'+this.opt.filters[key].title+'
');
- var filterOptions = jQuery('');
- filterContainer.append(filterTitle);
- filterContainer.append(filterOptions);
- jQuery("#"+this._filtersTarget).append(filterContainer);
- if(this.opt.filters[key].presentation == "radio"){
- this._createRadioButtons(this.opt.filters[key].data, key, '#'+key+'Options');
- } else if (this.opt.filters[key].presentation == "checkbox"){
- // todo
- } else {
- Biojs.console.log("ERROR: " + "filter presentation value unknown for filter " + key);
- }
- }
- }
- }
- },
-
- /*
- * Function: Biojs.HpaSummaryFeatures._createCheckBox
- * Purpose: Create checkbox options
- * Returns: -
- * Inputs: -
- */
- _createCheckBox: function(data, filterName, target){
- },
- /*
- * Function: Biojs.HpaSummaryFeatures._createRadioButtons
- * Purpose: Create radio button options
- * Returns: -
- * Inputs: data -> {Object} Data for one filter.
- * filterName -> {String} Filter name.
- * target -> {String} HTML tag where to draw.
- */
- _createRadioButtons: function(data, filterName, target){
- for (key in data) {
- if (data.hasOwnProperty(key)){
- var br = jQuery(''); - var radioBtnContainer = jQuery(''); - var radioBtn = jQuery(''); - var radioBtnName = jQuery(''+key+''); - radioBtnContainer.append(radioBtn); - radioBtnContainer.append(radioBtnName); - radioBtnContainer.appendTo(target); - //br.appendTo('#timeSeriesRadioButtons'); - } - } - var nondeRadioBtn = jQuery(''); //checked="checked" - var noneRadioBtnName = jQuery('None'); - nondeRadioBtn.appendTo(target); - noneRadioBtnName.appendTo(target); - }, - - - /* - * Function: Biojs.HpaSummaryFeatures._setHtmlTemplate - * Purpose: Create an HTML template to later on populate with information - * Returns: - - * Inputs: - - */ - _setHtmlTemplate: function(){ - this.opt.graphWidth = this.opt.graphWidth.toString(); - var width = this.opt.graphWidth + "px"; - if(this.opt.graphWidth.indexOf("%") != -1 || this.opt.graphWidth.indexOf("px") != -1){ - width = this.opt.graphWidth; - } - var interactionFilters = jQuery(''); - var cytoscape = jQuery(''); - var information = jQuery(''); - jQuery("#"+this.opt.target).append(interactionFilters); - jQuery("#"+this.opt.target).append(cytoscape); - jQuery("#"+this.opt.target).append(information); - }, - - /* - * Variable: Biojs.HpaSummaryFeatures._setHtmlTemplate - * Purpose: Create an HTML template to later on populate with information - * Returns: - - * Inputs: - - */ - _cytoscapeTarget: "miCy", - _filtersTarget: "miInteractionFilters", - _informationTarget: "miInformation" - - - - - -}); \ No newline at end of file diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.InteractionsTable.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.InteractionsTable.js deleted file mode 100755 index dda7668fc5..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.InteractionsTable.js +++ /dev/null @@ -1,668 +0,0 @@ -/** - * Table to show binary molecular interactions. - * - * @class - * @extends Biojs.Table - * - * @author John Gomez - * @version 1.0.0 - * @category 3 - * - * @param {Object} options - * An object with the options for InteractionTable' component. - * - * @option {string[][]|Object} dataSet - * Either 2D string array containing the whole data to be displayed or a plain object defining the data source. - * - *
- * {
- * url: <url>,
- * proxyUrl: <proxy>,
- * paramsMap: { "iDisplayStart": <newName1>, "iDisplayLength": <newName2>, ... },
- * filter: <flag>,
- * version: <MITAB_VERSION>,
- * totalRecords:<number>
- * }
- *
- * where:
- * -
- *
- url is string containing the url data source. - *
- paramsMap Customize the name of the following params which will be passed to server:
- *
-
- *
- iDisplayStart: index of the first expected record for paging. - *
- iDisplayLength: size of the fetched data (page size). - *
- sSearch: filter string entered by the user in case of filter is enabled. - *
- * - filter is a boolean to show/hide the search box on the table top. - * The entered string will be passed to the server by means of 'sSearch' parameter. - * Personalize the parameter name using paramsMap. - *
- proxyUrl optional string containing the url of the proxy in case of needing access to server through a proxy. - *
- version either string or integer containing the version of MITAB format as follows:
- *
-
- *
- "MITAB_VERSION_2_5" or 15: to set MITAB format v2.5 - *
- "MITAB_VERSION_2_5_EXT" or 31: to set MITAB format v2.5 extended - *
- "MITAB_VERSION_2_6" or 36: to set MITAB format v2.6 - *
- "MITAB_VERSION_2_7" or 42: to set MITAB format v2.7 - *
- * - totalRecords integer containing the number of total records. MITAB format does not contains this value on the response. - * You must do a request to ask for it. - *
- * {
- * psiquicUrl: 'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query',
- * proxyUrl: '../biojs/dependencies/proxy/proxy.php',
- * version: "MITAB_VERSION_2_5_EXT",
- * query: "species:human",
- * filter: false
- * }
- *
- *
- * - * ...soon - *- * - * @example - * var myTable = new Biojs.InteractionsTable({ - * target: "YourOwnDivId", - * dataSet: { - * psicquicUrl: 'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query', - * proxyUrl: '../biojs/dependencies/proxy/proxy.php', - * query: "brca2", - * version: "MITAB_VERSION_2_5", - * filter: false - * }, - * rowSelection: true - * }); - * - */ -Biojs.InteractionsTable = Biojs.Table.extend( -/** @lends Biojs.InteractionsTable# */ -{ - constructor: function (options) { - //Biojs.console.enable(); - - options.dataSet.version = (options.dataSet.version != undefined) ? options.dataSet.version : Biojs.InteractionsTable.MITAB_VERSION_2_5 - - this._useVersion ( options.dataSet.version ); - - // Calling super's constructor - this.base(options); - - }, - - /** - * Default values for the options - * @name Biojs.InteractionsTable-opt - */ - opt: { - target: "YourOwnDivId", - rowSelection: false, - version: "MITAB_VERSION_2_5", - psiquicUrl: 'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query', - proxyUrl: '../biojs/dependencies/proxy/proxy.php' - }, - - /** - * Array containing the supported event names - * @name Biojs.InteractionsTable-eventTypes - */ - eventTypes: [], - - /** - * Do a query to PSICQUIC server by using the provided query in MIQL. - * Uses the structure of the URL to fetch data from PSICQUIC. - * @param {string} columns Column indexes to be hided. - * - * @example - * myTable.setQuery("species:human"); - * - */ - setQuery: function ( query ) { - - // remove this properties to set a new query - delete this.opt.dataSet.url; - delete this.opt.totalRecords; - - // set the new query - this.opt.dataSet.query = query; - - // request data - this.setDataSource(this.opt.dataSet); - }, - - /** - * Get the actual query. - * Uses the structure of the URL to fetch data from PSICQUIC. - * - * @return {string} Current query. - * - * @example - * alert( "The query is " + myTable.getQuery() ); - */ - getQuery: function () { - return unescape(this.opt.dataSet.query); - }, - - /* - * Function: Biojs.InteractionTable._requestQueryCount - * Purpose: Request total rows counting with the provided query for pagination purposes. - * Since the PSIQUIC service does not provides the total row count with retrieved data, - * it's necessary to do another request in order to get it. - * Inputs: dataSet -> {Object} Settings of the data set. - * action -> {function} Callback function having the dataSet as argument. - */ - _requestQueryCount: function ( dataSet, action ) { - var self = this; - - dataSet.url = dataSet.psicquicUrl + '/' + dataSet.query; - dataSet.paramsMap = { "iDisplayStart": "firstResult", "iDisplayLength": "maxResults" }; - - jQuery.ajax({ - url: dataSet.proxyUrl, - dataType: "text", - data: [{ name: "url", value: dataSet.url + '?format=count' }], - success: function ( data ) { - dataSet.totalRecords = parseInt(data) | 0; - action.call( self, dataSet ); - } - }); - }, - - /** - * Rebuild the table - * - * @example - * myTable.setDataSource({ - * psicquicUrl: 'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query', - * proxyUrl: '../biojs/dependencies/proxy/proxy.php', - * query: "pubid:(10837477 OR 12029088)", - * version: "MITAB_VERSION_2_5", - * filter: false - * }); - * - */ - setDataSource: function ( dataSet ) { - - if ( dataSet instanceof Array ) { - // Local data - // invoke parent's setDataSource - this.base( dataSet ); - - } else { - // Remote data - if ( dataSet.hasOwnProperty("totalRecords") && dataSet.hasOwnProperty("url") ) { - // Already have the number of records for pagination - // then, invoke parent's setDataSource - this.base( dataSet ); - - } else { - // Set the new query - this.opt.dataSet = {}; - this.opt.dataSet.psicquicUrl = dataSet.psicquicUrl; - this.opt.dataSet.proxyUrl = dataSet.proxyUrl; - this.opt.dataSet.version = dataSet.version; - this.opt.dataSet.filter = dataSet.filter; - this.opt.dataSet.query = escape(dataSet.query); - this.opt.dataSet.url = dataSet.psicquicUrl + '/' + dataSet.query; - this.opt.dataSet.paramsMap = { "iDisplayStart": "firstResult", "iDisplayLength": "maxResults" }; - // Request query counting rows and apply setDataSource then - this._requestQueryCount( this.opt.dataSet, this.base ); - } - } - }, - /* - * Function: Biojs.InteractionTable._decodeToJSON - * Purpose: Overrides the parent method to decode the received MITAB data into the expected JSON format. - * Returns: {Object} formatted in the expected JSON. - * Inputs: data -> {*} MITAB data received from the PSIQUIC server or another one. - */ - _decodeToJSON: function ( mitabData ) { - Biojs.console.log("DATA DECODING FROM MITAB to JSON"); - - var jsonData = {}; - var decoder = new Biojs.InteractionsTable.MITabTxtDecoder(mitabData); - - jsonData.aaData = decoder.decodeData(); - jsonData.iTotalRecords = this.getTotalRecords(); - jsonData.iTotalDisplayRecords = this.getTotalRecords(); - - delete decoder; - return jsonData; - }, - - /* - * Function: Biojs.InteractionTable._useVersion - * Purpose: Set the columns depending on the MITAB format version. - * Returns: - * Inputs: {string|int} Either the name or the number of columns of the MITAB version. - * Use values defined in the static members of Biojs.InteractionsTable declared at the end of this class. - */ - _useVersion: function (version) { - - var length = ( (typeof version) == "string" ) ? Biojs.InteractionsTable[version] : version; - - var columnsToHide = []; - - switch (length) { - - case Biojs.InteractionsTable.MITAB_VERSION_2_7: - for ( var i = 36; i < 42; i++ ) { - this.opt.columns[i] = Biojs.InteractionsTable.MITAB_COLUMNS[i]; - } - columnsToHide = [36,37,38,39,40,41]; - - case Biojs.InteractionsTable.MITAB_VERSION_2_6: - for ( var i = 31; i < 36; i++ ) { - this.opt.columns[i] = Biojs.InteractionsTable.MITAB_COLUMNS[i]; - } - columnsToHide = columnsToHide.concat([31,32,33,34,35]); - - case Biojs.InteractionsTable.MITAB_VERSION_2_5_EXT: - for ( var i = 15; i < 31; i++ ) { - this.opt.columns[i] = Biojs.InteractionsTable.MITAB_COLUMNS[i]; - } - columnsToHide = columnsToHide.concat([15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30]); - - // Complex expansion - this.opt.columns[15].render = this._columnRender.showDescXRef; - - // Biological Role A - this.opt.columns[16].render = this._columnRender.showDescXRef; - - // Biological Role B - this.opt.columns[17].render = this._columnRender.showDescXRef; - - // Experimental Role A - this.opt.columns[18].render = this._columnRender.showRowDescXRef; - - // Experimental Role B - this.opt.columns[19].render = this._columnRender.showRowDescXRef; - - // Interactor Type A - this.opt.columns[20].render = this._columnRender.showDescXRef; - - // Interactor Type B - this.opt.columns[21].render = this._columnRender.showDescXRef; - - // XRef Interactor Type A - this.opt.columns[22].render = this._columnRender.showDescXRef; - - // Xref Interactor Type B - this.opt.columns[23].render = this._columnRender.showDescXRef; - - // XRef Interaction - this.opt.columns[24].render = this._columnRender.showDescXRef; - - // Annotation Interactor A - this.opt.columns[25].render = this._columnRender.showRowDescXRef; - - // Annotations Interactor B - this.opt.columns[26].render = this._columnRender.showRowDescXRef; - - // Annotations Interaction - this.opt.columns[27].render = this._columnRender.showRowDescXRef; - - // NCBI Taxonomy - this.opt.columns[28].render = this._columnRender.showDescXRef; - - // Parameters - this.opt.columns[29].render = this._columnRender.showRowDescXRef; - - // Creation Date - this.opt.columns[30].render = this._columnRender.showRowDescXRef; - - case Biojs.InteractionsTable.MITAB_VERSION_2_5: - - for ( var i = 0; i < 15; i++ ) { - this.opt.columns[i] = Biojs.InteractionsTable.MITAB_COLUMNS[i]; - } - columnsToHide = columnsToHide.concat([2,3,7,8,11,12,13]); - - this.opt.columns[0].render = this._columnRender.showProteinXRef; - this.opt.columns[1].render = this._columnRender.showProteinXRef; - this.opt.columns[2].render = this._columnRender.showValueXRef; - this.opt.columns[3].render = this._columnRender.showValueXRef; - this.opt.columns[4].render = this._columnRender.showValueXRef; - this.opt.columns[5].render = this._columnRender.showValueXRef; - - this.opt.columns[6].render = this._columnRender.showDescXRef; - - // NCBI Taxon - this.opt.columns[9].render = this._columnRender.showDescXRef; - this.opt.columns[10].render = this._columnRender.showDescXRef; - - // Interaction type - this.opt.columns[11].render = this._columnRender.showDescXRef; - - // source - this.opt.columns[12].render = this._columnRender.showDescXRef; - - // Interaction AC - this.opt.columns[13].render = this._columnRender.showInteractionXRef; - - // Confidence Score - this.opt.columns[14].render = this._columnRender.showRawValueXRef; - - break; - - default : - Biojs.console.log("Wrong version <"+length+"> "); - } - - - this.opt.hideColumns = columnsToHide; - - }, - - /* - * Object: Biojs.InteractionTable._columnRender.showProteinXRef - * Purpose: Store the render functions to format values on the table cells. - */ - _columnRender: { - - /** - * @ignore - * - * Function: Biojs.InteractionTable._columnRender - * Purpose: Format the string
'; - } - delete tk; - return newValue; - }, - /** - * @ignore - * - * Function: Biojs.InteractionTable._columnRender.showInteractionXRef - * Purpose: Format the string
'; - } - delete tk; - return newValue; - }, - /** - * @ignore - * - * Function: Biojs.InteractionTable._columnRender.showValueXRef - * Purpose: Format the string
'; - } - delete tk; - return newValue; - }, - /** - * @ignore - * - * Function: Biojs.InteractionTable._columnRender.showDescXRef - * Purpose: Format the string
').appendTo('#'+opt.target);
-
- $( "#play" ).button({
- text: false,
- icons: {
- primary: "ui-icon-play"
- }
- }).click(function() {
- var options;
- if ( $(this).text() === "play" ) {
- options = {
- label: "stop",
- icons: {
- primary: "ui-icon-stop"
- }
- };
- $("#refresh").button("disable");
-
- self._conditions = $("#condition > option");
- self._interval = setInterval(function(){
-
- var conditions = self._conditions;
- var selected = $('#condition').val();
-
- var index;
- for(var i=0; i
' ); - self.pdbid = options.pdbid; - self.catable = null; - jQuery.ajax({ - url: 'http://puck.ebi.ac.uk:4000/mmcif/'+self.pdbid+'/categories', - data: {'varname':'catlist'}, - dataType: 'script', - crossDomain: 'true', - type: 'GET', - success: function(response, callOptions) { self.showCategoriesList(catlist); } - }); - }, - - showCategoriesList: function(catlist) { - var self = this; - for(var ci=0; ci < catlist.length; ci++) catlist[ci] = [catlist[ci]]; - var dtable = jQuery('#catlistTable').dataTable( { - "aaData": catlist, - "aoColumns": [ { "sTitle": "Categories" } ] - } ); - dtable.$('td').click( function () { - var sData = dtable.fnGetData( this ); - self.showAcategory(sData); - } ); - }, - standardizeVals: function(vals) { - if(vals instanceof Array) return vals; - return [vals]; - }, - showAcategory: function(catname) { - var self = this; - console.log( 'Start showing category '+catname ); - jQuery.ajax({ - url: 'http://puck.ebi.ac.uk:4000/mmcif/'+self.pdbid+'/'+catname, - data: {'varname':'catinfo'}, - dataType: 'script', - crossDomain: 'true', - type: 'GET', - success: function(response, callOptions) { self.showCategoryTable(catinfo); } - }); - //var dtable = jQuery('#catlistTable').dataTable( { - // "aaData": catlist, - // "aoColumns": [ { "sTitle": "Categories" } ] - //} ); - }, - - showCategoryTable: function(catinfo) { - var self = this; - var colinfo = [], rows = []; - for(var item in catinfo) { - colinfo.push( {"sTitle":item} ); - var vals = self.standardizeVals(catinfo[item]); - if(rows.length == 0) { - for(ri=0; ri < vals.length; ri++) rows.push([]); - } - for(ri=0; ri < vals.length; ri++) - rows[ri].push(vals[ri]); - } - if(self.catable!=null) { self.catable.fnDestroy(); jQuery("#categoryTable").html(""); } - //self.catable = null; - self.catable = jQuery('#categoryTable').dataTable( { - "aaData": rows, "aoColumns": colinfo, bDestroy:true //, "bRetrieve": true, "bDestroy": true - } ); - }, - - /** - * Array containing the supported event names - * @name Biojs.MmcifViewer-eventTypes - */ - eventTypes : [ - /** - * @name Biojs.MmcifViewer#onClick - * @event - * @param {function} actionPerformed A function which receives an {@link Biojs.Event} object as argument. - * @eventData {Object} source The component which did triggered the event. - * @eventData {string} type The name of the event. - * @eventData {int} selected Selected character. - * @example - * instance.onClick( - * function( objEvent ) { - * alert("The character " + objEvent.selected + " was clicked."); - * } - * ); - * - * */ - "onClick", - - /** - * @name Biojs.MmcifViewer#onHelloSelected - * @event - * @param {function} actionPerformed A function which receives an {@link Biojs.Event} object as argument. - * @eventData {Object} source The component which did triggered the event. - * @eventData {string} type The name of the event. - * @eventData {int} textSelected Selected text, will be 'Hello' obviously. - * @example - * instance.onHelloSelected( - * function( objEvent ) { - * alert("The word " + objEvent.textSelected + " was selected."); - * } - * ); - * - * */ - "onHelloSelected" - ] -}); - diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.PDBLogos.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.PDBLogos.js deleted file mode 100755 index ac0dd21d3d..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.PDBLogos.js +++ /dev/null @@ -1,261 +0,0 @@ -/** - * PDBLogos shows a set of icons to give a quick summary of salient features of a PDB entry. - * See more info on PDBLogos at http://pdbe.org/prints - * - * @class - * @extends Biojs - * - * @author John Gomez-Carvajal - * @version 1.0.0 - * @category 2 - * - * @requires Raphael 2.1.0 - * @dependency - * - * @requires jQuery Core 1.6.4 - * @dependency - * - * @param {Object} options An object with the options for PDBLogos component. - * - * @option {string} target - * Identifier/HTMLElement of the div container where the component should be rendered. - * - * @option {string} identifier - * PDB entry id for which prints will be rendered. - * - * @option {Object} raphael - * A Raphael object instead of div to render PDBprints into. - * - * @option {int} startX - * X-coordinate of point where rendering the array of PDBprints will start in the Raphael canvas - * - * @option {int} startY - * Y-coordinate of point point where rendering the array of PDBprints will start in the Raphael canvas - * - * @option {int} interval - * Gap size between successive PDBprints in a vertical or horizontal array - * - * @option {int} size - * Length of an icon logo - * - * @option {string} [color="#588FE5"] - * Color for background as HTML color code. - * - * @option {char} orient - * Rendering orientation either vertical or horizontal - * - * @option {string} [pdb3DIcon='biojs/css/images/3d.png'] - * Image URL to be used as 3D structure's icon - * - * @example - * var instance = new Biojs.PDBLogos({ - * target: "YourOwnDivId", - * identifier: "1cbs" - * }); - * - */ -Biojs.PDBLogos = Biojs.extend ( -/** @lends Biojs.PDBLogos# */ -{ - /** - * Default values for the options - * @name Biojs.PDBLogos-opt - */ - opt: { - target: "YourOwnDivId", - raphael: null, - identifier:"", - startX: 10, - startY: 10, - interval: 10, - size: 40, - orient: 'h', - logosURL: 'http://www.ebi.ac.uk/pdbe-apps/widgets/pdbprints', - logos: [], - color: "#588FE5", - pdb3DIcon: 'biojs/css/images/3d.png' - }, - - /** - * Array containing the supported event names - * @name Biojs.PDBLogos-eventTypes - */ - eventTypes : [ - /** - * @name Biojs.PDBLogos#onClick - * @event - * @param {function} actionPerformed A function which receives an {@link Biojs.Event} object as argument. - * @eventData {Object} source The component which did triggered the event. - * @eventData {string} type The name of the event. - * @eventData {string} identifier PDB actual entry. - * @eventData {string} category Name of the PDBLogo category clicked. - * @eventData {string} printsUrl Url of the PDB general information. - * @example - * instance.onClick( - * function( e ) { - * alert("Logo " + e.category + " of PDB " + e.identifier + " was clicked."); - * } - * ); - * - * */ - "onClick" - ], - - constructor: function (options) { - this._initCanvas(); - if( !Biojs.Utils.isEmpty(this.opt.identifier) ) { - this._doRequest(this.opt.identifier); - } - }, - - _initCanvas: function() { - var config = this.opt; - - // Make Raphael object if not provided already - if ( !Biojs.Utils.isEmpty( config.raphael ) ){ - config.raphael.remove(); - config.raphael = null; - } - - var sizex = config.startX + config.size * Biojs.PDBLogos.CATEGORY.lenght; - var sizey = config.startY + (config.interval+config.size); - - if(config.orient == Biojs.PDBLogos.VERTICAL) { - sizey = config.startY + config.size * Biojs.PDBLogos.CATEGORY.lenght; - sizex = config.startX + (config.interval+config.size); - } - config.raphael = Raphael(config.target, sizex, sizey); - }, - - /** - * Sets the pdb identifier generating a new request of logos. - * - * @param {string} value PDB entry. - * - * @example - * instance.setIdentifier("1j3s"); - * - */ - setIdentifier: function ( value ) { - this.opt.identifier = value; - this._initCanvas(); - this._doRequest(value); - }, - - _doRequest: function(identifier){ - - var self = this; - - jQuery.ajax({ - url: 'http://www.ebi.ac.uk/pdbe-apps/widgets/pdbprints', - data: { 'varname':'printsdata', 'pdbid': identifier, color: "transparent" }, - dataType: 'script', - crossDomain: 'true', - type: 'GET', - success: function(response, callOptions) { self._printsLayout(printsdata); } - }); - }, - - - _printsLayout: function(data) { - var self = this; - var config = this.opt; - var ix = config.startX; - var iy = config.startY; - var i=0; - - config.logos = []; - - data[config.identifier].PDBStructure = [ config.pdb3DIcon, 'structure']; - - for( category in Biojs.PDBLogos.CATEGORY ) { - - var isizeY = config.size, isizeX = config.size; - var imgUrl = data[config.identifier][category][0]; - var printsURL = "http://www.pdbe.org"; - - ix = config.startX; - iy = config.startY; - - if( config.orient == Biojs.PDBLogos.VERTICAL ) { - iy += config.size * (i++); - } else { - ix += config.size * (i++); - } - - if(category == "PDBeLogo") { - config.logos.push( - config.raphael.text(ix, iy + self.opt.size/4, config.identifier) - .attr({ - 'font-family':'Mono', - 'text-anchor':'start', - 'font-size': self.opt.size/3, - 'cursor':'pointer', - 'title':'View all about PDB ' + config.identifier - }) - .data("identifier", config.identifier) - .mouseup( function() { - window.open( "http://www.pdbe.org/" + this.data("identifier") ); - }) - ); - - imgUrl = "http://www.ebi.ac.uk/pdbe-apps/widgets/html/PDBeWatermark_horizontal_128.png"; - isizeX = config.size * 0.9; - isizeY = config.size/2; - iy += config.size/2; - - } else { - - printsURL += "/"+config.identifier+"/" + Biojs.PDBLogos.CATEGORY[category]; - - if ( category == "PDBStructure" ) { - printsURL = "http://www.ebi.ac.uk/pdbe-srv/view/entry/" + config.identifier + "/openastex"; - } - - // Add icon background - config.raphael.rect(ix, iy, isizeX, isizeY, 7).attr({'fill':self.opt.color}); - } - - config.logos.push( - config.raphael.image(imgUrl, ix, iy, isizeX, isizeY) - .attr({ - 'cursor':'pointer', - 'title':'View '+category - }) - .data({ - "printsURL": printsURL, - "category": category - }) - .mouseup( function() { - self.raiseEvent( Biojs.PDBLogos.EVT_ON_CLICK, { - printsURL: this.data("printsURL"), - identifier: config.identifier, - category: this.data("category") - }); - }) - .mouseover( function() { } ) - ); - - } - - } - -},{ - HORIZONTAL: 'h', - VERTICAL: 'v', - - CATEGORY: { - "PDBeLogo": "", - "PrimaryCitation": "citation", - "Taxonomy": "taxonomy", - "Expressed": "taxonomy", - "Experimental": "experimental", - "Protein": "primary", - "NucleicAcid": "primary", - "Ligands": "ligands", - "PDBStructure": "PDBStructure" - }, - - EVT_ON_CLICK: "onClick" - -}); \ No newline at end of file diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.PDBprints.