFile[i] = { url: this.params.configFile[i] };
 
         (function(config) {
              Util.maybeLoad(
@@ -127,7 +127,7 @@ Browser.prototype.loadConfig = function () {
                              brwsr.addConfig( o, { sourceUrl: config.url });
                          });
                  });
-         })(this.params.config[i]);
+         })(this.params.configFile[i]);
     }
 };
 

From 4e280d9b3fbba6804ea04a243f52b0d075c4d8ad Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 10:40:58 -0400
Subject: [PATCH 20/49] tweak ArrayRepr accessor pregeneration to not collide
 with builtin properties of Function

---
 js/ArrayRepr.js | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/js/ArrayRepr.js b/js/ArrayRepr.js
index 147540936e..c34f128704 100644
--- a/js/ArrayRepr.js
+++ b/js/ArrayRepr.js
@@ -218,20 +218,22 @@ ArrayRepr.prototype._makeAccessors = function() {
     var that = this,
         accessors = {
             get: function(field) {
-                var f = this.get[field];
+                var f = this.get.field_accessors[field];
                 if( f )
                     return f.call(this);
                 else
                     return undefined;
             },
             set: function(field,val) {
-                var f = this.set[field];
+                var f = this.set.field_accessors[field];
                 if( f )
                     return f.call(this,val);
                 else
                     return undefined;
             }
         };
+    accessors.get.field_accessors = {};
+    accessors.set.field_accessors = {};
 
     // make a data structure as: { attr_name: [offset,offset,offset], }
     // that will be convenient for finding the location of the attr
@@ -245,19 +247,20 @@ ArrayRepr.prototype._makeAccessors = function() {
         });
     });
 
+    // use that to make precalculated get and set accessors for each field
     for( var attrname in indices ) {
         if( ! indices.hasOwnProperty(attrname) ) continue;
 
-        // make a get accessor
-        accessors.get[ attrname ] = (function() {
+        // get
+        accessors.get.field_accessors[ attrname ] = (function() {
             var attr_indices = indices[attrname];
             return !attr_indices ? function() { return undefined; } : function() {
                 return this[ attr_indices[ this[0] ] ];
             };
         })();
 
-        // make a set accessor
-        accessors.set[ attrname ] = (function() {
+        // set
+        accessors.set.field_accessors[ attrname ] = (function() {
             var attr_indices =  indices[attrname];
             return !attr_indices ? function() { return undefined; } : function(v) {
                 return ( this[ attr_indices[ this[0] ] ] = v );

From 9cfa458d303f662d11d2b26d41c02ff42de2ec3b Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 10:44:28 -0400
Subject: [PATCH 21/49] fix regression with missing labels

---
 js/FeatureTrack.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index 355f23ed4d..fbb26ac4eb 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -240,7 +240,7 @@ FeatureTrack.prototype.fillHist = function(blockIndex, block,
 };
 
 FeatureTrack.prototype.endZoom = function(destScale, destBlockBases) {
-    if (destScale < (this.density * this.config.scaleThresh.hist)) {
+    if (destScale < (this.featureStore.density * this.config.scaleThresh.hist)) {
         this.setLabel(this.key + "<br>per " + Math.round(destBlockBases / this.numBins) + "bp");
     } else {
         this.setLabel(this.key);
@@ -255,7 +255,7 @@ FeatureTrack.prototype.fillBlock = function(blockIndex, block,
                                             containerStart, containerEnd) {
     //console.log("scale: %d, histScale: %d", scale, this.histScale);
     if (this.featureStore.histograms &&
-        (scale < (this.density * this.config.scaleThresh.hist)) ) {
+        (scale < (this.featureStore.density * this.config.scaleThresh.hist)) ) {
 	this.fillHist(blockIndex, block, leftBase, rightBase, stripeWidth,
                       containerStart, containerEnd);
     } else {
@@ -445,7 +445,7 @@ FeatureTrack.prototype.renderFeature = function(feature, uniqueId, block, scale,
     // if the label extends beyond the feature, use the
     // label end position as the end position for layout
     var name = feature.get('name');
-    var labelScale = this.density * this.config.scaleThresh.label;
+    var labelScale = this.featureStore.density * this.config.scaleThresh.label;
     if (name && (scale > labelScale)) {
 	featureEnd = Math.max(featureEnd,
                               featureStart + ((name ? name.length : 0)

From 786d9d8afb0ef25a5107b1b5fe73e59e07be0d41 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 11:57:14 -0400
Subject: [PATCH 22/49] make Util.maybeLoad take an object instead of just a
 URL, to give more control over how the xhr is done

---
 js/Browser.js |  7 +++++--
 js/NCList.js  |  4 +++-
 js/Util.js    | 42 +++++++++++++++++++++---------------------
 3 files changed, 29 insertions(+), 24 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index eac6db8bd3..e31ffd3016 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -100,7 +100,7 @@ Browser.prototype.initialize = function() {
     var brwsr = this;
     if( typeof this.params.refSeqs == 'string' )
         this.params.refSeqs = { url: this.params.refSeqs };
-    Util.maybeLoad(this.params.refSeqs.url, this.params.refSeqs,
+    Util.maybeLoad({ url: this.config.refSeqs.url, handleAs: 'json'}, this.config.refSeqs,
                    function(o) {
                        brwsr.addRefseqs(o);
                    });
@@ -121,7 +121,10 @@ Browser.prototype.loadConfig = function () {
 
         (function(config) {
              Util.maybeLoad(
-                 config.url,
+                 {
+                     url: config.url,
+                     handleAs: 'json'
+                 },
                  config,
                  function(o) {
                      brwsr.addDeferred(
diff --git a/js/NCList.js b/js/NCList.js
index 184a21d291..7597f7eb0b 100644
--- a/js/NCList.js
+++ b/js/NCList.js
@@ -124,10 +124,12 @@ NCList.prototype.iterHelper = function(arr, from, to, fun, finish,
             }
             var chunk = this.lazyChunks[chunkNum];
             finish.inc();
-            Util.maybeLoad(Util.resolveUrl(this.baseURL,
+            Util.maybeLoad({ url: Util.resolveUrl(this.baseURL,
                                            this.lazyUrlTemplate.replace(
                                                    /\{Chunk\}/g, chunkNum
                                            ) ),
+                             handleAs: 'json'
+                           },
                            chunk,
                            (function (myChunkNum) {
                                return function(o) {
diff --git a/js/Util.js b/js/Util.js
index feed5e3384..93c98a9cb6 100644
--- a/js/Util.js
+++ b/js/Util.js
@@ -98,12 +98,13 @@ Util.fillTemplate = function(template, fillWith) {
 
 /**
  * function to load a specified resource only once
- * @param url URL to get
- * @param stateObj object that stores the state of the load
- * @param successCallback function to call on a successful load
- * @param errorCallback function to call on an unsuccessful load
+ * @param {Object}   dojoXhrArgs object containing arguments for dojo.xhrGet,
+ *                               like <code>url</code> and <code>handleAs</code>
+ * @param {Object}   stateObj object that stores the state of the load
+ * @param {Function} successCallback function to call on a successful load
+ * @param {Function} errorCallback function to call on an unsuccessful load
  */
-Util.maybeLoad = function (url, stateObj, successCallback, errorCallback) {
+Util.maybeLoad = function ( dojoXhrArgs, stateObj, successCallback, errorCallback) {
     if (stateObj.state) {
         if ("loaded" == stateObj.state) {
             successCallback(stateObj.data);
@@ -117,22 +118,21 @@ Util.maybeLoad = function (url, stateObj, successCallback, errorCallback) {
         stateObj.state = "loading";
         stateObj.successCallbacks = [successCallback];
         stateObj.errorCallbacks = [errorCallback];
-        dojo.xhrGet(
-            {
-                url: url,
-                handleAs: "json",
-                load: function(o) {
-                    stateObj.state = "loaded";
-                    stateObj.data = o;
-                    var cbs = stateObj.successCallbacks;
-                    for (var c = 0; c < cbs.length; c++) cbs[c](o);
-                },
-                error: function() {
-                    stateObj.state = "error";
-                    var cbs = stateObj.errorCallbacks;
-                    for (var c = 0; c < cbs.length; c++) cbs[c]();
-                }
-            });
+
+        var args = dojo.clone( dojoXhrArgs );
+        args.load = function(o) {
+            stateObj.state = "loaded";
+            stateObj.data = o;
+            var cbs = stateObj.successCallbacks;
+            for (var c = 0; c < cbs.length; c++) cbs[c](o);
+        };
+        args.error = function() {
+            stateObj.state = "error";
+            var cbs = stateObj.errorCallbacks;
+            for (var c = 0; c < cbs.length; c++) cbs[c]();
+        };
+
+        dojo.xhrGet( args );
     }
 };
 

From c2c62478965fccc0cb6a2ac1258b70cb59bc6187 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 12:31:23 -0400
Subject: [PATCH 23/49] change the `params` Browser property to be called
 `config`

Moving toward the params passed to the browser constructor, and the
data in the tracklist, being treated the same, as configuration data.
---
 js/Browser.js | 131 ++++++++++++++++++++++++--------------------------
 1 file changed, 64 insertions(+), 67 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index e31ffd3016..23ee98183d 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -29,14 +29,12 @@ var Browser = function(params) {
     dojo.require("dijit.layout.ContentPane");
     dojo.require("dijit.layout.BorderContainer");
 
-    this.params = params;
-
     this.deferredFunctions = [];
-
-    if (params.nameUrl)
-        this.names = new LazyTrie(params.nameUrl, "lazy-{Chunk}.json");
     this.tracks = [];
     this.isInitialized = false;
+
+    this.config = params;
+
     var browser = this;
     dojo.addOnLoad( function() { browser.initialize(); } );
     // TODO: refactor the touch stuff
@@ -47,9 +45,12 @@ Browser.prototype.initialize = function() {
 
     this.loadConfig();
 
+    if (this.config.nameUrl)
+        this.names = new LazyTrie(this.config.nameUrl, "lazy-{Chunk}.json");
+
     //set up top nav/overview pane and main GenomeView pane
     dojo.addClass(document.body, "tundra");
-    this.container = dojo.byId(this.params.containerID);
+    this.container = dojo.byId(this.config.containerID);
     this.container.genomeBrowser = this;
     var topPane = document.createElement("div");
     this.container.appendChild(topPane);
@@ -58,7 +59,7 @@ Browser.prototype.initialize = function() {
     overview.className = "overview";
     overview.id = "overview";
     // overview=0 hides the overview, but we still need it to exist
-    if( this.params.show_overview == 0 ) overview.style.cssText = "display: none";
+    if( this.config.show_overview == 0 ) overview.style.cssText = "display: none";
     topPane.appendChild(overview);
 
     //try to come up with a good estimate of how big the location box
@@ -90,16 +91,16 @@ Browser.prototype.initialize = function() {
     //    from a param passed to our instance, or from a cookie, or
     //    the passed defaults, or the last-resort default of "DNA"?
     this.origTracklist =
-           this.params.tracks
+           this.config.tracks
         || dojo.cookie( this.container.id + "-tracks" )
-        || this.params.defaultTracks
+        || this.config.defaultTracks
         || "DNA";
 
 
     // load our ref seqs
     var brwsr = this;
-    if( typeof this.params.refSeqs == 'string' )
-        this.params.refSeqs = { url: this.params.refSeqs };
+    if( typeof this.config.refSeqs == 'string' )
+        this.config.refSeqs = { url: this.config.refSeqs };
     Util.maybeLoad({ url: this.config.refSeqs.url, handleAs: 'json'}, this.config.refSeqs,
                    function(o) {
                        brwsr.addRefseqs(o);
@@ -112,12 +113,12 @@ Browser.prototype.loadConfig = function () {
     var brwsr = this;
 
     // load any configuration files we've been passed
-    if( typeof this.params.configFile != 'object' || !this.params.configFile.length )
-        this.params.configFile = [ this.params.configFile ];
+    if( typeof this.config.configFile != 'object' || !this.config.configFile.length )
+        this.config.configFile = [ this.config.configFile ];
 
-    for (var i = 0; i < this.params.configFile.length; i++) {
-        if( typeof this.params.configFile[i] == 'string' )
-            this.params.configFile[i] = { url: this.params.configFile[i] };
+    for (var i = 0; i < this.config.configFile.length; i++) {
+        if( typeof this.config.configFile[i] == 'string' )
+            this.config.configFile[i] = { url: this.config.configFile[i] };
 
         (function(config) {
              Util.maybeLoad(
@@ -129,10 +130,10 @@ Browser.prototype.loadConfig = function () {
                  function(o) {
                      brwsr.addDeferred(
                          function() {
-                             brwsr.addConfig( o, { sourceUrl: config.url });
+                             brwsr.addConfigData( o, { sourceUrl: config.url });
                          });
                  });
-         })(this.params.configFile[i]);
+         })(this.config.configFile[i]);
     }
 };
 
@@ -147,34 +148,31 @@ Browser.prototype.addDeferred = function(f) {
         this.deferredFunctions.push(f);
 };
 
-Browser.prototype.addConfig = function( config, additional ) {
+Browser.prototype.addConfigData = function( newconfig, additional ) {
 
-    // add any additional data to the config hash
-    for( p in additional ) {
-        if( additional.hasOwnProperty(p) )
-            config[p] = additional[p];
-    }
+    newconfig = dojo.clone(newconfig);
+
+    // add any additional data to the conf that's coming in
+    Util.deepUpdate( newconfig, additional );
 
     // make a default baseUrl if one is not already set
-    if( !config.baseUrl ) {
-        config.baseUrl = Util.resolveUrl( config.sourceUrl, '.' );
+    if( !newconfig.baseUrl ) {
+        newconfig.baseUrl = Util.resolveUrl( newconfig.sourceUrl, '.' );
     }
-    if( ! /\/$/.test( config.baseUrl ) )
-        config.baseUrl += "/";
+    if( ! /\/$/.test( newconfig.baseUrl ) )
+        newconfig.baseUrl += "/";
 
+    // and now add that to our overall config
+    Util.deepUpdate( this.config, newconfig );
 
-    if (1 == config.formatVersion) {
-        if( config.tracks ) {
-            if( config.sourceUrl ) {
-                for (var i = 0; i < config.tracks.length; i++)
-                    if( ! config.tracks[i].baseUrl )
-                        config.tracks[i].baseUrl = config.baseUrl;
-            }
-            this.trackListWidget.insertNodes(false, config.tracks);
-            this.showTracks(this.origTracklist);
+    if( this.config.tracks ) {
+        if( this.config.sourceUrl ) {
+            for (var i = 0; i < this.config.tracks.length; i++)
+                if( ! this.config.tracks[i].baseUrl )
+                    this.config.tracks[i].baseUrl = this.config.baseUrl;
         }
-    } else {
-        throw "track list format " + trackList.formatVersion + " not supported";
+        this.trackListWidget.insertNodes(false, this.config.tracks);
+        this.showTracks(this.origTracklist);
     }
 };
 
@@ -185,7 +183,7 @@ Browser.prototype.addRefseqs = function(refSeqs) {
     for (var i = 0; i < refSeqs.length; i++)
         this.allRefs[refSeqs[i].name] = refSeqs[i];
 
-    var refCookie = dojo.cookie(this.params.containerID + "-refseq");
+    var refCookie = dojo.cookie(this.config.containerID + "-refseq");
     this.refSeq = refSeqs[0];
     for (var i = 0; i < refSeqs.length; i++) {
         this.chromList.options[i] = new Option(refSeqs[i].name,
@@ -198,13 +196,13 @@ Browser.prototype.addRefseqs = function(refSeqs) {
 
     //hook up GenomeView
     var gv = new GenomeView(this.viewElem, 250, this.refSeq, 1/200,
-                            this.params.browserRoot);
+                            this.config.browserRoot);
     this.view = gv;
     //gv.setY(0);
     this.viewElem.view = gv;
 
     //set up track list
-    var trackListDiv = this.createTrackList(this.container, this.params);
+    var trackListDiv = this.createTrackList( this.container );
     this.containerWidget.startup();
 
     var brwsr = this;
@@ -224,12 +222,12 @@ Browser.prototype.addRefseqs = function(refSeqs) {
 
     //set initial location
     var oldLocMap = dojo.fromJson(dojo.cookie(brwsr.container.id + "-location")) || {};
-    if (this.params.location) {
-        this.navigateTo(this.params.location);
+    if (this.config.location) {
+        this.navigateTo(this.config.location);
     } else if (oldLocMap[this.refSeq.name]) {
         this.navigateTo( oldLocMap[this.refSeq.name] );
-    } else if (this.params.defaultLocation){
-        this.navigateTo(this.params.defaultLocation);
+    } else if (this.config.defaultLocation){
+        this.navigateTo(this.config.defaultLocation);
     } else {
         this.navigateTo( Util.assembleLocString({
                              ref:   this.refSeq.name,
@@ -292,11 +290,10 @@ Browser.prototype.onFineMove = function(startbp, endbp) {
  * @private
  */
 
-
-Browser.prototype.createTrackList = function(parent, params) {
+Browser.prototype.createTrackList = function( /**Element*/ parent ) {
     var leftPane = document.createElement("div");
     leftPane.id = "trackPane";
-    leftPane.style.cssText= params.show_tracklist == 0 ? "width: 0": "width: 10em";
+    leftPane.style.cssText= this.config.show_tracklist == 0 ? "width: 0": "width: 10em";
     parent.appendChild(leftPane);
     //splitter on left side
     var leftWidget = new dijit.layout.ContentPane({region: "left", splitter: true}, leftPane);
@@ -307,7 +304,7 @@ Browser.prototype.createTrackList = function(parent, params) {
         "width: 100%; height: 100%; overflow-x: hidden; overflow-y: auto;";
     trackListDiv.innerHTML =
         "Available Tracks:<br/>(Drag <img src=\""
-        + (params.browserRoot ? params.browserRoot : "")
+        + (this.config.browserRoot ? this.config.browserRoot : "")
         + "img/right_arrow.png\"/> to view)<br/><br/>";
     leftPane.appendChild(trackListDiv);
 
@@ -337,7 +334,7 @@ Browser.prototype.createTrackList = function(parent, params) {
                                                 accept: ["track"], // accepts tracks into left div
                                                 withHandles: false});
 
-    var trackCreate = function( trackConfig, hint) {
+    var trackCreate = /**@inner*/ function( trackConfig, hint) {
         var node;
         if ("avatar" == hint) {
             return trackListCreate( trackConfig, hint);
@@ -590,12 +587,12 @@ Browser.prototype.visibleTracks = function() {
 Browser.prototype.makeBookmarkLink = function (area) {
     // don't make the link if we were explicitly passed a 'bookmark'
     // param of 'false'
-    if( typeof this.params.bookmark != 'undefined' && !this.params.bookmark )
+    if( typeof this.config.bookmark != 'undefined' && !this.config.bookmark )
         return;
 
     // if a function was not passed, make a default bookmarking function
-    if( typeof this.params.bookmark != 'function' )
-        this.params.bookmark = function( browser_obj ) {
+    if( typeof this.config.bookmark != 'function' )
+        this.config.bookmark = function( browser_obj ) {
                return "".concat(
                    window.location.protocol,
                    "//",
@@ -605,13 +602,13 @@ Browser.prototype.makeBookmarkLink = function (area) {
                    dojo.objectToQuery({
                        loc:    browser_obj.visibleRegion(),
                        tracks: browser_obj.visibleTracks(),
-                       data:   browser_obj.params.queryParams.data
+                       data:   browser_obj.config.queryParams.data
                    })
                );
         };
 
     // make the bookmark link
-    var fullview = this.params.show_nav == 0 || this.params.show_tracklist == 0 || this.params.show_overview == 0;
+    var fullview = this.config.show_nav == 0 || this.config.show_tracklist == 0 || this.config.show_overview == 0;
     this.link = document.createElement("a");
     this.link.className = "topLink";
     this.link.href  = window.location.href;
@@ -625,7 +622,7 @@ Browser.prototype.makeBookmarkLink = function (area) {
 
     // connect moving events to update it
     var update_bookmark = function() {
-        this.link.href = this.params.bookmark.call( this, this );
+        this.link.href = this.config.bookmark.call( this, this );
     };
     dojo.connect( this, "onCoarseMove",           update_bookmark, this );
     dojo.connect( this, "onVisibleTracksChanged", update_bookmark, this );
@@ -675,7 +672,7 @@ Browser.prototype.onCoarseMove = function(startbp, endbp) {
 Browser.prototype.createNavBox = function( parent, locLength ) {
     var brwsr = this;
     var navbox = document.createElement("div");
-    var browserRoot = this.params.browserRoot ? this.params.browserRoot : "";
+    var browserRoot = this.config.browserRoot ? this.config.browserRoot : "";
     navbox.id = "navbox";
     parent.appendChild(navbox);
     navbox.style.cssText = "text-align: center; z-index: 10;";
@@ -687,7 +684,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
     moveLeft.id = "moveLeft";
     moveLeft.className = "icon nav";
     moveLeft.style.height = "40px";
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         dojo.connect(moveLeft, "click",
                 function(event) {
                 dojo.stopEvent(event);
@@ -701,7 +698,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
     moveRight.id="moveRight";
     moveRight.className = "icon nav";
     moveRight.style.height = "40px";
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         dojo.connect(moveRight, "click",
                      function(event) {
                      dojo.stopEvent(event);
@@ -715,7 +712,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
     bigZoomOut.id = "bigZoomOut";
     bigZoomOut.className = "icon nav";
     bigZoomOut.style.height = "40px";
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         dojo.connect(bigZoomOut, "click",
                  function(event) {
                      dojo.stopEvent(event);
@@ -729,7 +726,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
     zoomOut.id = "zoomOut";
     zoomOut.className = "icon nav";
     zoomOut.style.height = "40px";
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         dojo.connect(zoomOut, "click",
                  function(event) {
                      dojo.stopEvent(event);
@@ -743,7 +740,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
     zoomIn.id = "zoomIn";
     zoomIn.className = "icon nav";
     zoomIn.style.height = "40px";
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         dojo.connect(zoomIn, "click",
                  function(event) {
                      dojo.stopEvent(event);
@@ -757,7 +754,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
     bigZoomIn.id = "bigZoomIn";
     bigZoomIn.className = "icon nav";
     bigZoomIn.style.height = "40px";
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         dojo.connect(bigZoomIn, "click",
                  function(event) {
                      dojo.stopEvent(event);
@@ -771,7 +768,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
     this.locationBox.size=locLength;
     this.locationBox.type="text";
     this.locationBox.id="location";
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         dojo.connect(this.locationBox, "keydown", function(event) {
             if (event.keyCode == dojo.keys.ENTER) {
                 brwsr.navigateTo(brwsr.locationBox.value);
@@ -787,7 +784,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
     this.goButton = document.createElement("button");
     this.goButton.appendChild(document.createTextNode("Go"));
     this.goButton.disabled = true;
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         dojo.connect(this.goButton, "click", function(event) {
             brwsr.navigateTo(brwsr.locationBox.value);
             //brwsr.locationBox.blur();
@@ -796,7 +793,7 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
         });
     };
 
-    if( this.params.show_nav != 0 ) {
+    if( this.config.show_nav != 0 ) {
         navbox.appendChild(document.createTextNode("\u00a0\u00a0\u00a0\u00a0"));
         navbox.appendChild(moveLeft);
         navbox.appendChild(moveRight);

From 36a268c8fa5dc1afebe7ae30e4ad7309a58a8ec6 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 14:41:28 -0400
Subject: [PATCH 24/49] add a little more inline doc

---
 js/Browser.js | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index 23ee98183d..75a142481a 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -41,6 +41,11 @@ var Browser = function(params) {
     this.deferredFunctions.push(function() { loadTouch(); });
 };
 
