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Merge pull request #463 from carlfeberhard/fix.trackster-chrint

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Trackster, chromosome interaction: fix display of chrint files in tra…
This commit is contained in:
John Chilton
2015-07-17 14:50:32 +01:00
parent 223583470b d31822e6d4
commit 70ef7e5561
9 changed files with 428 additions and 421 deletions
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client/galaxy/scripts/utils/config.js
+24 -24
View File
@@ -4,7 +4,7 @@ define(['libs/underscore', 'viz/trackster/util', 'utils/config'], function(_, ut
* A configuration setting. Currently key is used as id.
*/
var ConfigSetting = Backbone.Model.extend({
initialize: function(options) {
// Use key as id for now.
var key = this.get('key');
@@ -16,8 +16,8 @@ var ConfigSetting = Backbone.Model.extend({
this.set(_.extend({}, defaults, options));
}
if (this.get('value') === undefined) {
// Use default to set value.
if (this.get('value') === undefined && this.get('default_value') !== undefined) {
// Use default to set value (if present).
this.set_value(this.get('default_value'));
// If no default value for color config, set random color.
@@ -134,7 +134,7 @@ var ConfigSettingCollection = Backbone.Collection.extend({
return _.extend({}, m, { value: saved_values[m.key] });
});
}
return new ConfigSettingCollection(models);
}
});
@@ -150,7 +150,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
*/
render: function() {
var container = this.$el;
this.collection.each(function(param, index) {
// Hidden params have no representation in the form
if (param.get('hidden')) { return; }
@@ -165,7 +165,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
if ( type === 'bool' ) {
row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) );
}
// Draw parameter as textbox
// Draw parameter as textbox
else if ( type === 'text' ) {
row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); }));
}
@@ -177,39 +177,39 @@ var ConfigSettingCollectionView = Backbone.View.extend({
});
select.val( value );
row.append( select );
}
// Draw parameter as color picker
// Draw parameter as color picker
else if ( type === 'color' ) {
var
var
container_div = $("<div/>").appendTo(row),
input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left")
input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left")
.appendTo(container_div).click(function(e) {
// Hide other pickers.
$(".tooltip").removeClass( "in" );
// Show input's color picker.
var tip = $(this).siblings(".tooltip").addClass( "in" );
tip.css( {
tip.css( {
// left: $(this).position().left + ( $(input).width() / 2 ) - 60,
// top: $(this).position().top + $(this.height)
// top: $(this).position().top + $(this.height)
left: $(this).position().left + $(this).width() + 5,
top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(this).height() / 2 )
} ).show();
// Click management:
// Click management:
// Keep showing tip if clicking in tip.
tip.click(function(e) {
e.stopPropagation();
});
// Hide tip if clicking outside of tip.
$(document).bind( "click.color-picker", function() {
tip.hide();
$(document).unbind( "click.color-picker" );
});
// No propagation to avoid triggering document click (and tip hiding) above.
e.stopPropagation();
}),
@@ -222,20 +222,20 @@ var ConfigSettingCollectionView = Backbone.View.extend({
tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip),
tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(tip),
farb_obj = $.farbtastic(tip_inner, { width: 100, height: 100, callback: input, color: value });
// Clear floating.
container_div.append( $("<div/>").css("clear", "both"));
// Use function to fix farb_obj value.
(function(fixed_farb_obj) {
new_color_icon.click(function() {
fixed_farb_obj.setColor(util_mod.get_random_color());
});
});
})(farb_obj);
}
}
else {
row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) );
row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) );
}
// Help text
if ( param.help ) {
client/galaxy/scripts/viz/trackster/painters.js
+88 -92
View File
@@ -8,7 +8,7 @@ define( ["libs/underscore"], function( _ ) {
*/
var BEFORE = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005, AFTER = 1006;
var compute_overlap = function(first_region, second_region) {
var
var
first_start = first_region[0], first_end = first_region[1],
second_start = second_region[0], second_end = second_region[1],
overlap;
@@ -34,7 +34,7 @@ var compute_overlap = function(first_region, second_region) {
overlap = OVERLAP_END;
}
}
return overlap;
};
@@ -60,7 +60,7 @@ var dashedLine = function(ctx, x1, y1, x2, y2, dashLen) {
var dashX = dX / dashes;
var dashY = dY / dashes;
var q;
for (q = 0; q < dashes; q++, x1 += dashX, y1 += dashY) {
if (q % 2 !== 0) {
continue;
@@ -74,11 +74,11 @@ var dashedLine = function(ctx, x1, y1, x2, y2, dashLen) {
*/
var drawDownwardEquilateralTriangle = function(ctx, down_vertex_x, down_vertex_y, side_len) {
// Compute other two points of triangle.
