1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ddabb9a875cb/ changeset: ddabb9a875cb user: jgoecks date: 2012-08-19 21:42:11 summary: Trackster: for explicit coverage histogram mode in Feature Tracks, use coverage indices rather than computing on client side. affected #: 2 files diff -r 2d937ad3e1b47492f64fa0b9c668529a735118e8 -r ddabb9a875cb27d172d499d979a329e0f682164e lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -387,7 +387,21 @@ 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 diff -r 2d937ad3e1b47492f64fa0b9c668529a735118e8 -r ddabb9a875cb27d172d499d979a329e0f682164e static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -4433,7 +4433,7 @@ // 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 @@ 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 @@ 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. @@ -4650,86 +4650,6 @@ 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. */ get_mode: function(data) { @@ -4766,8 +4686,7 @@ * 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 @@ 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 @@ 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; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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