+/**
+ * Does most of the actual initialization work.  Scheduled by
+ * constructor, and called after page load.
+ * @returns nothing meaningful
+ */
 Browser.prototype.initialize = function() {
 
     this.loadConfig();
@@ -107,8 +112,12 @@ Browser.prototype.initialize = function() {
                    });
 };
 
-// load our configuration files based on the parameters the
-// constructor was passed
+/**
+ *  Load our configuration file(s) based on the parameters thex
+ *  constructor was passed.  Does not return until all files are
+ *  loaded and merged in.
+ *  @returns nothing meaningful
+ */
 Browser.prototype.loadConfig = function () {
     var brwsr = this;
 

From 22973d173174dca66895b819d4125cb7a4fc1c5f Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 18:58:40 -0400
Subject: [PATCH 25/49] make Util.maybeLoad log errors when they happen

---
 js/Util.js | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/js/Util.js b/js/Util.js
index 93c98a9cb6..e555675767 100644
--- a/js/Util.js
+++ b/js/Util.js
@@ -126,7 +126,8 @@ Util.maybeLoad = function ( dojoXhrArgs, stateObj, successCallback, errorCallbac
             var cbs = stateObj.successCallbacks;
             for (var c = 0; c < cbs.length; c++) cbs[c](o);
         };
-        args.error = function() {
+        args.error = function(error) {
+            console.error(''+error);
             stateObj.state = "error";
             var cbs = stateObj.errorCallbacks;
             for (var c = 0; c < cbs.length; c++) cbs[c]();
@@ -145,10 +146,11 @@ Util.deepUpdate = function(a, b) {
             && ("object" == typeof b[prop])
             && ("object" == typeof a[prop]) ) {
             Util.deepUpdate(a[prop], b[prop]);
-        } else {
+        } else if( typeof a[prop] == 'undefined' || typeof b[prop] != undefined ){
             a[prop] = b[prop];
         }
     }
+    return a;
 };
 
 // from http://bugs.dojotoolkit.org/ticket/5794

From 15d3469d79752a060bf684f1f1c5b83c4b2175bb Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 19:28:25 -0400
Subject: [PATCH 26/49] make load failure in SeqFeatureStore/NCList log errors

---
 js/SeqFeatureStore/NCList.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/SeqFeatureStore/NCList.js b/js/SeqFeatureStore/NCList.js
index 1264c5948d..b350585906 100644
--- a/js/SeqFeatureStore/NCList.js
+++ b/js/SeqFeatureStore/NCList.js
@@ -33,7 +33,7 @@ SeqFeatureStore.NCList.prototype.load = function() {
     dojo.xhrGet({ url: url,
                   handleAs: "json",
                   load:  function(o) { that.loadSuccess(o, url); },
-                  error: function(o) { that.loadFail(o, url);    }
+                  error: function(e) { console.error(''+e); that.loadFail(e, url);    }
 	        });
 };
 

From 030476c34005d11a2ddae2cfd898b75c3d20c34b Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 19:30:23 -0400
Subject: [PATCH 27/49] big commit: add a system of configuration format
 adaptors, and refactor browser initialization code to be more event-based

---
 index.html                     |   3 +-
 js/Browser.js                  | 349 ++++++++++++++++++++-------------
 js/ConfigAdaptor/JB_json_v1.js |  24 +++
 3 files changed, 239 insertions(+), 137 deletions(-)
 create mode 100644 js/ConfigAdaptor/JB_json_v1.js

diff --git a/index.html b/index.html
index d08805e2a1..03647fa8e3 100644
--- a/index.html
+++ b/index.html
@@ -17,6 +17,7 @@
 <!-- the files between the "js_source_files" comments get replaced
      when the JS gets minified (see the minification rule in the Makefile) -->
     <script type="text/javascript" src="js/Browser.js"></script>
+    <script type="text/javascript" src="js/ConfigAdaptor/JB_json_v1.js"></script>
     <script type="text/javascript" src="js/Util.js"></script>
     <script type="text/javascript" src="js/ArrayRepr.js"></script>
     <script type="text/javascript" src="js/NCList.js"></script>
@@ -56,7 +57,7 @@
                                    defaultTracks: "DNA,gene,mRNA,noncodingRNA",
                                    queryParams: queryParams,
                                    location: queryParams.loc,
-                                   tracks: queryParams.tracks,
+                                   forceTracks: queryParams.tracks,
 				   show_nav: queryParams.nav,
 				   show_tracklist: queryParams.tracklist,
 				   show_overview: queryParams.overview
diff --git a/js/Browser.js b/js/Browser.js
index 75a142481a..9b53dde1f1 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -35,24 +35,52 @@ var Browser = function(params) {
 
     this.config = params;
 
-    var browser = this;
-    dojo.addOnLoad( function() { browser.initialize(); } );
-    // TODO: refactor the touch stuff
+    // load our touch device support
+    // TODO: refactor this
     this.deferredFunctions.push(function() { loadTouch(); });
+
+    // schedule the config load, the first step in the initialization
+    // process, to happen when the page is done loading
+    var browser = this;
+    dojo.addOnLoad( function() { browser.loadConfig(); } );
+
+    dojo.connect( this, 'onConfigLoaded',  this, 'loadRefSeqs' );
+    dojo.connect( this, 'onConfigLoaded',  this, 'loadNames'   );
+    dojo.connect( this, 'onRefSeqsLoaded', this, 'initView'   );
+};
+
+Browser.prototype.loadRefSeqs = function() {
+    // load our ref seqs
+    var that = this;
+    if( typeof this.config.refSeqs == 'string' )
+        this.config.refSeqs = { url: this.config.refSeqs };
+    dojo.xhrGet(
+        {
+            url: this.config.refSeqs.url,
+            handleAs: 'json',
+            load: function(o) {
+                that.addRefseqs(o);
+                //that.onRefSeqsLoaded();
+                window.setTimeout(function() { that.onRefSeqsLoaded();},1);
+            }
+        });
 };
 
 /**
- * Does most of the actual initialization work.  Scheduled by
- * constructor, and called after page load.
- * @returns nothing meaningful
+ * Event that fires when the reference sequences have been loaded.
  */
-Browser.prototype.initialize = function() {
-
-    this.loadConfig();
+Browser.prototype.onRefSeqsLoaded = function() {};
 
+/**
+ * Load our name index.
+ */
+Browser.prototype.loadNames = function() {
+    // load our name index
     if (this.config.nameUrl)
         this.names = new LazyTrie(this.config.nameUrl, "lazy-{Chunk}.json");
+};
 
+Browser.prototype.initView = function() {
     //set up top nav/overview pane and main GenomeView pane
     dojo.addClass(document.body, "tundra");
     this.container = dojo.byId(this.config.containerID);
@@ -67,8 +95,6 @@ Browser.prototype.initialize = function() {
     if( this.config.show_overview == 0 ) overview.style.cssText = "display: none";
     topPane.appendChild(overview);
 
-    //try to come up with a good estimate of how big the location box
-    //actually has to be
     this.navbox = this.createNavBox( topPane, 25 );
 
     var viewElem = document.createElement("div");
@@ -96,20 +122,62 @@ Browser.prototype.initialize = function() {
     //    from a param passed to our instance, or from a cookie, or
     //    the passed defaults, or the last-resort default of "DNA"?
     this.origTracklist =
-           this.config.tracks
+           this.config.forceTracks
         || dojo.cookie( this.container.id + "-tracks" )
         || this.config.defaultTracks
         || "DNA";
 
+    // hook up GenomeView
+    this.view = this.viewElem.view =
+        new GenomeView(this.viewElem, 250, this.refSeq, 1/200,
+                       this.config.browserRoot);
+    dojo.connect( this.view, "onFineMove",   this, "onFineMove"   );
+    dojo.connect( this.view, "onCoarseMove", this, "onCoarseMove" );
 
-    // load our ref seqs
-    var brwsr = this;
-    if( typeof this.config.refSeqs == 'string' )
-        this.config.refSeqs = { url: this.config.refSeqs };
-    Util.maybeLoad({ url: this.config.refSeqs.url, handleAs: 'json'}, this.config.refSeqs,
-                   function(o) {
-                       brwsr.addRefseqs(o);
-                   });
+    //set up track list
+    var trackListDiv = this.createTrackList( this.container );
+    this.containerWidget.startup();
+    dojo.connect( this.browserWidget, "resize", this, 'onResize' );
+    this.onResize();
+
+    //set initial location
+    var oldLocMap = dojo.fromJson(dojo.cookie(this.container.id + "-location")) || {};
+    if (this.config.location) {
+        this.navigateTo(this.config.location);
+    } else if (oldLocMap[this.refSeq.name]) {
+        this.navigateTo( oldLocMap[this.refSeq.name] );
+    } else if (this.config.defaultLocation){
+        this.navigateTo(this.config.defaultLocation);
+    } else {
+        this.navigateTo( Util.assembleLocString({
+                             ref:   this.refSeq.name,
+                             start: 0.4 * ( this.refSeq.start + this.refSeq.end ),
+                             end:   0.6 * ( this.refSeq.start + this.refSeq.end )
+                         })
+                       );
+    }
+
+    dojo.connect(this.chromList, "onchange", this, function(event) {
+        var newRef = this.allRefs[this.chromList.options[this.chromList.selectedIndex].value];
+        this.navigateTo( newRef.name );
+    });
+
+    this.isInitialized = true;
+
+    //if someone calls methods on this browser object
+    //before it's fully initialized, then we defer
+    //those functions until now
+    for (var i = 0; i < this.deferredFunctions.length; i++)
+        this.deferredFunctions[i]();
+    this.deferredFunctions = [];
+};
+
+Browser.prototype.onResize = function() {
+    this.view.sizeInit();
+    this.view.locationTrapHeight = dojo.marginBox( this.navbox ).h;
+    this.view.showVisibleBlocks();
+    this.view.showFine();
+    this.view.showCoarse();
 };
 
 /**
@@ -119,146 +187,133 @@ Browser.prototype.initialize = function() {
  *  @returns nothing meaningful
  */
 Browser.prototype.loadConfig = function () {
-    var brwsr = this;
+    var that = this;
 
-    // load any configuration files we've been passed
+    // coerce configFile to an array
     if( typeof this.config.configFile != 'object' || !this.config.configFile.length )
         this.config.configFile = [ this.config.configFile ];
 
+    // coerce bare strings in the configs to URLs
     for (var i = 0; i < this.config.configFile.length; i++) {
         if( typeof this.config.configFile[i] == 'string' )
             this.config.configFile[i] = { url: this.config.configFile[i] };
-
-        (function(config) {
-             Util.maybeLoad(
-                 {
-                     url: config.url,
-                     handleAs: 'json'
-                 },
-                 config,
-                 function(o) {
-                     brwsr.addDeferred(
-                         function() {
-                             brwsr.addConfigData( o, { sourceUrl: config.url });
-                         });
-                 });
-         })(this.config.configFile[i]);
     }
-};
 
-/**
- * Add a function to be executed once JBrowse is initialized
- * @param f function to be executed
- */
-Browser.prototype.addDeferred = function(f) {
-    if (this.isInitialized)
-        f();
-    else
-        this.deferredFunctions.push(f);
-};
+    // fetch and parse all the configuration data
+    var configs_remaining = this.config.configFile.length;
+    dojo.forEach( this.config.configFile, function(config) {
 
-Browser.prototype.addConfigData = function( newconfig, additional ) {
+        // set defaults for format and version
+        if( !config.format ) config.format = 'JB_json';
+        if( typeof config.version == 'undefined' ) config.version = 1;
 
-    newconfig = dojo.clone(newconfig);
-
-    // add any additional data to the conf that's coming in
-    Util.deepUpdate( newconfig, additional );
-
-    // make a default baseUrl if one is not already set
-    if( !newconfig.baseUrl ) {
-        newconfig.baseUrl = Util.resolveUrl( newconfig.sourceUrl, '.' );
-    }
-    if( ! /\/$/.test( newconfig.baseUrl ) )
-        newconfig.baseUrl += "/";
+        // instantiate the adaptor and load the config
+        var adaptor = this.getConfigAdaptor( config );
+        if( !adaptor ) {
+            console.log( "WARNING: could not load config: " );
+            console.log( config );
+            return;
+        }
 
-    // and now add that to our overall config
-    Util.deepUpdate( this.config, newconfig );
+        adaptor.load({
+            config: config,
+            context: this,
+            onSuccess: function( config_data, request_info ) {
+                config.data = config_data;
+                config.loaded = true;
+                if( ! --configs_remaining )
+                    this.onConfigLoaded();
+                    //if you need a backtrace: window.setTimeout( function() { that.onConfigLoaded(); }, 1 );
+            },
+            onFailure: function( request_info ) {
+                config.loaded = false;
+                if( ! --configs_remaining )
+                    this.onConfigLoaded();
+                    //if you need a backtrace: window.setTimeout( function() { that.onConfigLoaded(); }, 1 );
+            }
+        });
 
-    if( this.config.tracks ) {
-        if( this.config.sourceUrl ) {
-            for (var i = 0; i < this.config.tracks.length; i++)
-                if( ! this.config.tracks[i].baseUrl )
-                    this.config.tracks[i].baseUrl = this.config.baseUrl;
-        }
-        this.trackListWidget.insertNodes(false, this.config.tracks);
-        this.showTracks(this.origTracklist);
-    }
+    }, this);
 };
 
-Browser.prototype.addRefseqs = function(refSeqs) {
-    //currently only meant to be called once
+Browser.prototype.onConfigLoaded = function() {
 
-    this.allRefs = {};
-    for (var i = 0; i < refSeqs.length; i++)
-        this.allRefs[refSeqs[i].name] = refSeqs[i];
+    var initial_config = this.config;
+    this.config = {};
 
-    var refCookie = dojo.cookie(this.config.containerID + "-refseq");
-    this.refSeq = refSeqs[0];
-    for (var i = 0; i < refSeqs.length; i++) {
-        this.chromList.options[i] = new Option(refSeqs[i].name,
-                                               refSeqs[i].name);
-        if (refSeqs[i].name.toUpperCase() == String(refCookie).toUpperCase()) {
-            this.refSeq = this.allRefs[refSeqs[i].name];
-            this.chromList.selectedIndex = i;
-        }
-    }
+    // load all the configuration data in order
+    dojo.forEach( initial_config.configFile, function( config ) {
+                      if( config.loaded && config.data )
+                          this.addConfigData( config.data );
+                  }, this );
 
-    //hook up GenomeView
-    var gv = new GenomeView(this.viewElem, 250, this.refSeq, 1/200,
-                            this.config.browserRoot);
-    this.view = gv;
-    //gv.setY(0);
-    this.viewElem.view = gv;
+    // load the initial config (i.e. constructor params) last so that
+    // it overrides the other config
+    this.addConfigData( initial_config );
 
-    //set up track list
-    var trackListDiv = this.createTrackList( this.container );
-    this.containerWidget.startup();
+    this.validateConfig();
+};
 
-    var brwsr = this;
-    this.resizeCallback = function() {
-        gv.sizeInit();
+/**
+ * Examine the loaded and merged configuration for errors.  Throws
+ * exceptions if it finds anything amiss.
+ * @returns nothing meaningful
+ */
+Browser.prototype.validateConfig = function() {
+    var c = this.config;
+    if( ! c.baseUrl ) {
+        throw "Must provide a baseUrl in config.";
+    }
+};
 
-        brwsr.view.locationTrapHeight = dojo.marginBox(brwsr.navbox).h;
-        gv.showVisibleBlocks();
-        gv.showFine();
-        gv.showCoarse();
-    };
-    dojo.connect(this.browserWidget, "resize", this.resizeCallback);
-    this.resizeCallback();
+/**
+ * Instantiate the right config adaptor for a given configuration source.
+ * @param {Object} config the configuraiton
+ * @returns {Object} the right configuration adaptor to use, or
+ * undefined if one could not be found
+ */
 
-    dojo.connect(gv, "onFineMove", brwsr, "onFineMove");
-    dojo.connect(gv, "onCoarseMove", brwsr, "onCoarseMove");
+Browser.prototype.getConfigAdaptor = function( config_def ) {
+    var adaptor_name = "ConfigAdaptor." + config_def.format;
+    if( config_def.version )
+        adaptor_name += '_v'+config_def.version;
+    adaptor_name.replace( /\W/g,'' );
+    var adaptor_class = eval( adaptor_name );
+    if( ! adaptor_class )
+        return undefined;
 
-    //set initial location
-    var oldLocMap = dojo.fromJson(dojo.cookie(brwsr.container.id + "-location")) || {};
-    if (this.config.location) {
-        this.navigateTo(this.config.location);
-    } else if (oldLocMap[this.refSeq.name]) {
-        this.navigateTo( oldLocMap[this.refSeq.name] );
-    } else if (this.config.defaultLocation){
-        this.navigateTo(this.config.defaultLocation);
-    } else {
-        this.navigateTo( Util.assembleLocString({
-                             ref:   this.refSeq.name,
-                             start: 0.4 * ( this.refSeq.start + this.refSeq.end ),
-                             end:   0.6 * ( this.refSeq.start + this.refSeq.end )
-                         })
-                       );
-    }
+    return new adaptor_class( config_def );
+};
 
-    dojo.connect(this.chromList, "onchange", function(event) {
-        var newRef = brwsr.allRefs[brwsr.chromList.options[brwsr.chromList.selectedIndex].value];
-        brwsr.navigateTo( newRef.name );
-    });
+/**
+ * Add a function to be executed once JBrowse is initialized
+ * @param f function to be executed
+ */
+Browser.prototype.addDeferred = function(f) {
+    if (this.isInitialized)
+        f();
+    else
+        this.deferredFunctions.push(f);
+};
 
-    this.isInitialized = true;
+/**
+ * Merge in some additional configuration data.  Properties in the
+ * passed configuration will override those properties in the existing
+ * configuration.
+ */
+Browser.prototype.addConfigData = function( /**Object*/ config_data ) {
+    Util.deepUpdate( this.config, config_data );
+};
 
-    //if someone calls methods on this browser object
-    //before it's fully initialized, then we defer
-    //those functions until now
-    for (var i = 0; i < brwsr.deferredFunctions.length; i++)
-        brwsr.deferredFunctions[i]();
-    brwsr.deferredFunctions = [];
+/**
+ * @param refSeqs {Array} array of refseq records to add to the browser
+ */
+Browser.prototype.addRefseqs = function( refSeqs ) {
+    this.allRefs = this.allRefs || {};
+    this.refSeq  = this.refSeq  || refSeqs[0];
+    dojo.forEach( refSeqs, function(r) {
+        this.allRefs[r.name] = r;
+    },this);
 };
 
 /**
@@ -343,6 +398,17 @@ Browser.prototype.createTrackList = function( /**Element*/ parent ) {
                                                 accept: ["track"], // accepts tracks into left div
                                                 withHandles: false});
 
+    // instantiate our track objects
+    if( this.config.tracks ) {
+        if( this.config.sourceUrl ) {
+            for (var i = 0; i < this.config.tracks.length; i++)
+                if( ! this.config.tracks[i].baseUrl )
+                    this.config.tracks[i].baseUrl = this.config.baseUrl;
+        }
+        this.trackListWidget.insertNodes(false, this.config.tracks);
+        this.showTracks(this.origTracklist);
+    }
+
     var trackCreate = /**@inner*/ function( trackConfig, hint) {
         var node;
         if ("avatar" == hint) {
@@ -633,8 +699,8 @@ Browser.prototype.makeBookmarkLink = function (area) {
     var update_bookmark = function() {
         this.link.href = this.config.bookmark.call( this, this );
     };
-    dojo.connect( this, "onCoarseMove",           update_bookmark, this );
-    dojo.connect( this, "onVisibleTracksChanged", update_bookmark, this );
+    dojo.connect( this, "onCoarseMove",           update_bookmark );
+    dojo.connect( this, "onVisibleTracksChanged", update_bookmark );
 
 };
 
@@ -773,6 +839,17 @@ Browser.prototype.createNavBox = function( parent, locLength ) {
 
     this.chromList = document.createElement("select");
     this.chromList.id="chrom";
+    var refCookie = dojo.cookie(this.config.containerID + "-refseq");
+    var i = 0;
+    for ( var name in this.allRefs ) {
+        this.chromList.add( new Option( name, name), null );
+        if ( name.toUpperCase() == String(refCookie).toUpperCase()) {
+            this.refSeq = this.allRefs[name];
+            this.chromList.selectedIndex = i;
+        }
+        i++;
+    }
+
     this.locationBox = document.createElement("input");
     this.locationBox.size=locLength;
     this.locationBox.type="text";
diff --git a/js/ConfigAdaptor/JB_json_v1.js b/js/ConfigAdaptor/JB_json_v1.js
new file mode 100644
index 0000000000..03bde95db4
--- /dev/null
+++ b/js/ConfigAdaptor/JB_json_v1.js
@@ -0,0 +1,24 @@
+var ConfigAdaptor; if( !ConfigAdaptor ) ConfigAdaptor = {};
+ConfigAdaptor.JB_json_v1 = function() {
+};
+
+ConfigAdaptor.JB_json_v1.prototype.load = function( args ) {
+    var config_def = args.config;
+    dojo.xhrGet({
+        url: config_def.url,
+        handleAs: 'json',
+        load: function( o ) {
+            o.sourceUrl = o.sourceUrl || config_def.url;
+            o.baseUrl   = o.baseUrl || Util.resolveUrl( o.sourceUrl, '.' );
+            if( ! /\/$/.test( o.baseUrl ) )
+                o.baseUrl += "/";
+
+            args.onSuccess.call( args.context || this, o );
+        },
+        error: function( i ) {
+            console.error( ''+i );
+            if( args.onFailure )
+                args.onFailure.call( args.context || this, i);
+        }
+    });
+};

From d8a4d97f97d744be695c911cd16a94b2c95ac76d Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Tue, 13 Mar 2012 20:01:43 -0400
Subject: [PATCH 28/49] allow .5 seconds for all elements to be created before
 running selenium tests

---
 tests/selenium_tests/jbrowse_selenium.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/selenium_tests/jbrowse_selenium.py b/tests/selenium_tests/jbrowse_selenium.py
index 6611a82021..495c18a134 100644
--- a/tests/selenium_tests/jbrowse_selenium.py
+++ b/tests/selenium_tests/jbrowse_selenium.py
@@ -22,6 +22,7 @@ def setUp( self ):
             self.base_url
             + ( "?data="+self.data_dir if self.data_dir else "" )
         )
+        time.sleep(0.5)
 
     ## convenience methods for us
 

From 792b4a7df99b23056c528754329833acce9850b1 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 08:22:44 -0400
Subject: [PATCH 29/49] rename the `configFile` conf variable to `include`

---
 index.html    |  2 +-
 js/Browser.js | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/index.html b/index.html
index 03647fa8e3..53f2e68e7d 100644
--- a/index.html
+++ b/index.html
@@ -50,7 +50,7 @@
            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: dataRoot + "/seq/refSeqs.json",
-                                   configFile: [
+                                   include: [
                                      dataRoot + "/trackList.json",
                                    ],
                                    nameUrl: dataRoot + "/names/root.json",
diff --git a/js/Browser.js b/js/Browser.js
index 9b53dde1f1..7726c9f477 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -189,19 +189,19 @@ Browser.prototype.onResize = function() {
 Browser.prototype.loadConfig = function () {
     var that = this;
 
-    // coerce configFile to an array
-    if( typeof this.config.configFile != 'object' || !this.config.configFile.length )
-        this.config.configFile = [ this.config.configFile ];
+    // coerce include to an array
+    if( typeof this.config.include != 'object' || !this.config.include.length )
+        this.config.include = [ this.config.include ];
 
