8c908f948b09826c6cb4452ee5b282aca41be85e
galt
  Tue Dec 8 21:52:59 2015 -0800
Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.

diff --git src/hg/js/utils.js src/hg/js/utils.js
index 73e83d2..6394fe2 100644
--- src/hg/js/utils.js
+++ src/hg/js/utils.js
@@ -1,2783 +1,2823 @@
 // Utility JavaScript
 
 // "use strict";
 
 // Don't complain about line break before '||' etc:
 /* jshint -W014 */
 
 var debug = false;
 
 function clickIt(obj,state,force)
 {
 // calls click() for an object, and click();click() if force
     if (obj.checked !== state) {
         obj.click();
     } else if (force) {
         obj.click();
         obj.click();    //force onclick event
     }
 }
 function setCheckBoxesWithPrefix(obj, prefix, state)
 {
 // Set all checkboxes with given prefix to state boolean
     var list = inputArrayThatMatches("checkbox","id",prefix,"");
     for (var i=0;i<list.length;i++) {
         var ele = list[i];
             if (ele.checked !== state)
                 ele.click();  // Forces onclick() javascript to run
     }
 }
 
 function setCheckBoxesThatContain(nameOrId, state, force, sub1)
 {
 // Set all checkboxes which contain 1 or more given substrings in NAME or ID to state boolean
 // First substring: must begin with it; 2 subs: beg and end; 3: begin, middle and end.
 // This can force the 'onclick() js of the checkbox, even if it is already in the state
     if (debug)
         alert("setCheckBoxesContains is about to set the checkBoxes to "+state);
     var list;
     if (arguments.length === 4)
         list = inputArrayThatMatches("checkbox",nameOrId,sub1,"");
     else if (arguments.length === 5)
         list = inputArrayThatMatches("checkbox",nameOrId,sub1,arguments[4]);
     else if (arguments.length === 6)
         list = inputArrayThatMatches("checkbox",nameOrId,sub1,arguments[4],arguments[5]);
     for (var ix=0;ix<list.length;ix++) {
         clickIt(list[ix],state,force);
     }
     return true;
 }
 
 function inputArrayThatMatches(inpType,nameOrId,prefix,suffix)
 {
     // returns an array of input controls that match the criteria
     var found = [];
     var fIx = 0;
     if (document.getElementsByTagName)
     {
         var list;
         if (inpType === 'select')
             list = document.getElementsByTagName('select');
         else
             list = document.getElementsByTagName('input');
         for (var ix=0;ix<list.length;ix++) {
             var ele = list[ix];
             if (inpType.length > 0 && inpType !== 'select' && ele.type !== inpType)
                 continue;
             var identifier = ele.name;
             if (nameOrId.search(/id/i) !== -1)
                 identifier = ele.id;
             var failed = false;
             if (prefix.length > 0)
                 failed = (identifier.indexOf(prefix) !== 0);
             if (!failed && suffix.length > 0)
                 failed = (identifier.lastIndexOf(suffix) !== (identifier.length - suffix.length));
             if (!failed) {
                 for (var aIx=4;aIx<arguments.length;aIx++) {
                     if (identifier.indexOf(arguments[aIx]) === -1) {
                         failed = true;
                         break;
                     }
                 }
             }
             if (!failed) {
                 found[fIx] = ele;
                 fIx++;
             }
         }
     } else {
         // NS 4.x - I gave up trying to get this to work.
         if (debugLevel>2)
            alert("arrayOfInputsThatMatch is unimplemented for this browser");
     }
     return found;
 }
 
 
 function normed(thing)
 {   // RETURNS undefined, the lone member of the set or the full set if more than one member.
     // Used for normalizing returns from jquery DOM selects (e.g. $('tr.track').children('td.data'))
     // jquery returns an "array like 'object'" with 0 or more entries.  
     // May be used on non-jquery objects and will reduce single element arrays to the element.
     // Use this to treat 0 entries the same as undefined and 1 entry as the item itself
     if (typeof(thing) === 'undefined' || thing === null
     ||  (thing.length !== undefined && thing.length === 0)  // Empty array (or 'array like object')
     ||  ($.isPlainObject(thing) && $.isEmptyObject(thing))) // Empty simple object
         return undefined;
     if (thing.length && thing.length === 1 && jQuery.type(thing) !== 'string') // string is overkill
         return thing[0]; // Container of one item should return the item itself.
     return thing;
 }
 
 var theClient = (function() {
 // Object that detects client browser if requested              
     
     // - - - - - Private variables and/or methods - - - - - 
     var ieVersion = null;
     var browserNamed = null;
     
     // - - - - - Public methods - - - - - 
     return { // returns an object with public methods
     
         getIeVersion: function ()
         { // Adapted from the web: stackOverflow.com answer by Joachim Isaksson
             if (ieVersion === null) {
                 ieVersion = -1.0;
                 var re = null;
                 if (navigator.appName === 'Microsoft Internet Explorer') {
                     browserNamed = 'MSIE';
                     re = new RegExp("MSIE ([0-9]{1,}[.0-9]{0,})");
                     if (re.exec(navigator.userAgent) !== null)
                         ieVersion = parseFloat( RegExp.$1 );
                 } else if (navigator.appName === 'Netscape') {
                     re = new RegExp("Trident/.*rv:([0-9]{1,}[.0-9]{0,})");
                     if (re.exec(navigator.userAgent) !== null) {
                         browserNamed = 'MSIE';
                         ieVersion = parseFloat( RegExp.$1 );
                     }
                 }
             }
             return ieVersion;
         },
         
         isIePre11: function ()
         {
             var ieVersion = theClient.getIeVersion();
             if ( ieVersion !== -1.0 && ieVersion < 11.0 )
                 return true;
             return false;
         },
         
         isIePost11: function ()
         {
             if (theClient.getIeVersion() >= 11.0 )
                 return true;
             return false;
         },
         
         isIe: function ()
         {
             if (theClient.getIeVersion() === -1.0 )
                 return false;
             return true;
         },
         
         isChrome: function () 
         {
             if (browserNamed !== null)
                 return (browserNamed === 'Chrome');
             
             if (navigator.userAgent.indexOf("Chrome") !== -1) {
                 browserNamed = 'Chrome';
                 return true;
             }
             return false;
         },
         
         isNetscape: function () 
         {   // IE sometimes mimics netscape
             if (browserNamed !== null)
                 return (browserNamed === 'Netscape');
         
             if (navigator.appName === 'Netscape'
             &&  navigator.userAgent.indexOf("Trident") === -1) {
                 browserNamed = 'Netscape';
                 return true;
             }
             return false;
         },
         
         isFirefox: function () 
         {
             if (browserNamed !== null)
                 return (browserNamed === 'FF');
             
             if (navigator.userAgent.indexOf("Firefox") !== -1) {
                 browserNamed = 'FF';
                 return true;
             }
             return false;
         },
         
         isSafari: function () 
         {   // Chrome sometimes mimics Safari
             if (browserNamed !== null)
                 return (browserNamed === 'Safari');
             
             if (navigator.userAgent.indexOf("Safari") !== -1 
             &&  navigator.userAgent.indexOf('Chrome') === -1) {
                 browserNamed = 'Safari';
                 return true;
             }
             return false;
         },
         
         isOpera: function () 
         {
             if (browserNamed !== null)
                 return (browserNamed === 'Opera');
             
             if (navigator.userAgent.indexOf("Presto") !== -1) {
                 browserNamed = 'Opera';
                 return true;
             }
             return false;
         },
         
         nameIs: function () 
         {   // simple enough, this needs no comment!
             if (browserNamed === null
             &&  theClient.isChrome() === false   // Looking in the order of popularity
             &&  theClient.isFirefox() === false
             &&  theClient.isIe()       === false
             &&  theClient.isSafari()    === false
             &&  theClient.isOpera()      === false
             &&  theClient.isNetscape()    === false)
                 browserNamed = navigator.appName; // Don't know what else to look for.
             
             return browserNamed;
         }
 
     };
 }());
 
 function waitCursor(obj)  // DEAD CODE?
 {
     //document.body.style.cursor="wait"
     obj.style.cursor="wait";
 }
 
 function endWaitCursor(obj)  // DEAD CODE?
 {
     obj.style.cursor="";
 }
 
 function getURLParam()
 {
 // Retrieve variable value from an url.
 // Can be called either:
 //     getURLParam(url, name)
 // or:
 //     getURLParam(name)
 // Second interface will default to using window.location.href
     var strHref, strParamName;
     var strReturn = "";
     if (arguments.length === 1) {
           strHref = window.location.href;
           strParamName = arguments[0];
     } else {
           strHref = arguments[0];
           strParamName = arguments[1];
     }
     if ( strHref.indexOf("?") > -1) {
       var strQueryString = strHref.substr(strHref.indexOf("?")).toLowerCase();
       var aQueryString = strQueryString.split("&");
       for (var iParam = 0; iParam < aQueryString.length; iParam++) {
          if (aQueryString[iParam].indexOf(strParamName.toLowerCase() + "=") > -1) {
             var aParam = aQueryString[iParam].split("=");
             strReturn = aParam[1];
             break;
          }
       }
     }
     return unescape(strReturn);
 }
 
 function makeHiddenInput(theForm,aName,aValue)
 {   // Create a hidden input to hold a value
     $(theForm).find("input:last").after("<input type=hidden name='"+aName+"' value='"+aValue+"'>");
 }
 
 function updateOrMakeNamedVariable(theForm,aName,aValue)
 {   // Store a value to a named input.  Will make the input if necessary
     var inp = normed($(theForm).find("input[name='"+aName+"']:last"));
     if (inp) {
         $(inp).val(aValue);
         inp.disabled = false;
     } else
         makeHiddenInput(theForm,aName,aValue);
 }
 
 function disableNamedVariable(theForm,aName)
 {   // Store a value to a named input.  Will make the input if necessary
     var inp = normed($(theForm).find("input[name='"+aName+"']:last"));
     if (inp)
         inp.disabled = true;
 }
 
 function parseUrlAndUpdateVars(theForm,href)  // DEAD CODE?
 {   // Parses the URL and converts GET vals to POST vals
     var url = href;
     var extraIx = url.indexOf("?");
     if (extraIx > 0) {
         var extra = url.substring(extraIx+1);
         url = url.substring(0,extraIx);
         // now extra must be repeatedly broken into name=var
         extraIx = extra.indexOf("=");
         for (; extraIx > 0;extraIx = extra.indexOf("=")) {
             var aValue;
             var aName = extra.substring(0,extraIx);
             var endIx = extra.indexOf("&");
             if (endIx>0) {
                 aValue = extra.substring(extraIx+1,endIx);
                 extra  = extra.substring(endIx+1);
             } else {
                 aValue = extra.substring(extraIx+1);
                 extra  = "";
             }
             if (aName.length > 0 && aValue.length > 0)
                 updateOrMakeNamedVariable(theForm,aName,aValue);
         }
     }
     return url;
 }
 
 function postTheForm(formName,href)
 {   // posts the form with a passed in href
     var goodForm = normed($("form[name='"+formName+"']"));
     if (goodForm) {
         if (href && href.length > 0) {
             $(goodForm).attr('action',href); // just attach the straight href
         }
         $(goodForm).attr('method','POST');
 
         $(goodForm).submit();
     }
     return false; // Meaning do not continue with anything else
 }
 function setVarAndPostForm(aName,aValue,formName)
 {   // Sets a specific variable then posts
     var goodForm = normed($("form[name='"+formName+"']"));
     if (goodForm) {
         updateOrMakeNamedVariable(goodForm,aName,aValue);
     }
     return postTheForm(formName,window.location.href);
 }
 
