mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fix to ba44452: properly scope mod_icon_btn in define not require
This commit is contained in:
Carl Eberhard
@@ -1,16 +1,20 @@
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// load required libraries
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require(
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[
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require([
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'utils/utils',
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'mvc/ui/icon-button',
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'libs/farbtastic',
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], function(mod_utils, mod_icon_btn)
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], function(mod_utils)
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{
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// load css
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mod_utils.cssLoadFile("static/style/circster.css");
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});
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define(["libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(_, d3, visualization, config) {
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define([
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"libs/underscore",
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"libs/d3",
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"viz/visualization",
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"utils/config",
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'mvc/ui/icon-button',
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'libs/farbtastic'
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], function(_, d3, visualization, config, mod_icon_btn) {
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/**
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* Utility class for working with SVG.
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@@ -71,7 +75,7 @@ var UsesTicks = {
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else {
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tick_coords = [1, 0, 4, 0];
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text_coords = [0, 4, ".35em", ""];
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}
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ticks.append("line")
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@@ -80,7 +84,7 @@ var UsesTicks = {
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.attr("x2", tick_coords[2])
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.attr("y1", tick_coords[3])
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.style("stroke", "#000");
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return ticks.append("text")
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.attr("x", text_coords[0])
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.attr("y", text_coords[1])
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@@ -98,11 +102,11 @@ var UsesTicks = {
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// Use default of 2 sig. digits.
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if (sigDigits === undefined)
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sigDigits = 2;
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// Verify input number
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if (num === null)
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return null;
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// Calculate return value
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var rval = null;
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if (Math.abs(num) < 1) {
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@@ -141,7 +145,7 @@ var CircsterLabelTrack = Backbone.Model.extend({});
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*/
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var CircsterView = Backbone.View.extend({
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className: 'circster',
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initialize: function(options) {
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this.genome = options.genome;
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this.label_arc_height = 50;
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@@ -188,7 +192,7 @@ var CircsterView = Backbone.View.extend({
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track_gap = this.model.get('config').get_value('track_gap'),
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// Subtract 20 to make sure chrom labels are on screen.
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min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20,
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// Compute radius start based on model, will be centered
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// Compute radius start based on model, will be centered
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// and fit entirely inside element by default.
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radius_start = min_dimension / 2 -
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circular_tracks.length * (dataset_arc_height + track_gap) +
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@@ -198,14 +202,14 @@ var CircsterView = Backbone.View.extend({
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// Compute range of track starting radii.
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tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap);
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// Map from track start to bounds.
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var self = this;
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return _.map(tracks_start_radii, function(radius) {
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return [radius, radius + dataset_arc_height];
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});
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},
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/**
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* Renders circular tracks, chord tracks, and label tracks.
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*/
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@@ -254,7 +258,7 @@ var CircsterView = Backbone.View.extend({
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}))
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.attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
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.append('svg:g').attr('class', 'tracks');
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// -- Render circular tracks. --
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// Create a view for each track in the visualization and render.
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@@ -266,12 +270,12 @@ var CircsterView = Backbone.View.extend({
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genome: self.genome,
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total_gap: total_gap
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});
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view.render();
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return view;
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});
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// -- Render chords tracks. --
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this.chords_views = chords_tracks.map(function(track) {
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@@ -289,10 +293,10 @@ var CircsterView = Backbone.View.extend({
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});
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// -- Render label track. --
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// Track bounds are:
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// (a) outer radius of last circular track;
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// (b)
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// (b)
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var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1],
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track_bounds = [
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outermost_radius,
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@@ -305,7 +309,7 @@ var CircsterView = Backbone.View.extend({
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genome: self.genome,
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total_gap: total_gap
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});
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this.label_track_view.render();
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},
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@@ -356,7 +360,7 @@ var CircsterView = Backbone.View.extend({
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// Update label track.
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/*
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FIXME: should never have to update label track because vis always expands to fit area
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FIXME: should never have to update label track because vis always expands to fit area
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within label track.
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var track_bounds = new_track_bounds[ new_track_bounds.length-1 ];
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track_bounds[1] = track_bounds[0];
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@@ -373,7 +377,7 @@ var CircsterView = Backbone.View.extend({
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var track_view = this.circular_views[options.index];
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this.circular_views.splice(options.index, 1);
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track_view.$el.remove();
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// Recompute and update track bounds.
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var new_track_bounds = this.get_tracks_bounds();
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_.each(this.circular_views, function(track_view, i) {
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@@ -392,7 +396,7 @@ var CircsterView = Backbone.View.extend({
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_.each(this.chords_views, function(track_view) {
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track_view.update_radius_bounds(new_track_bounds[0]);
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});
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}
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});
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@@ -455,7 +459,7 @@ var CircsterTrackView = Backbone.View.extend({
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// Append titles to paths.
