documents/inc/secretary.js

   1 /*** Third-party Javascript Code **************************************************************************
   2 **********************************************************************************************************
   3 */
   4
   5 /** NOTICE: This code has been modified for ease of use.  Please download the original from
   6 http://www.jaaulde.com/test_bed/cookieLib/ for the original (and latest) versions
   7 /*
   8 Copyright (c) 2005, James Auldridge
   9 All rights reserved.
  10 Code licensed under the BSD License:
  11   http://www.jaaulde.com/license.txt
  12 Version 1.2
  13 */
  14 var Cookie = window.Cookie || {};
  15 Cookie = {
  16         get: function(cookieName) {
  17                 var cookieNameStart,valueStart,valueEnd,value;
  18                 cookieNameStart = document.cookie.indexOf(cookieName+'=');
  19                 if (cookieNameStart < 0) {return null;}
  20                 valueStart = document.cookie.indexOf(cookieName+'=') + cookieName.length + 1;
  21                 valueEnd = document.cookie.indexOf(";",valueStart);
  22                 if (valueEnd == -1){valueEnd = document.cookie.length;}
  23                 value = document.cookie.substring(valueStart,valueEnd );
  24                 value = unescape(value);
  25                 if (value == "") {return null;}
  26                 return value;
  27         },
  28         set: function(cookieName,value,hoursToLive,path,domain,secure) {
  29                 var domainRegEx = /[^.]+\.[^.]+$/;
  30                 domain = window.location.hostname.match(domainRegEx);
  31                 if(domain == 'cornell.edu') domain = 'sgn.cornell.edu';
  32                 var expireString,timerObj,expireAt,pathString,domainString,secureString,setCookieString;
  33                 if (!hoursToLive || typeof hoursToLive != 'number' || parseInt(hoursToLive)=='NaN'){
  34                         expireString = "";
  35                 }
  36                 else {
  37                         timerObj = new Date();
  38                         timerObj.setTime(timerObj.getTime()+(parseInt(hoursToLive)*60*60*1000));
  39                         expireAt = timerObj.toGMTString();
  40                         expireString = "; expires="+expireAt;
  41                 }
  42                 pathString = "; path=";
  43                 (!path || path=="") ? pathString += "/" : pathString += path;
  44                 domainString = "; domain=";
  45                 (!domain || domain=="") ? domainString += window.location.hostname : domainString += domain;
  46                 (secure === true) ? secureString = "; secure" : secureString = "";
  47                 value = escape(value);
  48                 setCookieString = cookieName+"="+value+expireString+pathString+domainString;
  49                 document.cookie = setCookieString;
  50         },
  51         del: function(cookieName,path,domain){
  52           (!path || !path.length) ? path="" : path=path;
  53           (!domain || !domain.length) ? domain="" : domain=domain;
  54                 Cookie.utils.cookies.set(cookieName,"",-8760,path,domain);
  55         },
  56         test: function(){
  57                 Cookie.utils.cookies.set('cT','acc');
  58                 var runTest = Cookie.utils.cookies.get('cT');
  59                 if (runTest == 'acc'){
  60                         Cookie.utils.cookies.del('cT');
  61                         testStatus = true;
  62                 }
  63                 else {
  64                         testStatus = false;
  65                 }
  66                 return testStatus;
  67         }
  68 };
  69
  70
  71
  72 /** Javascript Code written by C. Carpita and ******* ***************************************************
  73 *********************************************************************************************************
  74 *********************************************************************************************************
  75
  76
  77
  78
  79 /**
  80 ************** Misc Secretary Functions ***********************************HEADER************************
  81 **/
  82
  83 function getSel() {
  84         var txt = '';
  85         var foundIn = '';
  86         document.getElementById('selectedblastp').innerHTML = "";
  87         document.getElementById('selectedblastnfull').innerHTML = "";
  88         document.getElementById('selectedblastncds').innerHTML = "";
  89
  90         if (window.getSelection)
  91         {
  92                 txt = window.getSelection();
  93                 foundIn = 'window.getSelection()';
  94         }
  95         else if (document.getSelection)
  96         {
  97                 txt = document.getSelection();
  98                 foundIn = 'document.getSelection()';
  99         }
 100         else if (document.selection)
 101         {
 102                 txt = document.selection.createRange().text;
 103                 foundIn = 'document.selection.createRange()';
 104         }
 105         else return false;
 106         //fixtxt = txt.replace(/<br>/ig, "");
 107         var fixtxt = new String(txt);
 108
 109         fixtxt = fixtxt.replace(/\W/ig, "");
 110         if (fixtxt.match(/^[A-Z]+$/)) {
 111                 return fixtxt;
 112         }
 113         else return false;
 114 }
 115
 116 function selectedblastp(selection){
 117       HTML = "<a class='external' href='http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&QUERY=" + selection + "&DATABASE=nr&PROGRAM=blastp&FILTER=L&HITLIST_SZE=500'>Perform BLASTP on Selection (" + selection.length + " aa)</a>";
 118       document.getElementById('selectedblastp').innerHTML = HTML;
 119
 120 }
 121
 122 function selectedblastnfull(selection){
 123       HTML = "<a class='external' href='http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&QUERY=" + selection + "&DATABASE=nr&PROGRAM=blastn&FILTER=L&HITLIST_SZE=500'>Perform BLASTN on Selection (" + selection.length + " bp)</a>";
 124       document.getElementById('selectedblastnfull').innerHTML = HTML;