 // json help routines
 function tdbGetJsonRecord(trackName)  { return hgTracks.trackDb[trackName]; }
 // NOTE: These must jive with tdbKindOfParent() and tdbKindOfChild() in trackDb.h
 function tdbIsFolder(tdb)             { return (tdb.kindOfParent === 1); } 
 function tdbIsComposite(tdb)          { return (tdb.kindOfParent === 2); }
 function tdbIsMultiTrack(tdb)         { return (tdb.kindOfParent === 3); }
 function tdbIsView(tdb)               { return (tdb.kindOfParent === 4); } // Don't expect to use
 function tdbIsContainer(tdb)          { return (tdb.kindOfParent === 2 || tdb.kindOfParent === 3); }
 function tdbIsLeaf(tdb)               { return (tdb.kindOfParent === 0); }
 function tdbIsFolderContent(tdb)      { return (tdb.kindOfChild  === 1); }
 function tdbIsCompositeSubtrack(tdb)  { return (tdb.kindOfChild  === 2); }
 function tdbIsMultiTrackSubtrack(tdb) { return (tdb.kindOfChild  === 3); }
 function tdbIsSubtrack(tdb)           { return (tdb.kindOfChild  === 2 || tdb.kindOfChild === 3); }
 function tdbHasParent(tdb)            { return (tdb.kindOfChild  !== 0 && tdb.parentTrack); }
 
 function aryFind(ary,val)
 {// returns the index of a value on the array or -1;
     for (var ix=0; ix < ary.length; ix++) {
         if (ary[ix] === val) {
             return ix;
         }
     }
     return -1;
 }
 
 function aryRemove(ary,vals)
 { // removes one or more variables that are found in the array
     for (var vIx=0; vIx < vals.length; vIx++) {
         var ix = aryFind(ary,vals[vIx]);
         if (ix !== -1)
             ary.splice(ix,1);
     }
     return ary;
 }
 
 function arysToObj(names,values)
 {   // Make hash type obj with two parallel arrays.
     var obj = {};
     for (var ix=0; ix < names.length; ix++) {
         obj[names[ix]] = values[ix]; 
     }
     return obj;
 }
 
 function objNotEmpty(obj)
 {   // returns true on non empty object.  Obj should pass $.isPlainObject()
     if ($.isPlainObject(obj) === false)
         warn("Only use plain js objects in objNotEmpty()");
     return ($.isEmptyObject(obj) === false);
 }
 
 function objKeyCount(obj)
 {   // returns number of keys in object.
     if (!Object.keys) {
         var count = 0;
         for (var key in obj) {
             count++;
         }
         return count;
     } else
         return Object.keys(obj).length;
 }
 
 function isInteger(s)
 {
     return (!isNaN(parseInt(s)) && isFinite(s) && s.toString().indexOf('.') < 0);
 }
 function isFloat(s)
 {
     return (!isNaN(parseFloat(s)) && isFinite(s));
 }
 
 function validateInt(obj,min,max)
 {   // validates an integer which may be restricted to a range (if min and/or max are numbers)
     var title = obj.title;
     var rangeMin=parseInt(min);
     var rangeMax=parseInt(max);
     if (title.length === 0)
         title = "Value";
     var popup=( theClient.isIePre11() === false );
     for (;;) {
         if ((obj.value === undefined || obj.value === null || obj.value === "") 
         &&  isInteger(obj.defaultValue))
             obj.value = obj.defaultValue;
         if (!isInteger(obj.value)) {
             if (popup) {
                 obj.value = prompt(title +" is invalid.\nMust be an integer.",obj.value);
                 continue;
             } else {
                 alert(title +" of '"+obj.value +"' is invalid.\nMust be an integer.");
                 obj.value = obj.defaultValue;
                 return false;
             }
         }
         var val = parseInt(obj.value);
         if (isInteger(min) && isInteger(max)) {
             if (val < rangeMin || val > rangeMax) {
                 if (popup) {
                     obj.value = prompt(title +" is invalid.\nMust be between "+rangeMin+
                                                                    " and "+rangeMax+".",obj.value);
                     continue;
                 } else {
                     alert(title +" of '"+obj.value +"' is invalid.\nMust be between "+
                                                                      rangeMin+" and "+rangeMax+".");
                     obj.value = obj.defaultValue;
                     return false;
                 }
             }
         } else if (isInteger(min)) {
             if (val < rangeMin) {
                 if (popup) {
                     obj.value = prompt(title +" is invalid.\nMust be no less than "+
                                                                            rangeMin+".",obj.value);
                     continue;
                 } else {
                     alert(title +" of '"+obj.value +"' is invalid.\nMust be no less than "+
                                                                                       rangeMin+".");
                     obj.value = obj.defaultValue;
                     return false;
                 }
             }
         } else if (isInteger(max)) {
             if (val > rangeMax) {
                 if (popup) {
                     obj.value = prompt(title +" is invalid.\nMust be no greater than "+
                                                                            rangeMax+".",obj.value);
                     continue;
                 } else {
                     alert(title +" of '"+obj.value +"' is invalid.\nMust be no greater than "+
                                                                                       rangeMax+".");
                     obj.value = obj.defaultValue;
                     return false;
                 }
             }
         }
         return true;
     }
 }
 
 function validateFloat(obj,min,max)
 {   // validates an float which may be restricted to a range (if min and/or max are numbers)
     var title = obj.title;
     var rangeMin=parseFloat(min);
     var rangeMax=parseFloat(max);
     if (title.length === 0)
         title = "Value";
     var popup=( theClient.isIePre11() === false );
     for (;;) {
         if ((obj.value === undefined || obj.value === null || obj.value === "") 
         &&  isFloat(obj.defaultValue))
             obj.value = obj.defaultValue;
         if (!isFloat(obj.value)) {
             if (popup) {
                 obj.value = prompt(title +" is invalid.\nMust be a number.",obj.value);
                 continue;
             } else {
                 alert(title +" of '"+obj.value +"' is invalid.\nMust be a number."); // try a prompt box!
                 obj.value = obj.defaultValue;
                 return false;
             }
         }
         var val = parseFloat(obj.value);
         if (isFloat(min) && isFloat(max)) {
             if (val < rangeMin || val > rangeMax) {
                 if (popup) {
                     obj.value = prompt(title +" is invalid.\nMust be between "+rangeMin+" and "+
                                                                            rangeMax+".",obj.value);
                     continue;
                 } else {
                     alert(title +" of '"+obj.value +"' is invalid.\nMust be between "+rangeMin+
                                                                               " and "+rangeMax+".");
                     obj.value = obj.defaultValue;
                     return false;
                 }
             }
         } else if (isFloat(min)) {
             if (val < rangeMin) {
                 if (popup) {
                     obj.value = prompt(title +" is invalid.\nMust be no less than "+rangeMin+
                                                                                    ".",obj.value);
                     continue;
                 } else {
                     alert(title +" of '"+obj.value +"' is invalid.\nMust be no less than "+
                                                                                       rangeMin+".");
                     obj.value = obj.defaultValue;
                     return false;
                 }
             }
         } else if (isFloat(max)) {
             if (val > rangeMax) {
                 if (popup) {
                     obj.value = prompt(title +" is invalid.\nMust be no greater than "+
                                                                            rangeMax+".",obj.value);
                     continue;
                 } else {
                     alert(title +" of '"+obj.value +"' is invalid.\nMust be no greater than "+
                                                                                       rangeMax+".");
                     obj.value = obj.defaultValue;
                     return false;
                 }
             }
         }
         return true;
     }
 }
 
 function validateUrl(url)
 {   // returns true if url is a valid url, otherwise returns false and shows an alert
 
     // I got this regexp from http://stackoverflow.com/questions/1303872/url-validation-using-javascript
     var regexp = /^(https?|ftp):\/\/(((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&amp;'\(\)\*\+,;=]|:)*@)?(((\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5]))|((([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])*([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])))\.)+(([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])*([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])))\.?)(:\d*)?)(\/((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&amp;'\(\)\*\+,;=]|:|@)+(\/(([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&amp;'\(\)\*\+,;=]|:|@)*)*)?)?(\?((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&amp;'\(\)\*\+,;=]|:|@)|[\uE000-\uF8FF]|\/|\?)*)?(\#((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&amp;'\(\)\*\+,;=]|:|@)|\/|\?)*)?$/i;
     if (regexp.test(url)) {
         return true;
     } else {
         alert(url + " is an invalid url");
         return false;
     }
 }
 
 function metadataIsVisible(trackName)
 {
     var divit = normed($("#div_"+trackName+"_meta"));
     if (!divit)
         return false;
     return ($(divit).css('display') !== 'none');
 }
 
 function metadataShowHide(trackName,showLonglabel,showShortLabel)
 {
 // Will show subtrack specific configuration controls
 // Config controls not matching name will be hidden
     var divit = normed($("#div_"+trackName+"_meta"));
     if (!divit)
         return false;
     var img = normed($(divit).prev('a').find("img"));
     if (img) {
         if ($(divit).css('display') === 'none')
             $(img).attr('src','../images/upBlue.png');
         else
             $(img).attr('src','../images/downBlue.png');
     }
     if ($(divit).css('display') === 'none') {
         if (typeof(subCfg) === "object") {// subCfg.js file included?
             var cfg = normed($("#div_cfg_"+trackName));
             if (cfg)   // Hide any configuration when opening metadata
                 $(cfg).hide();
         }
 
         if ($(divit).find('table').length === 0) {
             lookupMetadata(trackName,showLonglabel,showShortLabel);
             return false;
         }
     }
     var tr = $(divit).parents('tr');
     if (tr.length > 0) {
         tr = tr[0];
         var bgClass = null;
         var classes = $( tr ).attr("class").split(" ");
         for (var ix=0;ix<classes.length;ix++) {
             if (classes[ix].substring(0,'bgLevel'.length) === 'bgLevel')
                 bgClass = classes[ix];
         }
         if (bgClass) {
             $(divit).children('table').removeClass('bgLevel1 bgLevel2 bgLevel3 bgLevel4');
             $(divit).children('table').addClass(bgClass);
         }
     }
     $(divit).toggle();  // jQuery hide/show
     return false;
 }
 
 function setTableRowVisibility(button, prefix, hiddenPrefix, titleDesc, doAjax)
 {
 // Show or hide one or more table rows whose id's begin with prefix followed by "-".
 // This code also modifies the corresponding hidden field (cart variable) and the
 // src of the +/- img button.
     var retval = true;
     var hidden = normed($("input[name='"+hiddenPrefix+"_"+prefix+"_close']"));
     if (button && hidden) {
 	var newVal = -1;
         if (arguments.length > 5)
             newVal = arguments[5] ? 0 : 1;
         var oldSrc = $(button).attr("src");
         if (oldSrc && oldSrc.length > 0) {
             // Old img version of the toggleButton
             if (newVal === -1)
                 newVal = oldSrc.indexOf("/remove") > 0 ? 1 : 0;
             if (newVal === 1)
                 $(button).attr("src", oldSrc.replace("/remove", "/add") );
             else
                 $(button).attr("src", oldSrc.replace("/add", "/remove") );
         } else {
             // new BUTTONS_BY_CSS
             if (newVal === -1) {
                 oldSrc = $(button).text();
                 if (oldSrc && oldSrc.length === 1)
                     newVal = (oldSrc === '+') ? 0 : 1;
                 else {
                     warn("Uninterpretable toggleButton!");
                     newVal = 0;
                 }
             }
             if (newVal === 1)
                 $(button).text('+');
             else
                 $(button).text('-');
         }
         var contents = $("tr[id^='"+prefix+"-']");
         if(newVal === 1) {
             $(button).attr('title', 'Expand this '+titleDesc);
             contents.hide();
         } else {
             $(button).attr('title', 'Collapse this '+titleDesc);
             contents.show().trigger('show');
         }
         $(hidden).val(newVal);
 	if (doAjax) {
 	    setCartVar(hiddenPrefix+"_"+prefix+"_close", newVal);
 	}
         retval = false;
     }
     return retval;
 }
 
 function warnBoxJsSetup()
 {   // Sets up warnBox if not already established.  This is duplicated from htmshell.c
     var html = "";
     html += "<center>";
     html += "<div id='warnBox' style='display:none;'>";
     html += "<CENTER><B id='warnHead'></B></CENTER>";
     html += "<UL id='warnList'></UL>";
     html += "<CENTER><button id='warnOK' onclick='hideWarnBox();return false;'></button></CENTER>";
     html += "</div></center>";
 
     html += "<script type='text/javascript'>";
     html += "function showWarnBox() {";
     html += "document.getElementById('warnOK').innerHTML='&nbsp;OK&nbsp;';";
     html += "var warnBox=document.getElementById('warnBox');";
     html += "warnBox.style.display=''; warnBox.style.width='65%%';";
     html += "document.getElementById('warnHead').innerHTML='Warning/Error(s):';";
     html +=  "window.scrollTo(0, 0);";
     html += "}";
     html += "function hideWarnBox() {";
     html += "var warnBox=document.getElementById('warnBox');";
     html += "warnBox.style.display='none';warnBox.innerHTML='';";
     html += "var endOfPage = document.body.innerHTML.substr(document.body.innerHTML.length-20);";
     html += "if(endOfPage.lastIndexOf('-- ERROR --') > 0) { history.back(); }";
     html += "}";
     html += "</script>";
 
     $('body').prepend(html);
 }
 
 function warn(msg)
 { // adds warnings to the warnBox
     var warnList = normed($('#warnList')); // warnBox contains warnList
     if (!warnList) {
         warnBoxJsSetup();
         warnList = normed($('#warnList'));
     }
     if (!warnList)
         alert(msg);
     else {
         $( warnList ).append('<li>'+msg+'</li>');
         if ($.isFunction(showWarnBox))
             showWarnBox();
         else
             alert(msg);
     }
 }
 
 var gWarnSinceMSecs = 0;
 function warnSince(msg)  // DEAD CODE?
 {   // Warn messages with msecs since last warnSince msg
     // This is necessary because IE Developer tools are hanging
     var now = new Date();
     var msecs = now.getTime();
     var since = 0;
     if (gWarnSinceMSecs > 0)
         since = msecs - gWarnSinceMSecs;
     gWarnSinceMSecs = msecs;
     warn('['+since+'] '+msg);
 }
 
 function cgiBooleanShadowPrefix()
 // Prefix for shadow variable set with boolean variables.
 // Exact copy of code in cheapcgi.c
 {
     return "boolshad.";
 }
 
 function getAllVars(obj,subtrackName)
 {
 // Returns a hash for all inputs and selects in an obj.
 // If obj is undefined then obj is document!
     var urlData = {};
     if (!obj)
         obj = $('document');
     var inp = $(obj).find('input');
     var sel = $(obj).find('select');
     //warn("obj:"+$(obj).attr('id') + " inputs:"+$(inp).length+ " selects:"+$(sel).length);
     $(inp).filter('[name]:enabled').each(function (i) {
         var name  = $(this).attr('name');
         var val = $(this).val();
         if ($(this).attr('type') === 'checkbox') {
             name = cgiBooleanShadowPrefix() + name;
             val = $(this).attr('checked') ? 1 : 0;
         } else if ($(this).attr('type') === 'radio') {
             if (!$(this).attr('checked')) {
                 name = undefined;
             }
         }
         if (name && name !== "Submit" && val !== undefined && val !== null) {
             urlData[name] = val;
         }
     });
     $(sel).filter('[name]:enabled').each(function (i) {
         var name  = $(this).attr('name');
         var val = $(this).val();
         if (name && val !== undefined && val !== null) {
             if (subtrackName && name === subtrackName) {
                 if (val === 'hide') {
                    urlData[name+"_sel"] = 0;    // Can't delete "_sel" because default takes over
                    urlData[name]        = "[]"; // Can delete vis because
                 } else {                        //     subtrack vis should be inherited.
                     urlData[name+"_sel"] = 1;
                     urlData[name]        = val;
                 }
             } else {
                 if ($.isArray( val) && val.length > 1) {
                     urlData[name] = "[" + val.toString() + "]";
                 } else
                     urlData[name] = val;
             }
         }
     });
     return urlData;
 }
 