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chroms_paths.append("title").text(function(d) { return d.data.chrom; });
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// -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. --
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var self = this,
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@@ -490,7 +494,7 @@ var CircsterTrackView = Backbone.View.extend({
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var new_d = d3.svg.arc()
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.innerRadius(this.radius_bounds[0])
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.outerRadius(this.radius_bounds[1]);
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this.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d);
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this._transition_chrom_data();
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@@ -511,7 +515,7 @@ var CircsterTrackView = Backbone.View.extend({
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}
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// -- Scale increased, so render visible data with more detail. --
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var self = this,
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utils = new SVGUtils();
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@@ -539,7 +543,7 @@ var CircsterTrackView = Backbone.View.extend({
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$.when(data_deferred).then(function(data) {
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// Remove current data path.
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path_elt.remove();
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// Update data bounds with new data.
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self._update_data_bounds();
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@@ -598,12 +602,12 @@ var CircsterTrackView = Backbone.View.extend({
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_transition_labels: function() {},
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/**
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* Update data bounds. If there are new_bounds, use them; otherwise use
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* Update data bounds. If there are new_bounds, use them; otherwise use
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* default data bounds.
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*/
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_update_data_bounds: function(new_bounds) {
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var old_bounds = this.data_bounds;
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this.data_bounds = new_bounds ||
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this.data_bounds = new_bounds ||
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this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome));
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this._transition_chrom_data();
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},
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@@ -624,7 +628,7 @@ var CircsterTrackView = Backbone.View.extend({
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// Set min, max value in config so that they can be adjusted. Make this silent
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// because these attributes are watched for changes and the viz is updated
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// accordingly (set up in initialize). Because we are setting up, we don't want
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// accordingly (set up in initialize). Because we are setting up, we don't want
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// the watch to trigger events here.
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track.get('config').set_value('min_value', self.data_bounds[0], {silent: true});
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track.get('config').set_value('max_value', self.data_bounds[1], {silent: true});
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@@ -660,7 +664,7 @@ var CircsterTrackView = Backbone.View.extend({
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_get_path_function: function(chrom_arc, chrom_data) {},
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/**
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* Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle
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* Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle
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* separated by gaps.
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*/
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_chroms_layout: function() {
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@@ -700,14 +704,14 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({
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* Render labels.
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*/
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_render_data: function(svg) {
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// -- Add chromosome label where it will fit; an alternative labeling mechanism
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// -- Add chromosome label where it will fit; an alternative labeling mechanism
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// would be nice for small chromosomes. --
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var self = this,
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chrom_arcs = svg.selectAll('g');
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chrom_arcs.selectAll('path')
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.attr('id', function(d) { return 'label-' + d.data.chrom; });
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chrom_arcs.append("svg:text")
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.filter(function(d) {
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return d.endAngle - d.startAngle > self.min_arc_len;
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@@ -857,12 +861,12 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
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return "rotate(90)";
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};
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// FIXME:
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// FIXME:
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// (1) using min_max class below is needed for _update_min_max, which could be improved.
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// (2) showing config on tick click should be replaced by proper track config icon.
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// Draw min, max on first chrom only.
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var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ],
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var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ],
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this._data_bounds_ticks_fn(), textTransform, true)
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.classed('min_max', true);
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@@ -872,7 +876,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
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var view = new config.ConfigSettingCollectionView({
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collection: self.track.get('config')
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});
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view.render_in_modal('Configure Track');
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view.render_in_modal('Configure Track');
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});
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});
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@@ -951,7 +955,7 @@ _.extend(CircsterQuantitativeTrackView.prototype, UsesTicks);
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var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({
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get_data_bounds: function(data) {
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// Set max across dataset by extracting all values, flattening them into a
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// Set max across dataset by extracting all values, flattening them into a
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// single array, and getting third quartile.
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var values = _.flatten( _.map(data, function(d) {
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if (d) {
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@@ -965,8 +969,8 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({
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return 0;
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}
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}) );
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// For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0
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// For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0
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// for sparsely populated data, so use max in that case.