 125 }
 126
 127 function selectedblastncds(selection){
 128       HTML = "<a class='external' href='http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&QUERY=" + selection + "&DATABASE=nr&PROGRAM=blastn&FILTER=L&HITLIST_SZE=500'>Perform BLASTN on Selection (" + selection.length + " bp)</a>";
 129       document.getElementById('selectedblastncds').innerHTML = HTML;
 130 }
 131
 132
 133 function closebox(boxID) {
 134         document.getElementById(boxID).style.display="none";
 135         return false;
 136 }
 137
 138 /** Only works on <span> tags for a given class name, currently alters the following properties:
 139 ***** color, backgroundColor, border, fontWeight  **/
 140 function classAlter(className, styleProperty, styleValue) {
 141         for (i=0;i<document.getElementsByTagName("span").length; i++) {
 142                 if (document.getElementsByTagName("span").item(i).className == className){
 143                         if(styleProperty == "color"){
 144                                 document.getElementsByTagName("span").item(i).style.color = styleValue;
 145                         }
 146                         else if(styleProperty == "backgroundColor"){
 147                                 document.getElementsByTagName("span").item(i).style.backgroundColor = styleValue;
 148                         }
 149                         else if(styleProperty == "border"){
 150                                 document.getElementsByTagName("span").item(i).style.border = styleValue;
 151                         }
 152                         else if(styleProperty == "fontWeight"){
 153                                 document.getElementsByTagName("span").item(i).style.fontWeight = styleValue;
 154                         }
 155                 }
 156         }
 157 }
 158
 159 /* Must match value in class highlightColor of the css file
 160 */
 161 var searchHighlightColor = "#c9c9ff";
 162 var searchHighlight = 0;
 163
 164 //Ensures that cookie object is instantiated, as well as Highlight Toggle-dependent functions
 165 function prepareSearchHighlight(){
 166         if(Cookie){
 167                 if(UserPrefs.get('searchHighlight')){
 168                         searchHighlight = UserPrefs.get('searchHighlight');
 169                 }
 170         }
 171         //Ok, this may look weird.  What we are doing is priming browser cache by calling the toggle function, which calls the classAlter function
 172         // and iterates through all of the <span> tags.  Therefore, the switches occur more quickly when the user first clicks the button.
 173         if (searchHighlight == 1){
 174                 searchHighlight = 0;
 175                 toggleSearchHighlight();  //this will set searchHighlight back to 1, don't worry ;)
 176         }
 177         else{
 178                 searchHighlight = 1;
 179                 toggleSearchHighlight();
 180         }
 181 }
 182
 183 function toggleSearchHighlight(nocookieset){
 184         if(searchHighlight){
 185                 classAlter("searchHighlight", "backgroundColor", "white");
 186                 document.getElementById("highlightSelector").style.display = "inline";
 187                 document.getElementById("unhighlightSelector").style.display = "none";
 188                 searchHighlight = 0;
 189                 UserPrefs.set('searchHighlight', 0);
 190                 if(!nocookieset) UserPrefs.setCookie();
 191         }
 192         else {
 193                 classAlter("searchHighlight", "backgroundColor", searchHighlightColor);
 194                 document.getElementById("highlightSelector").style.display = "none";
 195                 document.getElementById("unhighlightSelector").style.display = "inline";
 196                 searchHighlight = 1;
 197                 UserPrefs.set('searchHighlight', 1);
 198                 if(!nocookieset) UserPrefs.setCookie();
 199         }
 200 }
 201
 202 /**
 203 ************** Secretary Database Query Functions *********************HEADER*****************************
 204 **/
 205
 206
 207 var selectTextColorBg = "#771111"; //background color of active text
 208 var selectTextColor = "#332277";  //color of unselected checkbox text
 209
 210 var joiners = new Array();
 211
 212 for(var i=0; i<10; i++) joiners.push("AND");
 213
 214 function selectModify(num, type){
 215
 216         if(type=='rem'){
 217                 document.getElementById("condcontainer" + num).style.display = "none";
 218                 document.getElementById("selrem" + num).style.display = "none";
 219                 if(num<10) document.getElementById("seladd" + num).style.display = "none";
 220                 document.getElementById("seladd" + (num-1)).style.display = "inline";
 221                 if (num > 1) document.getElementById("selrem" + (num-1)).style.display = "inline";
 222                 document.getElementById("condvar"+num).value="";
 223                 document.getElementById("condop"+num).value="=";
 224                 document.getElementById("condoperand"+num).value="";
 225         }
 226         if(type=='add'){
 227                 if(num<10) document.getElementById("condcontainer" + (num+1)).style.display="inline";
 228                 if(num<10) document.getElementById("selrem" + (num+1)).style.display="inline";
 229                 if(num<9) document.getElementById("seladd" + (num+1)).style.display="inline";
 230                 document.getElementById("seladd" + num).style.display="none";
 231                 if(num>0) document.getElementById("selrem" + num).style.display="none"
 232         }
 233 }
 234
 235 function selectSwitch(value, item){
 236         box = document.getElementById("cb." + value);
 237         text = document.getElementById("text." + value);
 238
 239         if(item){
 240                 box = document.getElementById("cb." + value + "." + item);
 241                 text = document.getElementById("text." + value + "." + item);
 242         }
 243         if(box.checked) {
 244                 box.checked = false;
