CXGN/Onto/Browser.js

   1 //
   2 // AJAX-based ontology browser
   3 //
   4 // Lukas Mueller and Naama Menda
   5 //
   6 // Sol Genomics Network (http://sgn.cornell.edu/ )
   7 //
   8 // Spring 2008
   9 //
  10
  11 JSAN.use('MochiKit.DOM');
  12 JSAN.use('MochiKit.Visual');
  13 JSAN.use('MochiKit.Logging');
  14 JSAN.use('MochiKit.Async');
  15 JSAN.use('Prototype');
  16 JSAN.use('CXGN.Effects');
  17 //JSAN.use('CXGN');
  18 //JSAN.use('CXGN.Onto');
  19 JSAN.use('CXGN.Onto.Browser');
  20 //JSAN.use('CXGN.Phenome.Tools');
  21
  22
  23 CXGN = function () {};
  24 CXGN.Onto = function () {};
  25
  26 CXGN.Onto.Browser = function () {
  27
  28     this.nodelist = new Array();
  29     this.resetNodeKey();
  30     //this.workingMessage(false);
  31     //document.write('<p id="ontology_browser">&nbsp;</p>');
  32     //var dom = MochiKit.DOM.getElement('ontology_browser');
  33     //MochiKit.Logging.log('DOM: '+dom);
  34     //this.setDOMElement(dom);
  35
  36     //MochiKit.Logging.log('In browser constructor.');
  37
  38 };
  39
  40 CXGN.Onto.Browser.prototype = {
  41
  42     fetchTestRoots: function() {
  43         //MochiKit.Logging.log('creating root node.');
  44         this.rootnode = new Node(this);
  45         this.rootnode.setName('ROOT');
  46         this.rootnode.openNode();
  47         var p2;
  48         for (var i=0; i<5; i++) {
  49             //MochiKit.Logging.log('adding child node '+i);
  50             var n = new Node(this);
  51
  52             var nodeName = 'node';
  53             n.setName(nodeName);
  54             n.openNode();
  55             if (i==2) {
  56                 p2=n;
  57                 p2.openNode();
  58                 p2.unHide();
  59                 //MochiKit.Logging.log('p2 is now ' + p2.getName());
  60             }
  61             this.rootnode.addChild(n);
  62
  63         }
  64
  65         for (i=0; i<3; i++) {
  66             //MochiKit.Logging.log('adding second level child nodes...');
  67             n = new Node(this);
  68             nodeName = 'subnode';
  69             n.setName(nodeName);
  70             n.openNode();
  71             p2.addChild(n);
  72         }
  73
  74     },
  75
  76     resetBrowser: function() {
  77
  78         //this.setSearchTerm();
  79         //this.setSearchValue();
  80         document.getElementById("ontology_browser_input").value='';
  81         document.getElementById("ontology_term_input").value='';
  82         //this.setSearchResults(); //this works
  83
  84         this.initializeBrowser();
  85
  86         this.render();
  87     },
  88
  89     setUpBrowser: function() {
  90         document.write('<div id="ontology_browser_input" >&nbsp;&nbsp;&nbsp;</div><div id="working"></div> '); // the element for the go id parentage search
  91         document.write('<div id="ontology_term_input" ></div>');     // the element for the search
  92         document.write('<input id="hide_link" type="button" value="show results" display="none" onClick="MochiKit.Visual.toggle(\'search_results\', \'blind\'); o.toggleSearchResultsVisible(); o.setSearchButtonText();  "><br />');
  93
  94         document.write('<div id="search_results" ></div>');
  95         document.write('<div id="ontology_browser" style="font-size:12px; line-height:10px; font-face:arial,helvetica" >&nbsp;</div>');  // the element for the browser
  96
  97
  98
  99     },
 100
 101     initializeBrowser: function() {
 102         this.setSelected();
 103         this.setSearchTerm('');
 104         this.setSearchValue('');
 105         this.setSearchResults('');
 106         this.fetchRoots();
 107         this.hideSearchButton();
 108         this.setSearchResponseCount(0);
 109         this.render();
 110     },
 111
 112     fetchRoots: function() {
 113         //MochiKit.Logging.log('THis in fetchRoots: ' + this);
 114
 115         new Ajax.Request("/chado/ajax_ontology_browser.pl", {
 116             parameters:   { action: 'roots' },
 117             asynchronous: false,
 118             on503: function() {
 119                 alert('An error occurred! The database may currently be unavailable. Please check back later.');
 120             },
 121             onSuccess: function(request) {
 122
 123                 //MochiKit.Logging.log('COMPLETE!');
 124
 125                 var responseText = request.responseText;
 126
 127                 //MochiKit.Logging.log('RESPONSETEXT = ' + responseText);
 128
 129                 //MochiKit.Logging.log('This = ' + this);
 130
 131                 o.rootnode = new Node(o);