     // coerce bare strings in the configs to URLs
-    for (var i = 0; i < this.config.configFile.length; i++) {
-        if( typeof this.config.configFile[i] == 'string' )
-            this.config.configFile[i] = { url: this.config.configFile[i] };
+    for (var i = 0; i < this.config.include.length; i++) {
+        if( typeof this.config.include[i] == 'string' )
+            this.config.include[i] = { url: this.config.include[i] };
     }
 
     // fetch and parse all the configuration data
-    var configs_remaining = this.config.configFile.length;
-    dojo.forEach( this.config.configFile, function(config) {
+    var configs_remaining = this.config.include.length;
+    dojo.forEach( this.config.include, function(config) {
 
         // set defaults for format and version
         if( !config.format ) config.format = 'JB_json';
@@ -242,7 +242,7 @@ Browser.prototype.onConfigLoaded = function() {
     this.config = {};
 
     // load all the configuration data in order
-    dojo.forEach( initial_config.configFile, function( config ) {
+    dojo.forEach( initial_config.include, function( config ) {
                       if( config.loaded && config.data )
                           this.addConfigData( config.data );
                   }, this );

From 6654bc680961a6c0cdb1274848ccf5d620e75141 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 08:23:14 -0400
Subject: [PATCH 30/49] refactor JB_json_v1 conf adaptor to be extendible

---
 js/ConfigAdaptor/JB_json_v1.js | 48 ++++++++++++++++++++++++++++------
 1 file changed, 40 insertions(+), 8 deletions(-)

diff --git a/js/ConfigAdaptor/JB_json_v1.js b/js/ConfigAdaptor/JB_json_v1.js
index 03bde95db4..7d3180d1a2 100644
--- a/js/ConfigAdaptor/JB_json_v1.js
+++ b/js/ConfigAdaptor/JB_json_v1.js
@@ -1,18 +1,21 @@
 var ConfigAdaptor; if( !ConfigAdaptor ) ConfigAdaptor = {};
+
+/**
+ * Configuration adaptor for JBrowse JSON version 1 configuration
+ * files (formerly known as trackList.json files).
+ * @class
+ */
 ConfigAdaptor.JB_json_v1 = function() {
 };
 
 ConfigAdaptor.JB_json_v1.prototype.load = function( args ) {
-    var config_def = args.config;
+    var that = this;
     dojo.xhrGet({
-        url: config_def.url,
-        handleAs: 'json',
+        url: args.config.url,
+        handleAs: 'text',
         load: function( o ) {
-            o.sourceUrl = o.sourceUrl || config_def.url;
-            o.baseUrl   = o.baseUrl || Util.resolveUrl( o.sourceUrl, '.' );
-            if( ! /\/$/.test( o.baseUrl ) )
-                o.baseUrl += "/";
-
+            o = that.parse_conf( o, args );
+            o = that.regularize_conf( o, args );
             args.onSuccess.call( args.context || this, o );
         },
         error: function( i ) {
@@ -22,3 +25,32 @@ ConfigAdaptor.JB_json_v1.prototype.load = function( args ) {
         }
     });
 };
+
+/**
+ * In this adaptor, just evals the conf text to parse the JSON, but
+ * other conf adaptors might want to inherit and override this.
+ * @param {String} conf_text the configuration text
+ * @param {Object} load_args the arguments that were passed to <code>load()</code>
+ * @returns {Object} the parsed JSON
+ */
+ConfigAdaptor.JB_json_v1.prototype.parse_conf = function( conf_text, load_args ) {
+    var conf;
+    return eval( 'conf = ' + conf_text );
+};
+
+/**
+ * Applies defaults and any other necessary tweaks to the loaded JSON
+ * configuration.  Called by <code>load()</code> on the JSON
+ * configuration before it calls the <code>onSuccess</code> callback.
+ * @param {Object} o the object containing the configuration, which it
+ *                   modifies in-place
+ * @param {Object} load_args the arguments that were passed to <code>load()</code>
+ * @returns the same object it was passed
+ */
+ConfigAdaptor.JB_json_v1.prototype.regularize_conf = function( o, load_args ) {
+    o.sourceUrl = o.sourceUrl || load_args.config.url;
+    o.baseUrl   = o.baseUrl || Util.resolveUrl( o.sourceUrl, '.' );
+    if( ! /\/$/.test( o.baseUrl ) )
+        o.baseUrl += "/";
+    return o;
+};

From 942a51ff75fe5ae23fcbca78a847a7f6f966d099 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 08:45:20 -0400
Subject: [PATCH 31/49] tweak adaptor-not-found failure messages

---
 js/Browser.js | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index 7726c9f477..028cccec38 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -210,8 +210,7 @@ Browser.prototype.loadConfig = function () {
         // instantiate the adaptor and load the config
         var adaptor = this.getConfigAdaptor( config );
         if( !adaptor ) {
-            console.log( "WARNING: could not load config: " );
-            console.log( config );
+            console.error( "Could not load config "+config.url+", no configuration adaptor found for config format "+config.format+' version '+config.version );
             return;
         }
 

From 88a9f966d6d0b0817cd58ab5d2ccbbdde8784c1c Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 09:14:57 -0400
Subject: [PATCH 32/49] add a function to Util for wrapping handlers to give
 better stack traces

---
 js/Util.js | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/js/Util.js b/js/Util.js
index e555675767..6e2a6c6912 100644
--- a/js/Util.js
+++ b/js/Util.js
@@ -260,6 +260,19 @@ Util.matchRefSeqName = function( name, refseqs ) {
     return null;
 };
 
+/**
+ * Wrap a handler function to be called 1ms later in a window timeout.
+ * This will usually give a better stack trace for figuring out where
+ * errors are happening.
+ */
+Util.debugHandler = function( context, func ) {
+    var debuggedHandler = function() {
+        var args = arguments;
+        window.setTimeout( function() { func.apply(context,args);}, 1);
+    };
+    return debuggedHandler;
+};
+
 if (!Array.prototype.reduce)
 {
   Array.prototype.reduce = function(fun /*, initial*/)

From eaad5bea7c5fd9e65948cf30aaf23dd74c2cf97f Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 09:23:39 -0400
Subject: [PATCH 33/49] add bam_simulated to the volvox_1_2_1 test data set

---
 .../data/volvox_formatted_1_2_1/trackInfo.js  | 30 +++++++++++--------
 .../tracks/ctgA/bam_simulated/hist-100-0.json |  1 +
 .../ctgA/bam_simulated/hist-1000-0.json       |  1 +
 .../tracks/ctgA/bam_simulated/hist-20-0.json  |  1 +
 .../tracks/ctgA/bam_simulated/hist-200-0.json |  1 +
 .../tracks/ctgA/bam_simulated/hist-40-0.json  |  1 +
 .../tracks/ctgA/bam_simulated/hist-400-0.json |  1 +
 .../ctgA/bam_simulated/lazyfeatures-0.json    |  1 +
 .../ctgA/bam_simulated/lazyfeatures-1.json    |  1 +
 .../ctgA/bam_simulated/lazyfeatures-2.json    |  1 +
 .../ctgA/bam_simulated/lazyfeatures-3.json    |  1 +
 .../tracks/ctgA/bam_simulated/trackData.json  |  1 +
 12 files changed, 29 insertions(+), 12 deletions(-)
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-100-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-1000-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-20-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-200-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-40-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-400-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-0.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-1.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-2.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-3.json
 create mode 100644 tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/trackData.json

diff --git a/tests/data/volvox_formatted_1_2_1/trackInfo.js b/tests/data/volvox_formatted_1_2_1/trackInfo.js
index e2f4d85762..bcdd9e5b7d 100644
--- a/tests/data/volvox_formatted_1_2_1/trackInfo.js
+++ b/tests/data/volvox_formatted_1_2_1/trackInfo.js
@@ -1,74 +1,80 @@
 trackInfo = 
 [
    {
-      "url" : "seq/{refseq}/",
       "args" : {
          "chunkSize" : 20000
       },
-      "label" : "DNA",
+      "url" : "seq/{refseq}/",
       "type" : "SequenceTrack",
+      "label" : "DNA",
       "key" : "DNA"
    },
    {
       "url" : "tracks/{refseq}/ExampleFeatures/trackData.json",
-      "type" : "FeatureTrack",
       "label" : "ExampleFeatures",
+      "type" : "FeatureTrack",
       "key" : "Example Features"
    },
    {
       "url" : "tracks/{refseq}/NameTest/trackData.json",
-      "label" : "NameTest",
       "type" : "FeatureTrack",
+      "label" : "NameTest",
       "key" : "Name test track"
    },
    {
       "url" : "tracks/{refseq}/Motifs/trackData.json",
-      "type" : "FeatureTrack",
       "label" : "Motifs",
+      "type" : "FeatureTrack",
       "key" : "Example motifs"
    },
    {
       "url" : "tracks/{refseq}/Alignments/trackData.json",
-      "label" : "Alignments",
       "type" : "FeatureTrack",
+      "label" : "Alignments",
       "key" : "Example alignments"
    },
    {
       "url" : "tracks/{refseq}/Genes/trackData.json",
-      "type" : "FeatureTrack",
       "label" : "Genes",
+      "type" : "FeatureTrack",
       "key" : "Protein-coding genes"
    },
    {
       "url" : "tracks/{refseq}/ReadingFrame/trackData.json",
-      "label" : "ReadingFrame",
       "type" : "FeatureTrack",
+      "label" : "ReadingFrame",
       "key" : "Frame usage"
    },
    {
       "url" : "tracks/{refseq}/CDS/trackData.json",
-      "type" : "FeatureTrack",
       "label" : "CDS",
+      "type" : "FeatureTrack",
       "key" : "Predicted genes"
    },
    {
       "url" : "tracks/{refseq}/Transcript/trackData.json",
-      "label" : "Transcript",
       "type" : "FeatureTrack",
+      "label" : "Transcript",
       "key" : "Exonerate predictions"
    },
    {
       "url" : "tracks/{refseq}/Clones/trackData.json",
-      "type" : "FeatureTrack",
       "label" : "Clones",
+      "type" : "FeatureTrack",
       "key" : "Fingerprinted BACs"
    },
    {
       "url" : "tracks/{refseq}/EST/trackData.json",
-      "label" : "EST",
       "type" : "FeatureTrack",
+      "label" : "EST",
       "key" : "ESTs"
    },
+   {
+      "url" : "tracks/{refseq}/bam_simulated/trackData.json",
+      "label" : "bam_simulated",
+      "type" : "FeatureTrack",
+      "key" : "Simulated next-gen reads"
+   },
    {
       "url" : "tracks/{refseq}/volvox_microarray.wig.json",
       "type" : "ImageTrack",
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-100-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-100-0.json
new file mode 100644
index 0000000000..e124da4ac7
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-100-0.json
@@ -0,0 +1 @@
+[13,22,12,13,22,31,33,28,33,38,41,38,26,33,44,40,42,54,38,36,49,50,51,39,37,39,41,41,22,29,42,39,35,38,40,37,45,39,34,37,46,48,42,37,36,31,30,39,52,46,41,43,35,34,37,31,31,41,38,32,38,40,36,31,31,39,42,39,33,38,40,36,38,38,39,45,44,37,37,36,33,37,39,36,38,40,46,39,39,43,35,37,36,38,45,45,34,31,40,42,38,31,38,47,48,38,42,46,34,40,35,31,38,38,42,41,37,35,39,41,42,41,34,46,50,46,41,41,50,47,51,52,40,38,44,43,37,38,40,52,49,35,35,31,39,44,42,43,45,43,33,43,46,38,33,33,34,31,38,27,30,41,40,38,38,43,45,46,40,31,36,39,38,35,28,28,42,45,30,27,34,40,49,44,35,40,40,41,51,42,32,33,30,31,32,36,44,35,34,39,35,41,49,45,32,32,36,40,39,37,34,37,40,37,38,36,33,34,38,34,32,35,38,44,42,37,52,71,53,44,46,38,43,50,51,46,40,36,34,39,40,36,44,50,53,53,43,41,46,41,46,45,36,28,38,49,43,36,36,41,40,37,35,35,40,36,34,34,31,31,39,50,44,30,31,39,44,49,48,39,32,36,37,34,41,46,39,35,31,31,35,38,41,38,38,46,50,40,33,36,36,32,32,42,45,37,37,39,34,38,44,42,44,45,43,41,43,41,43,38,32,36,33,33,36,30,33,28,18,33,40,34,25,27,32,35,51,53,52,41,28,35,32,48,49,29,23,31,37,45,49,47,42,35,30,38,43,34,33,34,41,43,44,49,40,37,38,31,36,37,36,36,36,34,29,31,42,46,41,42,34,28,34,34,27,30,33,38,45,42,39,37,33,35,33,30,32,40,48,48,36,35,37,42,38,46,53,43,44,38,34,33,27,35,41,38,49,50,37,32,42,45,46,48,43,49,44,37,43,37,34,34,36,43,48,41,35,37,39,48,45,30,32,39,44,45,42,41,32,47,50,31,39,47,41,28,31,39,35,37,36,37,43,42,44,42,43,46,48,45,43,37,30,46,57,45,35,37,43,42,46,43,39,39,37,42,37,32,38,45,40,37,48,41,38,35,19,15,20,11,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-1000-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-1000-0.json
new file mode 100644
index 0000000000..999a2cf7ab
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-1000-0.json
@@ -0,0 +1 @@
+[131,217,223,214,220,197,202,215,211,211,224,210,239,244,229,191,208,190,224,189,210,197,243,236,243,220,194,221,197,215,207,230,172,209,196,214,214,203,191,208,223,204,232,217,228,215,233,229,221,164,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-20-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-20-0.json
new file mode 100644
index 0000000000..5f5d6714a5
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-20-0.json
@@ -0,0 +1 @@
+[5,5,9,11,13,14,12,16,12,11,9,9,7,3,4,6,10,10,9,11,12,12,9,10,14,15,12,12,21,22,22,24,25,26,19,17,18,15,17,16,16,17,18,23,22,22,21,24,23,20,24,27,31,26,27,29,25,21,17,20,19,16,14,14,17,19,16,16,21,24,29,29,29,31,27,29,25,22,21,19,19,19,18,22,26,27,34,34,36,36,31,31,25,21,16,15,19,22,24,28,31,29,30,27,27,28,33,33,31,33,36,35,28,28,26,23,20,16,20,20,19,24,25,27,24,24,28,23,21,22,25,27,23,24,28,27,25,21,21,24,20,17,13,10,9,8,12,15,22,26,28,29,27,25,22,26,27,24,23,25,27,20,19,18,17,17,18,22,24,26,27,26,25,22,19,20,23,25,23,23,23,22,23,25,28,25,27,28,25,24,17,20,21,20,22,21,27,27,26,25,22,25,23,21,28,29,27,32,29,31,24,24,27,23,26,20,21,24,26,22,20,27,25,22,22,20,21,16,19,17,18,19,19,20,18,20,23,24,24,24,24,28,26,28,34,32,32,30,27,25,18,22,25,23,30,29,33,27,26,28,22,21,18,22,20,18,22,19,20,22,24,24,24,24,24,23,20,21,16,14,19,19,20,19,20,20,20,22,21,25,25,29,27,23,22,19,18,17,14,18,20,24,25,29,27,24,25,21,24,20,20,20,18,21,20,21,23,21,21,20,18,18,20,22,21,25,23,24,23,22,26,25,23,26,24,26,24,23,25,20,24,23,20,20,18,21,18,20,26,25,24,20,23,20,19,20,21,22,23,25,23,20,22,23,24,26,24,30,28,26,20,19,23,21,22,25,31,31,29,28,28,27,23,24,22,26,28,24,24,21,24,18,19,22,22,22,22,23,19,20,19,20,20,20,21,22,21,22,23,22,26,25,29,24,21,22,20,20,18,20,24,24,27,23,24,24,22,26,22,24,27,29,30,27,29,28,22,20,19,17,18,22,25,28,28,27,27,23,21,22,20,21,19,21,24,19,25,26,27,25,23,24,21,19,19,21,22,25,22,25,26,24,26,28,28,30,32,29,25,25,26,21,18,18,18,15,15,17,19,22,24,26,25,22,25,28,27,26,24,28,26,18,20,20,21,18,19,21,16,18,19,16,17,24,28,29,29,33,33,28,26,25,28,30,28,27,27,25,23,19,23,24,27,27,31,30,27,24,24,25,20,19,22,20,21,20,23,27,26,29,31,28,24,21,15,17,14,18,18,21,20,19,18,16,22,21,26,26,25,27,22,25,23,25,27,27,30,31,29,24,21,22,21,19,19,21,25,20,21,20,22,22,20,21,25,25,23,25,23,27,21,24,27,27,29,32,33,29,24,22,19,12,12,17,19,21,27,31,34,32,32,29,28,29,26,26,30,32,31,29,28,24,22,22,23,23,24,25,29,29,29,23,29,32,30,31,30,33,29,27,32,33,32,32,33,34,35,28,30,29,31,26,18,20,19,20,20,26,25,26,24,22,24,25,26,25,24,29,30,23,22,21,22,23,17,19,23,24,28,27,26,28,28,26,24,25,25,28,29,36,38,34,33,27,25,19,17,20,21,22,24,24,25,21,20,19,20,16,17,18,23,25,24,26,26,26,26,25,26,26,22,24,21,24,25,29,32,32,30,25,25,22,22,31,26,28,28,30,27,23,22,20,19,17,17,17,20,24,30,32,33,33,30,28,23,21,24,22,26,25,23,21,19,20,15,15,18,20,24,23,22,21,22,21,16,17,20,21,20,21,24,21,22,24,22,22,19,17,12,10,11,12,12,19,24,25,27,23,27,26,23,21,21,28,26,21,21,25,26,21,23,27,25,21,26,25,24,22,28,30,27,26,25,30,27,29,30,31,33,27,27,25,24,19,17,18,19,17,17,19,20,24,27,24,24,24,24,23,20,21,23,21,21,20,22,23,25,26,24,20,21,18,17,13,13,17,15,19,18,18,21,18,19,23,26,26,24,29,30,25,20,24,23,18,16,11,14,14,18,20,22,25,23,21,20,21,18,24,26,27,30,31,33,28,30,30,26,23,23,24,20,22,22,22,22,21,22,23,23,27,27,25,27,23,24,23,23,27,27,28,28,27,30,28,31,30,31,29,22,23,20,19,16,16,20,20,22,21,22,20,19,20,15,17,16,19,21,21,20,20,23,20,17,16,17,20,18,20,21,25,26,24,25,27,28,28,26,21,18,18,16,15,20,24,25,25,27,27,23,21,22,20,24,21,18,22,25,27,24,24,28,27,26,30,29,28,27,31,26,23,21,19,18,15,17,18,18,17,20,21,22,20,20,22,25,24,19,23,22,28,24,21,24,23,27,21,21,22,23,25,21,20,25,23,21,20,22,21,19,24,27,25,26,26,24,19,19,22,23,23,25,26,28,24,21,21,19,22,19,19,20,18,22,15,18,19,22,22,24,25,22,20,20,24,23,20,19,24,21,19,16,20,23,18,20,23,26,25,20,22,24,24,24,22,24,24,23,22,20,27,27,27,26,23,26,23,24,24,26,23,22,27,31,35,36,41,44,41,39,41,40,41,34,32,26,24,23,24,28,27,30,28,29,24,23,22,23,23,22,23,24,27,29,28,28,32,30,28,28,29,30,31,32,32,30,30,29,28,24,25,23,23,22,22,24,22,23,25,24,21,20,20,21,17,20,20,23,24,23,27,24,23,21,24,25,20,20,22,24,23,25,26,26,25,29,32,30,31,34,35,29,31,30,29,31,31,34,32,34,33,32,30,28,25,22,19,16,22,23,25,30,30,31,26,28,24,25,28,25,26,27,25,26,24,29,26,26,26,25,28,23,27,26,25,23,18,17,15,15,15,21,20,22,26,29,29,25,31,29,28,24,23,23,22,26,23,25,27,28,23,22,23,23,23,22,26,25,26,25,25,23,24,22,20,22,20,25,22,20,22,21,24,19,22,22,19,19,24,24,21,24,27,28,25,24,25,22,19,22,19,20,24,23,23,19,23,22,19,18,17,19,18,17,15,17,18,15,17,18,20,19,22,28,26,29,28,33,32,27,30,33,32,30,28,25,23,16,16,11,11,11,13,18,18,24,26,28,26,23,26,24,21,25,25,28,28,30,31,31,31,31,30,28,30,28,27,23,23,21,21,21,19,18,20,22,25,20,19,25,23,23,19,23,26,20,21,20,20,18,17,20,19,25,29,28,28,30,34,25,25,24,29,24,23,24,21,19,17,19,19,19,19,19,18,18,16,18,21,21,22,24,25,22,22,22,23,21,19,24,22,28,24,24,28,24,21,19,20,22,19,22,25,24,25,23,28,24,26,28,29,30,28,37,32,32,27,24,25,17,19,17,16,18,18,21,20,23,26,27,24,23,23,22,19,20,18,17,14,16,20,17,18,18,22,22,18,24,29,32,31,30,32,28,25,24,21,20,21,22,23,20,20,20,23,25,22,21,23,24,24,23,24,24,23,22,22,21,21,26,26,29,26,23,28,24,23,23,23,28,26,24,29,27,31,28,26,30,28,32,24,28,28,26,25,23,27,22,26,27,24,23,25,28,24,24,27,29,27,26,23,23,21,24,24,26,27,24,26,20,20,18,23,25,21,22,21,20,18,20,20,19,21,21,20,17,19,23,22,21,19,21,22,19,23,21,20,16,17,17,14,16,22,27,22,24,23,20,16,9,11,7,10,13,13,14,19,18,17,17,21,20,22,24,28,27,23,26,23,21,16,16,15,14,13,13,14,13,13,16,18,21,21,21,22,22,21,20,19,23,22,24,27,29,36,36,40,36,34,31,25,26,26,30,31,34,34,31,24,21,16,13,15,16,22,21,23,25,21,20,17,19,19,17,20,21,19,22,23,27,36,34,34,29,32,29,20,21,19,20,15,15,16,16,15,14,18,17,18,18,20,23,23,19,19,23,24,26,26,28,32,30,28,30,27,29,26,32,29,30,31,28,25,20,21,22,20,23,26,26,24,20,18,15,14,14,17,18,21,24,30,31,30,31,30,25,20,16,16,17,18,19,21,25,22,19,22,23,22,19,21,24,20,21,22,26,27,26,25,27,27,25,25,24,28,27,30,27,26,25,30,29,26,26,26,26,19,20,20,23,24,26,27,27,25,21,17,17,18,15,16,18,24,22,22,23,25,25,23,22,20,23,23,26,23,23,25,19,21,16,18,22,22,21,20,24,21,18,18,19,18,17,20,21,19,19,17,14,19,16,19,18,22,31,28,30,29,33,28,23,23,24,25,23,23,27,26,23,21,26,28,22,23,24,25,18,17,16,14,13,15,17,19,22,25,25,23,22,20,19,16,15,15,15,18,17,18,19,19,21,19,20,19,19,21,20,21,23,25,25,24,27,26,24,23,27,28,30,28,26,25,23,20,20,22,23,21,23,24,23,20,20,24,21,20,18,19,21,20,20,22,23,22,20,19,19,17,16,16,22,18,19,18,20,21,17,23,27,30,29,27,31,27,24,27,26,30,23,30,33,25,27,24,26,20,14,17,18,21,21,24,23,22,21,23,20,20,20,24,27,29,28,27,25,21,20,22,24,25,31,35,37,33,29,31,29,26,26,27,28,28,25,26,24,24,27,24,24,25,23,22,22,21,21,18,21,23,20,23,21,20,17,17,15,14,14,17,18,18,19,24,29,29,27,26,26,20,20,19,19,23,26,33,32,35,36,35,32,27,25,25,23,20,21,20,21,19,24,24,20,20,22,26,24,26,29,30,29,25,22,24,29,30,28,33,33,32,24,26,25,23,24,23,25,25,27,30,31,33,33,33,30,24,25,24,21,18,21,20,18,24,25,28,29,31,30,24,23,20,15,19,24,25,25,28,25,22,19,18,19,16,19,20,23,23,22,25,27,26,22,27,26,29,26,25,32,29,26,20,24,25,18,17,20,23,24,23,25,25,24,22,24,26,28,25,24,27,25,22,23,29,31,28,27,28,26,21,19,19,18,17,15,17,18,21,23,24,24,25,25,22,28,29,31,27,28,27,19,19,20,23,25,28,31,34,29,27,26,23,23,19,18,18,16,19,18,23,31,36,37,37,36,32,28,22,21,18,20,19,17,18,17,22,19,24,26,32,33,30,31,29,27,20,22,23,23,19,16,16,16,13,13,15,19,26,23,26,29,27,28,20,25,22,20,20,17,19,18,20,20,24,26,25,22,21,21,20,15,19,25,25,27,26,30,28,25,26,22,21,25,25,28,25,27,28,25,24,25,25,27,26,29,28,26,25,24,26,28,32,32,30,30,32,28,26,25,25,28,25,26,26,26,29,27,25,22,24,24,23,21,21,18,18,17,16,15,20,24,30,36,35,35,34,37,31,27,29,33,28,24,24,22,21,16,22,20,20,21,22,27,24,25,27,26,28,26,25,28,25,26,24,26,25,24,25,30,30,28,28,27,24,25,24,25,26,26,25,24,22,23,19,19,21,20,22,21,23,23,26,25,26,27,28,27,22,21,20,16,16,16,20,21,16,19,20,26,21,23,33,34,32,29,30,26,17,19,18,17,23,26,28,30,31,31,27,31,27,23,22,22,23,21,22,22,24,28,27,25,24,24,19,14,10,9,7,6,7,8,10,10,11,11,11,13,11,13,11,9,8,4,3,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-200-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-200-0.json
new file mode 100644
index 0000000000..7eff81dd89
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-200-0.json
@@ -0,0 +1 @@
+[22,22,40,46,51,55,46,60,71,65,78,68,56,59,47,64,60,62,61,53,67,59,48,52,68,60,54,49,53,54,56,50,52,60,56,59,57,64,62,54,53,57,58,59,57,55,58,67,54,62,54,62,63,61,59,55,58,61,54,58,60,63,75,66,72,74,62,65,59,73,68,50,59,63,64,62,67,54,52,46,50,58,61,70,56,55,54,45,62,47,57,67,58,64,66,48,47,53,57,53,59,69,49,57,58,56,60,56,52,53,50,62,60,88,79,65,69,72,57,56,58,69,79,67,66,66,48,61,59,57,58,53,54,49,46,64,55,50,69,64,51,53,62,56,48,56,59,63,65,51,52,58,63,57,57,65,66,63,61,56,49,50,47,39,38,54,41,50,71,61,44,64,60,42,64,75,60,56,60,51,61,69,62,53,52,52,50,45,62,60,47,47,43,54,63,56,52,49,56,71,58,62,70,75,60,49,50,61,70,53,61,67,70,65,59,50,59,63,52,66,57,50,63,60,65,64,62,52,50,56,58,64,66,68,71,60,62,77,57,64,63,56,59,54,63,62,64,51,28,20,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-40-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-40-0.json
new file mode 100644
index 0000000000..cc7cc039c3
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-40-0.json
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-400-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-400-0.json
new file mode 100644
index 0000000000..3111c9a55b
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-400-0.json
@@ -0,0 +1 @@
+[35,68,88,86,107,116,96,86,97,98,104,87,111,84,85,87,91,92,102,98,89,97,94,103,96,100,109,89,99,95,105,116,124,105,110,99,102,107,100,79,88,107,95,82,89,101,99,98,83,96,104,89,95,96,86,94,130,117,115,96,108,120,111,97,100,93,88,95,94,108,85,97,86,104,101,94,102,99,107,99,82,75,72,75,112,92,91,111,98,94,109,93,88,81,102,81,81,100,82,103,98,113,93,88,102,109,107,93,99,100,95,104,96,90,87,100,112,108,107,99,102,91,100,99,39,0]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-0.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-0.json
new file mode 100644
index 0000000000..0748c2d47c
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-0.json
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\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-1.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-1.json
new file mode 100644
index 0000000000..55ed618f04
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-1.json
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-2.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-2.json
new file mode 100644
index 0000000000..38148d539c
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-2.json
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-3.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-3.json
new file mode 100644
index 0000000000..c2a56bd328
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-3.json
@@ -0,0 +1 @@
+[[48340,48441,1],[48341,48442,-1],[48356,48457,1],[48366,48467,-1],[48375,48476,1],[48376,48477,-1],[48377,48478,-1],[48378,48479,1],[48379,48480,-1],[48403,48504,1],[48415,48516,1],[48425,48526,-1],[48426,48527,1],[48426,48527,-1],[48430,48531,1],[48436,48537,-1],[48444,48545,-1],[48446,48547,1],[48453,48554,-1],[48454,48555,1],[48460,48561,1],[48470,48571,1],[48470,48571,1],[48477,48578,-1],[48478,48579,1],[48481,48582,-1],[48489,48590,-1],[48489,48590,-1],[48491,48592,1],[48501,48602,1],[48505,48606,1],[48516,48617,-1],[48527,48628,-1],[48530,48631,-1],[48540,48641,-1],[48544,48645,1],[48546,48647,-1],[48554,48655,1],[48555,48656,1],[48558,48659,-1],[48558,48659,-1],[48559,48660,-1],[48565,48666,1],[48567,48668,-1],[48577,48678,1],[48581,48682,-1],[48584,48685,1],[48588,48689,1],[48591,48692,1],[48595,48696,-1],[48598,48699,-1],[48601,48702,1],[48601,48702,1],[48606,48707,1],[48610,48711,-1],[48614,48715,1],[48628,48729,-1],[48629,48730,-1],[48630,48731,1],[48633,48734,1],[48647,48748,1],[48660,48761,-1],[48673,48774,1],[48685,48786,1],[48688,48789,-1],[48699,48800,-1],[48705,48806,-1],[48711,48812,-1],[48713,48814,-1],[48715,48816,-1],[48716,48817,1],[48720,48821,1],[48741,48842,-1],[48749,48850,1],[48751,48852,1],[48751,48852,-1],[48769,48870,1],[48781,48882,-1],[48783,48884,1],[48788,48889,1],[48793,48894,1],[48794,48895,-1],[48796,48897,1],[48805,48906,-1],[48812,48913,-1],[48819,48920,1],[48837,48938,1],[48852,48953,1],[48852,48953,1],[48857,48958,1],[48858,48959,1],[48860,48961,-1],[48866,48967,-1],[48871,48972,1],[48872,48973,-1],[48877,48978,-1],[48880,48981,1],[48882,48983,-1],[48887,48988,1],[48888,48989,1],[48888,48989,-1],[48888,48989,1],[48889,48990,-1],[48919,49020,-1],[48928,49029,-1],[48928,49029,-1],[48929,49030,1],[48936,49037,-1],[48942,49043,1],[48944,49045,1],[48944,49045,-1],[48947,49048,1],[48947,49048,-1],[48950,49051,-1],[48951,49052,-1],[48953,49054,1],[48955,49056,-1],[48956,49057,-1],[48956,49057,1],[48957,49058,1],[48961,49062,1],[48962,49063,1],[48964,49065,1],[48972,49073,-1],[48979,49080,1],[48984,49085,1],[48994,49095,1],[48995,49096,-1],[49000,49101,1],[49004,49105,-1],[49009,49110,1],[49017,49118,-1],[49024,49125,-1],[49056,49157,1],[49062,49163,-1],[49072,49173,-1],[49073,49174,-1],[49081,49182,-1],[49092,49193,-1],[49092,49193,-1],[49093,49194,-1],[49096,49197,1],[49099,49200,1],[49107,49208,1],[49115,49216,1],[49118,49219,1],[49129,49230,1],[49137,49238,1],[49138,49239,-1],[49140,49241,-1],[49142,49243,-1],[49145,49246,1],[49146,49247,-1],[49147,49248,1],[49148,49249,-1],[49153,49254,-1],[49161,49262,-1],[49168,49269,1],[49174,49275,-1],[49179,49280,1],[49183,49284,1],[49184,49285,-1],[49191,49292,1],[49191,49292,1],[49197,49298,-1],[49206,49307,1],[49207,49308,1],[49209,49310,1],[49213,49314,-1],[49213,49314,1],[49217,49318,-1],[49217,49318,1],[49228,49329,1],[49231,49332,1],[49234,49335,1],[49236,49337,-1],[49238,49339,1],[49241,49342,-1],[49251,49352,1],[49259,49360,-1],[49265,49366,1],[49270,49371,1],[49272,49373,1],[49282,49383,-1],[49284,49385,1],[49289,49390,1],[49289,49390,1],[49291,49392,1],[49291,49392,-1],[49297,49398,-1],[49304,49405,-1],[49311,49412,-1],[49323,49424,1],[49329,49430,1],[49332,49433,1],[49341,49442,-1],[49345,49446,-1],[49347,49448,1],[49359,49460,-1],[49374,49475,1],[49379,49480,-1],[49381,49482,-1],[49395,49496,1],[49396,49497,-1],[49397,49498,1],[49397,49498,-1],[49404,49505,1],[49410,49511,-1],[49411,49512,1],[49412,49513,-1],[49418,49519,1],[49426,49527,1],[49427,49528,-1],[49438,49539,-1],[49445,49546,-1],[49450,49551,-1],[49454,49555,1],[49460,49561,-1],[49463,49564,1],[49466,49567,1],[49473,49574,1],[49477,49578,-1],[49480,49581,-1],[49483,49584,-1],[49486,49587,-1],[49491,49592,-1],[49494,49595,1],[49496,49597,1],[49500,49601,1],[49501,49602,1],[49511,49612,1],[49514,49615,1],[49518,49619,1],[49532,49633,-1],[49534,49635,1],[49539,49640,-1],[49545,49646,-1],[49558,49659,-1],[49562,49663,-1],[49577,49678,-1],[49578,49679,-1],[49615,49716,-1],[49637,49738,-1],[49657,49758,-1],[49668,49769,-1],[49686,49787,-1],[49693,49794,-1],[49713,49814,-1],[49720,49821,-1],[49724,49825,-1],[49741,49842,-1],[49741,49842,-1],[49747,49848,-1],[49763,49864,-1],[49781,49882,-1],[49798,49899,-1],[49808,49909,-1],[49814,49915,-1],[49836,49937,-1],[49841,49942,-1],[49845,49946,-1],[49847,49948,-1],[49854,49955,-1],[49876,49977,-1],[49886,49987,-1],[49886,49987,-1],[49886,49987,-1]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/trackData.json b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/trackData.json
new file mode 100644
index 0000000000..b9117f2a4f
--- /dev/null
+++ b/tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/trackData.json
@@ -0,0 +1 @@
+{"histogramMeta":[{"basesPerBin":"20","arrayParams":{"length":2501,"chunkSize":10000,"urlTemplate":"hist-20-{chunk}.json"}},{"basesPerBin":"40","arrayParams":{"length":1251,"chunkSize":10000,"urlTemplate":"hist-40-{chunk}.json"}},{"basesPerBin":"100","arrayParams":{"length":501,"chunkSize":10000,"urlTemplate":"hist-100-{chunk}.json"}},{"basesPerBin":"200","arrayParams":{"length":251,"chunkSize":10000,"urlTemplate":"hist-200-{chunk}.json"}},{"basesPerBin":"400","arrayParams":{"length":126,"chunkSize":10000,"urlTemplate":"hist-400-{chunk}.json"}},{"basesPerBin":"1000","arrayParams":{"length":51,"chunkSize":10000,"urlTemplate":"hist-1000-{chunk}.json"}}],"subfeatureClasses":null,"headers":["start","end","strand"],"lazyIndex":2,"featureCount":9596,"histStats":[{"bases":20,"max":44,"mean":23.2163134746102},{"bases":40,"max":50,"mean":27.123101518785},{"bases":100,"max":71,"mean":38.497005988024},{"bases":200,"max":88,"mean":57.7450199203187},{"bases":400,"max":130,"mean":95.531746031746},{"bases":1000,"max":244,"mean":207.352941176471}],"featureNCList":[[2,17152,{"chunk":0}],[17055,32741,{"chunk":1}],[32644,48432,{"chunk":2}],[48340,49987,{"chunk":3}]],"key":"Simulated next-gen reads","className":"basic","clientConfig":{"histScale":"2","featureCss":"background-color: #66F; height: 8px","histCss":"background-color: #88F"},"arrowheadClass":null,"subfeatureHeaders":null,"label":"bam_simulated","type":"FeatureTrack","sublistIndex":3,"lazyfeatureUrlTemplate":"lazyfeatures-{chunk}.json"}
\ No newline at end of file