 245                 text.style.backgroundColor = "white";
 246                 text.style.color = selectTextColor;
 247                 text.style.fontWeight = "normal";
 248         }
 249         else {
 250                 box.checked = true;
 251                 text.style.backgroundColor = selectTextColorBg;
 252                 text.style.color = "white";
 253                 text.style.fontWeight = "bold";
 254
 255                 if(value != "COUNT"){
 256                                 document.getElementById("cb.COUNT").checked = false;
 257                                 text = document.getElementById("text.COUNT");
 258                                 text.style.color = "#332277"
 259                                 text.style.backgroundColor = "white";
 260                                 text.style.fontWeight = "normal";
 261                 }
 262         }
 263 }
 264
 265
 266
 267 function cbColorSwitch(value, item){
 268
 269         box = document.getElementById("cb." + value);
 270         text = document.getElementById("text." + value);
 271
 272         if(item){
 273                 box = document.getElementById("cb." + value + "." + item);
 274                 text = document.getElementById("text." + value + "." + item);
 275         }
 276
 277
 278         if(!box.checked) {
 279                 text.style.backgroundColor = "white";
 280                 text.style.color = selectTextColor;
 281                 text.style.fontWeight = "normal";
 282         }
 283         else {
 284                 text.style.backgroundColor = selectTextColorBg;
 285                 text.style.color = "white";
 286                 text.style.fontWeight = "bold";
 287         }
 288 }
 289
 290
 291 function switchJoin(id){
 292         joinercontent = document.getElementById("joinercontent"+id);
 293         formjoiner = document.getElementById("formjoiner" + id);
 294         if (joinercontent.innerHTML=="AND"){
 295                 joinercontent.innerHTML="OR";
 296                 joiners[id-1] = "OR";
 297                 formjoiner.value = "OR";
 298         }
 299         else{
 300                 joinercontent.innerHTML="AND";
 301                 joiners[id-1] = "AND";
 302                 formjoiner.value = "AND";
 303         }
 304 }
 305
 306 function switchParen(id){
 307         formparen = document.getElementById("formparen"+id);
 308         parencontent = document.getElementById("parencontent"+id);
 309         jointop = document.getElementById("jointop"+id);
 310         joinbottom = document.getElementById("joinbottom"+id);
 311
 312         if(formparen.value=='0'){
 313                 formparen.value=1;
 314                 parencontent.innerHTML = "<span style='color:#442277'>(Unjoin)</span>";
 315                 jointop.innerHTML="";
 316                 joinbottom.innerHTML="";
 317         }
 318         else{
 319                 formparen.value=0;
 320                 parencontent.innerHTML = "(Join)";
 321                 jointop.innerHTML="<br>";
 322                 joinbottom.innerHTML="<br>";
 323         }
 324
 325 }
 326
 327 function variableChange(id){
 328         variable = document.getElementById("condvar" + id);
 329         operator = document.getElementById("condop" + id);
 330         type = variable.value.charAt(0);
 331         if(type=="f" || type=="i") operator.value = ">";
 332         else if(type=="r") operator.value = "REGEXP";
 333         else if(type=="t") operator.value = "FULLTEXT";
 334 }
 335
 336 function chartTypeChange(){
 337         ctype = document.getElementById("charttype");
 338         pie_opt = document.getElementById("pie_options");
 339         bar_opt = document.getElementById("bar_options");
 340         if(ctype.value==''){
 341                 pie_opt.style.display = "none";
 342                 bar_opt.style.display = "none";
 343         }
 344         else if(ctype.value=="pie"){
 345                 pie_opt.style.display = "block";
 346                 bar_opt.style.display = "none";
 347         }
 348         else{
 349                 pie_opt.style.display = "none";
 350                 bar_opt.style.display = "block";
 351         }
 352 }
 353
 354 var num=0;
 355 var live=1;
 356 var last=3;
 357
 358 function killAnimateDots(){
 359         live = 0;
 360 }
 361
 362 function animateDots(){
 363         num = num+1;
 364         if(num>3) num = 0;
 365         last = num - 1;
 366         if(last<0) last = 3;
 367
 368         document.getElementById("dots"+last).style.display="none";
 369         document.getElementById("dots"+num).style.display="inline";
 370
 371         if(live) setTimeout("animateDots()", 500);
 372 }
 373
 374
 375 function closeBox(name){
 376         document.getElementById(name+"_hide").style.display="none";
 377         document.getElementById(name+"_show").style.display="inline";
 378         document.getElementById(name+"_table").style.display="none";
 379         document.getElementById(name+"_box").style.borderColor="#555555";
 380         document.getElementById(name+"_header").style.backgroundColor="#555555";
 381 }
 382
 383 function openBox(name){
 384         document.getElementById(name+"_hide").style.display="inline";
 385         document.getElementById(name+"_show").style.display="none";
 386         document.getElementById(name+"_table").style.display="inline";
 387
 388         var activeColor = "";
 389         if(name=="chart") activeColor = "#444499";
 390         else if(name=="select") activeColor = "#770000";
 391         else if(name=="cond") activeColor = "#551155";
 392
 393         document.getElementById(name+"_box").style.borderColor = activeColor;
 394         document.getElementById(name+"_header").style.backgroundColor = activeColor;
 395 }
 396
 397
 398 /**
 399 *************** Hotlist Functions ***************************HEADER****************************************
 400 **/
 401
 402 //var user_pref_string is used (global already set in header))
 403 //Used to set user_pref_string variables for the current user.
