e08ae97dc288749c2454fd98a10dc79f06e27cb5
max
  Tue Aug 11 06:16:20 2026 -0700
hgBlat/hgc: fixes from the v502 code review of the BLAT results pages, refs #37893

#4 blatOldTracks now falls back to "keep" (with a warning) on any value other
than keep/hide/delete, instead of dropping into the destructive delete branch,
so a typo in hg.conf can never silently discard a user's earlier BLAT tracks.

#5 htmlEncode() (js/utils.js) now also escapes " and ', which the browser's
text->markup conversion leaves alone. Every hgBlat caller puts the result in a
double-quoted attribute, so an unescaped quote in the cart position string could
break out of the attribute; the shared helper now honors its documented contract.

#6 The non-BLAT alignment title no longer starts with a stray space.

#7 open_memstream() is checked for NULL: on that failure the alignment renders
straight to stdout instead of writing to a NULL FILE and calling fclose(NULL).
The section reorder keys on the literal "<H4><A NAME=genomic>"/"<H4><A NAME=ali>"
strings, so a note was added in fuzzyShow.c and pslShow.c to keep them intact.

Found in the v502 final-build code review, refs #38069.

diff --git src/hg/js/utils.js src/hg/js/utils.js
index 72bbd6f4408..da93bb1447a 100644
--- src/hg/js/utils.js
+++ src/hg/js/utils.js
@@ -1,5071 +1,5077 @@
 // Utility JavaScript
 
 // "use strict";
 
 // Don't complain about line break before '||' etc:
 /* jshint -W014 */
 /* jshint -W087 */
 /* jshint esnext: true */
 
 var debug = false;
 
 /* Support these formats for range specifiers.  Note the ()'s around chrom,
  * start and end portions for substring retrieval: */
 // \s = whitespace, \w = azAZ0-9_, 
 var canonicalRangeExp = /^[\s]*([\w._#-]+)[\s]*:[\s]*([-0-9,]+)[\s]*[-_][\s]*([0-9,]+)[\s]*$/;
 var gbrowserRangeExp =  /^[\s]*([\w._#-]+)[\s]*:[\s]*([0-9,]+)[\s]*\.\.[\s]*([0-9,]+)[\s]*$/;
 var lengthRangeExp =    /^[\s]*([\w._#-]+)[\s]*:[\s]*([0-9,]+)[\s]*\+[\s]*([0-9,]+)[\s]*$/;
 var bedRangeExp =       /^[\s]*([\w._#-]+)[\s]+([0-9,]+)[\s]+([0-9,]+)[\s]*$/;
 var sqlRangeExp =       /^[\s]*([\w._#-]+)[\s]*\|[\s]*([0-9,]+)[\s]*\|[\s]*([0-9,]+)[\s]*$/;
 var singleBaseExp =     /^[\s]*([\w._#-]+)[\s]*:[\s]*([0-9,]+)[\s]*$/;
 // also allow gnomad variants, ex: 12-1234-A-C
 var gnomadVarExp = "^(([0-9]+)|(X|Y|M|MT))-([0-9]+)-([A-Za-z]+)-([A-Za-z]+)$";
 
 // allow gnomad ranges, ex: 12-1234-11223344
 var gnomadRangeExp = "^(([0-9]+)|(X|Y|M|MT))-([0-9]+)-([0-9]+)$";
 
 // gene symbol + exon number: "TP53 exon 5", "BRCA1 exon 10"
 var geneExonExp = /^[\s]*([A-Za-z][A-Za-z0-9._-]*)[\s]+exon[\s]+([0-9]+)[\s]*$/i;
 // compact exon notation: "TP53:e.5", "NM_000546:e.5+2", "BRCA2:e.10-3"
 var geneExonCoordExp = /^[\s]*([A-Za-z0-9._-]+):e\.([0-9]+)([+-][0-9]+)?[\s]*$/i;
 
 function createInfoIcon(text) {
     /* Create an info icon (i in circle) with tooltip text.
      * Returns a span element containing the SVG icon.
      * Uses addMouseover() for consistent tooltip behavior. */
     var span = document.createElement("span");
     span.style.marginLeft = "4px";
     span.innerHTML = "<svg style='height:1.1em; vertical-align:top' viewBox='0 0 24 24' fill='none' xmlns='http://www.w3.org/2000/svg'>" +
         "<circle cx='12' cy='12' r='10' stroke='#1C274C' stroke-width='1.5'/>" +
         "<path d='M12 17V11' stroke='#1C274C' stroke-width='1.5' stroke-linecap='round'/>" +
         "<circle cx='1' cy='1' r='1' transform='matrix(1 0 0 -1 11 9)' fill='#1C274C'/>" +
         "</svg>";
     addMouseover(span, text);
     return span;
 }
 
 function copyToClipboard(ev) {
     /* copy a piece of text to clipboard. event.target is some DIV or SVG that is an icon. 
      * The attribute data-target of this element is the ID of the element that contains the text to copy. 
      * The text is either in the attribute data-copy or the innerText.
      * see C function printCopyToClipboardButton(iconId, targetId);
      * */
      
     ev.preventDefault();
 
     var buttonEl = ev.target.closest("button"); // user can click SVG or BUTTON element
 
     var targetId = buttonEl.getAttribute("data-target");
     if (targetId===null)
         targetId = ev.target.parentNode.getAttribute("data-target");
     var textEl = document.getElementById(targetId);
     var text = textEl.getAttribute("data-copy");
     if (text===null)
         text = textEl.innerText;
 
     var textArea = document.createElement("textarea");
     textArea.value = text;
     // Avoid scrolling to bottom
     textArea.style.top = "0";
     textArea.style.left = "0";
     textArea.style.position = "fixed";
     document.body.appendChild(textArea);
     textArea.focus();
     textArea.select();
     document.execCommand('copy');
     document.body.removeChild(textArea);
     buttonEl.innerHTML = 'Copied';
     ev.preventDefault();
 }
 
 function cfgPageOnVisChange(ev) {
     /* configuration page event listener when user changes visibility in dropdown */
     if (ev.target.value === 'hide')
         ev.target.classList.replace("normalText", "hiddenText");
     else
         ev.target.classList.replace("hiddenText", "normalText");
 }
 
 function cfgPageAddListeners() {
     /* add event listener to dropdowns */
     var els = document.querySelectorAll(".trackVis");
     for (var i=0; i < els.length; i++) {
         var el = els[i];
         el.addEventListener("change", cfgPageOnVisChange );
     }
 }
 
