[galaxy-commits] commit/galaxy-central: carlfeberhard: History panel: refactoring for dataset collections

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/50a273de6cd7/ Changeset: 50a273de6cd7 User: carlfeberhard Date: 2014-07-09 19:40:43 Summary: History panel: refactoring for dataset collections Affected #: 17 files diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/collection/hdca-model.js --- /dev/null +++ b/static/scripts/mvc/collection/hdca-model.js @@ -0,0 +1,69 @@ +define([ + "mvc/history/history-content-base", + "utils/localization" +], function( historyContent, _l ){ +//============================================================================== +var HistoryDatasetCollectionAssociation = historyContent.HistoryContent.extend( +/** @lends HistoryDatasetCollectionAssociation.prototype */{ + /** default attributes for a model */ + defaults : { + // parent (containing) history + history_id : null, + // often used with tagging + model_class : 'HistoryDatasetCollectionAssociation', + history_content_type : 'dataset_collection', + hid : 0, + + id : null, + name : '(unnamed dataset collection)', + // one of HistoryDatasetAssociation.STATES, calling them all 'ok' for now. + state : 'ok', + + accessible : true, + deleted : false, + visible : true, + + purged : false, // Purged doesn't make sense for collections - at least right now. + + tags : [], + annotation : '' + }, + urls : function(){ + }, + + inReadyState : function(){ + return true; // TODO + }, + + // ........................................................................ search + /** what attributes of an collection will be used in a text search */ + searchAttributes : [ + 'name' + ], + + /** our attr keys don't often match the labels we display to the user - so, when using + * attribute specifiers ('name="bler"') in a term, allow passing in aliases for the + * following attr keys. + */ + searchAliases : { + title : 'name' + // TODO: Add tag... + }, + + // ........................................................................ misc + /** String representation */ + toString : function(){ + var nameAndId = this.get( 'id' ) || ''; + if( this.get( 'name' ) ){ + nameAndId = this.get( 'hid' ) + ' :"' + this.get( 'name' ) + '",' + nameAndId; + } + return 'HDCA-' + this.get( 'collection_type' ) + '(' + nameAndId + ')'; + } +}); + + +//============================================================================== + return { + HistoryDatasetCollectionAssociation : HistoryDatasetCollectionAssociation + }; +}); diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -1,169 +1,7 @@ define([ - "mvc/base-mvc", + "mvc/history/history-content-base", "utils/localization" -], function( baseMVC, _l ){ -//============================================================================== -/** @class model for contents related to a history. - * @name HistoryContent - * - * @augments Backbone.Model - * @borrows LoggableMixin#logger as #logger - * @borrows LoggableMixin#log as #log - * @constructs - */ -var HistoryContent = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( { - idAttribute : 'type_id', - - /** fetch location of this HDA's history in the api */ - urlRoot: galaxy_config.root + 'api/histories/', - - constructor : function( attrs, options ){ - attrs.type_id = HistoryContent.typeIdStr( attrs.history_content_type, attrs.id ); - Backbone.Model.apply( this, arguments ); - }, - - initialize : function( attrs, options ){ - // assumes type won't change - this.on( 'change:id', this._createTypeId ); - //TODO: not sure this covers all the bases... - }, - - /** full url spec. for this HDA */ - url : function(){ - return this.urlRoot + this.get( 'history_id' ) + '/contents/' + this.get('history_content_type') + 's/' + this.get( 'id' ); - }, - - /** the more common alias of visible */ - hidden : function(){ - return !this.get( 'visible' ); - }, - - // ........................................................................ ajax - - /** save this HDA, _Mark_ing it as deleted (just a flag) */ - 'delete' : function _delete( options ){ - if( this.get( 'deleted' ) ){ return jQuery.when(); } - return this.save( { deleted: true }, options ); - }, - /** save this HDA, _Mark_ing it as undeleted */ - undelete : function _undelete( options ){ - if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); } - return this.save( { deleted: false }, options ); - }, - - /** save this HDA as not visible */ - hide : function _hide( options ){ - if( !this.get( 'visible' ) ){ return jQuery.when(); } - return this.save( { visible: false }, options ); - }, - /** save this HDA as visible */ - unhide : function _uhide( options ){ - if( this.get( 'visible' ) ){ return jQuery.when(); } - return this.save( { visible: true }, options ); - }, - - /** based on show_deleted, show_hidden (gen. from the container control), - * would this ds show in the list of ds's? - * @param {Boolean} show_deleted are we showing deleted hdas? - * @param {Boolean} show_hidden are we showing hidden hdas? - */ - isVisible : function( show_deleted, show_hidden ){ - var isVisible = true; - if( ( !show_deleted ) - && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){ - isVisible = false; - } - if( ( !show_hidden ) - && ( !this.get( 'visible' ) ) ){ - isVisible = false; - } - return isVisible; - }, - - /** search the attribute with key attrKey for the string searchFor; T/F if found */ - searchAttribute : function( attrKey, searchFor ){ - var attrVal = this.get( attrKey ); - //console.debug( 'searchAttribute', attrKey, attrVal, searchFor ); - // bail if empty searchFor or unsearchable values - if( !searchFor - || ( attrVal === undefined || attrVal === null ) ){ - return false; - } - // pass to sep. fn for deep search of array attributes - if( _.isArray( attrVal ) ){ return this._searchArrayAttribute( attrVal, searchFor ); } - return ( attrVal.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 ); - }, - - /** deep(er) search for array attributes; T/F if found */ - _searchArrayAttribute : function( array, searchFor ){ - //console.debug( '_searchArrayAttribute', array, searchFor ); - searchFor = searchFor.toLowerCase(); - //precondition: searchFor has already been validated as non-empty string - //precondition: assumes only 1 level array - //TODO: could possibly break up searchFor more (CSV...) - return _.any( array, function( elem ){ - return ( elem.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 ); - }); - }, - - /** search all searchAttributes for the string searchFor, - * returning a list of keys of attributes that contain searchFor - */ - search : function( searchFor ){ - var model = this; - return _.filter( this.searchAttributes, function( key ){ - return model.searchAttribute( key, searchFor ); - }); - }, - - /** alias of search, but returns a boolean; accepts attribute specifiers where - * the attributes searched can be narrowed to a single attribute using - * the form: matches( 'genome_build=hg19' ) - * (the attribute keys allowed can also be aliases to the true attribute key; - * see searchAliases above) - * @param {String} term plain text or ATTR_SPECIFIER sep. key=val pair - * @returns {Boolean} was term found in (any) attribute(s) - */ - matches : function( term ){ - var ATTR_SPECIFIER = '=', - split = term.split( ATTR_SPECIFIER ); - // attribute is specified - search only that - if( split.length >= 2 ){ - var attrKey = split[0]; - attrKey = this.searchAliases[ attrKey ] || attrKey; - return this.searchAttribute( attrKey, split[1] ); - } - // no attribute is specified - search all attributes in searchAttributes - return !!this.search( term ).length; - }, - - /** an implicit AND search for all terms; IOW, an hda must match all terms given - * where terms is a whitespace separated value string. - * e.g. given terms of: 'blah bler database=hg19' - * an HDA would have to have attributes containing blah AND bler AND a genome_build == hg19 - * To include whitespace in terms: wrap the term in double quotations. - */ - matchesAll : function( terms ){ - var model = this; - // break the terms up by whitespace and filter out the empty strings - terms = terms.match( /(".*"|\w*=".