+function debugDumpFormCollection(collectionName,vars)
+{ // dumps form vars collection in an alert
+    var debugStr = ""; 
+    for (var thisVar in vars) {
+	debugStr += thisVar + "==" + vars[thisVar]+"\n";
+    }
+    alert("DEBUG "+ collectionName + ":\n"+debugStr);  
+}
+
 function varHashChanges(newVars,oldVars)
 {   // Returns a hash of all vars that are changed between old and new hash.
     // New vars not found in old are changed.
     var changedVars = {};
     for (var newVar in newVars) {
-        if (!oldVars[newVar] || oldVars[newVar] !== newVars[newVar])
+        if (oldVars[newVar] === null || oldVars[newVar] !== newVars[newVar])
             changedVars[newVar] = newVars[newVar];
     }
     return changedVars;
 }
 
 function varHashToQueryString(varHash)
 {
 // return a CGI QUERY_STRING for name/vals in given object
     var retVal = "";
     var count = 0;
     for (var aVar in varHash) {
         if (count++ > 0) {
             retVal += "&";
         }
         var val = varHash[aVar];
         if (typeof(val) === 'string'
         && val.length >= 2
         && val.indexOf('[') === 0
         && val.lastIndexOf(']') === (val.length - 1)) {
             var vals = val.substr(1,val.length - 2).split(',');
             /* jshint loopfunc: true */// function inside loop works and replacement is awkward.
             $(vals).each(function (ix) {
                 if (ix > 0)
                     retVal += "&";
                 retVal += aVar + "=" + encodeURIComponent(this);
             });
         } else {
             retVal += aVar + "=" + encodeURIComponent(val);
         }
     }
     return retVal;
 }
 
 function getAllVarsAsUrlData(obj)  // DEAD CODE?
 {
 // Returns a string in the form of var1=val1&var2=val2... for all inputs and selects in an obj
 // If obj is undefined then obj is document!
     return varHashToQueryString(getAllVars(obj));
 }
 
 /*
 function popupBox(popit, content, popTitle)
 {
 // Kicks off a Modal Dialog for the provided content.
 // Requires jquery-ui.js
 // NEEDS SOME WORK
 
     warn(content);
 
     // Set up the popit div if necessary
     if (!popit) {
         popit = $('#popit');
 
         if (!popit ) {
             $('body').prepend("<div id='popit' style='display: none'></div>");
             popit = $('#popit');
         }
     }
 
     // Set up the modal dialog
     $(popit).html("<div style='font-size:80%'>" + content + "</div>");
     $(popit).dialog({
                                ajaxOptions: {
                                    // This doesn't work
                                    cache: true
                                },
                                resizable: true,
                                bgiframe: true,
                                height: 'auto',
                                width: 'auto',
                                minHeight: 200,
                                minWidth: 400,
                                modal: true,
                                closeOnEscape: true,
                                autoOpen: false,
                                close: function() {    // clear out html after close to prevent
                                    $(popDiv).empty(); // problems caused by duplicate html elements
                                }
                            });
     // Apparently the options above to dialog take only once, so we set title explicitly.
     if (popTitle && popTitle.length > 0)
         $(popit).dialog('option' , 'title' , popTitle );
     else
         $(popit).dialog('option' , 'title' , "Please Respond");
     jQuery('body').css('cursor', '');
     $(popit).dialog('open');
 }
 */
 
 function embedBoxOpen(boxit, content, reenterable)  // DEAD CODE?
 {   // embeds a box for the provided content.
     // This box has 1 button (close) by default and 2 buttons if the name of an applyFunc
     // is provided (apply, cancel) If there is no apply function, the box may be reentrent, 
     // meaning subsequent calls do not need to provide content
     // NOTE: 4 extra STRING Params: boxWidth, boxTitle, applyFunc, applyName
 
     // Define extra params now
     var boxWidth = "80%";
     var boxTitle = "";
     var applyFunc = "";
     var applyName = "Apply";
     if (arguments.length > 3 && arguments[3].length > 0) // FIXME: could check type
         boxWidth = arguments[3];
     if (arguments.length > 4 && arguments[4].length > 0)
         boxTitle = arguments[4];
     if (arguments.length > 5 && arguments[5].length > 0)
         applyFunc = arguments[5];
     if (arguments.length > 6 && arguments[6].length > 0)
         applyName = arguments[6];
 
     // Set up the popit div if necessary
     if (!boxit) {
         boxit = $('div#boxit');
 
         if (!boxit) {
             $('body').prepend("<div id='boxit'></div>");
             //$('body').prepend("<div id='boxit' style='display: none'></div>");
             boxit = $('div#boxit');
         }
     }
     if (!reenterable || (content.length > 0)) { // Can reenter without changing content!
 
         var buildHtml = "<center>";
         if (boxTitle.length > 0)
             buildHtml += "<div style='background-color:#D9E4F8;'><B>" +  boxTitle + "</B></div>";
 
         buildHtml += "<div>" + content + "</div>";
 
         // Set up closing code
         var closeButton = "Close";
         var closeHtml = "embedBoxClose($(\"#"+ $(boxit).attr('id') + "\"),";
         if (reenterable && applyFunc.length === 0)
             closeHtml += "true);";
         else
             closeHtml += "false);";
 
         // Buttons
         buildHtml += "<div>";
         if (applyFunc.length > 0) { // "Apply" button and "Cancel" button.  Apply also closes!
             buildHtml += "&nbsp;<INPUT TYPE='button' value='" + applyName + "' onClick='"+ 
                             applyFunc + "(" + $(boxit).attr('id') + "); " + closeHtml + "'>&nbsp;";
             closeButton = "Cancel"; // If apply button then close is cancel
         }
         buildHtml += "&nbsp;<INPUT TYPE='button' value='" + closeButton + "' onClick='" + closeHtml;
         buildHtml += "'>&nbsp;</div>";
 
         $(boxit).html("<div class='blueBox' style='width:" + boxWidth + 
                           "; background-color:#FFF9D2;'>" + buildHtml + "</div>"); // Make it boxed
     }
 
     var boxedHtml = $(boxit).html();
     if (!boxedHtml || boxedHtml.length === 0)
         warn("embedHtmlBox() called without content");
     else
         $(boxit).show();
 }
 
 function embedBoxClose(boxit, reenterable)  // DEAD CODE?
 {   // Close an embedded box
     // NOTE  4 extra STRING Params: boxWidth, boxTitle, applyFunc, applyName
     if (boxit) {
         $(boxit).hide();
         if (!reenterable)
             $(boxit).empty();
     }
 }
 
 function startTiming()  // DEAD CODE?
 {
     var now = new Date();
     return now.getTime();
 }
 
 function showTiming(start,whatTookSoLong)  // DEAD CODE?
 {
     var now = new Date();
     var end = (now.getTime() - start);
     warn(whatTookSoLong+" took "+end+" msecs.");
     return end;
 }
 
 function getHgsid()
 {// return current session id
 
     // .first() because hgTracks turned up 3 of these!
     var hgsid = normed($("input[name='hgsid']").first());
     if (hgsid)
         return hgsid.value;
 
     hgsid = getURLParam(window.location.href, "hgsid");
     if (hgsid.length > 0)
         return hgsid;
 
     // This may be moved to 1st position as the most likely source
     if (typeof(common) !== 'undefined' && common.hgsid !== undefined && common.hgsid !== null)
         return common.hgsid;
 
     hgsid = normed($("input#hgsid").first());
     if (hgsid)
         return hgsid.value;
 
     return "";
 }
 
 function getDb()
 {
     var db = normed($("input[name='db']").first());
     if (db)
         return db.value;
 
     db = getURLParam(window.location.href, "db");
     if (db.length > 0)
         return db;
 
     // This may be moved to 1st position as the most likely source
     if (typeof(common) !== 'undefined' && common.db)
         return common.db;
 
     db = normed($("input#db").first());
     if (db)
         return db.value;
 
     return "";
 }
 
 function getTrack()
 {
     var track = normed($("input[name='g']").first());
     if (track)
         return track.value;
 
     track = getURLParam(window.location.href, "g");
     if (track.length > 0)
         return track;
 
     // This may be moved to 1st position as the most likely source
     if (typeof(common) !== 'undefined' && common.track)
         return common.track;
 
     track = normed($("input#g").first());
     if (track)
         return track.value;
 
     return "";
 }
 
 function Rectangle()  // DEAD CODE?
 {
 // Rectangle object constructor:
 // calling syntax:
 //
 // new Rectangle(startX, endX, startY, endY)
 // new Rectangle(coords) <-- coordinate string from an area item
     if (arguments.length === 4) {
         this.startX = arguments[0];
         this.endX = arguments[1];
         this.startY = arguments[2];
         this.endY = arguments[3];
     } else if (arguments.length > 0)  {
         var coords = arguments[0].split(",");
         this.startX = coords[0];
         this.endX = coords[2];
         this.startY = coords[1];
         this.endY = coords[3];
     } else { // what else to do?
         this.startX = 0;
         this.endX = 100;
         this.startY = 0;
         this.endY = 100;
     }
 }
 
 Rectangle.prototype.contains = function(x, y)  // DEAD CODE?
 {
 // returns true if given points are in the rectangle
     var retval = x >= this.startX && x <= this.endX && y >= this.startY && y <= this.endY;
     return retval;
 };
 
 function commify (str) {
     if (typeof(str) === "number")
 	str = str + "";
     var n = str.length;
     if (n <= 3) {
 	return str;
     } else {
 	var pre = str.substring(0, n-3);
 	var post = str.substring(n-3);
 	pre = commify(pre);
 	return pre + "," + post;
     }
 }
 
 function parsePosition(position)
 // Parse chr:start-end string into a chrom, start, end object
 {
     if (position && position.length > 0) {
         position = position.replace(/,/g, "");
         var a = /(\S+):(\d+)-(\d+)/.exec(position);
         if (a && a.length === 4) {
             var o = {};
             o.chrom = a[1];
             o.start = parseInt(a[2]);
             o.end = parseInt(a[3]);
             return o;
         }
     }
     return null;
 }
 
 function parsePositionWithDb(position)
 // Parse db.chr:start-end string into a db, chrom, start, end object
 // Also supports be db.chr:start-end#color string
 {
     var out = {};
     var parts = position.split(".");
     if (parts.length === 2) {
         out.db = parts[0];
         position = parts[1];
     } else {
         out.db = getDb(); // default the db 
     }
     parts = position.split("#"); // Highlight Region may carry its color
     if (parts.length === 2) {
         position = parts[0];
         out.color = '#' + parts[1];
     }
     var pos = parsePosition(position);
     if (pos) {
         out.chrom = pos.chrom;
         out.start = pos.start;
         out.end   = pos.end;
         return out;
     }
     return null;
 }
 
 function getSizeFromCoordinates(position)
 {
 // Parse size out of a chr:start-end string
     var o = parsePosition(position);
     if (o) {
         return o.end - o.start + 1;
     }
     return null;
 }
 
 // This code is intended to allow setting up a wait cursor while waiting on the function
 var gWaitFuncArgs = [];
 var gWaitFunc;
 
 function waitMaskClear()
 { // Clears the waitMask
     var  waitMask = normed($('#waitMask'));
     if (waitMask)
         $(waitMask).hide();
 }
 
 function waitMaskSetup(timeOutInMs)
 { // Sets up the waitMask to block page manipulation until cleared
 
     // Find or create the waitMask (which masks the whole page)
     var  waitMask = normed($('#waitMask'));
     if (!waitMask) {
         // create the waitMask
         $("body").append("<div id='waitMask' class='waitMask');'></div>");
         waitMask = normed($('#waitMask'));
     }
     $(waitMask).css({opacity:0.0,display:'block',top: '0px', 
                         height: $(document).height().toString() + 'px' });
     // Special for IE, since it takes so long, make mask obvious
     //if (theClient.isIePre11())
     //    $(waitMask).css({opacity:0.4,backgroundColor:'gray'});
 
     // Things could fail, so always have a timeout.
     if (!timeOutInMs)  // works for undefined, null and 0
         timeOutInMs = 30000; // IE can take forever!
 