 // Google Analytics helper functions to send events, see src/hg/lib/googleAnalytics.c
 
 function gaOnButtonClick(ev) {
 /* user clicked a button: send event to GA, then execute the old handler */
     var button = ev.currentTarget;
     var buttonName = button.name;
     if (buttonName==="")
         buttonName = button.id;
     if (buttonName==="")
         buttonName = button.value;
     // add the original label, makes logs a lot easier to read
     buttonName = button.value + " / "+buttonName;
 
     ga('send', 'event', 'buttonClick', buttonName);
     if (button.oldOnClick) // most buttons did not have an onclick function at all (the default click is a listener)
     {
         button.oldOnClick(ev);
     }
 }
 
 function gaTrackButtons() {
   /* replace the click handler on all buttons with one the sends a GA event first, then handles the click */
   if (!window.ga || ga.loaded) // When using an Adblocker, the ga object does not exist
       return;
   var buttons = document.querySelectorAll('input[type=submit],input[type=button]');
   var isFF = theClient.isFirefox();
   for (var i = 0; i < buttons.length; i++) {
        var b = buttons[i];
        // some old Firefox versions <= 78 do not allow submit buttons to also send AJAX requests
        // so Zoom/Move buttons are skipped in FF (even though newer versions allow it again, certainly FF >= 90)
        if (isFF && b.name.match(/\.out|\.in|\.left|\.right/))
            continue;
        b.oldOnClick = b.onclick;
        b.onclick = gaOnButtonClick; // addEventHandler would not work here, the default click stops propagation.
   }
 }
 // end Google Analytics helper functions
 
 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 && typeof 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 parentIsAllWiggle(tdb)
 {   // True if every subtrack of tdb's parent composite is a wiggle type.
     if (!tdb.parentTrack)
         return false;
     var parentName = tdb.parentTrack, found = false;
     for (var name in hgTracks.trackDb) {
         var t = hgTracks.trackDb[name];
         if (t.parentTrack === parentName) {
             found = true;
             if (/^wigMaf/.test(t.type) || !/^(wig|bigWig|bedGraph)/.test(t.type))
                 return false;
         }
     }
     return found;
 }
 
 function cartHideAnyTrack (id, cartVars, cartVals) {
     /* set the right cart variables to hide a track, changes cartVars and cartVals */
     var rec = hgTracks.trackDb[id];
     if (tdbIsSubtrack(rec)) {
         cartVars.push(id);
         cartVals.push('[]');
 
         cartVars.push(id+"_sel");
         cartVals.push(0);
     } else if (tdbIsFolderContent(rec)) {
         // supertrack children need to have _sel set to trigger superttrack reshaping
         cartVars.push(id);
         cartVals.push('hide');
 
         cartVars.push(id+"_sel");
         cartVals.push(0);
     } else {
         // normal, top-level track
         cartVars.push(id);
         cartVals.push('hide');
     }
 }
 
 function tdbCountChildren(trackDb, parentType) {
     /* return dicts with count of children, uses either the .parentTrack or .topParent trackDb attributes */
     var familySize = {};
     var families = {};
     // sort trackDb into object topParent -> count of children
     for (var trackName of Object.keys(hgTracks.trackDb)) {
         var rec = hgTracks.trackDb[trackName];
         // when looking at superTracks, only look at those children that are in superTracks
         if (rec[parentType]===undefined) {
             continue; // ignore tracks without parents
         }
 
         var parentTrack = rec[parentType];
         if (!familySize.hasOwnProperty(parentTrack)) {
             familySize[parentTrack] = 0;
             families[parentTrack] = [];
         }
         familySize[parentTrack]++;
         families[parentTrack].push(trackName);
     }
 
     var ret = {};
     ret.familySize = familySize;
     ret.families = families;
     return ret;
 }
 
 function tdbFindChildless(trackDb, delTracks) {
     /* Find parents that have no children left anymore in hgTracks.trackDb if you remove delTracks.
      * return obj with o.loneParents as array of [parent, array of children] , and o.others as an array of all other tracks
      * The caller needs the children names, as we want to hide the children with Javascript right away */
 
     // This functions uses a somewhat weird strategy: it counts the children of the composites, also counts the children of superTracks,
     // and compares both at the end. There may be a better strategy but our data structures are so strange that I didn't know what
     // else to do.
     var parentType = "parentTrack";
     others = [];
 
     var compLinks = tdbCountChildren(trackDb, "parentTrack"); // look only at direct parents: superTracks and composites
     var topLinks = tdbCountChildren(trackDb, "topParent");  // look at top parents, so only superTracks
 
     // decrease the parent's count for each track to delete
     for (var delTrack of delTracks) {
         var tdbRec = hgTracks.trackDb[delTrack];
         let parentName = tdbRec.parentTrack;
         if (parentName)
             compLinks.familySize[parentName]--;
 
         parentName = tdbRec.topParent;
         if (parentName)
             topLinks.familySize[parentName]--;
     }
 
     // for the parents of deleted tracks with a count of 0, create an array of [parentName, children]
     var loneParents = [];
     var doneParents = [];
     for (delTrack of delTracks) {
         var parentName = hgTracks.trackDb[delTrack].parentTrack;
         var topParentName = hgTracks.trackDb[delTrack].topParent;
         if (parentName) {
             // hide a superTrack parent only if that superTrack does not have any other tracks open
             // This addresses the case where you hide the last child of a composite under a superTrack
             // E.g. All Gencode / Gencode V46 or FANTOM5/Max count 
             if (compLinks.familySize[parentName]===0 && topLinks.familySize[topParentName]===0) {
                 if (!doneParents.includes(parentName)) {
                     loneParents.push([topParentName, compLinks.families[parentName]]);
                     doneParents.push(topParentName);
                 }
             } else
                 for (var child of compLinks.families[parentName])
                     // do not hide tracks of lone parents that are not in delTracks
                     if (delTracks.includes(child))
                         others.push(child);
         } else {
             others.push(delTrack);
         }
     }
 
     o = {};
     o.loneParents = loneParents;
     o.others = Array.from(new Set(others)); // remove duplicates (rare bug in the above)
     return o;
 }
 
 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 validateLabel(label)
 {   // returns true if label is valid in trackDb as short or long label
 
     var regexp = /^[a-z][ a-z0-9/'!\$()*,\-.:;<=>?@\[\]^_`{|}~]*$/i;
     if (regexp.test(label)) {
         return true;
     } else {
         alert(label + " is an invalid label. The first character must be alphabetical and the rest of the string be alphanumeric or the following puncuation ~`!@$/^*.()_-=[{]}?|;:'<,>");
         return false;
     }
 }
 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|gs|s3|drs):\/\/(((([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();
         }
 