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.PDBprints.js deleted file mode 100755 index 5b38cc36dd..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.PDBprints.js +++ /dev/null @@ -1,187 +0,0 @@ -/** - * This is the description of the PDBprints component. This component renders a set of icons to give a quick summary of salient features of a PDB entry. - * See more info on PDBprints at http://pdbe.org/prints - * - * @class - * @extends Biojs - * - * @author Swanand Gore - * @version 1.0.0 - * @category 0 - * - * @requires Raphael 2.1.0 - * @dependency - * - * @requires jQuery Core 1.6.4 - * @dependency - * - * @param {Object} options An object with the options for PDBprints component. - * - * @option {list} targets - * This is a list of configuration options, each corresponding to PDBprints to be rendered in a div. - * Each config consists of following: - *
-
- *
- pdbids: PDB entry ids for which prints are to be rendered. - *
- divid: the id of div in which the prints are to be rendered. - *
- rapha: A Raphael object instead of div to render PDBprints into. - *
- startX: X-coordinate of point where rendering the array of PDBprints will start in the Raphael canvas - *
- startY: Y-coordinate of point point where rendering the array of PDBprints will start in the Raphael canvas - *
- interval: gap between successive PDBprints in a vertical or horizontal array - *
- size: length of an icon logo in PDBprints - *
- orient: vertical or horizontal rendering fo PDBprints - *
Display:
' + - ' Hydrophylic residues' + - ' Hydrophobic residues
' + - ' Basic(+) residues
' + - ' Acidic(-) residues
' + - ' Antialias
'+ - ' Black background
'+ - ' Rotation'+ - - '
Style:
'+ - - 'Color:
'+ - - 'Surface:
'+ - - 'Show selection using:
' + - ' Translucent ' + - ' Halos') - - .change( function ( e ) { - - var targetId = jQuery(e.target).attr('id'); - - switch ( targetId ) { - case "polarCheck": - self.displayPolar( undefined, e.target.checked ); - break; - case "unpolarCheck": - self.displayUnPolar( undefined, e.target.checked ); - break; - case "positiveCheck": - self.displayPositive( undefined, e.target.checked ); - break; - case "negativeCheck": - self.displayNegative( undefined, e.target.checked ); - break; - case "antialiasCheck": - self.displayAntialias( event.target.checked ); - break; - case "rotationCheck": - self.rotate( event.target.checked ); - break; - case "backgroundCheck": - self.changeBackgroundColor( "black", e.target ); - break; - case "styleSelect": - self.displayStyle( e.target.value ); - break; - case "colorSelect": - self.displayColorScheme( e.target.value ); - break; - case "surfaceSelect": - self.displaySurface( e.target.value ); - break; - case "translucentRadio": - self.setHalosVisible(false); - break; - case "halosRadio": - self.setHalosVisible(true); - break; - default: - ; - } - - }); - - this._controlsReady = true; - - Biojs.console.log("_buildControls done"); - }, - - _controlsAreVisible: function () { - return this._controlsContainer.find('.toggle.collapse').is(':visible'); - }, - - _toggleControls: function(){ - - if ( this._controlsAreVisible() ) { - this._controlsContainer.find('.toggle.collapse').click(); - } else { - this._controlsContainer.find('.toggle.expand').click(); - } - }, - - _addControl: function(html){ - this._controlsDiv.append( html ); - }, - - _getDisplayStyle: function ( text ) { - if (text == Biojs.Protein3D.STYLE_CARTOON ) { - - return "hide null; select all; spacefill off; wireframe off; backbone off;" + - " cartoon on; " + - " select ligand; wireframe 0.16;spacefill 0.5; color cpk; " + - " select *.FE; spacefill 0.7; color cpk ; " + - " select *.CU; spacefill 0.7; color cpk ; " + - " select *.ZN; spacefill 0.7; color cpk ; " + - " select all; "; - } - else if (text == Biojs.Protein3D.STYLE_BACKBONE ) { - - return "hide null; select all; spacefill off; wireframe off; backbone 0.4;" + - " cartoon off; " + - " select ligand; wireframe 0.16;spacefill 0.5; color cpk; " + - " select *.FE; spacefill 0.7; color cpk ; " + - " select *.CU; spacefill 0.7; color cpk ; " + - " select *.ZN; spacefill 0.7; color cpk ; " + - " select all; "; - - } else if (text == Biojs.Protein3D.STYLE_CPK ) { - - return "hide null; select all; spacefill off; wireframe off; backbone off;" + - " cartoon off; cpk on;" + - " select ligand; wireframe 0.16;spacefill 0.5; color cpk; " + - " select *.FE; spacefill 0.7; color cpk ; " + - " select *.CU; spacefill 0.7; color cpk ; " + - " select *.ZN; spacefill 0.7; color cpk ; " + - " select all; "; - - } - else if (text == Biojs.Protein3D.STYLE_LIGANDS ) { - return "restrict ligand; cartoon off; wireframe on; display selected;"+ - " select *.FE; spacefill 0.7; color cpk ; " + - " select *.CU; spacefill 0.7; color cpk ; " + - " select *.ZN; spacefill 0.7; color cpk ; " + - " select all; "; - } - - else if (text == Biojs.Protein3D.STYLE_LIGANDS_POCKET ) { - return " select within (6.0, true, ligand); cartoon off; wireframe on; backbone off; display selected; " + - " select *.FE; spacefill 0.7; color cpk ; " + - " select *.CU; spacefill 0.7; color cpk ; " + - " select *.ZN; spacefill 0.7; color cpk ; " + - " select all; "; - } - else if (text == Biojs.Protein3D.STYLE_BALL_STICK ) { - - return "hide null; restrict not water; wireframe 0.2; spacefill 25%;" + - " cartoon off; backbone off; " + - " select ligand; wireframe 0.16; spacefill 0.5; color cpk; " + - " select *.FE; spacefill 0.7; color cpk ; " + - " select *.CU; spacefill 0.7; color cpk ; " + - " select *.ZN; spacefill 0.7; color cpk ; " + - " select all; "; - - } else { - return undefined; - } - }, - - _getDisplayColor: function ( text ) { - if ( text == Biojs.Protein3D.COLOR_BY_CHAIN ) { - return "hide null; select all; cartoon on; wireframe off; spacefill off; color chain; select ligand; wireframe 0.16; spacefill 0.5; color chain ; select all; "; - } - else if ( text == Biojs.Protein3D.COLOR_BY_TEMPERATURE ) { - return "hide null; select all;spacefill off; wireframe off; backbone 0.4; cartoon off; set defaultColors Jmol; color relativeTemperature; color cartoon relateiveTemperature select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " ; - } - else if ( text == Biojs.Protein3D.COLOR_RAINBOW ){ - return "hide null; select all; set defaultColors Jmol; color group; color cartoon group; select ligand;wireframe 0.16;spacefill 0.5; color cpk ; select all; " ; - } - else if ( text == Biojs.Protein3D.COLOR_SECONDARY_STRUCTURE ){ - return "hide null; select all; set defaultColors Jmol; color structure; color cartoon structure;select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " ; - } - else if ( text == Biojs.Protein3D.COLOR_BY_ELEMENT ){ - return "hide null; select all; set defaultColors Jmol; color cpk; color cartoon cpk; select ligand;wireframe 0.16; spacefill 0.5; color cpk ; select all; " ; - } - else if ( text == Biojs.Protein3D.COLOR_BY_AMINO_ACID ){ - return "hide null; select all; set defaultColors Jmol; color amino; color cartoon amino; select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " ; - } - else if ( text == Biojs.Protein3D.COLOR_HIDROPHOBICITY ){ - return "hide null; set defaultColors Jmol; select hydrophobic; color red; color cartoon red; select not hydrophobic ; color blue ; color cartoon blue; select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " ; - } else { - return undefined; - } - }, - - _getDisplaySurface: function ( text ) { - if ( text == Biojs.Protein3D.SURFACE_NONE ){ - return "select all; isosurface off; select none;"; - } - else if ( text == Biojs.Protein3D.SURFACE_ACCESSIBLE ){ - return "select all; isosurface sasurface 1.2; color isoSurface translucent 0.8; select none;"; - } - else if ( text == Biojs.Protein3D.SURFACE_EXCLUDED ){ - return "select all; isosurface solvent 1.2; color isoSurface translucent 0.8; select none;"; - } - else if ( text == Biojs.Protein3D.SURFACE_CAVITIES ){ - return "select all; isosurface cavity 1.2 10; color isoSurface translucent 0.8; select none;"; - } else { - return undefined; - } - }, - - toString: function() { - return "Biojs.Protein3D"; - }, - /* - * Function: Biojs.Protein3D._functionCbName - * Purpose: enable controls an triggers the loading pdb file event. - * It is invoked by JmolApplet. - * Returns: - - * Inputs: - * appletId -> {string} Applet identifier. - * url -> {string} URL of the loaded file (full path+filename). - * file -> {string} the filename of the loaded file (without the path). - * title -> {string} the internal title of the model in the loaded file. - * message -> {string} any error messages generated. - * code -> {int} A numeric code: - * 3 when the file loaded successfully, - * 0 when the model was zapped, - * -1 when the loading failed. - * formerFrame -> {string} a text string with the frame - * number prior to loading the current model, in file.model syntax - * (for example, "3.1" or "1.1 - 3.31" if a whole range of models was framed). - * frame -> {string} A text string with the last frame number after loading the current model, - * in file.model syntax. - */ - _loadStructCallback: function ( appletId, url, file, title, message, code, formerFrame, frame ) { - - Biojs.console.log("executing _loadStructCallback for " + appletId); - - switch (code) { - case 3 : result = 'success'; break; - case 0 : result = 'zapped'; break; - case -1 : result = 'failure'; break; - default : result = 'undefined'; break; - } - - // Ignore the execution of the callback on replacing pdb file. - if ( "zapped" != result ) { - var instanceId = parseInt( appletId.replace("jmolApplet",'') ); - var instance = Biojs.getInstance(instanceId); - - if ( "success" == result ) { - instance.showControls(); - instance.displayAntialias(instance.opt.antialias); - instance.rotate(instance.opt.rotate); - } - - instance.raiseEvent(Biojs.Protein3D.EVT_ON_PDB_LOADED, { - "file": title, - "result": result, - "message": message - }); - - } - - } - - -},{ - // - // Coloring Schemes - // - COLOR_BY_CHAIN: "By Chain", - COLOR_SECONDARY_STRUCTURE: "Secondary Structure", - COLOR_RAINBOW: "Rainbow", - COLOR_BY_ELEMENT: "By Element", - COLOR_BY_AMINO_ACID: "By Amino Acid", - COLOR_BY_TEMPERATURE: "By Temperature", - COLOR_HIDROPHOBICITY: "Hidrophobicity", - // - // Surfaces - // - SURFACE_NONE: "None", - SURFACE_ACCESSIBLE: "Solvent Accessible", - SURFACE_EXCLUDED: "Solvent Excluded", - SURFACE_CAVITIES: "Cavities", - // - // Drawing Style - // - STYLE_CARTOON: "Cartoon", - STYLE_BACKBONE: "Backbone", - STYLE_CPK: "CPK", - STYLE_BALL_STICK: "Ball and Stick", - STYLE_LIGANDS: "Ligands", - STYLE_LIGANDS_POCKET: "Ligands and Pocket", - // - // Events - // - EVT_ON_PDB_LOADED: "onPdbLoaded", - EVT_ON_SELECTION: "onSelection" -}); diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DCanvas.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DCanvas.js deleted file mode 100755 index 0a2b4ac465..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DCanvas.js +++ /dev/null @@ -1,289 +0,0 @@ -/** - * Pdb file 3D viewer component using JSMol and Canvas HTML5 technology if available (downgrade to Applet technology otherwise). - * - * - * @class - * @extends Biojs.Protein3D - * - * @author Francesco Talo - * @version 1.0.0 - * @category 3 - * - * @requires jQuery Core 1.8.2 (not necessaty if you import the JSmol.min.js) - * @dependency - * - * @requires jsMol 14.0.2 - * @dependency - * - * @requires jsMol 14.0.2 (use this if you import separately jQuery) - * @dependency - - * - * - * @requires jsMol 14.0.2 (use this if you don't import already jQuery in your application) - * @dependency - * - * - * - * @requires Protein3D CSS - * @dependency - * - * @param {Object} options An object with the options for Biojs.Protein3DCanvas component. - * - * @option {string} target - * Identifier of the DIV tag where the component should be displayed. - * - * @option {int} [width=597] - * Width in pixels. - * - * @option {int} [height=400] - * Height in pixels. - * - * @option {string} [jsmolFolder="{BIOJS_HOME}/dependencies/jmol-12.0.48"] - * Relative path of the jSMol library. - - * @option {string} [use="HTML5 JAVA"] - * This string determines the various options to be tried (HTML5, Java Applet and surrogates) and the order in which to try them. - * The default setting is HTML5 CANVAS and then Java if Canvas is not available. - * - * @option {string} [urlProxy="{BIOJS_HOME}/dependencies/jsmol-14.0.2/jsmol/proxy/jsmol.jsp"] - * Path of the proxy to use for transformation of the gzip file in base64 files for MSIE and CHROME. - * - * @option {string} [loadingStatusImage="{BIOJS_HOME}/css/images/ajax-loader-1.gif"] - * Relative path of the image to be displayed on loading status. - * - * @option {string} [unpolarColor="salmon"] - * This value is used by displayUnpolar() method for coloring hydrophobic residues. - * - * @option {string} [negativeColor="red"] - * This value is used by displayNegative() method for coloring acidic(-) residues. - * - * @option {string} [positiveColor="blue"] - * This value is used by displayNegative() method for coloring basic(+) residues. - * - * @option {string} [polarColor="yellow"] - * This value is used by displayNegative() method for coloring hydrophylic residues. - * - * @option {string} [backgroundColor="white"] - * Background color of the jMol applet - * - * @option {bool} [enableControls=true] - * Enable for showing the control panel. If value is 'false', it disables both methods showControls and hideControls. - - @option {bool} [viewControls=true] - * Show/Hide controls panel after the loading of the PDB structure. - * - * - * @example - * // Example of loading a pdb file by means of an HTTP request to get the zip file - * // 'http://www.rcsb.org/pdb/files/"+pdb+".pdb.gz' containing the structure of the protein. - * //The file id downloaded form the server as a zipped file and then it's unzipped on the client - * var instance = new Biojs.Protein3DCanvas({ - * target: "YourOwnDivId", - * jsmolFolder: '/bioJs/dependencies/jsmol-14.0.2/jsmol', - * height: 440, - * width: 440, - * style: Biojs.Protein3D.STYLE_CARTOON, - * use:"HTML5 JAVA", - * urlProxy:"/bioJs/dependencies/jsmol-14.0.2/jsmol/proxy/jsmol.jsp", - * viewControls: true - * }); - * instance.onPdbLoaded( - * function( objEvent ) { - * alert('PDB LOADED'); - * } - * ); - * //trigger to download the zip file containing the pdb structure from the server and unzip the file on the client - * instance.setPdb('2al6'); - * - * - */ -Biojs.Protein3DCanvas = Biojs.Protein3D.extend( -/** @lends Biojs.Protein3DCanvas# */ -{ - constructor: function (options) { - - this.opt.jmolFolder= this.opt.jsmolFolder; - Biojs.Protein3D.call(this, options); - - //JMol configuraion - if ( this.opt.use == undefined ) { - Jmol.Info["use"] = "HTML5 JAVA"; - - }else{ - Jmol.Info["use"] = this.opt.use; - } - - - if ( this.opt.proxyUrl != undefined ) { - Jmol.Info["serverURL"] = this.opt.proxyUrl; - } - - Jmol.Info["jarPath"] = this.opt.jsmolFolder+"/java", - Jmol.Info["jarFile"] = this.opt.jsmolFolder+"/java/JmolApplet0.jar", - Jmol.Info["j2sPath"] = this.opt.jsmolFolder+"/j2s"; - - Jmol.Info["addSelectionOptions"]= false; - Jmol.Info["color"]= "#ffffff"; - Jmol.Info["debug"]= false; - Jmol.Info["memoryLimit"]= 512; // Java only - Jmol.Info["readyFunction"]= null; - Jmol.Info["src"]= null; - Jmol.Info["disableInitialConsole"]=true; - Jmol.Info["disableJ2SLoadMonitor"]= true; - Jmol.Info["deferUncover"]=true; - Jmol.Info["deferApplet"]= false; - }, - - /** - * Default options (and its values) for the Protein3DCanvas component. - * @name Biojs.Protein3DCanvas-opt - * @type Object - */ - opt: - { - use: "HTML5 JAVA", - jsmolFolder: "../biojs/dependencies/jsmol-14.0.2/jsmol", - viewControls: true - }, - - /** - * Array containing the supported event names - * @name Biojs.Protein3DCanvas-eventTypes - */ - eventTypes : [], - - /** - * Sets the pdb file to be displayed. - * Also triggers the event whenever a new pdb file is loaded. - * It demands entirely to JSMol the download from the server and unzip of of the PDB file on the browser - * - * @param The pdb id to use to download the gz file from the server http://www.rcsb.org/pdb/files/"+pdb+".pdb.gz. - * - * @example - * var instance = new Biojs.Protein3DCanvas({ - * target: "YourOwnDivId", - * jsmolFolder: '/bioJs/dependencies/jsmol-14.0.2/jsmol', - * height: 440, - * width: 440, - * style: Biojs.Protein3D.STYLE_CARTOON, - * use:"HTML5 JAVA", - urlProxy:"/bioJs/dependencies/jsmol-14.0.2/jsmol/proxy/jsmol.jsp", - viewControls: true - * }); - * - * instance.onPdbLoaded( - * function( objEvent ) { - * alert('PDB LOADED'); - * } - * ); - * - * //trigger the downloading of the zip containing the pdb file from the server and unzip the file on the client - * instance.setPdb('2al6'); - * - * - */ - setPdb: function( pdb ){ - Biojs.console.log("LOADING pdb content"); - - var self = this; - - var surfaceCmd = this._getDisplaySurface( this.opt.surface ); - var styleCmd = this._getDisplayStyle( this.opt.style ); - var colorSchemeCmd = this._getDisplayColor( this.opt.colorScheme ); - - var scr = colorSchemeCmd + styleCmd + surfaceCmd + this._getSelectionScript( this._selection ); - - this.showLoadingImage(true); - - if ( this._jmolAppletInitialized ) { - this.reset(); - } - Jmol.setDocument(0); - htmlContent = jmolApplet([self._appletContainer.width(), self._appletContainer.height()], " load 'http://www.rcsb.org/pdb/files/"+pdb+".pdb.gz';"+ scr, self.getId()); - - this._appletContainer.html(Jmol.getAppletHtml(eval(htmlContent._id))); - - this._jmolAppletInitialized = true; - - Biojs.console.log("setPdb() ending"); - }, - - toString: function() { - return "Biojs.Protein3DCanvas"; - }, - - /* - * Function: Biojs.Protein3D._functionCbName - * Purpose: enable controls an triggers the loading pdb file event. - * It is invoked by JmolApplet. - * Returns: - - * Inputs: - * appletId -> {string} Applet identifier. - * url -> {string} URL of the loaded file (full path+filename). - * file -> {string} the filename of the loaded file (without the path). - * title -> {string} the internal title of the model in the loaded file. - * message -> {string} any error messages generated. - * code -> {int} A numeric code: - * 3 when the file loaded successfully, - * 0 when the model was zapped, - * -1 when the loading failed. - * formerFrame -> {string} a text string with the frame - * number prior to loading the current model, in file.model syntax - * (for example, "3.1" or "1.1 - 3.31" if a whole range of models was framed). - * frame -> {string} A text string with the last frame number after loading the current model, - * in file.model syntax. - */ - - _loadStructCallback: function ( appletId, url, file, title, message, code, formerFrame, frame ) { - -Biojs.console.log("executing _loadStructCallback for " + appletId); - - switch (code) { - case 3 : result = 'success'; break; - case 0 : result = 'zapped'; break; - case -1 : result = 'failure'; break; - default : result = 'undefined'; break; - } - - // Ignore the execution of the callback on replacing pdb file. - - if ( "zapped" != result ) { - //uncover the loading image - var instanceId = parseInt( appletId.replace("jmolApplet",'') ); - var instance = Biojs.getInstance(instanceId); - - if ( "success" == result ) { - instance.displayAntialias(instance.opt.antialias); - instance.rotate(instance.opt.rotate); - } - - instance.showLoadingImage(false); - if (instance.opt.viewControls){ - instance.showControls(); - instance._controlsContainer.css('display','block'); - jmolResizeApplet([ instance._container.width() - instance._controlsContainer.outerWidth(), instance._container.height()], instance.getId()); - instance._appletContainer.css('float','right'); - - }else{ - instance.hideControls(); - instance._controlsContainer.css('display','none'); - jmolResizeApplet([ instance._container.width(), instance._container.height()], instance.getId()); - instance._appletContainer.css('float','left'); - } - - instance.raiseEvent(Biojs.Protein3D.EVT_ON_PDB_LOADED, { - "file": title, - "result": result, - "message": message - }); - - instance._appletContainer.css('display','block'); - - - } - - - } - -}); diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DUniprot.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DUniprot.js deleted file mode 100755 index 5a261c5035..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DUniprot.js +++ /dev/null @@ -1,582 +0,0 @@ -/** - * - * Protein viewer to show the pdb files aligned to an Uniprot Accession - * - * @class - * @extends Biojs.Protein3DWS - * - * @author John Gomez - * @version 1.0.0 - * @category 2 - * - * @param {Object} options An object with the options for the component. - * - * @option {string} [proteinId] - * Uniprot identifier of the protein. - * - * @option {string} [mapping=Biojs.Protein3DUniprot.ALIGNMENTS_UNIPROT_MAPPING] - * Mapping function to obtain the protein's alignments: - *-