 404 var UserPrefs = {
 405         _preferences: new Object,
 406         init: function() {
 407
 408                 //the string is initially set server-side, so if we don't get
 409                 //anything, we try the client-side cookie
 410                 if(!user_pref_string.length) UserPrefs.loadCookie();
 411
 412                 if(user_pref_string.length && user_pref_string.indexOf('=') && user_pref_string.indexOf(":")) {
 413                         var pref_array = user_pref_string.split(":");
 414                         for(var n = 0; n < pref_array.length; n++) {
 415                                 var key_val = pref_array[n].split("=");
 416                                 if(key_val[0].length>0 && key_val[1].length>0){
 417                                         UserPrefs._preferences[key_val[0]] = key_val[1];
 418                                 }
 419                         }
 420                 }
 421                 UserPrefs.setCookie();
 422         },
 423         setCookie: function() {
 424                 var thisDate = new Date();
 425                 var base = new Date(0);
 426                 var skew = base.getTime();
 427                 var unix_epoch_time = thisDate.getTime();
 428         if (skew > 0)  unix_epoch_time -= skew;  //Steve Jobs is a prick!
 429                 UserPrefs._preferences.timestamp = unix_epoch_time;
 430                 UserPrefs._preferences.sp_person_id = user_id;
 431                 UserPrefs._buildString();
 432                 Cookie.set('user_prefs', user_pref_string, 1000);
 433         },
 434         //sendPrefs will make an AJAX request to the server, writing the cookie string to the database.  neat-o!
 435         //ONLY use this when you anticipate that the user will set a preference and not load another page.  The page-loading process will update the user_prefs string in the database from the user's cookie.
 436         send: function() {
 437                 var req = new Request();
 438                 if(req.isValid()){
 439
 440                         var parameters = "?sp_person_id=" + user_id + "&user_prefs=" + encodeURIComponent(user_pref_string);
 441                         req.sendRequest("/scraps/set_user_prefs.pl", parameters);
 442                         return true;
 443                 }
 444                 return false;
 445         },
 446         loadCookie: function() {
 447                 user_pref_string = Cookie.get('user_prefs');
 448         },
 449         _buildString: function() {
 450                 var new_string = '';
 451                 var i = 0;
 452                 for(var name in UserPrefs._preferences){
 453                         if(i>0) new_string += ":";
 454                         new_string += name + "=" + UserPrefs._preferences[name];
 455                         i++;
 456                 }
 457                 user_pref_string = new_string;
 458         },
 459         set: function(name, value) {
 460                 UserPrefs._preferences[name] = value;
 461         },
 462         get: function(name) {
 463                 return UserPrefs._preferences[name];
 464         }
 465 }
 466 UserPrefs.init();
 467
 468
 469 //Encapsulates all of our visual effects on Secretary
 470 var Effects = {
 471
 472         switchHotlistButton: function(buttonId, switchTo, content, clearOnClick){
 473                 var button = document.getElementById(buttonId);
 474                 var imgAdd = document.getElementById(buttonId + ":imgAdd");
 475                 var imgRemove = document.getElementById(buttonId + ":imgRemove");
 476
 477                 var optionalText = "All AGIs on this Page ";
 478                 if(!content.match(/:/)) optionalText = "";
 479                 if(switchTo == 'remove'){
 480                         imgAdd.style.display = "none";
 481                         imgRemove.style.display = "inline";
 482                         button.firstChild.nodeValue = "Remove " + optionalText + "from Hotlist";
 483                         if(clearOnClick){
 484                                 button.setAttribute("onClick", "alert('some')");
 485                         }
 486                         else {
 487                                 button.setAttribute("onClick", "Hotlist.remove('" + buttonId + "', '" + content + "'); return false;");
 488                         }
 489                 }
 490                 else if (switchTo == 'add'){
 491                         imgAdd.style.display = "inline";
 492                         imgRemove.style.display = "none";
 493                         button.firstChild.nodeValue = "Add " + optionalText + "to Hotlist";
 494                         if(clearOnClick){
 495                                 button.setAttribute("onClick", "alert('some')");
 496                         }
 497                         else {