     }
     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 getNonce(debug)
 {   // Gets nonce value from page meta header
 var content = $("meta[http-equiv='Content-Security-Policy']").attr("content");
 if (!content)
     return "";
 // parse nonce like 'nonce-JDPiW8odQkiav4UCeXsa34ElFm7o'
 var sectionBegin = "'nonce-";
 var sectionEnd   = "'";
 var ix = content.indexOf(sectionBegin);
 if (ix < 0)
     return "";
 content = content.substring(ix+sectionBegin.length);
 ix = content.indexOf(sectionEnd);
 if (ix < 0)
     return "";
 content = content.substring(0,ix);
 if (debug)
     alert('page nonce='+content);
 return content;
 }
 
 function notifBoxShow(cgiName, keyName) {
     /* move the notification bar div under '#TrackHeaderForm' */
     let lsKey = cgiName + "_" + keyName;
     if (localStorage.getItem(lsKey))
         return;
     var notifEl = document.getElementById(lsKey + "notifBox");
     if (!notifEl) {
         // missing call to setup function (ie generated server side like a udcTimeout message)
         notifBoxSetup(cgiName, keyName);
     }
     // TODO: make a generic element for positioning this
     var parentEl = document.getElementById('TrackHeaderForm');
     if (parentEl) {
         parentEl.appendChild(notifEl);
         notifEl.style.display = 'block';
     }
 }
 
 function notifBoxSetup(cgiName, keyName, msg, skipCloseButton) {
 /* Create a notification box if one hasn't been created, and
  * add msg to the list of shown notifications.
  * cgiName.keyName will be saved to localStorage in order to show
  * or hide this notification.
  * Must call notifBoxShow() in order to display the notification */
     lsKey = cgiName + "_" + keyName;
     if (localStorage.getItem(lsKey))
         return;
     let alreadyPresent = false;
     let notifBox = document.getElementById(lsKey+"notifBox");
     if (notifBox) {
         alreadyPreset = true;
         if (msg) {
             notifBox.innerHTML += "<br>" + msg;
         }
     } else {
         notifBox = document.createElement("div");
         notifBox.className = "notifBox";
         notifBox.style.display = "none";
         notifBox.style.width = "90%";
         notifBox.style.marginLeft = "100px";
         notifBox.id = lsKey+"notifBox";
         if (msg) {
             notifBox.innerHTML = msg;
         }
     }
     var closeHtml = "<button id='" + lsKey + "notifyHide'>Close</button>&nbsp;";
     var buttonStyles = "text-align: center";
     // XX code review: The close button does not sense at all, why not just always remove it?
     if (skipCloseButton===true) {
         closeHtml = "";
         buttonStyles += "; display: inline; margin-left: 20px";
     }
 
     notifBox.innerHTML += "<div style='"+buttonStyles+"'>"+
         closeHtml +
         "<button id='" + lsKey + "notifyHideForever'>Don't show again</button>"+
         "</div>";
     if (!alreadyPresent) {
         document.body.appendChild(notifBox);
     }
     $("#"+lsKey+"notifyHide").click({"id":lsKey}, function() {
         let key = arguments[0].data.id;
         $("#"+key+"notifBox").remove();
     });
     $("#"+lsKey+"notifyHideForever").click({"id": lsKey}, function() {
         let key = arguments[0].data.id;
         $("#"+key+"notifBox").remove();
         localStorage.setItem(key, "1");
     });
 }
 
 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'></button></CENTER>";
     html += "</div></center>";
 
 
     // GALT TODO either add nonce or move the showWarnBox and hideWarnBox to some universal javascript 
     //   file that is always included. Or consider if we can just dynamically define the functions
     //   right here inside this function?  maybe prepend function names with "window." to (re)define the global functions.
     //  maybe something like window.showWarnBox = function(){stuff here}; 
     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';";
     html += "var warnList=document.getElementById('warnList');";
     html += "warnList.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);
     document.getElementById('warnOK').onclick = function() {hideWarnBox();return false;};
 }
 
 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 {
         // don't add warnings that already exist:
         var oldMsgs = [];
         $('#warnList li').each(function(i, elem) {
             oldMsgs.push(elem.innerHTML);
         });
         // make the would-be new message into an <li> element so the case and quotes
         // match any pre-existing ones
         var newNode = document.createElement('li');
         newNode.innerHTML = msg;
         if (oldMsgs.indexOf(newNode.innerHTML) === -1) {
             $( warnList ).append(newNode);
         }
         if ($.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(':not([name^="boolshad"]):enabled').each(function (i) {
         var name  = $(this).attr('name');
         var val = $(this).val();
         if ($(this).attr('type') === 'checkbox' || $(this).attr('type') === "CHECKBOX") {
             name = cgiBooleanShadowPrefix() + name;
             val = $(this).prop('checked') ? 1 : 0;
         } else if ($(this).attr('type') === 'radio') {
             if (!$(this).prop('checked')) {
                 name = undefined;
             }
         }
         if (name && name !== "Submit" && val !== undefined && val !== null) {
             urlData[name] = val;
         }
     });
     // special case the vcfSampleOrder variable because it is a hidden input type that
     // changes based on click-drag
     $(inp).filter('[name$="vcfSampleOrder"]').each(function (i) {
         var name  = $(this).attr('name');
         var val = $(this).val();
         if (name && name !== "Submit" && val !== undefined && val !== null) {
             urlData[name] = val;
         }
     });
     // special case the highlight/color picker inputs
     $(inp).filter('[id^=colorPicker],[id^=colorInput]').each(function(i) {
         // remove the prefix that lets us recognize this setting, what remains
         // is specific to the track or for the back end
         var name = $(this)[0].id.replace("colorPicker.", "").replace("colorInput.", "");
         var val = $(this).val();
         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 (Array.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] === 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 if (typeof(val) === 'string') {
             // sometimes val is already encoded or partially encoded
             // the CGI cannot know if user input is double encoded
             // so test for already encoded characters here and only
             // encode what we need to
             retVal += aVar + "=" + val.replace(/(%[0-9A-Fa-f]{2})+|[^%]+/g, (match) => {
                 if (/%[0-9A-Fa-f]{2}/.test(match)) {
                     // Already percent-encoded, leave as-is
                     return match;
                 }
                 // Encode unencoded parts
                 return encodeURIComponent(match);
             });
         } 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 undecoratedDb(db)
 // return the db name with any hub_id_ stripped
 {
 var retDb = db;
 if (db.startsWith("hub_")) {
     retDb = db.split('_').slice(2).join('_');
 }
 return retDb;
 }
 
