2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/def88c93886e/ Changeset: def88c93886e User: jeremy goecks Date: 2014-02-07 21:02:49 Summary: Backbone config settings view: hide modal before updating model. Affected #: 1 file
diff -r a253d56a0dd6be3816581a0c7ed0ada191a1693b -r def88c93886e490e70f449644e002277be996b30 static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -225,9 +225,9 @@ var self = this, cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { - self.update_from_form(); Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); + self.update_from_form(); }, check_enter_esc = function(e) { if ((e.keyCode || e.which) === 27) { // Escape key
https://bitbucket.org/galaxy/galaxy-central/commits/749db2ae03b4/ Changeset: 749db2ae03b4 User: jeremy goecks Date: 2014-02-07 21:04:42 Summary: Circster: (a) fix bad math that led to incorrect track positioning and (b) make gap between tracks a configurable option. Affected #: 1 file
diff -r def88c93886e490e70f449644e002277be996b30 -r 749db2ae03b4ff4c83053322ef291af3b9173325 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -134,7 +134,6 @@
initialize: function(options) { this.genome = options.genome; - this.track_gap = 10; this.label_arc_height = 50; this.scale = 1; this.circular_views = null; @@ -147,6 +146,7 @@ // When config settings change, update view. var vis_config = this.model.get('config'); vis_config.get('arc_dataset_height').on('change:value', this.update_track_bounds, this); + vis_config.get('track_gap').on('change:value', this.update_track_bounds, this); },
// HACKs: using track_type for circular/chord distinction in the functions below for now. @@ -175,16 +175,20 @@ get_tracks_bounds: function() { var circular_tracks = this.get_circular_tracks(), dataset_arc_height = this.model.get('config').get_value('arc_dataset_height'), - min_dimension = Math.min(this.$el.width(), this.$el.height()), + track_gap = this.model.get('config').get_value('track_gap'), + // Subtract 20 to make sure chrom labels are on screen. + min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20, // Compute radius start based on model, will be centered // and fit entirely inside element by default. radius_start = min_dimension / 2 - - circular_tracks.length * (dataset_arc_height + this.track_gap) - - (this.label_arc_height + this.track_gap), + circular_tracks.length * (dataset_arc_height + track_gap) + + // Add track_gap back in because no gap is needed for last track. + track_gap - + this.label_arc_height,
// Compute range of track starting radii. - tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + this.track_gap); - + 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) { @@ -317,7 +321,7 @@ else { // Added circular track.
- // Recompute and update track bounds. + // Recompute and update circular track bounds. var new_track_bounds = this.get_tracks_bounds(); _.each(this.circular_views, function(track_view, i) { track_view.update_radius_bounds(new_track_bounds[i]); @@ -341,9 +345,13 @@ this.circular_views.push(track_view);
// Update label track. + /* + 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]; this.label_track_view.update_radius_bounds(track_bounds); + */ } },
@@ -369,6 +377,12 @@ _.each(this.circular_views, function(track_view, i) { track_view.update_radius_bounds(new_track_bounds[i]); }); + + // Update chords tracks. + _.each(this.chords_views, function(track_view) { + track_view.update_radius_bounds(new_track_bounds[0]); + }); + } });
@@ -381,11 +395,11 @@ /* ----------------------- Public Methods ------------------------- */
initialize: function(options) { - this.bg_stroke = 'ccc'; + this.bg_stroke = 'ddd'; // Fill color when loading data. - this.loading_bg_fill = '000'; + this.loading_bg_fill = 'ffc'; // Fill color when data has been loaded. - this.bg_fill = 'ccc'; + this.bg_fill = 'ddd'; this.total_gap = options.total_gap; this.track = options.track; this.radius_bounds = options.radius_bounds; @@ -898,7 +912,7 @@
// 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) ]; + return [ _.min(values), this._quantile(values, 0.5) || _.max(values) ]; } });
@@ -987,6 +1001,7 @@ // Add Circster-specific config options. vis.get('config').add([ { key: 'arc_dataset_height', label: 'Arc Dataset Height', type: 'int', value: 25, view: 'circster' }, + { key: 'track_gap', label: 'Gap Between Tracks', type: 'int', value: 5, view: 'circster' }, { key: 'total_gap', label: 'Gap [0-1]', type: 'float', value: 0.4, view: 'circster', hidden: true } ]);
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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