From 4665ba827fac24848874b7ea2bc3b403b3227a4b Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 09:31:04 -0400
Subject: [PATCH 34/49] bugfixes to config adaptor loading

---
 js/Browser.js | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/js/Browser.js b/js/Browser.js
index 028cccec38..aadaa54b0c 100644
--- a/js/Browser.js
+++ b/js/Browser.js
@@ -204,8 +204,12 @@ Browser.prototype.loadConfig = function () {
     dojo.forEach( this.config.include, function(config) {
 
         // set defaults for format and version
-        if( !config.format ) config.format = 'JB_json';
-        if( typeof config.version == 'undefined' ) config.version = 1;
+        if( ! ('format' in config) ) {
+            config.format = 'JB_json';
+        }
+        if( config.format == 'JB_json' && ! ('version' in config) ) {
+            config.version = 1;
+        }
 
         // instantiate the adaptor and load the config
         var adaptor = this.getConfigAdaptor( config );
@@ -274,7 +278,7 @@ Browser.prototype.validateConfig = function() {
 
 Browser.prototype.getConfigAdaptor = function( config_def ) {
     var adaptor_name = "ConfigAdaptor." + config_def.format;
-    if( config_def.version )
+    if( 'version' in config_def )
         adaptor_name += '_v'+config_def.version;
     adaptor_name.replace( /\W/g,'' );
     var adaptor_class = eval( adaptor_name );

From e6524815aef849de509815e2095408affe2e695a Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 09:31:47 -0400
Subject: [PATCH 35/49] add JB_json_v0 conf adaptor to javascript files being
 loaded.  we need a module loading system.

---
 index.html | 1 +
 1 file changed, 1 insertion(+)

diff --git a/index.html b/index.html
index 53f2e68e7d..b8b6d40a5f 100644
--- a/index.html
+++ b/index.html
@@ -18,6 +18,7 @@
      when the JS gets minified (see the minification rule in the Makefile) -->
     <script type="text/javascript" src="js/Browser.js"></script>
     <script type="text/javascript" src="js/ConfigAdaptor/JB_json_v1.js"></script>
+    <script type="text/javascript" src="js/ConfigAdaptor/JB_json_v0.js"></script>
     <script type="text/javascript" src="js/Util.js"></script>
     <script type="text/javascript" src="js/ArrayRepr.js"></script>
     <script type="text/javascript" src="js/NCList.js"></script>

From 7e7707a8fe4147de8a9ff09d16d9cb69c16eb273 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 10:56:48 -0400
Subject: [PATCH 36/49] flatten feature config format, having the feature's
 configuration in two levels of keys (root and config) is unnecessarily
 complicated, especially if users are eventually going to write configuration
 files directly, which is the direction i'm moving in

---
 bin/prepare-refseqs.pl                        |   7 +-
 js/FeatureTrack.js                            |  15 +-
 js/ImageTrack.js                              |   8 +-
 js/SequenceTrack.js                           |   9 +-
 lib/GenomeDB.pm                               |  19 +-
 .../mahoney_formatted/trackList.json          |   6 +-
 tests/data/hg19_formatted/trackList.json      |   4 +-
 .../volvox_formatted_refseqs/trackList.json   |   6 +-
 tests/perl_tests/bam-to-json.pl.t             |   4 +-
 tests/perl_tests/biodb-to-json.pl.t           | 501 +++++++++---------
 tests/perl_tests/draw-basepair-track.pl.t     |  20 +-
 tests/perl_tests/flatfile-to-json.pl.t        |   2 +-
 tests/perl_tests/wig-to-json.pl.t             |  19 +-
 tests/selenium_tests/yeast_biodb_test.py      |  11 +-
 14 files changed, 318 insertions(+), 313 deletions(-)

diff --git a/bin/prepare-refseqs.pl b/bin/prepare-refseqs.pl
index dd4b904dc4..55bc6b13b3 100755
--- a/bin/prepare-refseqs.pl
+++ b/bin/prepare-refseqs.pl
@@ -247,11 +247,8 @@ =head1 OPTIONS
                                        'label' => $seqTrackName,
                                        'key' => $seqTrackName,
                                        'type' => "SequenceTrack",
-                                       'config' =>
-                                       {
-                                        'chunkSize' => $chunkSize,
-                                        'urlTemplate' => "$seqRel/{refseq}/",
-                                       }
+                                       'chunkSize' => $chunkSize,
+                                       'urlTemplate' => "$seqRel/{refseq}/",
                                       };
                                     return $trackList;
                             });
diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index fbb26ac4eb..378583084e 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -3,8 +3,8 @@
 /**
  * @class
  */
-function FeatureTrack( trackMeta, refSeq, browserParams ) {
-    //trackMeta: object with:
+function FeatureTrack( config, refSeq, browserParams ) {
+    //config: object with:
     //            key:   display text track name
     //            label: internal track name (no spaces, odd characters)
     //            baseUrl: base URL to use for resolving relative URLs
@@ -17,16 +17,16 @@ function FeatureTrack( trackMeta, refSeq, browserParams ) {
     //browserParams: object with:
     //                changeCallback: function to call once JSON is loaded
     //                trackPadding: distance in px between tracks
-    //                baseUrl: base URL for the URL in trackMeta
+    //                baseUrl: base URL for the URL in config
 
-    Track.call(this, trackMeta.label, trackMeta.key,
+    Track.call(this, config.label, config.key,
                false, browserParams.changeCallback);
     this.fields = {};
     this.refSeq = refSeq;
 
     this.featureStore = new SeqFeatureStore.NCList({
-        urlTemplate: trackMeta.config.urlTemplate,
-        baseUrl: trackMeta.baseUrl,
+        urlTemplate: config.urlTemplate,
+        baseUrl: config.baseUrl,
         refSeq: refSeq
     });
 
@@ -43,8 +43,7 @@ function FeatureTrack( trackMeta, refSeq, browserParams ) {
     this.padding = 5;
     this.trackPadding = browserParams.trackPadding;
 
-    this.trackMeta = trackMeta;
-    this.config = trackMeta.config;
+    this.config = config;
 }
 
 FeatureTrack.prototype = new Track("");
diff --git a/js/ImageTrack.js b/js/ImageTrack.js
index 5753494199..0ec640d65f 100644
--- a/js/ImageTrack.js
+++ b/js/ImageTrack.js
@@ -3,15 +3,15 @@
 /**
  * @class
  */
-function ImageTrack(trackMeta, refSeq, browserParams) {
-    Track.call(this, trackMeta.label, trackMeta.key,
+function ImageTrack(config, refSeq, browserParams) {
+    Track.call(this, config.label, config.key,
                false, browserParams.changeCallback);
     this.refSeq = refSeq;
     this.trackPadding = browserParams.trackPadding;
     this.tileToImage = {};
     this.zoomCache = {};
-    this.url = Util.resolveUrl(trackMeta.baseUrl,
-                               Util.fillTemplate(trackMeta.config.urlTemplate,
+    this.url = Util.resolveUrl(config.baseUrl,
+                               Util.fillTemplate(config.urlTemplate,
                                                  {'refseq': refSeq.name}) );
     this.load(this.url);
 
diff --git a/js/SequenceTrack.js b/js/SequenceTrack.js
index ca59869403..bf04d4e69a 100644
--- a/js/SequenceTrack.js
+++ b/js/SequenceTrack.js
@@ -7,9 +7,8 @@ function SequenceTrack(trackMeta, refSeq, browserParams) {
     //trackMeta: object with:
     //  key:   display text track name
     //  label: internal track name (no spaces or odd characters)
-    //  config: object with:
-    //    urlTemplate: url of directory in which to find the sequence chunks
-    //    chunkSize: size of sequence chunks, in characters
+    //  urlTemplate: url of directory in which to find the sequence chunks
+    //  chunkSize: size of sequence chunks, in characters
     //refSeq: object with:
     //  start: refseq start
     //  end:   refseq end
@@ -26,9 +25,9 @@ function SequenceTrack(trackMeta, refSeq, browserParams) {
     this.trackMeta = trackMeta;
     this.setLoaded();
     this.chunks = [];
-    this.chunkSize = trackMeta.config.chunkSize;
+    this.chunkSize = trackMeta.chunkSize;
     this.url = Util.resolveUrl(trackMeta.baseUrl,
-                               Util.fillTemplate(trackMeta.config.urlTemplate,
+                               Util.fillTemplate(trackMeta.urlTemplate,
                                                  {'refseq': refSeq.name}) );
 
 }
diff --git a/lib/GenomeDB.pm b/lib/GenomeDB.pm
index ec45aae2bf..1394a4d6b6 100644
--- a/lib/GenomeDB.pm
+++ b/lib/GenomeDB.pm
@@ -87,10 +87,10 @@ sub writeTrackEntry {
         $trackIndex = ($#{$trackList} + 1) unless defined($trackIndex);
 
         $trackList->[$trackIndex] = {
+                                     %{ $track->config || {} },
                                      label => $track->label,
                                      key => $track->key,
                                      type => $track->type,
-                                     config => $track->config
                                     };
         return $trackData;
     };
@@ -158,7 +158,7 @@ sub getTrack {
     return $type->new( $self->trackDir($trackLabel),
                        $baseUrl,
                        $trackDesc->{label},
-                       $trackDesc->{config},
+                       $trackDesc,
                        $trackDesc->{key},
                      );
 }
@@ -201,15 +201,12 @@ Return an arrayref of track definition hashrefs similar to:
 
