[galaxy-commits] commit/galaxy-central: 3 new changesets

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b1e3adfafb4/ Changeset: 5b1e3adfafb4 User: jgoecks Date: 2013-10-12 03:59:34 Summary: Trackster: clean up link attributes. Affected #: 1 file diff -r 34ff4b571205e3d28adcf2d553e6aa0c15364d94 -r 5b1e3adfafb419eb8b3ec61af04a00604b02712c static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -367,7 +367,7 @@ */ add_action_icon: function(name, title, css_class, on_click_fn, prepend, hide) { var drawable = this; - this.action_icons[name] = $("<a/>").attr("href", "").attr("title", title) + this.action_icons[name] = $("<a/>").attr("title", title) .addClass("icon-button").addClass(css_class).tooltip() .click( function() { on_click_fn(drawable); } ) .appendTo(this.icons_div); @@ -942,7 +942,10 @@ // Overview (scrollbar and overview plot) at bottom this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container); this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview); - this.overview_close = $("<a/>").attr("href", "").attr("title", "Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport); + this.overview_close = $("<a/>").attr("title", "Close overview") + .addClass("icon-button overview-close tooltip") + .hide() + .appendTo(this.overview_viewport); this.overview_highlight = $("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport); this.overview_box_background = $("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport); this.overview_box = $("<div/>").addClass("overview-box").appendTo(this.overview_viewport); https://bitbucket.org/galaxy/galaxy-central/commits/a7837763dbaf/ Changeset: a7837763dbaf User: jgoecks Date: 2013-10-13 21:39:08 Summary: Trackster: simplify constructor and config logic using object attributes. Affected #: 1 file diff -r 5b1e3adfafb419eb8b3ec61af04a00604b02712c -r a7837763dbaf2ec540a39c6d0c24bfae5645a1f4 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -208,15 +208,13 @@ this.view = view; this.container = container; this.config = new Config({ - track: this, - params: [ - { key: 'name', label: 'Name', type: 'text', default_value: this.name } - ], - saved_values: obj_dict.prefs, - onchange: function() { - this.track.set_name(this.track.config.get('values').name); - } + params: this.config_params, + onchange: this.config_onchange, + saved_values: obj_dict.prefs }); + if (this.config_onchange) { + this.config.on('change:values', this.config_onchange, this); + } this.prefs = this.config.get('values'); this.drag_handle_class = obj_dict.drag_handle_class; this.is_overview = false; @@ -297,10 +295,20 @@ ]; extend(Drawable.prototype, { + config_params: [ + { key: 'name', label: 'Name', type: 'text', default_value: this.name } + ], + + config_onchange: function() { + this.track.set_name(this.track.config.get('values').name); + }, + init: function() {}, + changed: function() { this.view.changed(); }, + can_draw: function() { if (this.enabled && this.content_visible) { return true; @@ -308,6 +316,7 @@ return false; }, + request_draw: function() {}, _draw: function(options) {}, @@ -1909,13 +1918,6 @@ } this.set('values', values); - - // HACK: to make onchange work as written, attach track at the - // top level of model and call onchange on custom event. - if (options.onchange) { - this.track = options.track; - this.on('change:values', options.onchange, this); - } }, /** @@ -2161,7 +2163,7 @@ canvas = this.html_elt.children()[0], message_div = $("<div/>").addClass("tile-message") // -1 to account for border. - .css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt); + .css({'height': ERROR_PADDING, 'width': canvas.width}).prependTo(this.html_elt); // Handle message; only message currently is that only the first N elements are displayed. var tile_region = new visualization.GenomeRegion({ @@ -2170,10 +2172,10 @@ end: this.high }), num_features = data.length, - more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down") + more_down_icon = $("<a/>").addClass("icon more-down") .attr("title", "For speed, only the first " + num_features + " features in this region were obtained from server. Click to get more data including depth") .tooltip().appendTo(message_div), - more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across") + more_across_icon = $("<a/>").addClass("icon more-across") .attr("title", "For speed, only the first " + num_features + " features in this region were obtained from server. Click to get more data excluding depth") .tooltip().appendTo(message_div); @@ -2356,7 +2358,7 @@ // Height attributes: min height, max height, and visible height. this.min_height_px = 16; this.max_height_px = 800; - this.visible_height_px = 0; + this.visible_height_px = this.prefs.height; // // Create content div, which is where track is displayed, and add to container if available. @@ -3529,7 +3531,6 @@ * bigwig data for now. */ var CompositeTrack = function(view, container, obj_dict) { - this.display_modes = CONTINUOUS_DATA_MODES; TiledTrack.call(this, view, container, obj_dict); // Init drawables; each drawable is a copy so that config/preferences @@ -3564,6 +3565,8 @@ }; extend(CompositeTrack.prototype, TiledTrack.prototype, { + display_modes: CONTINUOUS_DATA_MODES, + action_icons_def: [ // Create composite track from group's tracks. @@ -3728,7 +3731,6 @@ var ReferenceTrack = function (view) { TiledTrack.call(this, view, { content_div: view.top_labeltrack }, { resize: false }); - this.visible_height_px = 13; // Use offset to ensure that bases at tile edges are drawn. this.left_offset = view.canvas_manager.char_width_px; this.container_div.addClass("reference-track"); @@ -3741,6 +3743,10 @@ this.hide_contents(); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + config_params: [ + { name: 