     if (timeOutInMs > 0)
         setTimeout(waitMaskClear,timeOutInMs); // Just in case
 
     return waitMask;  // The caller could add css if they wanted.
 }
 
 function _launchWaitOnFunction()
 { // should ONLY be called by waitOnFunction()
   // Launches the saved function
     var func = gWaitFunc;
     gWaitFunc = null;
     var funcArgs = gWaitFuncArgs;
     gWaitFuncArgs = [];
 
     if (!func || !jQuery.isFunction(func))
         warn("_launchWaitOnFunction called without a function");
     else
         func.apply(this, funcArgs);
 
     // Special if the first var is a button that can visually be inset
     if (funcArgs.length > 0 && funcArgs[0].type) {
         if (funcArgs[0].type === 'button' && $(funcArgs[0]).hasClass('inOutButton')) {
             $(funcArgs[0]).css('borderStyle',"outset");
         }
     }
     // Now we can get rid of the wait cursor
     waitMaskClear();
 }
 
 function waitOnFunction(func)
 {   // sets the waitMask (wait cursor and no clicking),
     // then launches the function with up to 5 arguments
     if (!jQuery.isFunction(func)) {
         warn("waitOnFunction called without a function");
         return false;
     }
     if (gWaitFunc) {
         if (gWaitFunc === func) // already called (sometimes hapens when onchange event is triggered
             return true;       // by js (rather than direct user action).  Happens in IE8
         warn("waitOnFunction called but already waiting on a function");
         return false;
     }
 
     waitMaskSetup(0);  // Find or create waitMask (which masks whole page) but gives up after 5sec
 
     // Special if the first var is a button that can visually be inset
     if (arguments.length > 1 && arguments[1].type) {
         if (arguments[1].type === 'button' && $(arguments[1]).hasClass('inOutButton')) {
             $(arguments[1]).css( 'borderStyle',"inset");
         }
     }
 
     // Build up the aruments array
     for (var aIx=1; aIx < arguments.length; aIx++) {
         gWaitFuncArgs.push(arguments[aIx]);
     }
     gWaitFunc = func;
 
     setTimeout(_launchWaitOnFunction,10);
 
 }
 
 // --- yielding iterator ---
 function _yieldingIteratorObject(yieldingFunc)  // DEAD CODE?
 { // This is the "recusive object" or ro which is instantiated in waitOnIteratingFunction
   // yieldingFunc is passed in from waitOnIteratingFunction
   // and will recurse which recursively calls an iterator
     this.step = function(msecs,args) {
         setTimeout(function() { yieldingFunc(args); }, msecs); // recursive timeouts
         return;
     };
 }
 
 function yieldingIterator(iteratingFunc,continuingFunc,args)  // DEAD CODE?
 {   // Will run iteratingFunc function with "yields", then run continuingFunc
     // Based upon design by Guido Tapia, PicNet
     // iteratingFunc must return number of msecs to pause before next interation.
     //                return 0 ends iteration with call to continuingFunc
     //                return < 0 ends iteration with no call to continuingFunc
     // Both iteratingFunc and continuingFunc will receive the single "args" param.
     // Hint. for multiple args, create a single struct object
 
     var ro = new _yieldingIteratorObject(function() {
             var msecs = iteratingFunc(args);
             if (msecs > 0)
                 ro.step(msecs,args);      // recursion
             else if (msecs === 0)
                 continuingFunc(args);     // completion
             // else (msec < 0) // abandon
         });
     ro.step(1,args);                      // kick-off
 }
 
 function showLoadingImage(id)
 // Show a loading image above the given id; return's id of div added (allowing later removal).
 {
     var loadingId = id + "LoadingOverlay";
     var overlay = $("<div id='"+loadingId+"' class='loading'></div>");
     var ele = $(document.getElementById(id));
     overlay.appendTo("body");
     var divLeft = ele.position().left + 2;
     var width = ele.width() - 1;
     var height = ele.height();
     overlay.width(width);
     overlay.height(height);
     overlay.css({top: (ele.position().top + 1) + 'px', left: divLeft + 'px'});
     return loadingId;
 }
 
 function hideLoadingImage(id)
 {
     $(document.getElementById(id)).remove();
 }
 
 function codonColoringChanged(name)
 {   // Updated disabled state of codonNumbering checkbox based on current value
     // of track coloring select.
     var val = $("select[name='" + name + ".baseColorDrawOpt'] option:selected").text();
     $("input[name='" + name + ".codonNumbering']").attr('disabled', val === "OFF");
 }
 
 
 var bindings = {
     // This object is for finding a subtring using tokens as bounds
     // The tokens can be literal strings or regular expressions.
     // If regular expressions are used, then only the first expression found will count
     // If not using regexp, then you can pass in limits to the original string
 
     _raw: function (begToken,endToken,someString,ixBeg,ixEnd)
     { // primitive not meant to be called directly but by bindings.inside and bindings.outside
         if (someString.length <= 0)
             return '';
         if (ixBeg === undefined || ixBeg === null)
             ixBeg = 0;
         if (ixEnd === undefined || ixEnd === null)
             ixEnd = someString.length;
         var insideBeg = ixBeg;
         var insideEnd = ixEnd;
         if (jQuery.type(begToken) === "regexp")
             insideBeg = someString.search(begToken);
         else if (begToken.length > 0)
             insideBeg = someString.indexOf(begToken,ixBeg);
         if (jQuery.type(endToken) === "regexp")
             insideEnd = someString.search(endToken);
         else if (endToken.length > 0)
             insideEnd = someString.indexOf(endToken,ixBeg);
         if (ixBeg <= insideBeg && insideBeg <= insideEnd && insideEnd <= ixEnd)
             return {start : insideBeg, stop : insideEnd};
 
         return {start : -1, stop : -1};
     },
 
     inside: function (begToken,endToken,someString,ixBeg,ixEnd)
     { // returns the inside bounds of 2 tokens within a string
     // Note ixBeg and ixEnd are optional bounds already established within string
     // Pattern match can be used instead of literal token if a regexp is passed in for the tokens
         var bounds = bindings._raw(begToken,endToken,someString,ixBeg,ixEnd);
         if (bounds.start > -1) {
             if (jQuery.type(begToken) === "regexp")
-                bounds.start += someString.match(begToken).length;
+                bounds.start += someString.match(begToken)[0].length;
             else
                 bounds.start += begToken.length;
         }
         return bounds;
     },
 
     outside: function (begToken,endToken,someString,ixBeg,ixEnd)
     { // returns the outside bounds of 2 tokens within a string
     // Note ixBeg and ixEnd are optional bounds already established within string
     // Pattern match can be used instead of literal token if a regexp is passed in for the tokens
         var bounds = bindings._raw(begToken,endToken,someString,ixBeg,ixEnd);
         if (bounds.start > -1) {
             if (jQuery.type(endToken) === "regexp") 
-                bounds.stop  += someString.match(endToken).length;
+                bounds.stop  += someString.match(endToken)[0].length;
             else
                 bounds.stop  += endToken.length;
         }
         return bounds;
     },
 
     insideOut: function (begToken,endToken,someString,ixBeg,ixEnd)
     { // returns what falls between begToken and endToken as found in the string provided
     // Note ixBeg and ixEnd are optional bounds already established within string
         var bounds = bindings.inside(begToken,endToken,someString,ixBeg,ixEnd);
         if (bounds.start < bounds.stop)
             return someString.slice(bounds.start,bounds.stop);
 
         return '';
     }
 };
 
 function stripHgErrors(returnedHtml, whatWeDid)
 {   // strips HGERROR style 'early errors' and shows them in the warnBox
     // If whatWeDid !== null, we use it to return info about what we stripped out and
     // processed (current just warnMsg).
     var cleanHtml = returnedHtml;
     while (cleanHtml.length > 0) {
         var bounds = bindings.outside('<!-- HGERROR-START -->','<!-- HGERROR-END -->',cleanHtml);
         if (bounds.start === -1)
             break;
         var warnMsg = bindings.insideOut('<P>','</P>',cleanHtml,bounds.start,bounds.stop);
         if (warnMsg.length > 0) {
             warn(warnMsg);
             if (whatWeDid)
                 whatWeDid.warnMsg = warnMsg;
         }
         cleanHtml = cleanHtml.slice(0,bounds.start) + cleanHtml.slice(bounds.stop);
     }
     return cleanHtml;
 }
 
 function stripJsFiles(returnedHtml,debug)
 { // strips javascript files from html returned by ajax
     var cleanHtml = returnedHtml;
     var shlurpPattern=/<script type=\'text\/javascript\' SRC\=\'.*\'\><\/script\>/gi;
     if (debug) {
         var jsFiles = cleanHtml.match(shlurpPattern);
         if (jsFiles && jsFiles.length > 0)
             alert("jsFiles:'"+jsFiles+"'\n---------------\n"+cleanHtml); // warn() interprets html
     }
     cleanHtml = cleanHtml.replace(shlurpPattern,"");
 
     return cleanHtml;
 }
 
 function stripCssFiles(returnedHtml,debug)
 { // strips csst files from html returned by ajax
     var cleanHtml = returnedHtml;
     var shlurpPattern=/<LINK rel=\'STYLESHEET\' href\=\'.*\' TYPE=\'text\/css\' \/\>/gi;
     if (debug) {
         var cssFiles = cleanHtml.match(shlurpPattern);
         if (cssFiles && cssFiles.length > 0)
             alert("cssFiles:'"+cssFiles+"'\n---------------\n"+cleanHtml);
     }
     cleanHtml = cleanHtml.replace(shlurpPattern,"");
 
     return cleanHtml;
 }
 
 function stripJsEmbedded(returnedHtml, debug, whatWeDid)
 { // strips embedded javascript from html returned by ajax
   // NOTE: any warnBox style errors will be put into the warnBox
   // If whatWeDid !== null, we use it to return info about
   // what we stripped out and processed (current just warnMsg).
     var cleanHtml = returnedHtml;
     // embedded javascript?
     while (cleanHtml.length > 0) {
         var begPattern = /<script type=\'text\/javascript\'\>/i;
         var endPattern = /<\/script\>/i;
         var bounds = bindings.outside(begPattern,endPattern,cleanHtml);
         if (bounds.start === -1)
             break;
         var jsEmbeded = cleanHtml.slice(bounds.start,bounds.stop);
         if (-1 === jsEmbeded.indexOf("showWarnBox")) {
             if (debug)
                 alert("jsEmbedded:'"+jsEmbeded+"'\n---------------\n"+cleanHtml);
         } else {
             var warnMsg = bindings.insideOut('<li>','</li>',cleanHtml,bounds.start,bounds.stop);
             if (warnMsg.length > 0) {
                 warn(warnMsg);
                 if (whatWeDid)
                     whatWeDid.warnMsg = warnMsg;
             }
         }
         cleanHtml = cleanHtml.slice(0,bounds.start) + cleanHtml.slice(bounds.stop);
     }
     return stripHgErrors(cleanHtml, whatWeDid); // Certain early errors are not called via warnBox
 }
 
+function stripMainMenu(returnedHtml, debug, whatWeDid)
+{ // strips main menu div from html returned by ajax
+  // NOTE: any warnBox style errors will be put into the warnBox
+  // If whatWeDid !== null, we use it to return info about
+  // what we stripped out and processed (current just warnMsg).
+    var cleanHtml = returnedHtml;
+    // embedded javascript?
+    while (cleanHtml.length > 0) {
+	
+        var begPattern = '<div id="main-menu-whole">';
+        var endPattern = '</div><!-- end main-menu-whole -->';
+        var bounds = bindings.outside(begPattern,endPattern,cleanHtml);
+        if (bounds.start === -1)
+            break;
+        var mainMenu = cleanHtml.slice(bounds.start,bounds.stop);
+        if (-1 === mainMenu.indexOf("showWarnBox")) {
+            if (debug)
+                alert("mainMenu:'"+mainMenu+"'\n---------------\n"+cleanHtml);
+        } else {
+            var warnMsg = bindings.insideOut('<li>','</li>',cleanHtml,bounds.start,bounds.stop);
+            if (warnMsg.length > 0) {
+                warn(warnMsg);
+                if (whatWeDid)
+                    whatWeDid.warnMsg = warnMsg;
+            }
+        }
+        cleanHtml = cleanHtml.slice(0,bounds.start) + cleanHtml.slice(bounds.stop);
+    }
+    return stripHgErrors(cleanHtml, whatWeDid); // Certain early errors are not called via warnBox
+}
+
 function visTriggersHiddenSelect(obj)
 { // SuperTrack child changing vis should trigger superTrack reshaping.
   // This is done by setting hidden input "_sel"
     var trackName_Sel = $(obj).attr('name') + "_sel";
     var theForm = $(obj).closest("form");
     var visible = (obj.selectedIndex !== 0);
     if (visible) {
         updateOrMakeNamedVariable(theForm,trackName_Sel,"1");
     } else
         disableNamedVariable(theForm,trackName_Sel);
     return true;
 }
 
 function setCheckboxList(list, value)
 { // set value of all checkboxes in semicolon delimited list
     var names = list.split(";");
     for (var i=0; i < names.length; i++) {
         $("input[name='" + names[i] + "']").attr('checked', value);
     }
 }
 
 function calculateHgTracksWidth()
 {
 // return appropriate width for hgTracks image given users current window width
     return $(window).width() - 20;
 }
 
 function hgTracksSetWidth()
 {
     var winWidth = calculateHgTracksWidth();
     if ($("#imgTbl").length === 0) {
         // XXXX what's this code for?
         $("#TrackForm").append('<input type="hidden" name="pix" value="' + winWidth + '"/>');
         //$("#TrackForm").submit();
     } else {
         $("input[name=pix]").val(winWidth);
     }
 }
 
 function filterByMaxHeight(multiSel)
 {   // Setting a max height to scroll dropdownchecklists but
     // multiSel is hidden when this is done, so it's position and height must be estimated.
     var pos = $(multiSel).closest(':visible').offset().top + 30;
     if (pos <= 0)
         pos = 260;
 