*"|\S*)/g ).filter( function( s ){ return !!s; }); - return _.all( terms, function( term ){ - term = term.replace( /"/g, '' ); - return model.matches( term ); - }); - }, - - _createTypeId : function(){ - this.set( 'type_id', TypeIdModel.typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) ) ); - }, - -} ); - -/** create a type + id string for use in mixed collections */ -HistoryContent.typeIdStr = function _typeId( type, id ){ - return [ type, id ].join( '-' ); -}; - +], function( historyContent, _l ){ //============================================================================== /** @class (HDA) model for a Galaxy dataset * related to a history. @@ -174,7 +12,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HistoryDatasetAssociation = HistoryContent.extend( +var HistoryDatasetAssociation = historyContent.HistoryContent.extend( /** @lends HistoryDatasetAssociation.prototype */{ ///** logger used to record this.log messages, commonly set to console */ @@ -456,326 +294,9 @@ HistoryDatasetAssociation.STATES.NEW ]; -//============================================================================== -/** @class Backbone collection of (HDA) models - * TODO: Rename HistoryContentCollection - * - * @borrows LoggableMixin#logger as #logger - * @borrows LoggableMixin#log as #log - * @constructs - */ -var HDACollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend( -/** @lends HDACollection.prototype */{ - model : function( attrs, options ) { - if( attrs.history_content_type == "dataset" ) { - return new HistoryDatasetAssociation( attrs, options ); - } else if( attrs.history_content_type == "dataset_collection" ) { - return new HistoryDatasetCollectionAssociation( attrs, options ); - } else { - // TODO: Handle unknown history_content_type... - } - }, - - ///** logger used to record this.log messages, commonly set to console */ - //// comment this out to suppress log output - //logger : console, - - /** root api url */ - urlRoot : galaxy_config.root + 'api/histories', - /** complete api url */ - url : function(){ - return this.urlRoot + '/' + this.historyId + '/contents'; - }, - - /** Set up. - * @see Backbone.Collection#initialize - */ - initialize : function( models, options ){ - options = options || {}; - this.historyId = options.historyId; - //this._setUpListeners(); - }, - - //_setUpListeners : function(){ - //}, - - // ........................................................................ common queries - /** Get the ids of every hda in this collection - * @returns array of encoded ids - */ - ids : function(){ - return this.map( function( hda ){ return hda.get('id'); }); - }, - - /** Get hdas that are not ready - * @returns array of HDAs - */ - notReady : function(){ - return this.filter( function( hda ){ - return !hda.inReadyState(); - }); - }, - - /** Get the id of every hda in this collection not in a 'ready' state (running). - * @returns an array of hda ids - * @see HistoryDatasetAssociation#inReadyState - */ - running : function(){ - var idList = []; - this.each( function( item ){ - if( !item.inReadyState() ){ - idList.push( item.get( 'id' ) ); - } - }); - return idList; - }, - - /** Get the hda with the given hid - * @param {Int} hid the hid to search for - * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found - */ - getByHid : function( hid ){ - return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); - }, - - /** Get every 'shown' hda in this collection based on show_deleted/hidden - * @param {Boolean} show_deleted are we showing deleted hdas? - * @param {Boolean} show_hidden are we showing hidden hdas? - * @returns array of hda models - * @see HistoryDatasetAssociation#isVisible - */ - getVisible : function( show_deleted, show_hidden, filters ){ - filters = filters || []; - //console.debug( 'filters:', filters ); - //TODO:?? why doesn't this return a collection? - // always filter by show deleted/hidden first - var filteredHdas = new HDACollection( this.filter( function( item ){ - return item.isVisible( show_deleted, show_hidden ); - })); - - _.each( filters, function( filter_fn ){ - if( !_.isFunction( filter_fn ) ){ return; } - filteredHdas = new HDACollection( filteredHdas.filter( filter_fn ) ); - }); - //if( filteredHdas.length ){ - // console.debug( 'filteredHdas:' ); - // filteredHdas.each( function( hda ){ - // console.debug( '\t', hda ); - // }); - //} else { - // console.warn( 'no visible hdas' ); - //} - return filteredHdas; - }, - - /** return true if any hdas don't have details */ - haveDetails : function(){ - return this.all( function( hda ){ return hda.hasDetails(); }); - }, - - // ........................................................................ ajax - /** fetch detailed model data for all HDAs in this collection */ - fetchAllDetails : function( options ){ - options = options || {}; - var detailsFlag = { details: 'all' }; - options.data = ( options.data )?( _.extend( options.data, detailsFlag ) ):( detailsFlag ); - return this.fetch( options ); - }, - - /** using a queue, perform hdaModelAjaxFn on each of the hdas in this collection */ - ajaxQueue : function( hdaAjaxFn, options ){ - var deferred = jQuery.Deferred(), - startingLength = this.length, - responses = []; - - if( !startingLength ){ - deferred.resolve([]); - return deferred; - } - - // use reverse order (stylistic choice) - var ajaxFns = this.chain().reverse().map( function( hda, i ){ - return function(){ - var xhr = hdaAjaxFn.call( hda, options ); - // if successful, notify using the deferred to allow tracking progress - xhr.done( function( response ){ - deferred.notify({ curr: i, total: startingLength, response: response, model: hda }); - }); - // (regardless of previous error or success) if not last ajax call, shift and call the next - // if last fn, resolve deferred - xhr.always( function( response ){ - responses.push( response ); - if( ajaxFns.length ){ - ajaxFns.shift()(); - } else { - deferred.resolve( responses ); - } - }); - }; - }).value(); - // start the queue - ajaxFns.shift()(); - - return deferred; - }, - - // ........................................................................ sorting/filtering - /** return a new collection of HDAs whose attributes contain the substring matchesWhat */ - matches : function( matchesWhat ){ - return this.filter( function( hda ){ - return hda.matches( matchesWhat ); - }); - }, - - // ........................................................................ misc - set : function( models, options ){ - // arrrrrrrrrrrrrrrrrg... - // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone) - // w/o this partial models from the server will fill in missing data with model defaults - // and overwrite existing data on the client - // see Backbone.Collection.set and _prepareModel - var collection = this; - models = _.map( models, function( model ){ - var attrs = model.attributes || model; // Handle raw json or Backbone model. - var typeId = HistoryContent.typeIdStr( attrs.history_content_type, attrs.id ); - var existing = collection.get( typeId ); - if( !existing ){ return model; } - - // merge the models _BEFORE_ calling the superclass version - var merged = existing.toJSON(); - _.extend( merged, model ); - return merged; - }); - // now call superclass when the data is filled - Backbone.Collection.prototype.set.call( this, models, options ); - }, - - /** Convert this ad-hoc collection of HDAs to a formal collection tracked - by the server. - **/ - promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){ - options = options || {}; - options.url = this.url(); - options.type = "POST"; - var full_collection_type = collection_type; - var element_identifiers = [], - name = null; - - // This mechanism is rough - no error handling, allows invalid selections, no way - // for user to pick/override element identifiers. This is only really meant - if( collection_type == "list" ) { - this.chain().each( function( hda ) { - // TODO: Handle duplicate names. - var name = hda.attributes.name; - var id = hda.get('id'); - var content_type = hda.attributes.history_content_type; - if( content_type == "dataset" ) { - if( full_collection_type != "list" ) { - console.log( "Invalid collection type" ); - } - element_identifiers.push( { name: name, src: "hda", id: id } ); - } else { - if( full_collection_type == "list" ) { - full_collection_type = "list:" + hda.attributes.collection_type; - } else { - if( full_collection_type != "list:" + hda.attributes.collection_type ) { - console.log( "Invalid collection type" ); - } - } - element_identifiers.push( { name: name, src: "hdca", id: id } ); - } - }); - name = "New Dataset List"; - } else if( collection_type == "paired" ) { - var ids = this.ids(); - if( ids.length != 2 ){ - // TODO: Do something... - } - element_identifiers.push( { name: "forward", src: "hda", id: ids[ 0 ] } ); - element_identifiers.push( { name: "reverse", src: "hda", id: ids[ 1 ] } ); - name = "New Dataset Pair"; - } - options.data = {type: "dataset_collection", - name: name, - collection_type: full_collection_type, - element_identifiers: JSON.stringify(element_identifiers), - }; - - var xhr = jQuery.ajax( options ); - xhr.done( function( message, status, responseObj ){ - history.refresh( ); - }); - xhr.fail( function( xhr, status, message ){ - if( xhr.responseJSON && xhr.responseJSON.error ){ - error = xhr.responseJSON.error; - } else { - error = xhr.responseJSON; - } - xhr.responseText = error; - // Do something? - }); - return xhr; - }, - - /** String representation. */ - toString : function(){ - return ([ 'HDACollection(', [ this.historyId, this.length ].join(), ')' ].join( '' )); - } -}); - -var HistoryDatasetCollectionAssociation = HistoryContent.extend( -/** @lends HistoryDatasetCollectionAssociation.prototype */{ - /** default attributes for a model */ - defaults : { - // parent (containing) history - history_id : null, - // often used with tagging - model_class : 'HistoryDatasetCollectionAssociation', - history_content_type : 'dataset_collection', - hid : 0, - - id : null, - name : '(unnamed dataset collection)', - // one of HistoryDatasetAssociation.STATES, calling them all 'ok' for now. - state : 'ok', - - accessible : true, - deleted : false, - visible : true, - - purged : false, // Purged doesn't make sense for collections - at least right now. - - tags : [], - annotation : '' - }, - urls : function(){ - }, - - inReadyState : function(){ - return true; // TODO - }, - - // ........................................................................ search - /** what attributes of an collection will be used in a text search */ - searchAttributes : [ - 'name' - ], - - /** our attr keys don't often match the labels we display to the user - so, when using - * attribute specifiers ('name="bler"') in a term, allow passing in aliases for the - * following attr keys. - */ - searchAliases : { - title : 'name' - // TODO: Add tag... - }, - -}); - - //============================================================================== -return { - HistoryDatasetAssociation : HistoryDatasetAssociation, - HDACollection : HDACollection -};}); + return { + HistoryDatasetAssociation : HistoryDatasetAssociation + }; +}); diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/current-history-panel.js --- a/static/scripts/mvc/history/current-history-panel.js +++ b/static/scripts/mvc/history/current-history-panel.js @@ -53,7 +53,7 @@ noneFoundMsg : _l( "No matching datasets found" ), // ......................................................................... SET UP - /** Set up the view, set up storage, bind listeners to HDACollection events + /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes */ initialize : function( attributes ){ diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/history-content-base.js --- /dev/null +++ b/static/scripts/mvc/history/history-content-base.js @@ -0,0 +1,181 @@ +define([ + "mvc/base-mvc", + "utils/localization" +], function( baseMVC, _l ){ +//============================================================================== +/** @class base model for content items contained in a history or hdca. + * @name HistoryContent + * + * @augments Backbone.Model + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var HistoryContent = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( { + idAttribute : 'type_id', + + constructor : function( attrs, options ){ + attrs.type_id = HistoryContent.typeIdStr( attrs.history_content_type, attrs.id ); + Backbone.Model.apply( this, arguments ); + }, + + initialize : function( attrs, options ){ + // assumes type won't change + this.on( 'change:id', this._createTypeId ); + //TODO: not sure this covers all the bases... + }, + _createTypeId : function(){ + this.set( 'type_id', TypeIdModel.typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) ) ); + }, + + // ........................................................................ common queries + /** the more common alias of visible */ + hidden : function(){ + return !this.get( 'visible' ); + }, + + /** based on show_deleted, show_hidden (gen. from the container control), + * would this ds show in the list of ds's? + * @param {Boolean} show_deleted are we showing deleted hdas? + * @param {Boolean} show_hidden are we showing hidden hdas? + */ + isVisible : function( show_deleted, show_hidden ){ + var isVisible = true; + if( ( !show_deleted ) + && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){ + isVisible = false; + } + if( ( !show_hidden ) + && ( !this.get( 'visible' ) ) ){ + isVisible = false; + } + return isVisible; + }, + + // ........................................................................ ajax + /** */ + urlRoot: galaxy_config.root + 'api/histories/', + + /** full url spec. for this HDA */ + url : function(){ + return this.urlRoot + this.get( 'history_id' ) + '/contents/' + + this.get('history_content_type') + 's/' + this.get( 'id' ); + }, + + /** save this HDA, _Mark_ing it as deleted (just a flag) */ + 'delete' : function _delete( options ){ + if( this.get( 'deleted' ) ){ return jQuery.when(); } + return this.save( { deleted: true }, options ); + }, + /** save this HDA, _Mark_ing it as undeleted */ + undelete : function _undelete( options ){ + if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); } + return this.save( { deleted: false }, options ); + }, + + /** save this HDA as not visible */ + hide : function _hide( options ){ + if( !this.get( 'visible' ) ){ return jQuery.when(); } + return this.save( { visible: false }, options ); + }, + /** save this HDA as visible */ + unhide : function _uhide( options ){ + if( this.get( 'visible' ) ){ return jQuery.when(); } + return this.save( { visible: true }, options ); + }, + + // ........................................................................ searching + /** search the attribute with key attrKey for the string searchFor; T/F if found */ + searchAttribute : function( attrKey, searchFor ){ + var attrVal = this.get( attrKey ); + //console.debug( 'searchAttribute', attrKey, attrVal, searchFor ); + // bail if empty searchFor or unsearchable values + if( !searchFor + || ( attrVal === undefined || attrVal === null ) ){ + return false; + } + // pass to sep. fn for deep search of array attributes + if( _.isArray( attrVal ) ){ return this._searchArrayAttribute( attrVal, searchFor ); } + return ( attrVal.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 ); + }, + + /** deep(er) search for array attributes; T/F if found */ + _searchArrayAttribute : function( array, searchFor ){ + //console.debug( '_searchArrayAttribute', array, searchFor ); + searchFor = searchFor.toLowerCase(); + //precondition: searchFor has already been validated as non-empty string + //precondition: assumes only 1 level array + //TODO: could possibly break up searchFor more (CSV...) + return _.any( array, function( elem ){ + return ( elem.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 ); + }); + }, + + /** search all searchAttributes for the string searchFor, + * returning a list of keys of attributes that contain searchFor + */ + search : function( searchFor ){ + var model = this; + return _.filter( this.searchAttributes, function( key ){ + return model.searchAttribute( key, searchFor ); + }); + }, + + /** alias of search, but returns a boolean; accepts attribute specifiers where + * the attributes searched can be narrowed to a single attribute using + * the form: matches( 'genome_build=hg19' ) + * (the attribute keys allowed can also be aliases to the true attribute key; + * see searchAliases above) + * @param {String} term plain text or ATTR_SPECIFIER sep. key=val pair + * @returns {Boolean} was term found in (any) attribute(s) + */ + matches : function( term ){ + var ATTR_SPECIFIER = '=', + split = term.split( ATTR_SPECIFIER ); + // attribute is specified - search only that + if( split.length >= 2 ){ + var attrKey = split[0]; + attrKey = this.searchAliases[ attrKey ] || attrKey; + return this.searchAttribute( attrKey, split[1] ); + } + // no attribute is specified - search all attributes in searchAttributes + return !!this.search( term ).length; + }, + + /** an implicit AND search for all terms; IOW, an hda must match all terms given + * where terms is a whitespace separated value string. + * e.g. given terms of: 'blah bler database=hg19' + * an HDA would have to have attributes containing blah AND bler AND a genome_build == hg19 + * To include whitespace in terms: wrap the term in double quotations. + */ + matchesAll : function( terms ){ + var model = this; + // break the terms up by whitespace and filter out the empty strings + terms = terms.match( /(".*"|\w*=".*"|\S*)/g ).filter( function( s ){ return !!s; }); + return _.all( terms, function( term ){ + term = term.replace( /"/g, '' ); + return model.matches( term ); + }); + }, + + // ........................................................................ misc + /** String representation */ + toString : function(){ + var nameAndId = this.get( 'id' ) || ''; + if( this.get( 'name' ) ){ + nameAndId = this.get( 'hid' ) + ' :"' + this.get( 'name' ) + '",' + nameAndId; + } + return 'HistoryContent(' + nameAndId + ')'; + } +}); + +/** create a type + id string for use in mixed collections */ +HistoryContent.typeIdStr = function _typeId( type, id ){ + return [ type, id ].join( '-' ); +}; + + +//============================================================================== +return { + HistoryContent : HistoryContent +};}); diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/history-contents.js --- /dev/null +++ b/static/scripts/mvc/history/history-contents.js @@ -0,0 +1,277 @@ +define([ + "mvc/history/history-content-base", + "mvc/dataset/hda-model", + "mvc/collection/hdca-model", + "mvc/base-mvc", + "utils/localization" +], function( historyContent, hdaModel, hdcaModel, baseMVC, _l ){ +//============================================================================== +/** @class Backbone collection for history content. + * NOTE: history content seems like a dataset collection, but differs in that it is mixed: + * each element can be either an HDA (dataset) or a DatasetCollection and co-exist on + * the same level. + * Dataset collections on the other hand are not mixed and (so far) can only contain either + * HDAs or child dataset collections on one level. + * This is why this does not inherit from any of the DatasetCollections (currently). + * + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var HistoryContents = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend( +/** @lends HistoryContents.prototype */{ + + ///** logger used to record this.log messages, commonly set to console */ + //// comment this out to suppress log output + //logger : console, + + /** since history content is a mix, override model fn into a factory, creating based on history_content_type */ + model : function( attrs, options ) { + if( attrs.history_content_type === "dataset" ) { + return new hdaModel.HistoryDatasetAssociation( attrs, options ); + } else if( attrs.history_content_type === "dataset_collection" ) { + return new hdcaModel.HistoryDatasetCollectionAssociation( attrs, options ); + } + // TODO: Handle unknown history_content_type... + throw new TypeError( 'Unknown history_content_type:' + attrs.history_content_type ); + }, + + /** Set up. + * @see Backbone.Collection#initialize + */ + initialize : function( models, options ){ + options = options || {}; + this.historyId = options.historyId; + //this._setUpListeners(); + }, + + /** root api url */ + urlRoot : galaxy_config.root + 'api/histories', + /** complete api url */ + url : function(){ + return this.urlRoot + '/' + this.historyId + '/contents'; + }, + + // ........................................................................ common queries + /** Get the ids of every hda in this collection + * @returns array of encoded ids + */ + ids : function(){ + return this.map( function( hda ){ return hda.get('id'); }); + }, + + /** Get hdas that are not ready + * @returns array of HDAs + */ + notReady : function(){ + return this.filter( function( hda ){ + return !hda.inReadyState(); + }); + }, + + /** Get the id of every hda in this collection not in a 'ready' state (running). + * @returns an array of hda ids + * @see HistoryDatasetAssociation#inReadyState + */ + running : function(){ + var idList = []; + this.each( function( item ){ + if( !item.inReadyState() ){ + idList.push( item.get( 'id' ) ); + } + }); + return idList; + }, + + /** Get the hda with the given hid + * @param {Int} hid the hid to search for + * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found + */ + getByHid : function( hid ){ + return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); + }, + + /** Get every 'shown' hda in this collection based on show_deleted/hidden + * @param {Boolean} show_deleted are we showing deleted hdas? + * @param {Boolean} show_hidden are we showing hidden hdas? + * @returns array of hda models + * @see HistoryDatasetAssociation#isVisible + */ + getVisible : function( show_deleted, show_hidden, filters ){ + filters = filters || []; + //console.debug( 'filters:', filters ); + //TODO:?? why doesn't this return a collection? + // always filter by show deleted/hidden first + var filteredHdas = new HistoryContents( this.filter( function( item ){ + return item.isVisible( show_deleted, show_hidden ); + })); + + _.each( filters, function( filter_fn ){ + if( !_.isFunction( filter_fn ) ){ return; } + filteredHdas = new HistoryContents( filteredHdas.filter( filter_fn ) ); + }); + return filteredHdas; + }, + + /** return true if any hdas don't have details */ + haveDetails : function(){ + return this.all( function( hda ){ return hda.hasDetails(); }); + }, + + // ........................................................................ ajax + /** fetch detailed model data for all HDAs in this collection */ + fetchAllDetails : function( options ){ + options = options || {}; + var detailsFlag = { details: 'all' }; + options.data = ( options.data )?( _.extend( options.data, detailsFlag ) ):( detailsFlag ); + return this.fetch( options ); + }, + + /** using a queue, perform hdaModelAjaxFn on each of the hdas in this collection */ + ajaxQueue : function( hdaAjaxFn, options ){ + var deferred = jQuery.Deferred(), + startingLength = this.length, + responses = []; + + if( !startingLength ){ + deferred.resolve([]); + return deferred; + } + + // use reverse order (stylistic choice) + var ajaxFns = this.chain().reverse().map( function( hda, i ){ + return function(){ + var xhr = hdaAjaxFn.call( hda, options ); + // if successful, notify using the deferred to allow tracking progress + xhr.done( function( response ){ + deferred.notify({ curr: i, total: startingLength, response: response, model: hda }); + }); + // (regardless of previous error or success) if not last ajax call, shift and call the next + // if last fn, resolve deferred + xhr.always( function( response ){ + responses.push( response ); + if( ajaxFns.length ){ + ajaxFns.shift()(); + } else { + deferred.resolve( responses ); + } + }); + }; + }).value(); + // start the queue + ajaxFns.shift()(); + + return deferred; + }, + + // ........................................................................ sorting/filtering + /** return a new collection of HDAs whose attributes contain the substring matchesWhat */ + matches : function( matchesWhat ){ + return this.filter( function( hda ){ + return hda.matches( matchesWhat ); + }); + }, + + // ........................................................................ misc + set : function( models, options ){ + // arrrrrrrrrrrrrrrrrg... + // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone) + // w/o this partial models from the server will fill in missing data with model defaults + // and overwrite existing data on the client + // see Backbone.Collection.set and _prepareModel + var collection = this; + models = _.map( models, function( model ){ + var attrs = model.attributes || model; // Handle raw json or Backbone model. + var typeId = historyContent.HistoryContent.typeIdStr( attrs.history_content_type, attrs.id ); + var existing = collection.get( typeId ); + if( !existing ){ return model; } + + // merge the models _BEFORE_ calling the superclass version + var merged = existing.toJSON(); + _.extend( merged, model ); + return merged; + }); + // now call superclass when the data is filled + Backbone.Collection.prototype.set.call( this, models, options ); + }, + + /** Convert this ad-hoc collection of HDAs to a formal collection tracked + by the server. + **/ + promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){ + options = options || {}; + options.url = this.url(); + options.type = "POST"; + var full_collection_type = collection_type; + var element_identifiers = [], + name = null; + + // This mechanism is rough - no error handling, allows invalid selections, no way + // for user to pick/override element identifiers. This is only really meant + if( collection_type === "list" ) { + this.chain().each( function( hda ) { + // TODO: Handle duplicate names. + var name = hda.attributes.name; + var id = hda.get('id'); + var content_type = hda.attributes.history_content_type; + if( content_type === "dataset" ) { + if( full_collection_type !== "list" ) { + console.log( "Invalid collection type" ); + } + element_identifiers.push( { name: name, src: "hda", id: id } ); + } else { + if( full_collection_type === "list" ) { + full_collection_type = "list:" + hda.attributes.collection_type; + } else { + if( full_collection_type !== "list:" + hda.attributes.collection_type ) { + console.log( "Invalid collection type" ); + } + } + element_identifiers.push( { name: name, src: "hdca", id: id } ); + } + }); + name = "New Dataset List"; + } else if( collection_type === "paired" ) { + var ids = this.ids(); + if( ids.length !