1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/edff37d76463/ Changeset: edff37d76463 User: jeremy goecks Date: 2014-02-28 21:27:59 Summary: Trackster: replace custom config settings model and view with generic model/view from config.js. Improvements for generic config model/view. Whitespace fixes. Affected #: 4 files

diff -r e059dbc01b575b856509c2e2baccac3750b6eeb5 -r edff37d76463a468753477080f65886d4a53619e static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -16,9 +16,14 @@ this.set(_.extend({}, defaults, options)); }

- // If type color and no value, get random color. - if (this.get('type') === 'color' && !this.get('value')) { - this.set('value', util_mod.get_random_color()); + if (!this.get('value')) { + if (this.get('type') === 'color') { + // For color setting, set random color. + this.set('value', util_mod.get_random_color()); + } + else { + this.set_value(this.get('default_value')); + } } },

@@ -90,23 +95,49 @@ }

return undefined; - } + }, + + /** + * Set value for a setting. + */ + set_value: function(key, value) { + var s = this.get(key); + if (s) { + return s.set_value(value); + } + + return undefined; + }, + + /** + * Set default value for a setting. + */ + set_default_value: function(key, default_value) { + var s = this.get(key); + if (s) { + return s.set('default_value', default_value); + } + + return undefined; + } }, { /** - * Utility function that creates a ConfigSettingsCollection from a standard dictionary - * with configuration key-value pairs. + * Utility function that creates a ConfigSettingsCollection from a set of models + * and a saved_values dictionary. */ - from_config_dict: function(config_dict) { - // Create a list of key-value dicts suitable for sending to a collection. - var settings_list = _.map(_.keys(config_dict), function(key) { - return { - key: key, - value: config_dict[key] - }; - }); - - return new ConfigSettingCollection(settings_list); + from_models_and_saved_values: function(models, saved_values) { + // Update models with saved values. + if (saved_values) { + _.each(models, function(m) { + if (saved_values[m.key]) { + // Found saved value, so update model. + m.value = saved_values[m.key]; + } + }); + } + + return new ConfigSettingCollection(models); } });

@@ -265,7 +296,7 @@ var id = 'param_' + index; var value = self.$el.find( '#' + id ).val(); if ( setting.get('type') === 'bool' ) { - value = container.find( '#' + id ).is( ':checked' ); + value = self.$el.find( '#' + id ).is( ':checked' ); } setting.set_value(value); }

diff -r e059dbc01b575b856509c2e2baccac3750b6eeb5 -r edff37d76463a468753477080f65886d4a53619e static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -199,7 +199,7 @@ init_editor : function () { // set title - $("#center .unified-panel-title").text(view.prefs.name + " (" + view.dbkey + ")"); + $("#center .unified-panel-title").text(view.config.get_value('name') + " (" + view.dbkey + ")");

// add dataset if (galaxy_config.app.add_dataset) @@ -208,7 +208,7 @@ data: { hda_ldda: 'hda', data_type: 'track_config' }, dataType: "json", success: function(track_data) { view.add_drawable( trackster_ui.object_from_template(track_data, view, view) ); } - }); + });

// initialize icons $("#add-bookmark-button").click(function()

diff -r e059dbc01b575b856509c2e2baccac3750b6eeb5 -r edff37d76463a468753477080f65886d4a53619e static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,7 +1,7 @@ define( ["libs/underscore", "viz/visualization", "viz/trackster/util", "viz/trackster/slotting", "viz/trackster/painters", "viz/trackster/filters", - "mvc/data", "mvc/tools" ], - function(_, visualization, util, slotting, painters, filters_mod, data, tools_mod) { + "mvc/data", "mvc/tools", "utils/config" ], + function(_, visualization, util, slotting, painters, filters_mod, data, tools_mod, config_mod) {

var extend = _.extend;

@@ -207,26 +207,23 @@

// -- Set up drawable configuration. --

- this.config = new Config({ - params: this.config_params, - onchange: this.config_onchange, - saved_values: obj_dict.prefs - }); - this.prefs = this.config.get('values'); - + this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values(this.config_params, obj_dict.prefs); + console.log(obj_dict.prefs); + this.config.each(function(s) { console.log(s.id, s.get('value')) }) + // If there's no saved name, use object name. - if (!this.prefs.name) { - this.prefs.name = obj_dict.name; + if (!this.config.get_value('name')) { + this.config.set_value('name', obj_dict.name); } if (this.config_onchange) { - this.config.on('change:values', this.config_onchange, this); + this.config.on('change', this.config_onchange, this); }