var
var
x1 = down_vertex_x - side_len/2,
x2 = down_vertex_x + side_len/2,
y = down_vertex_y - Math.sqrt( side_len*3/2 );
// Draw and fill.
ctx.beginPath();
ctx.moveTo(x1, y);
@@ -198,16 +198,16 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
ctx.fillStyle = "#aaa";
ctx.fillRect( 0, y_zero, width, 1 );
}
ctx.beginPath();
var x_scaled, y, delta_x_px;
if (data.length > 1) {
delta_x_px = Math.ceil((data[1][0] - data[0][0]) * w_scale);
}
}
else {
delta_x_px = 10;
}
// Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack).
var painter_color = this.prefs.block_color || this.prefs.color,
// Extract RGB from preference color.
@@ -215,10 +215,10 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
pref_r = (pref_color & 0xff0000) >> 16,
pref_g = (pref_color & 0x00ff00) >> 8,
pref_b = pref_color & 0x0000ff,
top_overflow = false,
top_overflow = false,
bot_overflow = false;
// Paint track.
for (var i = 0, len = data.length; i < len; i++) {
// Reset attributes for next point.
@@ -241,20 +241,20 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
if (y < min_value) {
bot_overflow = true;
y = min_value;
}
}
else if (y > max_value) {
top_overflow = true;
y = max_value;
}
// Draw point.
if (mode === "Histogram") {
// y becomes the bar height in pixels, which is the negated for canvas coords
y = Math.round( y / vertical_range * height_px );
ctx.fillRect(x_scaled, y_zero, delta_x_px, - y );
}
}
else if (mode === "Intensity") {
var
var
saturation = (y - min_value) / vertical_range,
// Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color
new_r = Math.round( pref_r + (255 - pref_r) * (1 - saturation) ),
@@ -262,23 +262,23 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
new_b = Math.round( pref_b + (255 - pref_b) * (1 - saturation) );
ctx.fillStyle = "rgb(" + new_r + "," + new_g + "," + new_b + ")";
ctx.fillRect(x_scaled, 0, delta_x_px, height_px);
}
}
else { // mode is Coverage/Line or Filled.
// Scale Y value.
y = Math.round( height_px - (y - min_value) / vertical_range * height_px );
if (in_path) {
ctx.lineTo(x_scaled, y);
}
}
else {
in_path = true;
if (mode === "Filled") {
ctx.moveTo(x_scaled, height_px);
ctx.lineTo(x_scaled, y);
}
}
else {
ctx.moveTo(x_scaled, y);
// Use this approach (note: same as for filled) to draw line from 0 to
// Use this approach (note: same as for filled) to draw line from 0 to
// first data point.
//ctx.moveTo(x_scaled, height_px);
//ctx.lineTo(x_scaled, y);
@@ -292,7 +292,7 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
var overflow_x;
if (mode === "Histogram" || mode === "Intensity") {
overflow_x = delta_x_px;
}
}
else { // Line and Filled, which are points
x_scaled -= 2; // Move it over to the left so it's centered on the point
overflow_x = 4;
@@ -312,11 +312,11 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
ctx.lineTo( 0, y_zero );
}
ctx.fill();
}
}
else {
ctx.stroke();
}
ctx.restore();
};
@@ -356,7 +356,7 @@ FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
if (!this.feature_positions[slot]) {
return null;
}
// Find feature using X.
x += this.translation;
for (var i = 0; i < this.feature_positions[slot].length; i++) {
@@ -404,8 +404,8 @@ _.extend(FeaturePainter.prototype, {
* a FeaturePositionMapper object with information about where features were drawn.
