[galaxy-commits] commit/galaxy-central: jgoecks: Trackster: subset reference data when available.

21 Feb 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/b7b000557d12/
changeset:   b7b000557d12
user:        jgoecks
date:        2013-02-21 20:11:09
summary:     Trackster: subset reference data when available.
affected #:  2 files

diff -r 5a910304b25466d3781821bc35f7d0a6c1eae28a -r b7b000557d128c537dfeb5bb4a9260853463793b static/scripts/viz/trackster/tracks.js

--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -2915,6 +2915,10 @@
             if ( is_deferred( seq_data ) ) {
                 can_draw_now = false;
             }
+            else {
+                // Sequence data is available, subset to get only data in region.
+                seq_data = view.reference_track.data_manager.subset_entry(seq_data, region);
+            }
         }
                 
         // If we can draw now, do so.
@@ -3440,7 +3444,8 @@
     this.data_url = reference_url + "/" + this.view.dbkey;
     this.data_url_extra_params = {reference: true};
     this.data_manager = new visualization.ReferenceTrackDataManager({
-        data_url: this.data_url
+        data_url: this.data_url,
+        can_subset: this.can_subset
     });
     this.hide_contents();
 };
@@ -3456,10 +3461,11 @@
     can_draw: Drawable.prototype.can_draw,
 
     /**
-     * Only retrieves data and draws tile if reference data can be displayed.
+     * Retrieves data and draws tile if reference data can be displayed.
      */
     draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) {
         if (w_scale > this.view.canvas_manager.char_width_px) {
+            this.show_contents();
             return TiledTrack.prototype.draw_helper.call(this, force, region, resolution, parent_element, w_scale, kwargs);
         }
         else {
@@ -3468,28 +3474,27 @@
         }
     },
 
+    can_subset: function(data) { return true; },
+
     /**
      * Draw ReferenceTrack tile.
      */
-    draw_tile: function(seq, ctx, mode, resolution, region, w_scale) {
-        var track = this;        
-        
+    draw_tile: function(data, ctx, mode, resolution, region, w_scale) {
         if (w_scale > this.view.canvas_manager.char_width_px) {
-            if (seq.data === null) {
-                this.hide_contents();
-                return;
-            }
+            // Try to subset data.
+            var subset = this.data_manager.subset_entry(data, region),
+                seq_data = subset.data;
+            
+            // Draw sequence data.
             var canvas = ctx.canvas;
             ctx.font = ctx.canvas.manager.default_font;
-            ctx.textAlign = "center";
-            seq = seq.data;
-            for (var c = 0, str_len = seq.length; c < str_len; c++) {
-                var c_start = Math.floor(c * w_scale);
-                ctx.fillText(seq[c], c_start, 10);
+            ctx.textAlign = "center";            
+            for (var c = 0, str_len = seq_data.length; c < str_len; c++) {
+                ctx.fillText(seq_data[c], Math.floor(c * w_scale), 10);
             }
-            this.show_contents();
-            return new Tile(track, region, resolution, canvas, seq);
+            return new Tile(this, region, resolution, canvas, subset);
         }
+
         this.hide_contents();
     }
 });

diff -r 5a910304b25466d3781821bc35f7d0a6c1eae28a -r b7b000557d128c537dfeb5bb4a9260853463793b static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -318,6 +318,8 @@
         // Do request.
         var manager = this,
             entry = $.getJSON(dataset.url(), params, function (result) {
+                // Add region to the result.
+                result.region = region;
                 manager.set_data(region, result);
             });
 
@@ -582,7 +584,25 @@
             return { data: null };
         }
         return GenomeDataManager.prototype.load_data.call(this, region, mode, resolution, extra_params);
-    } 
+    },
+
+    /**
+     * Return an entry that includes only data in the subregion.
+     */
+    subset_entry: function(entry, subregion) {
+        var seq_data = entry.data;
+        if (!entry.region.same(subregion)) {
+            // Need to subset sequence data.
+            var seq_start = subregion.get('start') - entry.region.get('start'),
+                seq_end = entry.data.length - ( entry.region.get('end') - subregion.get('end') );
+            seq_data = entry.data.slice(seq_start, seq_end);
+        }
+
+        return {
+            region: subregion,
+            data: seq_data
+        };
+    }
 });
  
 /**
@@ -639,6 +659,16 @@
         end: 0,
         genome: null
     },
+
+    /**
+     * Returns true if this region is the same as a given region.
+     * It does not test the genome right now.
+     */
+    same: function(region) {
+        return this.attributes.chrom === region.get('chrom') &&
+               this.attributes.start === region.get('start') &&
+               this.attributes.end === region.get('end');
+    },
     
     /**
      * If from_str specified, use it to initialize attributes.

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[galaxy-commits] commit/galaxy-central: jgoecks: Trackster: subset reference data when available.

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