// Build Drawable HTML and behaviors. this.container_div = this.build_container_div(); this.header_div = this.build_header_div();

- if (this.header_div) { + if (this.header_div) { this.container_div.append(this.header_div);

// Icons container. @@ -257,14 +254,14 @@ title: "Hide/show content", css_class: "toggle", on_click_fn: function(drawable) { - if ( drawable.prefs.content_visible ) { + if ( drawable.config.get_value('content_visible') ) { drawable.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"); drawable.hide_contents(); - drawable.prefs.content_visible = false; - } + drawable.config.set_value('content_visible', false); + } else { drawable.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"); - drawable.prefs.content_visible = true; + drawable.config.set_value('content_visible', true); drawable.show_contents(); } } @@ -275,10 +272,10 @@ title: "Edit settings", css_class: "gear", on_click_fn: function(drawable) { - var view = new ConfigView({ - model: drawable.config + var view = new config_mod.ConfigSettingCollectionView({ + collection: drawable.config }); - view.render(); + view.render_in_modal('Configure Track'); } }, // Remove. @@ -295,7 +292,7 @@ ];

extend(Drawable.prototype, { - config_params: [ + config_params: [ { key: 'name', label: 'Name', type: 'text', default_value: '' }, { key: 'content_visible', type: 'bool', default_value: true, hidden: true } ], @@ -311,7 +308,7 @@ },

can_draw: function() { - if (this.enabled && this.prefs.content_visible) { + if (this.enabled && this.config.get_value('content_visible')) { return true; }

@@ -330,11 +327,11 @@

/** * Set drawable name. - */ + */ set_name: function(new_name) { - this.old_name = this.prefs.name; - this.prefs.name = new_name; - this.name_div.text(this.prefs.name); + this.old_name = this.config.get_value('name'); + this.config.set_value('name', new_name); + this.name_div.text(new_name); },

/** @@ -342,8 +339,8 @@ */ revert_name: function() { if (this.old_name) { - this.prefs.name = this.old_name; - this.name_div.text(this.prefs.name); + this.config.set_value('name', this.old_name); + this.name_div.text(this.old_name); } },

@@ -355,7 +352,7 @@

this.container.remove_drawable(this); var view = this.view; - this.container_div.hide(0, function() { + this.container_div.hide(0, function() { $(this).remove(); // HACK: is there a better way to update the view? view.update_intro_div(); @@ -364,7 +361,7 @@

/** * Build drawable's container div; this is the parent div for all drawable's elements. - */ + */ build_container_div: function() {},

/** @@ -473,7 +470,7 @@ dictified_drawables.push(this.drawables[i].to_dict()); } return { - prefs: this.prefs, + prefs: this.config.to_key_value_dict(), obj_type: this.obj_type, drawables: dictified_drawables }; @@ -668,7 +665,7 @@ build_header_div: function() { var header_div = $("<div/>").addClass("track-header"); header_div.append($("<div/>").addClass(this.drag_handle_class)); - this.name_div = $("<div/>").addClass("track-name").text(this.prefs.name).appendTo(header_div); + this.name_div = $("<div/>").addClass("track-name").text(this.config.get_value('name')).appendTo(header_div); return header_div; },

@@ -829,7 +826,7 @@ */ show_composite_track: function() { var composite_track = new CompositeTrack(this.view, this.view, { - name: this.prefs.name, + name: this.config.get_value('name'), drawables: this.drawables }); var index = this.container.replace_drawable(this, composite_track, true); @@ -898,19 +895,15 @@ this.reset();

// Define track configuration - this.config = new Config( { - track: this, - params: [ + this.config = new config_mod.ConfigSettingCollection({ + models: [ { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" }, { key: 'c_color', label: 'C Color', type: 'color', default_value: "#00FF00" }, { key: 'g_color', label: 'G Color', type: 'color', default_value: "#0000FF" }, { key: 't_color', label: 'T Color', type: 'color', default_value: "#FF00FF" }, { key: 'n_color', label: 'N Color', type: 'color', default_value: "#AAAAAA" } - ], + ], saved_values: obj_dict.prefs, - onchange: function() { - track.request_redraw({ clear_tile_cache: true }); - } }); },