     // Special mess since the filterBy's on non-current tabs will calculate pos badly.
     var tabbed = normed($('input#currentTab'));
     if (tabbed) {
         var tabDiv = $(multiSel).parents('div#'+ $(tabbed).attr('value'));
         if (!tabDiv || $(tabDiv).length === 0) {
             pos = 360;
         }
     }
     var maxHeight = $(window).height() - pos;
     var selHeight = $(multiSel).children().length * 21;
     if (maxHeight > selHeight)
         maxHeight = null;
 
     return maxHeight;
 }
 
 //////////// Drag and Drop ////////////
 function tableDragAndDropRegister(thisTable)
 {// Initialize a table with tableWithDragAndDrop
     if ($(thisTable).hasClass("tableWithDragAndDrop") === false)
         return;
 
     $(thisTable).tableDnD({
         onDragClass: "trDrag",
         dragHandle: "dragHandle",
         onDrop: function(table, row, dragStartIndex) {
                 if (row.rowIndex !== dragStartIndex) {
                     if (sortTable.savePositions) {
                         sortTable.savePositions(table);
                     }
                 }
             }
     });
     $(thisTable).find("td.dragHandle").hover(
         function(){ $(this).closest('tr').addClass('trDrag'); },
         function(){ $(this).closest('tr').removeClass('trDrag'); }
     );
 }
 
   ///////////////////////////////
  ////////// Sort Table /////////
 ///////////////////////////////
 var sortTable = {
 // The sortTable object handles sorting HTML tables on columns.
 // Just add the 'sortable' class to your table and in ready() call 
 //                                                       sortTable.initialize($('table.sortable')).
 //
 // Details you don't need to know until you want to do something fancy.
 // A sortable table requires:
 // TABLE.sortable: TABLE class='sortable' containing a THEAD header and sortable TBODY filled
 //                 with the rows to sort.
 //   THEAD.sortable: (NOTE: created if not found) THEAD can contain multiple rows must contain:
 //     TR.sortable: exactly 1 header TH (tr) class='sortable' which will declare the sort columns:
 //     TH.sortable: 1 or more TH (column headers) with class='sortable sort1 [sortRev]'
 //                  (or sort2, sort3) declaring sort order and whether reversed.  e.g.:
 //                  <TH id='factor' class='sortable sortRev sort3' nowrap>...</TH>
 //                  (this means that factor is currently the third sort column and reverse sorted)
 //            NOTE: If no TH.sortable is found, then every th in the TR.sortable will be converted
 //                  for you and will be in sort1,2,3 order.
 //       ONCLICK: Each TH.sortable must call sortTable.sortOnButtonPress(this) directly
 //                or indirectly in the onclick event e.g.:
 //                <TH id='factor' class='sortable sortRev sort3' nowrap title='Sort on this column' 
 //                                           onclick="return sortTable.sortOnButtonPress(this);">
 //          NOTE: onclick function will automatically be added if not found.
 //       SUP: Each TH.sortable *may* contain a <sup> which will be filled with an
 //                          up or down arrow and the column's sort order: e.g. <sup>&darr;2</sup>
 //            NOTE: The sup can be added via the addSuperscript option in sortTable.initialize().
 //   TBODY.sortable: (NOTE: created if not found) The TBODY class='sortable' contains the
 //                   table rows that get sorted:
 //                   TBODY->TR & ->TD: Each row contains a TD for each sortable column.
 //                   The innerHTML (entire contents) of the cell will be used for sorting.
 //     TRICK: You can use the 'abbr' field to subtly alter the sortable contents.
 //            Otherwise sorts on td contents ($(td).text()).  Use the abbr field to make
 //            case-insensitive sorts or force exceptions to alpha-text order
 //            (such as. ZCTRL vs Control forcing controls to bottom)  e.g.:
 //                <TD id='wgEncodeBroadHist...' nowrap abbr='ZCTRL' align='left'>Control</TD>
 //            This is also the method to ensure a numeric sort e.g.:
 //                <td align="right" abbr="000003416800354">3.2 GB</td>
 //            IMPORTANT: You must add abbr='use' to the TH.sortable definitions.
 // Finally if you want the tableSort to alternate the table row colors (using #FFFEE8 and #FFF9D2)
 // then TBODY.sortable should also have class 'altColors'
 // NOTE: This class can be added by using the altColors option to sortTable.initialize().
 //
 // PRESERVING TO CART: To send the sort column on a form 'submit', the header tr (TR.sortable)
 //   needs a named hidden input of class='sortOrder' as:
 //      <INPUT TYPE=HIDDEN NAME='wgEncodeBroadHistone.sortOrder'
 //                                              class='sortOrder' VALUE="factor=- cell=+ view=+">
 //   AND each sortable column header (TH.sortable) must have id='{name}' which is the name of
 //   the sortable field (e.g. 'factor', 'shortLabel').  The value preserves the column sort order
 //   and direction based upon the id={name} of each sort column.  In the example, while 'cell' may
 //   be the first column, the table is currently reverse ordered by 'factor', then by cell and view.
 // And to send the sorted row orders on form 'submit', each TBODY->TR will need a named hidden
 //   input field of class='trPos'.  e.g.:
 //      <INPUT TYPE=HIDDEN NAME='wgEncodeHaibTfbsA549ControlPcr2xDexaRawRep1.priority'
 //                                                                        class='trPos' VALUE="2">
 //   A reason to preserve the order in the cart is if the order will affect other cgis.
 //   For instance: sort subtracks and see that order in the hgTracks image.
 
     // Sorting a table by columns relies upon the columns obj, whose C equivalent would look like:
     //struct column
     //    {
     //    char *  tags[];     // a list of field names in sort order (e.g. 'cell', 'shortLabel')
     //    boolean reverse[];  // the sort direction for each sort field
     //    int     cellIxs[];  // The indexes of the columns in the table to be sorted
     //    boolean useAbbr[];  // Compare on Abbr or on text()?
     //    };
 
     // These 2 globals are used during setTimeout, so that rows can be hidden while sorting
     // and javascript timeout on slow (IE) browsers is less likely
     columns: null,
     tbody: null,
     loadingId: null,
     caseSensitive: false, // sorts are case INSENSITIVE by default
 
     sortCaseSensitive: function (sensitive)
     {   // set case senstivity, which can be added to each sortable columnn's onclick event.
         // or set for the whole table right after initialize()
         sortTable.caseSensitive = sensitive;
     },
 
     row: function (tr,sortColumns)
     {
         this.fields  = [];
         this.reverse = [];
         this.row = tr;
         for (var ix=0; ix < sortColumns.cellIxs.length; ix++)
             {
             var cell = tr.cells[sortColumns.cellIxs[ix]];
             this.fields[ix]  = (sortColumns.useAbbr[ix] ? cell.abbr : $(cell).text());
             if (!sortTable.caseSensitive) 
                 this.fields[ix]  = this.fields[ix].toLowerCase(); // case insensitive sorts
             this.reverse[ix] = sortColumns.reverse[ix];
             }
     },
 
     rowCmp: function (a,b)
     {
         for (var ix=0; ix < a.fields.length; ix++) {
             if (a.fields[ix] > b.fields[ix])
                 return (a.reverse[ix] ? -1:1);
             else if (a.fields[ix] < b.fields[ix])
                 return (a.reverse[ix] ? 1:-1);
         }
         return 0;
     },
 
     field: function (value,reverse,row)
     {
         if (sortTable.caseSensitive || typeof(value) !== 'string') 
             this.value   = value;
         else
             this.value   = value.toLowerCase(); // case insensitive sorts
         this.reverse = reverse;
         this.row     = row;
     },
 
     fieldCmp: function (a,b)
     {
         if (a.value > b.value)
             return (a.reverse ? -1:1);
         else if (a.value < b.value)
             return (a.reverse ? 1:-1);
         return 0;
     },
 
     sort: function (tbody,sortColumns)
     {// Sorts table based upon rules passed in by function reference
     // Expects tbody to not sort thead, but could take table
 
         // The sort routine available is javascript array.sort(), which cannot sort rows directly
         // Until we have jQuery >=v1.4, we cannot easily convert tbody.rows[] inot a javascript array
         // So we will make our own array, sort, then then walk through the table and reorder
         // FIXME: Until better methods are developed, only sortOrder based sorts are supported
         //        and fnCompare is obsolete
 
         // Create an array of rows to sort
         var rows = [];
         var trs = tbody.rows;
         $(trs).each(function(ix) {
             rows.push(new sortTable.row(this, sortColumns));
         });
 
         // Sort the array
         rows.sort(sortTable.rowCmp);
 
         // most efficient reload of sorted rows I have found
         var sortedRows = jQuery.map(rows, function(row, i) { 
                 return row.row; 
         });
         $(tbody).append(sortedRows);
 
         sortTable.tbody=tbody;
         sortTable.columns=sortColumns;
         // Avoid js timeout
         setTimeout(function() { 
                         sortTable.sortFinish(sortTable.tbody,sortTable.columns); 
                     },5);
     },
 
     sortFinish: function (tbody,sortColumns)
     {   // Additional sort cleanup.
         // This is in a separate function to allow calling with setTimeout() which will
         // prevent javascript timeouts (I hope)
         sortTable.savePositions(tbody);
         if ($(tbody).hasClass('altColors'))
             sortTable.alternateColors(tbody,sortColumns);
         $(tbody).parents("table.tableWithDragAndDrop").each(function (ix) {
             tableDragAndDropRegister(this);
         });
         if (sortTable.loadingId)
             hideLoadingImage(sortTable.loadingId);
     },
 
     sortByColumns: function (tbody,sortColumns)
     {   // Will sort the table based on the abbr values on a set of <TH> colIds
         // Expects tbody to not sort thead, but could take table
 
         // Used to use 'sorting' class, but showLoadingImage results in much less screen redrawing
         // For IE especially this was difference between dead/timedout scripts and working sorts!
         var id = $(tbody).attr('id');
         if (!id || id.length === 0) {
             $(tbody).attr('id',"tbodySort"); // Must have some id!
             id = $(tbody).attr('id');
         }
         sortTable.loadingId = showLoadingImage(id);
         sortTable.tbody=tbody;
         sortTable.columns=sortColumns;
         // This allows hiding the rows while sorting!
         setTimeout(function() { 
                         sortTable.sort(sortTable.tbody,sortTable.columns); 
                     },50); 
     },
 
     trAlternateColors: function (tbody,rowGroup,cellIx)
     {   // Will alternate colors for visible table rows.
         // If cellIx(s) provided then color changes when the column(s) abbr or els innerHtml changes
         // If no cellIx is provided then alternates on rowGroup (5= change color 5,10,15,...)
         // Expects tbody to not color thead, but could take table
         var darker   = false; // === false will trigger first row to be change color = darker
 
         if (arguments.length<3) { // No columns to check so alternate on rowGroup
 
             if (!rowGroup || rowGroup === 0)
                 rowGroup = 1;
             var curCount = 0; // Always start with a change
             $(tbody).children('tr:visible').each( function(i) {
                 if (curCount === 0) {
                     curCount = rowGroup;
                     darker = (!darker);
                 }
                 if (darker) {
                     $(this).removeClass("bgLevel1");
                     $(this).addClass(   "bgLevel2");
                 } else {
                     $(this).removeClass("bgLevel2");
                     $(this).addClass(   "bgLevel1");
                 }
                 curCount--;
             });
 
