1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/fd21bfd6d257/ changeset: fd21bfd6d257 user: jgoecks date: 2012-07-31 17:55:41 summary: Trackster bug fixes: (a) fix 1-base offset bug in LineTracks; (b) fix overview track resolution calculation; and (c) code cleanup via JSHint. affected #: 1 file

diff -r eb4206636dd9b385cc84f20b81d61f9ea11727c5 -r fd21bfd6d2577090013e005f20e174b2a1d9f128 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -3325,8 +3325,7 @@ var TiledTrack = function(view, container, obj_dict) { Track.call(this, view, container, obj_dict);

- var track = this, - view = track.view; + var track = this;

// Make track moveable. moveable(track.container_div, track.drag_handle_class, ".group", track); @@ -3506,8 +3505,8 @@ if (this.is_overview) { low = this.view.max_low; high = this.view.max_high; - resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / TILE_SIZE ) / Math.log(RESOLUTION) )); - w_scale = width / (view.max_high - view.max_low); + resolution = ( view.max_high - view.max_low ) / width; + w_scale = 1 / resolution; }

this.before_draw(); @@ -3558,8 +3557,6 @@ * drawn/fetched and shown. */ postdraw_actions: function(tiles, width, w_scale, clear_after) { - var track = this; - // // If some tiles have icons, set padding of tiles without icons so features and rows align. // @@ -3995,19 +3992,19 @@

this.tile_predraw_init();

- var - canvas = track.view.canvas_manager.new_canvas(), + var canvas = track.view.canvas_manager.new_canvas(), tile_bounds = track._get_tile_bounds(tile_index, resolution), tile_low = region.get('start'), tile_high = region.get('end'), all_data_index = 0, width = Math.ceil( (tile_high - tile_low) * w_scale ) + this.left_offset, height = 0, - track_modes = []; + track_modes = [], + i;

// Get max height for all tracks and record track modes. var track_canvas_height = 0; - for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) { + for (i = 0; i < this.drawables.length; i++, all_data_index += 2) { track = this.drawables[i]; tile_data = all_data[ all_data_index ];

@@ -4035,7 +4032,7 @@ ctx.translate(this.left_offset, 0); ctx.globalAlpha = 0.5; ctx.globalCompositeOperation = "source-over"; - for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) { + for (i = 0; i < this.drawables.length; i++, all_data_index += 2) { track = this.drawables[i]; tile_data = all_data[ all_data_index ]; seq_data = all_data[ all_data_index + 1 ]; @@ -4509,12 +4506,13 @@ postdraw_actions: function(tiles, width, w_scale, clear_after) { TiledTrack.prototype.postdraw_actions.call(this, tiles, clear_after);

- var track = this; + 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") { // Get global max. - var i, global_max = -1; + var global_max = -1; for (i = 0; i < tiles.length; i++) { var cur_max = tiles[i].max_val; if (cur_max > global_max) { @@ -4547,7 +4545,7 @@ var filters_available = false, example_feature, filter; - for (var i = 0; i < tiles.length; i++) { + for (i = 0; i < tiles.length; i++) { if (tiles[i].data.length) { example_feature = tiles[i].data[0]; for (var f = 0; f < filters.length; f++) { @@ -4597,7 +4595,7 @@ // if (first_tile instanceof FeatureTrackTile) { var all_slotted = true; - for (var i = 0; i < tiles.length; i++) { + for (i = 0; i < tiles.length; i++) { if (!tiles[i].all_slotted) { all_slotted = false; break; @@ -4671,8 +4669,7 @@ data_interval, bin_index = 0, bin_interval = [], - cur_bin, - overlap; + cur_bin;

// Set bin interval. var set_bin_interval = function(interval, low, bin_index, bin_size) { @@ -4790,7 +4787,6 @@ canvas = ctx.canvas, tile_low = region.get('start'), tile_high = region.get('end'), - min_height = 25, left_offset = this.left_offset;