@@ -1819,7 +1812,7 @@ // already in group, add track to group. if (current_track.container === view) { // Create new group. - var group = new DrawableGroup(view, view, { name: track.prefs.name }); + var group = new DrawableGroup(view, view, { name: track.config.get_value('name') });

// Replace track with group. var index = current_track.container.replace_drawable(current_track, group, false); @@ -1923,241 +1916,6 @@ };

/** - * Configuration object. - */ -var Config = Backbone.Model.extend({ - initialize: function(options) { - // values is a simple param_key-to-value dictionary used to store - // param values. - var values = {}; - - // Set default values. - _.each(options.params, function(p) { - // For color parameters without a default value, assign a random color. - values[p.key] = (p.type === 'color' && !p.default_value ? util.get_random_color() : p.default_value ); - - }); - - // Restore saved values. - if (options.saved_values) { - _.each( this.get('params'), function(p) { - if (p.key in options.saved_values) { - values[p.key] = options.saved_values[p.key]; - } - }); - } - - this.set('values', values); - }, - - /** - * Set default value for parameter. - */ - set_param_default_value: function(key, default_value) { - var param = _.find(this.get('params'), function(p) { - return p.key === key; - }); - - if (param) { - param.default_value = default_value; - } - }, - - /** - * Set a parameter's value. Returns true if value changed, false if value changed. - */ - set_param_value: function(key, value) { - // Find param. - var param = _.find(this.get('params'), function(p) { - return p.key === key; - }); - - if (param) { - // Parse value from string. - if (typeof value === "string" || value instanceof String) { - // Parse string. - if (value.trim() === '') { - // If empty value, use default. - value = param.default_value; - } else if ( param.type === 'float' ) { - value = parseFloat( value ); - } else if ( param.type === 'int' ) { - value = parseInt( value, 10 ); - } - } - } - - // Set value and return true if changed, false otherwise. - if (this.get('values')[key] !== value) { - this.get('values')[key] = value; - // HACK: custom event trigger needed to indicate that values were updated. - this.trigger('change:values'); - return true; - } - else { - return false; - } - } -}); - -var ConfigView = Backbone.View.extend({ - - /** - * Build and show form for modifying configuration. Currently uses Galaxy modals. - */ - render: function() { - // - // Build config selection UI. - // - - var track_config = this.model; - - // Prevent propagation of keydown events to viz to avoid inadvertent navigation. - var container = $("<div/>").keydown(function(e) { - e.stopPropagation(); - }); - var param; - // Function to process parameters recursively - function handle_params( params, container ) { - for ( var index = 0; index < params.length; index++ ) { - param = params[index]; - // Hidden params have no representation in the form - if ( param.hidden ) { continue; } - // Build row for param - var id = 'param_' + index; - var value = track_config.get('values')[ param.key ]; - var row = $("<div class='form-row' />").appendTo( container ); - row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); - // Draw parameter as checkbox - if ( param.type === 'bool' ) { - row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); - // Draw parameter as textbox - } - else if ( param.type === 'text' ) { - row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); })); - // Draw paramter as select area - } - else if ( param.type === 'select' ) { - var select = $('<select />').attr("id", id); - for ( var i = 0; i < param.options.length; i++ ) { - $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); - } - select.val( value ); - row.append( select ); - // Draw parameter as color picker - } - else if ( param.type === 'color' ) { - var - container_div = $("<div/>").appendTo(row), - input = $('<input/>').attr({ - id: id, - name: id - }).val( value ).addClass('color-input') - .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( { - // left: $(this).position().left + ( $(input).width() / 2 ) - 60, - // top: $(this).position().top + $(this.height) - left: $(this).position().left + $(this).width() + 5, - top: $(this).position().top + Galaxy.modal.scrollTop() - ( $(tip).height() / 2 ) + ( $(this).height() / 2 ) - } ).show(); - // 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(); - }), - // Icon for setting a new random color; behavior set below. - new_color_icon = $("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(container_div) - .attr("title", "Set new random color").tooltip(), - // Color picker in tool tip style. - tip = $( "<div class='tooltip right' style='position: absolute;' />" ).appendTo(container_div).hide(), - // Inner div for padding purposes - 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.get_random_color()); - }); - })(farb_obj); - - } - else { - row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) ); - } - // Help text - if ( param.help ) { - row.append( $("<div class='help'/>").text( param.help ) ); - } - } - } - // Handle top level parameters in order - handle_params( track_config.get('params'), container ); - - // - // Use Galaxy modal to display config. - // - - var self = this, - cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - self.update_from_form( $(Galaxy.modal.el) ); - Galaxy.modal.hide(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - Galaxy.modal.show({title: "Configure", body: container, buttons : {'Cancel' : cancel_fn, 'Ok' : ok_fn } }); - }, - - /** - * Update configuration from form. - */ - update_from_form: function( container ) { - var model = this.model; - var changed = false; - _.each(model.get('params'), function(param, index) { - if ( !param.hidden ) { - // Get value from form element. - var id = 'param_' + index; - var value = container.find( '#' + id ).val(); - if ( param.type === 'bool' ) { - value = container.find( '#' + id ).is( ':checked' ); - } - changed = model.set_param_value(param.key, value) || changed; - } - }); - } -}); - -/** * Tiles drawn by tracks. */ var Tile = function(track, region, w_scale, canvas, data) { @@ -2376,8 +2134,8 @@ this.data_url_extra_params = {}; this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); // A little ugly creating data manager right now due to transition to Backbone-based objects. - this.data_manager = ('data_manager' in obj_dict ? - obj_dict.data_manager : + this.data_manager = ('data_manager' in obj_dict ? + obj_dict.data_manager : new visualization.GenomeDataManager({ dataset: this.dataset, // HACK: simulate 'genome' attributes from view for now. @@ -2395,13 +2153,13 @@ // Height attributes: min height, max height, and visible height. this.min_height_px = 16; this.max_height_px = 800; - this.visible_height_px = this.prefs.height; + this.visible_height_px = this.config.get_value('height');

