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Alexandre Masselot
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Aug 1, 2014
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,23 @@ | ||
| /* | ||
| * Copyright (c) 2013, Genentech Inc. | ||
| * Authors: Alexandre Masselot, Kiran Mukhyala, Bioinformatics & Computational Biology | ||
| */ | ||
| define(['backbone', '../models/PositionedFeature'], function(bb, PositionedFeature) { | ||
| return bb.Collection.extend({ | ||
| model : PositionedFeature, | ||
| group : function() { | ||
| var self = this; | ||
| return _.groupBy(self.models, function(ft) { | ||
| return (ft.groupSet ? (ft.groupSet + '/:') : '') + ft.category; | ||
| define( | ||
| /** | ||
| @exports FeatureLayerCollection | ||
| @author Alexandre Masselot | ||
| @author Kiran Mukhyala | ||
| @copyright 2013, Bioinformatics & Computational Biology Department, Genentech Inc. | ||
| */ | ||
| ['backbone', '../models/FeatureLayer'], function (bb, FeatureLayer) { | ||
| /** | ||
| * a collection of FeatureLayer, follows backbone collection mechanisms | ||
| * @constructor | ||
| * @augments Backbone.Collection | ||
| */ | ||
| var FeatureLayerCollection = bb.Collection.extend( | ||
| /** | ||
| * @lends module:FeatureLayerCollection~FeatureLayerCollection.prototype | ||
| */ | ||
| { | ||
| model: FeatureLayer | ||
|
|
||
| }) | ||
| } | ||
| }) | ||
|
|
||
| }) | ||
| }); | ||
| return FeatureLayerCollection; | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,40 @@ | ||
| /* | ||
| * Copyright (c) 2013, Genentech Inc. | ||
| * Authors: Alexandre Masselot, Kiran Mukhyala, Bioinformatics & Computational Biology | ||
| */ | ||
| define(['underscore', 'backbone'], function(_, bb) { | ||
| var FeatureLayer = bb.Model.extend({ | ||
| defaults : { | ||
| visible : true | ||
| }, | ||
| initialize : function(options) { | ||
| }, | ||
| type : function() { | ||
| return this.get('type') || this.get('name'); | ||
| } | ||
| }); | ||
|
|
||
| return FeatureLayer; | ||
| }); | ||
| define( | ||
| /** | ||
| @exports FeatureLayer | ||
| @author Alexandre Masselot | ||
| @author Kiran Mukhyala | ||
| @copyright 2013, Bioinformatics & Computational Biology Department, Genentech Inc. | ||
| */ | ||
| ['underscore', 'backbone'], function (_, bb) { | ||
|
|
||
| /** | ||
| * FeatureLayer regroups all the PositionedFeature of a same type | ||
| * @constructor | ||
| * @augments Backbone.Model | ||
| * | ||
| * @param {Map} options | ||
| * @param {String} options.type is only compulsory member | ||
| * @param {boolean} options.visible is the layer to be shown. Default is true | ||
| */ | ||
| var FeatureLayer = bb.Model.extend( | ||
| /** | ||
| * @lends module:FeatureLayer~FeatureLayer.prototype | ||
| */ | ||
| { | ||
| defaults: { | ||
| visible: true | ||
| }, | ||
| initialize: function (options) { | ||
| }, | ||
| /** | ||
| * The object type, based on the type or name attribute | ||
| * | ||
| * @return {String} the type key | ||
| */ | ||
| type: function () { | ||
| return this.get('type') || this.get('name'); | ||
| } | ||
| }); | ||
| return FeatureLayer; | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,30 @@ | ||
| /* | ||
| * Copyright (c) 2013, Genentech Inc. | ||
| * Authors: Alexandre Masselot, Kiran Mukhyala, Bioinformatics & Computational Biology | ||
| */ | ||
| define(['underscore'], function(_) { | ||
| var PositionedFeature = function(options) { | ||
| var self = this; | ||
| _.each(['start', 'end', 'type', 'category', 'description', 'displayTrack', 'text', 'groupSet'], function(name) { | ||
| self[name] = options[name] | ||
| }) | ||
| } | ||
|
|
||
| return PositionedFeature; | ||
| }); | ||
| define( | ||
| /** | ||
| @exports PositionedFeature | ||
| @author Alexandre Masselot | ||
| @author Kiran Mukhyala | ||
| @copyright 2013, Bioinformatics & Computational Biology Department, Genentech Inc. | ||
| */ | ||
| ['underscore'], function (_) { | ||
| /** | ||
| * @class PositionedFeature, corresponding to the basic component to be displayed. There is no limit among the feature member. However, a few a given by default | ||
| * @constructor | ||
| * @param {Map} options | ||
| * @param {int} options.start [compulsory] the starting position, (first one is 0) | ||
| * @param {int} options.end [compulsory] the ending position | ||
| * @param {String} options.type [compulsory] will be used to define how to draw the feature | ||