 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;
 
     if (typeof uiState !== "undefined" && uiState.db)
         return uiState.db;
 
     db = document.getElementById("selectAssembly");
     if (db)
         return db.selectedOptions[0].value;
 
     return "";
 }
 
 function undecoratedTrack(track)
 // return the track name with any hub_id_ stripped
 {
 var retTrack = track;
 if (track.startsWith("hub_")) {
     retTrack = track.split('_').slice(2).join("_");
 }
 return retTrack;
 }
 
 function getTrack()
 {
     var track = normed($("input#g").first());
     if (track)
         return track.value;
 
     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;
 
     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 makeHighlightString(db, chrom, start, end, color) {
 /* given db and a range on it and a color (color must be prefixed by #),
  * return the highlight string in the cart for it. See parsePositionWithDb for the history
  * of the various accepted highlight strings */
     return db+"#"+chrom+"#"+start+"#"+end+color;
 }
 
 function parsePositionWithDb(position)
 // returns an object with chrom, start, end and optionally color attributes
 // position is a string and can be in one of five different formats:
 // 0) chr:start-end 
 // 1) db.chr:start-end 
 // 2) db.chr:start-end#color
 // 3) db#chr#start#end#color
 // Formats 0-2 are only supported for backwards compatibility with old carts
 {
     var out = {};
     var parts = null;
     if (position.split("#").length !==5 ) {
         // formats of old carts: 0-2
         parts = position.split(".");
         // handle the db part
         if (parts.length === 2) {
             out.db = parts[0];
             position = parts[1];
         } else {
             out.db = getDb(); // default the db 
         }
         // position now contains chr:start-end#color
         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;
         }
     } else {
         // new format
         parts = position.split("#");
         out.db = parts[0];
         out.chrom = parts[1];
         out.start = parseInt(parts[2]);
         out.end = parseInt(parts[3]);
         out.color = "#" + parts[4];
     }
     return out;
 }
 
 function getHighlight(highlightStr, index) 
 /* Parse out highlight at index and return as a position object (see parsePositionWithDb) */
 {
     var hlStrings = highlightStr.split("|");
     var myHlStr = hlStrings[index];
     var posObj = parsePositionWithDb(myHlStr);
     return posObj;
 }
 
 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");
     $("#" + name + "CodonNumberingLabel").toggleClass("disabled", val === "OFF" ? true : false);
 }
 
 function gtexTransformChanged(name)
 { // Disable view limits settings if log transform enabled
 
     // NOTE: selector strings are a bit complex due to dots GB vars/attributes (track.var)
     // so can't use more concise jQuery syntax
 
     // check log transform
     var logCheckbox = $("input[name='" + name + ".logTransform']");
     var isLogChecked = logCheckbox.attr('checked');
 
     // enable/disable view limits
     var maxTextbox = $("input[name='" + name + ".maxViewLimit']");
     maxTextbox.attr('disabled', isLogChecked);
     var maxTextLabel = $("." + name + "ViewLimitsMaxLabel");
     maxTextLabel.toggleClass("disabled", isLogChecked ? true : false);
 }
 
 function barChartUiTransformChanged(name) {
 // Disable view limits settings if log transform enabled
     gtexTransformChanged(name);
 }
 
 function gtexSamplesChanged(name)
 { // Disable and comparison controls if all samples selected
 
     // check sample select
     var sampleSelect = $("input[name='" + name + ".samples']:checked");
     var isAllSamples = (sampleSelect.val() === 'all');
 
     // enable/disable comparison options
     // limiting to radio buttons as there is a problem with tissue checkbox naming on popup
     var comparisonButtons = $("input[type='radio' name='" + name + ".comparison']");
     comparisonButtons.attr('disabled', isAllSamples);
     var comparisonLabel = $("." + name + "ComparisonLabel");
     comparisonLabel.toggleClass("disabled", isAllSamples ? true : false);
 }
 
 
 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 (begToken.constructor.name === "RegExp")
             insideBeg = someString.search(begToken);
         else if (begToken.length > 0)
             insideBeg = someString.indexOf(begToken,ixBeg);
         if (endToken.constructor.name === "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 (begToken.constructor.name === "RegExp")
                 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 (endToken.constructor.name === "RegExp") 
                 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;
     var begToken = '<!-- HGERROR-START -->';
     var endToken = '<!-- HGERROR-END -->';
     while (cleanHtml.length > 0) {
         var bounds = bindings.outside(begToken,endToken,cleanHtml);
         if (bounds.start === -1)
             break;
         // OLD WAY var warnMsg = bindings.insideOut('<P>','</P>',cleanHtml,bounds.start,bounds.stop);
 	var warnMsg = cleanHtml.slice(bounds.start+begToken.length,bounds.stop-endToken.length);
         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, whatWeDid)
 { // strips javascript files from html returned by ajax
     var cleanHtml = returnedHtml;
     // Match script tags with src attribute - handles single/double quotes, with/without type attr
     var shlurpPattern=/<script[^>]*\ssrc\s*=\s*(['"])[^'"]*\1[^>]*>\s*<\/script>/gi;
     if (debug || whatWeDid) {
         var jsFiles = cleanHtml.match(shlurpPattern);
         if (jsFiles && jsFiles.length > 0) {
 	    if (debug)
 		alert("jsFiles:'"+jsFiles+"'\n---------------\n"+cleanHtml); // warn() interprets html
 	    if (whatWeDid)
 		whatWeDid.jsFiles = jsFiles;
 	}
     }
     cleanHtml = cleanHtml.replace(shlurpPattern,"");
 
     return cleanHtml;
 }
 
 function stripCspHeader(html, debug, whatWeDid)
 { // strips CSP Header from html returned by ajax
     var shlurpPattern=/<meta http-equiv=\'Content-Security-Policy\' content=".*"\>/i;
     if (debug || whatWeDid) {
         var csp = html.match(shlurpPattern);
         if (csp && csp.length > 0) {
 	    if (debug)
 		alert("csp:'"+csp+"'\n---------------\n"+html); // warn() interprets html
 	    if (whatWeDid)
 		whatWeDid.csp = csp[0];
 	}
     }
     return html.replace(shlurpPattern,""); // Clean CSP meta tag.
 }
 
 function parseNonce(content, debug)
 { // parse nonce from returned ajax page csp header
 
     if (!content)
 	return "";
     // parse nonce like 'nonce-JDPiW8odQkiav4UCeXsa34ElFm7o'
     var sectionBegin = "'nonce-";
     var sectionEnd   = "'";
     var ix = content.indexOf(sectionBegin);
     if (ix < 0)
 	return "";
     content = content.substring(ix+sectionBegin.length);
     ix = content.indexOf(sectionEnd);
     if (ix < 0)
 	return "";
     content = content.substring(0,ix);
     if (debug)
 	alert('ajax nonce='+content);
     return content;
 }
 