// // Create content div, which is where track is displayed, and add to container if available. // this.content_div = $("<div class='track-content'>").appendTo(this.container_div); - if (this.container) { + if (this.container) { this.container.content_div.append(this.container_div); if ( !("resize" in obj_dict) || obj_dict.resize ) { this.add_resize_handle(); @@ -2459,7 +2217,7 @@

// Update track name. if (track.tool.is_visible()) { - track.set_name(track.prefs.name + track.tool_region_and_parameters_str()); + track.set_name(track.config.get_value('name') + track.tool_region_and_parameters_str()); } else { track.revert_name(); @@ -2475,8 +2233,8 @@ css_class: "arrow-split", on_click_fn: function(track) { var template = - '<strong>Tool</strong>: <%= track.tool.get("name") %><br/>' + - '<strong>Dataset</strong>: <%= track.prefs.name %><br/>' + + '<strong>Tool</strong>: <%= track.tool.get("name") %><br/>' + + '<strong>Dataset</strong>: <%= track.config.get("name") %><br/>' + '<strong>Region(s)</strong>: <select name="regions">' + '<option value="cur">current viewing area</option>' + '<option value="bookmarks">bookmarks</option>' + @@ -2492,7 +2250,7 @@ start: view.low, end: view.high }), - bookmarked_regions = _.map($(".bookmark"), function(elt) { + bookmarked_regions = _.map($(".bookmark"), function(elt) { return new visualization.GenomeRegion({from_str: $(elt).children(".position").text()}); });

@@ -2548,8 +2306,8 @@ build_header_div: function() { var header_div = $("<div class='track-header'/>"); if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(header_div); } - this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.prefs.name) - .attr( "id", this.prefs.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9-]/g,'').toLowerCase() ); + this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.config.get_value('name')) + .attr( "id", this.config.get_value('name').replace(/\s+/g,'-').replace(/[^a-zA-Z0-9-]/g,'').toLowerCase() ); return header_div; },