         } else {
 
             var lastContent = "startWithChange";
             var cIxs = [];
             for (var aIx=2; aIx < arguments.length; aIx++) {   // multiple columns
                 cIxs[aIx-2] = arguments[aIx];
             }
             $(tbody).children('tr:visible').each( function(i) {
                 curContent = "";
                 for (var ix=0; ix < cIxs.length; ix++) {
                     if (this.cells[cIxs[ix]]) {
                         curContent += (this.cells[cIxs[ix]].abbr !== "" ?
                                     this.cells[cIxs[ix]].abbr       :
                                     this.cells[cIxs[ix]].innerHTML );
                     }
                 }
                 if (lastContent !== curContent) {
                     lastContent  = curContent;
                     darker = (!darker);
                 }
                 if (darker) {
                     $(this).removeClass("bgLevel1");
                     $(this).addClass(   "bgLevel2");
                 } else {
                     $(this).removeClass("bgLevel2");
                     $(this).addClass(   "bgLevel1");
                 }
             });
         }
     },
 
     alternateColors: function (tbody)
     {   // Will alternate colors based upon sort columns (which may be passed in as second arg,
         // or discovered).  Expects tbody to not color thead, but could take table
         var sortColumns;
         if (arguments.length > 1)
             sortColumns = arguments[1];
         else {
             var table = tbody;
             if ($(table).is('tbody'))
                 table = $(tbody).parent();
             sortColumns = new sortTable.columnsFromTable(table);
         }
 
         if (sortColumns) {
             if (sortColumns.cellIxs.length === 1)
                 sortTable.trAlternateColors(tbody,0,sortColumns.cellIxs[0]);
             else if (sortColumns.cellIxs.length === 2)
                 sortTable.trAlternateColors(tbody,0,sortColumns.cellIxs[0],sortColumns.cellIxs[1]);
             else // Three columns is plenty
                 sortTable.trAlternateColors(tbody,0,sortColumns.cellIxs[0],sortColumns.cellIxs[1],
                                                                             sortColumns.cellIxs[2]);
         } else {
             sortTable.trAlternateColors(tbody,5); // alternates every 5th row
         }
     },
 
     orderFromColumns: function (sortColumns)
     {// Creates the trackDB setting entry sortOrder subGroup1=+ ... from a sortColumns structure
         fields = [];
         for (var ix=0; ix < sortColumns.cellIxs.length; ix++) {
             if (sortColumns.tags[ix] && sortColumns.tags[ix].length > 0)
                 fields[ix] = sortColumns.tags[ix] + "=" + (sortColumns.reverse[ix] ? "-":"+");
             else
                 fields[ix] = sortColumns.cellIxs[ix] + "=" + (sortColumns.reverse[ix] ? "-":"+");
         }
         var sortOrder = fields.join(' ');
         return sortOrder;
     },
 
     orderUpdate: function (table,sortColumns,addSuperscript)
     {// Updates the sortOrder in a sortable table
         if (addSuperscript === undefined || addSuperscript === null)
             addSuperscript = false;
         if ($(table).is('tbody'))
             table = $(table).parent();
         var tr = $(table).find('tr.sortable')[0];
         if (tr) {
             for (cIx=0; cIx < sortColumns.cellIxs.length; cIx++) {
                 var th = tr.cells[sortColumns.cellIxs[cIx]];
                 /* jshint loopfunc: true */// function inside loop works and replacement is awkward.
                 $(th).each(function(i) {
                     // First remove old sort classes
                     var classList = $( this ).attr("class").split(" ");
                     if (classList.length < 2) // assertable
                         return;
                     classList = aryRemove(classList,["sortable"]);
                     while (classList.length > 0) {
                         var aClass = classList.pop();
                         if (aClass.indexOf("sort") === 0)
                             $(this).removeClass(aClass);
                     }
 
                     // Now add current sort classes
                     $(this).addClass("sort"+(cIx+1));
                     if (sortColumns.reverse[cIx])
                         $(this).addClass("sortRev");
 
                     // update any superscript
                     sup = $(this).find('sup')[0];
                     if (sup || addSuperscript) {
                         var content = (sortColumns.reverse[cIx] === false ? "&darr;":"&uarr;");
 
                         if (sortColumns.cellIxs.length>1) { // Number only if more than one
                             if (cIx < 5)  // Show numbering and direction only for the first 5
                                 content += (cIx+1);
                             else
                                 content = "";
                         }
 
                         if (sup)
                             sup.innerHTML = content;
                         else
                             $(th).append("<sup>"+content+"</sup>");
                     }
                 });
             }
             // There may be a hidden input that gets updated to the cart
             var inp = $(tr).find('input.sortOrder')[0];
             if (inp) {
                 $(inp).val(sortTable.orderFromColumns(sortColumns));
                 if (!addSuperscript && typeof(subCfg) === "object") // subCfg.js file included?
                     subCfg.markChange(null,inp);     // use instead of change() because type=hidden!
             }
         }
     },
 
     orderFromTr: function (tr)
     {   // Looks up the sortOrder input value from a *.sortable header row of a sortable table
         var inp = $(tr).find('input.sortOrder')[0];
         if (inp)
             return $(inp).val();
         else {
             // create something like "cellType=+ rep=+ protocol=+ treatment=+ factor=+ view=+"
             var fields = [];
             var cells = $(tr).find('th.sortable');
             $(cells).each(function (i) {
                 var classList = $( this ).attr("class").split(" ");
                 if (classList.length < 2) // assertable
                     return;
                 classList = aryRemove(classList,["sortable"]);
                 var reverse = false;
                 var sortIx = -1;
                 while (classList.length > 0) {
                     var aClass = classList.pop();
                     if (aClass.indexOf("sort") === 0) {
                         if (aClass === "sortRev")
                             reverse = true;
                         else {
                             aClass = aClass.substring(4);  // clip off the "sort" portion
                             var ix = parseInt(aClass);
                             if (!isNaN(ix)) {
                                 sortIx = ix;
                             }
                         }
                     }
                 }
                 if (sortIx >= 0) {
                     if (this.id && this.id.length > 0)
                         fields[sortIx] = this.id + "=" + (reverse ? "-":"+");
                     else
                         fields[sortIx] = this.cellIndex + "=" + (reverse ? "-":"+");
                 }
             });
             if (fields.length > 0) {
                 if (!fields[0])
                     fields.shift();  // 1 based sort ix and 0 based fields ix
                 return fields.join(' ');
             }
         }
         return "";
     },
 
     columnsFromSortOrder: function (sortOrder)
     {   // Creates sortColumns struct (without cellIxs[]) from a trackDB.sortOrder setting string
         this.tags = [];
         this.reverse = [];
         var fields = sortOrder.split(" "); // sortOrder looks like: "cell=+ factor=+ view=+"
         while (fields.length > 0) {
             var pair = fields.shift().split("=");  // Take first and split into
             if (pair.length === 2) {
                 this.tags.push(pair[0]);
                 this.reverse.push(pair[1] !== '+');
             }
         }
     },
 
     columnsFromTr: function (tr,silent)
     {   // Creates a sortColumns struct from entries in the 'tr.sortable' heading row of the table
         this.inheritFrom = sortTable.columnsFromSortOrder;
         var sortOrder = sortTable.orderFromTr(tr);
         if (sortOrder.length === 0 && !silent) {
             // developer needs to know something is wrong
             warn("Unable to obtain sortOrder from sortable table.");   
             return;
         }
 
         this.inheritFrom(sortOrder);
         // Add two additional arrays
         this.cellIxs = [];
         this.useAbbr = [];
         var ths = $(tr).find('th.sortable');
         for (var tIx=0; tIx < this.tags.length; tIx++) {
             for (ix=0; ix < ths.length; ix++) {
                 if ((ths[ix].id && ths[ix].id === this.tags[tIx])
                 ||  (ths[ix].cellIndex === parseInt(this.tags[tIx])))
                 {
                     this.cellIxs[tIx] = ths[ix].cellIndex;
                     this.useAbbr[tIx] = (ths[ix].abbr.length > 0);
                 }
             }
         }
         if (this.cellIxs.length === 0 && !silent) {
             warn("Unable to find any sortOrder.cells for sortable table.  ths.length:"+ths.length + 
                  " tags.length:"+this.tags.length + " sortOrder:["+sortOrder+"]");
             return;
         }
     },
 
     columnsFromTable: function (table)
     {// Creates a sortColumns struct from the contents of a 'table.sortable'
         this.inheritNow = sortTable.columnsFromTr;
         var tr = $(table).find('tr.sortable')[0];
         this.inheritNow(tr);
     },
 
     _sortOnButtonPress: function (anchor)
     {   // Updates the sortColumns struct and sorts the table when a column header has been pressed
         // If the current primary sort column is pressed, its direction is toggled then the table
         // is sorted. If a secondary sort column is pressed, it is moved to the primary spot and
         // sorted in fwd direction
         var th=$(anchor).closest('th')[0];  // Note that anchor is <a href> within th, not th
         var tr=$(th).parent();
         var theOrder = new sortTable.columnsFromTr(tr);
         var oIx = th.cellIndex;
         for (oIx=0; oIx < theOrder.cellIxs.length; oIx++) {
             if (theOrder.cellIxs[oIx] === th.cellIndex)
                 break;
         }
         if (oIx === theOrder.cellIxs.length) {
             // Developer must be warned that something is wrong with sortable table setup
             warn("Failure to find '"+th.id+"' in sort columns."); 
             return;
         }
         if (oIx > 0) { // Need to reorder
             var newOrder = new sortTable.columnsFromTr(tr);
             var nIx=0; // button pushed puts this 'tagId' column first in new order
             newOrder.tags[nIx] = theOrder.tags[oIx];
             newOrder.reverse[nIx] = false;  // When moving to the first position sort forward
             newOrder.cellIxs[nIx] = theOrder.cellIxs[oIx];
             newOrder.useAbbr[nIx] = theOrder.useAbbr[oIx];
             for (var ix=0; ix < theOrder.cellIxs.length; ix++) {
                 if (ix !== oIx) {
                     nIx++;
                     newOrder.tags[nIx]    = theOrder.tags[ix];
                     newOrder.reverse[nIx] = theOrder.reverse[ix];
                     newOrder.cellIxs[nIx] = theOrder.cellIxs[ix];
                     newOrder.useAbbr[nIx] = theOrder.useAbbr[ix];
                 }
             }
             theOrder = newOrder;
         } else { // if (oIx === 0) {   // need to reverse directions
             theOrder.reverse[oIx] = (theOrder.reverse[oIx] === false);
         }
         var table=$(tr).closest("table.sortable")[0];
         if (table) { // assertable
             sortTable.orderUpdate(table,theOrder);  // Must update sortOrder first!
             var tbody = $(table).find("tbody.sortable")[0];
             sortTable.sortByColumns(tbody,theOrder);
         }
         return;
     },
 
     sortOnButtonPress: function (anchor,tagId)
     {   // wrapper for the real worker: _sortOnButtonPress()
         var table = $( anchor ).closest("table.sortable")[0];
         if (table) {
             waitOnFunction( sortTable._sortOnButtonPress, anchor, tagId);
         }
         return false;  // called by link so return false means don't try to go anywhere
     },
 
     sortUsingColumns: function (table) // NOT USED
     {   // Sorts a table body based upon the marked columns
         var columns = new sortTable.columnsFromTable(table);
         tbody = $(table).find("tbody.sortable")[0];
         if (tbody)
             sortTable.sortByColumns(tbody,columns);
     },
 
     savePositions: function (table)
     {   // Sets the value for the input.trPos of a table row.  Typically this is a "priority" for
         // a track.  This gets called by sort or dragAndDrop in order to allow the new order to
         // affect hgTracks display
         var inputs = $(table).find("input.trPos");
         $( inputs ).each( function(i) {
             var tr = $( this ).closest('tr')[0];
             var trIx = $( tr ).attr('rowIndex').toString();
             if ($( this ).val() != trIx) {
                 $( this ).val( trIx );
                 if (typeof(subCfg) === "object")  // NOTE: couldn't get $(this).change() to work.
                     subCfg.markChange(null,this); //    probably because this is input type=hidden!
             }
         });
     },
 
     ///// Following functions are for Sorting by priority
     trPriorityFind: function (tr)
     {   // returns the position (*.priority) of a sortable table row
         var inp = $(tr).find('input.trPos')[0];
         if (inp)
             return $(inp).val();
         return 999999;
     },
 
     trPriorityCmp: function (tr1,tr2)  // UNUSED FUNCTION
     {   // Compare routine for sorting by *.priority
         var priority1 = sortTable.trPriorityFind(tr1);
         var priority2 = sortTable.trPriorityFind(tr2);
         return priority2 - priority1;
     },
 
     tablesSortAtStartup: function ()  // DEAD CODE?
     {   // Called at startup if you want javascript to initialize and sort all your
         // class='sortable' tables
         // IMPORTANT: This function WILL ONLY sort by first column.
         // If there are multiple sort columns, please presort the list for accurtacy!!!
         var tables = $("table.sortable");
         $(tables).each(function(i) {
             sortTable.initialize(this,true); // Will initialize superscripts
             sortTable.sortUsingColumns(this);
         });
     },
 
     initialize: function (table,addSuperscript,altColors)
     {// Called if you want javascript to initialize your class='sortable' table.
     // A sortable table requires:
     // TABLE.sortable: TABLE class='sortable' containing a THEAD header and
     //                 sortable TBODY filled with the rows to sort.
     // THEAD.sortable: (NOTE: created if not found) THEAD can contain multiple rows must contain:
     //   TR.sortable: exactly 1 header TH (table row) class='sortable' which will declare
     //                the sort columnns:
     //   TH.sortable: 1 or more TH (table column headers) with class='sortable sort1 [sortRev]'
     //                (or sort2, sort3) declaring sort order and whether reversed. e.g.:
     //                <TH id='factor' class='sortable sortRev sort3' nowrap>...</TH>
     //                (this means that factor is currently the third sort column and reverse sorted)
     //          NOTE: If no TH.sortable is found, then every th in the TR.sortable will be
     //                converted for you and will be in sort1,2,3 order.)
     //     ONCLICK: Each TH.sortable must call sortTable.sortOnButtonPress(this) directly or
     //              indirectly in the onclick event.  e.g.:
     //              <TH id='factor' class='sortable sortRev sort3' nowrap title='Sort on column' 
     //                              onclick="return sortTable.sortOnButtonPress(this);">
     //              NOTE: onclick function will automatically be added if not found.
     //     SUP: Each TH.sortable *may* contain a <sup> which will be filled with an up or down
     //          arrow and the column's sort order: e.g. <sup>&darr;2</sup>
     //          NOTE: If no sup is found but addSuperscript is requested, then they will be added.
     // TBODY.sortable: (NOTE: created if not found) The TBODY class='sortable' contains the
     //                 table rows that get sorted:
     //                 TBODY->TR & ->TD: Each row contains a TD for each sortable column.
     //                 The innerHTML (entire contents) of the cell will be used for sorting.
     //   TRICK: You can use the 'abbr' field to subtly alter the sortable contents.
     //          Otherwise sorts on td contents ($(td).text()).  Use the abbr field to make
     //          case-insensitive sorts or force exceptions to alpha-text order 
     //          (such as ZCTRL vs Control forcing controls to bottom). e.g.:
     //             <TD id='wgEncodeBroadHist...' nowrap abbr='ZCTRL' align='left'>Control</TD>
     //          IMPORTANT: You must add abbr='use' to the TH.sortable definitions.
     // Finally if you want the tableSort to alternate the table row colors
     // (using #FFFEE8 and #FFF9D2) then TBODY.sortable should also have class 'altColors'
     // NOTE: This class can be added by using the altColors option to this function
     
         if (altColors === undefined || altColors === null) // explicitly default this boolean
             altColors = false;
 
         if ($(table).hasClass('sortable') === false) {
             warn('Table is not sortable');
             return;
         }
         var tr = $(table).find('tr.sortable')[0];
         if (!tr) {
             tr = $(table).find('tr')[0];
             if (!tr) {
                 warn('Sortable table has no rows');
                 return;
             }
             $(tr).addClass('sortable');
             //warn('Made first row tr.sortable');
         }
         if ($(table).find('tr.sortable').length !== 1) {
             warn('sortable table contains more than 1 header row declaring sort columns.');
             return;
         }
 