 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 stripJsNonce(html, nonce, debug, whatWeDid)
 { // Strips and returns embedded javascript from html returned by ajax with nonce
     var results=[];
     var content = "";
     var sectionBegin = "<script type='text/javascript' nonce='"+nonce+"'>";
     var sectionEnd   = "</script>";
     var lastIx = 0;
     while (1) {
 	var ix = html.indexOf(sectionBegin, lastIx);
 	if (ix < 0)
 	    break;
 	var ix2 = ix + sectionBegin.length;
 	var ex = html.indexOf(sectionEnd, ix2);
 	if (ex < 0)
 	    break;
 	content += html.substring(lastIx,ix);
 	var jsNonce = html.substring(ix2,ex);
 	if (debug)
 	    alert("jsNonce:"+jsNonce);
 	results.push(jsNonce);
 	lastIx = ex + sectionEnd.length;
 	}
     // grab the last piece.
     content += html.substring(lastIx);
 
     //return results;
     if (whatWeDid)
 	whatWeDid.js = results;
 
     return content;
 
 }
 
 function charsAreHex(s)
 // are all the chars found hex?
 {
     var hexChars = "01234566789abcdefABCDEF";
     var d = false;
     var i = 0;
     if (s) {
 	d = true;
 	while (i < s.length) {
 	    if (hexChars.indexOf(s.charAt(i++)) < 0)
 		d = false;
 	}
     }
     return d;
 }
 
 function nonAlphaNumericHexDecodeText(s, prefix, postfix)
 // For html tag attributes, it decodes non-alphanumeric characters
 // with <prefix>HH<postfix> hex codes.
 // Decoding happens in-place, changing the input string s.
 // prefix must not be empty string or null, but postfix can be empty string.
 // Because the decoded string is always equal to or shorter than the input string,
 // the decoding is just done in-place modifying the input string.
 // Accepts upper and lower case values in entities.
 //
 {
     var d = ""; 
     var pfxLen = prefix.length;
     var postLen = postfix.length;
     var i = 0;
     if (s) {
 	while (i < s.length) {
 	    var matched = false;
 	    if (i+pfxLen+postLen+2 <= s.length) {
 		var pre = s.substr(i, pfxLen).toLowerCase();
 		if (pre === prefix) {
 		    var post = s.substr(i+pfxLen+2, postLen).toLowerCase();
 		    if (post === postfix) {
 			var hex = s.substr(i+pfxLen, 2);
 			if (charsAreHex(hex)) {
 			    d = d + String.fromCharCode(parseInt(hex,16));
 			    i += pfxLen + 2 + postLen;
 			    matched = true;
 			}
 		    }
 		}
 	    }
 	    if (!matched)
 		d = d + s.charAt(i++);
 	    }
     }
     return d;
 }
 
 
 function jsDecode(s)
 // For JS string values decode "\xHH" 
 {
     return nonAlphaNumericHexDecodeText(s, "\\x", "");
 }
 
 
 function stripCSPAndNonceJs(content,  debug, whatWeDid)
 // Strip CSP Header and script blocks with the ajax nonce.
 {
 
     var pageNonce = getNonce(debug);
 
     var csp = {};
     content = stripCspHeader(content, debug, csp);
 
     var ajaxNonce = parseNonce(csp.csp, debug);
 	
     var jsBlocks = {};
     content = stripJsNonce(content, ajaxNonce, debug, jsBlocks);
 
     if (whatWeDid) {
 	whatWeDid.pageNonce = pageNonce;
 	whatWeDid.ajaxNonce = ajaxNonce;  // Not in use yet.
 	whatWeDid.js = jsBlocks.js;
     }
 
     return stripHgErrors(content, whatWeDid); // Certain early errors are not called via warnBox
 	
 }
 
 function appendNonceJsToPage(jsNonce)
 // Append ajax js blocks with nonce.
 // Create jsNonce by calling stripCSPAndNonceJs.
 // Call this after ajax html content has been added to the page/DOM.
 {
     var i;
     for (i=0; i<jsNonce.js.length; ++i) {
 	var sTag = document.createElement("script");
 	sTag.type = "text/javascript";
 	sTag.text = jsNonce.js[i];
 	sTag.setAttribute('nonce', jsNonce.pageNonce); // CSP2 Requires
 	document.head.appendChild(sTag);
     }		
 }
 
 function stripJsEmbedded(returnedHtml, debug, whatWeDid)
 { 
   // GALT NOTE: this may have been mostly obsoleted by CSP2 changes.
   // There were 3 or 4 places in the code that even in production
   // had called this function stripJsEmbedded with debug=true, which means that
   // if any script tag blocks are present, they would be seen and shown
   // to the user.  This probably was because if these blocks were found
   // simply adding them to the div html from the ajax callback would result in 
   // their being ignored by the browser. It seems to be a security feature of browsers.
   // Meanwhile however inline event handlers in the html worked and were allowed.
   // So this was just a way to warn developers that their script blocks would have been ignored
   // and have no effect. I think this concern no longer applies after my CSP2 changes
   // because it is able to pull in all the js, whether from event handlers or what would
   // have been individual script blocks in the old days, and adds it to
   // the page with a nonce and appendChild.
   //
   // 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.*\>/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) {
                 warnMsg = jsDecode(warnMsg);
                 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 addPixAndReloadPage()
 /* users who do not come in from hgGateway have no pix variable in the URL nor the cart.
  * This is a rare case, and the solution is brute force: if it happens, set pix, then reload the entire page.
  * This will only happen once to these users, as afterwards the cookie is set. */
 {
     var winWidth = calculateHgTracksWidth();
     var myUrl = window.location.href;
     var sep = '?';
     if (myUrl.indexOf('?')!==-1)
         sep = '&';
     var newUrl = myUrl+sep+"pix="+winWidth;
     window.location.href = newUrl;
 }
 
 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 + 1) * 22;
     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 = $(tbody).attr('id');
         }
         if ($(tbody).css('display') === 'none') {
             // suppress loading image if element is hidden (and consequently has no position)
             sortTable.loadingId = null;
         } else {
             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 = $( tr ).prop('rowIndex').toString();
             if ($( 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
     // To override, specify <TBODY class='sortable noAltColors'>
     // NOTE: Add class 'initBySortOrder' to have an sort by column performed at document initialization time, using
     // the saved sortOrder cart variable 
     
         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).hasClass('noAltColors') === 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') && $(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
                     $(this).attr('title',"Sort list on column." );
             }
         });
         // Now update all of those cells
         sortTable.orderUpdate(table,sortColumns,addSuperscript);
         if ($(tbody).hasClass('initBySortOrder')) {
             sortTable.sortByColumns(tbody,sortColumns);
         }
 