- *
- Biojs.Protein3DUniprot.ALIGNMENTS_UNIPROT_MAPPING - *
- Biojs.Protein3DUniprot.ALIGNMENTS_PDBe_MAPPING - *
Structures for ' + self.opt.proteinId + '
' + ''); - jQuery('#' + self.opt.target + ' #pdbFile_select').val(pdb); - jQuery('#' + self.opt.target + ' #pdbFile_select').change(function() { - self._onAlignmentSelectionChange(); - }); - jQuery('#' + self.opt.target).find('#pdbStructures').show(); - var alignmentId = pdb; - var pdbId = alignmentId.substring(0, pdb.indexOf('.')).toLowerCase(); - var alignment = self.getAlignmentsByPdb(alignmentId); - if (alignment.hasOwnProperty(alignmentId)) { - var start = alignment[alignmentId][1].start; - var end = alignment[alignmentId][1].end; - self.raiseEvent('onPdbSelected', {"pdbId": pdbId,"alignmentId": alignmentId,"start": start,"end": end}); - } - self._alignmentsJustArrived = false; - } - }); - - if (this.opt.proteinId != undefined) { - var proteinId = this.opt.proteinId; - this.opt.proteinId = ''; - this.setProtein(proteinId); - } - }, - - opt: { - proteinId: undefined, - mapping: 'http://www.ebi.ac.uk/pdbe-apps/widgets/unipdb?uniprot=', - proxyUrl: '../biojs/dependencies/proxy/proxy.php' - }, - - eventTypes : [ - /** - * @name Biojs.Protein3DUniprot#onPdbSelected - * @event - * @param {function} actionPerformed An function which receives an {@link Biojs.Event} object as argument. - * @eventData {Object} source The component which did triggered the event. - * @eventData {string} pdbId The name of the loaded file. - * @eventData {string} alignmentId Alignment identifier. - * @eventData {string} start Starting base index. - * @eventData {string} end Ending base index. - * - * @example - * instance.onPdbSelected( - * function( e ) { - * alert( "Alignment " + e.alignmentId + " selected. Start: " + e.start + " End: " + e.end ); - * } - * ); - * - * */ - "onPdbSelected" - ], - - _aligments: undefined, - - - /** - * Get all pdb files for a given uniprot id. - * Also triggers the event that a new pdb file was loaded. - * - * @option {string} proteinId Uniprot identifier of the protein. - * - * @example - * instance.setProtein("P99999"); - * - */ - setProtein: function(proteinId){ - if (proteinId != this.opt.proteinId) { - this.opt.proteinId = proteinId; - this._selection = undefined; - this._minStart = Number.MAX_VALUE; - this._maxEnd = 0; - this._alignments = undefined; - - if ( this.opt.mapping == Biojs.Protein3DUniprot.ALIGNMENTS_UNIPROT_MAPPING ) { - this._requestAligmentsFromUniprot(); - } else if ( this.opt.mapping == Biojs.Protein3DUniprot.ALIGNMENTS_PDBe_MAPPING ) { - this._requestAligmentsFromPdbe(); - } else { - throw "Error in mapping function. this.opt.mapping="+this.opt.mapping; - } - } - }, - - // makes an ajax request to get the pdb files for the given uniprot id - _requestAligmentsFromUniprot: function(){ - var self = this; - jQuery.ajax({ - url: self.opt.mapping + self.opt.proteinId, - data: {biojsmapping:'1', varname:'pdbmappings'}, - dataType: "script", - crossDomain: true, - success: function(){ - Biojs.console.log("SUCCESS: data received"); - self._alignments = pdbmappings; - //change proteinId to the one retrieved from pdbmappings (in case it is a protein id rather than an accession) - //Warning: Here we suppose that position [0] always give the info for the pdb and position [1] always give the info for the accession - for (obj in pdbmappings) { - if ( pdbmappings[obj][1].intObjectId != self.opt.proteinId ) { - self.opt.proteinId = pdbmappings[obj][1].intObjectId; - } - break; - } - self._aligmentsArrived(); - }, - async: false, - error: function(qXHR, textStatus, errorThrown){ - Biojs.console.log("ERROR: requesting "+this.data); - self.raiseEvent('onRequestError', {message: textStatus}); - } - }); - }, - - // makes an ajax request to get the pdb files for the given uniprot id - _requestAligmentsFromPdbe: function(){ - var self = this; - - jQuery.ajax({ - url: self.opt.proxyUrl, - dataType: "text", - data: { url: self.opt.mapping + self.opt.proteinId + '/'}, - success: function(data){ - Biojs.console.log("SUCCESS: data received"); - self._parseResponse(data); - }, - async: false, - error: function(qXHR, textStatus, errorThrown){ - Biojs.console.log("ERROR: requesting "+this.data); - self.raiseEvent('onRequestError', { message: textStatus}); - } - }); - }, - - // parses the xml file from the request and stores the information in an easy to access way - _parseResponse: function (text) { - this._alignments = {}; - var i = 0; - var self = this; - var data; - - Biojs.console.log("Decoding " + text); - - if ( !Biojs.Utils.isEmpty(text) ) { - - try { - data = jQuery.parseJSON(text); - - } catch (e) { - Biojs.console.log("Error decoding response: " + e.message ); - } - - for ( var i in data ) { - - try { - var segments = []; - - segments.push({ - "start": data[i].pdb_range[0], - "end": data[i].pdb_range[1], - "intObjectId": data[i].pdbid + '.' + data[i].chain } ); - - segments.push({ - "start": data[i].uniprot_range[0], - "end": data[i].uniprot_range[1], - "intObjectId": data[i].uniprot_acc } ); - - self._alignments[ segments[0].intObjectId ] = segments; - - if (self._minStart > segment[1].start) { - self._minStart = segment[1].start; - } - - if (self._maxEnd < segment[1].end) { - self._maxEnd = segment[1].end; - } - - } catch (e) { - Biojs.console.log("Error decoding alignment: " + e.message ); - } - } - } - - Biojs.console.log("Alignments decoded:"); - Biojs.console.log(self._alignments); - this._aligmentsArrived(); - }, - - // adds all available pdb files to a dropdown box - // or displays the fact that there are no pdb files for the given id - _aligmentsArrived: function(){ - - this._alignmentsJustArrived = true; - - var alignments = this._filterAligmentsBySelection(this._selection); - - if (!Biojs.Utils.isEmpty(alignments)) { - var pdb = undefined; - for (pdb in alignments) { - break; - } - - Biojs.console.log("Requesting pdb " + pdb); - this.requestPdb(pdb.substring(0, pdb.indexOf('.')).toLowerCase()); - - } else { - this._container.html("No structural information for " + this.opt.proteinId ); - this.raiseEvent('onRequestError', { message: "No structural information available for " + this.opt.proteinId }); - } - }, - - _onAlignmentSelectionChange: function(){ - var pdb = jQuery('#pdbFile_select').val(); - - if ( pdb != undefined ) { - - var alignmentId = pdb.substring(0, pdb.indexOf(' ')); - var pdbId = alignmentId.substring(0, pdb.indexOf('.')).toLowerCase(); - - var alignment = this.getAlignmentsByPdb(alignmentId); - - if ( alignment.hasOwnProperty( alignmentId ) ) { - var start = alignment[alignmentId][1].start; - var end = alignment[alignmentId][1].end; - - this.raiseEvent('onPdbSelected', { - "pdbId": pdbId, - "alignmentId": alignmentId, - "start": start, - "end": end - }); - } - - this.requestPdb(pdbId); - - } else { - Biojs.console.log("No structural information available for "+this.opt.proteinId); - } - }, - - /** - * Request and display a pdb file by means of its identifier. - * - * @param {string} pdbId Pdb file identifier. - * - * @example - * instance.requestPdb('3t6f'); - * - */ - requestPdb: function(pdbId) { - var self = this; - - self.showLoadingImage(); - self.opt.id = pdbId; - - jQuery.ajax({ - url: self.opt.proxyUrl, - data: 'url='+self.opt.pdbUrl+'/pdb'+pdbId+'.ent', - dataType: 'text', - success: function (pdbContent) { - Biojs.console.log("DATA ARRIVED"); - //reset the PDB selected area if a uniprot selection has been made already - if (self._uniprotSelection != undefined) { - self._selection = self._translateSelection(self._uniprotSelection); - } - self.setPdb(pdbContent); - }, - error: function(qXHR, textStatus, errorThrown){ - self.raiseEvent('onRequestError', {message: textStatus}); - } - }); - }, - - - /** - * Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region). - * - * @example - * // Selection of the region in the interval [100,150]. - * instance.setSelection({start: 120, end: 150}); - * - * @example - * // Get the alignments matching with bases 4, 8 and 100. - * alert ( instance.filterAlignments([4,8,100]) ); - * - * @param {Object|Array} selection Can be either a plain object or an array. - * If object, it must have the fields start and end; Where "start" is greater than or equal to "end". - * If array, it must contain numbers representing the positions to be selected. - */ - getAlignmentsBySelection: function ( selection ) { - - var alignments = this._alignments; - - if ( selection != undefined ) { - this._filterAligmentsBySelection(selection); - } - - return alignments; - }, - - /** - * Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region). - * - * @example - * // Get the alignments matching with bases 4, 8 and 100. - * alert ( instance.getAlignmentsByPdb("2F73") ); - * - * @param {string} pdb identifier. - * @returns {Object} . - * - */ - getAlignmentsByPdb: function ( pdbId ) { - - var alignments = {}; - - for (al in this._alignments) { - if ( this._alignments[al][0].intObjectId.indexOf( pdbId ) != -1 ) { - alignments[this._alignments[al][0].intObjectId] = this._alignments[al]; - } - } - - Biojs.console.log("Alignments for pdb " + pdbId ); - Biojs.console.log(alignments); - - return alignments; - }, - - /** - * Filters the alignments available for the current protein: Only PDB files containing a part of the requested region - * are selectable. The specified region is highlighted in the displayed PDB file. - * - * @example - * // Selection of the region in the interval [100,150]. - * instance.filterAlignments({start: 120, end: 150}); - * - * @param {Object|Array} selection Can be either a plain object or an array. - * If object, it must have the fields start and end; Where "start" is greater than or equal to "end". - * If array, it must contain numbers representing the positions to be selected. - */ - filterAlignments: function ( selection ) { - - var alignments = this._filterAligmentsBySelection(selection); - var selectedAlignment = jQuery('#pdbFile_select').val(); - - // Update the drop-down box showing the filtered alignments - jQuery('#pdbFile_select').html(this._createOptions(alignments)); - - // Select an alignment - if ( alignments.hasOwnProperty( selectedAlignment.slice(0,selectedAlignment.indexOf(' '))) ) { - // Select current alignment if it belongs to filtered alignments - jQuery('#pdbFile_select').val(selectedAlignment); - - } else { - // Select any alignment - for ( a in alignments ){ - jQuery('#pdbFile_select').val(a); - break; - } - this._onAlignmentSelectionChange(); - } - - // invoke setSelection on the parent - this.base(selection); - }, - - _createOptions: function(alignments) { - var pdbOptions = ""; - for (pdb in alignments) { - text = pdb + " (" + alignments[pdb][1].start + ".." + alignments[pdb][1].end + ")"; - pdbOptions += ''; - } - Biojs.console.log("_createOptions: " + pdbOptions); - return pdbOptions; - }, - - _filterAligmentsBySelection: function(selection) { - var alignments = undefined; - if (selection instanceof Array) { - alignments = {}; - for (al in this._alignments) { - var uniprot = this._alignments[al][1]; - for (i in selection) { - if (selection[i] >= uniprot.start && selection[i] <= uniprot.end) { - alignments[this._alignments[al][0].intObjectId] = this._alignments[al]; - break; - } - } - } - } else if (selection instanceof Object) { - alignments = {}; - var i = 0; - for (al in this._alignments) { - var uniprot = this._alignments[al][1]; - if ((selection.start >= uniprot.start && selection.start <= uniprot.end) || (selection.end >= uniprot.start && selection.end <= uniprot.end) || (selection.start < uniprot.start && selection.end > uniprot.end)) { - alignments[this._alignments[al][0].intObjectId] = this._alignments[al]; - i++; - } - } - } else { - alignments = this._alignments; - } - Biojs.console.log("Filtered alignments:"); - Biojs.console.log(alignments); - return alignments; - }, - - /** - * Selection of a region using the uniprot positions. - * - * @example - * // Selection of the region in the interval [100,150]. - * instance.setSelection({start: 100, end: 150}); - * - * @example - * // Selection of the positions 4, 8 and 100. - * instance.setSelection([4,8,100]); - * - * @param {Object|Array} selection Can be either a plain object or an array. - * If object, it must have the fields start and end; Where "start" is greater than or equal to "end". - * If array, it must contain numbers representing the positions to be selected. - */ - setSelection: function ( s ) { - this._uniprotSelection = Biojs.Utils.clone(s); - var selection = this._translateSelection(s); - this.base(selection); - }, - - _translateSelection: function (s) { - //Selection in Uniprot regions needs to be translated into PDB regions - var selection = Biojs.Utils.clone(s); - var alignmentId = this.getCurrentAlignmentId(); - var proteinId = this.getCurrentProteinId(); - var segment = this.getAlignmentsByPdb(alignmentId)[alignmentId]; - var offset = 0; - for ( i in segment ) { - if ( segment[i].intObjectId == alignmentId ) { - pdbSegment = segment[i]; - } else if ( segment[i].intObjectId == proteinId ) { - uniprotSegment = segment[i]; - } - } - offset = uniprotSegment.start - pdbSegment.start; - if ( selection instanceof Array ) { - var toDelete = new Array(selection.length); - for ( i in selection ) { - if (selection[i] instanceof Object) {//a range - if ( (selection[i].start > uniprotSegment.end) || (selection[i].end < uniprotSegment.start) ){ - //we first check whether it is completely out of the range - selection[i].start = 0; - selection[i].end = 0; - toDelete[i] = true; - } else if ( (selection[i].start >= uniprotSegment.start) && (selection[i].end <= uniprotSegment.end) ){ - selection.start -= offset; - selection.end -= offset; - toDelete[i] = false; - } else if ( (selection[i].start < uniprotSegment.start) && (selection[i].end <= uniprotSegment.end) ){ - selection[i].start = pdbSegment.start - 0; - selection[i].end -= offset; - toDelete[i] = false; - } else if ( (selection[i].start >= uniprotSegment.start) && (selection[i].end > uniprotSegment.end) ){ - selection[i].start -= offset; - selection[i].end = pdbSegment.end - 0; - toDelete[i] = false; - } else if ( (selection[i].start < uniprotSegment.start) && (selection[i].end > uniprotSegment.end) ){ - selection[i].start = pdbSegment.start - 0 - selection[i].end = pdbSegment.end - 0; - toDelete[i] = false; - } - } else { //a position - if ( (uniprotSegment.start <= selection[i]) && (selection[i] <= uniprotSegment.end) ) { - selection[i] -= offset; - toDelete[i] = false; - } else { - toDelete[i] = true; - } - } - } - var deleted = 0; - for (j in toDelete) { - if (toDelete[j] == true) { - selection.splice(j-deleted,j-deleted); - deleted += 1; - } - } - } else if ( selection instanceof Object && selection.start <= selection.end ){ - if ( (selection.start > uniprotSegment.end) || (selection.end < uniprotSegment.start) ){ - //we first check whether it is completely out of the range - selection.start = 0; - selection.end = 0; - this.removeSelection(); - } else if ( (selection.start >= uniprotSegment.start) && (selection.end <= uniprotSegment.end) ){ - selection.start -= offset; - selection.end -= offset; - } else if ( (selection.start < uniprotSegment.start) && (selection.end <= uniprotSegment.end) ){ - selection.start = pdbSegment.start - 0; - selection.end -= offset; - } else if ( (selection.start >= uniprotSegment.start) && (selection.end > uniprotSegment.end) ){ - selection.start -= offset; - selection.end = pdbSegment.end - 0; - } else if ( (selection.start < uniprotSegment.start) && (selection.end > uniprotSegment.end) ){ - selection.start = pdbSegment.start - 0 - selection.end = pdbSegment.end - 0; - } - } - return (selection); - }, - - getCurrentAlignmentId: function () { - var selectedValue = jQuery('#pdbFile_select').val(); - var alignmentId = selectedValue.substring(0, selectedValue.indexOf(' ')); - //var pdbId = alignmentId.substring(0, pdb.indexOf('.')).toLowerCase(); - return alignmentId; - }, - - getCurrentProteinId: function () { - return this.opt.proteinId; - }, - - /** - * Removes selection in the current displayed structure. - * - * @example - * instance.removeSelection(); - */ - removeSelection: function() { - this.base(); - } -}, { - - // Mapping services - ALIGNMENTS_UNIPROT_MAPPING: 'http://www.ebi.ac.uk/pdbe-apps/widgets/unipdb?uniprot=', - ALIGNMENTS_PDBe_MAPPING: 'http://wwwdev.ebi.ac.uk/pdbe-apps/jsonizer/mappings/best/all/' - -}); diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DWS.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DWS.js deleted file mode 100755 index 48746b433c..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.Protein3DWS.js +++ /dev/null @@ -1,106 +0,0 @@ -/** - * - * Extension of the pdb file viewer getting data from a web service - * - * @class - * @extends Biojs.Protein3D - * - * @author John Gomez - * @version 1.0.0 - * @category 2 - * - * @requires Server side proxy - * - * @param {Object} options An object with the options for the component. - * - * @option {string} [pdbUrl="http://www.ebi.ac.uk/pdbe/entry-files"] - * Url of the web service in order to require the pdb file. - * - * @option {string} [id] - * Identifier of the pdb to be displayed (i.e. '3nuc' to require 3nuc.pdb file). You can load another pbd by using requestPdb method. - * - * @option {string} [proxyUrl="../biojs/dependencies/proxy/proxy.php"] - * Server side proxy server. - * - * @example - * - * var instance = new Biojs.Protein3DWS({ - * target: 'YourOwnDivId', - * id: '3nuc' - * }); - * - * - */ -Biojs.Protein3DWS = Biojs.Protein3D.extend( -/** @lends Biojs.Protein3DWS# */ -{ - constructor: function(options){ - this.base(options); - //constructor of Biojs.Protein3DWS - if (this.opt.id !== undefined) { - this.requestPdb(this.opt.id); - } - }, - - opt: { - id: undefined, - pdbUrl: 'http://www.ebi.ac.uk/pdbe/entry-files', - proxyUrl: '../biojs/dependencies/proxy/proxy.php' - }, - - eventTypes : [ - /** - * @name Biojs.Protein3DWS#onRequestError - * @event - * @param {function} actionPerformed An function which receives an {@link Biojs.Event} object as argument. - * @eventData {Object} source The component which did triggered the event. - * @eventData {string} file The name of the loaded file. - * @eventData {string} result A string with either value 'success' or 'failure'. - * @eventData {string} message Error message in case of result be 'failure'. - * - * @example - * instance.onRequestError( - * function( e ) { - * alert( e.message ); - * } - * ); - * - * */ - "onRequestError" - ], - - /** - * Request and display a pdb file by means of its identifier. - * - * @param {string} pdbId Pdb file identifier. - * - * @example - * instance.requestPdb('3t6f'); - * - */ - requestPdb: function(pdbId) { - var self = this; - - self.showLoadingImage(); - self.opt.id = pdbId; - - jQuery.ajax({ - url: self.opt.proxyUrl, - data: 'url='+self.opt.pdbUrl+'/pdb'+pdbId+'.ent', - dataType: 'text', - success: function (pdbContent) { - Biojs.console.log("DATA ARRIVED"); - self.setPdb(pdbContent); - }, - error: function(qXHR, textStatus, errorThrown){ - self.raiseEvent('onRequestError', {message: textStatus}); - } - }); - }, - - getPdbId: function(pdb) { - return opt.id; - } - - -}); \ No newline at end of file diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.ProteinPortafolio.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.ProteinPortafolio.js deleted file mode 100755 index 1d7e978ff9..