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Merge.

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Dannon Baker
2011-04-13 19:05:45 -04:00
parent ef2b1b9e7b bfbe47327a
commit 1f59ddfa7d
1 changed files with 110 additions and 73 deletions
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static/scripts/trackster.js
+110 -73
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@@ -741,7 +741,7 @@ extend( View.prototype, {
this.high = Math.ceil(high);
// 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width
this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / 200 ) / Math.LN10 ) );
this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) );
this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )));
// Overview
@@ -1016,14 +1016,16 @@ extend(NumberFilter.prototype, {
return false;
},
/**
* Returns true iff element is in [low, high]; range is inclusive.
* Returns true if (a) element's value is in [low, high] (range is inclusive)
* or (b) if value is non-numeric and hence unfilterable.
*/
keep: function(element) {
if ( !this.applies_to( element ) ) {
// No element to filter on.
return true;
}
return (element[this.index] >= this.low && element[this.index] <= this.high);
var val = parseInt(element[this.index]);
return (isNaN(val) || (val >= this.low && val <= this.high));
},
/**
* Update filter's min and max values based on element's values.
@@ -1306,11 +1308,22 @@ extend( TrackConfig.prototype, {
});
/**
* Tiles for TiledTracks.
* Tiles drawn by tracks.
*/
var Tile = function(track, canvas) {
this.track = track;
this.canvas = canvas;
var Tile = function(index, resolution, canvas) {
// Wrap element in div for background
this.index = index;
this.resolution = resolution;
this.canvas = $("<div class='track-tile'/>").append(canvas);
};
var SummaryTreeTile = function(index, resolution, canvas, max_val) {
Tile.call(this, index, resolution, canvas);
this.max_val = max_val;
};
var FeatureTrackTile = function(index, resolution, canvas) {
Tile.call(this, index, resolution, canvas);
};
/**
@@ -1669,30 +1682,33 @@ extend(TiledTrack.prototype, Track.prototype, {
// w_scale units are pixels per base.
w_scale = width / range,
resolution = this.view.resolution,
parent_element = $("<div style='position: relative;'></div>");
parent_element = $("<div style='position: relative;'></div>"),
gen_key = function(width, w_scale, tile_index) {
return width + '_' + w_scale + '_' + tile_index;
};
if (!clear_after) { this.content_div.children().remove(); }
this.content_div.append( parent_element );
this.max_height = 0;
// Index of first tile that overlaps visible region
var tile_index = Math.floor( low / resolution / DENSITY );
// A set of setTimeout() ids used when drawing tiles. Each ID indicates
// a tile has been requested to be drawn or is being drawn.
var draw_tile_dict = {};
// A list of tiles drawn/retrieved.
var drawn_tiles = [];
var tile_count = 0
while ( ( tile_index * DENSITY * resolution ) < high ) {
// Check in cache
var key = width + '_' + w_scale + '_' + tile_index;
var key = gen_key(width, w_scale, tile_index);
var cached = this.tile_cache.get(key);
var tile_low = tile_index * DENSITY * this.view.resolution;
var tile_high = tile_low + DENSITY * this.view.resolution;
// console.log(cached, this.tile_cache);
if ( !force && cached ) {
drawn_tiles[drawn_tiles.length] = cached;
this.show_tile(cached, parent_element, tile_low, w_scale);
} else {
this.delayed_draw(force, key, tile_low, tile_high, tile_index,
resolution, parent_element, w_scale, draw_tile_dict);
this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles);
}
tile_index += 1;
tile_count++;
}
//
@@ -1700,7 +1716,7 @@ extend(TiledTrack.prototype, Track.prototype, {
//
var track = this;
var intervalId = setInterval(function() {
if (obj_length(draw_tile_dict) === 0) {
if (drawn_tiles.length === tile_count) {
// All tiles have been drawn.
clearInterval(intervalId);
@@ -1724,6 +1740,29 @@ extend(TiledTrack.prototype, Track.prototype, {
}
}
//
// 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 global_max = -1;
for (var i = 0; i < drawn_tiles.length; i++) {
var cur_max = drawn_tiles[i].max_val;
if (cur_max > global_max) {
global_max = cur_max;
}
}
for (var i = 0; i < drawn_tiles.length; i++) {
if (drawn_tiles[i].max_val !== global_max) {
var tile = drawn_tiles[i];
tile.canvas.remove();
track.delayed_draw(true, gen_key(width, w_scale, tile.index), tile.index,
tile.resolution, parent_element, w_scale, [], { max: global_max });
}
}
}
//
// Update filter attributes, UI.