 132
 133                 //MochiKit.Logging.log('Created root node. Yay!');
 134                 o.rootnode.setName('');
 135                 o.rootnode.setAccession('root');
 136                 o.rootnode.openNode();
 137                 o.rootnode.unHide();
 138                 o.rootnode.setHasChildren(true);
 139                 //MochiKit.Logging.log('root: ' + o.rootnode + ' ---- ' + o.rootnode.name);
 140
 141                 //MochiKit.Logging.log('fetching roots...');
 142
 143                 var t = responseText.split('#');
 144
 145                 //MochiKit.Logging.log('Children count ' +  t.length + '<br />');
 146
 147                 for (var i=0; i<t.length; i++) {
 148                     var j = t[i].split('*');
 149                     //  MochiKit.Logging.log(i + '. Child: ID: '+ j[0] + ' Name: ' + j[1] +  ' <br />');
 150
 151
 152                     //MochiKit.Logging.log('Processing '+j[0]);
 153
 154
 155                     var childNode = new Node(o);
 156
 157                     o.rootnode.addChild(childNode);
 158                     childNode.setAccession(j[0]);
 159                     //childNode.setHilite(true);
 160                     childNode.closeNode();
 161                     childNode.unHide();
 162                     childNode.setName(j[1]);
 163                     childNode.setCVtermID(j[2]);
 164                     childNode.setRelType(j[4]);
 165                     //MochiKit.Logging.log('hasChildren = '+j[2]);
 166                     if (j[3]==1) {
 167                         childNode.setHasChildren(true);
 168                     }
 169                     else {
 170                         childNode.setHasChildren(false);
 171                     }
 172
 173                     //MochiKit.Logging.log('Root node name: '+o.rootnode.getName()+'<br />');
 174                     //MochiKit.Logging.log('Child accession: '+childNode.getAccession()+'<br />');
 175
 176                 }
 177             }
 178         });
 179     },
 180
 181     workingMessage: function(status) {
 182         MochiKit.Logging.log('the working message = ' , status );
 183         var w = document.getElementById('working');
 184
 185         if (status) {
 186             //      MochiKit.Logging.log('status is true! ' , status);
 187             w.style.visibility='visible';
 188         }
 189         else {
 190             w.style.visibility='hidden';
 191         }
 192     },
 193
 194     renderSearchById: function() {
 195         //this.workingMessage(false);
 196         //MochiKit.Logging.log('the value of ontology_browser_input is ...', (document.getElementById('ontology_browser_input')).value);
 197
 198         var s = '<form name="search_id_form" style="margin-bottom:0" onSubmit="javascript:o.showParentage(this.ontology_browser_input.value); return false;" >';
 199         s += '<div id="search_by_id" style="width:700" style="margin-bottom:0" >';
 200         s += '<table summary="" cellpadding="5" cellspacing="0" ><tr><td align="center">';
 201         s += 'Ontology id&nbsp;&nbsp;&nbsp;&nbsp; <input id="ontology_browser_input" name="ontology_browser_input_name" type="text"  size="12" style="margin-bottom:0" /><input id="ontology_browser_submit" type="submit" style="margin-bottom:0" />';
 202         s += '&nbsp;|&nbsp;<input id="reset_hiliting" type="button" value="clear hiliting" onClick="javascript:o.clearHiliting()" style="margin-bottom:0" /> | <input id="reset_tree" type="button" value="reset" onClick="javascript:o.resetBrowser()" style="margin-bottom:0" />';
 203                 s += '</td><td align="right" width="*" ></td></tr></table>';
 204         s +='</div></form>';
 205
 206         var e = document.getElementById('ontology_browser_input');
 207         //MochiKit.Logging.log('the value of ontology_browser_input is ...',document.getElementById('ontology_browser_input').value);
 208         e.innerHTML = s;
 209         document.getElementById('ontology_browser_input').value=(o.getSearchTerm());
 210                 this.workingMessage(false);
 211     },
 212
 213     renderSearchByName: function() {
 214         //this.workingMessage(false);
 215         var s = '<form style="margin-bottom:0" name="SearchByNameForm" onsubmit="javascript:o.getOntologies(this.cv_select.value, this.ontology_term_input.value); return false;" >';
 216         s += '<div id="search_by_name"  style="margin-bottom:0" >';
 217         //s += '<form name="search_name_form" style="margin-bottom:0" >';
 218         s += '<table summary="" cellpadding="5" cellspacing="0"><tr><td align="center" >';