*/
draw: function(ctx, width, height, w_scale, slots) {
var data = this.data,
view_start = this.view_start,
var data = this.data,
view_start = this.view_start,
view_end = this.view_end;
ctx.save();
@@ -423,11 +423,11 @@ _.extend(FeaturePainter.prototype, {
feature_uid = feature[0],
feature_start = feature[1],
feature_end = feature[2],
// Slot valid only if features are slotted and this feature is slotted;
// Slot valid only if features are slotted and this feature is slotted;
// feature may not be due to lack of space.
slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid].slot : null);
// Draw feature if (a) mode is dense or feature is slotted (as it must be for all non-dense modes) and
// Draw feature if (a) mode is dense or feature is slotted (as it must be for all non-dense modes) and
// (b) there's overlap between the feature and drawing region.
if ( (this.mode === "Dense" || slot !== null) && ( feature_start < view_end && feature_end > view_start ) ) {
x_draw_coords = this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, width);
@@ -449,7 +449,7 @@ _.extend(FeaturePainter.prototype, {
});
},
/**
/**
* Abstract function for drawing an individual feature.
*/
draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {
@@ -486,7 +486,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
get_row_height: function() {
var mode = this.mode, height;
if (mode === "Dense") {
height = DENSE_TRACK_HEIGHT;
height = DENSE_TRACK_HEIGHT;
}
else if (mode === "no_detail") {
height = NO_DETAIL_TRACK_HEIGHT;
@@ -520,20 +520,20 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
// For now, assume '.' === '+'
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.
ctx.globalAlpha = this.alpha_scaler.gen_val(feature);
// In dense mode, put all data in top slot.
if (mode === "Dense") {
slot = 1;
}
if (mode === "no_detail") {
// No details for feature, so only one way to display.
ctx.fillStyle = block_color;
ctx.fillRect(f_start, y_start + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT);
}
}
else { // Mode is either Squish or Pack:
// Feature details.
var feature_ts = feature[5],
@@ -541,12 +541,12 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
feature_blocks = feature[7],
// Whether we are drawing full height or squished features
full_height = true;
if (feature_ts && feature_te) {
thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) );
thick_end = Math.ceil( Math.min(width, Math.max(0, (feature_te - tile_low) * w_scale)) );
}
// Set vars that depend on mode.
var thin_height, thick_height;
if (mode === "Squish" ) {
@@ -560,7 +560,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
thin_height = 5;
thick_height = PACK_FEATURE_HEIGHT;
}
// Draw feature/feature blocks + connectors.
if (!feature_blocks) {
// If there are no blocks, treat the feature as one big exon.
@@ -575,15 +575,15 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
}
ctx.fillRect(f_start, y_start + 1, f_end - f_start, thick_height);
}
} else {
} else {
//
// There are feature blocks and mode is either Squish or Pack.
//
// Approach: (a) draw whole feature as connector/intron and (b) draw blocks as
// Approach: (a) draw whole feature as connector/intron and (b) draw blocks as
// needed. This ensures that whole feature, regardless of whether it starts with
// a block, is visible.
//
// Compute y axis start position and height
var cur_y_start, cur_height;
if (mode === "Squish" || mode === "Dense") {
@@ -620,7 +620,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
}
ctx.fillRect(f_start, cur_y_start, f_end - f_start, cur_height);
}
// Draw blocks.
var start_and_height;
for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
@@ -630,7 +630,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low - 0.5) * w_scale)) ),
last_block_start, last_block_end;
// Skip drawing if block not on tile.
// Skip drawing if block not on tile.
if (block_start > block_end) { continue; }
// Draw thin block.
@@ -666,15 +666,15 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
last_block_start = block_start;
last_block_end = block_end;
}
// FIXME: Height scaling only works in Pack mode right now.
if (mode === "Pack") {
// Reset alpha so height scaling is not impacted by alpha scaling.
ctx.globalAlpha = 1;
// Height scaling: draw white lines to reduce height according to height scale factor.
ctx.fillStyle = "white"; // TODO: set this to background color.
var
var
hscale_factor = this.height_scaler.gen_val(feature),
// Ceil ensures that min height is >= 1.
new_height = Math.ceil(thick_height * hscale_factor),
@@ -682,13 +682,13 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
if (hscale_factor !== 1) {
ctx.fillRect(f_start, cur_y_start + 1, f_end - f_start, ws_height);
ctx.fillRect(f_start, cur_y_start + thick_height - ws_height + 1, f_end - f_start, ws_height);
}
}
}
}
}
// Reset alpha so that label is not transparent.