         // 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 = "hgsid=" + getHgsid() + "&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 isHub = trackName.slice(0,4) === "hub_";
         var hubUrl = isHub ? tdb.hubUrl : "";
         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);
             }
         }
 
         // if we selected a track in a public hub that is unconnected, we need to get the
         // hubUrl into the form so the genome browser knows to load that hub. If the hub
         // was already a connected hub, then we don't need to specify anything because it
         // will already be in the cart and we handle the visibility settings like normal.
         // The hubUrl field present in the json indicates this is an unconnected hub
         if (justClicked && hubUrl !== undefined && hubUrl.length > 0) {
             var form = $("form[id='searchResults'");
             var newHubInput = document.createElement("input");
             // if we are a subtrack we need to explicitly hide the parent
             // track so ALL subtracks of the parent don't show up unexpectedly
             if (needSel) {
                 var parentTrack = tdb.parentTrack;
                 var parentTrackInput = document.createElement("input");
                 parentTrackInput.setAttribute("type", "hidden");
                 parentTrackInput.setAttribute("name", parentTrack);
                 parentTrackInput.setAttribute("value", "hide");
                 form.append(parentTrackInput);
             }
             newHubInput.setAttribute("type", "hidden");
             newHubInput.setAttribute("name", "hubUrl");
             newHubInput.setAttribute("value", hubUrl);
             form.append(newHubInput);
         }
 
         // 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
 
         id = ui.newPanel[0].id;
         if (id === 'simpleTab' && $('div#found').length < 1) {
             // delay necessary, since select event not afterSelect event
             setTimeout(function() { 
                             $('input#simpleSearch').focus(); 
                         },20); 
         } else if (id === 'advancedTab') {
             // Advanced tab has DDCL wigets which were sized badly because the hidden width
             // was unknown delay necessary, since select event not afterSelect event
             setTimeout(function() { 
                             ddcl.reinit($('div#advancedTab').find('select.filterBy'),false); 
                         },20);
         }
         if ($('div#filesFound').length === 1) {
             if (id === 'filesTab')
                 $('div#filesFound').show();
             else
                 $('div#filesFound').hide();
         }
         if ($('div#found').length === 1) {
             if (id !== 'filesTab')
                 $('div#found').show();
             else
                 $('div#found').hide();
         }
         // explicitly set the hidden form input for the current tab because jquery-ui won't do
         // it for us anymore
         $("#currentTab").val(id);
     }
 };
 
 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++;
 }
 
 
   ///////////////////
  /////  mouse  /////
 ///////////////////
 var mouse = {
 
     savedOffset: {x:0, y:0},
 
     saveOffset: function (ev)
     {   // Save the mouse offset associated with this event
         mouse.savedOffset = {x: ev.clientX, y: ev.clientY};
     },
 
     hasMoved: function (ev)
     {   // return true if mouse has moved a significant amount
         var minPixels = 10;
         var movedX = ev.clientX - mouse.savedOffset.x;
         var movedY = ev.clientY - mouse.savedOffset.y;
         if (arguments.length === 2) {
             var num = Number(arguments[1]);
             if (isNaN(num)) {
                 if ( arguments[1].toLowerCase() === "x" )
                     return (movedX > minPixels || movedX < (minPixels * -1));
                 if ( arguments[1].toLowerCase() === "y" )
                     return (movedY > minPixels || movedY < (minPixels * -1));
             }
             else
                 minPixels = num;
         }
         return (   movedX > minPixels || movedX < (minPixels * -1)
                 || movedY > minPixels || movedY < (minPixels * -1));
     }
 };
 
   ///////////////////////////
  //// Drag Reorder Code ////
 ///////////////////////////
 var dragReorder = {
     originalHeights: {}, // trackName: startHeight
 
     setOrder: function (table)
     {   // Sets the 'order' value for the image table after a drag reorder
         var varsToUpdate = {};
         $("tr.imgOrd").each(function (i) {
             if ($(this).prop('abbr') !== $(this).prop('rowIndex').toString()) {
                 $(this).attr('abbr', $(this).prop('rowIndex').toString());
                 var name = this.id.substring('tr_'.length) + '_imgOrd';
                 varsToUpdate[name] = $(this).attr('abbr');
             }
         });
         if (objNotEmpty(varsToUpdate)) {
             cart.setVarsObj(varsToUpdate);
             imageV2.markAsDirtyPage();
         }
     },
 
     sort: function (table)
     {   // Sets the table row order to match the order of the abbr attribute.
         // This is needed for back-button, and for visBox changes combined with refresh.
         var tbody = $(table).find('tbody')[0];
         if (!tbody)
             tbody = table;
 
         // Do we need to sort?
         var trs = tbody.rows;
         var needToSort = false;
         $(trs).each(function(ix) {
             if (this.getAttribute('abbr') !== this.getAttribute('rowIndex')) {
                 needToSort = true;
                 return false;  // break for each() loops
             }
         });
         if (!needToSort)
             return false;
 
         // Create array of tr holders to sort
         var ary = [];
         $(trs).each(function(ix) {  // using sortTable found in utils.js
             ary.push(new sortTable.field(parseInt($(this).attr('abbr')),false,this));
         });
 
         // Sort the array
         ary.sort(sortTable.fieldCmp);
 
         // most efficient reload of sorted rows I have found
         var sortedRows = jQuery.map(ary, function(ary, i) { return ary.row; });
         $(tbody).append( sortedRows ); // removes tr from current position and adds to end.
         return true;
     },
 
     showCenterLabel: function (tr, show)
     {   // Will show or hide centerlabel as requested
         // adjust button, sideLabel height, sideLabelOffset and centerlabel display
 
         if (!$(tr).hasClass('clOpt'))
             return;
         var center = normed($(tr).find(".sliceDiv.cntrLab"));
         if (!center)
             return;
         var seen = ($(center).css('display') !== 'none');
         if (show === seen)
             return;
 
         var centerHeight = $(center).height();
 
         var btn = normed($(tr).find("p.btn"));
         var side = normed($(tr).find(".sliceDiv.sideLab"));
         if (btn && side) {
             var sideImg = normed($(side).find("img"));
             if (sideImg) {
                 var top = parseInt($(sideImg).css('top'));
                 if (show) {
                     $(btn).css('height',$(btn).height() + centerHeight);
                     $(side).css('height',$(side).height() + centerHeight);
                     top += centerHeight; // top is a negative number
                     $(sideImg).css( {'top': top.toString() + "px" });
                     $( center ).show();
                 } else if (!show) {
                     $(btn).css('height',$(btn).height() - centerHeight);
                     $(side).css('height',$(side).height() - centerHeight);
                     top -= centerHeight; // top is a negative number
                     $(sideImg).css( {'top': top.toString() + "px" });
                     $( center ).hide();
                 }
             }
         }
     },
 
     getContiguousRowSet: function (row)
     {   // Returns the set of rows that are of the same class and contiguous
         if (!row)
             return null;
         var btn = $( row ).find("p.btn");
         if (btn.length === 0)
             return null;
         var classList = $( btn ).attr("class").split(" ");
         var matchClass = classList[0];
         var table = $(row).parents('table#imgTbl')[0];
         var rows = $(table).find('tr');
 