         // If not TBODY is found, then create, wrapping all but those already in a thead
         tbody = $(table).find('tbody')[0];
         if (!tbody) {
             trs = $(table).find('tr').not('thead tr');
             $(trs).wrapAll("<TBODY class='sortable' />");
             tbody = $(table).find('tbody')[0];
             //warn('Wrapped all trs not in thead.sortable in tbody.sortable');
         }
         if ($(tbody).hasClass('sortable') === false) {
             $(tbody).addClass('sortable');
             //warn('Added sortable class to tbody');
         }
         if (altColors && $(tbody).hasClass('altColors') === false) {
             $(tbody).addClass('altColors');
             //warn('Added altColors class to tbody.sortable');
         }
         $(tbody).hide();
 
         // If not THEAD is found, then create, wrapping first row.
         thead = $(table).find('thead')[0];
         if (!thead) {
             $(tr).wrapAll("<THEAD class='sortable' />");
             thead = $(table).find('thead')[0];
             $(thead).insertBefore(tbody);
             //warn('Wrapped tr.sortable with thead.sortable');
         }
         if ($(thead).hasClass('sortable') === false) {
             $(thead).addClass('sortable');
             //warn('Added sortable class to thead');
         }
 
         var sortColumns = new sortTable.columnsFromTr(tr,"silent");
         if (!sortColumns || sortColumns.cellIxs.length === 0) {
             // could mark all columns as sortable!
             $(tr).find('th').each(function (ix) {
                 $(this).addClass('sortable');
                 $(this).addClass('sort'+(ix+1));
                 //warn("Added class='sortable sort"+(ix+1)+"' to th:"+this.innerHTML);
             });
             sortColumns = new sortTable.columnsFromTr(tr,"silent");
             if (!sortColumns || sortColumns.cellIxs.length === 0) {
                 warn("sortable table's header row contains no sort columns.");
                 return;
             }
         }
         // Can wrap all columnn headers with link
         $(tr).find("th.sortable").each(function (ix) {
             if ( ! $(this).attr('onclick') ) {
                 $(this).click( function () { sortTable.sortOnButtonPress(this);} );
             }
             if (theClient.isIePre11()) { // Special case for IE since CSS :hover doesn't work
                 $(this).hover(
                     function () { $(this).css( { backgroundColor: '#CCFFCC', cursor: 'hand' } ); },
                     function () { $(this).css( { backgroundColor: '#FCECC0', cursor: '' } ); }
                 );
             }
             if ( $(this).attr('title').length === 0) {
                 var title = $(this).text().replace(/[^a-z0-9 ]/ig,'');
                 if (title.length > 0 && $(this).find('sup'))
                     title = title.replace(/[0-9]$/g,'');
                 if (title.length > 0)
                     $(this).attr('title',"Sort list on '" + title + "'." );
                 else
                     $(this).attr('title',"Sort list on column." );
             }
         });
         // Now update all of those cells
         sortTable.orderUpdate(table,sortColumns,addSuperscript);
 
         // Alternate colors if requested
         if (altColors)
             sortTable.alternateColors(tbody);
 
         // Highlight rows?  But on subtrack list, this will mess up "metadata dropdown" coloring.
         // So just exclude tables with drag and drop
         if ($(table).hasClass('tableWithDragAndDrop') === false) {
             $('tbody.sortable').find('tr').hover(
                 function(){ $(this).addClass('bgLevel3');
                             $(this).find('table').addClass('bgLevel3'); },
                 function(){ $(this).removeClass('bgLevel3');
                             $(this).find('table').removeClass('bgLevel3'); }
             );
         }
 
         // Finally, make visible
         $(tbody).removeClass('sorting');
         $(tbody).show();
     }
 };
 
 function sortTableInitialize(table,addSuperscript,altColors)
 {   // legacy in case some static pages still initialize the table the old way
     sortTable.initialize(table,addSuperscript,altColors);
 }
 
 
  //////////////////////////////
 //// findTracks functions ////
 /////////////////////////////
 var findTracks = {
 
     updateMdbHelp: function (index)
     {   // update the metadata help links based on currently selected values.
         // If index === 0 we update all help items, otherwise we only update the one === index.
         var db = getDb();
         var disabled = {  // blackList 
             'accession':          1, 'dataVersion':      1, 'dccAccession':    1, 'expId':    1, 
             'geoSampleAccession': 1, 'grant':            1, 'lab':             1, 'labExpId': 1, 
             'labVersion':         1, 'origAssembly':     1, 'obtainedBy':      1, 'region':   1, 
             'replicate':          1, 'setType':          1, 'softwareVersion': 1, 'subId':    1, 
             'tableName':          1, 'tissueSourceType': 1, 'view':            1
         };
         var expected = $('tr.mdbSelect').length;
         var ix=1;
         if (index !== 0) {
             ix=index;
             expected=index;
         }
         for (; ix <= expected; ix++) {
             var helpLink = $("span#helpLink" + ix);
             if (helpLink.length > 0) {
                 // NOTE must match METADATA_NAME_PREFIX in hg/hgTracks/searchTracks.c
                 var val = $("select[name='hgt_mdbVar" + ix + "']").val();  
                 var text = $("select[name='hgt_mdbVar" + ix + "'] option:selected").text();
                 helpLink.html("&nbsp;"); // Do not want this with length === 0 later!
                 if ( ! disabled[val] ) {
                     var str;
                     if (val === 'cell') {
                         if (db.substr(0, 2) === "mm") {
                             str = "../ENCODE/cellTypesMouse.html";
                         } else {
                             str = "../ENCODE/cellTypes.html";
                         }
                     } else if (val.toLowerCase() === 'antibody') {
                         str = "../ENCODE/antibodies.html";
                     } else {
                         str = "../ENCODE/otherTerms.html#" + val;
                     }
                     helpLink.html("&nbsp;<a target='_blank' " +
                                   "title='detailed descriptions of terms'" + 
                                   " href='" + str + "'>" + text + "</a>");
                 }
             }
         }
     },
 
     mdbVarChanged: function (obj)
     {   // Ajax call to repopulate a metadata vals select when mdb var changes
         // This handles the currnet case when 2 vars have the same name (e.g. advanced, files tabs)
 
         findTracks.clearFound();  // Changing values so abandon what has been found
 
         var newVar = $(obj).val();
         // NOTE must match METADATA_NAME_PREFIX in hg/hgTracks/searchTracks.c
         var a = /hgt_mdbVar(\d+)/.exec(obj.name); 
         if (newVar !== undefined && newVar !== null && a && a[1]) {
             var num = a[1];
             if ($('#advancedTab').length === 1 && $('#filesTab').length === 1) {
                 $("select.mdbVar[name='hgt_mdbVar"+num+"'][value!='"+newVar+"']").val(newVar);
             }
             var cgiVars = "db=" + getDb() +  "&cmd=hgt_mdbVal" + num + "&var=" + newVar;
             if (document.URL.search('hgFileSearch') !== -1)
                 cgiVars += "&fileSearch=1";
             else
                 cgiVars += "&fileSearch=0";
 
             $.ajax({
                     type: "GET",
                     url: "../cgi-bin/hgApi",
                     data: cgiVars,
                     dataType: 'html',
                     trueSuccess: findTracks.handleNewMdbVals,
                     success: catchErrorOrDispatch,
                     error: errorHandler,
                     cache: true,
                     cmd: "hgt_mdbVal" + num, // NOTE must match METADATA_VALUE_PREFIX
                     num: num                 //      in hg/hgTracks/searchTracks.c
                 });
         }
         // NOTE: with newJquery, the response is getting a new error (missing ; before statement)
         //       There were also several XML parsing errors.
         // This error is fixed with the addition of "dataType: 'html'," above.
     },
 
     handleNewMdbVals: function (response, status)
     {   // Handle ajax response (repopulate a metadata val select)
         // This handles the currnet case when 2 vars have the same name (e.g. advanced, files tabs)
 
         var td = normed($('td#' + this.cmd));
         if (td) {
             $(td).empty();
             $(td).append(response);
             var inp = normed($(td).find('.mdbVal'));
             var tdIsLike = normed($('td#isLike'+this.num));
             if (inp && tdIsLike) {
                 if ($(inp).hasClass('freeText')) {
                     $(tdIsLike).text('contains');
                 } else if ($(inp).hasClass('wildList') ||  $(inp).hasClass('filterBy')) {
                     $(tdIsLike).text('is among');
                 } else {
                     $(tdIsLike).text('is');
                 }
             }
             // Do this by 'each' to set noneIsAll individually
             $(td).find('.filterBy').each( function(i) { 
                 ddcl.setup(this,'noneIsAll');
             });
         }
         findTracks.updateMdbHelp(this.num);
     },
 
     mdbValChanged: function (obj)
     {   // Keep all tabs with same selects in sync
         // TODO: Change from name to id based identification and only have one set of inputs in form
         // This handles the currnet case when 2 vars have the same name (e.g. advanced, files tabs)
 
         findTracks.clearFound();  // Changing values so abandon what has been found
 
         if ($('#advancedTab').length === 1 && $('#filesTab').length === 1) {
             var newVal = $(obj).val();
             // NOTE must match METADATA_NAME_PREFIX in hg/hgTracks/searchTracks.c
             var a = /hgt_mdbVal(\d+)/.exec(obj.name); 
             if (newVal !== undefined && newVar !== null && a && a[1]) {
                 var num = a[1];
                 $("input.mdbVal[name='hgt_mdbVal"+num+"'][value!='"+newVal+"']").val(newVal);
                 $("select.mdbVal[name='hgt_mdbVal"+num+"'][value!='"+newVal+"']").each( function (i) {
                     $(this).val(newVal);
                     if ($(this).hasClass('filterBy')) {
                         $(this).dropdownchecklist("destroy");
                         ddcl.setup(this,'noneIsAll');
                     }
                 });
             }
         }
         //findTracks.searchButtonsEnable(true);
     },
 
     changeVis: function (seenVis)
     {   // called by onchange of vis
         var visName = $(seenVis).attr('id');
         var trackName = visName.substring(0,visName.length - "_id".length);
         var hiddenVis = $("input[name='"+trackName+"']");
         var tdb = tdbGetJsonRecord(trackName);
         if ($(seenVis).val() !== "hide")
             $(hiddenVis).val($(seenVis).val());
         else {
             var selCb = $("input#"+trackName+"_sel_id");
             $(selCb).attr('checked',false);    // Can't set these to [] because that means default
             $(seenVis).attr('disabled',true);  // setting is used. However, we're explicitly hiding!
             var needSel = (tdb.parentTrack !== undefined && tdb.parentTrack !== null);
             if (needSel) {
                 var hiddenSel = $("input[name='"+trackName+"_sel']");
                 $(hiddenSel).val('0');  // Can't set it to [] because it means default setting used.
                 $(hiddenSel).attr('disabled',false);
             }
             if (tdbIsSubtrack(tdb))
                 $(hiddenVis).val("[]");
             else
                 $(hiddenVis).val("hide");
         }
         $(hiddenVis).attr('disabled',false);
 
         $('input.viewBtn').val('View in Browser');
     },
 
     clickedOne: function (selCb,justClicked)
     {   // called by on click of CB and findTracks.checkAll()
         var selName = $(selCb).attr('id');
         var trackName = selName.substring(0,selName.length - "_sel_id".length);
         var hiddenSel = $("input[name='"+trackName+"_sel']");
         var seenVis = $('select#' + trackName + "_id");
         var hiddenVis = $("input[name='"+trackName+"']");
         var tr = $(selCb).parents('tr.found');
         var tdb = tdbGetJsonRecord(trackName);
         var needSel = (typeof(tdb.parentTrack) === 'string' && tdb.parentTrack !== '');
         var shouldPack = tdb.canPack && tdb.kindOfParent === 0; // If parent then not pack but full
         if (shouldPack
         &&  tdb.shouldPack !== undefined && tdb.shouldPack !== null && !tdb.shouldPack)
             shouldPack = false;
         var checked = $(selCb).attr('checked');
 