@@ -2578,7 +2336,7 @@ var drag_control = $( "<div class='track-resize'>" ); // Control shows on hover over track, stays while dragging $(track.container_div).hover( function() { - if ( track.prefs.content_visible ) { + if ( track.config.get_value('content_visible') ) { in_handle = true; drag_control.show(); } @@ -2597,10 +2355,10 @@ track.visible_height_px = (track.max_height_px === new_height ? 0 : new_height); track.on_resize(); }).bind( "dragend", function( e, d ) { - track.tile_cache.clear(); + track.tile_cache.clear(); in_drag = false; if (!in_handle) { drag_control.hide(); } - track.config.get('values').height = track.visible_height_px; + track.config.set('height', track.visible_height_px); track.changed(); }).appendTo(track.container_div); }, @@ -2611,16 +2369,15 @@ set_display_modes: function(new_modes, init_mode) { // Set modes, init mode. this.display_modes = new_modes; - this.mode = (init_mode ? init_mode : - (this.config && this.config.get('values').mode ? - this.config.get('values').mode : this.display_modes[0]) + this.mode = (init_mode ? init_mode : + (this.config && this.config.get_value('mode') ? + this.config.get_value('mode') : this.display_modes[0]) );

this.action_icons.mode_icon.attr("title", "Set display mode (now: " + this.mode + ")");

// Setup popup menu for changing modes. - var - track = this, + var track = this, mode_mapping = {}; for (var i = 0, len = track.display_modes.length; i < len; i++) { var mode = track.display_modes[i]; @@ -2822,10 +2579,10 @@ min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) ); max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) ); // Update config, prefs - track.config.set_param_default_value('min_value', min_value); - track.config.set_param_default_value('max_value', max_value); - track.prefs.min_value = min_value; - track.prefs.max_value = max_value; + track.config.set_default_value('min_value', min_value); + track.config.set_default_value('max_value', max_value); + track.config.set_value('min_value', min_value); + track.config.set_value('max_value', max_value); } }); }, @@ -2879,7 +2636,7 @@

// Add tiles_div, overlay_div to content_div. this.tiles_div = $("<div/>").addClass("tiles").appendTo(this.content_div); - if (!this.prefs.content_visible) { + if (!this.config.get_value('content_visible')) { this.tiles_div.hide(); } this.overlay_div = $("<div/>").addClass("overlay").appendTo(this.content_div); @@ -2934,13 +2691,14 @@ * Use from_dict to recreate object. */ to_dict: function() { + console.log(this.config.to_key_value_dict()); return { track_type: this.get_type(), dataset: { id: this.dataset.id, hda_ldda: this.dataset.get('hda_ldda') }, - prefs: this.prefs, + prefs: this.config.to_key_value_dict(), mode: this.mode, filters: this.filters_manager.to_dict(), tool_state: (this.tool ? this.tool.state_dict() : {}) @@ -2958,7 +2716,8 @@ high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) { var data = result.data; - if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { + if ( isNaN(parseFloat(track.config.get_value('min_value'))) || + isNaN(parseFloat(track.config.get_value('max_value'))) ) { // Compute default minimum and maximum values var min_value = data.min, max_value = data.max; @@ -2967,8 +2726,8 @@ min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) ); max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) ); // Update the prefs - track.prefs.min_value = min_value; - track.prefs.max_value = max_value; + track.config.set_value('min_value', min_value); + track.config.set_value('max_value', max_value); } }); }, @@ -2980,7 +2739,7 @@ var track = this; // TODO: is it necessary to store the mode in two places (.mode and track_config)? track.mode = new_mode; - track.config.get('values').mode = new_mode; + track.config.set_value('mode', new_mode); // FIXME: find a better way to get Auto data w/o clearing cache; using mode in the // data manager would work if Auto data were checked for compatibility when a specific // mode is chosen. @@ -3151,11 +2910,11 @@

if (label.length !== 0) { // Label already exists, so update value. - label.text(track.prefs[pref_name]); + label.text(track.config.get_value(pref_name)); } else { // Add label. - label = $("<div/>").text(track.prefs[pref_name]).make_text_editable({ + label = $("<div/>").text(track.config.get_value(pref_name)).make_text_editable({ num_cols: 12, on_finish: function(new_val) { $(".tooltip").remove(); @@ -3163,7 +2922,7 @@ on_change(); }, help_text: "Set " + text + " value" - }).addClass('yaxislabel ' + css_class).css("color", this.prefs.label_color); + }).addClass('yaxislabel ' + css_class).css("color", this.config.get_value('label_color')); this.container_div.prepend(label); } }, @@ -3376,7 +3135,7 @@ */ _draw_line_track_tile: function(result, ctx, mode, region, w_scale) { var canvas = ctx.canvas, - painter = new painters.LinePainter(result.data, region.get('start'), region.get('end'), this.prefs, mode); + painter = new painters.LinePainter(result.data, region.get('start'), region.get('end'), this.config.to_key_value_dict(), mode); painter.draw(ctx, canvas.width, canvas.height, w_scale);

return new LineTrackTile(this, region, w_scale, canvas, result.data); @@ -3691,7 +3450,7 @@ show_group: function() { // Create group with individual tracks. var group = new DrawableGroup(this.view, this.container, { - name: this.prefs.name + name: this.config.get_value('name') }), track; for (var i = 0; i < this.drawables.length; i++) { @@ -3718,16 +3477,16 @@ //