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.ProteinPortafolio.js +++ /dev/null @@ -1,522 +0,0 @@ -/** - * ProteinPortafolio component shows the description of a protein as well as its PDB alignments if there is any. - * Component shows the PDBLogos of the selected alignment and ables to play with the sequence and - * the 3D draw of the alignment. - * - * @class - * @extends Biojs - * - * @author John Gomez - * @version 1.0.0 - * @category 3 - * - * @requires jQuery Core 1.6.4 - * @dependency - * - * @requires Raphael 2.1.0 - * @dependency - * - * @requires PDBLogos - * @dependency - * - * @requires Sequence - * @dependency - * - * @requires Protein3DWS - * @dependency - * @dependency - * - * @requires jMol 12.0.48 - * @dependency - * - * @requires Protein3D CSS - * @dependency - * - * @requires ProteinPortafolio CSS - * @dependency - * - * @param {Object} options An object with the options for ProteinPortafolio component. - * - * @option {string} target - * Identifier of the DIV tag where the component should be displayed. - * - * @option {string} [fontFamily='"Andale mono", courier, monospace'] - * Font list to be applied to the component content. - * - * @option {string} [fontColor="white"] - * HTML color code for the font. - * - * @option {string} [backgroundColor="#7BBFE9"] - * Background color for the entire div content. - * - * @option {Object} [selectionFontColor="white"] - * This color will be used to change the font color of selected text. - * - * @option {Object} [ selectionBackgroundColor="yellow"] - * This color will be used to change the background of selected text. - * - * @option {string} [pdb3DIcon='../biojs/css/images/3d.png'] - * The only PDB icon is able to defines the 3D structure. - * Set source URL for 3D icon - * - * @example - * var instance = new Biojs.ProteinPortafolio({ - * target : "YourOwnDivId", - * accession : 'P99999' - * }); - * - */ -Biojs.ProteinPortafolio = Biojs.extend ( -/** @lends Biojs.ProteinPortafolio# */ -{ - constructor: function (options) { - // In JavaScript "this" always refers to the owner of the function we're executing (http://www.quirksmode.org/js/this.html) - // Let's preserve the reference to 'this' through the variable self. In this way, we can invoke/execute - // our component instead of the object where 'this' is being invoked/executed. - var self = this; - - Biojs.console.enable(); - - // For practical use, create an object with the main DIV container - // to be used in all of the code of our component - this._container = jQuery("#"+self.opt.target); - - this._initialize(); - - if ( !Biojs.Utils.isEmpty( options.accession ) ) { - this.setProtein(options.accession); - } - - }, - - /** - * Default values for the options - * @name Biojs.ProteinPortafolio-opt - */ - opt: { - target: "YourOwnDivId", - accession: "", - mappingUrl: 'http://www.ebi.ac.uk/pdbe-apps/widgets/unipdb?uniprot=', - featuresUrl: 'http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot-summary/features', - proxyUrl: '../biojs/dependencies/proxy/proxy.php', - jmolFolder: '../biojs/dependencies/jmol-12.0.48', - pdb3DIcon: '../biojs/css/images/3d.png', - pdbIconSize: 40 - }, - - /** - * Array containing the supported event names - * @name Biojs.ProteinPortafolio-eventTypes - */ - eventTypes : [ - /** - * @name Biojs.ProteinPortafolio#onClick - * @event - * @param {function} actionPerformed A function which receives an {@link Biojs.Event} object as argument. - * @eventData {Object} source The component which did triggered the event. - * @eventData {string} type The name of the event. - * @eventData {int} selected Selected character. - * @example - * instance.onClick( - * function( objEvent ) { - * alert("The character " + objEvent.selected + " was clicked."); - * } - * ); - * - * */ - "onClick", - - /** - * @name Biojs.ProteinPortafolio#onPdbSelected - * @event - * @param {function} actionPerformed A function which receives an {@link Biojs.Event} object as argument. - * @eventData {Object} source The component which did triggered the event. - * @eventData {string} alignmentId Identifier . - * @eventData {string} pdbId Selected pdb entry. - * @eventData {int} start Start position of the alignment. - * @eventData {int} end End position of the alignment. - * @example - * instance.onPdbSelected( - * function( e ) { - * alert("Selected " + e.alignmentId + " alignment."); - * } - * ); - * - * */ - "onPdbSelected" - ], - - /** - * Change the font size. Do nothing it no value is provided. - * - * @param {string} [size] The new font size in pixels. - * - * @example - * instance.setSize("72px"); - */ - setSize: function(size) { - - }, - - _initialize: function() { - - this._alpha = jQuery('').appendTo( this._container ); - this._beta = jQuery('').appendTo( this._container ); - - this._header = jQuery('').appendTo( this._alpha ); - this._toolbar = jQuery('').appendTo( this._alpha ); - this._content = jQuery('').appendTo( this._alpha ); - - this._content.attr('id', 'ProteinPortafolio_content_' + this.getId() ); - - this._container.addClass('ProteinPortafolio'); - }, - - _clearAll: function () { - this._header.children().remove(); - this._toolbar.children().remove(); - this._content.children().remove(); - }, - - /** - * Sets the protein accession which changes everything to reflect the new protein information - * - * @param {string} accession The new protein identifier - * - * @example - * instance.setProtein("P07148"); - * - * @example - * instance.setProtein("P12345"); - */ - setProtein: function( accession ) { - - this.opt.accession = accession; - - this._requestAligments(accession, function(alignments){ - - this._alignments = alignments; - - this._container.removeClass('loading'); - - if (!Biojs.Utils.isEmpty(alignments)) { - // Alignments found - this._setHeader( this.opt.accession, this._createPDBSelect(alignments) ); - - } else { - // none alignment found - this._setHeader( this.opt.accession ); - } - }); - - this._showFeatures(accession); - }, - - _requestAligments: function( accession, action ){ - var self = this; - - this._clearAll(); - this._container.addClass('loading'); - - var xhr = jQuery.ajax({ - url: self.opt.mappingUrl + accession, - data: {biojsmapping:'1', varname:'pdbmappings'}, - dataType: "script", - crossDomain: true, - timeout: 5000, - success: function(){ - Biojs.console.log("SUCCESS: data received"); - self._alignments = pdbmappings; - action.call(self,pdbmappings); - }, - async: true, - error: function(qXHR, textStatus, errorThrown){ - Biojs.console.log("ERROR: " + textStatus ); - self.raiseEvent('onRequestError', {message: textStatus}); - action.call(self,{}); - } - }); - }, - - _createPDBSelect: function(alignments) { - var pdbOptions = ""; - for (pdb in alignments) { - text = pdb + " (" + alignments[pdb][1].start + ".." + alignments[pdb][1].end + ")"; - pdbOptions += ''; - } - Biojs.console.log("_createOptions: " + pdbOptions); - return pdbOptions; - }, - - _setHeader: function( accession, mappingsSelector ) { - var self = this; - - if ( mappingsSelector !== undefined ) { - this._header.html("Accession: "+ accession + ", PDB Alignments: " ); - this._onAlignmentSelectionChange(); - this._header.children('select').change( function(){ self._onAlignmentSelectionChange() }); - } else { - this._header.html("Accession: "+ accession + ", No PDB alignments found." ); - } - - this._adjustContentSize(); - - }, - - _onAlignmentSelectionChange: function(){ - - var alignment = this.getCurrentAlignment(); - - if ( !Biojs.Utils.isEmpty(alignment) ) { - - this.raiseEvent('onPdbSelected', { - "pdbId": alignment.pdbId, - "alignmentId": alignment.alignmentId, - "start": alignment.start, - "end": alignment.end - }); - - this._showPDBPrints(alignment.pdbId); - this._showImage(alignment.pdbId); - this._showFeatures(this.opt.accession); - - } else { - Biojs.console.log("No structural information available for " + this.opt.accession ); - } - }, - - _showPDBPrints: function(pdbId) { - - var self = this; - this._toolbar.children().remove(); - this._toolbar.attr('id', 'PDBLogos_toolbar_' + this.getId() ); - - var myprints = new Biojs.PDBLogos({ - target: this._toolbar.attr('id'), - identifier: pdbId, - size: self.opt.pdbIconSize, - pdb3DIcon: self.opt.pdb3DIcon - }); - - myprints.onClick( function(e) { - if ( e.category == "PDBStructure" ) { - self._showProtein3D(); - } else { - window.open( e.printsURL ); - } - }); - - this._adjustContentSize(); - }, - - /** - * Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region). - * - * @example - * // Get the alignments matching with bases 4, 8 and 100. - * alert ( instance.getAlignmentsByPdb("2F73") ); - * - * @param {string} pdb identifier. - * @returns {Object} . - * - */ - getAlignmentsByPdb: function ( pdbId ) { - - var alignments = {}; - - for (al in this._alignments) { - if ( this._alignments[al][0].intObjectId.indexOf( pdbId ) != -1 ) { - alignments[this._alignments[al][0].intObjectId] = this._alignments[al]; - } - } - - Biojs.console.log("Alignments for pdb " + pdbId ); - Biojs.console.log(alignments); - - return alignments; - }, - - getCurrentAlignment: function(){ - - var result = {}; - var pdbSelectedValue = this._header.find('select').val(); - - if ( pdbSelectedValue != undefined ) { - - result.accession = this.opt.accession; - result.alignmentId = pdbSelectedValue.substring(0, pdbSelectedValue.indexOf(' ')); - result.pdbId = pdbSelectedValue.substring(0, pdbSelectedValue.indexOf('.')).toLowerCase(); - - - var alignment = this.getAlignmentsByPdb(result.alignmentId); - - result.start = alignment[result.alignmentId][1].start; - result.end = alignment[result.alignmentId][1].end; - result.offset = 0; - - if ( alignment.hasOwnProperty( result.alignmentId ) ) { - result.offset = result.start - alignment[result.alignmentId][0].start; - } - - result.alignment = alignment; - } - - Biojs.console.log("Current alignment"); - Biojs.console.log(result); - - return result; - }, - - _showProtein3D: function( ){ - - var self = this; - var alignment = this.getCurrentAlignment(); - var height = this._container.height() - this._header.height() - this._toolbar.height(); - - self._content.children().remove(); - self._beta.children().remove(); - - self._beta.attr('id','biojs_protein3D_' + self._content.attr('id') ); - - // Calculate character width - var test = jQuery("X").appendTo(self._content); - var columns = Math.round( self._content.width() * (1/test.width()) ); - test.remove(); - - var sequence = new Biojs.Sequence({ - target : self._content.attr('id'), - format : 'FASTA', - id : alignment.accession, - formatSelectorVisible: false, - columns: { size: columns, spacedEach: 10 } - }); - - var proteinStructure = new Biojs.Protein3DWS({ - id: alignment.pdbId, - target: self._beta.attr('id'), - width: Math.round( self._beta.width() ), - height: self._container.height(), - proxyUrl: self.opt.proxyUrl, - jmolFolder: self.opt.jmolFolder - }); - - sequence.onSelectionChange( function (e) { - // [e.start, e.end] from the event data corresponds to the protein sequence positions - // which need to be aligned with PDB structure - var selection = {start: e.start, end: e.end}; - - selection.start -= alignment.offset; - selection.end -= alignment.offset; - - proteinStructure.setSelection( selection ); - }); - - }, - - _showSequence: function( accession ){ - - var self = this; - - this._content.children().remove(); - - var sequence = new Biojs.Sequence({ - target : this._content.attr('id'), - format : 'FASTA', - id : accession, - formatSelectorVisible: false, - columns: { size: Math.round( self._content.width()/20 ), spacedEach: 10 } - }); - }, - - _showImage: function( pdbId ){ - - this._beta.children().remove(); - - var img = jQuery('
')
- .appendTo(this._beta)
- .addClass('crop');
-
- },
-
- _showFeatures: function( accession ) {
-
- var self = this;
-
- this._content.children().remove();
- this._adjustContentSize();
-
- this._requestFeatures( accession, function(xml){
-
- Biojs.console.log("Features received " + xml );
-
- var xmlDoc = "";
-
- try {
- xmlDoc = jQuery.parseXML( xml );
- } catch (e) {
- Biojs.console.log("XML parser error" + e);
- }
-
- var features = jQuery('')); - var imgUrl = this.opt.chebiImgUrl + chebiId - + '&dimensions=' + this.opt.dimensions; - $('#'+compDivId).append(jQuery('
{
- "location": [ "Some part of the page" ],
- "action": ["Action 1", "Action 2", "Action 3" ],
- "target": [ {
- "name": "First Target",
- "conditions": [ {
- "name": "Select from",
- "type": "selects",
- "amount": 1,
- "values": ["An Option","another option" ]
- }, {
- "name": "number",
- "type": "numeric_comparison"
- }, {
- "name": "some text",
- "type": "text_comparison"
- } ]
- } ]
-}
- *
- * @example
- * var instance = new Biojs.Ruler({
- * target: "YourOwnDivId",
- * allowOrdering:true,
- * rules:{
- * "location": [
- * "all proteins",
- * "protein1",
- * "protein2",
- * "protein3",
- * "protein4"
- * ],
- * "target": [
- * {
- * "name": "Proteins",
- * "action": [
- * {name:"Show",type:"single"},
- * {name:"Hide",type:"single"},
- * {name:"Highlight",type:"single"},
- * {name:"Color",type:"color"},
- * {name:"Color Range",type:"colorRange"},
- * {name:"Show Label",type:"select",options:["ID","Functional Class","Organism","Gene Name"]}
- * ],
- * "conditions": [
- * {
- * "name": "interactions with",
- * "type": "selects",
- * "amount": 1,
- * "values": [
- * "protein1",
- * "protein2",
- * "protein3",
- * "protein4"
- * ]
- * },
- * {
- * "name": "number of interactions",
- * "type": "numeric_comparison"
- * },
- * {
- * "name": "accession number",
- * "type": "text_comparison"
- * }
- * ]
- * },
- * {
- * "name": "Interactions",
- * "action": [
- * {name:"Show",type:"single"},
- * {name:"Hide",type:"single"},
- * {name:"Highlight",type:"single"},
- * {name:"Color",type:"color"},
- * ],
- * "conditions": [
- * {
- * "name": "protein",
- * "type": "selects",
- * "amount": 1,
- * "values": [
- * "protein1",
- * "protein2",
- * "protein3",
- * "protein4"
- * ]
- * },
- * {
- * "name": "proteins",
- * "type": "selects",
- * "amount": 2,
- * "values": [
- * "protein1",
- * "protein2",
- * "protein3",
- * "protein4"
- * ]
- * },
- * {
- * "name": "score",
- * "type": "numeric_comparison"
- * }
- * ]
- * }
- * ]
- * }
- * });
- *
- */
-Biojs.Ruler = Biojs.extend (
-/** @lends Biojs.Ruler# */
-{
- _number: 1,
- constructor: function (options) {
- var self=this;
- var target =self.opt.target;
- var innerCode = ' - ';
- innerCode +='
- ';
- innerCode +='
| '; - var gotRule =!(typeof rule=="undefined"); - var selectedTarget=0; - - if (typeof self.opt.rules.location !='undefined' && self.opt.rules.location.length>0){ - code_rule+= "In"; - code_rule+= self._getSelect('location_'+number,self.opt.rules.location,"", - gotRule?rule.location:rule - ); - } - - if (gotRule) - for (var i in self.opt.rules.target) - if (self.opt.rules.target[i].name==rule.target) - selectedTarget=i; - - code_rule+= ' '+ self._getActionSpan(number,selectedTarget,rule)+''; - code_rule+= ' the '; - code_rule+= self._getSelect('target_'+number,self.opt.rules.target,"name", - gotRule?rule.target:rule - ); - code_rule+= ' with '; - - var visible=gotRule?"none":"inline"; - for (var i in self.opt.rules.target){ - visible=gotRule? - ((self.opt.rules.target[i].name==rule.target)?"inline":"none"): - visible; - code_rule+= self._getConditionsSpan(number,self.opt.rules.target[i],visible,rule); - visible="none"; - } - code_rule+= ' | '; - code_rule+= 'APPLY | '; - code_rule+= '
| '+rule.action.name+' '+parameter_span+' the '+rule.target+' with '+rule.condition+' '+rule.parameters.join(" ")+' | remove edit | 0 |
- * [
- * // Highlight aminoacids from 'start' to 'end' of the current strand using the specified 'color' (optional) and 'background' (optional).
- * { start: <startVal1>, end: <endVal1> [, id:<idVal1>] [, color: <HTMLColor>] [, background: <HTMLColor>]},
- * //
- * // Any others highlights
- * ...,
- * //
- * { start: <startValN>, end: <endValN> [, id:<idValN>] [, color: <HTMLColor>] [, background: <HTMLColor>]}
- * ]
- *
- *
- * highlights : [
- * { start:30, end:42, color:"white", background:"green", id:"spin1" },
- * { start:139, end:140 },
- * { start:631, end:633, color:"white", background:"blue" }
- * ]
- *
- *
- * @option {Object} [columns={size:40,spacedEach:10}]
- * Options for displaying the columns. Syntax: { size: <numCols>, spacedEach: <numCols>}
- *
- * @option {Object} [selection]
- * Positions for the current selected region. Syntax: { start: <startValue>, end: <endValue>}
- *
- * @option {Object[]} [annotations]
- * Set of overlapping annotations. Must be an array of objects following the syntax:
- *
- * [
- * // An annotation:
- * { name: <name>,
- * html: <message>,
- * color: <color_code>,
- * regions: [{ start: <startVal1>, end: <endVal1> color: <HTMLColor>}, ...,{ start: <startValN>, end: <endValN>, color: <HTMLColor>}]
- * },
- *
- * // ...
- * // more annotations here
- * // ...
- * ]
- *
- * where:
- * -
- *
- name is the unique name for the annotation - *
- html is the message (can be HTML) to be displayed in the tool tip. - *
- color is the default HTML color code for all the regions. - *
- regions array of objects defining the intervals which belongs to the annotation. - *
- regions[i].start is the starting character for the i-th interval. - *
- regions[i].end is the ending character for the i-th interval. - *
- regions[i].color is an optional color for the i-th interval. - *
- * formatOptions : {
- * title:false,
- * footer:false
- * }
- *
- *
- * @example
- * var theSequence = "METLCQRLNVCQDKILTHYENDSTDLRDHIDYWKHMRLECAIYYKAREMGFKHINHQVVPTLAVSKNKALQAIELQLTLETIYNSQYSNEKWTLQDVSLEVYLTAPTGCIKKHGYTVEVQFDGDICNTMHYTNWTHIYICEEAojs SVTVVEGQVDYYGLYYVHEGIRTYFVQFKDDAEKYSKNKVWEVHAGGQVILCPTSVFSSNEVSSPEIIRQHLANHPAATHTKAVALGTEETQTTIQRPRSEPDTGNPCHTTKLLHRDSVDSAPILTAFNSSHKGRINCNSNTTPIVHLKGDANTLKCLRYRFKKHCTLYTAVSSTWHWTGHNVKHKSAIVTLTYDSEWQRDQFLSQVKIPKTITVSTGFMSI";
- * var mySequence = new Biojs.Sequence({
- * sequence : theSequence,
- * target : "YourOwnDivId",
- * format : 'CODATA',
- * id : 'P918283',
- * annotations: [
- * { name:"CATH",
- * color:"#F0F020",
- * html: "Using color code #F0F020 ",
- * regions: [{start: 122, end: 135}]
- * },
- * { name:"TEST",
- * html:"<br> Example of <b>HTML</b>",
- * color:"green",
- * regions: [
- * {start: 285, end: 292},
- * {start: 293, end: 314, color: "#2E4988"}]
- * }
- * ],
- * highlights : [
- * { start:30, end:42, color:"white", background:"green", id:"spin1" },
- * { start:139, end:140 },
- * { start:631, end:633, color:"white", background:"blue" }
- * ]
- * });
- *
- */
-
-Biojs.Sequence = Biojs.extend(
-/** @lends Biojs.Sequence# */
-{
- constructor: function (options) {
- var self = this;
-
- this._container = jQuery( "#" + this.opt.target );
-
- // Lazy initialization
- this._container.ready(function() {
- self._initialize();
- });
- },
-
- /**
- * Default values for the options
- * @name Biojs.Sequence-opt
- */
- opt : {
-
- sequence : "",
- id : "",
- target : "",
- format : "FASTA",
- selection: { start: 0, end: 0 },
- columns: { size: 35, spacedEach: 10 },
- highlights : [],
- annotations: [],
- sequenceUrl: 'http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence',
-
- // Styles
- selectionColor : 'Yellow',
- selectionFontColor : 'black',
- highlightFontColor : 'red',
- highlightBackgroundColor : 'white',
- fontFamily: '"Andale mono", courier, monospace',
- fontSize: '12px',
- fontColor : 'inherit',
- backgroundColor : 'inherit',
- width: undefined,
- height: undefined,
- formatSelectorVisible: true
- },
-
- /**
- * Array containing the supported event names
- * @name Biojs.Sequence-eventTypes
- */
- eventTypes : [
- /**
- * @name Biojs.Sequence#onSelectionChanged
- * @event
- * @param {function} actionPerformed An function which receives an {@link Biojs.Event} object as argument.
- * @eventData {Object} source The component which did triggered the event.
- * @eventData {string} type The name of the event.
- * @eventData {int} start A number indicating the start of the selection.
- * @eventData {int} end A number indicating the ending of selection.
- * @example
- * mySequence.onSelectionChanged(
- * function( objEvent ) {
- * alert("Selected: " + objEvent.start + ", " + objEvent.end );
- * }
- * );
- *
- * */
- "onSelectionChanged",
-
- /**
- * @name Biojs.Sequence#onSelectionChange
- * @event
- * @param {function} actionPerformed An function which receives an {@link Biojs.Event} object as argument.
- * @eventData {Object} source The component which did triggered the event.
- * @eventData {string} type The name of the event.
- * @eventData {int} start A number indicating the start of the selection.
- * @eventData {int} end A number indicating the ending of selection.
- * @example
- * mySequence.onSelectionChange(
- * function( objEvent ) {
- * alert("Selection in progress: " + objEvent.start + ", " + objEvent.end );
- * }
- * );
- *
- *
- * */
- "onSelectionChange",
-
- /**
- * @name Biojs.Sequence#onAnnotationClicked
- * @event
- * @param {function} actionPerformed An function which receives an {@link Biojs.Event} object as argument.
- * @eventData {Object} source The component which did triggered the event.
- * @eventData {string} type The name of the event.
- * @eventData {string} name The name of the selected annotation.
- * @eventData {int} pos A number indicating the position of the selected amino acid.
- * @example
- * mySequence.onAnnotationClicked(
- * function( objEvent ) {
- * alert("Clicked " + objEvent.name + " on position " + objEvent.pos );
- * }
- * );
- *
- * */
- "onAnnotationClicked"
- ],
-
- // internal members
- _headerDiv : null,
- _contentDiv : null,
-
- // Methods
-
- _initialize: function () {
-
- if ( this.opt.width !== undefined ) {
- this._container.width( this.opt.width );
- }
-
- if ( this.opt.height !== undefined ) {
- this._container.height( this.opt.height );
- }
-
- // Disable text selection
-
- this._container.css({
- '-moz-user-select':'none',
- '-webkit-user-select':'none',
- 'user-select':'none'
- });
-
- // DIV for the format selector
- this._buildFormatSelector();
-
- // DIV for the sequence
- this._contentDiv = jQuery('').appendTo(this._container);
- this._contentDiv.css({
- 'font-family': this.opt.fontFamily,
- 'font-size': this.opt.fontSize,
- 'text-align': 'left'
- });
-
- // Initialize highlighting
- this._highlights = this.opt.highlights;
-
- // Initialize annotations
- this._annotations = this.opt.annotations;
-
- //Initialize tooltip
- jQuery('')
- .css({
- 'position': "absolute",
- 'z-index': "999999",
- 'color': "#fff",
- 'font-size': "12px",
- 'width': "auto",
- 'display': 'none'
- })
- .addClass("tooltip")
- .appendTo("body")
- .hide();
-
- if ( ! Biojs.Utils.isEmpty(this.opt.sequence) ) {
- this._redraw();
-
- } else if ( ! Biojs.Utils.isEmpty(this.opt.id) ) {
- this._requestSequence( this.opt.id );
-
- } else {
- this.clearSequence("No sequence available", "../biojs/css/images/warning_icon.png");
- }
-
- },
-
-
- /**
- * Shows the columns indicated by the indexes array.
- * @param {string} seq The sequence strand.
- * @param {string} [identifier] Sequence identifier.
- *
- * @example
- * mySequence.setSequence("P99999");
- *
- */
- setSequence: function ( seq, identifier ) {
-
- if ( seq.match(/^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$/i) ) {
- this._requestSequence( arguments[0] );
-
- } else {
- this.opt.sequence = seq;
- this.opt.id = identifier;
- this._highlights = [];
- this._highlightsCount = 0;
- this.opt.selection = { start: 0, end: 0 };
- this._annotations = [];
-
- this._contentDiv.children().remove();
- this._redraw();
- }
- },
-
- _requestSequence: function ( accession ) {
- var self = this;
-
- Biojs.console.log("Requesting sequence for: " + accession );
-
- jQuery.ajax({
- url: self.opt.sequenceUrl,
- dataType: "xml",
- data: { segment: accession },
- success: function ( xml ) {
- try {
-
- var sequenceNode = jQuery(xml).find('SEQUENCE:first');
- self.setSequence( sequenceNode.text(), sequenceNode.attr("id"), sequenceNode.attr("label") );
-
- } catch (e) {
- Biojs.console.log("Error decoding response data: " + e.message );
- self.clearSequence("No sequence available", "../biojs/css/images/warning_icon.png");
- }
-
- },
- error: function (jqXHR, textStatus, errorThrown) {
- Biojs.console.log("Error decoding response data: " + textStatus );
- self.clearSequence("Error requesting the sequence to the server " + this.url , "../biojs/css/images/warning_icon.png");
- }
- });
- },
-
- /**
- * Shows the columns indicated by the indexes array.