 498                                 button.setAttribute("onClick", "Hotlist.add('" + buttonId + "', '" + content + "'); return false;");
 499                         }
 500                 }
 501                 else { alert("You sent a bad switchTo variable to switchHotlistButton"); }
 502         },
 503         showElement: function(elementId, displayMethod) {
 504                 var element = document.getElementById(elementId);
 505                 var dispMethod;
 506                 if(displayMethod) {
 507                         dispMethod = displayMethod;
 508                 }
 509                 else { dispMethod = "inline" }
 510                 element.style.display = dispMethod;
 511         },
 512         hideElement: function(elementId, displayMethod) {
 513                 var element = document.getElementById(elementId);
 514                 var dispMethod = "";
 515                 if(displayMethod) {
 516                         dispMethod = displayMethod
 517                 }
 518                 else { dispMethod = "none"; } //alternative is "hidden", which causes it to continue occupying space on the page
 519                 element.style.display = dispMethod;
 520         },
 521         swapElements: function(elementIdFrom, elementIdTo, displayMethod){
 522                 try {
 523                         var dispMethod = displayMethod || "inline";
 524                         var elementFrom = document.getElementById(elementIdFrom);
 525                         var elementTo = document.getElementById(elementIdTo);
 526                         elementFrom.style.display = "none";
 527                         elementTo.style.display = dispMethod;
 528                 }
 529                 catch(e) { alert(e) }
 530         }
 531 }
 532
 533
 534
 535 function RequestWaitIndicator(waitElementId) {
 536
 537         RequestWaitIndicator.numWaits += 1;
 538         this.id = "RWI:" + RequestWaitIndicator.numWaits;
 539         RequestWaitIndicator.waitHash[this.id] = 1;
 540         this.waitElementId = waitElementId;
 541         setTimeout("RequestWaitIndicator.displayElement('" + this.id + "', '" + this.waitElementId + "')", 1000);
 542
 543         this.stopWait = function () {
 544                 RequestWaitIndicator.waitHash[this.id] = 0;
 545                 Effects.hideElement(waitElementId);
 546         }
 547 }
 548 RequestWaitIndicator.numWaits = 0;
 549 RequestWaitIndicator.waitHash = {};
 550 RequestWaitIndicator.displayElement = function (waitId, elementId) {
 551         if (RequestWaitIndicator.waitHash[waitId]){
 552                 Effects.showElement(elementId);
 553         }
 554 }
 555
 556
 557
 558 //Request Object
 559 //The returned XML file should contain all information needed to cause a page effect,
 560 //rather than creating a custom response for each request, which is not possible due
 561 //to the security issues that prevent the creation of instances of XMLHttpRequest()
 562 //with unique properties
 563 function Request() {
 564
 565         var request = null;
 566         var valid = false;
 567         var loader = this;
 568
 569         if(window.XMLHttpRequest) {
 570                 request = new XMLHttpRequest();
 571         }
 572         else if (window.ActiveXObject) {
 573                 try { request = new ActiveXObject("Msxml2.XMLHTTP");}
 574                 catch(e) {
 575                         try { request = new ActiveXObject ("Microsoft.XMLHTTP");}
 576                         catch (e) {}
 577                 }
 578         }
 579
 580         if(request) {
 581                 valid = true;
 582                 request.onreadystatechange = function() { loader.onReadyState.call() }
 583         }
 584
 585
 586         this.isValid= function () { return valid }
 587         this.onReadyState= function() { //override this function in a subclass!!
 588                 if(request.readyState==4){
 589                         if(request.responseText.indexOf('E:')==0) alert(request.responseText);
 590                         XMLroute(request.responseXML);
 591                 }
 592         }
 593         this.sendRequest= function(url, parameters, method) {
 594                 if(!method) { method = "GET" }
 595                 request.open(method, url + parameters, true);
 596                 request.send(null);
 597         }
 598 }
 599
 600 //finds the calling object name in the XML response and directs the document to the appropriate handler
 601 function XMLroute (response) {
 602         var doc = response;
 603         var caller = doc.getElementsByTagName("caller")[0].firstChild.nodeValue;
 604         if(caller=="Hotlist") {
 605                         Hotlist._response(doc);
 606         }
 607         else {
 608                 // insert 'if' statements to route to other handlers
 609         }
 610 }
 611
 612
 613 //Hotlist is defined as a single object instead of a class. We can't have more than one!