 219         s += 'Ontology term <input id="ontology_term_input" name="ontology_term_input_name" type="text" size="30"  />';
 220         s += '<select id="cv_select" >';
 221         s += '<option value="GO" ' + o.isSelected("GO") +'>GO (gene ontology)</option>';
 222         s += '<option value="PO" ' + o.isSelected("PO") +'>PO (plant ontology)</option>';
 223         s += '<option value="SP" ' + o.isSelected("SP") +'>SP (Solanaceae phenotypes)</option>';
 224         s += '<option value="PATO" ' + o.isSelected("PATO") +'>PATO (Phenotype and trait)</option>';
 225         s += '<option value="SO" ' + o.isSelected("SO") +'>SO (Sequence ontology)</option>';
 226
 227         s += '</select>';
 228         s += '<input id="term_search" type="submit" value="Search"  />';
 229         s += '</td></tr></table>';
 230         s += '</div></form>';
 231
 232         var e = document.getElementById('ontology_term_input');
 233         e.innerHTML = s;
 234         document.getElementById('ontology_term_input').value=(o.getSearchValue());
 235     },
 236
 237
 238     render: function() {
 239
 240         var s = '';
 241
 242         if (o.searchResults) {
 243             //s +='<input id="hide_link" type="button" value="'+o.getSearchButtonText()+'" onClick="MochiKit.Visual.toggle(\'search_results\', \'blind\'); o.toggleSearchResultsVisible(); o.setSearchButtonText(); "><br />';
 244             document.getElementById("hide_link").style.display="inline";
 245
 246         }
 247
 248         o.setSearchButtonText();
 249
 250         document.getElementById("search_results").innerHTML=this.getSearchResults();
 251         //      s +='<div id="search_results" >' + this.getSearchResults() + '</div>';
 252
 253         //s += '<div style="font-size:9pt; line-height:10px; font-face:arial,helvetica" >';
 254
 255         s = s + this.renderLevel(s, this.rootnode, 0);
 256         var e = document.getElementById('ontology_browser');
 257         s += '</div>';
 258         e.innerHTML = s;
 259
 260
 261
 262     },
 263
 264     renderLevel: function (s, node, level, last) {
 265         //MochiKit.Logging.log('renderLevel: ' + node.getName() + ', '+level);
 266
 267         var t = '';
 268
 269         if ((node == undefined) || (node.isHidden())) {
 270             //MochiKit.Logging.log('undefined or hidden node!');
 271         }
 272         else {
 273
 274             //MochiKit.Logging.log('level '+level);
 275             //for (var l=0; l<level; l++) {
 276             //              MochiKit.Logging.log('.');
 277             //}
 278
 279
 280             for (var i=0; i<level-1; i++) {
 281                 t += '<img src="/documents/img/tree_bar.png" border="0" />';
 282             }
 283
 284             if (node.hasChildren()) {
 285                 var key = node.getNodeKey();
 286                 if (node.getOpenNode()) {
 287
 288                     t +=  '<a href="javascript:o.closeNode('+key+')"><img src="/documents/img/tree_exp.png" border="0" /></a>';
 289
 290                 }
 291                 else {
 292
 293                     if (last) {
 294                         t += '<a href="javascript:o.openNode('+key+')"><img src="/documents/img/tree_col_end.png" border="0" /></a>';
 295                     }
 296                     else {
 297
 298                         t +=  '<b><a href="javascript:o.openNode('+key+')"><img src="/documents/img/tree_col.png" border="0" /></a></b>';
 299                     }
 300                 }
 301             }
 302             else {
 303                 if (last) {
 304                     t +=  '<img src="/documents/img/tree_end.png" border="0" />';
 305                 }
 306                 else {
 307                     t +=  '<img src="/documents/img/tree_bar_con.png" border="0" />';
 308                 }
 309             }
 310
 311
 312             t +=  node.renderNode(level);
 313
 314             level++;
 315
 316             if (node.getOpenNode()) {
 317
 318                 var c = node.children;
 319
 320                 //MochiKit.Logging.log('now processing node '+node.name + ', with '+c.length+' children nodes');
 321
 322                 var cs = new Array();
 323                 for(var i=0; i<c.length; i++) {
 324                     last = (i==c.length-1);
 325                     //MochiKit.Logging.log('<p>', c[i].accession, '</p>');
 326                     t = t + this.renderLevel(t, c[i], level, last);
 327
 328                 }
 329
 330             }
 331
 332         }
 333         return t;