- * @param {string} [showMessage] Message to be showed.
- * @param {string} [icon] Icon to be showed a side of the message
- *
- * @example
- * mySequence.clearSequence("No sequence available", "../biojs/css/images/warning_icon.png");
- *
- */
- clearSequence: function ( showMessage, icon ) {
-
- var message = undefined;
-
- this.opt.sequence = "";
- this.opt.id = "";
- this._highlights = [];
- this._highlightsCount = 0;
- this.opt.selection = { start: 0, end: 0 };
- this._annotations = [];
- this._contentDiv.children().remove();
-
- this._headerDiv.hide();
-
- if ( undefined !== showMessage ) {
- message = jQuery('' + showMessage + '
')
- .appendTo(this._contentDiv)
- .addClass("message");
-
- if ( undefined !== icon ) {
- message.css({
- 'background': 'transparent url("' + icon + '") no-repeat center left',
- 'padding-left': '20px'
- });
- }
- }
- },
-
- /**
- * Set the current selection in the sequence causing the event {@link Biojs.Sequence#onSelectionChanged}
- *
- * @example
- * // set selection from the position 100 to 150
- * mySequence.setSelection(100, 150);
- *
- * @param {int} start The starting character of the selection.
- * @param {int} end The ending character of the selection
- */
- setSelection : function(start, end) {
- if(start > end) {
- var aux = end;
- end = start;
- start = aux;
-
- }
-
- if(start != this.opt.selection.start || end != this.opt.selection.end) {
- this._setSelection(start, end);
- this.raiseEvent(
- Biojs.Sequence.EVT_ON_SELECTION_CHANGED,
- { "start" : start, "end" : end }
- );
- }
- },
-
- _buildFormatSelector: function () {
- var self = this;
-
- this._headerDiv = jQuery('').appendTo(this._container);
- this._headerDiv.css({
- 'font-family': '"Heveltica Neue", Arial, "sans serif"',
- 'font-size': '14px'
- }).append('Format: ');
-
- this._formatSelector = jQuery('').appendTo(self._headerDiv);
-
- this._formatSelector.change(function(e) {
- self.opt.format = jQuery(this).val();
- self._redraw();
- });
-
- this._formatSelector.val(self.opt.format);
-
- this.formatSelectorVisible( this.opt.formatSelectorVisible );
- },
-
- /**
- * Highlights a region using the font color defined in {Biojs.Protein3D#highlightFontColor} by default is red.
- *
- * @deprecated use addHighlight instead.
- *
- * @param {int} start The starting character of the highlighting.
- * @param {int} end The ending character of the highlighting.
- * @param {string} [color] HTML color code.
- * @param {string} [background] HTML color code.
- * @param {string} [id] Custom identifier.
- *
- * @return {int} representing the id of the highlight on the internal array. Returns -1 on failure
- */
- highlight : function (start, end, color, background, id ) {
- return this.addHighlight({ "start": start, "end": end, "color": color, "background": background, "id": id });
- },
-
- /**
- * Highlights a region using the font color defined in {Biojs.Sequence#highlightFontColor} by default is red.
- *
- * @example
- * // highlight the characters within the position 100 to 150, included.
- * mySequence.addHighlight( { "start": 100, "end": 150, "color": "white", "background": "red", "id": "aaa" } );
- *
- * @param {Object} h The highlight defined as follows:
- *
- *
- * @return {int} representing the id of the highlight on the internal array. Returns -1 on failure
- */
- addHighlight : function ( h ) {
- var id = '-1';
- var color = "";
- var background = "";
- var highlight = {};
-
- if ( h instanceof Object && h.start <= h.end ) {
-
- color = ( "string" == typeof h.color )? h.color : this.opt.highlightFontColor;
- background = ( "string" == typeof h.background )? h.background : this.opt.highlightBackgroundColor;
- id = ( "string" == typeof h.id )? h.id : (new Number(this._highlightsCount++)).toString();
-
- highlight = { "start": h.start, "end": h.end, "color": color, "background": background, "id": id };
-
- this._highlights.push(highlight);
- this._applyHighlight(highlight);
- this._restoreSelection(h.start,h.end);
- }
-
- return id;
- },
- /*
- * Function: Biojs.Sequence._applyHighlight
- * Purpose: Apply the specified color and background to a region between 'start' and 'end'.
- * Returns: -
- * Inputs: highlight -> {Object} An object containing the fields start (int), end (int),
- * color (HTML color string) and background (HTML color string).
- */
- _applyHighlight: function ( highlight ) {
- var seq = this._contentDiv.find('.sequence');
- for ( var i = highlight.start - 1; i < highlight.end; i++ ){
- zindex = jQuery(seq[i]).css("z-index");
- if (zindex=="auto"){
- z = 1;
- o = 1;
- }
- else{
- z = 0;
- o = 0.5;
- }
- jQuery(seq[i])
- .css({
- "color": highlight.color,
- "background-color": highlight.background,
- "z-index": z,
- "opacity": o
- })
- .addClass("highlighted");
- }
- },
- /*
- * Function: Biojs.Sequence._applyHighlights
- * Purpose: Apply the specified highlights.
- * Returns: -
- * Inputs: highlights -> {Object[]} An array containing the highlights to be applied.
- */
- _applyHighlights: function ( highlights ) {
- for ( var i in highlights ) {
- this._applyHighlight(highlights[i]);
- }
- },
- /*
- * Function: Biojs.Sequence._restoreHighlights
- * Purpose: Repaint the highlights in the specified region.
- * Returns: -
- * Inputs: start -> {int} Start of the region to be restored.
- * end -> {int} End of the region to be restored.
- */
- _restoreHighlights: function ( start, end ) {
- var h = this._highlights;
- // paint the region using default blank settings
- this._applyHighlight({
- "start": start,
- "end": end,
- "color": this.opt.fontColor,
- "background": this.opt.backgroundColor
- });
- // restore highlights in that region
- for ( var i in h ) {
- // interval intersects with highlight i ?
- if ( !( h[i].start > end || h[i].end < start ) ) {
- a = ( h[i].start < start ) ? start : h[i].start;
- b = ( h[i].end > end ) ? end : h[i].end;
- this._applyHighlight({
- "start": a,
- "end": b,
- "color": h[i].color,
- "background": h[i].background
- });
- }
- }
- },
- /*
- * Function: Biojs.Sequence._restoreSelection
- * Purpose: Repaint the current selection in the specified region.
- * It is used in the case of any highlight do overriding of the current selection.
- * Returns: -
- * Inputs: start -> {int} Start of the region to be restored.
- * end -> {int} End of the region to be restored.
- */
- _restoreSelection: function ( start, end ) {
- var sel = this.opt.selection;
- // interval intersects with current selection ?
- // restore selection
- if ( !( start > sel.end || end < sel.start ) ) {
- a = ( start < sel.start ) ? sel.start : start;
- b = ( end > sel.end ) ? sel.end : end;
-
- this._applyHighlight({
- "start": a,
- "end": b,
- "color": this.opt.selectionFontColor,
- "background": this.opt.selectionColor,
- });
- }
- },
-
- /**
- * Clear a highlighted region using.
- *
- * @deprecated use removeHighlight instead.
- *
- * @param {int} id The id of the highlight on the internal array. This value is returned by method highlight.
- */
- unHighlight : function (id) {
- this.removeHighlight(id);
- },
-
- /**
- * Remove a highlight.
- *
- * @example
- * // Clear the highlighted characters within the position 100 to 150, included.
- * mySequence.removeHighlight("spin1");
- *
- * @param {string} id The id of the highlight on the internal array. This value is returned by method highlight.
- */
- removeHighlight : function (id) {
- var h = this._highlights;
- for ( i in h ) {
- if ( h[i].id == id ) {
- start = h[i].start;
- end = h[i].end;
- h.splice(i,1);
-
- this._restoreHighlights(start,end);
- this._restoreSelection(start,end);
-
- break;
- }
- }
- },
-
- /**
- * Clear the highlights of whole sequence.
- * @deprecated use removeAllHighlights instead.
- */
- unHighlightAll : function () {
- this.removeAllHighlights();
- },
-
- /**
- * Remove all the highlights of whole sequence.
- *
- * @example
- * mySequence.removeAllHighlights();
- */
- removeAllHighlights : function () {
- this._highlights = [];
- this._restoreHighlights(1,this.opt.sequence.length);
- this._restoreSelection(1,this.opt.sequence.length);
- },
-
- /**
- * Changes the current displaying format of the sequence.
- *
- * @example
- * // Set format to 'FASTA'.
- * mySequence.setFormat('FASTA');
- *
- * @param {string} format The format for the sequence to be displayed.
- */
- setFormat : function(format) {
- if ( this.opt.format != format.toUpperCase() ) {
- this.opt.format = format.toUpperCase();
- this._redraw();
- }
-
- var self = this;
- // Changes the option in the combo box
- this._headerDiv.find('option').each(function() {
- if(jQuery(this).val() == self.opt.format.toUpperCase()) {
- jQuery(this).attr('selected', 'selected');
- }
- });
- },
-
- /**
- * Changes the current number of columns in the displayed sequence.
- *
- * @example
- * // Set the number of columns to 70.
- * mySequence.setNumCols(70);
- *
- * @param {int} numCols The number of columns.
- */
- setNumCols : function(numCols) {
- this.opt.columns.size = numCols;
- this._redraw();
- },
-
- /**
- * Set the visibility of the drop-down list of formats.
- *
- * @param {boolean} visible true: show; false: hide.
- */
- formatSelectorVisible : function (visible){
- if (visible) {
- this._headerDiv.show();
- } else {
- this._headerDiv.hide();
- }
- },
-
- /**
- * This is similar to a {Biojs.Protein3D#formatSelectorVisible} with the 'true' argument.
- *
- * @example
- * // Shows the format selector.
- * mySequence.showFormatSelector();
- *
- */
- showFormatSelector : function() {
- this._headerDiv.show();
- },
-
- /**
- * This is similar to a {Biojs.Protein3D#formatSelectorVisible} with the 'false' argument.
- *
- * @example
- * // Hides the format selector.
- * mySequence.hideFormatSelector();
- *
- */
- hideFormatSelector : function() {
- this._headerDiv.hide();
- },
-
- /**
- * Hides the whole component.
- *
- */
- hide : function () {
- this._headerDiv.hide();
- this._contentDiv.hide();
- },
-
- /**
- * Shows the whole component.
- *
- */
- show : function () {
- this._headerDiv.show();
- this._contentDiv.show();
- },
- /*
- * Function: Biojs.Sequence._setSelection
- * Purpose: Update the current selection.
- * Returns: -
- * Inputs: start -> {int} Start of the region to be selected.
- * end -> {int} End of the region to be selected.
- */
- _setSelection : function(start, end) {
- //alert("adsas");
-
- var current = this.opt.selection;
- var change = {};
-
- // Which is the change on selection?
- if ( current.start == start ) {
- // forward?
- if ( current.end < end ) {
- change.start = current.end;
- change.end = end;
- } else {
- this._restoreHighlights(end+1, current.end);
- }
- } else if ( current.end == end ) {
- // forward?
- if ( current.start > start ) {
- change.start = start;
- change.end = current.start;
- } else {
- this._restoreHighlights(current.start, start-1);
- }
- } else {
- this._restoreHighlights(current.start, current.end);
- change.start = start;
- change.end = end;
- }
-
- current.start = start;
- current.end = end;
-
- if ( change.start != undefined ) {
- this._applyHighlight({
- "start": change.start,
- "end": change.end,
- "color": this.opt.selectionFontColor,
- "background": this.opt.selectionColor
- });
- }
-
- },
-
- /*
- * Function: Biojs.Sequence._repaintSelection
- * Purpose: Repaint the whole current selection.
- * Returns: -
- * Inputs: -
- */
- _repaintSelection: function(){
- var s = Biojs.Utils.clone(this.opt.selection);
- this._setSelection(0,0);
- this._setSelection(s.start,s.end);
- },
-
- /*
- * Function: Biojs.Sequence._redraw
- * Purpose: Repaint the current sequence.
- * Returns: -
- * Inputs: -
- */
- _redraw : function() {
- var i = 0;
- var self = this;
-
- // Reset the content
- //this._contentDiv.text('');
- this._contentDiv.children().remove();
-
- // Rebuild the spans of the sequence
- // according to format
- if(this.opt.format == 'RAW') {
- this._drawRaw();
- } else if(this.opt.format == 'CODATA') {
- this._drawCodata();
- } else if (this.opt.format == 'FASTA'){
- this._drawFasta();
- } else {
- this.opt.format = 'PRIDE';
- this._drawPride();
- }
-
- // Restore the highlighted regions
- this._applyHighlights(this._highlights);
- this._repaintSelection();
- this._addSpanEvents();
- },
- /*
- * Function: Biojs.Sequence._drawFasta
- * Purpose: Repaint the current sequence using FASTA format.
- * Returns: -
- * Inputs: -
- */
- _drawFasta : function() {
- var self = this;
- var a = this.opt.sequence.toUpperCase().split('');
- var pre = jQuery('').appendTo(this._contentDiv);
-
- var i = 1;
- var arr = [];
- var str = '>' + this.opt.id + ' ' + a.length + ' bp'; - - /* Correct column size in case the sequence is as small peptide */ - var numCols = this.opt.columns.size; - if ( this.opt.sequence.length < this.opt.columns.size ) { - numCols = this.opt.sequence.length; - } - - var opt = { - numCols: numCols, - numColsForSpace: 0 - }; - - str += this._drawSequence(a, opt); - pre.html(str); - - this._drawAnnotations(opt); - }, - /* - * Function: Biojs.Sequence._drawCodata - * Purpose: Repaint the current sequence using CODATA format. - * Returns: - - * Inputs: - - */ - _drawCodata : function() { - - var self = this; - var a = this.opt.sequence.toUpperCase().split(''); - var pre = jQuery('').appendTo(this._contentDiv); - - var i = 0; - var str = 'ENTRY ' + this.opt.id + '
'; - str += 'SEQUENCE
'; - if ( this.opt.formatOptions !== undefined ){ - if(this.opt.formatOptions.title !== undefined ){ - if (this.opt.formatOptions.title == false) { - str = ''; - } - } - } - - /* Correct column size in case the sequence is as small peptide */ - var numCols = this.opt.columns.size; - if ( this.opt.sequence.length < this.opt.columns.size ) { - numCols = this.opt.sequence.length; - } - - var opt = { - numLeft: true, - numLeftSize: 7, - numLeftPad:' ', - numTop: true, - numTopEach: 5, - numCols: numCols, - numColsForSpace: 0, - spaceBetweenChars: true - }; - - str += this._drawSequence(a, opt); - - var footer = '
///'; - if (this.opt.formatOptions !== undefined) { - if (this.opt.formatOptions.footer !== undefined) { - if (this.opt.formatOptions.footer == false) { - footer = ''; - } - } - } - str += footer; - pre.html(str); - - this._drawAnnotations(opt); - }, - /* - * Function: Biojs.Sequence._drawAnnotations - * Purpose: Paint the annotations on the sequence. - * Returns: - - * Inputs: settings -> {object} - */ - _drawAnnotations: function ( settings ){ - - var self = this; - var a = this.opt.sequence.toLowerCase().split(''); - var annotations = this._annotations; - var leftSpaces = ''; - var row = ''; - var annot = ''; - - // Index at the left? - if ( settings.numLeft ) { - leftSpaces += this._formatIndex(' ', settings.numLeftSize+2, ' '); - } - - for ( var i = 0; i < a.length; i += settings.numCols ){ - row = ''; - for ( var key in annotations ){ - annotations[key].id = this.getId() + "_" + key; - annot = this._getHTMLRowAnnot(i+1, annotations[key], settings); - if (annot.length > 0) { - row += '
'; - row += leftSpaces; - row += annot; - row += '
'; - } - } - - var numCols = settings.numCols; - var charRemaining = a.length-i; - if(charRemaining < numCols){ - numCols = charRemaining; - } - - if ( settings.numRight ) { - jQuery(row).insertAfter('div#'+self.opt.target+' div pre span#numRight_' + this.getId() + '_' + (i + numCols) ); - } else { - jQuery(row).insertAfter('div#'+self.opt.target+' div pre span#'+ this.getId() + '_' + (i + numCols) ); - } - } - - // add tool tips and background' coloring effect - jQuery(this._contentDiv).find('.annotation').each( function(){ - self._addToolTip( this, function() { - return self._getAnnotationString( jQuery(this).attr("id") ); - }); - - jQuery(this).mouseover(function(e) { - jQuery('.annotation.'+jQuery(e.target).attr("id")).each(function(){ - jQuery(this).css("background-color", jQuery(this).attr("color") ); - }); - }).mouseout(function() { - jQuery('.annotation').css("background-color", "transparent"); - - }).click(function(e) { - self.raiseEvent( Biojs.Sequence.EVT_ON_ANNOTATION_CLICKED, { - "name": self._annotations[ jQuery(e.target).attr("id") ].name, - "pos": parseInt( jQuery(e.target).attr("pos") ) - }); - }); - - }); - - }, - /* - * Function: Biojs.Sequence._getAnnotationString - * Purpose: Get the annotation text message for the tooltip - * Returns: {string} Annotation text for the annotation - * Inputs: id -> {int} index of the internal annotation array - */ - _getAnnotationString: function ( id ) { - var annotation = this._annotations[id.substr(id.indexOf("_") + 1)]; - return annotation.name + "
" + ((annotation.html)? annotation.html : ''); - }, - - /* - * Function: Biojs.Sequence._getHTMLRowAnnot - * Purpose: Build an annotation - * Returns: HTML of the annotation - * Inputs: currentPos -> {int} - * annotation -> {Object} - * settings -> {Object} - */ - _getHTMLRowAnnot : function (currentPos, annotation, settings) { - var styleBegin = 'border-left:1px solid; border-bottom:1px solid; border-color:'; - var styleOn = 'border-bottom:1px solid; border-color:'; - var styleEnd = 'border-bottom:1px solid; border-right:1px solid; border-color:'; - var styleBeginAndEnd = 'border-left:1px solid; border-right:1px solid; border-bottom:1px solid; border-color:'; - - var row = []; - var end = (currentPos + settings.numCols); - var spaceBetweenChars = (settings.spaceBetweenChars)? ' ' : ''; - var defaultColor = annotation.color; - var id = annotation.id; - for ( var pos=currentPos; pos < end ; pos++ ) { - // regions - for ( var r in annotation.regions ) { - region = annotation.regions[r]; - - spaceAfter = ''; - spaceAfter += (pos % settings.numColsForSpace == 0 )? ' ' : ''; - spaceAfter += spaceBetweenChars; - - color = ((region.color)? region.color : defaultColor); - data = 'class="annotation '+id+'" id="'+id+'" color="'+color+'" pos="'+pos+'"'; - - if ( pos == region.start && pos == region.end) { - row[pos] = ' '; - row[pos] += spaceAfter; - row[pos] += ''; - } else if ( pos == region.start ) { - row[pos] = ' '; - row[pos] += spaceAfter; - row[pos] += ''; - } else if ( pos == region.end ) { - row[pos] = ' '; - //row[pos] += spaceAfter; - row[pos] += ''; - } else if ( pos > region.start && pos < region.end ) { - row[pos] = ' '; - row[pos] += spaceAfter; - row[pos] += ''; - } else if (!row[pos]) { - row[pos] = ' '; - row[pos] += spaceAfter; - } - } - } - - var str = row.join(""); - - return ( str.indexOf("span") == -1 )? "" : str; - }, - /* - * Function: Biojs.Sequence._drawRaw - * Purpose: Repaint the current sequence using RAW format. - * Returns: - - * Inputs: - - */ - _drawRaw : function() { - var self = this; - var a = this.opt.sequence.toLowerCase().split(''); - var i = 0; - var arr = []; - var pre = jQuery('').appendTo(this._contentDiv); - - /* Correct column size in case the sequence is as small peptide */ - var numCols = this.opt.columns.size; - if ( this.opt.sequence.length < this.opt.columns.size ) { - numCols = this.opt.sequence.length; - } - - var opt = { - numCols: numCols - }; - - pre.html( - this._drawSequence(a, opt) - ); - - this._drawAnnotations(opt); - }, - /* - * Function: Biojs.Sequence._drawPride - * Purpose: Repaint the current sequence using PRIDE format. - * Returns: - - * Inputs: - - */ - _drawPride : function() { - var self = this; - var a = this.opt.sequence.toUpperCase().split(''); - var pre = jQuery('').appendTo(this._contentDiv); - - /* Correct column size in case the sequence is as small peptide */ - var numCols = this.opt.columns.size; - if ( this.opt.sequence.length < this.opt.columns.size ) { - numCols = this.opt.sequence.length; - } - - opt = { - numLeft: true, - numLeftSize: 5, - numLeftPad:'0', - numRight: true, - numRightSize: 5, - numRightPad: '0', - numCols: numCols, - numColsForSpace: self.opt.columns.spacedEach - }; - - pre.html( - this._drawSequence(a, opt) - ); - - this._drawAnnotations(opt); - }, - /* - * Function: Biojs.Sequence._drawSequence - * Purpose: Repaint the current sequence using CUSTOM format. - * Returns: - - * Inputs: a -> {char[]} a The sequence strand. - * opt -> {Object} opt The CUSTOM format. - */ - _drawSequence : function(a, opt) { - var str = ''; - - var spaceStyle = "white-space: pre;"; - - // Index at top? - if( opt.numTop ) - { - str += '' - var size = (opt.spaceBetweenChars)? opt.numTopEach*2: opt.numTopEach; - - if (opt.numLeft) { - str += this._formatIndex(' ', opt.numLeftSize, ' '); - } - - str += this._formatIndex(' ', size, ' '); - - for(var x = opt.numTopEach; x < opt.numCols; x += opt.numTopEach) { - str += this._formatIndex(x, size, ' ', true); - } - str += '
' - } - - - // Index at the left? - if (opt.numLeft) { - str += this._formatIndex(1, opt.numLeftSize, opt.numLeftPad); - str += ' '; - } - - var j=1; - for (var i=1; i <= a.length; i++) { - - if( i % opt.numCols == 0) { - str += '' + a[i-1] + ''; - - if (opt.numRight) { - str += ''; - str += ' '; - str += this._formatIndex(i, opt.numRightSize, opt.numRightPad); - str += ''; - } - - str += '
'; - - var aaRemaining = a.length - i; - if (opt.numLeft && aaRemaining > 0) { - str += ''; - str += this._formatIndex(i+1, opt.numLeftSize, opt.numLeftPad); - str += ' '; - str += ''; - } - - j = 1; - - } else { - str += '' + a[i-1]; - str += ( j % opt.numColsForSpace == 0)? ' ' : ''; - str += (opt.spaceBetweenChars)? ' ' : ''; - str += ''; - j++; - } - } - - str += '
' - - if (jQuery.browser.msie) { - str = "