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return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ];
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}
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@@ -1068,13 +1072,13 @@ var Circster = Backbone.View.extend(
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genome : genome,
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model : vis
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});
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// Render vizualization
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viz_view.render();
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// setup title
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$('#center .unified-panel-header-inner').append(galaxy_config.app.viz_config.title + " " + galaxy_config.app.viz_config.dbkey);
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// setup menu
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var menu = mod_icon_btn.create_icon_buttons_menu([
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{
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@@ -1100,7 +1104,7 @@ var Circster = Backbone.View.extend(
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{
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// show saving dialog box
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Galaxy.modal.show({title: "Saving...", body: "progress" });
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// send to server
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$.ajax({
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url: galaxy_config.root + "visualization/save",
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@@ -1132,11 +1136,11 @@ var Circster = Backbone.View.extend(
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window.location = galaxy_config.root + "visualization/list";
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}
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}], { tooltip_config: { placement: 'bottom' } });
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// add menu
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menu.$el.attr("style", "float: right");
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$("#center .unified-panel-header-inner").append(menu.$el);
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// manual tooltip config because default gravity is S and cannot be changed
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$(".menu-button").tooltip( { placement: 'bottom' } );
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}
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File diff suppressed because one or more lines are too long
@@ -1,16 +1,20 @@
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// load required libraries
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require(
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[
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require([
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'utils/utils',
|
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'mvc/ui/icon-button',
|
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'libs/farbtastic',
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], function(mod_utils, mod_icon_btn)
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], function(mod_utils)
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{
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// load css
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mod_utils.cssLoadFile("static/style/circster.css");
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});
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define(["libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(_, d3, visualization, config) {
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define([
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"libs/underscore",
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"libs/d3",
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"viz/visualization",
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"utils/config",
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'mvc/ui/icon-button',
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'libs/farbtastic'
|
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], function(_, d3, visualization, config, mod_icon_btn) {
|
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|
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/**
|
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* Utility class for working with SVG.
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@@ -71,7 +75,7 @@ var UsesTicks = {
|
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else {
|
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tick_coords = [1, 0, 4, 0];
|
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text_coords = [0, 4, ".35em", ""];
|
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|
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|
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}
|
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|
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ticks.append("line")
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@@ -80,7 +84,7 @@ var UsesTicks = {
|
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.attr("x2", tick_coords[2])
|
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.attr("y1", tick_coords[3])
|
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.style("stroke", "#000");
|
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|
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|
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return ticks.append("text")
|
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.attr("x", text_coords[0])
|
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.attr("y", text_coords[1])
|
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@@ -98,11 +102,11 @@ var UsesTicks = {
|
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// Use default of 2 sig. digits.
|
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if (sigDigits === undefined)
|
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sigDigits = 2;
|
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|
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|
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// Verify input number
|
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if (num === null)
|
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return null;
|
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|
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|
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// Calculate return value
|
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var rval = null;
|
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if (Math.abs(num) < 1) {
|
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@@ -141,7 +145,7 @@ var CircsterLabelTrack = Backbone.Model.extend({});
|
||||
*/
|
||||
var CircsterView = Backbone.View.extend({
|
||||
className: 'circster',
|
||||
|
||||
|
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initialize: function(options) {
|
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this.genome = options.genome;
|
||||
this.label_arc_height = 50;
|
||||
@@ -188,7 +192,7 @@ var CircsterView = Backbone.View.extend({
|
||||
track_gap = this.model.get('config').get_value('track_gap'),
|
||||
// Subtract 20 to make sure chrom labels are on screen.
|
||||
min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20,
|
||||
// Compute radius start based on model, will be centered
|
||||
// Compute radius start based on model, will be centered
|
||||
// and fit entirely inside element by default.
|
||||
radius_start = min_dimension / 2 -
|
||||
circular_tracks.length * (dataset_arc_height + track_gap) +
|
||||
@@ -198,14 +202,14 @@ var CircsterView = Backbone.View.extend({
|
||||
|
||||
// Compute range of track starting radii.
|
||||
tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap);
|
||||
|
||||
|
||||
// Map from track start to bounds.
|
||||
var self = this;
|
||||
return _.map(tracks_start_radii, function(radius) {
|
||||
return [radius, radius + dataset_arc_height];
|
||||
});
|
||||
},
|
||||
|
||||
|
||||
/**
|
||||
* Renders circular tracks, chord tracks, and label tracks.
|
||||
*/
|
||||
@@ -254,7 +258,7 @@ var CircsterView = Backbone.View.extend({
|
||||
}))
|
||||
.attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
|
||||
.append('svg:g').attr('class', 'tracks');
|
||||
|
||||
|
||||
// -- Render circular tracks. --
|
||||
|
||||
// Create a view for each track in the visualization and render.