 334         //MochiKit.Logging.log('renderLevel end');
 335     },
 336
 337     addNode: function(node) {
 338         //MochiKit.Logging.log('addNode: adding node ' + node.getName());
 339         var key = this.newNodeKey();
 340         node.setNodeKey(key);
 341         //MochiKit.Logging.log('generated node key '+key);
 342         this.nodelist[key]=node;
 343     },
 344
 345     getNode: function(key) {
 346         return this.nodelist[key];
 347     },
 348
 349
 350     closeNode: function(key) {
 351         var n = this.getNode(key);
 352         n.closeNode();
 353         this.render();
 354     },
 355
 356     openNode: function(key) {
 357         //MochiKit.Logging.log('opening node ' + key);
 358         this.workingMessage(true);
 359         var n = this.getNode(key);
 360         n.openNode();
 361         var c = n.getChildren();
 362         for (var i=0; i<c.length; i++) {
 363             c[i].unHide();
 364         }
 365         this.render();
 366         this.workingMessage(false);
 367     },
 368
 369     hideNode: function(key) {
 370         var n = this.getNode(key);
 371         n.hide();
 372         this.render();
 373     },
 374
 375     unHideNode: function(key) {
 376         this.getNode().unHide();
 377         this.render();
 378     },
 379
 380     findNode: function(node) {
 381     },
 382
 383     newNodeKey: function() {
 384         this.nodeKey++;
 385         return this.nodeKey;
 386     },
 387
 388     resetNodeKey: function() {
 389         this.nodeKey=0;
 390     },
 391
 392     showParentage: function(accession) {
 393         MochiKit.Logging.log('the accession is :', accession );
 394         this.setSearchTerm(accession);
 395         if (accession.length < 5) {
 396             alert('The search text must be longer than 4 characters');
 397             return;
 398         }
 399         this.workingMessage(true);
 400         var pL = this.getParentsList(accession);
 401
 402         MochiKit.Logging.log('Retrieved parents '+pL.join(' '));
 403
 404         var c = this.rootnode.getChildren();
 405         for (var i=0; i<c.length; i++) {
 406             this.recursiveParentage(c[i], pL, accession);
 407             this.render();
 408         }
 409         this.workingMessage(false);
 410     },
 411
 412     //this is called when a search term is clicked from the search results list.
 413     //we explicitly hide the search results.
 414     searchTermParentage: function(accession) {
 415         o.hideSearchResults();
 416         o.showParentage(accession);
 417     },
 418
 419     getSearchTerm: function() {
 420         return this.searchTerm;
 421     },
 422
 423     setSearchTerm: function(searchTerm) {
 424         this.searchTerm = searchTerm;
 425     },
 426     getSearchValue: function() {
 427         return this.searchValue;
 428     },
 429
 430     setSearchValue: function(searchValue) {
 431         this.searchValue = searchValue;
 432     },
 433
 434     recursiveParentage: function(currentNode, parentsList, accession) {
 435
 436         if (currentNode.getAccession() == accession) {
 437             //MochiKit.Logging.log('unHiding '+currentNode.getAccession() + ' ' + accession);
 438             currentNode.unHide();
 439             currentNode.setHilite(true);
 440         }
 441         else {
 442
 443             //MochiKit.Logging.log('node is ' + currentNode.getAccession() + ' accession= ' , accession);
 444             if (this.hasMatch(parentsList, currentNode.getAccession())) { // indexOf does not seem to be implemented widely.
 445                 //MochiKit.Logging.log('Opening node '+ currentNode.getName());
 446                 currentNode.openNode();
 447                 currentNode.unHide();
 448             }
 449             else {
 450                 //MochiKit.Logging.log('Current node '+currentNode.getAccession()+' does not match parent list ' + parentsList.join(' '));
 451                 currentNode.hide();
 452             }
 453
 454             var c = currentNode.getChildren();
 455             for (var i=0; i<c.length; i++) {
 456                 this.recursiveParentage(c[i], parentsList, accession);
 457             }
 458         }
 459     },
 460
 461     //check if a list contains a certain member
 462     hasMatch: function(list, value) {
 463         for (var i=0; i<list.length; i++) {
 464             if (list[i] == value) {
 465                 return true;
 466             }
 467         }
 468         return false;
 469     },
 470
 471     //clears all hiliting in the tree.