'height', default: 13 } + ], + build_header_div: function() {}, init: function() { @@ -3796,33 +3802,25 @@ * Track displays continuous/numerical data. Track expects position data in 1-based format, i.e. wiggle format. */ var LineTrack = function (view, container, obj_dict) { - var track = this; - this.display_modes = CONTINUOUS_DATA_MODES; this.mode = "Histogram"; TiledTrack.call(this, view, container, obj_dict); - - // Define track configuration - this.config = new Config( { - track: this, - params: [ +}; +extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + display_modes: CONTINUOUS_DATA_MODES, + + config_params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, { key: 'color', label: 'Color', type: 'color', default_value: util.get_random_color() }, { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined }, { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, { key: 'height', type: 'int', default_value: 30, hidden: true } - ], - saved_values: obj_dict.prefs, - onchange: function() { - track.set_name(track.prefs.name); - track.request_redraw({ clear_tile_cache: true }); - } - }); - - this.prefs = this.config.get('values'); - this.visible_height_px = this.prefs.height; -}; -extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + ], + + config_onchange: function() { + this.set_name(this.prefs.name); + this.request_draw({ clear_tile_cache: true }); + }, /** * Actions to be taken before drawing. @@ -3854,35 +3852,32 @@ } }); +/** + * Diagonal heatmap for showing interactions data. + */ var DiagonalHeatmapTrack = function (view, container, obj_dict) { - var track = this; - this.display_modes = ["Heatmap"]; this.mode = "Heatmap"; TiledTrack.call(this, view, container, obj_dict); - - // Define track configuration - this.config = new Config( { - track: this, - params: [ - { key: 'name', label: 'Name', type: 'text', default_value: this.name }, - { key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" }, - { key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" }, - { key: 'min_value', label: 'Min Value', type: 'float', default_value: -1 }, - { key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 }, - { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, - { key: 'height', type: 'int', default_value: 500, hidden: true } - ], - saved_values: obj_dict.prefs, - onchange: function() { - track.set_name(track.prefs.name); - this.request_redraw({ clear_tile_cache: true }); - } - }); - - this.prefs = this.config.get('values'); - this.visible_height_px = this.prefs.height; }; + extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + display_modes: ["Heatmap"], + + config_params: [ + { key: 'name', label: 'Name', type: 'text', default_value: this.name }, + { key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" }, + { key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" }, + { key: 'min_value', label: 'Min Value', type: 'float', default_value: -1 }, + { key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 }, + { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, + { key: 'height', type: 'int', default_value: 500, hidden: true } + ], + + config_onchange: function() { + this.set_name(this.prefs.name); + this.request_draw({ clear_tile_cache: true }); + }, + /** * Draw tile. */ @@ -3900,51 +3895,8 @@ * A track that displays features/regions. Track expects position data in BED format, i.e. 0-based, half-open. */ var FeatureTrack = function(view, container, obj_dict) { - // - // Preinitialization: do things that need to be done before calling Track and TiledTrack - // initialization code. - // - var track = this; - this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"]; - - // - // Initialization. - // TiledTrack.call(this, view, container, obj_dict); - - // Define and restore track configuration. - var - block_color = util.get_random_color(), - reverse_strand_color = util.get_random_color( [ block_color, "#FFFFFF" ] ); - this.config = new Config( { - track: this, - params: [ - { key: 'name', label: 'Name', type: 'text', default_value: this.name }, - { key: 'block_color', label: 'Block color', type: 'color', default_value: block_color }, - { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: reverse_strand_color }, - { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, - { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true, - help: 'Show the number of items in each bin when drawing summary histogram' }, - { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' }, - { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' }, - { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones', - options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] }, - { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, - { key: 'height', type: 'int', default_value: this.visible_height_px, hidden: true} - ], - saved_values: obj_dict.prefs, - onchange: function() { - track.set_name(track.prefs.name); - track.set_painter_from_config(); - track.request_draw({ clear_tile_cache: true }); - } - }); - this.prefs = this.config.get('values'); - this.visible_height_px = this.prefs.height; - this.container_div.addClass( "feature-track" ); - this.show_labels_scale = 0.001; - this.showing_details = false; this.summary_draw_height = 30; this.slotters = {}; this.start_end_dct = {}; @@ -3954,6 +3906,28 @@ this.set_painter_from_config(); }; extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"], + + config_params: [ + { key: 'name', label: 'Name', type: 'text', default_value: this.name }, + { key: 'block_color', label: 'Block color', type: 'color', default_value: util.get_random_color() }, + { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() }, + { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, + { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true, + help: 