ctx.globalAlpha = 1;
// Draw label for Pack mode.
if (feature_name && mode === "Pack" && feature_start > tile_low) {
ctx.fillStyle = label_color;
@@ -705,10 +705,10 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
//ctx.fillStyle = block_color;
}
}
// Reset global alpha.
ctx.globalAlpha = 1;
return [draw_start, draw_end];
}
});
@@ -726,7 +726,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
get_row_height: function() {
var height, mode = this.mode;
if (mode === "Dense") {
height = DENSE_TRACK_HEIGHT;
height = DENSE_TRACK_HEIGHT;
}
else if (mode === "Squish") {
height = SQUISH_TRACK_HEIGHT;
@@ -821,7 +821,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
drawing_blocks = [],
s_start,
s_end;
// Keep list of items that need to be drawn on top of initial drawing layer.
var draw_last = [];
@@ -837,7 +837,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
if (is_overlap([feature_start + block[0], feature_start + block[1]], tile_region)) {
s_start = get_draw_coord(feature_start + block[0]);
s_end = get_draw_coord(feature_start + block[1]);
// Make sure that block is drawn even if it too small to be rendered officially; in this case,
// read is drawn at 1px.
// TODO: need to ensure that s_start, s_end are calculated the same for both slotting
@@ -861,7 +861,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
var seq_start = feature_start + base_offset;
s_start = get_draw_coord(seq_start);
s_end = get_draw_coord(seq_start + cig_len);
// Skip feature if it's not in tile.
if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) {
// Update offsets.
@@ -869,7 +869,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
seq_offset = update_seq_offset(seq_offset, cig_op, cig_len);
continue;
}
// Make sure that read is drawn even if it too small to be rendered officially; in this case,
// read is drawn at 1px.
// TODO: need to ensure that s_start, s_end are calculated the same for both slotting
@@ -877,8 +877,8 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
if (s_start === s_end) {
s_end += 1;
}
// Draw read feature.
// Draw read feature.
switch (cig_op) {
case "H": // Hard clipping.
case "S": // Soft clipping.
@@ -932,7 +932,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Move forward in sequence only if sequence used to get mismatches.
if (cig_op === 'X') { seq_offset += cig_len; }
base_offset += cig_len;
break;
case "N": // Skipped bases.
ctx.fillStyle = CONNECTOR_COLOR;
@@ -948,7 +948,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Check to see if sequence should be drawn at all by looking at the overlap between
// the sequence region and the tile region.
var insert_x_coord = s_start - gap;
if (is_overlap([seq_start, seq_start + cig_len], tile_region)) {
var seq = read_seq.slice(seq_offset, seq_offset + cig_len);
// Insertion point is between the sequence start and the previous base: (-gap) moves
@@ -992,7 +992,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Draw block.
ctx.fillStyle = "yellow";
// TODO: This is a pretty hack-ish way to fill rectangle based on mode.
ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5),
ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5),
s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT));
}
}
@@ -1011,7 +1011,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
break;
}
}
//
// Draw last items.
//
@@ -1032,7 +1032,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
}
}
},
/**
* Draw a complete read pair
*/
@@ -1048,7 +1048,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
draw_height = (mode === 'Pack' ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT),
label_color = this.prefs.label_color;
// Draw read.
if (feature[5] instanceof Array) {
// Read is paired.
@@ -1097,7 +1097,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 9, this.max_label_length);
}
}
// FIXME: provide actual coordinates for drawn read.