 472     clearHiliting: function() {
 473         this.recursiveHiliteClearing(this.rootnode);
 474         this.render();
 475     },
 476
 477     recursiveHiliteClearing: function(node) {
 478         node.setHilite(false);
 479         var c = node.getChildren();
 480         for (var i=0; i<c.length; i++) {
 481             this.recursiveHiliteClearing(c[i]);
 482         }
 483     },
 484
 485     getParentsList: function(accession) {
 486         //MochiKit.Logging.log('Fetching children for node '+this.getName());
 487
 488         var parentsList = new Array();
 489
 490
 491         new Ajax.Request('/chado/ajax_ontology_browser.pl', {
 492             parameters: { node: accession, action: 'parents' },
 493             asynchronous: false,
 494                               on503: function() {
 495                 alert('An error occurred! The database may currently be unavailable. Please check back later.');
 496             },
 497
 498             onSuccess: function(request) {
 499
 500                 var responseText = request.responseText;
 501
 502                 var t = responseText.split('#');
 503
 504                 //MochiKit.Logging.log('Children count ' +  t.length);
 505
 506                 for (var i=0; i<=t.length; i++) {
 507                     var j = t[i].split('*');
 508                     //MochiKit.Logging.log(i + '. Parent: ID: '+ j[0] + ' Name: ' + j[1], '' );
 509
 510                     //MochiKit.Logging.log('Processing '+j[0]);
 511                     parentsList.push(j[0]);
 512
 513                     //MochiKit.Logging.log('Child accession: '+childNode.getAccession());
 514
 515                 }
 516
 517                 //MochiKit.Logging.log('Rendering again...');
 518                 //parentNode.browser.render();
 519
 520             }
 521
 522                               });
 523         return parentsList;
 524     },
 525
 526     //Make an ajax response that finds all the ontology terms with names/definitions/synonyms/accessions like the current value of the ontology input
 527     getOntologies: function(db_name, search_string) {
 528         this.workingMessage(true);
 529         //      var search_string= document.getElementById('ontology_term_input').value;
 530         //      var db_name = document.getElementById('cv_select').value;
 531         o.setSelected(db_name);
 532         if(search_string.length<4){
 533             alert('The search text must be longer than 4 characters');
 534         }
 535         else{
 536             new Ajax.Request('/chado/ajax_ontology_browser.pl', {
 537                 parameters: {action: 'match', term_name: search_string, db_name: db_name },
 538                 asynchronous: false,
 539                             on503: function() {
 540                 alert('An error occurred! The database may currently be unavailable. Please check back later.');
 541             },
 542
 543                 onSuccess: function(request) {
 544                     var matchNodes = new Array();
 545                     var responseText = request.responseText;
 546
 547                     var responseArray = responseText.split('|');
 548                     responseArray.pop();
 549
 550                     var s='';
 551                     o.setSearchResponseCount(responseArray.length);
 552                     MochiKit.Logging.log('Matched '+responseArray.length+' terms');
 553                     for (var i=0; i<responseArray.length; i++) {
 554                         var ontologyObject = responseArray[i].split('--');
 555                         var searchResults= responseArray[i].split('*');
 556                         MochiKit.Logging.log('getOntologies found term ',  ontologyObject[1] );
 557                         MochiKit.Logging.log('search term ', search_string);
 558                         matchNodes.push(ontologyObject[0]); ///
 559                         s +='<a href=javascript:o.searchTermParentage(\''+ontologyObject[1]+'\')>'+searchResults[1]+'</a><br />';
 560                     }
 561         //                  MochiKit.Logging.log('the search results:' , s) ;
 562                     MochiKit.Logging.log('the search string:' , search_string) ;
 563
 564                     if (s === '') { s = '(no terms found) '; }
 565                     o.setSearchResults('<div class="topicbox">Search term: <b>'+search_string+'</b></div><div class="topicdescbox">'+s+'</div>');
 566                     o.showSearchResults();
 567                     o.setSearchValue(search_string);
 568
 569                     o.render();
 570                 }
 571             });
 572         }
 573         this.workingMessage(false);
 574
 575     },
 576
 577     getSearchResults: function() {
 578         return this.searchResults || '';
 579     },
 580
 581     setSearchResults: function(searchResults) {
 582         //MochiKit.Logging.log('searh results= ',searchResults);
 583         this.searchResults = searchResults;
 584     },
 585
 586     //showSearchResults, hideSearchResults
 587     //
 588     //hides the result section of the search but keeps the