     [
         {
-          config => {
-                      autocomplete => "all",
-                      compress => 0,
-                      feature => ["remark"],
-                      key => "Example Features",
-                      style => { className => "feature2" },
-                      track => "ExampleFeatures",
-                      urlTemplate => "tracks/ExampleFeatures/{refseq}/trackData.json",
-                    },
+          autocomplete => "all",
+          compress => 0,
+          feature => ["remark"],
+          style => { className => "feature2" },
+          track => "ExampleFeatures",
+          urlTemplate => "tracks/ExampleFeatures/{refseq}/trackData.json",
           key    => "Example Features",
           label  => "ExampleFeatures",
           type   => "FeatureTrack",
diff --git a/tests/data/base_pairing/mahoney_formatted/trackList.json b/tests/data/base_pairing/mahoney_formatted/trackList.json
index 1a0e8a8fc7..6a75f7abe3 100644
--- a/tests/data/base_pairing/mahoney_formatted/trackList.json
+++ b/tests/data/base_pairing/mahoney_formatted/trackList.json
@@ -1,10 +1,8 @@
 {
    "tracks" : [
       {
-         "config" : {
-            "chunkSize" : 20000,
-            "urlTemplate" : "seq/{refseq}/"
-         },
+         "chunkSize" : 20000,
+         "urlTemplate" : "seq/{refseq}/",
          "type" : "SequenceTrack",
          "label" : "DNA",
          "key" : "DNA"
diff --git a/tests/data/hg19_formatted/trackList.json b/tests/data/hg19_formatted/trackList.json
index a8b25da4df..f7fff23767 100644
--- a/tests/data/hg19_formatted/trackList.json
+++ b/tests/data/hg19_formatted/trackList.json
@@ -1,7 +1,6 @@
 {
    "tracks" : [
       {
-         "config" : {
             "urlTemplate" : "tracks/knownGene/{refseq}/trackData.jsonz",
             "style" : {
                "className" : "generic_parent",
@@ -16,8 +15,7 @@
             "compress" : 1,
             "hooks" : {
                "modify" : "function(track, feat, attrs, elem) {\n    var fType = attrs.get(feat, \"Type\");\n    if (fType) {\n        elem.className = \"basic\";\n        switch (fType]) {\n        case \"CDS\":\n        case \"thick\":\n            elem.style.height = \"10px\";\n            elem.style.marginTop = \"-3px\";\n            break;\n        case \"UTR\":\n        case \"thin\":\n            elem.style.height = \"6px\";\n            elem.style.marginTop = \"-1px\";\n            break;\n        }\n        elem.style.backgroundColor = \"#0c0c78\";\n    }\n}\n"
-            }
-         },
+            },
          "type" : "FeatureTrack",
          "label" : "knownGene",
          "key" : "knownGene"
diff --git a/tests/data/volvox_formatted_refseqs/trackList.json b/tests/data/volvox_formatted_refseqs/trackList.json
index 1a0e8a8fc7..6a75f7abe3 100644
--- a/tests/data/volvox_formatted_refseqs/trackList.json
+++ b/tests/data/volvox_formatted_refseqs/trackList.json
@@ -1,10 +1,8 @@
 {
    "tracks" : [
       {
-         "config" : {
-            "chunkSize" : 20000,
-            "urlTemplate" : "seq/{refseq}/"
-         },
+         "chunkSize" : 20000,
+         "urlTemplate" : "seq/{refseq}/",
          "type" : "SequenceTrack",
          "label" : "DNA",
          "key" : "DNA"
diff --git a/tests/perl_tests/bam-to-json.pl.t b/tests/perl_tests/bam-to-json.pl.t
index b0a1a5b1b5..da8c44ac16 100644
--- a/tests/perl_tests/bam-to-json.pl.t
+++ b/tests/perl_tests/bam-to-json.pl.t
@@ -34,8 +34,8 @@ is( ref(  $out->{ catfile(qw( tracks TestBAM ctgA lf-4.json  )) } ),
     'BAM! got some features up in there',
   );
 
-is( $out->{'trackList.json'}{tracks}[1]{config}{style}{foobee}, 1, 'got some style' );
-is( $out->{'trackList.json'}{tracks}[1]{config}{style}{className}, 'basic', 'got default CSS class' );
+is( $out->{'trackList.json'}{tracks}[1]{style}{foobee}, 1, 'got some style' );
+is( $out->{'trackList.json'}{tracks}[1]{style}{className}, 'basic', 'got default CSS class' );
 
 
 #system "find $tempdir";
diff --git a/tests/perl_tests/biodb-to-json.pl.t b/tests/perl_tests/biodb-to-json.pl.t
index 0be67b70fa..76aa3632ce 100644
--- a/tests/perl_tests/biodb-to-json.pl.t
+++ b/tests/perl_tests/biodb-to-json.pl.t
@@ -9,261 +9,286 @@ use File::Copy::Recursive 'dircopy';
 
 use JsonGenerator;
 
-my $tempdir   = File::Temp->newdir( CLEANUP => $ENV{KEEP_ALL} ? 0 : 1 );
-my $read_json = sub { JsonGenerator::readJSON( catfile( $tempdir, @_ ) ) };
+{ # test volvox
 
-dircopy( 'tests/data/volvox_formatted_refseqs', $tempdir );
+    my $tempdir   = File::Temp->newdir( CLEANUP => $ENV{KEEP_ALL} ? 0 : 1 );
+    my $read_json = sub { JsonGenerator::readJSON( catfile( $tempdir, @_ ) ) };
 
-diag "writing output to $tempdir";
-system $^X, 'bin/biodb-to-json.pl', (
-    '--quiet',
-    '--conf'  => 'sample_data/raw/volvox.json',
-    '--out'   => "$tempdir",
-  );
-ok( ! $?, 'biodb-to-json.pl ran ok' );
+    dircopy( 'tests/data/volvox_formatted_refseqs', $tempdir );
 
-my $hist_output = $read_json->(qw( tracks Transcript ctgA hist-100000-0.json ));
-is_deeply( $hist_output, [1], 'got right histogram output' ) or diag explain( $hist_output );
+    diag "writing output to $tempdir";
+    system $^X, 'bin/biodb-to-json.pl', (
+        '--quiet',
+        '--conf'  => 'sample_data/raw/volvox.json',
+        '--out'   => "$tempdir",
+      );
+    ok( ! $?, 'biodb-to-json.pl ran ok' );
 
-my $tracklist = $read_json->('trackList.json');
-is_deeply( $tracklist,
+    my $hist_output = $read_json->(qw( tracks Transcript ctgA hist-100000-0.json ));
+    is_deeply( $hist_output, [1], 'got right histogram output' ) or diag explain( $hist_output );
+
+    my $tracklist = $read_json->('trackList.json');
+    is_deeply( $tracklist,
+    {
+      'formatVersion' => 1,
+      'tracks' => [
+        {
+            'chunkSize' => 20000,
+            'urlTemplate' => 'seq/{refseq}/',
+            'key' => 'DNA',
+            'label' => 'DNA',
+            'type' => 'SequenceTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            style => { 'className' => 'feature2' },
+            'compress' => 0,
+            'feature' => [
+                'remark'
+                ],
+            'track' => 'ExampleFeatures',
+            'urlTemplate' => 'tracks/ExampleFeatures/{refseq}/trackData.json',
+            'key' => 'Example Features',
+            'label' => 'ExampleFeatures',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            style => { 'className' => 'feature2' },
+            'compress' => 0,
+            'feature' => [
+              'protein_coding_primary_transcript',
+              'polypeptide'
+              ],
+            'track' => 'NameTest',
+            'urlTemplate' => 'tracks/NameTest/{refseq}/trackData.json',
+            'key' => 'Name test track',
+            'label' => 'NameTest',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            'compress' => 0,
+            'feature' => [
+                'SNP'
+                ],
+            'style' => {
+                'className' => 'triangle hgred'
+                },
+            'track' => 'snps',
+            'urlTemplate' => 'tracks/snps/{refseq}/trackData.json',
+            'key' => 'Test SNPs',
+            'label' => 'snps',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            style => {'className' => 'feature3'},
+            'compress' => 0,
+            'description' => 1,
+            'feature' => [
+                'polypeptide_domain'
+                ],
+            'key' => 'Example motifs',
+            'track' => 'Motifs',
+            'urlTemplate' => 'tracks/Motifs/{refseq}/trackData.json',
+            'key' => 'Example motifs',
+            'label' => 'Motifs',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            'category' => 'Alignments',
+            style => { 'className' => 'feature4' },
+            'compress' => 0,
+            'feature' => [
+                'match'
+                ],
+            'track' => 'Alignments',
+            'urlTemplate' => 'tracks/Alignments/{refseq}/trackData.json',
+            'key' => 'Example alignments',
+            'label' => 'Alignments',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            style => {'className' => 'feature5'},
+            'compress' => 0,
+            'feature' => [
+                'gene'
+                ],
+            'track' => 'Genes',
+            'urlTemplate' => 'tracks/Genes/{refseq}/trackData.json',
+            'key' => 'Protein-coding genes',
+            'label' => 'Genes',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            'category' => 'Genes',
+            style => { 'className' => 'dblhelix' },
+            'compress' => 0,
+            'feature' => [
+                'mRNA'
+                ],
+            'track' => 'ReadingFrame',
+            'urlTemplate' => 'tracks/ReadingFrame/{refseq}/trackData.json',
+            'key' => 'Frame usage',
+            'label' => 'ReadingFrame',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            'category' => 'Genes',
+            style => { 'className' => 'cds' },
+            'compress' => 0,
+            'feature' => [
+                'CDS:predicted',
+                'mRNA:exonerate'
+            ],
+            'phase' => 1,
+            'track' => 'CDS',
+            'urlTemplate' => 'tracks/CDS/{refseq}/trackData.json',
+            'key' => 'Predicted genes',
+            'label' => 'CDS',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            'category' => 'Genes',
+            'compress' => 0,
+            'description' => 1,
+            'feature' => [
+              'mRNA:exonerate'
+              ],
+            'key' => 'Exonerate predictions',
+            'style' => {
+                'className' => 'transcript',
+                'arrowheadClass' => 'transcript-arrowhead',
+                'subfeatureClasses' => {
+                    'CDS' => 'transcript-CDS',
+                    'UTR' => 'transcript-UTR'
+                    },
+            },
+            'subfeatures' => 'true',
+            'track' => 'Transcript',
+            'urlTemplate' => 'tracks/Transcript/{refseq}/trackData.json',
+            'key' => 'Exonerate predictions',
+            'label' => 'Transcript',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            style => {'className' => 'exon'},
+            'compress' => 0,
+            'description' => 1,
+            'feature' => [
+              'BAC'
+            ],
+            'track' => 'Clones',
+            'urlTemplate' => 'tracks/Clones/{refseq}/trackData.json',
+            'key' => 'Fingerprinted BACs',
+            'label' => 'Clones',
+            'type' => 'FeatureTrack'
+        },
+        {
+            'autocomplete' => 'all',
+            style => {'className' => 'est'},
+            'compress' => 0,
+            'feature' => [
+                'EST_match:est'
+                ],
+            'track' => 'EST',
+            'urlTemplate' => 'tracks/EST/{refseq}/trackData.json',
+            'key' => 'ESTs',
+            'label' => 'EST',
+            'type' => 'FeatureTrack'
+        }
+      ]
+    },
+               'made right trackList.json',
+             ) or diag explain $tracklist;
+
+    my $names_output = $read_json->(qw( tracks Transcript ctgA names.json ));
+    is_deeply( $names_output,
+               [
+                   [
+                       [ 'Apple3' ],
+                       'Transcript',
+                       'Apple3',
+                       'ctgA',
+                       '17399',
+                       '23000',
+                       '192'
+                   ]
+               ],
+               'got the right names output'
+               ) or diag explain $names_output;
+
+    system $^X, 'bin/generate-names.pl', (
+        '--dir'   => "$tempdir",
+      );
+    ok( ! $?, 'generate-names.pl ran ok' );
+
+    system $^X, 'bin/generate-names.pl', (
+        '--out'   => "$tempdir",
+      );
+    ok( ! $?, 'generate-names.pl also ran ok with the --out option' );
+}
+
+{ # test yeast
+
+    my $tempdir   = File::Temp->newdir( CLEANUP => $ENV{KEEP_ALL} ? 0 : 1 );
+    my $read_json = sub { JsonGenerator::readJSON( catfile( $tempdir, @_ ) ) };
+
+    system $^X, 'bin/prepare-refseqs.pl', (
+        '--fasta' => 'sample_data/raw/yeast_scaffolds/chr1.fa.gz',
+        '--fasta' => 'sample_data/raw/yeast_scaffolds/chr2.fa.gzip',
+        '--out'   => "$tempdir",
+        );
+
+    system $^X, 'bin/biodb-to-json.pl', (
+        '--conf'  => 'sample_data/raw/yeast.json',
+        '--out'   => "$tempdir",
+      );
+
+    my $tracklist = $read_json->('trackList.json');
+    is_deeply( $tracklist,
 {
   'formatVersion' => 1,
   'tracks' => [
     {
-      'config' => {
-        'chunkSize' => 20000,
-        'urlTemplate' => 'seq/{refseq}/'
-      },
+      'chunkSize' => 20000,
       'key' => 'DNA',
       'label' => 'DNA',
-      'type' => 'SequenceTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        style => { 'className' => 'feature2' },
-        'compress' => 0,
-        'feature' => [
-          'remark'
-        ],
-        'key' => 'Example Features',
-        'track' => 'ExampleFeatures',
-        'urlTemplate' => 'tracks/ExampleFeatures/{refseq}/trackData.json'
-      },
-      'key' => 'Example Features',
-      'label' => 'ExampleFeatures',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        style => { 'className' => 'feature2' },
-        'compress' => 0,
-        'feature' => [
-          'protein_coding_primary_transcript',
-          'polypeptide'
-        ],
-        'key' => 'Name test track',
-        'track' => 'NameTest',
-        'urlTemplate' => 'tracks/NameTest/{refseq}/trackData.json'
-      },
-      'key' => 'Name test track',
-      'label' => 'NameTest',
-      'type' => 'FeatureTrack'
+      'type' => 'SequenceTrack',
+      'urlTemplate' => 'seq/{refseq}/'
     },
     {
-      'config' => {
-        'autocomplete' => 'all',
-        'compress' => 0,
-        'feature' => [
-          'SNP'
-        ],
-        'key' => 'Test SNPs',
-        'style' => {
-          'className' => 'triangle hgred'
-        },
-        'track' => 'snps',
-        'urlTemplate' => 'tracks/snps/{refseq}/trackData.json'
-      },
-      'key' => 'Test SNPs',
-      'label' => 'snps',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        style => {'className' => 'feature3'},
-        'compress' => 0,
-        'description' => 1,
-        'feature' => [
-          'polypeptide_domain'
-        ],
-        'key' => 'Example motifs',
-        'track' => 'Motifs',
-        'urlTemplate' => 'tracks/Motifs/{refseq}/trackData.json'
-      },
-      'key' => 'Example motifs',
-      'label' => 'Motifs',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        'category' => 'Alignments',
-        style => { 'className' => 'feature4' },
-        'compress' => 0,
-        'feature' => [
-          'match'
-        ],
-        'key' => 'Example alignments',
-        'track' => 'Alignments',
-        'urlTemplate' => 'tracks/Alignments/{refseq}/trackData.json'
-      },
-      'key' => 'Example alignments',
-      'label' => 'Alignments',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        style => {'className' => 'feature5'},
-        'compress' => 0,
-        'feature' => [
-          'gene'
-        ],
-        'key' => 'Protein-coding genes',
-        'track' => 'Genes',
-        'urlTemplate' => 'tracks/Genes/{refseq}/trackData.json'
-      },
+      'autocomplete' => 'all',
+      'category' => 'Genes',
+      'compress' => '0',
+      'feature' => [
+        'gene'
+      ],
       'key' => 'Protein-coding genes',
       'label' => 'Genes',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        'category' => 'Genes',
-        style => { 'className' => 'dblhelix' },
-        'compress' => 0,
-        'feature' => [
-          'mRNA'
-        ],
-        'key' => 'Frame usage',
-        'track' => 'ReadingFrame',
-        'urlTemplate' => 'tracks/ReadingFrame/{refseq}/trackData.json'
-      },
-      'key' => 'Frame usage',
-      'label' => 'ReadingFrame',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        'category' => 'Genes',
-        style => { 'className' => 'cds' },
-        'compress' => 0,
-        'feature' => [
-          'CDS:predicted',
-          'mRNA:exonerate'
-        ],
-        'key' => 'Predicted genes',
-        'phase' => 1,
-        'track' => 'CDS',
-        'urlTemplate' => 'tracks/CDS/{refseq}/trackData.json'
-      },
-      'key' => 'Predicted genes',
-      'label' => 'CDS',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        'category' => 'Genes',
-        'compress' => 0,
-        'description' => 1,
-        'feature' => [
-          'mRNA:exonerate'
-        ],
-        'key' => 'Exonerate predictions',
-        'style' => {
-           'className' => 'transcript',
-          'arrowheadClass' => 'transcript-arrowhead',
-           'subfeatureClasses' => {
-               'CDS' => 'transcript-CDS',
-               'UTR' => 'transcript-UTR'
-               },
-        },
-        'subfeatures' => 'true',
-        'track' => 'Transcript',
-        'urlTemplate' => 'tracks/Transcript/{refseq}/trackData.json'
-      },
-      'key' => 'Exonerate predictions',
-      'label' => 'Transcript',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        style => {'className' => 'exon'},
-        'compress' => 0,
-        'description' => 1,
-        'feature' => [
-          'BAC'
-        ],
-        'key' => 'Fingerprinted BACs',
-        'track' => 'Clones',
-        'urlTemplate' => 'tracks/Clones/{refseq}/trackData.json'
+      'style' => {
+        'arrowheadClass' => 'transcript-arrowhead',
+        'className' => 'feature5',
+        'subfeatureClasses' => {
+          'CDS' => 'transcript-CDS'
+        }
       },
-      'key' => 'Fingerprinted BACs',
-      'label' => 'Clones',
-      'type' => 'FeatureTrack'
-    },
-    {
-      'config' => {
-        'autocomplete' => 'all',
-        style => {'className' => 'est'},
-        'compress' => 0,
-        'feature' => [
-          'EST_match:est'
-        ],
-        'key' => 'ESTs',
-        'track' => 'EST',
-        'urlTemplate' => 'tracks/EST/{refseq}/trackData.json'
-      },
-      'key' => 'ESTs',
-      'label' => 'EST',
-      'type' => 'FeatureTrack'
+      'subfeatures' => bless( do{\(my $o = 1)}, 'JSON::XS::Boolean' ),
+      'track' => 'Genes',
+      'type' => 'FeatureTrack',
+      'urlTemplate' => 'tracks/Genes/{refseq}/trackData.json'
     }
   ]
 },
-           'made right trackList.json',
-         ) or diag explain $tracklist;
-
-my $names_output = $read_json->(qw( tracks Transcript ctgA names.json ));
-is_deeply( $names_output,
-           [
-               [
-                   [ 'Apple3' ],
-                   'Transcript',
-                   'Apple3',
-                   'ctgA',
-                   '17399',
-                   '23000',
-                   '192'
-               ]
-           ],
-           'got the right names output'
-           ) or diag explain $names_output;
-
-system $^X, 'bin/generate-names.pl', (
-    '--dir'   => "$tempdir",
-  );
-ok( ! $?, 'generate-names.pl ran ok' );
-
-system $^X, 'bin/generate-names.pl', (
-    '--out'   => "$tempdir",
-  );
-ok( ! $?, 'generate-names.pl also ran ok with the --out option' );
+               'made right trackList.json',
+             ) or diag explain $tracklist;
+}
 
 done_testing;
diff --git a/tests/perl_tests/draw-basepair-track.pl.t b/tests/perl_tests/draw-basepair-track.pl.t
index 6725b01f0b..eb7bf5a561 100644
--- a/tests/perl_tests/draw-basepair-track.pl.t
+++ b/tests/perl_tests/draw-basepair-track.pl.t
@@ -44,22 +44,18 @@ for my $args ( @testargs ) {
           'formatVersion' => 1,
           'tracks' => [
             {
-              'config' => {
                 'chunkSize' => 20000,
-                'urlTemplate' => 'seq/{refseq}/'
-              },
-              'key' => 'DNA',
-              'label' => 'DNA',
-              'type' => 'SequenceTrack'
+                'urlTemplate' => 'seq/{refseq}/',
+                'key' => 'DNA',
+                'label' => 'DNA',
+                'type' => 'SequenceTrack'
             },
             {
-              'config' => {
                 'compress' => 0,
-                'urlTemplate' => 'tracks/foo/{refseq}/trackData.json'
-              },
-              'key' => 'Fooish Test Data',
-              'label' => 'foo',
-              'type' => 'ImageTrack'
+                'urlTemplate' => 'tracks/foo/{refseq}/trackData.json',
+                'key' => 'Fooish Test Data',
+                'label' => 'foo',
+                'type' => 'ImageTrack'
             }
           ]
         },
diff --git a/tests/perl_tests/flatfile-to-json.pl.t b/tests/perl_tests/flatfile-to-json.pl.t
index 34ff9a7b8a..8c3773c31a 100644
--- a/tests/perl_tests/flatfile-to-json.pl.t
+++ b/tests/perl_tests/flatfile-to-json.pl.t
@@ -73,7 +73,7 @@ sub tempdir {
        or diag explain $cds_trackdata;
     is( scalar @{$cds_trackdata->{intervals}{nclist}[2][9]}, 5, 'exonerate mRNA has 5 subfeatures' );
 
-    is_deeply( $read_json->('trackList.json')->{tracks}[1]{config}{style},
+    is_deeply( $read_json->('trackList.json')->{tracks}[1]{style},
                { featureCss => 'height: 8px;',
                  histScale => 2,
                  className => 'feature2',
diff --git a/tests/perl_tests/wig-to-json.pl.t b/tests/perl_tests/wig-to-json.pl.t
index a19992359d..3794dc94dc 100644
--- a/tests/perl_tests/wig-to-json.pl.t
+++ b/tests/perl_tests/wig-to-json.pl.t
@@ -31,23 +31,18 @@ is_deeply( $tracklist,
                'formatVersion' => 1,
                'tracks' => [
                    {
-                       'config' => {
-                           'chunkSize' => 20000,
-                           'urlTemplate' => 'seq/{refseq}/'
-                           },
+                       'chunkSize' => 20000,
+                       'urlTemplate' => 'seq/{refseq}/',
                        'key' => 'DNA',
                        'label' => 'DNA',
                        'type' => 'SequenceTrack'
                    },
                    {
-                       'config' => {
-                           'compress' => 0,
-                           'key' => 'volvox_microarray.wig',
-                           'style' => {
-                               'className' => 'image',
-                               },
-                           'urlTemplate' => 'tracks/volvox_microarray.wig/{refseq}/trackData.json'
-                           },
+                       'compress' => 0,
+                       'style' => {
+                           'className' => 'image',
+                       },
+                       'urlTemplate' => 'tracks/volvox_microarray.wig/{refseq}/trackData.json',
                        'key' => 'volvox_microarray.wig',
                        'label' => 'volvox_microarray.wig',
                        'type' => 'ImageTrack'
diff --git a/tests/selenium_tests/yeast_biodb_test.py b/tests/selenium_tests/yeast_biodb_test.py
index 55c204a9e7..0e6adace0f 100644
--- a/tests/selenium_tests/yeast_biodb_test.py
+++ b/tests/selenium_tests/yeast_biodb_test.py
@@ -37,16 +37,16 @@ def test_yeast( self ):
     def search_yal024c( self ):
 
         # check that a YAL024C feature label is not yet in the DOM
-        yal024_xpath = "//div[@class='feature-label'][contains(.,'YAL024C')]"
-        self.assert_no_element( yal024_xpath )
+        yal024_label_xpath = "//div[@class='feature-label'][contains(.,'YAL024C')]"
+        self.assert_no_element( yal024_label_xpath )
 
         # Find the query box and put YAL024C into it and hit enter
         self.do_typed_query( 'YAL024C' )
 
-        # test that YAL024C appeared in the DOM (TODO: check that it's
+        # test that the YAL024C label appeared in the DOM (TODO: check that it's
         # actually centered in the window), and that the protein-coding
         # genes track is now selected
-        feature_labels = self.assert_elements( yal024_xpath )
+        feature_labels = self.assert_elements( yal024_label_xpath )
         assert feature_labels[0].text == 'YAL024C'
         assert len(feature_labels) == 1, "actually %d features match" % len(feature_labels)
 
@@ -54,6 +54,9 @@ def search_yal024c( self ):
         track_labels = self.get_track_labels_containing( 'Protein-coding genes' )
         assert len(track_labels) == 1, '%d tracks displayed with that name' % len(track_labels)
 