|
||||
@@ -266,12 +270,12 @@ var CircsterView = Backbone.View.extend({
|
||||
genome: self.genome,
|
||||
total_gap: total_gap
|
||||
});
|
||||
|
||||
|
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view.render();
|
||||
|
||||
|
||||
return view;
|
||||
});
|
||||
|
||||
|
||||
// -- Render chords tracks. --
|
||||
|
||||
this.chords_views = chords_tracks.map(function(track) {
|
||||
@@ -289,10 +293,10 @@ var CircsterView = Backbone.View.extend({
|
||||
});
|
||||
|
||||
// -- Render label track. --
|
||||
|
||||
|
||||
// Track bounds are:
|
||||
// (a) outer radius of last circular track;
|
||||
// (b)
|
||||
// (b)
|
||||
var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1],
|
||||
track_bounds = [
|
||||
outermost_radius,
|
||||
@@ -305,7 +309,7 @@ var CircsterView = Backbone.View.extend({
|
||||
genome: self.genome,
|
||||
total_gap: total_gap
|
||||
});
|
||||
|
||||
|
||||
this.label_track_view.render();
|
||||
},
|
||||
|
||||
@@ -356,7 +360,7 @@ var CircsterView = Backbone.View.extend({
|
||||
|
||||
// Update label track.
|
||||
/*
|
||||
FIXME: should never have to update label track because vis always expands to fit area
|
||||
FIXME: should never have to update label track because vis always expands to fit area
|
||||
within label track.
|
||||
var track_bounds = new_track_bounds[ new_track_bounds.length-1 ];
|
||||
track_bounds[1] = track_bounds[0];
|
||||
@@ -373,7 +377,7 @@ var CircsterView = Backbone.View.extend({
|
||||
var track_view = this.circular_views[options.index];
|
||||
this.circular_views.splice(options.index, 1);
|
||||
track_view.$el.remove();
|
||||
|
||||
|
||||
// Recompute and update track bounds.
|
||||
var new_track_bounds = this.get_tracks_bounds();
|
||||
_.each(this.circular_views, function(track_view, i) {
|
||||
@@ -392,7 +396,7 @@ var CircsterView = Backbone.View.extend({
|
||||
_.each(this.chords_views, function(track_view) {
|
||||
track_view.update_radius_bounds(new_track_bounds[0]);
|
||||
});
|
||||
|
||||
|
||||
}
|
||||
});
|
||||
|
||||
@@ -455,7 +459,7 @@ var CircsterTrackView = Backbone.View.extend({
|
||||
|
||||
// Append titles to paths.
|
||||
chroms_paths.append("title").text(function(d) { return d.data.chrom; });
|
||||
|
||||
|
||||
// -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. --
|
||||
|
||||
var self = this,
|
||||
@@ -490,7 +494,7 @@ var CircsterTrackView = Backbone.View.extend({
|
||||
var new_d = d3.svg.arc()
|
||||
.innerRadius(this.radius_bounds[0])
|
||||
.outerRadius(this.radius_bounds[1]);
|
||||
|
||||
|
||||
this.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d);
|
||||
|
||||
this._transition_chrom_data();
|
||||
@@ -511,7 +515,7 @@ var CircsterTrackView = Backbone.View.extend({
|
||||
}
|
||||
|
||||
// -- Scale increased, so render visible data with more detail. --
|
||||
|
||||
|
||||
var self = this,
|
||||
utils = new SVGUtils();
|
||||
|
||||
@@ -539,7 +543,7 @@ var CircsterTrackView = Backbone.View.extend({
|
||||
$.when(data_deferred).then(function(data) {
|
||||
// Remove current data path.
|
||||
path_elt.remove();
|
||||
|
||||
|
||||
// Update data bounds with new data.
|
||||
self._update_data_bounds();
|
||||
|
||||
@@ -598,12 +602,12 @@ var CircsterTrackView = Backbone.View.extend({
|
||||
_transition_labels: function() {},
|
||||
|
||||
/**
|
||||
* Update data bounds. If there are new_bounds, use them; otherwise use
|
||||
* Update data bounds. If there are new_bounds, use them; otherwise use
|
||||
* default data bounds.
|
||||
*/
|
||||
_update_data_bounds: function(new_bounds) {
|
||||
var old_bounds = this.data_bounds;
|
||||
this.data_bounds = new_bounds ||
|
||||
this.data_bounds = new_bounds ||
|
||||
this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome));
|
||||
this._transition_chrom_data();
|
||||
},
|
||||
@@ -624,7 +628,7 @@ var CircsterTrackView = Backbone.View.extend({
|
||||
|
||||
// Set min, max value in config so that they can be adjusted. Make this silent
|
||||
// because these attributes are watched for changes and the viz is updated
|
||||
// accordingly (set up in initialize). Because we are setting up, we don't want
|
||||
// accordingly (set up in initialize). Because we are setting up, we don't want
|
||||
// the watch to trigger events here.