 589     //the un/hide toggle button visible
 590     //
 591     showSearchResults: function() {
 592         this.showResults = true;
 593         this.showSearchButton();
 594         this.setSearchButtonText();
 595         document.getElementById('search_results').style.display='inline';
 596     },
 597
 598     hideSearchResults: function() {
 599         this.showResults = false;
 600         this.setSearchButtonText();
 601         document.getElementById('search_results').style.display='none';
 602     },
 603
 604     //accessor setSearchResponseCount, getSearchResponseCount
 605     //property defines how many items were found in the search
 606     //used to display that number in the un/hide toggle button
 607     setSearchResponseCount: function(c) {
 608         this.searchCount = c;
 609     },
 610
 611     getSearchResponseCount: function() {
 612         return this.searchCount || 0;
 613     },
 614
 615     toggleSearchResultsVisible: function() {
 616         if (this.isSearchResultsVisible() === true) { this.hideSearchResults(); }
 617         else {
 618             this.showSearchResults();
 619         }
 620     },
 621
 622     isSearchResultsVisible: function() {
 623         return this.showResults;
 624     },
 625
 626
 627     hideSearchButton: function() {
 628         document.getElementById("hide_link").style.display="none";
 629     },
 630
 631     showSearchButton: function() {
 632         document.getElementById("hide_link").style.display="inline";
 633     },
 634
 635
 636
 637
 638
 639     setSearchButtonText: function() {
 640
 641         if (this.getSearchResponseCount() === 0) {
 642             this.hideSearchButton();
 643         }
 644         else {
 645             this.showSearchButton();
 646         }
 647
 648
 649         if (this.isSearchResultsVisible()) {
 650             this.searchButtonText = 'hide ' + this.getSearchResponseCount() + ' results';
 651         }
 652         else {
 653             this.searchButtonText = 'show '+this.getSearchResponseCount()+ ' results';
 654         }
 655
 656
 657         if (document.getElementById('hide_link')) {
 658             document.getElementById('hide_link').value=this.searchButtonText;
 659         }
 660         return this.searchButtonText;
 661     },
 662
 663     getSelected: function() {
 664         return this.selected || '';
 665     },
 666
 667     setSelected: function(selected) {
 668         this.selected = selected;
 669     },
 670
 671     isSelected: function(db_name) {
 672         var selected_db_name=o.getSelected();
 673         if (selected_db_name == db_name) {
 674             return 'SELECTED' ;
 675         }else { return '' ; }
 676     },
 677
 678
 679     // the following function is deprecated.
 680     //
 681     fetchMatches: function (searchText) {
 682
 683         //MochiKit.Logging.log('Fetching children for node '+this.getName());
 684
 685         new Ajax.Request('/chado/ajax_ontology_browser.pl', {
 686             parameters: { node: searchText, action: 'match' },
 687             asynchronous: false,
 688                     on503: function() {
 689                 alert('An error occurred! The database may currently be unavailable. Please check back later.');
 690             },
 691
 692             onSuccess: function(request) {
 693
 694                 //MochiKit.Logging.log('HELLO WORLD!');
 695                 var matchNodes = new Array();
 696                 var responseText = request.responseText;
 697
 698                 var t = responseText.split('#');
 699
 700                 //             t.pop(); //remove last element from the array
 701
 702                 //MochiKit.Logging.log('Matched '+t.length+' nodes');
 703                 for (var i=0; i<t.length; i++) {
 704                     var j = t[i].split('*');
 705
 706                     //MochiKit.Logging.log('matching node: '+ j[0]);
 707                     matchNodes.push(j[0]); ///
 708                 }
 709
 710                 return matchNodes;
 711             }
 712         });
 713
 714     },
 715
 716     setLinkToTextField: function(linkToTextField) {
 717         this.linkToTextField=linkToTextField;
 718     },
 719
 720     setShowSelectTermButtons: function(showLinks) {
 721         this.showLinks = showLinks;
 722     },
 723
 724     getShowSelectTermButtons: function() {
 725         return this.showLinks;
 726     },
 727
 728     copySelectedToTextField: function(node) {
 729         var copyToElement = document.getElementById(node.linkToTextField);
 730         if (copyToElement != undefined) {
 731             copyToElement.setValue(node.getName());
 732         }
 733
 734     }
 735
 736 //     submitFormWithEnter: function(myfield,e) {
 737 //      var keycode;
 738 //      if (window.event) keycode = window.event.keyCode;
 739 //      else if (e) keycode = e.which;
 740 //      else return true;
 741
 742 //      if (keycode == 13)
 743 //      {
 744 //          myfield.form.submit();
 745 //          return false;
 746 //      }
 747 //      else
