trackster: much greater resolution for line tracks (might still need to tweak BLOCK_SIZE), fixed stacking issue in feature tracks for features sharing same name)

lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py

@@ -8,6 +8,8 @@ import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.arrays.array_tree import *
 from bx.arrays.wiggle import IntervalReader
 
+BLOCK_SIZE = 1000
+
 def main():
    
     input_fname = sys.argv[1]
@@ -16,7 +18,7 @@ def main():
     reader = IntervalReader( open( input_fname ) )
     
     # Fill array from wiggle
-    d = array_tree_dict_from_wiggle_reader( reader, {} )
+    d = array_tree_dict_from_wiggle_reader( reader, {}, block_size = BLOCK_SIZE )
     
     for value in d.itervalues():
         value.root.build_summary()

lib/galaxy/visualization/tracks/data/array_tree.py

@@ -31,11 +31,16 @@ class ArrayTreeDataProvider( object ):
         f.close()
         return { 'max': float( max(root_summary.maxs) ), 'min': float( min(root_summary.mins) ) }
     
-    def get_data( self, chrom, start, end ):
+    def get_data( self, chrom, start, end, **kwargs ):
         start = int( start )
         end = int( end )
-        level = int( ceil( log( end - start, BLOCK_SIZE ) ) ) - 1
-
+        resolution = max(1, ceil(float(kwargs['resolution'])))
+        
+        level = int( floor( log( resolution, BLOCK_SIZE ) ) )
+        level = max( level, 0 )
+        stepsize = BLOCK_SIZE ** level
+        step1 = stepsize * BLOCK_SIZE
+        
         # Open the file
         f = open( self.dataset.file_name )
         d = FileArrayTreeDict( f )
@@ -47,22 +52,20 @@ class ArrayTreeDataProvider( object ):
         # Is the requested level valid?
         assert 0 <= level <= chrom_array_tree.levels
         # Calculate the actual start/range/step of the block we're getting
-        size = BLOCK_SIZE ** (level+1)
-        block_start = ( start // BLOCK_SIZE ) * BLOCK_SIZE
-        block_step = size // BLOCK_SIZE
-        indexes = range( block_start, block_start + size, block_step )
-        # Return either data point or a summary depending on the level
-        if level > 0:
-            s = chrom_array_tree.get_summary( start, level )
-            f.close()
-            if s is not None:
-                return zip( indexes,  map( float, s.sums / s.counts ) )
+        
+        results = []
+        for block_start in range( start, end, stepsize * BLOCK_SIZE ):
+            # print block_start
+            # Return either data point or a summary depending on the level
+            indexes = range( block_start, block_start + stepsize * BLOCK_SIZE, stepsize )
+            if level > 0:
+                s = chrom_array_tree.get_summary( block_start, level )
+                if s is not None:
+                    results.extend( zip( indexes,  map( float, s.sums / s.counts ) ) )
             else:
-                return None
-        else:
-            v = chrom_array_tree.get_leaf( start )
-            f.close()
-            if v is not None:
-                return zip( indexes, map( float, v ) )
-            else:
-                return None
+                v = chrom_array_tree.get_leaf( block_start )
+                if v is not None:
+                    results.extend( zip( indexes, map( float, v ) ) )
+        
+        f.close()
+        return results

lib/galaxy/visualization/tracks/data/interval_index.py

@@ -11,17 +11,18 @@ class IntervalIndexDataProvider( object ):
         self.original_dataset = original_dataset
         self.converted_dataset = converted_dataset
     
-    def get_data( self, chrom, start, end ):
+    def get_data( self, chrom, start, end, **kwargs ):
         start, end = int(start), int(end)
         chrom = str(chrom)
         source = open( self.original_dataset.file_name )
         index = Indexes( self.converted_dataset.file_name )
         results = []
         
+        uid = 0
         for start, end, offset in index.find(chrom, start, end):
             source.seek(offset)
             feature = source.readline().split()
-            payload = { 'start': start, 'end': end, 'name': feature[3] }
+            payload = { 'uid': uid, 'start': start, 'end': end, 'name': feature[3] }
             try:
                 payload['strand'] = feature[5]
             except IndexError:
@@ -41,5 +42,6 @@ class IntervalIndexDataProvider( object ):
                 pass
 
             results.append(payload)
+            uid += 1
         
         return results

lib/galaxy/web/controllers/tracks.py

@@ -184,7 +184,7 @@ class TracksController( BaseController ):
         return manifest
 
     @web.json
-    def data( self, trans, dataset_id, track_type, chrom, low, high, stats=False ):
+    def data( self, trans, dataset_id, track_type, chrom, low, high, **kwargs ):
         """
         Called by the browser to request a block of data
         """
@@ -216,10 +216,10 @@ class TracksController( BaseController ):
         data_provider = dataset_type_to_data_provider[ converted_dataset_type ]( converted_dataset, dataset )
 
         # Return stats if we need them
-        if stats: return data_provider.get_stats( chrom )
+        if 'stats' in kwargs: return data_provider.get_stats( chrom )
 