== 2 ){ + // TODO: Do something... + } + element_identifiers.push( { name: "forward", src: "hda", id: ids[ 0 ] } ); + element_identifiers.push( { name: "reverse", src: "hda", id: ids[ 1 ] } ); + name = "New Dataset Pair"; + } + options.data = { + type: "dataset_collection", + name: name, + collection_type: full_collection_type, + element_identifiers: JSON.stringify( element_identifiers ) + }; + + var xhr = jQuery.ajax( options ); + xhr.done( function( message, status, responseObj ){ + history.refresh( ); + }); + xhr.fail( function( xhr, status, message ){ + if( xhr.responseJSON && xhr.responseJSON.error ){ + error = xhr.responseJSON.error; + } else { + error = xhr.responseJSON; + } + xhr.responseText = error; + // Do something? + }); + return xhr; + }, + + /** String representation. */ + toString : function(){ + return ([ 'HistoryContents(', [ this.parentId, this.length ].join(), ')' ].join( '' )); + } +}); + + +//============================================================================== + return { + HistoryContents : HistoryContents + }; +}); diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -1,8 +1,8 @@ define([ - "mvc/dataset/hda-model", + "mvc/history/history-contents", "mvc/base-mvc", "utils/localization" -], function( hdaModel, baseMVC, _l ){ +], function( historyContents, baseMVC, _l ){ //============================================================================== /** @class Model for a Galaxy history resource - both a record of user * tool use and a collection of the datasets those tools produced. @@ -45,8 +45,8 @@ this.logger = options.logger || null; this.log( this + ".initialize:", historyJSON, hdaJSON, options ); - /** HDACollection of the HDAs contained in this history. */ - this.hdas = new hdaModel.HDACollection( hdaJSON || [], { historyId: this.get( 'id' )}); + /** HistoryContents collection of the HDAs contained in this history. */ + this.hdas = new historyContents.HistoryContents( hdaJSON || [], { historyId: this.get( 'id' )}); // if we've got hdas passed in the constructor, load them if( hdaJSON && _.isArray( hdaJSON ) ){ this.hdas.reset( hdaJSON ); @@ -230,12 +230,12 @@ } var data = {}; if( hdaDetailIds.length ) { - data[ "dataset_details" ] = hdaDetailIds.join( ',' ); + data.dataset_details = hdaDetailIds.join( ',' ); } if( hdcaDetailIds.length ) { // for symmetry, not actually used by backend of consumed // by frontend. - data[ "dataset_collection_details" ] = hdcaDetailIds.join( ',' ); + data.dataset_collection_details = hdcaDetailIds.join( ',' ); } return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyData.id + '/contents', { data: data }); } diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -2,11 +2,12 @@ "mvc/dataset/hda-model", "mvc/dataset/hda-edit", "mvc/collection/dataset-collection-edit", + "mvc/history/history-contents", "mvc/history/readonly-history-panel", "mvc/tags", "mvc/annotations", "utils/localization" -], function( hdaModel, hdaEdit, datasetCollectionEdit, readonlyPanel, tagsMod, annotationsMod, _l ){ +], function( hdaModel, hdaEdit, datasetCollectionEdit, historyContents, readonlyPanel, tagsMod, annotationsMod, _l ){ /* ============================================================================= TODO: @@ -36,7 +37,7 @@ HDAViewClass : hdaEdit.HDAEditView, // ......................................................................... SET UP - /** Set up the view, set up storage, bind listeners to HDACollection events + /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes */ initialize : function( attributes ){ @@ -493,7 +494,7 @@ /** return an HdaCollection of the models of all currenly selected hdas */ getSelectedHdaCollection : function(){ - return new hdaModel.HDACollection( _.map( this.getSelectedHdaViews(), function( hdaView ){ + return new historyContents.HistoryContents( _.map( this.getSelectedHdaViews(), function( hdaView ){ return hdaView.model; }), { historyId: this.model.id }); }, diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -97,7 +97,7 @@ noneFoundMsg : _l( 'No matching datasets found' ), // ......................................................................... SET UP - /** Set up the view, set up storage, bind listeners to HDACollection events + /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes optional settings for the panel */ initialize : function( attributes ){ diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/collection/hdca-model.js --- /dev/null +++ b/static/scripts/packed/mvc/collection/hdca-model.js @@ -0,0 +1,1 @@ +define(["mvc/history/history-content-base","utils/localization"],function(b,c){var a=b.HistoryContent.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},toString:function(){var d=this.get("id")||"";if(this.get("name")){d=this.get("hid")+' :"'+this.get("name")+'",'+d}return"HDCA-"+this.get("collection_type")+"("+d+")"}});return{HistoryDatasetCollectionAssociation:a}}); \ No newline at end of file diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(e,c){var a=Backbone.Model.extend(e.LoggableMixin).extend({idAttribute:"type_id",urlRoot:galaxy_config.root+"api/histories/",constructor:function(o,n){o.type_id=a.typeIdStr(o.history_content_type,o.id);Backbone.Model.apply(this,arguments)},initialize:function(o,n){this.on("change:id",this._createTypeId)},url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},hidden:function(){return !this.get("visible")},"delete":function f(n){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},n)},undelete:function j(n){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},n)},hide:function d(n){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},n)},unhide:function i(n){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},n)},isVisible:function(o,p){var n=true;if((!o)&&(this.get("deleted")||this.get("purged"))){n=false}if((!p)&&(!this.get("visible"))){n=false}return n},searchAttribute:function(p,n){var o=this.get(p);if(!n||(o===undefined||o===null)){return false}if(_.isArray(o)){return this._searchArrayAttribute(o,n)}return(o.toString().toLowerCase().indexOf(n.toLowerCase())!==-1)},_searchArrayAttribute:function(o,n){n=n.toLowerCase();return _.any(o,function(p){return(p.toString().toLowerCase().indexOf(n.toLowerCase())!==-1)})},search:function(n){var o=this;return _.filter(this.searchAttributes,function(p){return o.searchAttribute(p,n)})},matches:function(o){var q="=",n=o.split(q);if(n.length>=2){var p=n[0];p=this.searchAliases[p]||p;return this.searchAttribute(p,n[1])}return !!this.search(o).length},matchesAll:function(o){var n=this;o=o.match(/(".*"|\w*=".*"|\S*)/g).filter(function(p){return !!p});return _.all(o,function(p){p=p.replace(/"/g,"");return n.matches(p)})},_createTypeId:function(){this.set("type_id",TypeIdModel.typeIdStr(this.get("history_content_type"),this.get("id")))},});a.typeIdStr=function h(n,o){return[n,o].join("-")};var m=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var o=this.get("id");if(!o){return{}}var n={purge:galaxy_config.root+"datasets/"+o+"/purge_async",display:galaxy_config.root+"datasets/"+o+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+o+"/edit",download:galaxy_config.root+"datasets/"+o+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+o,rerun:galaxy_config.root+"tool_runner/rerun?id="+o,show_params:galaxy_config.root+"datasets/"+o+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+o,set:galaxy_config.root+"dataset/annotate_async?id="+o},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+o+"&metadata_name="};return n},initialize:function(n){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",m.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(o,n){this.log(this+" has changed state:",o,n);if(this.inReadyState()){this.trigger("state:ready",o,n,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var n=_.contains(m.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||n)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function f(n){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},n)},undelete:function j(n){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},n)},hide:function d(n){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},n)},unhide:function i(n){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},n)},purge:function g(n){if(this.get("purged")){return jQuery.when()}n=n||{};n.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var o=this,p=jQuery.ajax(n);p.done(function(s,q,r){o.set({deleted:true,purged:true})});p.fail(function(u,q,t){var r=c("Unable to purge dataset");var s=("Removal of datasets by users is not allowed in this Galaxy instance");if(u.responseJSON&&u.responseJSON.error){r=u.responseJSON.error}else{if(u.responseText.indexOf(s)!==-1){r=s}}u.responseText=r;o.trigger("error",o,u,n,c(r),{error:r})});return p},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var n=this.get("id")||"";if(this.get("name")){n=this.get("hid")+' :"'+this.get("name")+'",'+n}return"HDA("+n+")"}});m.