 748 //      return true;
 749 //     }
 750
 751 };
 752
 753
 754
 755 Node = function(browser) {
 756     //MochiKit.Logging.log('Node constructor...');
 757     this.children = new Array();
 758     this.parents = new Array();
 759     this.browser = browser;
 760     //MochiKit.Logging.log('adding node to the browser...');
 761
 762     this.browser.addNode(this);
 763     //MochiKit.Logging.log('done...');
 764     this.nodeId=0;
 765
 766     //MochiKit.Logging.log('Node constructor: Created node.');
 767 };
 768
 769 Node.prototype = {
 770
 771     setName: function(name) {
 772         this.name=name;
 773     },
 774
 775     getName: function() {
 776         return this.name;
 777     },
 778
 779     setAccession: function(accession) {
 780         this.accession=accession;
 781     },
 782
 783     getAccession: function() {
 784         return this.accession;
 785     },
 786
 787     setCVtermID: function(cvtermid) {
 788         this.cvtermid=cvtermid;
 789     },
 790
 791     getCVtermID: function() {
 792         return this.cvtermid;
 793     },
 794
 795     setNodeKey: function(key) {
 796         this.nodeKey = key;
 797     },
 798
 799     getNodeKey: function() {
 800         return this.nodeKey;
 801     },
 802
 803     setBrowser: function(browser) {
 804         this.browser = browser;
 805     },
 806
 807     getBrowser: function() {
 808         return this.browser;
 809     },
 810
 811     setOpenNode: function(status) {
 812         this.nodeOpen = status;
 813     },
 814
 815     getOpenNode: function() {
 816         return this.nodeOpen;
 817     },
 818     setRelType: function(reltype) {
 819         this.reltype=reltype;
 820     },
 821
 822     getRelType: function() {
 823         return this.reltype;
 824     },
 825     openNode: function() {
 826         this.setOpenNode(true);
 827         if (this.hasChildren() && !this.getChildrenFetched()) {
 828             this.fetchChildren(this);
 829             this.setChildrenFetched(true);
 830         }
 831     },
 832
 833     closeNode: function() {
 834         this.setOpenNode(false);
 835     },
 836
 837     hide: function() {
 838         this.hidden = true;
 839     },
 840
 841     unHide: function() {
 842         this.hidden = false;
 843     },
 844
 845     isHidden: function() {
 846         return this.hidden;
 847     },
 848
 849     setChildrenFetched: function(fetched) {
 850         this.childrenFetched=fetched;
 851     },
 852
 853     getChildrenFetched: function() {
 854         return this.childrenFetched;
 855     },
 856
 857     setParentsFetched: function(fetched) {
 858         this.parentsFetched = fetched;
 859     },
 860
 861     getParentsFetched: function() {
 862         return this.parentsFetched;
 863     },
 864
 865     addChild: function (child) {
 866         //MochiKit.Logging.log('Adding child '+child.name + ' to '+ this.name);
 867         var c = child;
 868         var p = this;
 869         this.children.push(c);
 870         child.parents.push(p);
 871     },
 872
 873     getChildren: function () {
 874         return this.children;
 875     },
 876
 877     setParents: function(p) {
 878         this.parents = p;
 879     },
 880
 881     getParents: function() {
 882         return this.parents;
 883     },
 884
 885     setHasChildren: function(childrenFlag) {
 886         this.childrenFlag = childrenFlag;
 887     },
 888
 889     hasChildren: function() {
 890         //MochiKit.Logging.log('Number of children for node '+this.getName()+' is ' +this.children.length);
 891         //if (this.children.length > 0) {
 892         //    return true;
 893         //      }
 894         //else {
 895         //    return false;
 896         //}
 897         return this.childrenFlag;
 898     },
 899
 900     addParent: function (parent) {
 901         var p = parent;
 902         this.parents.push(p);
 903     },
 904
 905     getParents: function () {
 906         if (!this.getParentsFetched()) {
 907             var p = this.fetchParents;
 908             this.parents = p;
 909         }
 910         return this.parents;
 911     },
 912
 913     renderNode: function (level) {
 914         //MochiKit.Logging.log('Rendering node '+this.getName());
 915
 916         //      if (this.getOpenNode()) {
 917         //create indent
 918
 919         //write out link
 920
 921         var hiliteStyle = 'background-color:white';
 922         if (this.isHilited()) {
 923             hiliteStyle = 'background-color:yellow';
 924         }
 925
 926         // add a button to select this node and fill it into a textfield
 927         // as provided by linkToTextField
 928         var link = "";
 929         //      if (this.getBrowser().linkToTextField==true) {
 930         if (this.getBrowser().getShowSelectTermButtons()) {
 931             link = '<a href="javascript:o.copySelectedToTextField(this)"><img src="/documents/img/select.png" border="0" /></a>';
 932         }
 933
 934         var relType=this.getRelType() || '';