//
@@ -1755,6 +1794,19 @@ extend(TiledTrack.prototype, Track.prototype, {
track.make_name_popup_menu();
}
}
// Store initial canvas in case we need to use it for overview
/* This is completely broken, just saves the first tile it sees
regardless of if it should be the overview
if (!track.initial_canvas && !window.G_vmlCanvasManager) {
track.initial_canvas = $(tile_element).clone();
var src_ctx = tile_element.get(0).getContext("2d");
var tgt_ctx = track.initial_canvas.get(0).getContext("2d");
var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
tgt_ctx.putImageData(data, 0, 0);
track.set_overview();
}
*/
}
}, 50);
@@ -1765,44 +1817,28 @@ extend(TiledTrack.prototype, Track.prototype, {
this.child_tracks[i].draw(force, clear_after);
}
},
delayed_draw: function(force, key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_dict) {
var track = this;
// Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
delayed_draw: function(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) {
var track = this,
tile_low = tile_index * DENSITY * resolution,
tile_high = tile_low + DENSITY * resolution;
// Helper method.
var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) {
// DEBUG: this is still called too many times when moving slowly,
// console.log( "draw_and_show_tile", resolution, tile_index, w_scale );
returned_tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data)
// Wrap element in div for background
var wrapper_element = $("<div class='track-tile'>").prepend(returned_tile);
tile_element = wrapper_element;
track.tile_cache.set(key, tile_element);
track.show_tile(tile_element, parent_element, tile_low, w_scale);
// TODO: this should go in a post-draw function.
// Store initial canvas in case we need to use it for overview
/* This is completely broken, just saves the first tile it sees
regardless of if it should be the overview
if (!track.initial_canvas && !window.G_vmlCanvasManager) {
track.initial_canvas = $(tile_element).clone();
var src_ctx = tile_element.get(0).getContext("2d");
var tgt_ctx = track.initial_canvas.get(0).getContext("2d");
var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
tgt_ctx.putImageData(data, 0, 0);
track.set_overview();
}
*/
delete draw_tile_dict[id];
var tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data);
track.tile_cache.set(key, tile);
track.show_tile(tile, parent_element, tile_low, w_scale);
drawn_tiles[drawn_tiles.length] = tile;
};
// Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
var id = setTimeout(function() {
if (tile_low <= track.view.high && tile_high >= track.view.low) {
// Show/draw tile: check cache for tile; if tile not in cache, draw it.
var tile_element = (force ? undefined : track.tile_cache.get(key));
if (tile_element) {
track.show_tile(tile_element, parent_element, tile_low, w_scale);
delete draw_tile_dict[id];
var tile = (force ? undefined : track.tile_cache.get(key));
if (tile) {
track.show_tile(tile, parent_element, tile_low, w_scale);
drawn_tiles[drawn_tiles.length] = tile;
}
else {
//
@@ -1810,6 +1846,7 @@ extend(TiledTrack.prototype, Track.prototype, {
//
$.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode,
resolution, track.data_url_extra_params)).then(function(tile_data) {
extend(tile_data, more_tile_data);
// If sequence data needed, get that and draw. Otherwise draw.
if (view.reference_track && w_scale > view.canvas_manager.char_width_px) {
$.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high,
@@ -1825,12 +1862,11 @@ extend(TiledTrack.prototype, Track.prototype, {
}
}
}, 50);
draw_tile_dict[id] = true;
},
/**
* Show track tile and perform associated actions.
*/
show_tile: function(tile_element, parent_element, tile_low, w_scale) {
show_tile: function(tile, parent_element, tile_low, w_scale) {
// Readability.
var track = this;
@@ -1844,6 +1880,7 @@ extend(TiledTrack.prototype, Track.prototype, {
if (this.left_offset) {
left -= this.left_offset;
}
var tile_element = tile.canvas;
tile_element.css({ position: 'absolute', top: 0, left: left, height: '' });
// Setup and show tile element.
@@ -1966,7 +2003,7 @@ extend(ReferenceTrack.prototype, TiledTrack.prototype, {
var c_start = Math.round(c * w_scale);
ctx.fillText(seq[c], c_start + track.left_offset, 10);
}
return canvas;
return new Tile(tile_index, resolution, canvas);
}
this.content_div.css("height", "0px");
}
@@ -2106,7 +2143,7 @@ extend(LineTrack.prototype, TiledTrack.prototype, {
this.prefs, this.mode );
painter.draw( ctx, width, height );
return canvas;
return new Tile(tile_length, resolution, canvas);
}
});
@@ -2196,11 +2233,14 @@ extend(FeatureTrack.prototype, TiledTrack.prototype, {
* 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, bin_size) {
var num_bins = Math.floor((high - low)/bin_size),
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++)
@@ -2335,8 +2375,7 @@ extend(FeatureTrack.prototype, TiledTrack.prototype, {
// Deal with left_offset by translating
ctx.translate( left_offset, SUMMARY_TREE_TOP_PADDING );
painter.draw( ctx, width, required_height );
// Canvas element is returned
return canvas;
return new SummaryTreeTile(tile_index, resolution, canvas, result.max);
}
// Drawing coverage histogram. This is different from summary tree because data can feature
@@ -2359,13 +2398,15 @@ extend(FeatureTrack.prototype, TiledTrack.prototype, {
canvas.height = required_height + SUMMARY_TREE_TOP_PADDING;
// Paint summary tree into canvas.