" + str + ""; - } - - return str; - }, - /* - * Function: Biojs.Sequence._formatIndex - * Purpose: Build the HTML corresponding to counting numbers (top, left, right) in the strand. - * Returns: - - * Inputs: number -> {int} The number - * size -> {int} Number of bins to suit the number. - * fillingChar -> {char} Character to be used for filling out blank bins. - * alignLeft -> {bool} Tell if aligned to the left. - */ - _formatIndex : function( number, size, fillingChar, alignLeft) { - var str = number.toString(); - var filling = ''; - var padding = size - str.length; - if ( padding > 0 ) { - while ( padding-- > 0 ) { - filling += (""+fillingChar+""); - } - if (alignLeft){ - str = number+filling; - } else { - str = filling+number; - } - } - return str; - }, - /* - * Function: Biojs.Sequence._addSpanEvents - * Purpose: Add the event handlers to the strand. - * Returns: - - * Inputs: - - */ - _addSpanEvents : function() { - var self = this; - var isMouseDown = false; - var currentPos; - - self._contentDiv.find('.sequence').each( function () { - - // Register the starting position - jQuery(this).mousedown(function() { - var id = jQuery(this).attr('id'); - currentPos = parseInt(id.substr(id.indexOf("_") + 1)); - clickPos = currentPos; - self._setSelection(clickPos,currentPos); - isMouseDown = true; - - // Selection is happening, raise an event - self.raiseEvent( - Biojs.Sequence.EVT_ON_SELECTION_CHANGE, - { - "start" : self.opt.selection.start, - "end" : self.opt.selection.end - } - ); - - }).mouseover(function() { - // Update selection - // Show tooltip containing the position - var id = jQuery(this).attr('id'); - currentPos = parseInt(id.substr(id.indexOf("_") + 1)); - - if(isMouseDown) { - if( currentPos > clickPos ) { - self._setSelection(clickPos, currentPos); - } else { - self._setSelection(currentPos, clickPos); - } - - // Selection is happening, raise an event - self.raiseEvent( Biojs.Sequence.EVT_ON_SELECTION_CHANGE, { - "start" : self.opt.selection.start, - "end" : self.opt.selection.end - }); - } - - }).mouseup(function() { - isMouseDown = false; - // Selection is done, raise an event - self.raiseEvent( Biojs.Sequence.EVT_ON_SELECTION_CHANGED, { - "start" : self.opt.selection.start, - "end" : self.opt.selection.end - }); - }); - - // Add a tooltip for this sequence base. - self._addToolTip.call( self, this, function( ) { - if (isMouseDown) { - return "[" + self.opt.selection.start +", " + self.opt.selection.end + "]"; - } else { - return currentPos; - } - }); - - }) - .css('cursor', 'pointer'); - }, - /* - * Function: Biojs.Sequence._addTooltip - * Purpose: Add a tooltip around the target DOM element provided as argument - * Returns: - - * Inputs: target -> {Element} DOM element wich is the targeted focus for the tooltip. - * cbGetMessageFunction -> {function} A callback function wich returns the message to be displayed in the tip. - */ - _addToolTip : function ( target, cbGetMessageFunction ) { - - var tipId = '#sequenceTip' + this.getId(); - - jQuery(target).mouseover(function(e) { - - var offset = jQuery(e.target).offset(); - - if ( ! jQuery( tipId ).is(':visible') ) { - jQuery( tipId ) - .css({ - 'background-color': "#000", - 'padding': "3px 10px 3px 10px", - 'top': offset.top + jQuery(e.target).height() + "px", - 'left': offset.left + jQuery(e.target).width() + "px" - }) - .animate( {opacity: '0.85'}, 10) - .html( cbGetMessageFunction.call( target ) ) - .show(); - } - - }).mouseout(function() { - //Remove the appended tooltip template - jQuery( tipId ).hide(); - }); - }, - - /** - * Annotate a set of intervals provided in the argument. - * - * @deprecated Use addAnnotation() instead. - * - * @param {Object} annotation The intervals belonging to the same annotation. - * Syntax: { name: <value>, color: <HTMLColorCode>, html: <HTMLString>, regions: [{ start: <startVal1>, end: <endVal1>}, ..., { start: <startValN>, end: <endValN>}] } - */ - setAnnotation: function ( annotation ) { - this.addAnnotation(annotation); - }, - - /** - * Annotate a set of intervals provided in the argument. - * - * @example - * // Annotations using regions with different colors. - * mySequence.addAnnotation({ - * name:"UNIPROT", - * html:"<br> Example of <b>HTML</b>", - * color:"green", - * regions: [ - * {start: 540, end: 560}, - * {start: 561, end:580, color: "#FFA010"}, - * {start: 581, end:590, color: "red"}, - * {start: 690, end:710}] - * }); - * - * - * @param {Object} annotation The intervals belonging to the same annotation. - * Syntax: { name: <value>, color: <HTMLColorCode>, html: <HTMLString>, regions: [{ start: <startVal1>, end: <endVal1>}, ..., { start: <startValN>, end: <endValN>}] } - */ - addAnnotation: function ( annotation ) { - this._annotations.push(annotation); - this._redraw(); - }, - - /** - * Removes an annotation by means of its name. - * - * @example - * // Remove the UNIPROT annotation. - * mySequence.removeAnnotation('UNIPROT'); - * - * @param {string} name The name of the annotation to be removed. - * - */ - removeAnnotation: function ( name ) { - for (var i=0; i < this._annotations.length ; i++ ){ - if(name != this._annotations[i].name){ - this._annotations.splice(i,1); - this._redraw(); - break; - } - } - }, - /** - * Removes all the current annotations. - * - * @example - * mySequence.removeAllAnnotations(); - * - */ - removeAllAnnotations: function () { - this._annotations = []; - this._redraw(); - } - -}, -{ - EVT_ON_SELECTION_CHANGE: "onSelectionChange", - EVT_ON_SELECTION_CHANGED: "onSelectionChanged", - EVT_ON_ANNOTATION_CLICKED: "onAnnotationClicked" - -}); - - diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.SimpleFeatureViewer.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.SimpleFeatureViewer.js deleted file mode 100755 index d7a03dbf88..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.SimpleFeatureViewer.js +++ /dev/null @@ -1,649 +0,0 @@ -/** - * This component generates the JSON structure used by the FeatureViewer. It is a simplified version as it only - * includes a non-overlapping view. Regions are represented as rectangles while one-base/aa are represented as lines. - * Some few shapes are also supported for one-base/aa features, particularly{"diamond", "triangle", "hexagon", - * "wave", "circle"}. In proteins, we recommend "diamond" for active sites, "triangle" for PTMs, "hexagon" for glycosylation, - * "wave" for lipids, and "circle" for metals. Any other shape will be rendered as a rectangle. Bridges can be specified - * with the type "bridge". - * The legend is generated based on the first feature of each "typeLabel"; thus, if features with the same "typeLabel" - * have different colours, only the first one will be used in the legend. - * - * @class - * @extends Biojs.FeatureViewer - * - * @author Leyla Jael Garcia Castro - * @version 1.0.0 - * @category 2 - * - * - * @param {Object} options An object with the options for SimpleFeatureViewer component. - * - * @option {string} target - * Identifier of the DIV tag where the component should be displayed. - * - * @option {boolean} [showSlider=true] - * Should the slider for zooming be displayed? - * - * @option {boolean} [showPrintButton=true] - * Should the button for printing/exporting to image be displayed? - * - * @option {boolean} [showFeatureTooltipOnMouseOver=true] - * Should the tooltip for features be displayed? - * - * @option {boolean} [highlightFeatureOnMouseOver=true] - * Should the features be highlighted when mouse over? - * - * @option {boolean} [selectFeatureOnMouseClick=true] - * Should the features remain highlighted, i.e. being selected, after a mouse click, - * and deselected after a second click or whenever other feature is selected? - * - * @option {String} [selectionColor=#ff8c00] - * Color in hexa format so the features on mouse-over and click will change to it. - * Make sure you do not use that color for any feature. - * - * @option {string} sequenceId - * Sequence identifier - * - * @option {string} sequenceLength - * Sequence length - * - * @option {Array} features - * A JSON array containing the features to be displayed. type element for a feature is optional and can be either of - * {"rect", "bridge", "diamond", "triangle", "hexagon", "wave", "circle"} - * If you want bridges or one-single-position features to be rendered as rectangles, do not specify any type for the feature - * In proteins, we recommend "diamond" for active sites, "triangle" for PTMs, "hexagon" for glycosylation, - * "wave" for lipids, and "circle" for metals. Any other shape will be rendered as a rectangle - * Colours can be specified in hexa, string, or rgb; if no colour is specified, black will be used. - * features = [ - * { - * featureId:"UNIPROTKB_Q8LAX3_PROPEP_1_73", - * featureStart:1,featureEnd:73, - * typeLabel:"Propeptide", - * featureLabel:"Propeptide", - * typeCategory:"Molecule processing",typeCode:"SO:0001062", - * evidenceText:"UniProt",evidenceCode:"none", - * color: "red" - * }, - * { - * featureId:"UNIPROTKB_Q8LAX3_PEPTIDE_54_96", - * featureStart:54,featureEnd:96, - * typeLabel:"Peptide", - * featureLabel:"Elicitor peptide 3", - * typeCategory:"Molecule processing",typeCode:"SO:0001064", - * evidenceText:"UniProt",evidenceCode:"no ECO", - * color: "blue" - * }, - * { - * featureId:"UNIPROTKB_Q8LAX3_PEPTIDE_74_96", - * featureStart:74,featureEnd:96, - * typeLabel:"Active Site", - * featureLabel:"Elicitor peptide 3", - * typeCategory:"Molecule processing",typeCode:"SO:0001064", - * evidenceText:"UniProt",evidenceCode:"no ECO", - * type: "diamond" - * }, - * { - * featureId:"UNIPROTKB_Q8LAX3_DISULFID_75_96", - * featureStart:75,featureEnd:96, - * typeLabel:"Active Site", - * featureLabel:"Elicitor peptide 3", - * typeCategory:"Molecule processing",typeCode:"SO:0001064", - * evidenceText:"UniProt",evidenceCode:"no ECO", - * color: "#33FF66", - * type: "bridge" - * } - * ]; - * - * @option {int} [imageWidth=700] - * Image width - * - * @example - * var myFT = [ - * { - * featureId:"UNIPROTKB_Q8LAX3_PROPEP_1_73", - * featureStart:1,featureEnd:73, - * typeLabel:"Propeptide", - * featureLabel:"Propeptide", - * typeCategory:"Molecule processing",typeCode:"SO:0001062", - * evidenceText:"UniProt",evidenceCode:"none", - * color: "red" - * }, - * { - * featureId:"UNIPROTKB_Q8LAX3_PEPTIDE_54_96", - * featureStart:54,featureEnd:96, - * typeLabel:"Peptide", - * featureLabel:"Elicitor peptide 3", - * typeCategory:"Molecule processing",typeCode:"SO:0001064", - * evidenceText:"UniProt",evidenceCode:"no ECO", - * color: "blue" - * }, - * { - * featureId:"UNIPROTKB_Q8LAX3_PEPTIDE_74_96", - * featureStart:74,featureEnd:96, - * typeLabel:"Active Site", - * featureLabel:"Elicitor peptide 3", - * typeCategory:"Molecule processing",typeCode:"SO:0001064", - * evidenceText:"UniProt",evidenceCode:"no ECO", - * type: "diamond" - * }, - * { - * featureId:"UNIPROTKB_Q8LAX3_DISULFID_75_96", - * featureStart:75,featureEnd:96, - * typeLabel:"Active Site", - * featureLabel:"Elicitor peptide 3", - * typeCategory:"Molecule processing",typeCode:"SO:0001064", - * evidenceText:"UniProt",evidenceCode:"no ECO", - * color: "#33FF66", - * type: "bridge" - * } - * ]; - * var myPainter = new Biojs.SimpleFeatureViewer({ - * target: "YourOwnDivId", - * sequenceId: "a4_human", - * sequenceLength: 770, - * features: myFT - * }); - * - */ -Biojs.SimpleFeatureViewer = Biojs.FeatureViewer.extend( - /** @lends Biojs.SimpleFeatureViewer */ - { - /** - * Default values for the options - * @name Biojs.SimpleFeatureViewer-constructor - */ - constructor:function (options) { - this.base(options); - //Biojs.console.enable(); - this._generatesJSON(); - this.paintFeatures(this.opt.json); - }, - - /** - * Default values for the options: - * target: "", - * showSlider: true, - * showPrintButton: true, - * showFeatureTooltipOnMouseOver: true, - * highlightFeatureOnMouseOver: true, - * selectFeatureOnMouseClick: true, - * selectionColor: "#ff8c00" - * imageWidth: 700, - * sequenceId: "none" - * sequenceLength: 0 - * features: {} - * - * @name Biojs.SimpleFeatureViewer-opt - */ - opt:{ - //Parent - /* target:"YourOwnDivId", - json: {}, //will be created by this component - showSlider:true, - showPrintButton:true, - showFeatureTooltipOnMouseOver:true, - highlightFeatureOnMouseOver:true, - selectFeatureOnMouseClick:true, - selectionColor:"#ff8c00", - */ - dragSites: false, - imageWidth:700 - }, - - /** - * Array containing the supported event names - * @name Biojs.SimpleFeatureViewer-eventTypes - */ - eventTypes : [], - - /** - * Opens a new window/tab in the browser with the graphical representation as a plain image. - * Note: For IE it does not reflect the drags/drops on sites - * - * @example - * myPainter.exportFeaturesToImage(); - * - */ - exportFeaturesToImage: function() { - var config = this.opt.json.configuration; - var dataURL = ""; - if (jQuery.browser.msie) { //canvas does not work (not even with IE 9) - alert("Operation not supported for IE, please try from a different browser"); - } else { - svg = document.getElementById('uniprotFeaturePainter-holder').innerHTML; - var canvas = document.createElement("canvas"); - canvg(canvas, svg); - dataURL = canvas.toDataURL(); - this.$imageExported = jQuery('') - .html('
- * {
- * url: <url>,
- * proxyUrl: <proxy>,
- * paramsMap: { "iDisplayStart": <newName1>, "iDisplayLength": <newName2>, ... },
- * filter: <flag>
- * }
- *
- * where:
- * -
- *
- url is string containing the url data source. - *
- paramsMap Customize the name of the following params which will be passed to server:
- *
-
- *
- iDisplayStart: index of the first expected record for paging. - *
- iDisplayLength: size of the fetched data (page size). - *
- sSearch: filter string entered by the user in case of filter is enabled. - *
- * - filter is a boolean to show/hide the search box on the table top. - * The entered string will be passed to the server by means of 'sSearch' parameter. - * Personalize the parameter name using paramsMap. - *
- proxyUrl optional string containing the url of the proxy in case of needing access to server through a proxy. - *
- * {
- * url: 'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/species:human',
- * paramsMap: { "iDisplayStart": "firstResult", "iDisplayLength": "maxResults" },
- * filter: false
- * }
- *
- *
- * - * [ - * [ 1, "chi", "China", 1347350000, "December 31, 2011", "0.1925" ], - * [ 2, "ind", "India", 1210193422, "March 1, 2011", "0.1729" ], - * [ 3, "usa", "United States", 313149000, "March 9, 2012", "0.0447" ], - * [ 4, "ino", "Indonesia", 237641326, "May 1, 2010", "0.034" ], - * [ 5, "bra", "Brazil", 192376496, "July 1, 2011", "0.0275" ], - * [ 6, "pak", "Pakistan", 178945000, "March 9, 2012", "0.0256" ], - * [ 7, "nig", "Nigeria", 162471000, "July 1, 2011", "0.0232" ], - * [ 8, "rus", "Russia", 143030106, "January 1, 2012", "0.0204" ], - * [ 9, "ban", "Bangladesh", 142319000, "March 15, 2011", "0.0203" ], - * [ 10, "jap", "Japan", 127770000, "February 1, 2012", "0.0183" ], - * [ 11, "mex", "Mexico", 112336538, "June 12, 2010", "0.016" ], - * [ 12, "phi", "Philippines", 94013200, "July 1, 2010", "0.0134" ], - * [ 13, "vie", "Vietnam", 87840000, "December 31, 2011", "0.0125" ], - * [ 14, "eth", "Ethiopia", 84320987, "July 1, 2012", "0.012" ], - * [ 15, "ger", "Germany", 81796000, "August 31, 2011", "0.0117" ] - * ] - *- * - * @option {(string|Object)[]} columns - *
Array containing the column descriptors. A descriptor can be either a string or an object. - * Use a string to define column name only. Use an object to define column name, rendering function and fixed width. - *
- *
- * {
- * name: <string>,
- * render: <function>,
- * width: <string>
- * }
- *
- * where:
- * -
- *
- name will be used for the column title, and 'render'. - *
- render is a function to format each row value in that column.
- *
Returns a string containing the new formatted value. - *
Arguments: - *-
- *
- col: index of the column. - *
- dataRow: 1D array containing whole row. - *
- value: current value of the cell. - *
- *
- * // Formats a decimal value in a percentage value.
- * var numberToPercentageFormat = function (col, dataRow, value) {
- * return ( new Number(value) * 100 ).toFixed(2) + "%";
- * };
- *
- *
- * // Three columns: Identifier, Name and Location.
- * // Custom rendering function will apply bold to Identifier values.
- * columns: [
- * "Name",
- * "Location",
- * { name: "Population %", render: numberToPercentageFormat }
- * ]
- *
- *
- * @option {int[]} [hideColumns=[]]
- * Indexes (0-based) of the columns to be hided.
- *
- * @option {array[][int,string]} [orderBy=[]]
- * A 2D array to tell how to order the columns. Each 1D array must contains both column index and ordering direction.
- *
- * - * // order column 0 in ascending direction and column 3 in descending direction - * orderBy: [ [0,'asc'], [3,'desc'] ] - *- * - * @option {int} [pageLength=10] - * Number of rows per page. - * - * @option {bool} [rowSelection=true] - * Show/hide the first check boxes column used for selecting rows. - * - * @option {bool} [paginate=true] - * Enable/disable the pagination, so whole the data will be displayed. - * - * @option {int} [width=597] - * Horizontal size of the general container. - * - * @option {int} [height=400] - * Vertical size of the general container. - * - * @example - * // Adds a flag to the cell value. - * var flagRender = function (col, dataRow, value) { - * return '
' + value;
- * };
- *
- * // Formats a decimal value in a percentage value.
- * var numberToPercentageFormat = function (col, dataRow, value) {
- * return ( new Number(value) * 100 ).toFixed(2) + "%";
- * };
- *
- * // Example of instantiation of the Table
- * var myTable = new Biojs.Table({
- * target: "YourOwnDivId",
- * hideColumns: [1],
- * orderBy: [ [0,'asc'], [3,'desc'] ],
- * columns: [
- * "Rank",
- * "Flag",
- * { name: "Country", render: flagRender },
- * "Population",
- * "Date",
- * { name:"% World Population", render: numberToPercentageFormat }
- * ],
- * dataSet: [
- * [ 1, "chi", "China", 1347350000, "December 31, 2011", "0.1925" ],
- * [ 2, "ind", "India", 1210193422, "March 1, 2011", "0.1729" ],
- * [ 3, "usa", "United States", 313149000, "March 9, 2012", "0.0447" ],
- * [ 4, "ino", "Indonesia", 237641326, "May 1, 2010", "0.034" ],
- * [ 5, "bra", "Brazil", 192376496, "July 1, 2011", "0.0275" ],
- * [ 6, "pak", "Pakistan", 178945000, "March 9, 2012", "0.0256" ],
- * [ 7, "nig", "Nigeria", 162471000, "July 1, 2011", "0.0232" ],
- * [ 8, "rus", "Russia", 143030106, "January 1, 2012", "0.0204" ],
- * [ 9, "ban", "Bangladesh", 142319000, "March 15, 2011", "0.0203" ],
- * [ 10, "jap", "Japan", 127770000, "February 1, 2012", "0.0183" ],
- * [ 11, "mex", "Mexico", 112336538, "June 12, 2010", "0.016" ],
- * [ 12, "phi", "Philippines", 94013200, "July 1, 2010", "0.0134" ],
- * [ 13, "vie", "Vietnam", 87840000, "December 31, 2011", "0.0125" ],
- * [ 14, "eth", "Ethiopia", 84320987, "July 1, 2012", "0.012" ],
- * [ 15, "ger", "Germany", 81796000, "August 31, 2011", "0.0117" ]
- * ]
- *
- * });
- */
-Biojs.Table = Biojs.extend (
-/** @lends Biojs.Table# */
-{
- constructor: function (options) {
- var self = this;
-
- //Biojs.console.enable();
-
- // TODO: validate mandatory values
-
- self._tableId = 'biojs_Table_'+self.getId();
- self._tableSelector = '#'+self._tableId;
- self._topControls = jQuery('').appendTo("#"+self.opt.target);
- self._body = jQuery('').appendTo("#"+self.opt.target);
- self._table = jQuery('- * // Select all the links - * targetSelector: "a" - * - * // Select the element with the id 'target' - * targetSelector: "#target" - * - * // Select all elements whose belong to the class 'here' - * targetSelector: ".here" - * - * // Select all list elements whose belong to the class 'here' - * targetSelector: "li.here" - *- * - * @param {function} [cbRender] - * By default, BiojsTooltip uses the 'title' attribute to render the content. - * Set this option to customize the content rendering instead of using the default value. - * - *
- * cbRender: function( element ) {
- * return "This is my personalized content for element " + element.tagName;
- * }
- *
- *
- * @param {static} [arrowType=Biojs.Tooltip.ARROW_LEFT_TOP]
- * Automatic positioning of the tooltip depends on the arrow direction.
- * Possible arrow types are:
- * -
- *
- Biojs.Tooltip.ARROW_LEFT_TOP - *
- Biojs.Tooltip.ARROW_LEFT_MIDDLE - *
- Biojs.Tooltip.ARROW_LEFT_BOTTOM - *
- Biojs.Tooltip.ARROW_TOP_LEFT - *
- Biojs.Tooltip.ARROW_TOP_MIDDLE - *
- Biojs.Tooltip.ARROW_TOP_RIGHT - *
- Biojs.Tooltip.ARROW_RIGHT_TOP - *
- Biojs.Tooltip.ARROW_RIGHT_MIDDLE - *
- Biojs.Tooltip.ARROW_RIGHT_BOTTOM - *
- Biojs.Tooltip.ARROW_BOTTOM_LEFT - *
- Biojs.Tooltip.ARROW_BOTTOM_MIDDLE - *
- Biojs.Tooltip.ARROW_BOTTOM_RIGHT - *
- Biojs.Tooltip.ARROW_LEFT_TOP - *
- Biojs.Tooltip.ARROW_LEFT_MIDDLE - *
- Biojs.Tooltip.ARROW_LEFT_BOTTOM - *
- Biojs.Tooltip.ARROW_TOP_LEFT - *
- Biojs.Tooltip.ARROW_TOP_MIDDLE - *
- Biojs.Tooltip.ARROW_TOP_RIGHT - *
- Biojs.Tooltip.ARROW_RIGHT_TOP - *
- Biojs.Tooltip.ARROW_RIGHT_MIDDLE - *
- Biojs.Tooltip.ARROW_RIGHT_BOTTOM - *
- Biojs.Tooltip.ARROW_BOTTOM_LEFT - *
- Biojs.Tooltip.ARROW_BOTTOM_MIDDLE - *
- Biojs.Tooltip.ARROW_BOTTOM_RIGHT - *
- name is the unique name corresponding to an id in the tree - *
- species_name the species the annotation belong to. - *
- alignment_length the length of the alignment sequence - *
- seq_length the length of the sequence - *
- domains array of objects defining the intervals which belongs to the annotation. - *
- domains[i].domain_start domain's start position - *
- domains[i].domain_end domain's stop position. - *
- domains[i].name name of the domain, e.g. BRCA-2_OB1 . - *
- domains[i].id the domain's id in the source database. Here, e.g. PF09103.5 - *
- domains[i].evalue the domains evalue - *
-
- *
- * @param {static} [position=Biojs.Tooltip.ELEMENT_POSITION]
- * Position is calculated through either mouse position or element position.