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};m.READY_STATES=[m.STATES.OK,m.STATES.EMPTY,m.STATES.PAUSED,m.STATES.FAILED_METADATA,m.STATES.NOT_VIEWABLE,m.STATES.DISCARDED,m.STATES.ERROR];m.NOT_READY_STATES=[m.STATES.UPLOAD,m.STATES.QUEUED,m.STATES.RUNNING,m.STATES.SETTING_METADATA,m.STATES.NEW];var b=Backbone.Collection.extend(e.LoggableMixin).extend({model:function(o,n){if(o.history_content_type=="dataset"){return new m(o,n)}else{if(o.history_content_type=="dataset_collection"){return new k(o,n)}else{}}},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(o,n){n=n||{};this.historyId=n.historyId},ids:function(){return this.map(function(n){return n.get("id")})},notReady:function(){return this.filter(function(n){return !n.inReadyState()})},running:function(){var n=[];this.each(function(o){if(!o.inReadyState()){n.push(o.get("id"))}});return n},getByHid:function(n){return _.first(this.filter(function(o){return o.get("hid")===n}))},getVisible:function(n,q,p){p=p||[];var o=new b(this.filter(function(r){return r.isVisible(n,q)}));_.each(p,function(r){if(!_.isFunction(r)){return}o=new b(o.filter(r))});return o},haveDetails:function(){return this.all(function(n){return n.hasDetails()})},fetchAllDetails:function(o){o=o||{};var n={details:"all"};o.data=(o.data)?(_.extend(o.data,n)):(n);return this.fetch(o)},ajaxQueue:function(q,p){var o=jQuery.Deferred(),n=this.length,s=[];if(!n){o.resolve([]);return o}var r=this.chain().reverse().map(function(u,t){return function(){var v=q.call(u,p);v.done(function(w){o.notify({curr:t,total:n,response:w,model:u})});v.always(function(w){s.push(w);if(r.length){r.shift()()}else{o.resolve(s)}})}}).value();r.shift()();return o},matches:function(n){return this.filter(function(o){return o.matches(n)})},set:function(p,n){var o=this;p=_.map(p,function(s){var r=s.attributes||s;var t=a.typeIdStr(r.history_content_type,r.id);var u=o.get(t);if(!u){return s}var q=u.toJSON();_.extend(q,s);return q});Backbone.Collection.prototype.set.call(this,p,n)},promoteToHistoryDatasetCollection:function l(s,q,o){o=o||{};o.url=this.url();o.type="POST";var u=q;var r=[],n=null;if(q=="list"){this.chain().each(function(x){var v=x.attributes.name;var y=x.get("id");var w=x.attributes.history_content_type;if(w=="dataset"){if(u!="list"){console.log("Invalid collection type")}r.push({name:v,src:"hda",id:y})}else{if(u=="list"){u="list:"+x.attributes.collection_type}else{if(u!="list:"+x.attributes.collection_type){console.log("Invalid collection type")}}r.push({name:v,src:"hdca",id:y})}});n="New Dataset List"}else{if(q=="paired"){var p=this.ids();if(p.length!=2){}r.push({name:"forward",src:"hda",id:p[0]});r.push({name:"reverse",src:"hda",id:p[1]});n="New Dataset Pair"}}o.data={type:"dataset_collection",name:n,collection_type:u,element_identifiers:JSON.stringify(r),};var t=jQuery.ajax(o);t.done(function(x,v,w){s.refresh()});t.fail(function(x,v,w){if(x.responseJSON&&x.responseJSON.error){error=x.responseJSON.error}else{error=x.responseJSON}x.responseText=error});return t},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});var k=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},});return{HistoryDatasetAssociation:m,HDACollection:b}}); \ No newline at end of file +define(["mvc/history/history-content-base","utils/localization"],function(e,f){var d=e.HistoryContent.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var j=this.get("id");if(!j){return{}}var i={purge:galaxy_config.root+"datasets/"+j+"/purge_async",display:galaxy_config.root+"datasets/"+j+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+j+"/edit",download:galaxy_config.root+"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+j,rerun:galaxy_config.root+"tool_runner/rerun?id="+j,show_params:galaxy_config.root+"datasets/"+j+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+j,set:galaxy_config.root+"dataset/annotate_async?id="+j},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};return i},initialize:function(i){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(j,i){this.log(this+" has changed state:",j,i);if(this.inReadyState()){this.trigger("state:ready",j,i,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var i=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||i)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(i){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},i)},undelete:function a(i){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},i)},hide:function b(i){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},i)},unhide:function h(i){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},i)},purge:function g(i){if(this.get("purged")){return jQuery.when()}i=i||{};i.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var j=this,k=jQuery.ajax(i);k.done(function(n,l,m){j.set({deleted:true,purged:true})});k.fail(function(p,l,o){var m=f("Unable to purge dataset");var n=("Removal of datasets by users is not allowed in this Galaxy instance");if(p.responseJSON&&p.responseJSON.error){m=p.responseJSON.error}else{if(p.responseText.indexOf(n)!==-1){m=n}}p.responseText=m;j.trigger("error",j,p,i,f(m),{error:m})});return k},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var i=this.get("id")||"";if(this.get("name")){i=this.get("hid")+' :"'+this.get("name")+'",'+i}return"HDA("+i+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA,d.STATES.NEW];return{HistoryDatasetAssociation:d}}); \ No newline at end of file diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/history/history-content-base.js --- /dev/null +++ b/static/scripts/packed/mvc/history/history-content-base.js @@ -0,0 +1,1 @@ +define(["mvc/base-mvc","utils/localization"],function(b,e){var f=Backbone.Model.extend(b.LoggableMixin).extend({idAttribute:"type_id",constructor:function(j,i){j.type_id=f.typeIdStr(j.history_content_type,j.id);Backbone.Model.apply(this,arguments)},initialize:function(j,i){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",TypeIdModel.typeIdStr(this.get("history_content_type"),this.get("id")))},hidden:function(){return !this.get("visible")},isVisible:function(j,k){var i=true;if((!j)&&(this.get("deleted")||this.get("purged"))){i=false}if((!k)&&(!this.get("visible"))){i=false}return i},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},"delete":function d(i){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},i)},undelete:function a(i){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},i)},hide:function c(i){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},i)},unhide:function g(i){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},i)},searchAttribute:function(k,i){var j=this.get(k);if(!i||(j===undefined||j===null)){return false}if(_.isArray(j)){return this._searchArrayAttribute(j,i)}return(j.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)},_searchArrayAttribute:function(j,i){i=i.toLowerCase();return _.any(j,function(k){return(k.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)})},search:function(i){var j=this;return _.filter(this.searchAttributes,function(k){return j.searchAttribute(k,i)})},matches:function(j){var l="=",i=j.split(l);if(i.length>=2){var k=i[0];k=this.searchAliases[k]||k;return this.searchAttribute(k,i[1])}return !!this.search(j).length},matchesAll:function(j){var i=this;j=j.match(/(".*"|\w*=".*"|\S*)/g).filter(function(k){return !!k});return _.all(j,function(k){k=k.replace(/"/g,"");return i.matches(k)})},toString:function(){var i=this.get("id")||"";if(this.get("name")){i=this.get("hid")+' :"'+this.get("name")+'",'+i}return"HistoryContent("+i+")"}});f.typeIdStr=function h(i,j){return[i,j].join("-")};return{HistoryContent:f}}); \ No newline at end of file diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/history/history-contents.js --- /dev/null +++ b/static/scripts/packed/mvc/history/history-contents.js @@ -0,0 +1,1 @@ +define(["mvc/history/history-content-base","mvc/dataset/hda-model","mvc/collection/hdca-model","mvc/base-mvc","utils/localization"],function(b,d,f,a,c){var g=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){console.debug("HistoryContents.model:",i);if(i.history_content_type==="dataset"){return new d.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){return new f.HistoryDatasetCollectionAssociation(i,h)}}throw new TypeError("Unknown history_content_type:"+i.history_content_type)},initialize:function(i,h){h=h||{};console.debug("new HistoryContents",i,h);this.historyId=h.historyId},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new g(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new g(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m;var n=b.HistoryContent.typeIdStr(l.history_content_type,l.id);var o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function e(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){console.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){console.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},toString:function(){return(["HistoryContents(",[this.parentId,this.length].join(),")"].join(""))}});return{HistoryContents:g}}); \ No newline at end of file diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/base-mvc","utils/localization"],function(c,a,b){var e=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new c.HDACollection(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||e.