return [0,0];
}
@@ -1122,7 +1122,7 @@ _.extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeat
return longest_feature_length;
},
get_top_padding: function( width ) {
get_top_padding: function( width ) {
var view_range = this.view_end - this.view_start,
w_scale = width / view_range;
return Math.min( 128, Math.ceil( ( this.longest_feature_length / 2 ) * w_scale ) );
@@ -1131,7 +1131,7 @@ _.extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeat
draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_start ) {
// Arc drawing -- from closest endpoints
var x_center = ( block1_end + block2_start ) / 2,
radius = block2_start - x_center;
radius = block2_start - x_center;
// For full half circles
var angle1 = Math.PI, angle2 = 0;
if ( radius > 0 ) {
@@ -1290,32 +1290,33 @@ SplitRamp.prototype.map_value = function( 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 (i = 0, len = this.data.length; i < len; i++) {
min_value = Math.min( min_value, this.data[i][5] );
min_value = Math.min( min_value, this.data[i][6] );
}
this.prefs.min_value = min_value;
}
if ( this.prefs.max_value === undefined ) {
var max_value = -Infinity;
for (i = 0, len = this.data.length; i < len; i++) {
max_value = Math.max( max_value, this.data[i][5] );
max_value = Math.max( max_value, this.data[i][6] );
}
this.prefs.max_value = max_value;
}
};
DiagonalHeatmapPainter.prototype.default_prefs = {
min_value: undefined,
max_value: undefined,
mode: "Heatmap",
DiagonalHeatmapPainter.prototype.default_prefs = {
min_value: undefined,
max_value: undefined,
mode: "Heatmap",
pos_color: "#FF8C00",
neg_color: "#4169E1"
neg_color: "#4169E1"
};
DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
var
var
min_value = this.prefs.min_value,
max_value = this.prefs.max_value,
value_range = max_value - min_value,
@@ -1336,15 +1337,11 @@ DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
// Draw into triangle, then rotate and scale
ctx.rotate(-45 * Math.PI / 180);
ctx.scale( invsqrt2, invsqrt2 );
// Paint track.
for (var i = 0, len = data.length; i < len; i++) {
d = data[i];
// Ensure the cell is visible
// if ( )
s1 = scale( d[1] );
e1 = scale( d[2] );
s2 = scale( d[4] );
@@ -1352,10 +1349,9 @@ DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
value = d[6];
ctx.fillStyle = ( ramp.map_value( value ) );
ctx.fillRect( s1, s2, ( e1 - s1 ), ( e2 - s2 ) );
}
ctx.restore();
};
@@ -1372,7 +1368,7 @@ var ReadPainterUtils = function(ctx, row_height, px_per_base, mode) {
_.extend(ReadPainterUtils.prototype, {
/**
* Draw deletion of base(s).
* Draw deletion of base(s).
* @param draw_detail if true, drawing in detail and deletion is drawn more subtly
*/
draw_deletion: function(x, y, len) {
@@ -1399,7 +1395,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
get_row_height: function() {
var mode = this.mode, height;
if (mode === "Dense") {
height = DENSE_TRACK_HEIGHT;
height = DENSE_TRACK_HEIGHT;
}
else if (mode === "Squish") {
height = SQUISH_TRACK_HEIGHT;
@@ -1431,8 +1427,8 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
draw: function(ctx, width, height, w_scale) {
ctx.save();
var
/**
var
/**
* Returns dictionary of information about an indel; returns empty if there no indel. Assumes indel is left-aligned.
* Dict attributes:
* -type: 'insertion' or 'deletion'
@@ -1485,7 +1481,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
row_height = (this.mode === 'Squish' ? SQUISH_TRACK_HEIGHT : PACK_TRACK_HEIGHT),
// If zoomed out, fill the whole row with feature to make it easier to read;
// when zoomed in, use feature height so that there are gaps in sample rows.
feature_height = (w_scale < 0.1 ?
feature_height = (w_scale < 0.1 ?
row_height :
(this.mode === 'Squish' ? SQUISH_FEATURE_HEIGHT : PACK_FEATURE_HEIGHT)
),
@@ -1495,7 +1491,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
// If there's a single sample, update drawing variables.
if (num_samples === 1) {
row_height = feature_height =
row_height = feature_height =
(w_scale < ctx.canvas.manager.char_width_px ? this.prefs.summary_height : row_height);
paint_utils.row_height = row_height;
// No summary when there's a single sample.
@@ -1519,7 +1515,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
alt = [ locus_data[4].split(',') ];
sample_gts = locus_data[7].split(',');
allele_counts = locus_data.slice(8);
// Process alterate values to derive information about each alt.
alt = _.map(_.flatten(alt), function(a) {
var alt_info = {
@@ -1528,7 +1524,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
start: 0
},
indel_info = get_indel_info(ref, a);
return _.extend(alt_info, indel_info);
});
@@ -1541,7 +1537,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
if (draw_summary) {
ctx.fillStyle = '#999999';
ctx.globalAlpha = 1;
for (j = 0; j < alt.length; j++) {
for (j = 0; j < alt.length; j++) {
// Draw background for summary.