// Get smallest min, biggest max. - var min = _.min(_.map(this.drawables, function(d) { return d.prefs.min_value; })), - max = _.max(_.map(this.drawables, function(d) { return d.prefs.max_value; })); + var min = _.min(_.map(this.drawables, function(d) { return d.config.get_value('min_value'); })), + max = _.max(_.map(this.drawables, function(d) { return d.config.get_value('max_value') }));

- this.prefs.min_value = min; - this.prefs.max_value = max; + this.config.set_value('min_value', min); + this.config.set_value('max_value', max);

// Set all tracks to smallest min, biggest max. _.each(this.drawables, function(d) { - d.prefs.min_value = min; - d.prefs.max_value = max; + d.config.set_value('min_value', min); + d.config.set_value('max_value', max); }); },

@@ -3735,10 +3494,12 @@ * Update minimum, maximum for component tracks. */ update_all_min_max: function() { - var track = this; + var track = this, + min_value = this.config.get_value('min_value'), + max_value = this.config.get_value('max_value'); _.each(this.drawables, function(d) { - d.prefs.min_value = track.prefs.min_value; - d.prefs.max_value = track.prefs.max_value; + d.config.set_value('min_value', min_value); + d.config.set_value('max_value', max_value); }); this.request_draw({ clear_tile_cache: true }); }, @@ -3861,16 +3622,16 @@ display_modes: CONTINUOUS_DATA_MODES,

config_params: _.union( Drawable.prototype.config_params, [ - { key: 'color', label: 'Color', type: '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 } + { key: 'color', label: 'Color', type: '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 } ] ),

config_onchange: function() { - this.set_name(this.prefs.name); - this.request_draw({ clear_tile_cache: true }); + this.set_name(this.config.get_value('name')); + this.request_draw({ clear_tile_cache: true }); },

/** @@ -3924,7 +3685,7 @@ ] ),

config_onchange: function() { - this.set_name(this.prefs.name); + this.set_name(this.config.get_value('name')); this.request_draw({ clear_tile_cache: true }); },

@@ -3934,7 +3695,7 @@ draw_tile: function(result, ctx, mode, region, w_scale) { // Paint onto canvas. var canvas = ctx.canvas, - painter = new painters.DiagonalHeatmapPainter(result.data, region.get('start'), region.get('end'), this.prefs, mode); + painter = new painters.DiagonalHeatmapPainter(result.data, region.get('start'), region.get('end'), this.config.to_key_value_dict(), mode); painter.draw(ctx, canvas.width, canvas.height, w_scale);

return new Tile(this, region, w_scale, canvas, result.data); @@ -3973,7 +3734,7 @@ ] ),

config_onchange: function() { - this.set_name(this.prefs.name); + this.set_name(this.config.get_value('name')); this.set_painter_from_config(); this.request_draw({ clear_tile_cache: true }); }, @@ -4158,7 +3919,7 @@ var rows_required = this.incremental_slots(w_scale, result.data, mode); // HACK: use dummy painter to get required height. Painter should be extended so that get_required_height // works as a static function. - var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode); + var dummy_painter = new (this.painter)(null, null, null, this.config.to_key_value_dict(), mode); return Math.max(this.min_height_px, dummy_painter.get_required_height(rows_required, canvas_width) ); } }, @@ -4219,14 +3980,14 @@ // Create painter. var filter_alpha_scaler = (this.filters_manager.alpha_filter ? new FilterScaler(this.filters_manager.alpha_filter) : null), filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null), - painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, + painter = new (this.painter)(filtered, tile_low, tile_high, this.config.to_key_value_dict(), mode, filter_alpha_scaler, filter_height_scaler, // HACK: ref_seq only be defined for ReadTracks, and only the ReadPainter accepts that argument ref_seq, // Only the ReadPainer will use this function function(b) { return track.view.get_base_color(b); }); var feature_mapper = null;