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function f(h,s){s=s||{};var m=s.hdaDetailIds||[];var j=s.hdcaDetailIds||[];var o=jQuery.Deferred(),n=null;function i(t){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(t){if(!t||!t.state_ids){return 0}return _.reduce(t.state_ids,function(u,w,v){return u+w.length},0)}function r(u){if(!g(u)){return[]}if(_.isFunction(m)){m=m(u)}if(_.isFunction(j)){j=j(u)}var t={};if(m.length){t.dataset_details=m.join(",")}if(j.length){t.dataset_collection_details=j.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+u.id+"/contents",{data:t})}var q=s.historyFn||i,p=s.hdaFn||r;var l=q(h);l.done(function(t){n=t;o.notify({status:"history data retrieved",historyJSON:n})});l.fail(function(v,t,u){o.reject(v,"loading the history")});var k=l.then(p);k.then(function(t){o.notify({status:"dataset data retrieved",historyJSON:n,hdaJSON:t});o.resolve(n,t)});k.fail(function(v,t,u){o.reject(v,"loading the datasets",{history:n})});return o};var d=Backbone.Collection.extend(a.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories"});return{History:e,HistoryCollection:d}}); \ No newline at end of file +define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(e,a,b){var d=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new e.HistoryContents(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||d.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});d.UPDATE_DELAY=4000;d.getHistoryData=function f(h,s){s=s||{};var m=s.hdaDetailIds||[];var j=s.hdcaDetailIds||[];var o=jQuery.Deferred(),n=null;function i(t){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(t){if(!t||!t.state_ids){return 0}return _.reduce(t.state_ids,function(u,w,v){return u+w.length},0)}function r(u){if(!g(u)){return[]}if(_.isFunction(m)){m=m(u)}if(_.isFunction(j)){j=j(u)}var t={};if(m.length){t.dataset_details=m.join(",")}if(j.length){t.dataset_collection_details=j.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+u.id+"/contents",{data:t})}var q=s.historyFn||i,p=s.hdaFn||r;var l=q(h);l.done(function(t){n=t;o.notify({status:"history data retrieved",historyJSON:n})});l.fail(function(v,t,u){o.reject(v,"loading the history")});var k=l.then(p);k.then(function(t){o.notify({status:"dataset data retrieved",historyJSON:n,hdaJSON:t});o.resolve(n,t)});k.fail(function(v,t,u){o.reject(v,"loading the datasets",{history:n})});return o};var c=Backbone.Collection.extend(a.LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories"});return{History:d,HistoryCollection:c}}); \ No newline at end of file diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,b,h,d,a,c,e){var g=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(i){i=i||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=i.purgeAllowed||false;this.selecting=i.selecting||false;this.annotationEditorShown=i.annotationEditorShown||false;this.tagsEditorShown=i.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,i)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(i){this.model.fetch()},this)},renderModel:function(){var i=$("<div/>");i.append(g.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(i);this._renderAnnotation(i)}i.find(".history-secondary-actions").prepend(this._renderSelectButton());i.find(".history-dataset-actions").toggle(this.selecting);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDATagEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDATagEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".history-secondary-actions"))})},_renderAnnotation:function(i){var j=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:i.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDAAnnotationEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDAAnnotationEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".history-secondary-actions"))})},_renderSelectButton:function(i){return faIconButton({title:e("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(i){i=i||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,i);if(!this.model){return}this._setUpDatasetActionsPopup(i);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var j=this;i.find(".history-name").attr("title",e("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(k){var l=j.model.get("name");if(k&&k!==l){j.$el.find(".history-name").text(k);j.model.save({name:k}).fail(function(){j.$el.find(".history-name").text(j.model.previous("name"))})}else{j.$el.find(".history-name").text(l)}}})},_setUpDatasetActionsPopup:function(i){var j=this,k=[{html:e("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;j.getSelectedHdaCollection().ajaxQueue(l)}}];if(j.purgeAllowed){k.push({html:e("Permanently delete datasets"),func:function(){if(confirm(e("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;j.getSelectedHdaCollection().ajaxQueue(l)}}})}k.push({html:e("Build Dataset List (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"list")}});k.push({html:e("Build Dataset Pair (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"paired")}});k.push({html:e("Build List of Dataset Pairs (Experimental)"),func:_.bind(j._showPairedCollectionModal,j)});return new PopupMenu(i.find(".history-dataset-action-popup-btn"),k)},_showPairedCollectionModal:function(){var i=this,j=i.getSelectedHdaCollection().toJSON().filter(function(k){return k.history_content_type==="dataset"&&k.state===f.HistoryDatasetAssociation.STATES.OK});if(j.length){require(["mvc/collection/paired-collection-creator"],function(k){window.creator=k.pairedCollectionCreatorModal(j,{historyId:i.model.id})})}else{}},_handleHdaDeletionChange:function(i){if(i.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[i.id])}},_handleHdaVisibleChange:function(i){if(i.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[i.id])}},_createContentView:function(j){var i=j.id,l=j.get("history_content_type"),k=null;if(l==="dataset"){k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(l==="dataset_collection"){k=new h.DatasetCollectionEditView({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,j);j.on("selected",function(m,l){if(!l){return}var k=[];if((l.shiftKey)&&(i.lastSelectedViewId&&_.has(i.hdaViews,i.lastSelectedViewId))){var o=i.hdaViews[i.lastSelectedViewId];k=i.selectDatasetRange(m,o).map(function(p){return p.model.id})}else{var n=m.model.id;i.lastSelectedViewId=n;k=[n]}i.selectedHdaIds=_.union(i.selectedHdaIds,k)});j.on("de-selected",function(l,k){var m=l.model.id;i.selectedHdaIds=_.without(i.selectedHdaIds,m)})},toggleHDATagEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.annotationEditor){k.annotationEditor.toggle.apply(k.annotationEditor,j)}})},removeHdaView:function(j){if(!j){return}var i=this;j.$el.fadeOut(i.fxSpeed,function(){j.off();j.remove();delete i.hdaViews[j.model.id];if(_.isEmpty(i.hdaViews)){i.trigger("empty-history",i);i._renderEmptyMsg()}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(i);_.each(this.hdaViews,function(j){j.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(i);_.each(this.hdaViews,function(j){j.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.select(i)})},deselectAllDatasets:function(i){this.lastSelectedViewId=null;_.each(this.hdaViews,function(j){j.deselect(i)})},selectDatasetRange:function(k,j){var i=this.hdaViewRange(k,j);_.each(i,function(l){l.select()});return i},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(i){return i.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(i){return i.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:g}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/history-contents","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,h,b,g,c,d,i,a){var e=c.ReadOnlyHistoryPanel.extend({HDAViewClass:h.HDAEditView,initialize:function(j){j=j||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=j.purgeAllowed||false;this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this.tagsEditorShown=j.tagsEditorShown||false;c.ReadOnlyHistoryPanel.prototype.initialize.call(this,j)},_setUpModelEventHandlers:function(){c.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this)},renderModel:function(){var j=$("<div/>");j.append(e.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(j).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}j.find(".history-secondary-actions").prepend(this._renderSelectButton());j.find(".history-dataset-actions").toggle(this.selecting);j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},_renderTags:function(j){var k=this;this.tagsEditor=new d.TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:a("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))})},_renderAnnotation:function(j){var k=this;this.annotationEditor=new i.AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:a("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))})},_renderSelectButton:function(j){return faIconButton({title:a("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;c.