'Show the number of items in each bin when drawing summary histogram' }, + { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' }, + { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' }, + { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones', + options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] }, + { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, + { key: 'height', type: 'int', default_value: 0, hidden: true} + ], + + config_onchange: function() { + this.set_name(this.prefs.name); + this.set_painter_from_config(); + this.request_draw({ clear_tile_cache: true }); + }, set_painter_from_config: function() { if ( this.config.get('values').connector_style === 'arcs' ) { @@ -4221,27 +4195,7 @@ * Displays variant data. */ var VariantTrack = function(view, container, obj_dict) { - this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"]; TiledTrack.call(this, view, container, obj_dict); - - this.config = new Config( { - track: this, - params: [ - { key: 'name', label: 'Name', type: 'text', default_value: this.name }, - { key: 'color', label: 'Histogram color', type: 'color', default_value: util.get_random_color() }, - { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true }, - { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true }, - { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 }, - { key: 'mode', type: 'string', default_value: this.mode, hidden: true } - ], - saved_values: obj_dict.prefs, - onchange: function() { - this.track.set_name(this.track.prefs.name); - this.track.request_draw({ clear_tile_cache: true }); - } - }); - this.prefs = this.config.get('values'); - this.painter = painters.VariantPainter; this.summary_draw_height = 30; @@ -4251,6 +4205,22 @@ }; extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"], + + config_params: [ + { key: 'name', label: 'Name', type: 'text', default_value: this.name }, + { key: 'color', label: 'Histogram color', type: 'color', default_value: util.get_random_color() }, + { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true }, + { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true }, + { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 }, + { key: 'mode', type: 'string', default_value: this.mode, hidden: true } + ], + + config_onchange: function() { + this.set_name(this.prefs.name); + this.request_draw({ clear_tile_cache: true }); + }, + /** * Draw tile. */ @@ -4375,39 +4345,32 @@ * Track that displays mapped reads. Track expects position data in 1-based, closed format, i.e. SAM/BAM format. */ var ReadTrack = function (view, container, obj_dict) { - FeatureTrack.call(this, view, container, obj_dict); - - var - block_color = util.get_random_color(), - reverse_strand_color = util.get_random_color( [ block_color, "#ffffff" ] ); - this.config = new Config( { - track: this, - params: [ - { key: 'name', label: 'Name', type: 'text', default_value: this.name }, - { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: block_color }, - { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: reverse_strand_color }, - { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, - { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false }, - { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true }, - { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, - { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, - { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' }, - { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' } - ], - saved_values: obj_dict.prefs, - onchange: function() { - this.track.set_name(this.track.prefs.name); - this.track.request_draw({ clear_tile_cache: true }); - } - }); - this.prefs = this.config.get('values'); - + FeatureTrack.call(this, view, container, obj_dict); // Choose painter based on whether there is reference data. this.painter = (view.reference_track ? painters.RefBasedReadPainter : painters.ReadPainter); - this.update_icons(); }; -extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); + +extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, { + config_params: [ + { key: 'name', label: 'Name', type: 'text', default_value: this.name }, + { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: util.get_random_color() }, + { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() }, + { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, + { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false }, + { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true }, + { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, + { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, + { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' }, + { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' }, + { key: 'height', type: 'int', default_value: 0, hidden: true} + ], + + config_onchange: function() { + this.set_name(this.prefs.name); + this.request_draw({ clear_tile_cache: true }); + } +}); /** * Objects that can be added to a view. https://bitbucket.org/galaxy/galaxy-central/commits/5c10579e88db/ Changeset: 5c10579e88db User: jgoecks Date: 2013-10-13 21:46:27 Summary: Automated merge. Affected #: 1 file diff -r a7837763dbaf2ec540a39c6d0c24bfae5645a1f4 -r 5c10579e88db53ed05013c4314573d3919d72e17 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -46,6 +46,9 @@ // element var el = null; + // xml request element + var xhr = null; + // attach to element $.fn.uploadbox = function(options) { @@ -237,7 +240,7 @@ formData.append(opts.paramname, file, file.name); // prepare request - var xhr = new XMLHttpRequest(); + xhr = new XMLHttpRequest(); // captures state changes xhr.onreadystatechange = function() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.