- ctx.fillStyle = this.prefs.block_color; + ctx.fillStyle = this.config.get_value('block_color'); ctx.font = ctx.canvas.manager.default_font; ctx.textAlign = "right";

@@ -4262,11 +4023,11 @@ { 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 }, - { key: 'height', type: 'int', default_value: 0, hidden: true } + { key: 'height', type: 'int', default_value: 32, hidden: true } ] ),

config_onchange: function() { - this.set_name(this.prefs.name); + this.set_name(this.config.get_value('name')); this.request_draw({ clear_tile_cache: true }); },

@@ -4280,7 +4041,7 @@ } else { // result.dataset_type === 'variant' var view = this.view, - painter = new (this.painter)(result.data, region.get('start'), region.get('end'), this.prefs, mode, + painter = new (this.painter)(result.data, region.get('start'), region.get('end'), this.config.to_key_value_dict(), mode, function(b) { return view.get_base_color(b); }); painter.draw(ctx, ctx.canvas.width, ctx.canvas.height, w_scale); return new Tile(this, region, w_scale, ctx.canvas, result.data); @@ -4312,7 +4073,7 @@ } }

- var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode); + var dummy_painter = new (this.painter)(null, null, null, this.config.to_key_value_dict(), mode); return dummy_painter.get_required_height(num_samples); } }, @@ -4343,7 +4104,7 @@

// Add summary/sample labels if needed and not already included. var sample_names = this.dataset.get_metadata('sample_names'); - if (line_track_tiles.length === 0 && this.prefs.show_labels && sample_names && sample_names.length > 1) { + if (line_track_tiles.length === 0 && this.config.get_value('show_labels') && sample_names && sample_names.length > 1) { var font_size;

// Add and/or style labels. @@ -4351,21 +4112,21 @@ // Add summary and sample labels.

// Add summary label to middle of summary area. - font_size = this.prefs.summary_height / 2; + font_size = this.config.get_value('summary_height') / 2; this.tiles_div.prepend( $("<div/>").text('Summary').addClass('yaxislabel variant top').css({ 'font-size': font_size + 'px', - 'top': (this.prefs.summary_height - font_size) / 2 + 'px' + 'top': (this.config.get_value('summary_height') - font_size) / 2 + 'px' }) );

// Show sample labels. - if (this.prefs.show_sample_data) { + if (this.config.get_value('show_sample_data')) { var samples_div_html = sample_names.join('<br/>');

this.tiles_div.prepend( $("<div/>").html(samples_div_html).addClass('yaxislabel variant top sample').css({ - 'top': this.prefs.summary_height, + 'top': this.config.get_value('summary_height') }) ); } @@ -4380,7 +4141,7 @@ 'line-height': font_size }); // Color labels to preference color. - $(this.tiles_div).find('.yaxislabel').css('color', this.prefs.label_color); + $(this.tiles_div).find('.yaxislabel').css('color', this.config.get_value('label_color')); } else { // Remove all labels. @@ -4414,7 +4175,7 @@ ] ),

config_onchange: function() { - this.set_name(this.prefs.name); + this.set_name(this.config.get_value('name')); this.request_draw({ clear_tile_cache: true }); } });

diff -r e059dbc01b575b856509c2e2baccac3750b6eeb5 -r edff37d76463a468753477080f65886d4a53619e static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -75,7 +75,7 @@ });

// FIXME: give unique IDs to Drawables and save overview as ID. - var overview_track_name = (view.overview_drawable ? view.overview_drawable.prefs.name : null), + var overview_track_name = (view.overview_drawable ? view.overview_drawable.config.get_value('name') : null), viz_config = { 'view': view.to_dict(), 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, @@ -86,9 +86,9 @@ url: galaxy_config.root + "visualization/save", type: "POST", dataType: "json", - data: { + data: { 'id' : view.vis_id, - 'title' : view.prefs.name, + 'title' : view.config.get_value('name'), 'dbkey' : view.dbkey, 'type' : 'trackster', 'vis_json' : JSON.stringify(viz_config) @@ -265,7 +265,7 @@ // Set overview. var overview_drawable; for (var i = 0; i < view.drawables.length; i++) { - if (view.drawables[i].prefs.name === overview_drawable_name) { + if (view.drawables[i].config.get_value('name') === overview_drawable_name) { view.set_overview(view.drawables[i]); break; }

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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