|
||||
track.get('config').set_value('min_value', self.data_bounds[0], {silent: true});
|
||||
track.get('config').set_value('max_value', self.data_bounds[1], {silent: true});
|
||||
@@ -660,7 +664,7 @@ var CircsterTrackView = Backbone.View.extend({
|
||||
_get_path_function: function(chrom_arc, chrom_data) {},
|
||||
|
||||
/**
|
||||
* Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle
|
||||
* Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle
|
||||
* separated by gaps.
|
||||
*/
|
||||
_chroms_layout: function() {
|
||||
@@ -700,14 +704,14 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({
|
||||
* Render labels.
|
||||
*/
|
||||
_render_data: function(svg) {
|
||||
// -- Add chromosome label where it will fit; an alternative labeling mechanism
|
||||
// -- Add chromosome label where it will fit; an alternative labeling mechanism
|
||||
// would be nice for small chromosomes. --
|
||||
var self = this,
|
||||
chrom_arcs = svg.selectAll('g');
|
||||
|
||||
chrom_arcs.selectAll('path')
|
||||
.attr('id', function(d) { return 'label-' + d.data.chrom; });
|
||||
|
||||
|
||||
chrom_arcs.append("svg:text")
|
||||
.filter(function(d) {
|
||||
return d.endAngle - d.startAngle > self.min_arc_len;
|
||||
@@ -857,12 +861,12 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
|
||||
return "rotate(90)";
|
||||
};
|
||||
|
||||
// FIXME:
|
||||
// FIXME:
|
||||
// (1) using min_max class below is needed for _update_min_max, which could be improved.
|
||||
// (2) showing config on tick click should be replaced by proper track config icon.
|
||||
|
||||
// Draw min, max on first chrom only.
|
||||
var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ],
|
||||
var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ],
|
||||
this._data_bounds_ticks_fn(), textTransform, true)
|
||||
.classed('min_max', true);
|
||||
|
||||
@@ -872,7 +876,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
|
||||
var view = new config.ConfigSettingCollectionView({
|
||||
collection: self.track.get('config')
|
||||
});
|
||||
view.render_in_modal('Configure Track');
|
||||
view.render_in_modal('Configure Track');
|
||||
});
|
||||
});
|
||||
|
||||
@@ -951,7 +955,7 @@ _.extend(CircsterQuantitativeTrackView.prototype, UsesTicks);
|
||||
var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({
|
||||
|
||||
get_data_bounds: function(data) {
|
||||
// Set max across dataset by extracting all values, flattening them into a
|
||||
// Set max across dataset by extracting all values, flattening them into a
|
||||
// single array, and getting third quartile.
|
||||
var values = _.flatten( _.map(data, function(d) {
|
||||
if (d) {
|
||||
@@ -965,8 +969,8 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({
|
||||
return 0;
|
||||
}
|
||||
}) );
|
||||
|
||||
// For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0
|
||||
|
||||
// For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0
|
||||
// for sparsely populated data, so use max in that case.
|
||||
return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ];
|
||||
}
|
||||
@@ -1068,13 +1072,13 @@ var Circster = Backbone.View.extend(
|
||||
genome : genome,
|
||||
model : vis
|
||||
});
|
||||
|
||||
|
||||
// Render vizualization
|
||||
viz_view.render();
|
||||
|
||||
|
||||
// setup title
|
||||
$('#center .unified-panel-header-inner').append(galaxy_config.app.viz_config.title + " " + galaxy_config.app.viz_config.dbkey);
|
||||
|
||||
|
||||
// setup menu
|
||||
var menu = mod_icon_btn.create_icon_buttons_menu([
|
||||
{
|
||||
@@ -1100,7 +1104,7 @@ var Circster = Backbone.View.extend(
|
||||
{
|
||||
// show saving dialog box
|
||||
Galaxy.modal.show({title: "Saving...", body: "progress" });
|
||||
|
||||
|
||||
// send to server
|
||||
$.ajax({
|
||||
url: galaxy_config.root + "visualization/save",
|
||||
@@ -1132,11 +1136,11 @@ var Circster = Backbone.View.extend(
|
||||
window.location = galaxy_config.root + "visualization/list";
|
||||
}
|
||||
}], { tooltip_config: { placement: 'bottom' } });
|
||||
|
||||
|
||||
// add menu
|
||||
menu.$el.attr("style", "float: right");
|
||||
$("#center .unified-panel-header-inner").append(menu.$el);
|
||||
|
||||
|
||||
// manual tooltip config because default gravity is S and cannot be changed
|
||||
$(".menu-button").tooltip( { placement: 'bottom' } );
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user