         // Find start index
         var startIndex = $(row).prop('rowIndex');
         var endIndex = startIndex;
         for (var ix=startIndex-1; ix >= 0; ix--) {
             btn = $( rows[ix] ).find("p.btn");
             if (btn.length === 0)
                 break;
             classList = $( btn ).attr("class").split(" ");
             if (classList[0] !== matchClass)
                 break;
             startIndex = ix;
         }
 
         // Find end index
         for (var rIx=endIndex; rIx<rows.length; rIx++) {
             btn = $( rows[rIx] ).find("p.btn");
             if (btn.length === 0)
                 break;
             classList = $( btn ).attr("class").split(" ");
             if (classList[0] !== matchClass)
                 break;
             endIndex = rIx;
         }
         return rows.slice(startIndex,endIndex+1); // endIndex is 1 based!
     },
 
     getCompositeSet: function (row)
     {   // Returns the set of rows that are of the same class and contiguous
         if (!row)
             return null;
         var rowId = $(row).attr('id').substring('tr_'.length);
         var rec = hgTracks.trackDb[rowId];
         if (tdbIsSubtrack(rec) === false)
             return null;
 
         var rows = $('tr.trDraggable:has(p.' + rec.parentTrack+')');
         return rows;
     },
 
     zipButtons: function (table)
     {   // Goes through the image and binds composite track buttons when adjacent
         var rows = $(table).find('tr');
         var lastClass="";
         var lastBtn = null;
         var lastSide = null;
         var lastMatchesLast=false;
         var lastBlue=true;
         var altColors=false;
         var count=0;
         var countN=0;
         for (var ix=0; ix<rows.length; ix++) {    // Need to have buttons in order
             var btn = $( rows[ix] ).find("p.btn");
             var side = $( rows[ix] ).find(".sliceDiv.sideLab"); // added by GALT
             if (btn.length === 0)
                 continue;
             var classList = $( btn ).attr("class").split(" ");
             var curMatchesLast=(classList[0] === lastClass);
 
             // centerLabels may be conditionally seen
             if ($( rows[ix] ).hasClass('clOpt')) {
                 // if same composite and previous also centerLabel optional then hide center label
                 if (curMatchesLast && $( rows[ix - 1] ).hasClass('clOpt'))
                     dragReorder.showCenterLabel(rows[ix],false);
                 else
                     dragReorder.showCenterLabel(rows[ix],true);
             }
 
             // On with buttons
             if (lastBtn) {
                 $( lastBtn ).removeClass('btnN btnU btnL btnD');
                 if (curMatchesLast && lastMatchesLast) {
                     $( lastBtn ).addClass('btnL');
                     $( lastBtn ).css('height', $( lastSide ).height() - 0);  // added by GALT
                 } else if (lastMatchesLast) {
                     $( lastBtn ).addClass('btnU');
                     $( lastBtn ).css('height', $( lastSide ).height() - 1);  // added by GALT
                 } else if (curMatchesLast) {
                     $( lastBtn ).addClass('btnD');
                     $( lastBtn ).css('height', $( lastSide ).height() - 2);  // added by GALT
                 } else {
                     $( lastBtn ).addClass('btnN');
                     $( lastBtn ).css('height', $( lastSide ).height() - 3);  // added by GALT
                     countN++;
                 }
                 count++;
                 if (altColors) {
                     // lastMatch and lastBlue or not lastMatch and notLastBlue
                     lastBlue = (lastMatchesLast === lastBlue);
                     if (lastBlue)    // Too  smart by 1/3rd
                         $( lastBtn ).addClass(    'btnBlue' );
                     else
                         $( lastBtn ).removeClass( 'btnBlue' );
                 }
             }
             lastMatchesLast = curMatchesLast;
             lastClass = classList[0];
             lastBtn = btn;
             lastSide = side;
         }
         if (lastBtn) {
             $( lastBtn ).removeClass('btnN btnU btnL btnD');
             if (lastMatchesLast) {
                 $( lastBtn ).addClass('btnU');
                 $( lastBtn ).css('height', $( lastSide ).height() - 1);  // added by GALT
             } else {
                 $( lastBtn ).addClass('btnN');
                 $( lastBtn ).css('height', $( lastSide ).height() - 3);  // added by GALT
                 countN++;
             }
             if (altColors) {
                 // lastMatch and lastBlue or not lastMatch and notLastBlue
                 lastBlue = (lastMatchesLast === lastBlue);
                 if (lastBlue)    // Too  smart by 1/3rd
                     $( lastBtn ).addClass(    'btnBlue' );
                 else
                     $( lastBtn ).removeClass( 'btnBlue' );
             }
             count++;
         }
         //warn("Zipped "+count+" buttons "+countN+" are independent.");
     },
 
     dragHandleMouseOver: function ()
     {   // Highlights a single row when mouse over a dragHandle column (sideLabel and buttons)
         if ( ! jQuery.tableDnD ) {
             //var handle = $("td.dragHandle");
             //$(handle)
             //    .unbind('mouseenter')//, jQuery.tableDnD.mousemove);
             //    .unbind('mouseleave');//, jQuery.tableDnD.mouseup);
             return;
         }
         if ( ! jQuery.tableDnD.dragObject ) {
             $( this ).parents("tr.trDraggable").addClass("trDrag");
         }
     },
 
     dragHandleMouseOut: function ()
     {   // Ends row highlighting by mouse over
         $( this ).parents("tr.trDraggable").removeClass("trDrag");
     },
 
     buttonMouseOver: function ()
     {   // Highlights a composite set of buttons, regarless of whether tracks are adjacent
         if ( ! jQuery.tableDnD || ! jQuery.tableDnD.dragObject ) {
             var classList = $( this ).attr("class").split(" ");
             var btns = $( "p." + classList[0] );
             $( btns ).removeClass('btnGrey');
             $( btns ).addClass('btnBlue');
             if (jQuery.tableDnD) {
                 var rows = dragReorder.getContiguousRowSet($(this).parents('tr.trDraggable')[0]);
                 if (rows)
                     $( rows ).addClass("trDrag");
             }
         }
     },
 