         # Get the requested chunk of data
-        return data_provider.get_data( chrom, low, high )
+        return data_provider.get_data( chrom, low, high, **kwargs )
 
     def __dataset_as_type( self, trans, dataset, type ):
         """

static/scripts/trackster.js

@@ -1,13 +1,15 @@
 /* Trackster
     2009, James Taylor, Kanwei Li
 */
+var DEBUG = false;
 
 var DENSITY = 1000,
     DATA_ERROR = "There was an error in indexing this dataset.",
     DATA_NONE = "No data for this chrom/contig.",
     DATA_PENDING = "Currently indexing... please wait",
     DATA_LOADING = "Loading data...",
-    CACHED_TILES = 10,
+    CACHED_TILES_FEATURE = 10,
+    CACHED_TILES_LINE = 30,
     CACHED_DATA = 20,
     CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"),
     RIGHT_STRAND, LEFT_STRAND;
@@ -104,6 +106,9 @@ $.extend( View.prototype, {
         this.high = Math.ceil(high);
         this.center = Math.round( this.low + (this.high - this.low) / 2 );
         
+        // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width
+        this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) );
+        
         // Overview
         $("#overview-box").css( {
             left: ( this.low / this.span ) * $("#overview-viewport").width(),
@@ -157,18 +162,16 @@ $.extend( Track.prototype, {
 });
 
 var TiledTrack = function() {
-    this.tile_cache = new Cache(CACHED_TILES);
-    // this.tile_cache = {};
 };
 $.extend( TiledTrack.prototype, Track.prototype, {
     draw: function() {
         var low = this.view.low,
             high = this.view.high,
-            range = high - low;
-
-        var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) );
-        resolution = Math.max( resolution, 0.1 );
-        resolution = Math.min( resolution, 1000000 );
+            range = high - low,
+            resolution = this.view.resolution;
+            
+        
+        if (DEBUG) { $("#debug").text(resolution); }
 
         var parent_element = $("<div style='position: relative;'></div>");
             this.content_div.children( ":first" ).remove();
@@ -187,7 +190,7 @@ $.extend( TiledTrack.prototype, Track.prototype, {
                 // console.log("cached tile " + tile_index);
                 var tile_low = tile_index * DENSITY * resolution;
                 cached.css( {
-                    left: ( tile_low - this.view.low ) * w_scale
+                    left: ( tile_low - low ) * w_scale
                 });
                 // Our responsibility to move the element to the new parent
                 parent_element.append( cached );
@@ -229,6 +232,7 @@ $.extend( LabelTrack.prototype, Track.prototype, {
 });
 
 var LineTrack = function ( name, dataset_id, height ) {
+    this.tile_cache = new Cache(CACHED_TILES_LINE);
     Track.call( this, name, $("#viewport") );
     TiledTrack.call( this );
     
@@ -236,6 +240,7 @@ var LineTrack = function ( name, dataset_id, height ) {
     this.height_px = (height ? height : 100);
     this.container_div.addClass( "line-track" );
     this.dataset_id = dataset_id;
+    this.data_queue = {};
     this.cache = new Cache(CACHED_DATA); // We need to cache some data because of
                                          // asynchronous calls
 };
@@ -282,11 +287,17 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, {
             low = position * DENSITY * resolution,
             high = ( position + 1 ) * DENSITY * resolution,
             key = resolution + "_" + position;
-            
-        $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id }, function ( data ) {
-            track.cache[key] = data;
-            $(document).trigger( "redraw" );
-        });
+        
+        if (!track.data_queue[key]) {
+            track.data_queue[key] = true;
+            $.getJSON( data_url, {  track_type: this.track_type, chrom: this.view.chrom, 
+                                    low: low, high: high, dataset_id: this.dataset_id,
+                                    resolution: this.view.resolution }, function ( data ) {
+                track.cache[key] = data;
+                delete track.data_queue[key];
+                track.draw();
+            });
+        }            
     },
     draw_tile: function( resolution, tile_index, parent_element, w_scale ) {
         if (!this.vertical_range) { // We don't have the necessary information yet
@@ -340,6 +351,7 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, {
 });
 
 var FeatureTrack = function ( name, dataset_id, height ) {
+    this.tile_cache = new Cache(CACHED_TILES_FEATURE);
     Track.call( this, name, $("#viewport") );
     TiledTrack.call( this );
     
@@ -409,9 +421,9 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
                 if (end_ary[j] === undefined || end_ary[j] < f_start) {
                     end_ary[j] = f_end;
                     if (include_labels) {
-                        this.zi_slots[feature.name] = j;
+                        this.zi_slots[feature.uid] = j;
                     } else {
-                        this.zo_slots[feature.name] = j;
+                        this.zo_slots[feature.uid] = j;
                     }
                     break;
                 }
@@ -466,7 +478,7 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
             if (feature.start <= tile_high && feature.end >= tile_low) {
                 var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ),
                     f_end   = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ),
-                    y_center = this.slots[feature.name] * this.vertical_gap;
+                    y_center = this.slots[feature.uid] * this.vertical_gap;
                 
                 var thickness, y_start, thick_start = null, thick_end = null;
                 if (feature.thick_start && feature.thick_end) {

static/trackster.css

@@ -25,6 +25,7 @@ input {
     font-size: 100%;
 }
 
+/*canvas{ border-right: 1px solid red; } /* debugging */
 #nav {
     padding: 0.5em 0;
     background:#cccccc;

templates/tracks/browser.mako

@@ -122,6 +122,7 @@ ${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster" )}
                 <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a>
                 <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a>
             </form>
+            <div id="debug" style="float: right"></div>
         </div>
     </div>
 </div>