var binned_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200);
if (result.max) {
binned_data.max = result.max;
}
var painter = new painters.SummaryTreePainter(binned_data, tile_low, tile_high, this.prefs);
var ctx = canvas.getContext("2d");
// Deal with left_offset by translating
ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING);
painter.draw(ctx, width, required_height);
// Canvas element is returned
return canvas;
return new SummaryTreeTile(tile_index, resolution, canvas, binned_data.max);
}
// Start dealing with row-by-row tracks
@@ -2433,7 +2474,7 @@ extend(FeatureTrack.prototype, TiledTrack.prototype, {
// If there's no data, return.
if (!result.data) {
return canvas;
return new Tile(tile_index, resolution, canvas);
}
}
@@ -2444,7 +2485,7 @@ extend(FeatureTrack.prototype, TiledTrack.prototype, {
ctx.translate( left_offset, ERROR_PADDING );
painter.draw( ctx, width, required_height, slots );
return canvas;
return new FeatureTrackTile(tile_index, resolution, canvas);
}
});
@@ -2558,7 +2599,7 @@ exports.FeatureSlotter = function ( w_scale, include_label, max_rows, measureTex
this.include_label = include_label;
this.max_rows = max_rows;
this.measureText = measureText;
}
};
/**
* Slot a set of features, `this.slots` will be updated with slots by id, and
@@ -2704,7 +2745,7 @@ extend( exports.FeatureSlotter.prototype, {
// ---- Painters ----
var painters_module = function(require, exports){
/**
* Draw a dashed line on a canvas using filled rectangles. This function is based on:
* http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.html
@@ -2776,7 +2817,7 @@ var SummaryTreePainter = function( data, view_start, view_end, prefs, mode ) {
Painter.call( this, data, view_start, view_end, prefs, mode );
}
SummaryTreePainter.prototype.default_prefis = { show_counts: false };
SummaryTreePainter.prototype.default_prefs = { show_counts: false };
SummaryTreePainter.prototype.draw = function( ctx, width, height ) {
@@ -2790,16 +2831,15 @@ SummaryTreePainter.prototype.draw = function( ctx, width, height ) {
// max rectangle is required_height.
base_y = height;
delta_x_px = Math.ceil(delta * w_scale);
ctx.save();
for (var i = 0, len = points.length; i < len; i++) {
var x = Math.floor( (points[i][0] - view_start) * w_scale );
var y = points[i][1];
if (!y) { continue; }
var y_px = y / max * height;
var y_px = y / max * height
if (y !== 0 && y_px < 1) { y_px = 1; }
ctx.fillStyle = "black";
ctx.fillRect( x, base_y - y_px, delta_x_px, y_px );
@@ -2991,7 +3031,7 @@ extend( FeaturePainter.prototype, {
}
});
// Contstants specific to feature tracks moved here (HACKING, these should
// Constants specific to feature tracks moved here (HACKING, these should
// basically all be configuration options)
var DENSE_TRACK_HEIGHT = 10,
NO_DETAIL_TRACK_HEIGHT = 3,
@@ -3034,8 +3074,7 @@ extend( LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
var
feature_uid = feature[0],
feature_start = feature[1],
// -1 b/c intervals are half-open.
feature_end = feature[2] - 1,
feature_end = feature[2],
feature_name = feature[3],
f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
@@ -3134,8 +3173,7 @@ extend( LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
var block = feature_blocks[k],
block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
// -1 b/c intervals are half-open.
block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) );
block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) );
// Skip drawing if block not on tile.
if (block_start > block_end) { continue; }
@@ -3199,8 +3237,7 @@ extend( VariantPainter.prototype, FeaturePainter.prototype, {
var feature = data[i],
feature_uid = feature[0],
feature_start = feature[1],
// -1 b/c intervals are half-open.
feature_end = feature[2] - 1,
feature_end = feature[2],
feature_name = feature[3],
// All features need a start, end, and vertical center.
f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),