draw_x_start = this.get_start_draw_pos(pos + alt[j].start, w_scale);
ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height);
@@ -1564,7 +1560,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
draw_y_start = (draw_summary ? this.prefs.summary_height + this.divider_height : 0);
for (j = 0; j < sample_gts.length; j++, draw_y_start += row_height) {
genotype = (sample_gts[j] ? sample_gts[j].split(/\/|\|/) : ['0', '0']);
// Get variant to draw and set drawing properties.
variant = null;
if (genotype[0] === genotype[1]) {
client/galaxy/scripts/viz/trackster/tracks.js
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static/maps/utils/config.js.map
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static/maps/viz/trackster/painters.js.map
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static/maps/viz/trackster/tracks.js.map
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static/scripts/utils/config.js
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@@ -1,2 +1,2 @@
define(["libs/underscore","viz/trackster/util","utils/config"],function(a,b){var c=Backbone.Model.extend({initialize:function(d){var e=this.get("key");this.set("id",e);var f=a.find(c.known_settings_defaults,function(a){return a.key===e});f&&this.set(a.extend({},f,d)),void 0===this.get("value")&&(this.set_value(this.get("default_value")),this.get("value")||"color"!==this.get("type")||this.set("value",b.get_random_color()))},set_value:function(a,b){var c=this.get("type");"float"===c?a=parseFloat(a):"int"===c&&(a=parseInt(a,10)),this.set({value:a},b)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:32,hidden:!0},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0}]}),d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var a={};return this.each(function(b){a[b.get("key")]=b.get("value")}),a},get_value:function(a){var b=this.get(a);return b?b.get("value"):void 0},set_value:function(a,b,c){var d=this.get(a);return d?d.set_value(b,c):void 0},set_default_value:function(a,b){var c=this.get(a);return c?c.set("default_value",b):void 0}},{from_models_and_saved_values:function(b,c){return c&&(b=a.map(b,function(b){return a.extend({},b,{value:c[b.key]})})),new d(b)}}),e=Backbone.View.extend({className:"config-settings-view",render:function(){var c=this.$el;return this.collection.each(function(d,e){if(!d.get("hidden")){var f="param_"+e,g=d.get("type"),h=d.get("value"),i=$("<div class='form-row' />").appendTo(c);if(i.append($("<label />").attr("for",f).text(d.get("label")+":")),"bool"===g)i.append($('<input type="checkbox" />').attr("id",f).attr("name",f).attr("checked",h));else if("text"===g)i.append($('<input type="text"/>').attr("id",f).val(h).click(function(){$(this).select()}));else if("select"===g){var j=$("<select />").attr("id",f);a.each(d.get("options"),function(a){$("<option/>").text(a.label).attr("value",a.value).appendTo(j)}),j.val(h),i.append(j)}else if("color"===g){var k=$("<div/>").appendTo(i),l=$("<input />").attr("id",f).attr("name",f).val(h).css("float","left").appendTo(k).click(function(a){$(".tooltip").removeClass("in");var b=$(this).siblings(".tooltip").addClass("in");b.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-$(b).height()/2+$(this).height()/2}).show(),b.click(function(a){a.stopPropagation()}),$(document).bind("click.color-picker",function(){b.hide(),$(document).unbind("click.color-picker")}),a.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(k).attr("title","Set new random color").tooltip(),n=$("<div class='tooltip right' style='position: absolute;' />").appendTo(k).hide(),o=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(n),p=($("<div class='tooltip-arrow'></div>").appendTo(n),$.farbtastic(o,{width:100,height:100,callback:l,color:h}));k.append($("<div/>").css("clear","both")),function(a){m.click(function(){a.setColor(b.get_random_color())})}(p)}else i.append($("<input />").attr("id",f).attr("name",f).val(h));d.help&&i.append($("<div class='help'/>").text(d.help))}}),this},render_in_modal:function(a){var b=this,c=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc")},d=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc"),b.update_from_form()},e=function(a){27===(a.keyCode||a.which)?c():13===(a.keyCode||a.which)&&d()};$(window).bind("keypress.check_enter_esc",e),0===this.$el.children().length&&this.render(),Galaxy.modal.show({title:a||"Configure",body:this.$el,buttons:{Cancel:c,OK:d}})},update_from_form:function(){var a=this;this.collection.each(function(b,c){if(!b.get("hidden")){var d="param_"+c,e=a.$el.find("#"+d).val();"bool"===b.get("type")&&(e=a.$el.find("#"+d).is(":checked")),b.set_value(e)}})}});return{ConfigSetting:c,ConfigSettingCollection:d,ConfigSettingCollectionView:e}});
