details: http://www.bx.psu.edu/hg/galaxy/rev/edb48f2816b5 changeset: 2927:edb48f2816b5 user: Kanwei Li <kanwei(a)gmail.com&gt; date: Tue Oct 27 22:34:30 2009 -0400 description: trackster: y-axis labels for linetracks, thin/thick blocks are correct for featuretracks, messages when data is loading and being indexed diffstat: lib/galaxy/visualization/tracks/data/interval_index.py | 4 +- static/scripts/trackster.js | 171 ++++++++++++--------- static/trackster.css | 10 + templates/tracks/browser.mako | 4 - 4 files changed, 110 insertions(+), 79 deletions(-) diffs (326 lines): diff -r ea0342f2df03 -r edb48f2816b5 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Tue Oct 27 15:11:41 2009 -0400 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Tue Oct 27 22:34:30 2009 -0400 @@ -35,8 +35,8 @@ pass try: - payload['exon_start'] = int(feature[6]) - payload['exon_end'] = int(feature[7]) + payload['thick_start'] = int(feature[6]) + payload['thick_end'] = int(feature[7]) except IndexError: pass diff -r ea0342f2df03 -r edb48f2816b5 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Oct 27 15:11:41 2009 -0400 +++ b/static/scripts/trackster.js Tue Oct 27 22:34:30 2009 -0400 @@ -5,6 +5,8 @@ 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 = 50, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), @@ -34,11 +36,11 @@ function commatize( number ) { number += ''; // Convert to string - var rgx = /(\d+)(\d{3})/; - while (rgx.test(number)) { - number = number.replace(rgx, '$1' + ',' + '$2'); - } - return number; + var rgx = /(\d+)(\d{3})/; + while (rgx.test(number)) { + number = number.replace(rgx, '$1' + ',' + '$2'); + } + return number; } var View = function( chrom, max_high ) { this.chrom = chrom; @@ -88,7 +90,7 @@ $("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>'); }, zoom_in: function ( point ) { - if (this.max_high === 0 || this.high - this.low < 5) { + if (this.max_high === 0 || this.high - this.low < 30) { return; } @@ -96,6 +98,7 @@ this.center = point / $(document).width() * (this.high - this.low) + this.low; } this.zoom_level += 1; + this.redraw(); }, zoom_out: function () { if (this.max_high === 0) { @@ -106,6 +109,7 @@ return; } this.zoom_level -= 1; + this.redraw(); } }); @@ -137,13 +141,13 @@ resolution = Math.max( resolution, 1 ); resolution = Math.min( resolution, 100000 ); - var parent_element = $("<div style='position: relative;'></div>"); + var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); this.content_div.append( parent_element ); var w = this.content_div.width(), h = this.content_div.height(), - w_scale = w / range; + w_scale = w / range; var tile_element; // Index of first tile that overlaps visible region @@ -211,21 +215,38 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { var track = this; + track.content_div.text(DATA_LOADING); $.getJSON( data_url, { stats: true, track_type: track.track_type, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + track.content_div.text(DATA_ERROR); } else if (data == "no data") { track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); + track.content_div.text(DATA_NONE); + } else if (data == "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, 5000); } else { + track.content_div.text(""); track.content_div.css( "height", track.height_px + "px" ); track.min_value = data.min; track.max_value = data.max; track.vertical_range = track.max_value - track.min_value; - track.view.redraw(); + + // Draw y-axis labels + var min_label = $("<div class='yaxislabel'>" + track.min_value + "</div>"); + var max_label = $("<div class='yaxislabel'>" + track.max_value + "</div>"); + + max_label.css({ position: "relative", top: "20px" }); + max_label.prependTo(track.container_div) + + min_label.css({ position: "relative", top: track.height_px + 50 + "px", }); + min_label.prependTo(track.container_div); + + track.draw(); } }); }, @@ -307,16 +328,22 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { var track = this; + track.content_div.text(DATA_LOADING); $.getJSON( data_url, { track_type: track.track_type, low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { if (data == "error") { track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + track.content_div.text(DATA_ERROR); } else if (data.length === 0 || data == "no data") { track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); + track.content_div.text(DATA_NONE); + } else if (data == "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, 5000); } else { + track.content_div.text(""); track.content_div.css( "height", track.height_px + "px" ); track.values = data; track.calc_slots(); @@ -412,68 +439,66 @@ f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), y_center = this.slots[feature.name] * this.vertical_gap; - if (feature.strand && this.showing_labels) { - if (feature.strand == "+") { - ctx.fillStyle = RIGHT_STRAND; - } else if (feature.strand == "-") { - ctx.fillStyle = LEFT_STRAND; + var thickness, y_start, thick_start = null, thick_end = null; + if (feature.thick_start && feature.thick_end) { + thick_start = Math.floor( Math.max(0, (feature.thick_start - tile_low) * w_scale) ); + thick_end = Math.ceil( Math.min(width, (feature.thick_end - tile_low) * w_scale) ); + } + if (!this.showing_labels) { + // Non-detail levels + ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); + } else { + // Showing labels, blocks, details + if (ctx.fillText) { + ctx.fillText(feature.name, f_start - 1, y_center + 8); } - ctx.fillRect(f_start, y_center, f_end - f_start, 10); - ctx.fillStyle = "#000"; - } else { - ctx.fillStyle = "#000"; - ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); - } - - if (this.showing_labels && ctx.fillText) { - ctx.fillText(feature.name, f_start - 1, y_center + 8); - } - - // If there is no thickStart/thickEnd, draw the whole thing - // as thick. - var exon_start, exon_end; - if (feature.exon_start && feature.exon_end) { - exon_start = Math.floor( Math.max(0, (feature.exon_start - tile_low) * w_scale) ); - exon_end = Math.ceil( Math.min(width, (feature.exon_end - tile_low) * w_scale) ); - } else { - exon_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ); - exon_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ); - } - - if (this.showing_labels) { - // If there are no blocks, we treat the feature as one - // big exon - var blocks = feature.blocks; - var arrows_in_blocks = false; - if ( ! blocks ) { - blocks = [[feature.start,feature.end]]; - arrows_in_blocks = true - } - for (var k = 0, k_len = blocks.length; k < k_len; k++) { - var block = blocks[k], - block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); - var thickness, y_start; - if (exon_start && block_start >= exon_start && block_end <= exon_end) { - thickness = 9; - y_start = 1; - ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); - if ( feature.strand && arrows_in_blocks ) { - if (feature.strand == "+") { - ctx.fillStyle = RIGHT_STRAND_INV; - } else if (feature.strand == "-") { - ctx.fillStyle = LEFT_STRAND_INV; - } - ctx.fillRect(block_start, y_center, block_end - block_start, 10); - ctx.fillStyle = "#000"; - } - } else { - thickness = 5; - y_start = 3; - ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); - } + var blocks = feature.blocks; + if (blocks) { + // Draw introns + if (feature.strand) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND; + } + ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillStyle = "#000"; + } - // console.log(block_start, block_end); + for (var k = 0, k_len = blocks.length; k < k_len; k++) { + var block = blocks[k], + block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), + block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); + + // Draw the block + thickness = 5; + y_start = 3; + ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); + + if (thick_start && (block_start < thick_end || block_end > thick_start) ) { + thickness = 9; + y_start = 1; + var block_thick_start = Math.max(block_start, thick_start), + block_thick_end = Math.min(block_end, thick_end); + + ctx.fillRect(block_thick_start, y_center + y_start, block_thick_end - block_thick_start, thickness); + + } + } + } else { + // If there are no blocks, we treat the feature as one big exon + thickness = 9; + y_start = 1; + ctx.fillRect(f_start, y_center + y_start, f_end - f_start, thickness); + if ( feature.strand ) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND_INV; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND_INV; + } + ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillStyle = "#000"; + } } } j++; diff -r ea0342f2df03 -r edb48f2816b5 static/trackster.css --- a/static/trackster.css Tue Oct 27 15:11:41 2009 -0400 +++ b/static/trackster.css Tue Oct 27 22:34:30 2009 -0400 @@ -95,6 +95,16 @@ width: 100%; height: 100px; } + +.yaxislabel { + color: #777; +} +/* Line track needs borders to show range */ +.line-track .track-content { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; +} + .track { /* border-top: solid gray 1px; */ /* border-bottom: solid gray 1px; */ diff -r ea0342f2df03 -r edb48f2816b5 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Oct 27 15:11:41 2009 -0400 +++ b/templates/tracks/browser.mako Tue Oct 27 22:34:30 2009 -0400 @@ -30,16 +30,13 @@ $(document).bind("mousewheel", function( e, delta ) { if (delta > 0) { view.zoom_in(e.pageX); - view.redraw(); } else { view.zoom_out(); - view.redraw(); } }); $(document).bind("dblclick", function( e ) { view.zoom_in(e.pageX); - view.redraw(); }); // To let the overview box be draggable @@ -96,7 +93,6 @@ }); }); })(); - view.redraw(); $(window).trigger("resize"); });