 614 var Hotlist = window.Hotlist || {};
 615 Hotlist = { //buttonId: id of the clicked button, for changing the button
 616         add: function(buttonId, content) {
 617                 if(!buttonId) { alert("buttonId not sent!"); }
 618                 var waitIndicator;// = new RequestWaitIndicator("hotlistWait:" + content);
 619                 var request = new Request();
 620                 if(request.isValid()) {
 621                         Effects.switchHotlistButton(buttonId, 'remove', content, 1);  //last argument clears onClick to prevent user interaction
 622                         var parameters = "?owner=" + user_id + "&button_id=" + buttonId + "&cookie_string=" + cookie_string + "&action=add&content=" + content;
 623                         request.sendRequest("/scraps/hotlist.pl", parameters);
 624                 }
 625                 else { alert('invalid request') }
 626         },
 627         remove: function (buttonId, content) {
 628                 if(!buttonId) { alert("buttonId not sent!"); }
 629                 var waitIndicator;// = new RequestWaitIndicator("hotlistWait:" + content);
 630                 var request = new Request();
 631                 if(request.isValid()) {
 632                         Effects.switchHotlistButton(buttonId, 'add', content, 1);
 633                         var parameters = "?owner=" + user_id + "&button_id=" + buttonId + "&cookie_string=" + cookie_string + "&action=remove&content=" + content;
 634                         request.sendRequest("/scraps/hotlist.pl", parameters);
 635                 }
 636         },
 637         _response: function(doc) {
 638                 var newsize = doc.getElementsByTagName("newsize")[0].firstChild.nodeValue;
 639                 var oldsize = doc.getElementsByTagName("oldsize")[0].firstChild.nodeValue;
 640                 var content = doc.getElementsByTagName("content")[0].firstChild.nodeValue;
 641                 var action = doc.getElementsByTagName("action")[0].firstChild.nodeValue;
 642                 var buttonId = doc.getElementsByTagName("buttonId")[0].firstChild.nodeValue;
 643                 if(newsize > oldsize){
 644                         Hotlist._addResponse(buttonId, content, newsize);
 645                 }
 646                 else if(newsize < oldsize) {
 647                         Hotlist._removeResponse(buttonId, content, newsize);
 648                 }
 649                 else {
 650                         Hotlist._nullResponse(buttonId, content, action);
 651                         alert(doc);  //temporary
 652                 }
 653         },
 654         _addResponse: function(buttonId, content, newsize){
 655                 Effects.switchHotlistButton(buttonId, 'remove', content); //will restore onClick attribute
 656                 document.getElementById('hlsize').firstChild.nodeValue = newsize;
 657         },
 658         _removeResponse: function(buttonId, content, newsize){
 659                 Effects.switchHotlistButton(buttonId, 'add', content);
 660                 document.getElementById('hlsize').firstChild.nodeValue = newsize;
 661         },
 662         _nullResponse: function(buttonId, content, action) {
 663                 if(action == "add") {
 664                         Effects.switchHotlistButton(buttonId, 'add', content); //change back
 665                 }
 666                 if(action == "remove") {
 667                         Effects.switchHotlistButton(buttonId, 'add', content); //change back
 668                 }
 669         }
 670 }
 671
 672 /**
 673 ********* User account related functions ****************HEADER************************************************
 674 **/
 675
 676
 677
 678 var http_request = false;
 679
 680 function makeRequest(url, parameters, type) {
 681
 682       http_request = false;
 683
 684       if (window.XMLHttpRequest) { // Mozilla, Safari,...