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,j);if(!this.model){return}this._setUpDatasetActionsPopup(j);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",a("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){var m=k.model.get("name");if(l&&l!==m){k.$el.find(".history-name").text(l);k.model.save({name:l}).fail(function(){k.$el.find(".history-name").text(k.model.previous("name"))})}else{k.$el.find(".history-name").text(m)}}})},_setUpDatasetActionsPopup:function(j){var k=this,l=[{html:a("Hide datasets"),func:function(){var m=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(m)}},{html:a("Unhide datasets"),func:function(){var m=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(m)}},{html:a("Delete datasets"),func:function(){var m=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(m)}},{html:a("Undelete datasets"),func:function(){var m=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(m)}}];if(k.purgeAllowed){l.push({html:a("Permanently delete datasets"),func:function(){if(confirm(a("This will permanently remove the data in your datasets. Are you sure?"))){var m=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(m)}}})}l.push({html:a("Build Dataset List (Experimental)"),func:function(){k.getSelectedHdaCollection().promoteToHistoryDatasetCollection(k.model,"list")}});l.push({html:a("Build Dataset Pair (Experimental)"),func:function(){k.getSelectedHdaCollection().promoteToHistoryDatasetCollection(k.model,"paired")}});l.push({html:a("Build List of Dataset Pairs (Experimental)"),func:_.bind(k._showPairedCollectionModal,k)});return new PopupMenu(j.find(".history-dataset-action-popup-btn"),l)},_showPairedCollectionModal:function(){var j=this,k=j.getSelectedHdaCollection().toJSON().filter(function(l){return l.history_content_type==="dataset"&&l.state===f.HistoryDatasetAssociation.STATES.OK});if(k.length){require(["mvc/collection/paired-collection-creator"],function(l){window.creator=l.pairedCollectionCreatorModal(k,{historyId:j.model.id})})}else{}},_handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},_handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},_createContentView:function(k){var j=k.id,m=k.get("history_content_type"),l=null;if(m==="dataset"){l=new this.HDAViewClass({model:k,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[j],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(m==="dataset_collection"){l=new b.DatasetCollectionEditView({model:k,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[j],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(l);return l},_setUpHdaListeners:function(k){var j=this;c.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,k);k.on("selected",function(n,m){if(!m){return}var l=[];if((m.shiftKey)&&(j.lastSelectedViewId&&_.has(j.hdaViews,j.lastSelectedViewId))){var p=j.hdaViews[j.lastSelectedViewId];l=j.selectDatasetRange(n,p).map(function(q){return q.model.id})}else{var o=n.model.id;j.lastSelectedViewId=o;l=[o]}j.selectedHdaIds=_.union(j.selectedHdaIds,l)});k.on("de-selected",function(m,l){var n=m.model.id;j.selectedHdaIds=_.without(j.selectedHdaIds,n)})},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.trigger("empty-history",j);j._renderEmptyMsg()}})},events:_.extend(_.clone(c.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(j){j=(j!==undefined)?(j):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(j){j=(j!==undefined)?(j):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(j){_.each(this.hdaViews,function(k){k.select(j)})},deselectAllDatasets:function(j){this.lastSelectedViewId=null;_.each(this.hdaViews,function(k){k.deselect(j)})},selectDatasetRange:function(l,k){var j=this.hdaViewRange(l,k);_.each(j,function(m){m.select()});return j},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new g.HistoryContents(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:e}}); \ No newline at end of file diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{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"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);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);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(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+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){if(this.view.reference_track.tiles_div.is(":visible")){this.view.resize_viewport()}var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{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}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.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}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{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.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"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.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"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},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{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.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{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"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);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);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?U(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*Q)),ak,am,ah,ai=[],ao=[];while((ac*Q*af)<ag){ak=Math.floor(ac*Q*af);am=new w.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(Q*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{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}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.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}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{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.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"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.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(ar){ap.draw_tile({data:ab.values(ac)},ar.canvas.getContext("2d"),ar.mode,ar.region,aq,ar.seq_data,true)})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"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},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{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.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].config.get_value("name")===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});this.set_up_router({view:l});return l},set_up_router:function(k){new h.TrackBrowserRouter(k);Backbone.history.start()},init_keyboard_nav:function(k){$(document).keyup(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(f.extend(p,{header:false}));l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].config.get_value("name")===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});this.set_up_router({view:l});return l},set_up_router:function(k){new h.TrackBrowserRouter(k);Backbone.history.start()},init_keyboard_nav:function(k){$(document).keyup(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/viz/viz_views.js --- /dev/null +++ b/static/scripts/packed/viz/viz_views.js @@ -0,0 +1,1 @@ +define(["libs/underscore"],function(a){var b=Backbone.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this);this.render()},render:function(){this.$el.append($("<div/>").addClass(this.model.drag_handle_class));this.$el.append($("<div/>").addClass("track-name").text(this.model.config.get_value("name")));this.action_icons={};this.render_action_icons();this.$el.dblclick(function(c){c.stopPropagation()});this.$el.append($("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var c=this;this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.$el);a.each(this.model.action_icons_def,function(d){c.add_action_icon(d.name,d.title,d.css_class,d.on_click_fn,d.prepend,d.hide)});this.set_display_modes(this.model.display_modes)},add_action_icon:function(e,i,h,g,d,f){var c=this;this.action_icons[e]=$("<a/>").attr("title",i).addClass("icon-button").addClass(h).tooltip().click(function(){g(c.model)}).appendTo(this.icons_div);if(f){this.action_icons[e].hide()}},set_display_modes:function(g,k){if(!g){return}this.model.display_modes=g;this.model.mode=(k||this.model.config.get_value("mode")||this.model.display_modes[0]);this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var e=this,d=this.model,h={};for(var f=0,c=d.display_modes.length;f<c;f++){var j=d.display_modes[f];h[j]=function(i){return function(){d.change_mode(i)}}(j)}make_popupmenu(this.action_icons.mode_icon,h)}});return{TrackHeaderView:b}}); \ No newline at end of file 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.