+        # test that the features in the track have the right classes
+        self.assert_elements("//div[@class='track']//div[@class='minus-feature5']");
+
         # do the search again, and make sure that again, only one track is displayed
         # Find the query box and put YAL024C into it and hit enter
         self.do_typed_query( "YAL024C" )

From abe6af8bb0bbba3a3eba201179b04bf42879ed23 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 12:11:38 -0400
Subject: [PATCH 37/49] first crack at v0 configuration adaptor

---
 js/ConfigAdaptor/JB_json_v0.js | 52 ++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 js/ConfigAdaptor/JB_json_v0.js

diff --git a/js/ConfigAdaptor/JB_json_v0.js b/js/ConfigAdaptor/JB_json_v0.js
new file mode 100644
index 0000000000..e3b7621343
--- /dev/null
+++ b/js/ConfigAdaptor/JB_json_v0.js
@@ -0,0 +1,52 @@
+var ConfigAdaptor; if( !ConfigAdaptor ) ConfigAdaptor = {};
+
+/**
+ * Configuration adaptor for JBrowse JSON version 0
+ * <code>trackInfo.js</code> files.
+ * @class
+ * @extends ConfigAdaptor.JB_json_v1
+ */
+ConfigAdaptor.JB_json_v0 = function() {
+};
+ConfigAdaptor.JB_json_v0.prototype = new ConfigAdaptor.JB_json_v1();
+
+/**
+ * Munge the v0 configuration to conform to v1.
+ *
+ * @param {Object} o the object containing the configuration, which it
+ *                   modifies in-place
+ * @param {Object} load_args the arguments that were passed to <code>load()</code>
+ * @returns {Object} v1-compliant configuration
+ */
+ConfigAdaptor.JB_json_v0.prototype.regularize_conf = function( o, load_args ) {
+
+    console.log(o);
+
+    // transform the object to conform to format version 1
+    o = { tracks: o };
+    dojo.forEach( o.tracks, function( trackdef ) {
+        if( 'url' in trackdef ) {
+            trackdef.urlTemplate = trackdef.url;
+            //trackdef.urlTemplate = trackdef.url.replace(/\{refseq\}\/([^/]+)/, "$1/{refseq}");
+            delete trackdef.url;
+        }
+    });
+
+    console.log(o);
+
+    return ConfigAdaptor.JB_json_v1.prototype.regularize_conf.call( this, o, load_args );
+};
+
+/**
+ * Parse the trackInfo.js configuration text into JSON.
+ *
+ * @param {String} conf_text the text in the conf file
+ * @returns {Object} parsed JSON
+ */
+ConfigAdaptor.JB_json_v0.prototype.parse_conf = function( conf_text ) {
+    conf_text.replace( /^[^\{]+/, '' );
+    var conf;
+    return eval( 'conf = ' + conf_text );
+};
+
+

From 56df0e6d2005c4fc16f57fc36275a09a1ea0211f Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Wed, 14 Mar 2012 18:30:32 -0400
Subject: [PATCH 38/49] 1.2.1 backcompat working for feature tracks

---
 compat_121.html                 |  74 +++++++++++
 js/ConfigAdaptor/JB_json_v0.js  |   8 +-
 js/FeatureTrack.js              |   6 +-
 js/NCList_v0.js                 | 216 ++++++++++++++++++++++++++++++++
 js/SeqFeatureStore.js           |  11 --
 js/SeqFeatureStore/NCList.js    |  38 ++++--
 js/SeqFeatureStore/NCList_v0.js | 111 ++++++++++++++++
 7 files changed, 437 insertions(+), 27 deletions(-)
 create mode 100644 compat_121.html
 create mode 100644 js/NCList_v0.js
 create mode 100644 js/SeqFeatureStore/NCList_v0.js

diff --git a/compat_121.html b/compat_121.html
new file mode 100644
index 0000000000..8661224e9b
--- /dev/null
+++ b/compat_121.html
@@ -0,0 +1,74 @@
+<!DOCTYPE html
+	  PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+	  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+
+  <head>
+    <title>JBrowse</title>
+    <link rel="stylesheet" type="text/css" href="jslib/dijit/themes/tundra/tundra.css"></link>
+    <link rel="stylesheet" type="text/css" href="jslib/dojo/resources/dojo.css"></link>
+    <link rel="stylesheet" type="text/css" href="genome.css"></link>
+
+    <script type="text/javascript" src="jslib/dojo/dojo.js" djConfig="isDebug: false"></script>
+    <script type="text/javascript" src="jslib/dojo/jbrowse_dojo.js" ></script>
+
+<!-- js_source_files -->
+<!-- the files between the "js_source_files" comments get replaced
+     when the JS gets minified (see the minification rule in the Makefile) -->
+    <script type="text/javascript" src="js/Browser.js"></script>
+    <script type="text/javascript" src="js/ConfigAdaptor/JB_json_v1.js"></script>
+    <script type="text/javascript" src="js/ConfigAdaptor/JB_json_v0.js"></script>
+    <script type="text/javascript" src="js/Util.js"></script>
+    <script type="text/javascript" src="js/ArrayRepr.js"></script>
+    <script type="text/javascript" src="js/NCList.js"></script>
+    <script type="text/javascript" src="js/NCList_v0.js"></script>
+    <script type="text/javascript" src="js/LazyPatricia.js"></script>
+    <script type="text/javascript" src="js/LazyArray.js"></script>
+    <script type="text/javascript" src="js/Track.js"></script>
+    <script type="text/javascript" src="js/SequenceTrack.js"></script>
+    <script type="text/javascript" src="js/Layout.js"></script>
+    <script type="text/javascript" src="js/SeqFeatureStore.js"></script>
+    <script type="text/javascript" src="js/SeqFeatureStore/NCList.js"></script>
+    <script type="text/javascript" src="js/SeqFeatureStore/NCList_v0.js"></script>
+    <script type="text/javascript" src="js/FeatureTrack.js"></script>
+    <script type="text/javascript" src="js/StaticTrack.js"></script>
+    <script type="text/javascript" src="js/GridTrack.js"></script>
+    <script type="text/javascript" src="js/ImageTrack.js"></script>
+    <script type="text/javascript" src="js/GenomeView.js"></script>
+    <script type="text/javascript" src="js/touchJBrowse.js"></script>
+
+    <script type="text/javascript">
+        window.onerror=function(msg){
+            document.body.setAttribute("JSError",msg);
+        }
+    </script>
+
+<!-- js_source_files -->
+
+    <script type="text/javascript">
+    /* <![CDATA[ */
+           var queryParams = dojo.queryToObject( window.location.search.slice(1) );
+           var dataRoot = queryParams.data || 'data';
+           var b = new Browser({
+                                   include: { url: dataRoot+"/trackInfo.js", version: 0 },
+
+                                   containerID: "GenomeBrowser",
+                                   refSeqs: { url: dataRoot+"/refSeqs.js", version: 0 },
+                                   nameUrl: dataRoot + "/names/root.json",
+                                   defaultTracks: "DNA,gene,mRNA,noncodingRNA",
+                                   queryParams: queryParams,
+                                   location: queryParams.loc,
+                                   forceTracks: queryParams.tracks,
+				   show_nav: queryParams.nav,
+				   show_tracklist: queryParams.tracklist,
+				   show_overview: queryParams.overview
+                               });
+    /* ]]> */
+    </script>
+  </head>
+
+  <body>
+    <div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0; border: 0;"></div>
+  </body>
+</html>
diff --git a/js/ConfigAdaptor/JB_json_v0.js b/js/ConfigAdaptor/JB_json_v0.js
index e3b7621343..3738221f7c 100644
--- a/js/ConfigAdaptor/JB_json_v0.js
+++ b/js/ConfigAdaptor/JB_json_v0.js
@@ -22,14 +22,20 @@ ConfigAdaptor.JB_json_v0.prototype.regularize_conf = function( o, load_args ) {
 
     console.log(o);
 
-    // transform the object to conform to format version 1
+    // transform Ye Olde Confige to conform to format version 1
     o = { tracks: o };
     dojo.forEach( o.tracks, function( trackdef ) {
         if( 'url' in trackdef ) {
             trackdef.urlTemplate = trackdef.url;
             //trackdef.urlTemplate = trackdef.url.replace(/\{refseq\}\/([^/]+)/, "$1/{refseq}");
             delete trackdef.url;
+
+            // TODO: this backendVersion thing is a stopgap until we
+            // refactor far enough to have real pluggable datasources
+            trackdef.backendVersion = 0;
         }
+
+        
     });
 
     console.log(o);
diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index 378583084e..b631dd7d51 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -24,10 +24,12 @@ function FeatureTrack( config, refSeq, browserParams ) {
     this.fields = {};
     this.refSeq = refSeq;
 
-    this.featureStore = new SeqFeatureStore.NCList({
+    var storeclass = config.backendVersion == 0 ? SeqFeatureStore.NCList_v0 : SeqFeatureStore.NCList;
+    this.featureStore = new storeclass({
         urlTemplate: config.urlTemplate,
         baseUrl: config.baseUrl,
-        refSeq: refSeq
+        refSeq: refSeq,
+        track: this
     });
 
     // connect the store and track loadSuccess and loadFailed events
diff --git a/js/NCList_v0.js b/js/NCList_v0.js
new file mode 100644
index 0000000000..e64f295f0b
--- /dev/null
+++ b/js/NCList_v0.js
@@ -0,0 +1,216 @@
+/**
+ * Legacy-compatible NCList for 1.2.1 backcompat.
+ * @extends
+ */
+function NCList_v0() {}
+
+NCList_v0.prototype.importExisting = function(nclist, sublistIndex,
+                                           lazyIndex, baseURL,
+                                           lazyUrlTemplate) {
+    this.topList = nclist;
+    this.sublistIndex = sublistIndex;
+    this.lazyIndex = lazyIndex;
+    this.baseURL = baseURL;
+    this.lazyUrlTemplate = lazyUrlTemplate;
+};
+
+NCList_v0.prototype.fill = function(intervals, sublistIndex) {
+    //intervals: array of arrays of [start, end, ...]
+    //sublistIndex: index into a [start, end] array for storing a sublist
+    //              array. this is so you can use those arrays for something
+    //              else, and keep the NCList_v0 bookkeeping from interfering.
+    //              That's hacky, but keeping a separate copy of the intervals
+    //              in the NCList_v0 seems like a waste (TODO: measure that waste).
+    //half-open?
+    this.sublistIndex = sublistIndex;
+    var myIntervals = intervals;//.concat();
+    //sort by OL
+    myIntervals.sort(function(a, b) {
+        if (a[0] != b[0])
+            return a[0] - b[0];
+        else
+            return b[1] - a[1];
+    });
+    var sublistStack = new Array();
+    var curList = new Array();
+    this.topList = curList;
+    curList.push(myIntervals[0]);
+    var curInterval, topSublist;
+    for (var i = 1, len = myIntervals.length; i < len; i++) {
+        curInterval = myIntervals[i];
+        //if this interval is contained in the previous interval,
+        if (curInterval[1] < myIntervals[i - 1][1]) {
+            //create a new sublist starting with this interval
+            sublistStack.push(curList);
+            curList = new Array(curInterval);
+            myIntervals[i - 1][sublistIndex] = curList;
+        } else {
+            //find the right sublist for this interval
+            while (true) {
+                if (0 == sublistStack.length) {
+                    curList.push(curInterval);
+                    break;
+                } else {
+                    topSublist = sublistStack[sublistStack.length - 1];
+                    if (topSublist[topSublist.length - 1][1] > curInterval[1]) {
+                        //curList is the first (deepest) sublist that
+                        //curInterval fits into
+                        curList.push(curInterval);
+                        break;
+                    } else {
+                        curList = sublistStack.pop();
+                    }
+                }
+            }
+        }
+    }
+};
+
+NCList_v0.prototype.binarySearch = function(arr, item, itemIndex) {
+    var low = -1;
+    var high = arr.length;
+    var mid;
+
+    while (high - low > 1) {
+        mid = (low + high) >>> 1;
+        if (arr[mid][itemIndex] > item)
+            high = mid;
+        else
+            low = mid;
+    }
+
+    //if we're iterating rightward, return the high index;
+    //if leftward, the low index
+    if (1 == itemIndex) return high; else return low;
+};
+
+NCList_v0.prototype.iterHelper = function(arr, from, to, fun, finish,
+                                       inc, searchIndex, testIndex, path) {
+    var len = arr.length;
+    var i = this.binarySearch(arr, from, searchIndex);
+    while ((i < len)
+           && (i >= 0)
+           && ((inc * arr[i][testIndex]) < (inc * to)) ) {
+
+        if ("object" == typeof arr[i][this.lazyIndex]) {
+            var ncl = this;
+            // lazy node
+            if (arr[i][this.lazyIndex].state) {
+                if ("loading" == arr[i][this.lazyIndex].state) {
+                    // node is currenly loading; finish this query once it
+                    // has been loaded
+                    finish.inc();
+                    arr[i][this.lazyIndex].callbacks.push(
+                        function(parentIndex) {
+                            return function(o) {
+                                ncl.iterHelper(o, from, to, fun, finish, inc,
+                                               searchIndex, testIndex,
+                                               path.concat(parentIndex));
+                                finish.dec();
+                            };
+                        }(i)
+                    );
+                } else if ("loaded" == arr[i][this.lazyIndex].state) {
+                    // just continue below
+                } else {
+                    console.log("unknown lazy type: " + arr[i]);
+                }
+            } else {
+                // no "state" property means this node hasn't been loaded,
+                // start loading
+                arr[i][this.lazyIndex].state = "loading";
+                arr[i][this.lazyIndex].callbacks = [];
+                finish.inc();
+                dojo.xhrGet(
+                    {
+                        url: this.baseURL +
+                            this.lazyUrlTemplate.replace(
+                                /\{chunk\}/g,
+                                arr[i][this.lazyIndex].chunk
+                            ),
+                        handleAs: "json",
+                        load: function(lazyFeat, lazyObj,
+                                       sublistIndex, parentIndex) {
+                            return function(o) {
+                                lazyObj.state = "loaded";
+                                lazyFeat[sublistIndex] = o;
+                                ncl.iterHelper(o, from, to,
+                                               fun, finish, inc,
+                                               searchIndex, testIndex,
+                                               path.concat(parentIndex));
+                                for (var c = 0;
+                                     c < lazyObj.callbacks.length;
+                                     c++)
+                                     lazyObj.callbacks[c](o);
+                                finish.dec();
+                            };
+                        }(arr[i], arr[i][this.lazyIndex], this.sublistIndex, i),
+                        error: function() {
+                            finish.dec();
+                        }
+                    });
+            }
+        } else {
+            fun(arr[i], path.concat(i));
+        }
+
+        if (arr[i][this.sublistIndex])
+            this.iterHelper(arr[i][this.sublistIndex], from, to,
+                            fun, finish, inc, searchIndex, testIndex,
+                            path.concat(i));
+        i += inc;
+    }
+};
+
+NCList_v0.prototype.iterate = function(from, to, fun, postFun) {
+    // calls the given function once for each of the
+    // intervals that overlap the given interval
+    //if from <= to, iterates left-to-right, otherwise iterates right-to-left
+
+    //inc: iterate leftward or rightward
+    var inc = (from > to) ? -1 : 1;
+    //searchIndex: search on start or end
+    var searchIndex = (from > to) ? 0 : 1;
+    //testIndex: test on start or end
+    var testIndex = (from > to) ? 1 : 0;
+    var finish = new Finisher(postFun);
+    this.iterHelper(this.topList, from, to, fun, finish,
+                    inc, searchIndex, testIndex, []);
+    finish.finish();
+};
+
+NCList_v0.prototype.histogram = function(from, to, numBins, callback) {
+    //calls callback with a histogram of the feature density
+    //in the given interval
+
+    var result = new Array(numBins);
+    var binWidth = (to - from) / numBins;
+    for (var i = 0; i < numBins; i++) result[i] = 0;
+    //this.histHelper(this.topList, from, to, result, numBins, (to - from) / numBins);
+    this.iterate(from, to,
+                 function(feat) {
+	             var firstBin =
+                         Math.max(0, ((feat[0] - from) / binWidth) | 0);
+                     var lastBin =
+                         Math.min(numBins, ((feat[1] - from) / binWidth) | 0);
+	             for (var bin = firstBin; bin <= lastBin; bin++)
+                         result[bin]++;
+                 },
+                 function() {
+                     callback(result);
+                 }
+                 );
+};
+
+/*
+
+Copyright (c) 2007-2009 The Evolutionary Software Foundation
+
+Created by Mitchell Skinner <mitch_skinner@berkeley.edu>
+
+This package and its accompanying libraries are free software; you can
+redistribute it and/or modify it under the terms of the LGPL (either
+version 2.1, or at your option, any later version) or the Artistic
+License 2.0.  Refer to LICENSE for the full license text.
+
+*/
diff --git a/js/SeqFeatureStore.js b/js/SeqFeatureStore.js
index f93f81e0fd..cc5a7f4d13 100644
--- a/js/SeqFeatureStore.js
+++ b/js/SeqFeatureStore.js
@@ -17,14 +17,3 @@ function SeqFeatureStore(args) {
     this.changed = args.changeCallback;
 };
 
-
-
-/**
- * Return a stored feature given its primary unique identifier.
- */
-
-SeqFeatureStore.prototype.get_feature_by_id = function(id) {
-
-};
-
-
diff --git a/js/SeqFeatureStore/NCList.js b/js/SeqFeatureStore/NCList.js
index b350585906..fb1b013bca 100644
--- a/js/SeqFeatureStore/NCList.js
+++ b/js/SeqFeatureStore/NCList.js
@@ -1,5 +1,7 @@
+var SeqFeatureStore; if( !SeqFeatureStore) SeqFeatureStore = function() {};
+
 /**
- * Implementation of SeqFeatureStore using using nested containment
+ * Implementation of SeqFeatureStore using nested containment
  * lists held in static files that are lazily fetched from the web
  * server.
  *
@@ -7,12 +9,12 @@
  * @augments SeqFeatureStore
  */
 
-var SeqFeatureStore;
-
 SeqFeatureStore.NCList = function(args) {
     SeqFeatureStore.call( this, args );
+    if( !args )
+        return;
 
-    this.nclist = new NCList();
+    this.nclist = this.makeNCList();
 
     this.baseUrl = args.baseUrl;
     this.urlTemplates = { tracklist: args.urlTemplate };
@@ -21,6 +23,10 @@ SeqFeatureStore.NCList = function(args) {
 
 SeqFeatureStore.NCList.prototype = new SeqFeatureStore();
 
+SeqFeatureStore.NCList.prototype.makeNCList = function() {
+    return new NCList();
+};
+
 SeqFeatureStore.NCList.prototype.load = function() {
     var that = this,
          url = Util.resolveUrl(
@@ -29,10 +35,10 @@ SeqFeatureStore.NCList.prototype.load = function() {
                                       {'refseq': this.refSeq.name}
                                     )
                );
-    // fetch the trackList
+    // fetch the trackdata
     dojo.xhrGet({ url: url,
                   handleAs: "json",
-                  load:  function(o) { that.loadSuccess(o, url); },
+                  load:  Util.debugHandler(this,function(o) { that.loadSuccess(o, url); }),
                   error: function(e) { console.error(''+e); that.loadFail(e, url);    }
 	        });
 };
@@ -43,13 +49,7 @@ SeqFeatureStore.NCList.prototype.loadSuccess = function( trackInfo, url ) {
     // average feature density per base
     this.density = trackInfo.featureCount / this.refSeq.length;
 
-    this.attrs = new ArrayRepr(trackInfo.intervals.classes);
-    this.nclist.importExisting( trackInfo.intervals.nclist,
-                                this.attrs,
-                                url,
-                                trackInfo.intervals.urlTemplate,
-                                trackInfo.intervals.lazyClass
-                              );
+    this.loadNCList( trackInfo, url );
 
     if (trackInfo.histograms) {
         this.histograms = trackInfo.histograms;
@@ -60,6 +60,17 @@ SeqFeatureStore.NCList.prototype.loadSuccess = function( trackInfo, url ) {
     }
 };
 
+SeqFeatureStore.NCList.prototype.loadNCList = function( trackInfo, url ) {
+    this.attrs = new ArrayRepr(trackInfo.intervals.classes);
+    this.nclist.importExisting( trackInfo.intervals.nclist,
+                                this.attrs,
+                                url,
+                                trackInfo.intervals.urlTemplate,
+                                trackInfo.intervals.lazyClass
+                              );
+};
+
+
 SeqFeatureStore.NCList.prototype.loadFail = function(trackInfo,url) {
     this.empty = true;
     this.setLoaded();
@@ -70,6 +81,7 @@ SeqFeatureStore.NCList.prototype.histogram = function() {
     return this.nclist.histogram.apply( this.nclist, arguments );
 };
 
+
 SeqFeatureStore.NCList.prototype.iterate = function( startBase, endBase, origFeatCallback, finishCallback ) {
     var that = this;
     var accessors    = this.attrs.accessors(),
diff --git a/js/SeqFeatureStore/NCList_v0.js b/js/SeqFeatureStore/NCList_v0.js
new file mode 100644
index 0000000000..bc18405178
--- /dev/null
+++ b/js/SeqFeatureStore/NCList_v0.js
@@ -0,0 +1,111 @@
+var SeqFeatureStore; if( !SeqFeatureStore) SeqFeatureStore = function() {};
+
+/**
+ * Feature storage backend for backward-compatibility with JBrowse 1.2.1 stores.
+ * @class
+ * @extends SeqFeatureStore.NCList
+ */
+
+SeqFeatureStore.NCList_v0 = function(args) {
+    SeqFeatureStore.NCList.call( this, args );
+
+    this.fields = {};
+    this.track = args.track;
+};
+
+SeqFeatureStore.NCList_v0.prototype = new SeqFeatureStore.NCList('');
+
+
+/**
+ * Delete an object member and return the deleted value.
+ * @private
+ */
+SeqFeatureStore.NCList_v0.prototype._del = function( obj, old ) {
+    var x = obj[old];
+    delete obj[old];
+    return x;
+};
+
+SeqFeatureStore.NCList_v0.prototype.loadSuccess = function( trackInfo, url ) {
+
+    if( trackInfo ) {
+
+        // munge the trackInfo to make the histogram stuff work with v1 code
+        dojo.forEach( trackInfo.histogramMeta, function(m) {
+                          m.arrayParams.urlTemplate = m.arrayParams.urlTemplate.replace(/\{chunk\}/,'{Chunk}');
+                      });
+        trackInfo.histograms = {
+            meta: this._del( trackInfo, 'histogramMeta' ),
+            stats: this._del( trackInfo, 'histStats' )
+        };
+
+        // since the old format had config information inside the
+        // trackdata file, yuckily push it up to the track's config
+        dojo.forEach(
+            ['className','arrowheadClass','subfeatureClasses'],
+            function(varname) {
+                if( !this.track.config.style ) this.track.config.style = {};
+                if( varname in trackInfo )
+                    this.track.config.style[varname] = trackInfo[varname];
+            },this);
+
+        // remember the field offsets from the old-style trackinfo headers
+        this.fields = {};
+        var i;
+        for (i = 0; i < trackInfo.headers.length; i++) {
+            this.fields[trackInfo.headers[i]] = i;
+        }
+        this.subFields = {};
+        if (trackInfo.subfeatureHeaders) {
+            for (i = 0; i < trackInfo.subfeatureHeaders.length; i++) {
+                this.subFields[trackInfo.subfeatureHeaders[i]] = i;
+            }
+        }
+
+    }
+
+    return SeqFeatureStore.NCList.prototype.loadSuccess.call( this, trackInfo, url );
+};
+
+SeqFeatureStore.NCList_v0.prototype.makeNCList = function() {
+    return new NCList_v0();
+};
+
+SeqFeatureStore.NCList_v0.prototype.loadNCList = function( trackInfo, url ) {
+    this.nclist.importExisting(trackInfo.featureNCList,
+                                 trackInfo.sublistIndex,
+                                 trackInfo.lazyIndex,
+                                 url,
+                                 trackInfo.lazyfeatureUrlTemplate);
+};
+
+
+SeqFeatureStore.NCList_v0.prototype.iterate = function( startBase, endBase, origFeatCallback, finishCallback ) {
+    var that = this,
+        fields = this.fields,
+        subFields = this.subFields,
+        get = function(fieldname) {
+            var f = fields[fieldname];
+            if( f >= 0 )
+                return this[f];
+            else
+                return undefined;
+        },
+        subget = function(fieldname) {
+            var f = subFields[fieldname];
+            if( f >= 0 )
+                return this[f];
+            else
+                return undefined;
+        },
+        featCallBack = function( feature, path ) {
+            feature.get = get;
+            dojo.forEach( feature.get('subfeatures'), function(f) {
+                f.get = subget;
+            });
+            return origFeatCallback( feature, path );
+        };
+
+    return this.nclist.iterate.call( this.nclist, startBase, endBase, featCallBack, finishCallback );
+};
+

