added VCFTabix store. working and emitting features. still needs deep…

…er parsing.
GMOD · Mar 7, 2013 · 4b97bf7 · 4b97bf7
1 parent 022f7e5
commit 4b97bf7
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Showing 11 changed files with 275 additions and 40 deletions.
diff --git a/index.html b/index.html
@@ -17,6 +17,7 @@
                    packages: [ 'dojo', 'dijit', 'dojox', 'jszlib',
                                { name: 'lazyload', main: 'lazyload' },
                                'dgrid', 'xstyle', 'put-selector',
+                               { name: 'jDataView', location: 'jDataView/src', main: 'jdataview' },
                                'JBrowse'
                              ]
                  },

diff --git a/setup.sh b/setup.sh
@@ -48,6 +48,7 @@ echo -n "Formatting Volvox example data ...";
     bin/add-track-json.pl docs/tutorial/data_files/volvox_sine.bw.conf sample_data/json/volvox/trackList.json
     bin/add-track-json.pl docs/tutorial/data_files/volvox-sorted.bam.conf sample_data/json/volvox/trackList.json
     bin/add-track-json.pl docs/tutorial/data_files/volvox-sorted.bam.coverage.conf sample_data/json/volvox/trackList.json
+    bin/add-track-json.pl docs/tutorial/data_files/volvox.vcf.gz.conf sample_data/json/volvox/trackList.json
     bin/generate-names.pl -v --out sample_data/json/volvox;
 
     # also recreate some symlinks used by tests and such

diff --git a/src/JBrowse/Browser.js b/src/JBrowse/Browser.js
@@ -853,11 +853,14 @@ Browser.prototype.getStore = function( storeName, callback ) {
     }
 
     require( [ storeClassName ], dojo.hitch( this, function( storeClass ) {
-                 var storeArgs = dojo.mixin( conf,
-                                             {
-                                                 browser: this,
-                                                 refSeq: this.refSeq
-                                             });
+                 var storeArgs = dojo.clone( conf );
+                 dojo.mixin( storeArgs,
+                             {
+                                 config: conf,
+                                 browser: this,
+                                 refSeq: this.refSeq
+                             });
+
                  var store = new storeClass( storeArgs );
                  this._storeCache[ storeName ] = { refCount: 1, store: store };
                  callback( store );

diff --git a/src/JBrowse/Component.js b/src/JBrowse/Component.js
@@ -3,10 +3,12 @@
  */
 
 define([
-           'dojo/_base/declare'
+           'dojo/_base/declare',
+           'JBrowse/Util'
        ],
        function(
-           declare
+           declare,
+           Util
        ) {
 
 return declare( null, {
@@ -19,10 +21,25 @@ return declare( null, {
         this.config = this._mergeConfigs( dojo.clone( this._defaultConfig() ), this.config );
 
         this.browser = args.browser;
+
+        this.compiledConfig = {};
     },
 
     _defaultConfig: function() {
-        return {};
+        return {
+            baseUrl: '/'
+        };
+    },
+
+    resolveUrl: function( url, args ) {
+        args = args || {};
+        return Util.resolveUrl(
+            this.getConf('baseUrl',[]),
+            Util.fillTemplate( url,
+                               args
+                             )
+        );
+
     },
 
     _mergeConfigs: function(a, b) {

diff --git a/src/JBrowse/Model/TabixIndex.js b/src/JBrowse/Model/TabixIndex.js
@@ -1,12 +1,14 @@
 define([
            'dojo/_base/declare',
+           'dojo/_base/array',
            'dojo/_base/Deferred',
            'jDataView',
            'JBrowse/Util',
            'JBrowse/Model/BGZip/VirtualOffset'
        ],
        function(
            declare,
+           array,
            Deferred,
            jDataView,
            Util,
@@ -146,7 +148,7 @@ return declare( null, {
    getRefSeqs: function( refSeqCallback, finishCallback, errorCallback ) {
        var thisB = this;
        thisB.load().then( function() {
-           array.forEach( this.refIDToName || [], function( name ) {
+           array.forEach( thisB._refIDToName || [], function( name ) {
                 refSeqCallback({ name: name });
            });
            finishCallback();
@@ -160,6 +162,9 @@ return declare( null, {
    TAD_LIDX_SHIFT: 14,
 
    blocksForRange: function( refName, beg, end ) {
+       if( beg < 0 )
+           beg = 0;
+
        var tid = this.getRefId( refName );
        var indexes = this._indices[tid];
        if( ! indexes )
@@ -184,7 +189,7 @@ return declare( null, {
        }
 
        if( n_off == 0 )
-           return null;
+           return [];
 
        var off = [];
 
@@ -196,7 +201,7 @@ return declare( null, {
                        off[n_off++] = new Chunk( chunks[j].minv, chunks[j].maxv, chunks[j].bin );
 
        if( ! off.length )
-           return null;
+           return [];
 
        off = off.sort( function(a,b) { return a.compareTo(b); } );
 

diff --git a/src/JBrowse/Store.js b/src/JBrowse/Store.js
@@ -1,7 +1,13 @@
-define( [ 'dojo/_base/declare'],
-        function( declare ) {
+define( [
+            'dojo/_base/declare',
+            'JBrowse/Component'
+        ],
+        function(
+            declare,
+            Component
+        ) {
 
-return declare( null,
+return declare( Component,
 
 /**
  * @lends JBrowse.Store.prototype
@@ -14,7 +20,6 @@ return declare( null,
     constructor: function( args ) {
         this.refSeq = dojo.clone( args.refSeq );
         this.changeCallback = args.changeCallback || function() {};
-        this.browser = args.browser;
     },
 
     notifyChanged: function( changeDescription ) {

diff --git a/src/JBrowse/Store/SeqFeature/GlobalStatsEstimationMixin.js b/src/JBrowse/Store/SeqFeature/GlobalStatsEstimationMixin.js
@@ -20,24 +20,26 @@ return declare( null, {
     _estimateGlobalStats: function( finishCallback ) {
 
         var statsFromInterval = function( refSeq, length, callback ) {
+            var thisB = this;
             var sampleCenter = refSeq.start*0.75 + refSeq.end*0.25;
             var start = Math.max( 0, Math.round( sampleCenter - length/2 ) );
             var end = Math.min( Math.round( sampleCenter + length/2 ), refSeq.end );
-            this.bam.fetch( refSeq.name, start, end, dojo.hitch( this, function( features, error) {
-                if ( error ) {
-                    console.error( error );
-                    callback.call( this, length,  null, error );
-                }
-                else if( features ) {
-                    features = array.filter( features, function(f) { return f.get('start') >= start && f.get('end') <= end; } );
-                    callback.call( this, length,
-                                   {
-                                       featureDensity: features.length / length,
-                                       _statsSampleFeatures: features.length,
-                                       _statsSampleInterval: { ref: refSeq.name, start: start, end: end, length: length }
-                                   });
-                }
-            }));
+            var features = [];
+            this._getFeatures({ ref: refSeq.name, start: start, end: end},
+                              function( f ) { features.push(f); },
+                              function( error ) {
+                                  features = array.filter( features, function(f) { return f.get('start') >= start && f.get('end') <= end; } );
+                                  callback.call( thisB, length,
+                                                 {
+                                                     featureDensity: features.length / length,
+                                                     _statsSampleFeatures: features.length,
+                                                     _statsSampleInterval: { ref: refSeq.name, start: start, end: end, length: length }
+                                                 });
+                              },
+                              function( error ) {
+                                      console.error( error );
+                                      callback.call( thisB, length,  null, error );
+                              });
         };
 
         var maybeRecordStats = function( interval, stats, error ) {