// Drawing the summary tree (feature coverage histogram) @@ -5213,7 +5209,7 @@ // Drawing prefs this.prefs = extend( {}, this.default_prefs, prefs ); this.mode = mode; -} +};

Painter.prototype.default_prefs = {};

@@ -5229,13 +5225,12 @@ */ var SummaryTreePainter = function(data, view_start, view_end, prefs, mode) { Painter.call(this, data, view_start, view_end, prefs, mode); -} +};

SummaryTreePainter.prototype.default_prefs = { show_counts: false };

SummaryTreePainter.prototype.draw = function(ctx, width, height, w_scale) { var view_start = this.view_start, - view_range = this.view_end - this.view_start, points = this.data.data, max = (this.prefs.histogram_max ? this.prefs.histogram_max : this.data.max), // Set base Y so that max label and data do not overlap. Base Y is where rectangle bases @@ -5266,20 +5261,21 @@ }

ctx.restore(); -} +};

var LinePainter = function(data, view_start, view_end, prefs, mode) { Painter.call( this, data, view_start, view_end, prefs, mode ); + var i, len; if ( this.prefs.min_value === undefined ) { var min_value = Infinity; - for (var i = 0, len = this.data.length; i < len; i++) { + for (i = 0, len = this.data.length; i < len; i++) { min_value = Math.min( min_value, this.data[i][1] ); } this.prefs.min_value = min_value; } if ( this.prefs.max_value === undefined ) { var max_value = -Infinity; - for (var i = 0, len = this.data.length; i < len; i++) { + for (i = 0, len = this.data.length; i < len; i++) { max_value = Math.max( max_value, this.data[i][1] ); } this.prefs.max_value = max_value; @@ -5296,7 +5292,6 @@ vertical_range = max_value - min_value, height_px = height, view_start = this.view_start, - view_range = this.view_end - this.view_start, mode = this.mode, data = this.data;

@@ -5329,7 +5324,9 @@ // Paint track. for (var i = 0, len = data.length; i < len; i++) { ctx.fillStyle = ctx.strokeStyle = this.prefs.color; - x_scaled = Math.round((data[i][0] - view_start) * w_scale); + // -1 because LineTrack data uses 1-based coordinate system but painter + // uses 0-based system. + x_scaled = Math.round((data[i][0] - view_start - 1) * w_scale); y = data[i][1]; var top_overflow = false, bot_overflow = false; if (y === null) { @@ -5471,7 +5468,9 @@ extend(FeaturePainter.prototype, { get_required_height: function(rows_required, width) { // y_scale is the height per row - var required_height = y_scale = this.get_row_height(), mode = this.mode; + var required_height = this.get_row_height(), + y_scale = required_height, + mode = this.mode; // If using a packing mode, need to multiply by the number of slots used if (mode === "no_detail" || mode === "Squish" || mode === "Pack") { required_height = rows_required * y_scale; @@ -5485,7 +5484,7 @@ /** Extra padding after last row of features */ get_bottom_padding: function(width) { // Pad bottom by half a row, at least 5 px - return Math.max( Math.round( this.get_row_height() / 2 ), 5 ) + return Math.max( Math.round( this.get_row_height() / 2 ), 5 ); }, /** * Draw data on ctx using slots and within the rectangle defined by width and height. Returns @@ -5499,8 +5498,7 @@ ctx.fillStyle = this.prefs.block_color; ctx.textAlign = "right";

- var view_range = this.view_end - this.view_start, - y_scale = this.get_row_height(), + var y_scale = this.get_row_height(), feature_mapper = new FeaturePositionMapper(y_scale), x_draw_coords;

@@ -5595,7 +5593,7 @@ thickness, y_start, thick_start = null, thick_end = null, // TODO: is there any reason why block, label color cannot be set at the Painter level? // For now, assume '.' === '+' - block_color = block_color = (!feature_strand || feature_strand === "+" || feature_strand === "." ? this.prefs.block_color : this.prefs.reverse_strand_color); + block_color = (!feature_strand || feature_strand === "+" || feature_strand === "." ? this.prefs.block_color : this.prefs.reverse_strand_color); label_color = this.prefs.label_color;

