diff --git a/lib/galaxy/datatypes/indexers/coverage.py b/lib/galaxy/datatypes/indexers/coverage.py
index 2bfec91c25f..454f5f29b70 100644
--- a/lib/galaxy/datatypes/indexers/coverage.py
+++ b/lib/galaxy/datatypes/indexers/coverage.py
@@ -2,7 +2,7 @@
"""
Read a chromosome of coverage data, and write it as a npy array, as
-well as averages over regions of progessively larger size in powers of 10
+well as averages over regions of progressively larger size in powers of 10
"""
from __future__ import division
diff --git a/lib/galaxy/datatypes/indexers/wiggle.py b/lib/galaxy/datatypes/indexers/wiggle.py
index 5ba1380aaa1..88e8fd7aca3 100644
--- a/lib/galaxy/datatypes/indexers/wiggle.py
+++ b/lib/galaxy/datatypes/indexers/wiggle.py
@@ -2,7 +2,7 @@
"""
Read a chromosome of wiggle data, and write it as a npy array, as
-well as averages over regions of progessively larger size in powers of 10
+well as averages over regions of progressively larger size in powers of 10
"""
from __future__ import division
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 95660613c65..7a48ab867b0 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -49,7 +49,8 @@ dataset_type_to_data_provider = {
# FIXME: hardcoding this for now, but it should be derived from the available
# converters
-browsable_types = set( ["wig", "bed" ] )
+browsable_types = ( "wig", "bed" )
+
class TracksController( BaseController ):
"""
@@ -92,7 +93,7 @@ class TracksController( BaseController ):
if dataset.metadata.dbkey == dbkey and dataset.extension in browsable_types:
datasets[dataset.id] = (dataset.extension, dataset.name)
# Render the template
- return trans.fill_template( "tracks/new_browser.mako", dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets )
+ return trans.fill_template( "tracks/new_browser.mako", converters=browsable_types, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets )
@web.expose
def browser(self, trans, dataset_ids, chrom=""):
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 8c4d5c53c26..092855096ef 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -6,35 +6,6 @@ var DENSITY = 1000,
DATA_ERROR = "There was an error in indexing this dataset.",
DATA_NONE = "No data for this chrom/contig.";
-var DataCache = function( type, track ) {
- this.type = type;
- this.track = track;
- this.cache = Object();
-};
-$.extend( DataCache.prototype, {
- get: function( resolution, position ) {
- var cache = this.cache;
- if ( !( cache[resolution] && cache[resolution][position] ) ) {
- if ( !cache[resolution] ) {
- cache[resolution] = Object();
- }
- var low = position * DENSITY * resolution;
- var high = ( position + 1 ) * DENSITY * resolution;
- cache[resolution][position] = { state: "loading" };
-
- $.getJSON( data_url, { track_type: this.track.track_type, chrom: this.track.view.chrom, low: low, high: high, dataset_id: this.track.dataset_id }, function ( data ) {
- if( data == "pending" ) {
- setTimeout( fetcher, 5000 );
- } else {
- cache[resolution][position] = { state: "loaded", values: data };
- }
- $(document).trigger( "redraw" );
- });
- }
- return cache[resolution][position];
- }
-});
-
var View = function( chrom, max_length ) {
this.chrom = chrom;
this.tracks = [];
@@ -234,7 +205,7 @@ var LineTrack = function ( name, dataset_id, height ) {
this.container_div.addClass( "line-track" );
this.content_div.css( "height", this.height_px + "px" );
this.dataset_id = dataset_id;
- this.cache = new DataCache( "", this );
+ this.cache = new Cache(50);
};
$.extend( LineTrack.prototype, TiledTrack.prototype, {
init: function() {
@@ -254,6 +225,21 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, {
}
});
},
+ get_data: function( resolution, position ) {
+ var key = resolution + '-' + position,
+ cache = this.cache;
+
+ if ( !cache[key] ) {
+ var low = position * DENSITY * resolution,
+ high = ( position + 1 ) * DENSITY * resolution;
+
+ $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id }, function ( data ) {
+ cache[key] = data;
+ $(document).trigger( "redraw" );
+ });
+ }
+ return cache[key];
+ },
draw_tile: function( resolution, tile_index, parent_element, w_scale, h_scale ) {
if (!this.vertical_range) // We don't have the necessary information yet
return;
@@ -261,13 +247,13 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, {
var tile_low = tile_index * DENSITY * resolution,
tile_high = ( tile_index + 1 ) * DENSITY * resolution,
tile_length = DENSITY * resolution;
- var chunk = this.cache.get( resolution, tile_index );
- var element;
- if ( chunk.state == "loading" ) {
- element = $("");
- } else {
- element = $("");
+ var data = this.get_data( resolution, tile_index );
+ if ( !data ) {
+ in_path = false;
+ return null;
}
+ var element = $("");
+
element.css( {
position: "absolute",
top: 0,
@@ -275,18 +261,13 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, {
});
parent_element.append( element );
// Chunk is still loading, do nothing
- if ( chunk.state == "loading" ) {
- in_path = false;
- return null;
- }
+
var canvas = element;
canvas.get(0).width = Math.ceil( tile_length * w_scale );
canvas.get(0).height = this.height_px;
var ctx = canvas.get(0).getContext("2d");
var in_path = false;
ctx.beginPath();
- var data = chunk.values;
- if (!data) return;
for ( var i = 0; i < data.length - 1; i++ ) {
var x = data[i][0] - tile_low;
var y = data[i][1];
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 59abec82503..1953b4b7b4d 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -7,7 +7,7 @@ ${parent.stylesheets()}
<%def name="javascripts()">
${parent.javascripts()}
-${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster" )}
+${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "lrucache", "trackster" )}
-