define(["libs/underscore","viz/trackster/util","utils/config"],function(a,b){var c=Backbone.Model.extend({initialize:function(d){var e=this.get("key");this.set("id",e);var f=a.find(c.known_settings_defaults,function(a){return a.key===e});f&&this.set(a.extend({},f,d)),void 0===this.get("value")&&void 0!==this.get("default_value")&&(this.set_value(this.get("default_value")),this.get("value")||"color"!==this.get("type")||this.set("value",b.get_random_color()))},set_value:function(a,b){var c=this.get("type");"float"===c?a=parseFloat(a):"int"===c&&(a=parseInt(a,10)),this.set({value:a},b)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:32,hidden:!0},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0}]}),d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var a={};return this.each(function(b){a[b.get("key")]=b.get("value")}),a},get_value:function(a){var b=this.get(a);return b?b.get("value"):void 0},set_value:function(a,b,c){var d=this.get(a);return d?d.set_value(b,c):void 0},set_default_value:function(a,b){var c=this.get(a);return c?c.set("default_value",b):void 0}},{from_models_and_saved_values:function(b,c){return c&&(b=a.map(b,function(b){return a.extend({},b,{value:c[b.key]})})),new d(b)}}),e=Backbone.View.extend({className:"config-settings-view",render:function(){var c=this.$el;return this.collection.each(function(d,e){if(!d.get("hidden")){var f="param_"+e,g=d.get("type"),h=d.get("value"),i=$("<div class='form-row' />").appendTo(c);if(i.append($("<label />").attr("for",f).text(d.get("label")+":")),"bool"===g)i.append($('<input type="checkbox" />').attr("id",f).attr("name",f).attr("checked",h));else if("text"===g)i.append($('<input type="text"/>').attr("id",f).val(h).click(function(){$(this).select()}));else if("select"===g){var j=$("<select />").attr("id",f);a.each(d.get("options"),function(a){$("<option/>").text(a.label).attr("value",a.value).appendTo(j)}),j.val(h),i.append(j)}else if("color"===g){var k=$("<div/>").appendTo(i),l=$("<input />").attr("id",f).attr("name",f).val(h).css("float","left").appendTo(k).click(function(a){$(".tooltip").removeClass("in");var b=$(this).siblings(".tooltip").addClass("in");b.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-$(b).height()/2+$(this).height()/2}).show(),b.click(function(a){a.stopPropagation()}),$(document).bind("click.color-picker",function(){b.hide(),$(document).unbind("click.color-picker")}),a.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(k).attr("title","Set new random color").tooltip(),n=$("<div class='tooltip right' style='position: absolute;' />").appendTo(k).hide(),o=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(n),p=($("<div class='tooltip-arrow'></div>").appendTo(n),$.farbtastic(o,{width:100,height:100,callback:l,color:h}));k.append($("<div/>").css("clear","both")),function(a){m.click(function(){a.setColor(b.get_random_color())})}(p)}else i.append($("<input />").attr("id",f).attr("name",f).val(h));d.help&&i.append($("<div class='help'/>").text(d.help))}}),this},render_in_modal:function(a){var b=this,c=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc")},d=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc"),b.update_from_form()},e=function(a){27===(a.keyCode||a.which)?c():13===(a.keyCode||a.which)&&d()};$(window).bind("keypress.check_enter_esc",e),0===this.$el.children().length&&this.render(),Galaxy.modal.show({title:a||"Configure",body:this.$el,buttons:{Cancel:c,OK:d}})},update_from_form:function(){var a=this;this.collection.each(function(b,c){if(!b.get("hidden")){var d="param_"+c,e=a.$el.find("#"+d).val();"bool"===b.get("type")&&(e=a.$el.find("#"+d).is(":checked")),b.set_value(e)}})}});return{ConfigSetting:c,ConfigSettingCollection:d,ConfigSettingCollectionView:e}});
//# sourceMappingURL=../../maps/utils/config.js.map
static/scripts/viz/trackster/painters.js
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static/scripts/viz/trackster/tracks.js
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