// Set global alpha. @@ -5821,8 +5819,7 @@ */ draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, orig_seq) { ctx.textAlign = "center"; - var track = this, - tile_region = [tile_low, tile_high], + var tile_region = [tile_low, tile_high], base_offset = 0, seq_offset = 0, gap = 0, @@ -5839,7 +5836,7 @@ } if (!cigar) { // If no cigar string, then assume all matches - cigar = [ [0, orig_seq.length] ] + cigar = [ [0, orig_seq.length] ]; } for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) { var cig = cigar[cig_id], @@ -6001,8 +5998,8 @@ var item, type, data; for (var i = 0; i < draw_last.length; i++) { item = draw_last[i]; - type = item["type"]; - data = item["data"]; + type = item.type; + data = item.data; if (type === "text") { ctx.save(); ctx.font = "bold " + ctx.font; @@ -6154,7 +6151,7 @@ this.alpha = typeof(a) === 'number' ? a : 1; }; Color.prototype = { - eval: function () { return this }, + eval: function () { return this; },

// // If we have some transparency, the only way to represent it @@ -6241,7 +6238,8 @@ this.start_value = start_value; this.end_value = end_value; this.value_range = end_value - start_value; -} +}; + LinearRamp.prototype.map_value = function( value ) { value = Math.max( value, this.start_value ); value = Math.min( value, this.end_value ); @@ -6249,7 +6247,7 @@ // HACK: just red for now // return "hsl(0,100%," + (value * 100) + "%)" return this.start_color.mix( this.end_color, 1 - value ).toCSS(); -} +};

var SplitRamp = function( start_color, middle_color, end_color, start_value, end_value ) { /** @@ -6259,29 +6257,31 @@ this.negative_ramp = new LinearRamp( middle_color, start_color, 0, -start_value ); this.start_value = start_value; this.end_value = end_value; -} +}; + SplitRamp.prototype.map_value = function( value ) { value = Math.max( value, this.start_value ); value = Math.min( value, this.end_value ); if ( value >= 0 ) { - return this.positive_ramp.map_value( value ) + return this.positive_ramp.map_value( value ); } else { - return this.negative_ramp.map_value( -value ) + return this.negative_ramp.map_value( -value ); } -} +};

var DiagonalHeatmapPainter = function(data, view_start, view_end, prefs, mode) { Painter.call( this, data, view_start, view_end, prefs, mode ); + var i, len; if ( this.prefs.min_value === undefined ) { var min_value = Infinity; - for (var i = 0, len = this.data.length; i < len; i++) { + for (i = 0, len = this.data.length; i < len; i++) { min_value = Math.min( min_value, this.data[i][5] ); } this.prefs.min_value = min_value; } if ( this.prefs.max_value === undefined ) { var max_value = -Infinity; - for (var i = 0, len = this.data.length; i < len; i++) { + for (i = 0, len = this.data.length; i < len; i++) { max_value = Math.max( max_value, this.data[i][5] ); } this.prefs.max_value = max_value; @@ -6303,7 +6303,6 @@ value_range = max_value - min_value, height_px = height, view_start = this.view_start, - view_range = this.view_end - this.view_start, mode = this.mode, data = this.data, invsqrt2 = 1 / Math.sqrt(2); @@ -6312,7 +6311,7 @@

var d, s1, e1, s2, e2, value;

- var scale = function( p ) { return ( p - view_start ) * w_scale }; + var scale = function( p ) { return ( p - view_start ) * w_scale; };

ctx.save();

@@ -6334,7 +6333,7 @@ e2 = scale( d[5] ); value = d[6];

- ctx.fillStyle = ( ramp.map_value( value ) ) + ctx.fillStyle = ( ramp.map_value( value ) );

ctx.fillRect( s1, s2, ( e1 - s1 ), ( e2 - s2 ) ); }

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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