 685          http_request = new XMLHttpRequest();
 686          if (http_request.overrideMimeType) {
 687             http_request.overrideMimeType('text/xml');
 688          }
 689       } else if (window.ActiveXObject) { // IE
 690          try {
 691             http_request = new ActiveXObject("Msxml2.XMLHTTP");
 692          } catch (e) {
 693             try {
 694                http_request = new ActiveXObject("Microsoft.XMLHTTP");
 695             } catch (e) {}
 696          }
 697       }
 698         if (!http_request) {
 699              //print("<!--Async XML Request Failed-->");
 700          return false;
 701       }
 702       if (type=='username') http_request.onreadystatechange = alertContentsName;
 703       http_request.open('GET', url + parameters, true);
 704       http_request.send(null);
 705           return true;
 706  }
 707
 708 function alertContentsName() {
 709       if (http_request.readyState == 4) {
 710          if (http_request.status == 200) {
 711             check_name_response(http_request.responseText);
 712                 return true;
 713          }
 714           else return true;
 715       }
 716       else return false;
 717    }
 718
 719
 720 function check_password(password){
 721         if(password==""){
 722                 document.getElementById('quickwarning').innerHTML = "&nbsp;";
 723                 document.getElementById('choosepw').style.color= "black";
 724     }
 725         else if(password.length < 7){
 726                 document.getElementById('quickwarning').innerHTML = "Password must be at least 7 characters long";
 727                 document.getElementById('choosepw').style.color= "#dd4444";
 728         }
 729         else {
 730                 document.getElementById('quickwarning').innerHTML = "&nbsp;";
 731                 document.getElementById('choosepw').style.color = "black";
 732         }
 733 }
 734
 735 function check_password_match(passwordrep){
 736         password = document.cf.password.value;
 737         if(passwordrep=="" || password.length==0){
 738                 document.getElementById('quickwarning').innerHTML = "&nbsp;"
 739                 document.getElementById('confirmpw').style.color = "black";
 740         }
 741         else if(passwordrep != password){
 742                 document.getElementById('quickwarning').innerHTML = "Repeated password doesn't match";
 743                 document.getElementById('confirmpw').style.color = "#dd4444";
 744         }
 745         else{
 746                 document.getElementById('quickwarning').innerHTML = "&nbsp;";
 747                 document.getElementById('confirmpw').style.color = "black";
 748         }
 749 }
 750
 751
 752
 753 function check_name(username){
 754   if(username==""){
 755         document.getElementById('quickwarning').innerHTML = "&nbsp;";
 756         document.getElementById('chooseuname').style.color = "black";
 757         document.getElementById('uname_available').style.display = "none";
 758         document.getElementById('uname_taken').style.display = "none";
 759   }
 760   else if(username.length < 7){
 761         document.getElementById('quickwarning').firstChild.nodeValue = "Username must be at least 7 characters long";
 762         document.getElementById('chooseuname').style.color = "#dd4444";
 763         document.getElementById('uname_available').style.display = "none";
 764         document.getElementById('uname_taken').style.display = "none";
 765   }
 766   else  {
 767         document.getElementById('quickwarning').innerHTML = "&nbsp;";
 768         document.getElementById('chooseuname').style.color = "black";
 769         makeRequest('scraps/check_name_avail.pl', '?username=' + username, 'username');
 770   }
 771 }
 772
 773 function check_email(email){
 774
 775   var ereg = /^[^@]+@[^@]+$/;
 776   if(email==""){
 777         document.getElementById('quickwarning').innerHTML = "&nbsp;";
 778         document.getElementById('chooseemail').style.color = "black";
 779   }
 780   else if(!email.match(ereg)){
 781         document.getElementById('quickwarning').innerHTML = "E-mail not of the form: name@address";
 782         document.getElementById('chooseemail').style.color = "#dd4444";
 783
 784   }
 785   else  {
 786         document.getElementById('quickwarning').innerHTML = "&nbsp;";
 787         document.getElementById('chooseemail').style.color = "black";
 788   }
 789 }
 790
 791 function check_name_response(response){
 792         if (response=='1') {
 793                 document.getElementById('uname_available').style.display = "inline";
 794                 document.getElementById('uname_taken').style.display = "none";
 795         }
 796         else if(response=='0') {
 797                 document.getElementById('uname_available').style.display = "none";
 798                 document.getElementById('uname_taken').style.display = "inline";
 799         }
 800         else {
 801                 document.getElementById('uname_available').style.display = "none";
 802                 document.getElementById('uname_taken').style.display = "none";
 803         }
 804 }
 805
 806
 807 function hide_warning(){
 808         document.getElementById('login_warning').style.display="none";
 809 }
 810
 811 function new_user(){
 812         document.getElementById('login_box').style.display="none";
 813         document.getElementById('createaccount_box').style.display="block";
 814         document.getElementById('newuname').focus();
 815         return false;
 816 }
 817
 818 function hide_create(){
 819         document.getElementById("createaccount_box").style.display="none";
 820         document.getElementById("userbar_container").style.display="block";
 821         document.getElementById("login_warning").style.display="none";
 822         return false;
 823 }
 824
 825 function hide_login(){
 826         document.getElementById("login_box").style.display="none";
 827         document.getElementById("userbar_container").style.display="block";
 828         document.getElementById("login_warning").style.display="none";
 829         return false;
 830 }
 831
 832 function show_login(){
 833         document.getElementById("login_box").style.display="block";
 834         document.getElementById("userbar_container").style.display="none";
 835         document.getElementById("uname").focus();
 836         document.getElementById("login_warning").style.display="none";
 837         return false;
 838 }
 839
 840
 841
 842 /**
 843 **** List Functions ****************************HEADER**********************************************************
 844 **/
 845 var http_request_mylistpage = false;
 846 var workinglist = "";
 847
 848 var lastAction = "";
 849 var lastList = "";
 850 var lastNewList = "";
 851
 852
 853 function makeRequestMylist(url, parameters, type, list) {
 854
 855           workinglist = list;
 856       http_request_mylistpage = false;
 857
 858       if (window.XMLHttpRequest) { // Mozilla, Safari,...
