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Trackster: for explicit coverage histogram mode in Feature Tracks, use coverage indices rather than computing on client side.

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This commit is contained in:
Jeremy Goecks
2012-08-19 15:42:11 -04:00
parent 5ab62c8746
commit 871f72c956
2 changed files with 27 additions and 98 deletions
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lib/galaxy/web/controllers/tracks.py
+15 -1
View File
@@ -387,7 +387,21 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDat
return return_message
extra_info = None
if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and kwargs.get("mode", "Auto") == "Auto":
mode = kwargs.get( "mode", "Auto" )
# Handle histogram mode uniquely for now:
if mode == "Coverage":
# Get summary using minimal cutoffs.
tracks_dataset_type = data_sources['index']['name']
converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset )
summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 )
if summary == "detail":
# Use maximum level of detail--2--to get summary data no matter the resolution.
summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 )
frequencies, max_v, avg_v, delta = summary
return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta }
if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto":
# Only check for summary_tree if it's Auto mode (which is the default)
#
# Have to choose between indexer and data provider
static/scripts/viz/trackster.js
+12 -97
View File
@@ -4433,7 +4433,7 @@ var FeatureTrack = function(view, container, obj_dict) {
// initialization code.
//
var track = this;
this.display_modes = ["Auto", "Histogram", "Dense", "Squish", "Pack"];
this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"];
//
// Initialization.
@@ -4516,8 +4516,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
var track = this,
i;
// If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max.
if (track.mode === "Histogram") {
// If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.
if (track.mode === "Coverage") {
// Get global max.
var global_max = -1;
for (i = 0; i < tiles.length; i++) {
@@ -4534,7 +4534,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } );
}
}
}
}
//
// Update filter attributes, UI.
@@ -4649,86 +4649,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
return slotter.slot_features( features );
},
/**
* Given feature data, returns summary tree data. Feature data must be sorted by start
* position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data
* is a two-item list; first item is bin start, second is bin's count.
*/
get_summary_tree_data: function(data, low, high, num_bins) {
if (num_bins > high - low) {
num_bins = high - low;
}
var bin_size = Math.floor((high - low)/num_bins),
bins = [],
max_count = 0;
/*
// For debugging:
for (var i = 0; i < data.length; i++)
console.log("\t", data[i][1], data[i][2], data[i][3]);
*/
//
// Loop through bins, counting data for each interval.
//
var data_index_start = 0,
data_index = 0,
data_interval,
bin_index = 0,
bin_interval = [],
cur_bin;
// Set bin interval.
var set_bin_interval = function(interval, low, bin_index, bin_size) {
interval[0] = low + bin_index * bin_size;
interval[1] = low + (bin_index + 1) * bin_size;
};
// Loop through bins, data to compute bin counts. Only compute bin counts as long
// as there is data.
while (bin_index < num_bins && data_index_start !== data.length) {
// Find next bin that has data.
var bin_has_data = false;
for (; bin_index < num_bins && !bin_has_data; bin_index++) {
set_bin_interval(bin_interval, low, bin_index, bin_size);
// Loop through data and break if data found that goes in bin.
for (data_index = data_index_start; data_index < data.length; data_index++) {
data_interval = data[data_index].slice(1, 3);
if (is_overlap(data_interval, bin_interval)) {
bin_has_data = true;
break;
}
}
// Break from bin loop if this bin has data.
if (bin_has_data) {
break;
}
}
// Set start index to current data, which is the first to overlap with this bin
// and perhaps with later bins.
data_start_index = data_index;
// Count intervals that overlap with bin.
bins[bins.length] = cur_bin = [bin_interval[0], 0];
for (; data_index < data.length; data_index++) {
data_interval = data[data_index].slice(1, 3);
if (is_overlap(data_interval, bin_interval)) {
cur_bin[1]++;
}
else { break; }
}
// Update max count.
if (cur_bin[1] > max_count) {
max_count = cur_bin[1];
}
// Go to next bin.
bin_index++;
}
return {max: max_count, delta: bin_size, data: bins};
},
/**
* Returns appropriate display mode based on data.
*/
@@ -4766,8 +4686,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
* number of pixels required.
*/
get_canvas_height: function(result, mode, w_scale, canvas_width) {
if (mode === "summary_tree" || mode === "Histogram") {
// Extra padding at top of summary tree so label does not overlap data.
if (mode === "summary_tree" || mode === "Coverage") {
return this.summary_draw_height;
}
else {
@@ -4796,16 +4715,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
tile_high = region.get('end'),
left_offset = this.left_offset;
// Drawing the summary tree (feature coverage histogram)
if (mode === "summary_tree" || mode === "Histogram") {
// Get summary tree data if necessary and set max if there is one.
if (result.dataset_type !== "summary_tree") {
var st_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200);
if (result.max) {
st_data.max = result.max;
}
result = st_data;
}
// Drawing the summary tree.
if (mode === "summary_tree" || mode === "Coverage") {
// Paint summary tree into canvas
var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs);
painter.draw(ctx, canvas.width, canvas.height, w_scale);
@@ -4872,7 +4783,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
if (mode === "Auto") {
return true;
}
// All other modes--Histogram, Dense, Squish, Pack--require data + details.
// Histogram mode requires summary_tree data.
else if (mode === "Coverage") {
return data.dataset_type === "summary_tree";
}
// All other modes--Dense, Squish, Pack--require data + details.
else if (data.extra_info === "no_detail" || data.dataset_type === "summary_tree") {
return false;
}