From f4417dade7df862972cbd74439b602b0f78f9c43 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Thu, 15 Mar 2012 15:24:56 -0400
Subject: [PATCH 39/49] improved some inline documentation

---
 js/FeatureTrack.js           | 3 +++
 js/ImageTrack.js             | 3 +++
 js/SeqFeatureStore.js        | 1 +
 js/SeqFeatureStore/NCList.js | 2 +-
 4 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index b631dd7d51..db657b521d 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -24,6 +24,9 @@ function FeatureTrack( config, refSeq, browserParams ) {
     this.fields = {};
     this.refSeq = refSeq;
 
+    // TODO: this featureStore object should eventuallly be
+    // instantiated by Browser and passed into this constructor, not
+    // constructed here.
     var storeclass = config.backendVersion == 0 ? SeqFeatureStore.NCList_v0 : SeqFeatureStore.NCList;
     this.featureStore = new storeclass({
         urlTemplate: config.urlTemplate,
diff --git a/js/ImageTrack.js b/js/ImageTrack.js
index 0ec640d65f..fe2621a084 100644
--- a/js/ImageTrack.js
+++ b/js/ImageTrack.js
@@ -1,7 +1,10 @@
 // VIEW
 
 /**
+ * A track that displays tiled images (PNGs, or other images) along
+ * the reference sequence.
  * @class
+ * @extends Track
  */
 function ImageTrack(config, refSeq, browserParams) {
     Track.call(this, config.label, config.key,
diff --git a/js/SeqFeatureStore.js b/js/SeqFeatureStore.js
index cc5a7f4d13..1a3e2b6b9d 100644
--- a/js/SeqFeatureStore.js
+++ b/js/SeqFeatureStore.js
@@ -6,6 +6,7 @@
  * Bio::DB::SeqFeature::Store.
   *
  * @class
+ * @extends Store
  * @constructor
  *
  */
diff --git a/js/SeqFeatureStore/NCList.js b/js/SeqFeatureStore/NCList.js
index fb1b013bca..7ae75e6ed2 100644
--- a/js/SeqFeatureStore/NCList.js
+++ b/js/SeqFeatureStore/NCList.js
@@ -6,7 +6,7 @@ var SeqFeatureStore; if( !SeqFeatureStore) SeqFeatureStore = function() {};
  * server.
  *
  * @class
- * @augments SeqFeatureStore
+ * @extends SeqFeatureStore
  */
 
 SeqFeatureStore.NCList = function(args) {

From c59d0459da117ace2bdc98aab3ff0187fc6d8179 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Thu, 15 Mar 2012 15:40:24 -0400
Subject: [PATCH 40/49] added Store.js base class for datastores

---
 index.html            |  2 ++
 js/SeqFeatureStore.js |  4 +++-
 js/Store.js           | 38 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 43 insertions(+), 1 deletion(-)
 create mode 100644 js/Store.js

diff --git a/index.html b/index.html
index b8b6d40a5f..92cac3c8a0 100644
--- a/index.html
+++ b/index.html
@@ -27,6 +27,8 @@
     <script type="text/javascript" src="js/Track.js"></script>
     <script type="text/javascript" src="js/SequenceTrack.js"></script>
     <script type="text/javascript" src="js/Layout.js"></script>
+
+    <script type="text/javascript" src="js/Store.js"></script>
     <script type="text/javascript" src="js/SeqFeatureStore.js"></script>
     <script type="text/javascript" src="js/SeqFeatureStore/NCList.js"></script>
     <script type="text/javascript" src="js/FeatureTrack.js"></script>
diff --git a/js/SeqFeatureStore.js b/js/SeqFeatureStore.js
index 1a3e2b6b9d..cfc7897006 100644
--- a/js/SeqFeatureStore.js
+++ b/js/SeqFeatureStore.js
@@ -8,13 +8,15 @@
  * @class
  * @extends Store
  * @constructor
- *
  */
 
 function SeqFeatureStore(args) {
+    Store.call(this, args);
+
     if( !args ) return;
 
     this.loaded  = args.loaded;
     this.changed = args.changeCallback;
 };
 
+SeqFeatureStore.prototype = new Store('');
diff --git a/js/Store.js b/js/Store.js
new file mode 100644
index 0000000000..b721f4949d
--- /dev/null
+++ b/js/Store.js
@@ -0,0 +1,38 @@
+/**
+ * Base class for all JBrowse data stores.
+ * @class
+ */
+
+function Store( args ) {
+};
+
+Store.prototype.loadSuccess = function( data, url ) {
+};
+
+Store.prototype.loadFail = function(error) {
+    this.empty = true;
+    this.setLoaded();
+};
+
+Store.prototype.load = function(url) {
+    var that = this;
+    dojo.xhrGet({url: url,
+                 handleAs: "json",
+                 load: function(o)  { that.loadSuccess(o, url); },
+                 error: function(o) { that.loadFail(o, url); }
+	        });
+};
+
+Store.prototype.setLoaded = function() {
+    this.loaded = true;
+    this.hideAll();
+    this.changed();
+};
+
+
+Store.prototype.hideAll = function() {
+};
+
+
+Store.prototype.changed = function() {
+};

From 4c34db34d8285fdd42309f03acee2fab78c71ed2 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Fri, 16 Mar 2012 14:46:30 -0700
Subject: [PATCH 41/49] split data-representation code out of ImageTrack.js
 into TiledImageStore/Fixed.js

---
 index.html                  |   2 +
 js/ImageTrack.js            | 138 ++++++++++++++----------------------
 js/Store.js                 |   2 +-
 js/TiledImageStore/Fixed.js | 103 +++++++++++++++++++++++++++
 js/Track.js                 |   4 ++
 5 files changed, 165 insertions(+), 84 deletions(-)
 create mode 100644 js/TiledImageStore/Fixed.js

diff --git a/index.html b/index.html
index 92cac3c8a0..bd4f077a92 100644
--- a/index.html
+++ b/index.html
@@ -31,6 +31,8 @@
     <script type="text/javascript" src="js/Store.js"></script>
     <script type="text/javascript" src="js/SeqFeatureStore.js"></script>
     <script type="text/javascript" src="js/SeqFeatureStore/NCList.js"></script>
+    <script type="text/javascript" src="js/TiledImageStore/Fixed.js"></script>
+
     <script type="text/javascript" src="js/FeatureTrack.js"></script>
     <script type="text/javascript" src="js/StaticTrack.js"></script>
     <script type="text/javascript" src="js/GridTrack.js"></script>
diff --git a/js/ImageTrack.js b/js/ImageTrack.js
index fe2621a084..04ed9dac26 100644
--- a/js/ImageTrack.js
+++ b/js/ImageTrack.js
@@ -9,81 +9,56 @@
 function ImageTrack(config, refSeq, browserParams) {
     Track.call(this, config.label, config.key,
                false, browserParams.changeCallback);
+
     this.refSeq = refSeq;
     this.trackPadding = browserParams.trackPadding;
-    this.tileToImage = {};
-    this.zoomCache = {};
-    this.url = Util.resolveUrl(config.baseUrl,
-                               Util.fillTemplate(config.urlTemplate,
-                                                 {'refseq': refSeq.name}) );
-    this.load(this.url);
-
-    this.imgErrorHandler = function(ev) {
-        var img = ev.currentTarget || ev.srcElement;
-        img.style.display = "none";
-        dojo.stopEvent(ev);
-    };
+
+    this.config = config;
+
+    this.imagestore = new TiledImageStore.Fixed({
+                              refSeq: refSeq,
+                              urlTemplate: config.urlTemplate,
+                              baseUrl: config.baseUrl,
+                              track: this
+                          });
+    dojo.connect( this.imagestore, 'loadSuccess', this, 'loadSuccess' );
+    dojo.connect( this.imagestore, 'loadFail',    this, 'loadFail'    );
+
+    this.imagestore.load();
 }
 
 ImageTrack.prototype = new Track("");
 
-ImageTrack.prototype.loadSuccess = function(o) {
-    //tileWidth: width, in pixels, of the tiles
-    this.tileWidth = o.tileWidth;
-    this.align = o.align;
-    //zoomLevels: array of {basesPerTile, urlPrefix} hashes
-    this.zoomLevels = o.zoomLevels;
+ImageTrack.prototype.loadSuccess = function(o,url) {
+    this.empty = this.imagestore.empty;
     this.setLoaded();
 };
 
 ImageTrack.prototype.setViewInfo = function(heightUpdate, numBlocks,
                                             trackDiv, labelDiv,
                                             widthPct, widthPx, scale) {
-    Track.prototype.setViewInfo.apply(this, [heightUpdate, numBlocks,
-                                             trackDiv, labelDiv,
-                                             widthPct, widthPx, scale]);
-    this.setLabel(this.key);
+    Track.prototype.setViewInfo.apply( this, arguments );
+    this.setLabel( this.key );
 };
 
-ImageTrack.prototype.getZoom = function(scale) {
-    var result = this.zoomCache[scale];
-    if (result) return result;
-
-    result = this.zoomLevels[0];
-    var desiredBases = this.tileWidth / scale;
-    for (i = 1; i < this.zoomLevels.length; i++) {
-        if (Math.abs(this.zoomLevels[i].basesPerTile - desiredBases)
-            < Math.abs(result.basesPerTile - desiredBases))
-            result = this.zoomLevels[i];
-    }
-
-    this.zoomCache[scale] = result;
-    return result;
+ImageTrack.prototype.handleImageError = function(ev) {
+    var img = ev.currentTarget || ev.srcElement;
+    img.style.display = "none";
+    dojo.stopEvent(ev);
 };
 
-ImageTrack.prototype.getImages = function(zoom, startBase, endBase) {
-    //var startTile = ((startBase - this.refSeq.start) / zoom.basesPerTile) | 0;
-    //var endTile = ((endBase - this.refSeq.start) / zoom.basesPerTile) | 0;
-    var startTile = (startBase / zoom.basesPerTile) | 0;
-    var endTile = (endBase / zoom.basesPerTile) | 0;
-    startTile = Math.max(startTile, 0);
-    var result = [];
-    var im;
-    for (var i = startTile; i <= endTile; i++) {
-	im = this.tileToImage[i];
-	if (!im) {
-	    im = document.createElement("img");
-            dojo.connect(im, "onerror", this.imgErrorHandler);
-            im.src = Util.resolveUrl(this.url, zoom.urlPrefix + i + ".png");
-            //TODO: need image coord systems that don't start at 0?
-	    im.startBase = (i * zoom.basesPerTile); // + this.refSeq.start;
-	    im.baseWidth = zoom.basesPerTile;
-	    im.tileNum = i;
-	    this.tileToImage[i] = im;
-	}
-	result.push(im);
-    }
-    return result;
+
+/**
+ * @private
+ */
+ImageTrack.prototype._makeImageLoadHandler = function( img, blockIndex, blockWidth ) {
+    var that = this;
+    return function() {
+        img.style.height = img.height + "px";
+        img.style.width  = (100 * (img.baseWidth / blockWidth)) + "%";
+        that.heightUpdate( img.height, blockIndex );
+        return true;
+    };
 };
 
 ImageTrack.prototype.fillBlock = function(blockIndex, block,
@@ -91,48 +66,44 @@ ImageTrack.prototype.fillBlock = function(blockIndex, block,
                                           leftBase, rightBase,
                                           scale, stripeWidth,
                                           containerStart, containerEnd) {
-    var zoom = this.getZoom(scale);
     var blockWidth = rightBase - leftBase;
-    var images = this.getImages(zoom, leftBase, rightBase);
+    var images = this.imagestore.getImages( scale, leftBase, rightBase );
     var im;
 
-    var self = this;
-    var makeLoadHandler = function(img, bi) {
-        return function() {
-            img.style.height = img.height + "px";
-            img.style.width = (100 * (img.baseWidth / blockWidth)) + "%";
-            self.heightUpdate(img.height, bi);
-        };
-    };
-
-    for (var i = 0; i < images.length; i++) {
-	im = images[i];
+    dojo.forEach( images, function(im) {
         im.className = 'image-track';
 	if (!(im.parentNode && im.parentNode.parentNode)) {
             im.style.position = "absolute";
             im.style.left = (100 * ((im.startBase - leftBase) / blockWidth)) + "%";
-            switch (self.align) {
+            switch (this.config.align) {
             case "top":
                 im.style.top = "0px";
                 break;
             case "bottom":
+            default:
                 im.style.bottom = this.trackPadding + "px";
                 break;
             }
             block.appendChild(im);
 	}
-        if (im.complete) {
-            makeLoadHandler(im, blockIndex)();
-        } else {
-            dojo.connect(im, "onload", makeLoadHandler(im, blockIndex));
-        }
-    }
+
+        // make an onload handler for when the image is fetched that
+        // will update the height and width of the track
+        var loadhandler = this._makeImageLoadHandler( im, blockIndex, blockWidth );
+        if( im.complete )
+            // just call the handler ourselves if the image is already loaded
+            loadhandler();
+        else
+            // otherwise schedule it
+            dojo.connect( im, "onload", loadhandler );
+
+    }, this);
 };
 
 ImageTrack.prototype.startZoom = function(destScale, destStart, destEnd) {
     if (this.empty) return;
-    this.tileToImage = {};
-    this.getImages(this.getZoom(destScale), destStart, destEnd);
+    this.imagestore.clearCache();
+    this.imagestore.getImages( destScale, destStart, destEnd );
 };
 
 ImageTrack.prototype.endZoom = function(destScale, destBlockBases) {
@@ -141,7 +112,7 @@ ImageTrack.prototype.endZoom = function(destScale, destBlockBases) {
 
 ImageTrack.prototype.clear = function() {
     Track.prototype.clear.apply(this);
-    this.tileToImage = {};
+    this.imagestore.clearCache();
 };
 
 ImageTrack.prototype.transfer = function(sourceBlock, destBlock, scale,
@@ -162,7 +133,8 @@ ImageTrack.prototype.transfer = function(sourceBlock, destBlock, scale,
 		im.style.left = (100 * ((im.startBase - destLeft) / (destRight - destLeft))) + "%";
 		destBlock.appendChild(im);
 	    } else {
-		delete this.tileToImage[im.tileNum];
+                // don't move it, and even uncache it
+		this.imagestore.unCacheImage( im );
 	    }
 	}
     }
diff --git a/js/Store.js b/js/Store.js
index b721f4949d..76854f2616 100644
--- a/js/Store.js
+++ b/js/Store.js
@@ -16,7 +16,7 @@ Store.prototype.loadFail = function(error) {
 
 Store.prototype.load = function(url) {
     var that = this;
-    dojo.xhrGet({url: url,
+    dojo.xhrGet({url: url || this.url,
                  handleAs: "json",
                  load: function(o)  { that.loadSuccess(o, url); },
                  error: function(o) { that.loadFail(o, url); }
diff --git a/js/TiledImageStore/Fixed.js b/js/TiledImageStore/Fixed.js
new file mode 100644
index 0000000000..4c253d0a69
--- /dev/null
+++ b/js/TiledImageStore/Fixed.js
@@ -0,0 +1,103 @@
+/**
+ * @namespace
+ */
+var TiledImageStore; if( !TiledImageStore ) TiledImageStore = {};
+
+/**
+ * Implements a store for image tiles that are only available at a
+ * fixed set of sizes and zoom levels.  Most often used with
+ * pre-generated image tiles served statically.
+ * @class
+ * @extends Store
+ */
+
+TiledImageStore.Fixed = function(args) {
+    Store.call( this, args );
+
+    this.tileToImage = {};
+    this.zoomCache = {};
+
+    this.refSeq = args.refSeq;
+
+    this.url = Util.resolveUrl(
+                   args.baseUrl,
+                   Util.fillTemplate( args.urlTemplate,
+                                      {'refseq': this.refSeq.name } )
+               );
+};
+
+TiledImageStore.Fixed.prototype = new Store('');
+
+TiledImageStore.Fixed.prototype.loadSuccess = function(o) {
+    //tileWidth: width, in pixels, of the tiles
+    this.tileWidth = o.tileWidth;
+    this.align = o.align;
+    //zoomLevels: array of {basesPerTile, urlPrefix} hashes
+    this.zoomLevels = o.zoomLevels;
+    this.setLoaded();
+};
+
+TiledImageStore.Fixed.prototype.getZoom = function(scale) {
+    var result = this.zoomCache[scale];
+    if (result) return result;
+
+    result = this.zoomLevels[0];
+    var desiredBases = this.tileWidth / scale;
+    for (i = 1; i < this.zoomLevels.length; i++) {
+        if (Math.abs(this.zoomLevels[i].basesPerTile - desiredBases)
+            < Math.abs(result.basesPerTile - desiredBases))
+            result = this.zoomLevels[i];
+    }
+
+    this.zoomCache[scale] = result;
+    return result;
+};
+
+/**
+ * Fetch an array of <code>&lt;img&gt;</code> elements for the image
+ * tiles that should be displayed for a certain magnification scale
+ * and section of the reference.
+ * @param {Number} scale     the current ratio of pixels per base in the view
+ * @param {Number} startBase the start of the region (in interbase coordinates)
+ * @param {Number} endBase   the end of the region   (in interbase coordinates)
+ */
+TiledImageStore.Fixed.prototype.getImages = function( scale, startBase, endBase ) {
+
+    var zoom = this.getZoom( scale );
+
+    var startTile = Math.max( startBase / zoom.basesPerTile, 0 ) | 0;
+    var endTile   =           endBase   / zoom.basesPerTile      | 0;
+
+    var result = [];
+    var im;
+    for (var i = startTile; i <= endTile; i++) {
+	im = this.tileToImage[i];
+	if (!im) {
+	    im = document.createElement("img");
+            dojo.connect(im, "onerror", this.handleImageError );
+            im.src = Util.resolveUrl(this.url, zoom.urlPrefix + i + ".png");
+            //TODO: need image coord systems that don't start at 0?
+	    im.startBase = (i * zoom.basesPerTile); // + this.refSeq.start;
+	    im.baseWidth = zoom.basesPerTile;
+	    im.tileNum = i;
+	    this.tileToImage[i] = im;
+	}
+	result.push(im);
+    }
+    return result;
+};
+
+
+/**
+ * Clear the store's cache of image elements.
+ */
+TiledImageStore.Fixed.prototype.clearCache = function() {
+    this.tileToImage = {};
+};
+
+/**
+ * Remove the given image element from the cache.
+ */
+TiledImageStore.Fixed.prototype.unCacheImage = function( /**HTMLImageElement*/ im) {
+    delete this.tileToImage[ im.tileNum ];
+};
diff --git a/js/Track.js b/js/Track.js
index 5ae328f448..f61470ea34 100644
--- a/js/Track.js
+++ b/js/Track.js
@@ -22,6 +22,10 @@ Track.prototype.load = function(url) {
 	        });
 };
 
+Track.prototype.loadSuccess = function(error) {
+    this.setLoaded();
+};
+
 Track.prototype.loadFail = function(error) {
     this.empty = true;
     this.setLoaded();

From 496842385c46bd298fda3c0977c0cfd2dea66959 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Fri, 16 Mar 2012 14:50:08 -0700
Subject: [PATCH 42/49] make TiledImageStore.Fixed.getZoom() a private method

---
 js/TiledImageStore/Fixed.js | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/js/TiledImageStore/Fixed.js b/js/TiledImageStore/Fixed.js
index 4c253d0a69..de22d293ed 100644
--- a/js/TiledImageStore/Fixed.js
+++ b/js/TiledImageStore/Fixed.js
@@ -37,7 +37,10 @@ TiledImageStore.Fixed.prototype.loadSuccess = function(o) {
     this.setLoaded();
 };
 
-TiledImageStore.Fixed.prototype.getZoom = function(scale) {
+/**
+ * @private
+ */
+TiledImageStore.Fixed.prototype._getZoom = function(scale) {
     var result = this.zoomCache[scale];
     if (result) return result;
 
@@ -63,7 +66,7 @@ TiledImageStore.Fixed.prototype.getZoom = function(scale) {
  */
 TiledImageStore.Fixed.prototype.getImages = function( scale, startBase, endBase ) {
 
-    var zoom = this.getZoom( scale );
+    var zoom = this._getZoom( scale );
 
     var startTile = Math.max( startBase / zoom.basesPerTile, 0 ) | 0;
     var endTile   =           endBase   / zoom.basesPerTile      | 0;

From d7dc647f8888c9e2472b892138bffb092d1bd955 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Fri, 16 Mar 2012 16:26:21 -0700
Subject: [PATCH 43/49] remove some stray console.log() calls

---
 js/ConfigAdaptor/JB_json_v0.js | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/js/ConfigAdaptor/JB_json_v0.js b/js/ConfigAdaptor/JB_json_v0.js
index 3738221f7c..9dfefee25a 100644
--- a/js/ConfigAdaptor/JB_json_v0.js
+++ b/js/ConfigAdaptor/JB_json_v0.js
@@ -20,8 +20,6 @@ ConfigAdaptor.JB_json_v0.prototype = new ConfigAdaptor.JB_json_v1();
  */
 ConfigAdaptor.JB_json_v0.prototype.regularize_conf = function( o, load_args ) {
 
-    console.log(o);
-
     // transform Ye Olde Confige to conform to format version 1
     o = { tracks: o };
     dojo.forEach( o.tracks, function( trackdef ) {
@@ -34,12 +32,8 @@ ConfigAdaptor.JB_json_v0.prototype.regularize_conf = function( o, load_args ) {
             // refactor far enough to have real pluggable datasources
             trackdef.backendVersion = 0;
         }
-
-        
     });
 
-    console.log(o);
-
     return ConfigAdaptor.JB_json_v1.prototype.regularize_conf.call( this, o, load_args );
 };
 

From 771d661c1aac7d728340c2593bae5baad8c8c48f Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Fri, 16 Mar 2012 16:32:31 -0700
Subject: [PATCH 44/49] got 1.2.1 backcompat working for image tracks