- * Allowed values are: Biojs.Tooltip.ELEMENT_POSITION or Biojs.Tooltip.MOUSE_POSITION
- *
- * @param {int} [delay=200]
- * Time interval in milliseconds starting on mouse exiting from element/Tooltip until the Tooltip hides itself.
- *
- * @example
- * // These examples use the component's example div 'YourOwnDivId' to draw the links only.
- * jQuery('#YourOwnDivId')
- * .append('Pass the mouse over here.')
- * .css({
- * 'display': 'table-cell',
- * 'vertical-align': 'middle',
- * 'text-align': 'center',
- * 'width': '730px',
- * 'height': '400px'
- * });
- *
- * // Tooltip will come out whenever mouse enter to any anchor 'a' with class 'example'
- * var simpleTip = new Biojs.Tooltip({
- * targetSelector: "a.example"
- * });
- *
- * //
- * // Another example using rendering function instead of 'title' attribute
- * //
- * jQuery('#YourOwnDivId')
- * .append('
This example change the tooltip direction
for each mouse entry.'); - * - * // Tooltip will come out whenever mouse enter to any anchor 'a' with class 'example' - * var tipRendered = new Biojs.Tooltip({ - * targetSelector: "a.example.render", - * cbRender: function( element ) { - * return "Tooltip type Biojs.Tooltip.ARROW_" + this.getArrowType().toUpperCase() + " using rendering function to build up content dynamically" - * } - * }); - * - * // Changes the tooltip's direction - * var counter = 0; - * var arrowTypes = [ - * Biojs.Tooltip.ARROW_LEFT_TOP, - * Biojs.Tooltip.ARROW_LEFT_MIDDLE, - * Biojs.Tooltip.ARROW_LEFT_BOTTOM, - * Biojs.Tooltip.ARROW_TOP_LEFT, - * Biojs.Tooltip.ARROW_TOP_MIDDLE, - * Biojs.Tooltip.ARROW_TOP_RIGHT, - * Biojs.Tooltip.ARROW_RIGHT_TOP, - * Biojs.Tooltip.ARROW_RIGHT_MIDDLE, - * Biojs.Tooltip.ARROW_RIGHT_BOTTOM, - * Biojs.Tooltip.ARROW_BOTTOM_LEFT, - * Biojs.Tooltip.ARROW_BOTTOM_MIDDLE, - * Biojs.Tooltip.ARROW_BOTTOM_RIGHT - * ]; - * - * // Changes the Tooltip arrow type dynamically - * jQuery('#YourOwnDivId a.example.render').mouseover( function() { - * var arrowType = arrowTypes[ counter++ % 12 ]; - * tipRendered.setArrowType( arrowType ); - * }); - * - * // - * // Another example using rich content - * // - * jQuery('#YourOwnDivId') - * .append('
Rich content'); - * - * var richContent = - * '
'+
- * '
'+
- * '
';
- *
- * var tipRich = new Biojs.Tooltip({
- * targetSelector: "a.example.rich",
- * cbRender: function( element ) {
- * return richContent;
- * },
- * arrowType: Biojs.Tooltip.ARROW_BOTTOM_MIDDLE
- * });
- *
- * //
- * // Last example using mouse position instead of element's
- * //
- * jQuery('#YourOwnDivId')
- * .append('Santiago de Cali
' + - * ''+
- * ''+ - * 'Simply referred to as Cali, is a city located in western Colombia '+ - * 'It is the capital of the Valle del Cauca Department. With a population of 2.5 million, '+ - * 'Cali is the third largest city in the country, after Bogota and Medellin. The city '+ - * 'was founded on 25 July 1536.
Tooltip changes with mouse positioning.'); - * - * var tipPosition = new Biojs.Tooltip({ - * targetSelector: "a.example.position", - * position: Biojs.Tooltip.MOUSE_POSITION - * }); - * - **/ -Biojs.Tooltip = Biojs.extend ( -/** @lends Biojs.Tooltip# */ -{ - constructor: function (options) { - - var self = this; - var arrowType = this.opt.arrowType; - - this._container = jQuery('').addClass("Tooltip"); - - this._arrow = jQuery('').appendTo( self._container ); - this._body = jQuery('').appendTo( self._container ); - - this._container.appendTo('body'); - - this._initialize(); - }, - - /** - * Default values for the options - * @name Biojs.Tooltip-opt - */ - opt: { - targetSelector: "a", - cbRender: undefined, - arrowType: "left_top", - position: 2, // ELEMENT_POSITION - delay: 200 - }, - - /** - * Array containing the supported event names - * @name Biojs.Tooltip-eventTypes - */ - eventTypes: [ - /** - * @name Biojs.Tooltip#onShowUp - * @event - * @param {function} actionPerformed A function which receives an {@link Biojs.Event} object as argument. - * @eventData {Object} source The component which did triggered the event. - * @eventData {string} type The name of the event. - * @eventData {string} target Target element. - * - * @example - * simpleTip.onShowUp( - * function( e ) { - * alert("Mouse has passed over the first example."); - * } - * ); - * - */ - "onShowUp" - ], - - _initialize: function( ) { - - var self = this; - var timer = 0; - var targetSelector = this.opt.targetSelector; - var cbRender = this.opt.cbRender; - var refPos = this.opt.position; - var target; - - // Get the text from the title attribute by default - if ( "function" != typeof cbRender ) { - cbRender = function( element ) { - return jQuery( element ).attr('title'); - } - } - - // Add the class to the arrow - //arrow.addClass( self.opt.arrowType.match(/^(left|top|right|bottom)/g)[0] ); - this.setArrowType( this.opt.arrowType ); - - // Positioning - this._arrow.css({ - "position": "absolute", - "z-index": "99999" - }); - - this._body.css({ - 'position': 'absolute', - 'z-index': '99998', - 'margin': '0px' - }); - - if ( refPos == Biojs.Tooltip.MOUSE_POSITION ) { - jQuery( targetSelector ).mousemove( function (e) { - - target = jQuery(e.target); - - if (timer) { - clearTimeout(timer); - } - timer = 0; - - // Set the content - content = cbRender.call( self, e.target ); - - self._body.html( content ); - - // Show up - self._show(); - - // Positioning - self._setPosition( - { left: e.pageX - 10, top: e.pageY - 10 }, - { width: 20, height: 20 } - ); - - // Event triggering - self.raiseEvent( Biojs.Tooltip.EVT_ON_SHOW_UP, { 'target': target }); - - }).mouseout( function() { - timer = setTimeout( 'Biojs.getInstance(' + self.getId() + ')._hide()' , self.opt.delay ); - }); - - } else { - jQuery( targetSelector ).mouseover( function (e) { - - target = jQuery(e.target); - - if (timer) { - clearTimeout(timer); - } - timer = 0; - - // Set the content - content = cbRender.call( self, e.target ); - - self._body.html( content ); - - // Show up - self._show(); - - // Positioning - self._setPosition( - target.offset(), - { width: target.width(), height: target.height() } - ); - - // Event triggering - self.raiseEvent( Biojs.Tooltip.EVT_ON_SHOW_UP, { 'target': target }); - - }).mouseout( function() { - timer = setTimeout( 'Biojs.getInstance(' + self.getId() + ')._hide()' , self.opt.delay ); - }); - } - - self._container.mouseover( function(){ - clearTimeout(timer); - timer = 0; - self._show(); - - }).mouseout( function() { - timer = setTimeout( 'Biojs.getInstance(' + self.getId() + ')._hide()' , self.opt.delay ); - }); - - this._hide(); - }, - - _hide: function() { - this._container.hide(); - }, - - _show: function() { - this._container.show(); - }, - - _setPosition: function ( offset, dim ) { - - var arrow = this._arrow; - var arrowType = this.opt.arrowType; - var arrowPos = { top: offset.top, left: offset.left }; - - var body = this._body; - var bodyPos = {}; - - arrow.removeClass(); - arrow.addClass( 'arrow ' + arrowType.match(/^(left|top|right|bottom)/g)[0] ); - - if ( arrowType == Biojs.Tooltip.ARROW_LEFT_TOP ) { - - arrowPos.top += Math.floor(dim.height/2) - Math.floor(arrow.height()/2); - arrowPos.left += arrow.width() + dim.width ; - - bodyPos.left = arrowPos.left + arrow.width() - 1; - bodyPos.top = arrowPos.top + Math.floor(arrow.height()/2) - Math.floor(body.height()/4); - - } else if ( arrowType == Biojs.Tooltip.ARROW_LEFT_MIDDLE ) { - - arrowPos.top += Math.floor(dim.height/2) - Math.floor(arrow.height()/2); - arrowPos.left += arrow.width() + dim.width ; - - bodyPos.left = arrowPos.left + arrow.width() - 1; - bodyPos.top = arrowPos.top + Math.floor(arrow.height()/2) - Math.floor(body.height()/2); - - } else if ( arrowType == Biojs.Tooltip.ARROW_LEFT_BOTTOM ) { - - arrowPos.top += Math.floor(dim.height/2) - Math.floor(arrow.height()/2); - arrowPos.left += arrow.width() + dim.width ; - - bodyPos.left = arrowPos.left + arrow.width() - 1; - bodyPos.top = arrowPos.top + Math.floor(arrow.height()/2) - Math.floor(body.height()*(3/4)); - - } else if ( arrowType == Biojs.Tooltip.ARROW_TOP_LEFT ) { - - arrowPos.top += dim.height; - arrowPos.left += Math.floor(dim.width/2) - Math.floor(arrow.width()/2); - - bodyPos.left = arrowPos.left + Math.floor(arrow.height()/2) - Math.floor(body.width()/4); - bodyPos.top = arrowPos.top + arrow.height() -1; - - } else if ( arrowType == Biojs.Tooltip.ARROW_TOP_MIDDLE ) { - - arrowPos.top += dim.height; - arrowPos.left += Math.floor(dim.width/2) - Math.floor(arrow.width()/2); - - bodyPos.left = arrowPos.left + Math.floor(arrow.height()/2) - Math.floor(body.width()/2); - bodyPos.top = arrowPos.top + arrow.height() -1; - - } else if ( arrowType == Biojs.Tooltip.ARROW_TOP_RIGHT ) { - - arrowPos.top += dim.height; - arrowPos.left += Math.floor(dim.width/2) - Math.floor(arrow.width()/2); - - bodyPos.left = arrowPos.left + Math.floor(arrow.height()/2) - Math.floor( body.width()*(3/4) ); - bodyPos.top = arrowPos.top + arrow.height() -1; - - } else if ( arrowType == Biojs.Tooltip.ARROW_RIGHT_TOP ) { - - arrowPos.top += Math.floor(dim.height/2) - Math.floor(arrow.height()/2); - arrowPos.left -= arrow.width(); - - bodyPos.left = arrowPos.left - body.outerWidth() +1; - bodyPos.top = arrowPos.top + Math.floor(arrow.height()/2) - Math.floor(body.height()/4); - - } else if ( arrowType == Biojs.Tooltip.ARROW_RIGHT_MIDDLE ) { - - arrowPos.top += Math.floor(dim.height/2) - Math.floor(arrow.height()/2); - arrowPos.left -= arrow.width(); - - bodyPos.left = arrowPos.left - body.outerWidth() +1; - bodyPos.top = arrowPos.top + Math.floor(arrow.height()/2) - Math.floor(body.height()/2); - - } else if ( arrowType == Biojs.Tooltip.ARROW_RIGHT_BOTTOM ) { - - arrowPos.top += Math.floor(dim.height/2) - Math.floor(arrow.height()/2); - arrowPos.left -= arrow.width(); - - bodyPos.left = arrowPos.left - body.outerWidth() +1; - bodyPos.top = arrowPos.top + Math.floor(arrow.height()/2) - Math.floor(body.height()*(3/4)); - - } else if ( arrowType == Biojs.Tooltip.ARROW_BOTTOM_LEFT ) { - - arrowPos.top -= arrow.height(); - arrowPos.left += Math.floor(dim.width/2) + Math.floor(arrow.width()/2); - - bodyPos.left = arrowPos.left + Math.floor(arrow.width()/2) - Math.floor(body.width()/4); - bodyPos.top = arrowPos.top - body.outerHeight() +1; - - } else if ( arrowType == Biojs.Tooltip.ARROW_BOTTOM_MIDDLE ) { - - arrowPos.top -= arrow.height(); - arrowPos.left += Math.floor(dim.width/2) - Math.floor(arrow.width()/2); - - bodyPos.left = arrowPos.left + Math.floor(arrow.width()/2) - Math.floor(body.width()/2); - bodyPos.top = arrowPos.top - body.outerHeight() +1; - - } else if ( arrowType == Biojs.Tooltip.ARROW_BOTTOM_RIGHT ) { - - arrowPos.top -= arrow.height(); - arrowPos.left += Math.floor(dim.width/2) - Math.floor(arrow.width()/2); - - bodyPos.left = arrowPos.left + Math.floor(arrow.width()/2) - Math.floor(body.width()*(3/4)); - bodyPos.top = arrowPos.top - body.outerHeight() +1; - } - - this._arrow.css( arrowPos ); - this._body.css( bodyPos ); - }, - - /** - * Changes the Tooltip direction. The point of reference is the arrow's type. - * Choose one of the following available types: - *
-
- *
-
- *
- * @param {static} arrowType Static Biojs.Tooltip.ARROW_[TYPE] value.
- *
- * @example
- * simpleTip.setArrowType(Biojs.Tooltip.ARROW_BOTTOM_RIGHT);
- *
- */
- setArrowType: function( arrowType ) {
-
- var newClass = arrowType.match(/^(left|top|right|bottom)/g)[0];
-
- if ( newClass !== undefined ) {
- this.opt.arrowType = arrowType;
- }
- },
- /**
- * Returns the actual arrow type.
- * @returns {static} Static Biojs.Tooltip.ARROW_[TYPE] value.
- *
- * @example
- * alert ( "First example is using " + simpleTip.getArrowType() + " arrow." );
- *
- */
- getArrowType: function( arrowType ) {
- return this.opt.arrowType;
- },
-
- /**
- * Returns the actual id attribute value.
- * @returns {string} DOM element identifier of this component.
- *
- * @example
- * alert ( "Identifier of the second example is " + tipRendered.getIdentifier() + "." );
- *
- */
- getIdentifier: function( ) {
- return this._container.attr('id');
- },
-
- /**
- * Sets the id attribute value.
- * @param {string} DOM element identifier for this component.
- *
- * @example
- * tipRendered.setIdentifier("MyIdentifier");
- *
- */
- setIdentifier: function( value ) {
- return this._container.attr( 'id', value );
- }
-
-
-},{
- // Arrows height: 12px width: 7px;
- ARROW_LEFT_TOP: "left_top",
- ARROW_LEFT_MIDDLE: "left_middle",
- ARROW_LEFT_BOTTOM: "left_bottom",
- ARROW_TOP_LEFT: "top_left",
- ARROW_TOP_MIDDLE: "top_middle",
- ARROW_TOP_RIGHT: "top_right",
- ARROW_RIGHT_TOP: "right_top",
- ARROW_RIGHT_MIDDLE: "right_middle",
- ARROW_RIGHT_BOTTOM: "right_bottom",
- ARROW_BOTTOM_LEFT: "bottom_left",
- ARROW_BOTTOM_MIDDLE: "bottom_middle",
- ARROW_BOTTOM_RIGHT: "bottom_right",
-
- // Events
- EVT_ON_SHOW_UP: "onShowUp",
-
- MOUSE_POSITION: 1,
- ELEMENT_POSITION: 2
-
-});
\ No newline at end of file
diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.Tree.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.Tree.js
deleted file mode 100755
index fbe64772ad..0000000000
--- a/src/lib/biojs-1.0/src/main/javascript/Biojs.Tree.js
+++ /dev/null
@@ -1,3113 +0,0 @@
-/**
- * Tree component
- *
- * @class
- * @extends Biojs
- *
- * @author Fabian Schreiber
- * @version 1.0.0
- * @category 3
- *
- * @requires jQuery Core 1.9.2
- * @dependency
- *
- * @requires jQuery Tipsy
- * @dependency
- *
- * @requires D3
- * @dependency
- * @requires Additional tree functions
- * @dependency
-
- * @requires BioJS Tree css
- * @dependency
-
- * @requires jQuery Tipsy
- * @dependency
- *
- *
- * @param {Object} options An object with the options for Tree component.
- *
- * @option {string} target
- * Identifier of the DIV tag where the component should be displayed.
- *
- *
- * @option {file} tree
- * JSON that contains the tree information.
- *
- * [
- * //
- * { name: <name>,
- * display_label: <display_label>,
- * duplication: <duplication>,
- * branch_length: <endVal1>,
- * common_name: <common_name>,
- * seq_length: <seq_length>,
- * type: <type>,
- * uniprot_name: <uniprot_name>,
- *
- * children: []},
- * //
- * // Any others nodes
- * ...,
- * //
- * ]
- *
- *
- * tree : [
- * {"name":"Amniota_1","branch_length":"0.2212","binary_alignment":"N/A","children": [..]
- * ,"common_name":"Chicken","seq_length":3397,"swissprot_gene_name":"N/A","display_label":"BRCA2"}
- * ]
- *
- *
- * @option {file} domains_file
- * Set of annotations for the leaves of the tree. Must be an array of objects following the syntax:
- *
- * [
- * // An annotation:
- * { name: <name>,
- * species_name: <message>,
- * alignment_length: <message>,
- * seq_length: <message>,
- * cigar_string: <color_code>,
- * domains: [{ name: name; domain_start: <startVal1>, domain_end: <endVal1> id: <HTMLColor> name : name}, ...,{ start: <startValN>, end: <endValN>, color: <HTMLColor>}]
- * },
- *
- * // ...
- * // more annotations here
- * // ...
- * ]
- *
- *
- * tree : [
- * {
- * "cigar_string" : "4D22MD23M3D10MD13M2D44M2D23M3D7MD13M11D16MD57M5D27MD26M2D3M9D8MD9M2D3MD12MD11M2D10M3D3MD2MDMD9MD19M4D2MD17MD10MD24M5D7MD3MD24MD19MD10M3D6M10D26M6D5M2D17M12D11M2D10M2D52M2D7M2D12MD7M5D22M2D4M2D10M3D46MD20MD6M4D4M2D3M3DM2D11M4D4MDM2D4MDMD3MD5M4D5MD9M5D5M2DM7D18M3D5MD2MD6MD21MD5MDM2D6MDMD2MD23MD9M5D19M7D3M2D19MD2MD7M7D14M5D13MD9MD7M3D45MD7M2D4M3D7M8D3M13D2M12D3M5D4MD35MD44M3D2M2D18M15D17MD18M8D4M8DMD21MD36MD17MD2MD25M2D19MD6MD2MD3MD12M6D12MD21M4D11MD17MD18M2D79MD55M2D18M2D30M4D5MD5MD8MD11MD23MD42M8D26M4DMD25MD6M5D7M2D6M2D3MD15M6DMD14MD32M10D3MD6M5D43M3D13MD21MD6MD6M3D3MD8MD10M7D11M4D23M10D44MD12M5D4MDM3D19M13D34MD4MD15MD2MD6MD53M4D2MD10MD38MD13MD25MD104M3D62M2D15M5D5M6D37M2D6MDMD234MD3MD162MD11M2D30M2D45MD20MD2MD100M13D25M4D20M4D78M8D62MD38MD2MD8MD3MD4MD5MD41MD3MD4M16D11M2DM3D38M2D",
- * "species_name" : "Ailuropoda_melanoleuca",
- * "alignment_length" : 4010,
- * "domains" : [ ..]