 935         return relType + ' <span style="'+hiliteStyle+'"><a href="/chado/cvterm.pl?action=view&amp;cvterm_id='+this.getCVtermID()+'">'+this.getAccession() + '</a> ' + this.getName() + ' ' + link +'</span><br />';
 936     },
 937
 938     setHilite: function(h) {
 939         this.hilite=h;
 940     },
 941
 942
 943     isHilited: function() {
 944         return this.hilite;
 945     },
 946
 947     fetchChildren: function () {
 948
 949         //MochiKit.Logging.log('Fetching children for node '+this.getName());
 950
 951         var parentNode = this;
 952         new Ajax.Request('/chado/ajax_ontology_browser.pl', {
 953             parameters: { node: parentNode.getAccession(), action: 'children' },
 954                           asynchronous: false,
 955             on503: function() {
 956                 alert('An error occurred! The database may currently be unavailable. Please check back later.');
 957             },
 958
 959            onSuccess: function(request) {
 960
 961
 962                               //MochiKit.Logging.log('HELLO WORLD!');
 963
 964                               var responseText = request.responseText;
 965
 966                               var t = responseText.split('#');
 967
 968                               //MochiKit.Logging.log('Children count ' +  t.length + '<br />');
 969
 970                               for (var i=0; i<t.length; i++) {
 971                                   var j = t[i].split('*');
 972                                   //MochiKit.Logging.log(i + '. Child: ID: '+ j[0] + ' Name: ' + j[1] +  ' <br />');
 973
 974                                   //MochiKit.Logging.log('Processing '+j[0]);
 975
 976                                   var childNode = new Node(o);
 977
 978                                   childNode.setAccession(j[0]);
 979                                   childNode.closeNode();
 980                                   childNode.unHide();
 981                                   childNode.setName(j[1]);
 982                                   childNode.setCVtermID(j[2]);
 983                                   childNode.setRelType(j[4]);
 984                                   //MochiKit.Logging.log('hasChildren = '+j[2]);
 985                                   if (j[3]==1) {
 986                                       childNode.setHasChildren(true);
 987                                   }
 988                                   else {
 989                                       childNode.setHasChildren(false);
 990                                   }
 991
 992                                   parentNode.addChild(childNode);
 993
 994                                   //MochiKit.Logging.log('Child accession: '+childNode.getAccession()+'<br />');
 995
 996                               }
 997                               //MochiKit.Logging.log('Rendering again...');
 998                               parentNode.browser.render();
 999
1000                           }
1001                                             });
1002     },
1003
1004
1005     fetchParents: function() {
1006         //MochiKit.Logging.log('Fetching children for node '+this.getName());
1007
1008         var childNode = this;
1009
1010         new Ajax.Request("/chado/ajax_ontology_browser.pl", {
1011             parameters: { node: childNode.getAccession(), action: 'parents' },
1012               asynchronous: false,
1013               onSuccess: function(request) {
1014
1015                   //MochiKit.Logging.log('HELLO WORLD!');
1016
1017                   var responseText = request.responseText;
1018
1019                   var t = responseText.split('#');
1020
1021                   //MochiKit.Logging.log('Children count ' +  t.length + '<br />');
1022
1023                   for (var i=0; i<t.length; i++) {
1024                       var j = t[i].split('*');
1025                       //MochiKit.Logging.log(i + '. Child: ID: '+ j[0] + ' Name: ' + j[1] +  ' <br />');
1026
1027                       //MochiKit.Logging.log('Processing '+j[0]);
1028                       var parent = new Node(o);
1029
1030                       parent.setAccession(j[0]);
1031                       parent.closeNode();
1032                       parent.unHide();
1033                       parent.setName(j[1]);
1034                       parent.setCVtermID(j[2]);
1035                       parent.setRelType(j[4]);
1036                       //MochiKit.Logging.log('hasChildren = '+j[1]);
1037                       if (j[3]==1) {
1038                           parent.setHasChildren(true);
1039                       }
1040                       else {
1041                           parent.setHasChildren(false);
1042                       }
1043
1044                       parentList.push(parent);
1045
1046                       //MochiKit.Logging.log('Child accession: '+childNode.getAccession()+'<br />');
1047
1048                   }
1049                   //MochiKit.Logging.log('Rendering again...');
1050                   //parentNode.browser.render();
1051                   return parentList;
1052               }
1053                                 });
1054     }
1055
1056
1057 };