         // First deal with seenVis control
         if (checked) {
             $(seenVis).attr('disabled', false);
             if ($(seenVis).attr('selectedIndex') === 0) {
                 if (shouldPack)
                     $(seenVis).attr('selectedIndex',3);  // packed
                 else
                     $(seenVis).attr('selectedIndex',$(seenVis).attr('length') - 1);
             }
         } else {
             $(seenVis).attr('selectedIndex',0);  // hide
             $(seenVis).attr('disabled', true );
         }
 
         // Deal with hiddenSel and hiddenVis so that submit does the right thing
         // Setting these requires justClicked OR seen vs. hidden to be different
         var setHiddenInputs = justClicked;
         if (!justClicked) {
             if (needSel)
                 setHiddenInputs = (checked !== (parseInt($(hiddenSel).val()) === 1));
             else if (checked)
                 setHiddenInputs = ($(seenVis).val() !== $(hiddenVis).val());
             else
                 setHiddenInputs = ($(hiddenVis).val() !== "hide" && $(hiddenVis).val() !== "[]");
         }
         if (setHiddenInputs) {
             if (checked)
                 $(hiddenVis).val($(seenVis).val());
             else if (tdbIsSubtrack(tdb))
                 $(hiddenVis).val("[]");
             else
                 $(hiddenVis).val("hide");
             $(hiddenVis).attr('disabled',false);
 
             if (needSel) {
                 if (checked)
                     $(hiddenSel).val('1');
                 else
                     $(hiddenSel).val('0');  // Can't set it to [] because it means default is used.
                 $(hiddenSel).attr('disabled',false);
             }
         }
 
         // The "view in browser" button should be enabled/disabled
         if (justClicked) {
             $('input.viewBtn').val('View in Browser');
             findTracks.counts();
         }
     },
 
 
     normalize: function ()
     {   // Normalize the page based upon current state of all found tracks
         $('div#found').show();
         var selCbs = $('input.selCb');
 
         // All should have their vis enabled/disabled appropriately (false means don't update cart)
         $(selCbs).each( function(i) { findTracks.clickedOne(this,false); });
 
         findTracks.counts();
     },
 
     normalizeWaitOn: function ()  // UNUSED ?
     {   // Put up wait mask then Normalize the page based upon current state of all found tracks
         waitOnFunction( findTracks.normalize );
     },
 
     _checkAll: function (check)
     {   // Checks/unchecks all found tracks.
         var selCbs = $('input.selCb');
         $(selCbs).attr('checked',check);
 
         // All should have their vis enabled/disabled appropriately (false means don't update cart)
         $(selCbs).each( function(i) { findTracks.clickedOne(this,false); });
 
         $('input.viewBtn').val('View in Browser');
         findTracks.counts();
         return false;  // Pressing button does nothing more
     },
 
     checkAllWithWait: function (check)
     {
         waitOnFunction( findTracks._checkAll, check);
     },
 
     searchButtonsEnable: function (enable)
     {   // Displays visible and checked track count
         // NOTE: must match TRACK_SEARCH in hg/inc/searchTracks.h
         var searchButton = $('input[name="hgt_tSearch"]'); 
         var clearButton  = $('input.clear');
         if (enable) {
             $(searchButton).attr('disabled',false);
             $(clearButton).attr('disabled',false);
         } else {
             $(searchButton).attr('disabled',true);
             $(clearButton).attr('disabled',true);
         }
     },
 
     counts: function ()
     {   // Displays visible and checked track count
         var counter = normed($('.selCbCount'));
         if (counter) {
             var selCbs =  $("input.selCb");
             if (selCbs && selCbs.length > 0)
                 $(counter).text("("+$(selCbs).filter(":enabled:checked").length + " of " +
                                                                     $(selCbs).length+ " selected)");
         }
     },
 
     clearFound: function ()
     {   // Clear found tracks and all input controls
         var found = normed($('div#found'));
         if (found)
             $(found).remove();
         found = normed($('div#filesFound'));
         if (found)
             $(found).remove();
         return false;
     },
 
     clear: function ()
     {   // Clear found tracks and all input controls
         findTracks.clearFound();
         $('input[type="text"]').val(''); // This will always be found
         $('select.mdbVal').attr('selectedIndex',0); // Should be 'Any'
         $('select.filterBy').each( function(i) { // Do this by 'each' to set noneIsAll individually
             //$(this).dropdownchecklist("refresh");  // requires v1.1
             $(this).dropdownchecklist("destroy");
             $(this).show();
             ddcl.setup(this,'noneIsAll');
         });
 
         $('select.groupSearch').attr('selectedIndex',0);
         $('select.typeSearch').attr('selectedIndex',0);
         //findTracks.searchButtonsEnable(false);
         return false;
     },
 
     sortNow: function (obj)
     {   // Called by radio button to sort tracks
         if ($('#sortIt').length === 0)
             $('form#trackSearch').append("<input TYPE=HIDDEN id='sortIt' name='"+
                                              $(obj).attr('name')+"' value='"+$(obj).val()+"'>");
         else
             $('#sortIt').val($(obj).val());
 
         // How to hold onto selected tracks?  There are 2 separate forms.  
         // Scrape named inputs from searchResults form and dup them on trackSearch?
         var inp = $('form#searchResults').find('input:hidden').not(':disabled').not(
                                                                                 "[name='hgsid']");
         if ($(inp).length > 0) {
             $(inp).appendTo('form#trackSearch');
             // Must be post to avoid url too long  NOTE: probably needs to be post anyway
             $('form#trackSearch').attr('method','POST'); 
         }
 
         $('#searchSubmit').click();
         return true;
     },
 
     page: function (pageVar,startAt)
     {   // Called by radio button to sort tracks
         var pager = $("input[name='"+pageVar+"']");
         if ($(pager).length === 1)
             $(pager).val(startAt);
 
         // How to hold onto selected tracks?  There are 2 separate forms.  
         // Scrape named inputs from searchResults form and dup them on trackSearch?
         var inp = $('form#searchResults').find('input:hidden').not(':disabled').not(
                                                                                 "[name='hgsid']");
         if ($(inp).length > 0) {
             $(inp).appendTo('form#trackSearch');
             // Must be post to avoid url too long  NOTE: probably needs to be post anyway
             $('form#trackSearch').attr('method','POST'); 
         }
 
         $('#searchSubmit').click();
         return false;
     },
 
     configSet: function (name)
     {   // Called when configuring a composite or superTrack
         var thisForm =  $('form#searchResults');
         $(thisForm).attr('action',"../cgi-bin/hgTrackUi?hgt_tSearch=Search&g="+name);
         $(thisForm).find('input.viewBtn').click();
     },
 
     mdbSelectPlusMinus: function (obj)
     {   // Now [+][-] mdb var rows with javascript rather than cgi roundtrip
         // Will remove row or clone new one.  Complication is that 'advanced' and 'files'
         // tab duplicate the tables!
         var objId = $(obj).attr('id');
         var rowNum = objId.substring(objId.length - 1);
         var val = $(obj).text();
         if (!val || val.length === 0)
             val = $(obj).val(); // Remove this when non-CSS buttons go away
         var buttons;
         if (val === '+') {
             buttons = $("#plusButton"+rowNum);  // Two tabs may have the exact same buttons!
             if (buttons.length > 0) {
                 var table = null;
                 $(buttons).each(function (i) {
                     var tr = $(this).parents('tr.mdbSelect')[0];
                     if (tr) {
                         table = $(tr).parents('table')[0];
                         var newTr = $(tr).clone();
                         var element = $(newTr).find("td[id^='hgt_mdbVal']")[0];
                         if (element)
                             $(element).empty();
                         element = $(newTr).find("td[id^='isLike']")[0];
                         if (element)
                             $(element).empty();
                         $(tr).after( newTr );
                         element = $(newTr).find("select.mdbVar")[0];
                         if (element)
                             $(element).attr('selectedIndex',-1); // chrome needs this after 'after'
                     }
                 });
                 if (table)
                     findTracks.mdbSelectRowsNormalize(table); // magic is in this function
                 return false;
             }
         } else { // === '-'
             buttons = $("#minusButton"+rowNum);  // Two tabs may have the exact same buttons!
             if (buttons.length > 0) {
                 var remaining = 0;
                 $(buttons).each(function (i) {
                     var tr = $(this).parents('tr')[0];
                     var table = $(tr).parents('table')[0];
                     if (tr)
                         $(tr).remove();
                     // Must renormalize since 2nd of 3 rows may have been removed
                     remaining = findTracks.mdbSelectRowsNormalize(table);  
                 });
                 // Got to remove the cart vars, though it doesn't matter which as
                 // count must not be too many.
                 if (remaining > 0) {
                     removeNum = remaining + 1;  
                     setCartVars( ["hgt_mdbVar"+removeNum,"hgt_mdbVal"+removeNum ], [ "[]","[]" ] );
                 }
 
                 findTracks.clearFound();  // Changing values so abandon what has been found
                 return false;
             }
         }
         return true;
     },
 
     mdbSelectRowsNormalize: function (table)
     { // Called when [-][+] buttons changed the number of mdbSelects in findTracks\
       // Will walk through each row and get the numberings of addressable elements correct.
         if (table) {
             var mdbSelectRows = $(table).find('tr.mdbSelect');
             var needMinus = (mdbSelectRows.length > 2);
             $(table).find('tr.mdbSelect').each( function (ix) {
                 var rowNum = ix + 1;  // Each [-][+] and mdb var=val pair of selects must be numbered
 
                 // First the [-][+] buttons
                 var plusButton = $(this).find("[id^='plusButton']")[0];
                 if (plusButton) {  // should always be a plus button
                     var oldNum =  Number(plusButton.id.substring(plusButton.id.length - 1));
                     if (oldNum === rowNum)
                         return;  // that is continue with the next row
 
                     $(plusButton).attr('id',"plusButton"+rowNum);
                     var minusButton = $(this).find("[id^='minusButton']")[0];
                     if (needMinus) {
                         if (!minusButton) {
                             if ($(plusButton).hasClass('pmButton'))
                                 $(plusButton).before("<span class='pmButton' id='minusButton"+
                                          rowNum+"' title='delete this row' "+
                                          "onclick='findTracks.mdbSelectPlusMinus(this);'>-</span>");
                             else   // Remove this else when non-CSS buttons go away
                                 $(plusButton).before("<input type='button' id='minusButton"+rowNum+
                                      "' value='-' style='font-size:.7em;' title='delete this row'" +
                                      " onclick='return findTracks.mdbSelectPlusMinus(this);'>");
                         } else
                             $(minusButton).attr('id',"minusButton"+rowNum);
                     } else if (minusButton)
                         $(minusButton).remove();
                 }
 
                 // Now the mdb var=val pair of selects
                 var element = $(this).find(".mdbVar")[0];  // select var
                 if (element)
                     $(element).attr('name','hgt_mdbVar' + rowNum);
 
                 element = $(this).find(".mdbVal")[0];      // select val
                 if (element) {                // not there if new row
                     $(element).attr('name','hgt_mdbVal' + rowNum);
                     if ($(element).hasClass('filterBy')) {
                         $(element).attr('id',''); // removing id ensures renumbering id
                         ddcl.reinit([ element ],true);
                     }
                 }
 
                 // A couple more things
                 element = $(this).find("td[id^='isLike']")[0];
                 if (element)
                     $(element).attr('id','isLike' + rowNum);
                 element = $(this).find("td[id^='hgt_mdbVal']")[0];
                 if (element)
                     $(element).attr('id','hgt_mdbVal' + rowNum);
             });
 
             return mdbSelectRows.length;
         }
         return 0;
     },
 
     switchTabs: function (ui)
     {   // switching tabs on findTracks page
 
         if (ui.panel.id === 'simpleTab' && $('div#found').length < 1) {
             // delay necessary, since select event not afterSelect event
             setTimeout(function() { 
                             $('input#simpleSearch').focus(); 
                         },20); 
         } else if (ui.panel.id === 'advancedTab') {
             // Advanced tab has DDCL wigets which were sized badly because the hidden width
             // was unknown delay necessary, since select event not afterSelect event
             setTimeout(function() { 
                             ddcl.reinit($('div#advancedTab').find('select.filterBy'),false); 
                         },20);
         }
         if ($('div#filesFound').length === 1) {
             if (ui.panel.id === 'filesTab')
                 $('div#filesFound').show();
             else
                 $('div#filesFound').hide();
         }
         if ($('div#found').length === 1) {
             if (ui.panel.id !== 'filesTab')
                 $('div#found').show();
             else
                 $('div#found').hide();
         }
     }
 };
 
 function escapeJQuerySelectorChars(str)
 {   // replace characters which are reserved in jQuery selectors
     // (surprisingly jQuery does not have a built in function to do this).
     return str.replace(/([!"#$%&'()*+,./:;<=>?@[\]^`{|}~"])/g,'\\$1');
 }
 
 var preloadImages = [];
 var preloadImageCount = 0;
 function preloadImg(url)  // DEAD CODE?
 {
 // force an image to be loaded (e.g. for images in menus or dialogs).
     preloadImages[preloadImageCount] = new Image();
     preloadImages[preloadImageCount].src = url;
     preloadImageCount++;
 }