- * "seq_length" : 3460,
- * "name" : "ENSAMEP00000009909"}
- * ]
- *
- *
- * where:
- * -
- *
Loading tree data...Loading annotation data...| "+d.xref.protein_id+" | "} - else {table_html += ""} - if(d.xref.sf_name){table_html += " | "+d.xref.sf_name+" | "} - else {table_html += ""} - if(d.xref.definition){table_html += " | "+d.xref.definition+" | "} - else {table_html += ""} - if(d.xref.gene_id){table_html += " | "+d.xref.gene_id+" | "} - else {table_html += ""} - if(d.xref.molecular_function){table_html += " | "+d.xref.molecular_function+" | "} - else {table_html += ""} - if(d.xref.biological_process){table_html += " | "+d.xref.biological_process+" | "} - else {table_html += ""} - if(d.xref.cellular_component){table_html += " | "+d.xref.cellular_component+" | "} - else {table_html += ""} - if(d.xref.protein_class){table_html += " | "+d.xref.protein_class+" | "} - else {table_html += ""} - - } - table_html += " |
'+
- // ' '+
- // ' | '+
-
- //''+
- ' internal nodes: '+
- ''+
- ' '+
- ''+
- //' | '+
- //''+
- ''+
- ' '+
- ''+
- //' | '+
- //''+
- ''+
- ' '+
- ''+
- //' | '+
-
- //''+
- ''+
- ' '+
- ''+
- //' | '+
-
- // ''+
- // ' '+
- // ' | '+
- // ''+
- // ' '+
- // ' | '+
-
- // ''+
- // ''+
- // ' '+
-// ''+
-// ' | '+
-// ''+
-// ''+
-// ' '+
-// ''+
-// ' | '+
-
-
- //''+
- // ''+
- // ' '+
- // ''+
- //' | '+
- //''+
- 'leaves: '+
- ''+
- ' '+
- ''+
- //' | '+
-
- //''+
- // ''+
- // ''+
- // ''+
- //' | '+
- //''+
- ''+
- ''+
- ''+
- //' | '+
- //''+
- ''+
- ' '+
- ''
- //' | '+
- // ''+
- // ''+
- // ' '+
- // ''+
- // ' | '+
- // ''+
- // ''+
- // ' '+
- // ''+
- // ' | '+
-
-
-
-
-
-
-
- //'
Lappen
').appendTo('#tv_controls'); - Biojs.console.enable("finished building div"); - //jQuery('').appentTo(jQuery("#tv_controls")); - - - // font size - jQuery('img.increase_font').click(function() { - self.opt.fontSize = parseInt(self.opt.fontSize) + 1 + "px"; - d3.select("svg").selectAll(".text").attr("font-size", function(d){ return self.opt.fontSize; }); - }); - - jQuery('img.decrease_font').click(function() { - self.opt.fontSize = parseInt(self.opt.fontSize) - 1 + "px"; - d3.select("svg").selectAll(".text").attr("font-size", function(d){ return self.opt.fontSize; }); - }); - - - - }, - /* - * Shows the columns indicated by the indexes array. - * @param {string} seq The sequence strand. - * @param {string} [identifier] Sequence identifier. - * - * @example - * myTree.__setModelOrganisms(); - * - */ - _setTaxaToShow: function (){ - - var show_taxa = new Object(); - show_taxa['Metazoa'] = 1; - show_taxa['Bilateria'] = 1; - show_taxa['Mammalia'] = 1; - show_taxa['Dipteria'] = 1; - show_taxa['Primates'] = 1; - show_taxa['Arabidopsis_thaliana'] = 1; - - - this.opt.show_taxa = show_taxa; - }, - __drawProteinDomains: function (){ - Biojs.console.enable("drawing protein domains"); - // Sequences - var rects = draw_sequences({nodeEnter: this.nodeEnter, - domainScale : this.opt.domainScale , - leaf_group_x : this.opt.leaf_group_x, - sequence_start_y : this.opt.sequence_start_y, - visibility : ""}); - // Domains - var domains = rects.selectAll(".domain").data(function(d) { return d.domains; }) - var all_domains = draw_domains({domains : domains, - sequence_start_y : this.opt.sequence_start_y, - domainScale: this.opt.domainScale, - sequence_rect_width : this.opt.sequence_rect_width, - leaf_group_x : this.opt.leaf_group_x, - domain_colors : this.opt.domain_colors, - visibility: "" }); - - } -}, -{ - EVT_ON_SELECTION_CHANGE: "onSelectionChange", - EVT_ON_SELECTION_CHANGED: "onSelectionChanged", - EVT_ON_ANNOTATION_CLICKED: "onAnnotationClicked" - -}); - - diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.UniProtDiseaseSummary.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.UniProtDiseaseSummary.js deleted file mode 100755 index eb8d0934d5..0000000000 --- a/src/lib/biojs-1.0/src/main/javascript/Biojs.UniProtDiseaseSummary.js +++ /dev/null @@ -1,375 +0,0 @@ -/** - * Component to present UniProt disease information. - * - * @class - * @extends Biojs - * - * @author Rafael C Jimenez - * @version 1.0.0 - * @category 2 - * - * @requires jQuery 1.7.2 - * @dependency - * - * - * @requires Biojs.UniProtDiseaseSummary.css - * @dependency - * - * - * @param {Object} options An object with the options for this component. - * - * @option {string} target - * Identifier of the DIV tag where the component should be displayed. - * - * @option {string} uniProtDasUrl - * Url pointing to an XML including UniProt infomration in DAS format - * - * @option {string} keywordFiltereing [['cancer','brain']] - * List of keywords to filter disease information - * - * @option {string} [proxyUrl='../biojs/dependencies/proxy/proxy.php'] - * Since the same origin policy ({@link http://en.wikipedia.org/wiki/Same_origin_policy}) in the browsers - * Biojs include a proxy script in PHP which redirects Ajax requests from local to any other domain. - * You can use tour own proxy script by modifying this value. - * - * @option {string} width [100%] - * Defines the width of the component - * - * @option {string} referencesColumnWidth [200px] - * Defines the width of the columns with reference links - * - * @option {boolean} tableHeader - * Boolean value to control the display of the table header - * - * @option {boolean} componentTitle - * Boolean value to control the display of the title of the component - * - * @example - * var instance = new Biojs.UniProtDiseaseSummary({ - * target: 'YourOwnDivId', - * uniProtDasUrl: 'http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=P08123;type=BS:01019', - * keywordFiltereing: ['osteogenesis','lipoblastoma'], - * proxyUrl: '../biojs/dependencies/proxy/proxy.php', - * width: '100%', - * referencesColumnWidth: '150px', - * tableHeader: false, - * componentTitle: false - * }); - * - */ - - -Biojs.UniProtDiseaseSummary = Biojs.extend ( - /** @lends Biojs.UniProtDiseaseSummary# */ - { - constructor: function (options) { - //Biojs.console.enable(); - this.setUniProtDasUrl(this.opt.uniProtDasUrl); - this._component_wrapper_id = "UDS_component_wrapper"; - }, - - /** - * Set an URL to start the query and visualization - * @param {string} uniProtDasUrl DAS XML - * - * @example - * instance.setUniProtDasUrl("http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=P37173;type=BS:01019"); - * - * @example - * instance.setUniProtDasUrl("http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=P08123;type=BS:01019"); - * - */ - - setUniProtDasUrl: function(uniProtDasUrl){ - var self = this; - self._clearHtmlTemplate(); - /* URL where to get DAS XML */ - self._url; - if(self.opt.proxyUrl != ""){ - self._url= self.opt.proxyUrl + "?url=" + uniProtDasUrl; - } else { - self._url= uniProtDasUrl; - } - - /* get XML */ - jQuery.ajax({ - type: "GET", - url: self._url, - dataType: "xml", - success: function(a){self._processDasUniProtXml(a);}, - error: function(a){self._processErrorRequest(a);} - }); - }, - /* - * Function: Biojs.UniProtDiseaseSummary._processErrorRequest - * Purpose: Process request error - * Returns: - - * Inputs: textStatus -> {String} Text satus - */ - _processErrorRequest: function (textStatus){ - var self = this; - Biojs.console.log("ERROR: " + textStatus ); - self.raiseEvent( Biojs.UniProtDiseaseSummary.EVT_ON_REQUEST_ERROR, { message: textStatus } ); - }, - /* - * Function: Biojs.UniProtDiseaseSummary._drawHtmlTemplate - * Purpose: Create HTML template - * Returns: - - * Inputs: - - */ - _drawHtmlTemplate: function (){ - var _selector = "#" + this.opt.target; - var _container = jQuery(_selector); - var _tableTitle = jQuery('').appendTo(_container); - jQuery("").appendTo(_tableTitle); - jQuery("").appendTo(_tableTitle); - }, - /* - * Function: Biojs.UniProtDiseaseSummary._clearHtmlTemplate - * Purpose: Remove component content - * Returns: - - * Inputs: - - */ - _clearHtmlTemplate: function (){ - var _selector = "#" + this.opt.target; - var _container = jQuery(_selector).html(''); - }, - /* - * Function: Biojs.UniProtDiseaseSummary._drawComponentTitle - * Purpose: Draw component title - * Returns: - - * Inputs: - - */ - _drawComponentTitle: function (){ - if(this.opt.componentTitle){ - var _selector = "#" + this._component_wrapper_id; - var _container = jQuery(_selector); - var _tableTitle = jQuery("Involvement in disease
").appendTo(_container);
- }
- },
- /*
- * Function: Biojs.UniProtDiseaseSummary._drawComments
- * Purpose: Draw disease main summary using UniProt disease comments
- * Returns: -
- * Inputs: -
- */
- _drawComments: function (){
- var _container = jQuery("#UDS_info");
- var _tableWrapper = jQuery("");
- var _table = jQuery('" + omimAccs + "
";
-
- }
- /* Display Pubmed */
- for (k = 0; k < this._comments[i].pubmedAccs.length; k++) {
- pubmedAccs += '' + this._comments[i].pubmedAccs[k] + ', ';
- }
- if (pubmedAccs.length > 0) {
- pubmedAccs = pubmedAccs.substring(0, pubmedAccs.length - 2);
- pubmedAccs = "Links to Pubmed:" + pubmedAccs + "
";
-
- }
- jQuery("Keywords: " + links + "
";
- jQuery(links).appendTo(_container);
- } else {
- var _info = jQuery("#UDS_info").html();
- if(_info.length > 0){
- jQuery("#UDS_warnings").html("No disease keywords or notes found for this query");
- } else {
- jQuery("#UDS_warnings").html("No disease keywords found for this query");
- }
- }
-
- },
-
-
- /*
- * Function: Biojs.UniProtDiseaseSummary._processUniProtXml
- * Purpose: process XML
- * Returns: -
- * Inputs: xml -> {String} DAS XML
- */
- _processDasUniProtXml: function (xml){
- Biojs.console.log("SUCCESS: data received");
- this._keywords = new Array();
- this._comments = new Array();
- var self = this;
- jQuery(xml).find("FEATURE").each(function(){
- var xmlType = jQuery(this).find("TYPE")[0];
- var featureCategory = jQuery(xmlType).attr("category");
- if(featureCategory.toLowerCase() == "keyword"){
- self._setKeyword(this);
- } else if (featureCategory.toLowerCase() == "comment"){
- self._setComment(this);
- }
-
- });
- this._drawHtmlTemplate();
- this._drawComponentTitle()
- this._drawComments();
- this._drawKeywords();
- },
- /*
- * Function: Biojs.UniProtDiseaseSummary._setKeyword
- * Purpose: parse keyword information
- * Returns: -
- * Inputs: featureXml -> {String} DAS XML
- */
- _setKeyword: function (featureXml){
- var keyword = new Object();
- keyword.label = jQuery(featureXml).attr("label");
- keyword.link = "http://www.uniprot.org/keywords/?query=" + jQuery(featureXml).attr("label");
- this._keywords.push(keyword);
- },
- /*
- * Function: Biojs.UniProtDiseaseSummary._setComment
- * Purpose: parse comment information
- * Returns: -
- * Inputs: featureXml -> {String} DAS XML
- */
- _setComment: function (featureXml){
- /* Find OMIM accs and notes */
- var diseaseHeader = "DISEASE: ";
- var comment = new Object();
- comment.omimAccs = new Array();
- comment.pubmedAccs = new Array();
- comment.notes = new Array();
- jQuery(featureXml).find("NOTE").each(function(){
- var omimPatern = /\[MIM\:[0-9]*\]/i; //[MIM:166200]
- var note = jQuery(this).text();
- if (note.indexOf(diseaseHeader) == 0) {
- note = note.substring(diseaseHeader.length,note.length);
- }
- if(note.match(omimPatern) != null){
- var omim = note.match(omimPatern)[0];
- var omimIndexStart = note.indexOf(omim);
- var omimIndexEnd = parseInt(omimIndexStart) + omim.length;
- note = note.substring(0,omimIndexStart-1) + note.substring(omimIndexEnd,note.length);
- comment.omimAccs.push(omim.substring(5,omim.length-1));
- }
- comment.notes.push(note);
- });
- /* Find Pubmed accs */
- jQuery(featureXml).find("LINK").each(function(){
- var linkHref = jQuery(this).attr("href");
- pubmedAcc ="";
- var pubmedUrl = "http://www.ncbi.nlm.nih.gov/pubmed/";
- var pubmedUrlIndex = linkHref.indexOf(pubmedUrl);
- if(pubmedUrlIndex == 0){
- pubmedAcc = linkHref.substring(pubmedUrl.length,linkHref.length);
- comment.pubmedAccs.push(pubmedAcc);
- }
- });
- this._comments.push(comment);
- Biojs.console.log(comment.omimAccs);
- Biojs.console.log(comment.pubmedAccs);
- Biojs.console.log(comment.notes);
- },
-
-
-
- /**
- * Default values for the options
- * @name Biojs.UniProtDiseaseSummary-opt
- */
- opt: {
- target: 'uniprotDiseaseSummary',
- uniProtDasUrl: 'http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=P08123;type=BS:01019',
- keywordFiltereing: [],
- proxyUrl: '../biojs/dependencies/proxy/proxy.php',
- width: '100%',
- referencesColumnWidth: '150px',
- tableHeader: false,
- componentTitle: false
- },
- /**
- * Array containing the supported event names
- * @name Biojs.UniProtDiseaseSummary-eventTypes
- */
- eventTypes: []
-});
\ No newline at end of file
diff --git a/src/lib/biojs-1.0/src/main/javascript/Biojs.js b/src/lib/biojs-1.0/src/main/javascript/Biojs.js
deleted file mode 100755
index b09b92ccb2..0000000000
--- a/src/lib/biojs-1.0/src/main/javascript/Biojs.js
+++ /dev/null
@@ -1,727 +0,0 @@
-/**
- * Main container of the BioJS library. It is the parent class for all the components.
- *
- * @namespace
- *
- */
-var Biojs = function() {
- // dummy
-};
-
-/**
- * @class
- * @param {string} eventType The name of the event.
- */
-Biojs.EventHandler = function(eventType) {
- /**
- * The name of the event.
- * @type {string}
- */
- this.eventType = eventType;
- /**
- * Array of the registered listeners.
- * @type {function[]}
- */
- this.listeners = [];
- /**
- * Register action listeners for the event.
- * @param {function} actionPerformed The action listener to be registered.
- */
- this.addListener = function ( actionPerformed ) {
- if ( (typeof actionPerformed) == "function" ) {
- this.listeners.push(actionPerformed);
- }
- };
- /**
- * Removes an action listener for the event.
- * @param {function} actionPerformed The action listener to be removed.
- */
- this.removeListener = function ( actionPerformed ) {
- if ( (typeof actionPerformed) == "function" ) {
- var pos = Biojs.Utils.indexOf(this.listeners,actionPerformed);
- if (pos!=-1)
- this.listeners.splice(pos,1);
- }
- };
- /**
- * Executes all listener actions registered in the listeners field.
- * @param {Object} eventObject The event' object to be passed as argument to the listeners.
- */
- this.triggerEvent = function( eventObject ) {
- for ( var i in this.listeners ) {
- this.listeners[i](eventObject);
- }
- }
-};
-
-/**
- * @class
- * @param {string} type The name of the event.
- * @param {Object} data An object containing the data for copying it in this event.
- * @param {Biojs} source The component source of the event.
- */
-Biojs.Event = function ( type, data, source ) {
-
- /**
- * The component which did triggered the event.
- * @type {Biojs}
- */
- this.source = source;
- /**
- * The name of the event.
- * @type {string}
- */
- this.type = type;
-
- for ( var key in data ) {
- this[key] = data[key];
- }
-};
-
-/**
- * @class
- *
- */
-Biojs.Utils = {
- /**
- * Clone all members from an object.
- * @param {object} object The object to be cloned.
- * @returns {object} A Clone of the object passed as argument.
- *
- */
- clone: function(obj) {
- var newObj = (obj instanceof Array) ? [] : {};
- for (i in obj) {
- if (obj[i] && typeof obj[i] == "object") {
- newObj[i] = Biojs.Utils.clone(obj[i]);
- } else {
- newObj[i] = obj[i];
- }
- }
- return newObj;
- },
-
- /**
- * Determine if an onject or array is empty.
- * @param {object|array} o Either object or array to figure out if empty or not.
- * @returns {bool} true if empty, false if don't
- */
- isEmpty: function(o){
- if (o instanceof Array) {
- return (o.length<=0);
- } else {
- for (var i in o) {
- if (o.hasOwnProperty(i)) {
- return false;
- }
- }
- return true;
- }
- },
-
- /**
- * Searches the array for the specified item, and returns its position.
- * The search will start at the specified position, or at the beginning if no start position is specified,
- * and end the search at the end of the array.
- *
- * Returns -1 if the item is not found.
- * If the item is present more than once, the indexOf method returns the position of the first occurence.
- *
- * indexOf is not supported in IE < v9
- *
- * @param {array} The array containing the element to look for.
- * @param {object} Required. The item to search for.
- * @param {int} Optional. Where to start the search.
- */
- indexOf : function(elem, arr, i){
- var len;
-
- if ( arr ) {
- if ( indexOf ) {
- return indexOf.call( arr, elem, i );
- }
-
- len = arr.length;
- i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0;
-
- for ( ; i < len; i++ ) {
- // Skip accessing in sparse arrays
- if ( i in arr && arr[ i ] === elem ) {
- return i;
- }
- }
- }
-
- return -1;
- },
-
- /**
- * Cross-browser console for debugging.
- * The console is disabled by default. That means, all messages written by means Biojs.console.log("My Message") will be ignored.
- * Use Biojs.console.enable() to enable it.
- *
- * @example
- * // Enabling loggin messages
- * Biojs.console.enable();
- * ...
- * // Writing a log
- * Biojs.console.log("My Message");
- *
- * @type {Object}
- */
- console: {
- enable: function() {
- // Define a cross-browser window.console.log method.
- // For IE and FF without Firebug, fallback to using an alert.
- if (window.console) {
- /**
- * @ignore
- */
- // In this case, there are a console, perfect!
- this.log = function (msg) { console.log(msg) };
- } else {
- // We have not window.console, but it is Opera browser?
- if (window.opera) {
- /**
- * @ignore
- */
- // Right! then lets use window.opera.postError
- this.log = function (msg) { window.opera.postError(msg) };
- } else {
- // None console found!
- // Try to write the logs somewhere
- // That's it! in a new window, identified by 'Biojs.console'
- var consoleWin = window.open('','myconsole',
- 'width=350,height=250'
- +',menubar=0'
- +',toolbar=0'
- +',status=0'
- +',scrollbars=1'
- +',resizable=1');
-
- // We got it?
- if (consoleWin) {
- // Good, build a blank document into with a DIV 'Biojs.console'
- consoleWin.document.writeln(
- '- *
variableStep chrom=chr2 span=5 - * 10 34 - * 20 41 - * 30 46 - * 40 49 - * 50 52 - * - * ... - * - * or - * - * fixedStep chrom=chr2 start=10 step=10 span=5 - * 34 - * 41 - * 46 - * 49 - * 52 - * - * ...- * - * @option {string} [selectionBackgroundColor] - * Name of the colour to be set as background for area chart - * - */ - - -Biojs.wigExplorer = Biojs.extend( - /** @lends Biojs.wigExplorer# */ - - - { - zoomSlider: '', - slider_stop: 0, - slider_start: 0, - track: [], - width: 1, - height: 1, - data_last_start: 1, - data_first_start: 1, - max: 0, - span: null, - chrom: [], - data: [], - main_data: [], - - - constructor: function (options) { - - var self = this; - self.vis = null; - self.color = null; - self.foci = []; - - - this.track; // data - - - this._container = $("#wigFeaturePainter-holder"); - $(this._container).addClass("graph"); - - - // Apply options values - this._container.css({ - 'font-family': self.opt.fontFamily, // this is one example of the use of self instead of this - 'background-color': self.opt.selectionBackgroundColor, - 'color': self.opt.fontColor, - 'font-size': '36px', - 'text-align': 'center', - 'vertical-align': 'middle', - 'width': '700px', - 'height': '100px', - 'bottom': '0px' - }); - - // Disable text selection and - // Change the selection mouse pointer - // from text to hand. - this._container.css({ - '-moz-user-select': 'none', - '-webkit-user-select': 'none', - 'user-select': 'none' - }); - - this.color = self.opt.selectionBackgroundColor; - this.paintFeatures(self.opt.dataSet); - - }, - - /** - * Default values for the options - * @name Biojs.wigExplorer-opt - */ - opt: { - target: "YourOwnDivId", - dataSet: "", - fontFamily: '"Andale mono", courier, monospace', - fontColor: "white", - backgroundColor: "", - selectionFontColor: "black", - selectionBackgroundColor: "yellow", - width: "100%", - height: "130", - radius: 10, - reference: null - }, - - /** - * Array containing the supported event names - * @name Biojs.wigExplorer-eventTypes - */ - eventTypes: [ - /** - * No events added for now but can be added in future - */ - ], - - - /** - * Repaints everything: ruler, shapes, and legend. - * @param {int} [newStart] Zoom from this sequence start value. - * @param {int} [newStop] Zoom to this sequence end value. - * - * @example - * instance._updateDraw(); - * - */ - _updateDraw: function (newStart, newStop, target) { - var self = this; - //recalculate start and stop - if (newStart && newStop) { - this.slider_start += newStart; - this.slider_stop += newStop; - } - - if (target) { - } else { - target = self.opt.target; - } - if (this.slider_start < this.data_first_start) { - if (newStart == newStop) { - this.slider_stop += this.data_first_start - this.slider_start; - } - this.slider_start = this.data_first_start; - - } - - if (this.slider_stop > this.data_last_start) { - - if (newStart == newStop) { - this.slider_start += this.data_last_start - this.slider_stop; - } - this.slider_stop = this.data_last_start; - } - //recalculate start and stop - if ((parseFloat(this.slider_start) < parseFloat(this.slider_stop))) { - this.paintWig(this.slider_start, this.slider_stop, target); - } - }, - - /** - * Paint the features according to the values specified in the json object defined when creating the object. - * This method initializes the holder, paints the slider and print button depending on the options, and - * paints the features and legend. - * - * @example - * instance.paintFeatures("path-to-wig.txt"); - * - * @param {string} dataSet Location of the file with the input data in text format. - *
variableStep chrom=chr2 span=5 - * 10 34 - * 20 41 - * 30 46 - * 40 49 - * 50 52 - * - * ... - * - * or - * - * fixedStep chrom=chr2 start=10 step=10 span=5 - * 34 - * 41 - * 46 - * 49 - * 52 - * - * ...- * - */ - paintFeatures: function (dataSet) { - if (dataSet != undefined) { - this._setDataSource(dataSet); - this._init(); - } else { - alert('Dataset not defined '); - } - - }, - - /** - * Private: Initializes the component. - */ - _init: function () { - Biojs.wigExplorer.myself = this; - var self = this; - var painter_div = jQuery("#" + this.opt.target); - painter_div.text(''); - painter_div.append(this._withSliderOnly(100)); - - painter_div.append(''); - var holder = document.getElementById(this.opt.target + '_wigFeaturePainter-holder'); - if (!holder) { - this.$errorMsg = jQuery('') - .html('There was an unexpected failure, the image cannot be displayed.') - .dialog({ - autoOpen: true, - title: 'Error', - modal: true - }); - throw "Error"; - } - - - holder.innerHTML = ""; - holder.style.height = "250px"; - holder.style.width = "700px"; - this.width = $('#' + self.opt.target + '_wigFeaturePainter-holder').width(), - this.height = $('#' + self.opt.target + '_wigFeaturePainter-holder').height(), - this.r = self.opt.radius; - - self.opt.width = self.opt.width.toString(); - - if (self.opt.width.indexOf("%") >= 1) - self.opt.width = self.opt.width.toString(); - else - self.opt.width = parseInt(this.width); - - //had similar problem before so I used contains and it should works - self.opt.height = self.opt.height.toString(); - if (self.opt.height.indexOf("%") >= 1) - self.opt.height = self.opt.height.toString(); - if (self.opt.height.indexOf("%") != -1) - this.height = this.height * (self.opt.height.substring(0, self.opt.height.length - 1) * 1) / 100.0; - else - this.height = self.opt.height * 1; - self.opt.height = parseInt(this.height); - - self.color = function () { - return d3.scale.ordinal().range(self.colors); - }(); - - jQuery.ajax({ - type: "GET", - url: self.opt.dataSet, - dataType: "text", - success: function (data) { - var wig = []; - var max = 0 - var data_split = data.split("\n") - var data_len = data_split.length; - if (data.indexOf("variableStep") >= 0 || data.indexOf("fixedStep") >= 0) { - self.chrom = [] - for (var i = 0; i < data_len; i++) { - if (data_split[i].indexOf("chrom") >= 0) { - var chr = data_split[i].split(/\s+/)[1].split("=")[1]; - if (self.chrom.indexOf(chr) < 0) { - self.chrom.push(chr); - } - } - } - self._buildReferenceSelector(); - } else { - alert("Unknown format detected") - } - - }, - error: function (qXHR, textStatus, errorThrown) { - alert(textStatus); - } - }); - }, - - - /** - * Private: Function to create reference dropdown. - * @ignore - */ - _buildReferenceSelector: function () { - var self = this; - - this._headerDiv = jQuery('#' + self.opt.target + '_selectorMenu'); - this._headerDiv.css({ - 'font-family': '"Heveltica Neue", Arial, "sans serif"', - 'font-size': '14px' - }).append('Reference: '); - - var selector_html = "