tweak TabixIndexedFile interface, rename fetch to getLines, add a…

…n `indexLoaded` property the gives access to the index-loading promise
GMOD · Mar 7, 2013 · 01f2e87 · 01f2e87
1 parent 61431e5
commit 01f2e87
Show file tree

Hide file tree

Showing 2 changed files with 17 additions and 6 deletions.
diff --git a/src/JBrowse/Store/TabixIndexedFile.js b/src/JBrowse/Store/TabixIndexedFile.js
@@ -20,15 +20,17 @@ return declare( null, {
     constructor: function( args ) {
         this.index = new TabixIndex( new BGZBlob( args.tbi ) );
         this.data  = new BGZBlob( args.file );
+        this.indexLoaded = this.index.load();
     },
 
-    fetch: function() {
+    getLines: function() {
         var thisB = this;
         var args = Array.prototype.slice.call(arguments);
-        this.index.load().then(function() {
+        this.indexLoaded.then(function() {
             thisB._fetch.apply( thisB, args );
         });
     },
+
     _fetch: function( ref, min, max, itemCallback, finishCallback, errorCallback ) {
 
         errorCallback = errorCallback || dojo.hitch( console, 'error' );
@@ -143,7 +145,7 @@ return declare( null, {
             // later, avoiding blocking any UI stuff that needs to be done
             else {
                 window.setTimeout( function() {
-                    that.parseItems( parseState.data, parseState.offset, itemCallback, finishCallback );
+                    that.parseItems( data, parseState.offset, itemCallback, finishCallback );
                 }, 1);
                 return;
             }
@@ -162,12 +164,21 @@ return declare( null, {
         if( !line )
             return null;
 
-        var fields = line.split("\t");
+        // function extractColumn( colNum ) {
+        //     var skips = '';
+        //     while( colNum-- > 1 )
+        //         skips += '^[^\t]*\t';
+        //     var match = (new Regexp( skips+'([^\t]*)' )).exec( line );
+        //     if( ! match )
+        //         return null;
+        //     return match[1];
+        // }
+        var fields = line.split( "\t" );
         var item = { // note: index column numbers are 1-based
             ref:   fields[this.index.columnNumbers.ref-1],
             start: fields[this.index.columnNumbers.start-1],
             end:   fields[this.index.columnNumbers.end-1],
-            _fields: fields
+            fields: fields
         };
         return item;
     },

diff --git a/tests/js_tests/spec/TabixIndexedFile.spec.js b/tests/js_tests/spec/TabixIndexedFile.spec.js
@@ -19,7 +19,7 @@ describe( "tabix-indexed file", function() {
 
     it( 'can read ctgA:1000..4000', function() {
             var items = [];
-            f.fetch( 'ctgA', 1000, 4000,
+            f.getLines( 'ctgA', 1000, 4000,
                      function(i) {
                          items.push(i);
                      },