| * @param {String} options.category [compulsory] all the feature below the same category are regrouped together | ||
| * @param {String} options.groupSet a super category | ||
| * @param {String} options.text a description to be displayed by default | ||
| * | ||
| */ | ||
| var PositionedFeature = function (options) { | ||
| var self = this; | ||
| _.each(['start', 'end', 'type', 'category', 'description', 'displayTrack', 'text', 'groupSet'], function (name) { | ||
| self[name] = options[name] | ||
| }) | ||
| } | ||
|
|
||
| return PositionedFeature; | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,47 +1,77 @@ | ||
| /* | ||
| * Copyright (c) 2013, Genentech Inc. | ||
| * Authors: Alexandre Masselot, Kiran Mukhyala, Bioinformatics & Computational Biology | ||
| */ | ||
| define(['underscore', 'backbone'], function(_, Backbone) { | ||
| var SeqEntry = Backbone.Model.extend({ | ||
| defaults : { | ||
| define( | ||
| /** | ||
| @exports SeqEntry | ||
| @author Alexandre Masselot | ||
| @author Kiran Mukhyala | ||
| @copyright 2013, Bioinformatics & Computational Biology Department, Genentech Inc. | ||
| */ | ||
| ['underscore', 'backbone'], function (_, Backbone) { | ||
| /** | ||
| * A SeqEntry object holds the sequence and the list of PositionedFeature | ||
| * @constructor | ||
| * @augments Backbone.Model | ||
| * | ||
| * @param {Map} options | ||
| * @param {String} options.sequence is the layer to be shown. Default is true | ||
| * @param {Array} options.features an array of object (will be mapped into PositionedFeature) | ||
| */ | ||
| var SeqEntry = Backbone.Model.extend( | ||
| /** | ||
| * @lends module:SeqEntry~SeqEntry.prototype | ||
| */ | ||
| { | ||
| defaults: { | ||
|
|
||
| }, | ||
| initialize : function() { | ||
| this.set('features', []); | ||
| }, | ||
| length : function() { | ||
| var seq = this.get('sequence'); | ||
| return (seq === undefined) ? 0 : seq.length | ||
| }, | ||
| addFeatures : function(feats, options) { | ||
| var self = this; | ||
| options = options || {}; | ||
| }, | ||
| initialize: function () { | ||
| this.set('features', []); | ||
| }, | ||
| /** | ||
| * | ||
| * @return {integer} sequence length | ||
| */ | ||
| length: function () { | ||
| var seq = this.get('sequence'); | ||
| return (seq === undefined) ? 0 : seq.length | ||
| }, | ||
| /** | ||
| * Add san array or a single feature to the seq entry. A 'change' event will be triggered by default. The Backbone view will be binded to such changes | ||
| * @param {Array|Object} feats | ||
| * @param {Map} options | ||
| * @param {boolean} options.triggerChange defines is a 'change' event is to be fired (default is true) | ||
| * @return {SeqEntry} | ||
| */ | ||
| addFeatures: function (feats, options) { | ||
| var self = this; | ||
| options = options || {}; | ||
|
|
||
| var triggerChange = options.triggerChange || (options.triggerChange === undefined); | ||
| var triggerChange = options.triggerChange || (options.triggerChange === undefined); | ||
|
|
||
| if (_.isArray(feats)) { | ||
| _.each(feats, function(ft) { | ||
| ft.start = parseInt(ft.start); | ||
| ft.end = parseInt(ft.end); | ||
| self.get('features').push(ft); | ||
| }) | ||
| if (triggerChange) | ||
| self.trigger('change'); | ||
| return self; | ||
| } | ||
| self.get('features').push(feats); | ||
| if (triggerChange) | ||
| self.trigger('change'); | ||
| return self; | ||
| }, | ||
| clear : function() { | ||
| this.get('features').length = 0 | ||
| this.trigger('change'); | ||
| return this; | ||
| if (_.isArray(feats)) { | ||
| _.each(feats, function (ft) { | ||
| ft.start = parseInt(ft.start); | ||
| ft.end = parseInt(ft.end); | ||
| self.get('features').push(ft); | ||
| }) | ||
| if (triggerChange) | ||
| self.trigger('change'); | ||
| return self; | ||
| } | ||
| self.get('features').push(feats); | ||
| if (triggerChange) | ||
| self.trigger('change'); | ||
| return self; | ||
| }, | ||
| /** | ||
| * Removes all the features (and fire a 'change' event | ||
| * @return {SeqEntry} | ||
| */ | ||
| clear: function () { | ||
| this.get('features').length = 0 | ||
| this.trigger('change'); | ||
| return this; | ||
|
|
||
| } | ||
| //urlRoot:'das/json' | ||
| }) | ||
| return SeqEntry; | ||
| }) | ||
| } | ||
| }); | ||
| return SeqEntry; | ||
| }); |
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