 859          http_request_mylistpage = new XMLHttpRequest();
 860          if (http_request_mylistpage.overrideMimeType) {
 861             http_request_mylistpage.overrideMimeType('text/xml');
 862          }
 863       } else if (window.ActiveXObject) { // IE
 864          try {
 865             http_request_mylistpage = new ActiveXObject("Msxml2.XMLHTTP");
 866          } catch (e) {
 867             try {
 868                http_request_mylistpage = new ActiveXObject("Microsoft.XMLHTTP");
 869             } catch (e) {}
 870          }
 871       }
 872       if (!http_request_mylistpage) {
 873                  return false;
 874       }
 875       if (type=='alterlist') http_request_mylistpage.onreadystatechange = alertContentsList;
 876       if (type=='FASTA') http_request_mylistpage.onreadystatechange = alertContentsFASTA;
 877       http_request_mylistpage.open('GET', url + parameters, true);
 878       http_request_mylistpage.send(null);
 879           return true;
 880  }
 881
 882
 883 function alertContentsList() {
 884       if (http_request_mylistpage.readyState == 4) {
 885          if (http_request_mylistpage.status == 200) {
 886             mylist_response(http_request_mylistpage.responseText);
 887             return true;
 888          }
 889          else return true;
 890       }
 891       else return false;
 892    }
 893
 894 function alertContentsFASTA(list){
 895       if (http_request_mylistpage.readyState == 4) {
 896          if (http_request_mylistpage.status == 200) {
 897             fasta_response(http_request_mylistpage.responseText);
 898             return true;
 899          }
 900          else return true;
 901       }
 902       else return false;
 903    }
 904
 905
 906 function createFASTA(type, list) {
 907         document.getElementById(list+'_fetch').style.display='inline';
 908         document.getElementById(list+'_cleartool').style.display="none";
 909         document.getElementById(list+'_createfastalinks').style.display="none";
 910         if(type!="full" && type!="cds" && type!="prot" && type!="cdna") type="full";
 911
 912         var RequestURL = "fastacreate.php?user=<?php echo $username?>&type=" + type + "&list="+list;
 913         makeRequestMylist(RequestURL, "", "FASTA", list);
 914
 915 }
 916
 917 function fasta_response(output) {
 918         var list = workinglist;
 919         document.getElementById(list+"_FASTAbox").value = output;
 920         document.getElementById(list+"_FASTAholder").style.display="block";
 921         document.getElementById(list+"_fetch").style.display='none';
 922         document.getElementById(list+"_cleartool").style.display="inline";
 923         document.getElementById(list+"_createfastalinks").style.display = "inline";
 924 }
 925
 926 function undoLast(){
 927         var action;
 928         if(lastAction=="add") action = "remove";
 929         else if(lastAction=="remove") action = "add";
 930
 931         alterList()
 932
 933 }
 934
 935
 936 function alterList(newlist, action, list){
 937
 938         lastAction = action;
 939         lastList = list;
 940         lastNewList = newlist;
 941
 942         var RequestURL = "alterlist.php?user=<?php echo $username?>&md5pass=<?php echo $password?>";
 943         RequestURL += "&list="+list+"&newlist=" + newlist + "&action=" + action;
 944         makeRequestMylist(RequestURL, "", "alterlist", list);
 945 }
 946
 947 var clear_reload = 0;
 948 function clearList(list){
 949
 950         RequestURL = "alterlist.php?user=<?php echo $username?>&md5pass=<?php echo $password?>";
 951         RequestURL += "&list="+list+"&clear=1";
 952         makeRequestMylist(RequestURL, "", "alterlist", list);
 953         clear_reload = 1;
 954 }
 955
 956 function alterLink(id, action, list){
 957
 958         if(action=="add") HTML = "<a href='#' onclick='alterList(\"" + id + "\", \"add\", \""+list+"\"); alterLink(\"" + id + "\", \"remove\", \""+list+"\"); return false;' style='text-decoration:none'>[ <img src='/img/hotlist_add.png' border=0 align='absmiddle'> Re-Add ]</a>";
 959         else if (action=="remove") HTML = "<a href='#' onclick='alterList(\"" + id + "\", \"remove\", \""+list+"\"); alterLink(\"" + id + "\", \"add\", \""+list+"\"); return false;' style='text-decoration:none'>[ <img src='/img/hotlist_remove.png' border=0 align='absmiddle'> Remove ]</a>";
 960         document.getElementById(list + "_" + id).innerHTML = HTML;
 961 }
 962
 963
 964 function mylist_response(output){
 965
 966         var list = workinglist;
 967         output = output.toString();
 968
 969         if (output.charAt(0) == 'q'){
 970
 971         output = output.substring(1);
 972         listsize = output * 1;
 973         if(list=="hotlist") document.getElementById('hlsize').firstChild.nodeValue = listsize;
 974     document.getElementById(list+"_headercount").innerHTML = listsize + " Genes";
 975         if(listsize==0 && clear_reload==1) window.location.reload();
 976         clear_reload = 0;
 977         }
 978
 979
 980 }
 981
 982