---
 compat_121.html                |  5 +++++
 js/ImageTrack.js               |  5 ++++-
 js/TiledImageStore/Fixed.js    | 14 ++++++++++++--
 js/TiledImageStore/Fixed_v0.js | 17 +++++++++++++++++
 4 files changed, 38 insertions(+), 3 deletions(-)
 create mode 100644 js/TiledImageStore/Fixed_v0.js

diff --git a/compat_121.html b/compat_121.html
index 8661224e9b..e78adf553c 100644
--- a/compat_121.html
+++ b/compat_121.html
@@ -28,9 +28,14 @@
     <script type="text/javascript" src="js/Track.js"></script>
     <script type="text/javascript" src="js/SequenceTrack.js"></script>
     <script type="text/javascript" src="js/Layout.js"></script>
+
+    <script type="text/javascript" src="js/Store.js"></script>
     <script type="text/javascript" src="js/SeqFeatureStore.js"></script>
     <script type="text/javascript" src="js/SeqFeatureStore/NCList.js"></script>
     <script type="text/javascript" src="js/SeqFeatureStore/NCList_v0.js"></script>
+    <script type="text/javascript" src="js/TiledImageStore/Fixed.js"></script>
+    <script type="text/javascript" src="js/TiledImageStore/Fixed_v0.js"></script>
+
     <script type="text/javascript" src="js/FeatureTrack.js"></script>
     <script type="text/javascript" src="js/StaticTrack.js"></script>
     <script type="text/javascript" src="js/GridTrack.js"></script>
diff --git a/js/ImageTrack.js b/js/ImageTrack.js
index 04ed9dac26..ef2b32720f 100644
--- a/js/ImageTrack.js
+++ b/js/ImageTrack.js
@@ -15,7 +15,10 @@ function ImageTrack(config, refSeq, browserParams) {
 
     this.config = config;
 
-    this.imagestore = new TiledImageStore.Fixed({
+    // TODO: the imagestore should be passed in as an arg to the
+    // constructor, not instantiated here
+    var storeclass = config.backendVersion == 0 ? TiledImageStore.Fixed_v0 : TiledImageStore.Fixed;
+    this.imagestore = new storeclass({
                               refSeq: refSeq,
                               urlTemplate: config.urlTemplate,
                               baseUrl: config.baseUrl,
diff --git a/js/TiledImageStore/Fixed.js b/js/TiledImageStore/Fixed.js
index de22d293ed..5d6de7a2cb 100644
--- a/js/TiledImageStore/Fixed.js
+++ b/js/TiledImageStore/Fixed.js
@@ -13,6 +13,8 @@ var TiledImageStore; if( !TiledImageStore ) TiledImageStore = {};
 
 TiledImageStore.Fixed = function(args) {
     Store.call( this, args );
+    if( !args )
+        return;
 
     this.tileToImage = {};
     this.zoomCache = {};
@@ -46,7 +48,7 @@ TiledImageStore.Fixed.prototype._getZoom = function(scale) {
 
     result = this.zoomLevels[0];
     var desiredBases = this.tileWidth / scale;
-    for (i = 1; i < this.zoomLevels.length; i++) {
+    for (var i = 1; i < this.zoomLevels.length; i++) {
         if (Math.abs(this.zoomLevels[i].basesPerTile - desiredBases)
             < Math.abs(result.basesPerTile - desiredBases))
             result = this.zoomLevels[i];
@@ -78,7 +80,7 @@ TiledImageStore.Fixed.prototype.getImages = function( scale, startBase, endBase
 	if (!im) {
 	    im = document.createElement("img");
             dojo.connect(im, "onerror", this.handleImageError );
-            im.src = Util.resolveUrl(this.url, zoom.urlPrefix + i + ".png");
+            im.src = this._imageSource( zoom, i );
             //TODO: need image coord systems that don't start at 0?
 	    im.startBase = (i * zoom.basesPerTile); // + this.refSeq.start;
 	    im.baseWidth = zoom.basesPerTile;
@@ -90,6 +92,14 @@ TiledImageStore.Fixed.prototype.getImages = function( scale, startBase, endBase
     return result;
 };
 
+/**
+ * Gives the image source for a given zoom (as returned by _getZoom())
+ * and tileIndex.
+ * @private
+ */
+TiledImageStore.Fixed.prototype._imageSource = function( zoom, tileIndex ) {
+    return Util.resolveUrl(this.url, zoom.urlPrefix + tileIndex + ".png");
+};
 
 /**
  * Clear the store's cache of image elements.
diff --git a/js/TiledImageStore/Fixed_v0.js b/js/TiledImageStore/Fixed_v0.js
new file mode 100644
index 0000000000..b701269eb8
--- /dev/null
+++ b/js/TiledImageStore/Fixed_v0.js
@@ -0,0 +1,17 @@
+/**
+ * @namespace
+ */
+var TiledImageStore; if( !TiledImageStore ) TiledImageStore = {};
+
+/**
+ * Subclass of TiledImageStore.Fixed to provide backward-compatibility
+ * with image stores formatted with JBrowse 1.2.1.
+ * @class
+ * @extends TiledImageStore.Fixed
+ */
+TiledImageStore.Fixed_v0 = TiledImageStore.Fixed;
+TiledImageStore.Fixed_v0.prototype = new TiledImageStore.Fixed('');
+
+TiledImageStore.Fixed_v0.prototype._imageSource = function( zoom, tileIndex ) {
+    return Util.resolveUrl( this.url, '../../' + zoom.urlPrefix + tileIndex + ".png" );
+};

From 647a448097b1fb6de637016891ae9f3e2dadfc97 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Sat, 17 Mar 2012 10:16:51 -0700
Subject: [PATCH 45/49] tweak sequencetrack inline docs

---
 js/SequenceTrack.js | 37 +++++++++++++++++++------------------
 1 file changed, 19 insertions(+), 18 deletions(-)

diff --git a/js/SequenceTrack.js b/js/SequenceTrack.js
index bf04d4e69a..2b006fd5f1 100644
--- a/js/SequenceTrack.js
+++ b/js/SequenceTrack.js
@@ -1,23 +1,24 @@
 // VIEW
 
 /**
+ * Track to display the underlying reference sequence, when zoomed in
+ * far enough.
  * @class
+ * @constructor
+ * @param {Object} config
+ *   key:   display text track name
+ *   label: internal track name (no spaces or odd characters)
+ *   urlTemplate: url of directory in which to find the sequence chunks
+ *   chunkSize: size of sequence chunks, in characters
+ * @param {Object} refSeq
+ *  start: refseq start
+ *  end:   refseq end
+ * @param {Object} browserParams
+ *  changeCallback: function to call once JSON is loaded
+ *  trackPadding: distance in px between tracks
+ *  charWidth: width, in pixels, of sequence base characters
+ *  seqHeight: height, in pixels, of sequence elements
  */
-function SequenceTrack(trackMeta, refSeq, browserParams) {
-    //trackMeta: object with:
-    //  key:   display text track name
-    //  label: internal track name (no spaces or odd characters)
-    //  urlTemplate: url of directory in which to find the sequence chunks
-    //  chunkSize: size of sequence chunks, in characters
-    //refSeq: object with:
-    //  start: refseq start
-    //  end:   refseq end
-    //browserParams: object with:
-    //  changeCallback: function to call once JSON is loaded
-    //  trackPadding: distance in px between tracks
-    //  charWidth: width, in pixels, of sequence base characters
-    //  seqHeight: height, in pixels, of sequence elements
-
     Track.call(this, trackMeta.label, trackMeta.key,
                false, browserParams.changeCallback);
     this.browserParams = browserParams;
@@ -127,9 +128,9 @@ SequenceTrack.prototype.renderSeqDiv = function ( start, end, seq ) {
 };
 
 /**
- * @param start start coord, in interbase
- * @param end end coord, in interbase
- * @param callback function that takes ( start, end, seq )
+ * @param {Number} start start coord, in interbase
+ * @param {Number} end end coord, in interbase
+ * @param {Function} callback function that takes ( start, end, seq )
  */
 SequenceTrack.prototype.getRange = function( /**Number*/ start, /**Number*/ end, /**Function*/ callback) {
     var firstChunk = Math.floor( Math.max(0,start) / this.chunkSize);

From eacfaac876eaa1004218edfca44ecc2a7600af06 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Sat, 17 Mar 2012 10:32:15 -0700
Subject: [PATCH 46/49] refactor SequenceTrack variables a bit

---
 js/SequenceTrack.js | 39 ++++++++++++++++++++++-----------------
 1 file changed, 22 insertions(+), 17 deletions(-)

diff --git a/js/SequenceTrack.js b/js/SequenceTrack.js
index 2b006fd5f1..850fd71508 100644
--- a/js/SequenceTrack.js
+++ b/js/SequenceTrack.js
@@ -19,18 +19,23 @@
  *  charWidth: width, in pixels, of sequence base characters
  *  seqHeight: height, in pixels, of sequence elements
  */
-    Track.call(this, trackMeta.label, trackMeta.key,
-               false, browserParams.changeCallback);
-    this.browserParams = browserParams;
-    this.refSeq = refSeq;
-    this.trackMeta = trackMeta;
-    this.setLoaded();
+function SequenceTrack(config, refSeq, browserParams) {
+
+    Track.call( this, config.label, config.key,
+                false, browserParams.changeCallback );
+
+    this.config = config;
+
+    this.charWidth = browserParams.charWidth;
+    this.seqHeight = browserParams.seqHeight;
+
     this.chunks = [];
-    this.chunkSize = trackMeta.chunkSize;
-    this.url = Util.resolveUrl(trackMeta.baseUrl,
-                               Util.fillTemplate(trackMeta.urlTemplate,
-                                                 {'refseq': refSeq.name}) );
+    this.chunkSize = config.chunkSize;
+    this.url = Util.resolveUrl( config.baseUrl,
+                                Util.fillTemplate( config.urlTemplate,
+                                                   {'refseq': refSeq.name} ));
 
+    this.setLoaded();
 }
 
 SequenceTrack.prototype = new Track("");
@@ -41,7 +46,7 @@ SequenceTrack.prototype.startZoom = function(destScale, destStart, destEnd) {
 };
 
 SequenceTrack.prototype.endZoom = function(destScale, destBlockBases) {
-    if (destScale == this.browserParams.charWidth) this.show();
+    if (destScale == this.charWidth) this.show();
     Track.prototype.clear.apply(this);
 };
 
@@ -51,7 +56,7 @@ SequenceTrack.prototype.setViewInfo = function(genomeView, numBlocks,
     Track.prototype.setViewInfo.apply(this, [genomeView, numBlocks,
                                              trackDiv, labelDiv,
                                              widthPct, widthPx, scale]);
-    if (scale == this.browserParams.charWidth) {
+    if (scale == this.charWidth) {
         this.show();
     } else {
         this.hide();
@@ -67,7 +72,7 @@ SequenceTrack.prototype.fillBlock = function(blockIndex, block,
                                              scale, stripeWidth,
                                              containerStart, containerEnd) {
     var that = this;
-    if (scale == this.browserParams.charWidth) {
+    if (scale == this.charWidth) {
         this.show();
     } else {
         this.hide();
@@ -99,7 +104,7 @@ SequenceTrack.prototype.fillBlock = function(blockIndex, block,
                            seqNode.appendChild( comp );
                        }
                      );
-        this.heightUpdate(this.browserParams.seqHeight, blockIndex);
+        this.heightUpdate(this.seqHeight, blockIndex);
     } else {
         this.heightUpdate(0, blockIndex);
     }
@@ -132,10 +137,10 @@ SequenceTrack.prototype.renderSeqDiv = function ( start, end, seq ) {
  * @param {Number} end end coord, in interbase
  * @param {Function} callback function that takes ( start, end, seq )
  */
-SequenceTrack.prototype.getRange = function( /**Number*/ start, /**Number*/ end, /**Function*/ callback) {
-    var firstChunk = Math.floor( Math.max(0,start) / this.chunkSize);
-    var lastChunk = Math.floor((end - 1) / this.chunkSize);
+SequenceTrack.prototype.getRange = function( start, end, callback) {
     var chunkSize = this.chunkSize;
+    var firstChunk = Math.floor( Math.max(0,start) / chunkSize );
+    var lastChunk  = Math.floor( (end - 1)         / chunkSize );
     var chunk;
 
     // if a callback spans more than one chunk, we need to wrap the

From a3621d7b1d952fd22cc394f1ace0fdac59301672 Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Sat, 17 Mar 2012 13:50:32 -0700
Subject: [PATCH 47/49] extract model code out of SequenceTrack into new class
 SequenceStore.StaticChunked

---
 index.html                        |   1 +
 js/SequenceStore/StaticChunked.js | 111 ++++++++++++++++++++++++++++++
 js/SequenceTrack.js               |  92 +++----------------------
 3 files changed, 122 insertions(+), 82 deletions(-)
 create mode 100644 js/SequenceStore/StaticChunked.js

diff --git a/index.html b/index.html
index bd4f077a92..1945911350 100644
--- a/index.html
+++ b/index.html
@@ -32,6 +32,7 @@
     <script type="text/javascript" src="js/SeqFeatureStore.js"></script>
     <script type="text/javascript" src="js/SeqFeatureStore/NCList.js"></script>
     <script type="text/javascript" src="js/TiledImageStore/Fixed.js"></script>
+    <script type="text/javascript" src="js/SequenceStore/StaticChunked.js"></script>
 
     <script type="text/javascript" src="js/FeatureTrack.js"></script>
     <script type="text/javascript" src="js/StaticTrack.js"></script>
diff --git a/js/SequenceStore/StaticChunked.js b/js/SequenceStore/StaticChunked.js
new file mode 100644
index 0000000000..f9c813015c
--- /dev/null
+++ b/js/SequenceStore/StaticChunked.js
@@ -0,0 +1,111 @@
+/** @namespace */
+var SequenceStore; if( !SequenceStore ) SequenceStore = {};
+
+/**
+ * Storage backend for sequences broken up into chunks, stored and
+ * served as static text files.
+ * @class
+ * @constructor
+ * @extends Store
+ */
+SequenceStore.StaticChunked = function(args) {
+    Store.call( this, args );
+
+    this.chunkCache  = {};
+
+    this.urlTemplate = args.urlTemplate;
+    this.baseUrl     = args.baseUrl;
+};
+
+SequenceStore.StaticChunked.prototype = new Store('');
+
+/**
+ * @param {Object} seq object describing the sequence to operate on
+ * @param {Number} start start coord, in interbase
+ * @param {Number} end end coord, in interbase
+ * @param {Function} callback function that takes ( start, end, seq )
+ */
+SequenceStore.StaticChunked.prototype.getRange = function( seq, start, end, callback) {
+
+    var seqname    = seq.name;
+    var chunkSize  = seq.seqChunkSize;
+    var firstChunk = Math.floor( Math.max(0,start) / chunkSize );
+    var lastChunk  = Math.floor( (end - 1)         / chunkSize );
+    var chunk;
+
+    // if a callback spans more than one chunk, we need to wrap the
+    // callback in another one that will be passed to each chunk to
+    // concatenate the different pieces from each chunk and *then*
+    // call the main callback
+    if( firstChunk != lastChunk ) {
+        callback = (function() {
+            var chunk_seqs = [],
+                chunks_still_needed = lastChunk-firstChunk+1,
+                orig_callback = callback;
+            return function( start, end, seq, chunkNum) {
+                chunk_seqs[chunkNum] = seq;
+                if( --chunks_still_needed == 0 )
+                    orig_callback( start, end, chunk_seqs.join("") );
+            };
+         })();
+    }
+
+    var callbackInfo = { start: start, end: end, callback: callback };
+
+    if( !this.chunkCache[seqname] ) {
+        this.chunkCache[seqname] = [];
+    }
+    var chunkCacheForSeq = this.chunkCache[seqname];
+
+    for (var i = firstChunk; i <= lastChunk; i++) {
+        //console.log("working on chunk %d for %d .. %d", i, start, end);
+
+        chunk = chunkCacheForSeq[i];
+        if (chunk) {
+            if (chunk.loaded) {
+                callback( start,
+                          end,
+                          chunk.sequence.substring(
+                              start - i*chunkSize,
+                              end - i*chunkSize
+                          ),
+                          i
+                        );
+            } else {
+                //console.log("added callback for %d .. %d", start, end);
+                chunk.callbacks.push(callbackInfo);
+            }
+        } else {
+            chunk = {
+                loaded: false,
+                num: i,
+                callbacks: [callbackInfo]
+            };
+            chunkCacheForSeq[i] = chunk;
+
+            var sequrl = Util.resolveUrl( this.baseUrl,
+                                          Util.fillTemplate( this.urlTemplate,
+                                                     {'refseq': seq.name} ));
+
+            dojo.xhrGet({
+                            url: sequrl + i + ".txt",
+                            load: function (response) {
+                                var ci;
+                                chunk.sequence = response;
+                                for (var c = 0; c < chunk.callbacks.length; c++) {
+                                    ci = chunk.callbacks[c];
+                                    ci.callback( ci.start,
+                                                 ci.end,
+                                                 response.substring( ci.start - chunk.num*chunkSize,
+                                                                     ci.end   - chunk.num*chunkSize
+                                                                   ),
+                                                 i
+                                               );
+                                }
+                                chunk.callbacks = undefined;
+                                chunk.loaded = true;
+                            }
+                        });
+        }
+    }
+};
diff --git a/js/SequenceTrack.js b/js/SequenceTrack.js
index 850fd71508..a258196bd1 100644
--- a/js/SequenceTrack.js
+++ b/js/SequenceTrack.js
@@ -13,6 +13,7 @@
  * @param {Object} refSeq
  *  start: refseq start
  *  end:   refseq end
+ *  name:  refseq name
  * @param {Object} browserParams
  *  changeCallback: function to call once JSON is loaded
  *  trackPadding: distance in px between tracks
@@ -29,11 +30,14 @@ function SequenceTrack(config, refSeq, browserParams) {
     this.charWidth = browserParams.charWidth;
     this.seqHeight = browserParams.seqHeight;
 
-    this.chunks = [];
-    this.chunkSize = config.chunkSize;
-    this.url = Util.resolveUrl( config.baseUrl,
-                                Util.fillTemplate( config.urlTemplate,
-                                                   {'refseq': refSeq.name} ));
+    this.refSeq = refSeq;
+
+    // TODO: this should be passed into the constructor instead of
+    // being instantiated here
+    this.sequenceStore = new SequenceStore.StaticChunked({
+                               baseUrl: config.baseUrl,
+                               urlTemplate: config.urlTemplate
+                             });
 
     this.setLoaded();
 }
@@ -80,7 +84,7 @@ SequenceTrack.prototype.fillBlock = function(blockIndex, block,
     }
 
     if (this.shown) {
-        this.getRange( leftBase, rightBase,
+        this.sequenceStore.getRange( this.refSeq, leftBase, rightBase,
                        function( start, end, seq ) {
 
                            // fill with leading blanks if the
@@ -132,79 +136,3 @@ SequenceTrack.prototype.renderSeqDiv = function ( start, end, seq ) {
     return container;
 };
 
-/**
- * @param {Number} start start coord, in interbase
- * @param {Number} end end coord, in interbase
- * @param {Function} callback function that takes ( start, end, seq )
- */
-SequenceTrack.prototype.getRange = function( start, end, callback) {
-    var chunkSize = this.chunkSize;
-    var firstChunk = Math.floor( Math.max(0,start) / chunkSize );
-    var lastChunk  = Math.floor( (end - 1)         / chunkSize );
-    var chunk;
-
-    // if a callback spans more than one chunk, we need to wrap the
-    // callback in another one that will be passed to each chunk to
-    // concatenate the different pieces from each chunk and *then*
-    // call the main callback
-    if( firstChunk != lastChunk ) {
-        callback = (function() {
-            var chunk_seqs = [],
-                chunks_still_needed = lastChunk-firstChunk+1,
-                orig_callback = callback;
-            return function( start, end, seq, chunkNum) {
-                chunk_seqs[chunkNum] = seq;
-                if( --chunks_still_needed == 0 )
-                    orig_callback( start, end, chunk_seqs.join("") );
-            };
-         })();
-    }
-
-    var callbackInfo = { start: start, end: end, callback: callback };
-
-    for (var i = firstChunk; i <= lastChunk; i++) {
-        //console.log("working on chunk %d for %d .. %d", i, start, end);
-        chunk = this.chunks[i];
-        if (chunk) {
-            if (chunk.loaded) {
-                callback( start,
-                          end,
-                          chunk.sequence.substring(
-                              start - i*chunkSize,
-                              end - i*chunkSize
-                          ),
-                          i
-                        );
-            } else {
-                //console.log("added callback for %d .. %d", start, end);
-                chunk.callbacks.push(callbackInfo);
-            }
-        } else {
-            chunk = {
-                loaded: false,
-                num: i,
-                callbacks: [callbackInfo]
-            };
-            this.chunks[i] = chunk;
-            dojo.xhrGet({
-                            url: this.url + i + ".txt",
-                            load: function (response) {
-                                var ci;
-                                chunk.sequence = response;
-                                for (var c = 0; c < chunk.callbacks.length; c++) {
-                                    ci = chunk.callbacks[c];
-                                    ci.callback( ci.start,
-                                                 ci.end,
-                                                 response.substring( ci.start - chunk.num*chunkSize,
-                                                                     ci.end   - chunk.num*chunkSize
-                                                                   ),
-                                                 i
-                                               );
-                                }
-                                chunk.callbacks = undefined;
-                                chunk.loaded = true;
-                            }
-                        });
-        }
-    }
-};
\ No newline at end of file

From d133afda88e6d85f3ecd49f1613c6ecd19079a0c Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Sun, 18 Mar 2012 06:29:52 -0700
Subject: [PATCH 48/49] sequence tracks are backcompat with 1.2.1

---
 compat_121.html | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/compat_121.html b/compat_121.html
index e78adf553c..8caf0e4fd1 100644
--- a/compat_121.html
+++ b/compat_121.html
@@ -35,6 +35,7 @@
     <script type="text/javascript" src="js/SeqFeatureStore/NCList_v0.js"></script>
     <script type="text/javascript" src="js/TiledImageStore/Fixed.js"></script>
     <script type="text/javascript" src="js/TiledImageStore/Fixed_v0.js"></script>
+    <script type="text/javascript" src="js/SequenceStore/StaticChunked.js"></script>
 
     <script type="text/javascript" src="js/FeatureTrack.js"></script>
     <script type="text/javascript" src="js/StaticTrack.js"></script>
@@ -59,7 +60,7 @@
                                    include: { url: dataRoot+"/trackInfo.js", version: 0 },
 
                                    containerID: "GenomeBrowser",
-                                   refSeqs: { url: dataRoot+"/refSeqs.js", version: 0 },
+                                   refSeqs: dataRoot+"/refSeqs.js",
                                    nameUrl: dataRoot + "/names/root.json",
                                    defaultTracks: "DNA,gene,mRNA,noncodingRNA",
                                    queryParams: queryParams,

From ad94c59dc08419a6f15e1a4da806c94a1b4f9e5d Mon Sep 17 00:00:00 2001
From: Robert Buels <rmb32@cornell.edu>
Date: Sun, 18 Mar 2012 18:00:17 -0700
Subject: [PATCH 49/49] fix volvox 1.2.1 backcompat selenium tests

---
 tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt | 2 +-
 tests/selenium_tests/volvox_biodb_121_test.py    | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt b/tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt
index 5d5e213224..f23fb1ae81 100644
--- a/tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt
+++ b/tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt
@@ -1 +1 @@
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c
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c
\ No newline at end of file
diff --git a/tests/selenium_tests/volvox_biodb_121_test.py b/tests/selenium_tests/volvox_biodb_121_test.py
index 2d613e9dd0..3c3b4631f1 100644
--- a/tests/selenium_tests/volvox_biodb_121_test.py
+++ b/tests/selenium_tests/volvox_biodb_121_test.py
@@ -1,8 +1,10 @@
+import os
 import unittest
 from volvox_biodb_test import AbstractVolvoxBiodbTest
 
 class VolvoxBiodbTest121 ( AbstractVolvoxBiodbTest, unittest.TestCase ):
 
+    base_url = "file://%s/compat_121.html" % os.getcwd()
     data_dir = 'tests/data/volvox_formatted_1_2_1/'
 
     def setUp( self ):