     buttonMouseOut: function ()
     {   // Ends composite highlighting by mouse over
         var classList = $( this ).attr("class").split(" ");
         var btns = $( "p." + classList[0] );
         $( btns ).removeClass('btnBlue');
         $( btns ).addClass('btnGrey');
         if (jQuery.tableDnD) {
             var rows = dragReorder.getContiguousRowSet($(this).parents('tr.trDraggable')[0]);
             if (rows)
             $( rows ).removeClass("trDrag");
         }
     },
 
     trMouseOver: function (e)
     {   // Trying to make sure there is always a imageV2.lastTrack so that we know where we are
         var id = '';
         var a = /tr_(.*)/.exec($(this).attr('id'));  // voodoo
         if (a && a[1]) {
             id = a[1];
         }
         if (id.length > 0) {
             if ( ! imageV2.lastTrack || imageV2.lastTrack.id !== id) {
                 imageV2.lastTrack = rightClick.makeMapItem(id);
                 // currentMapItem gets set by mapItemMapOver.   This is just backup
             }
 
             if (typeof greyBarIcons !== 'undefined' && greyBarIcons === true) {
                 // show the gear icon over the grey bar to bring up the context menu
                 let tdBtn = document.getElementById("td_btn_" + id);
                 if (tdBtn) {
                     let span = document.getElementById("gear_btn_" + id);
                     if (span) {
                         // hide any gears that may be present from dragging
                         $(document.querySelectorAll("[id^=gear_btn]")).hide();
                         $(span).show();
                         if (!span.dataset.alreadySetup) {
                             tdBtn.style.position = "relative";
                             let tdbKey = tdBtn.id.replace("td_btn_","");
                             let tdb = hgTracks.trackDb[tdbKey];
                             let tooltip = " click or right click to configure... drag to reorder";
                             if (typeof tdb.parentLabel !== 'undefined') {
                                 addMouseover(span, tdb.parentLabel + tooltip + " highlighted subtracks");
                             } else {
                                 addMouseover(span, tdb.shortLabel + tooltip);
                             }
                             span.addEventListener("click", (e) => {
                                 // trigger a click on the <a> of the td
                                 e.preventDefault();
                                 e.stopPropagation();
                                 e.stopImmediatePropagation();
                                 const clickEvent = new MouseEvent("click", {
                                     bubbles: true,
                                     cancelable: true,
                                     view: window,
                                     clientX: tdBtn.getBoundingClientRect().left + 15,
                                     clientY: tdBtn.getBoundingClientRect().top,
                                     button: 1,
                                 });
                                 tdBtn.children[0].dispatchEvent(clickEvent);
                             });
                             let tdp = tdBtn.querySelector("p.btn");
                             if (tdp) {
                                 span.addEventListener("pointerenter", (e) => {
                                     // trigger a mouseover on the actual btn
                                     dragReorder.buttonMouseOver.call(tdp, e);
                                 });
                                 span.addEventListener("pointerleave", (e) => {
                                     dragReorder.buttonMouseOut.call(tdp, e);
                                 });
                             }
                             // prevent attaching multiple events every time the tr is moused over
                             span.dataset.alreadySetup = "true";
                         }
                     }
                 }
 
                 // add an 'x' icon in the label area to hide the track
                 let tdSide = document.getElementById("td_side_" + id);
                 if (tdSide) {
                     // mouseover event fires if you stop moving the mouse while still
                     // hovering the element and then move it again, don't make
                     // duplicate btns in that case
                     let btn = document.getElementById("close_btn_" + id);
                     if (btn) {
                         // hide any shown 'x' buttons from dragging
                         $(document.querySelectorAll("[id^=close_btn]")).hide();
                         $(btn).show();
                         if (!btn.dataset.alreadySetup) {
                             addMouseover(btn, btn.title);
                             tdSide.style.position = "relative";
                             if (hgTracks && hgTracks.revCmplDisp) {
                                 // set up 'x' icon to the right
                                 btn.classList.add("hgTracksCloseIconRight");
                             } else {
                                 // set up 'x' icon to the left
                                 btn.classList.add("hgTracksCloseIconLeft");
                             }
                             btn.addEventListener("click", (e) => {
                                rightClick.hideTracks([id]);
                             });
                             // prevent attaching multiple events every time the tr is moused over
                             btn.dataset.alreadySetup = "true";
                         }
                     }
                 }
             }
         }
     },
 
     trMouseLeave: function(e)
     {
         var id = '';
         var a = /tr_(.*)/.exec($(this).attr('id'));  // voodoo
         if (a && a[1]) {
             id = a[1];
         }
         if (id.length > 0) {
             // hide 'x' icon in the label area to hide the track
             let tdSide = document.getElementById("td_side_" + id);
             if (tdSide) {
                 let btn = document.getElementById("close_btn_" + id);
                 if (btn) {
                     $(btn).hide();
                 }
             }
 
             // hide gear icon over the grey bar
             let tdBtn = document.getElementById("td_btn_" + id);
             if (tdBtn) {
                 let btn = document.getElementById("gear_btn_" + id);
                 if (btn) {
                     $(btn).hide();
                 }
             }
         }
     },
 
     mapItemMouseOver: function ()
     {
         // Record data for current map area item
         var id = this.id;
         if (!id || id.length === 0) {
             id = '';
             var tr = $( this ).parents('tr.imgOrd');
             if ( $(tr).length === 1 ) {
                 var a = /tr_(.*)/.exec($(tr).attr('id'));  // voodoo
                 if (a && a[1]) {
                     id = a[1];
                 }
             }
         }
         if (id.length > 0) {
             rightClick.currentMapItem = rightClick.makeMapItem(id);
             if (rightClick.currentMapItem) {
                 rightClick.currentMapItem.href = this.href;
                 rightClick.currentMapItem.title = this.getAttribute("data-tooltip") || this.title;
             }
         }
     },
 
     mapItemMouseOut: function ()
     {
         imageV2.lastTrack = rightClick.currentMapItem; // Just a backup
         rightClick.currentMapItem = null;
     },
 
     
 
     init: function ()
     {   // Make side buttons visible (must also be called when updating rows in the imgTbl).
         var btns = $("p.btn");
         if (btns.length > 0) {
             dragReorder.zipButtons($('#imgTbl'));
             $(btns).on("mouseenter", dragReorder.buttonMouseOver );
             $(btns).on("mouseleave", dragReorder.buttonMouseOut  );
             $(btns).show();
         }
         var handle = $("td.dragHandle");
         if (handle.length > 0) {
             $(handle).on("mouseenter", dragReorder.dragHandleMouseOver );
             $(handle).on("mouseleave", dragReorder.dragHandleMouseOut  );
         }
 
         // setup mouse callbacks for the area tags
         $("#imgTbl").find("tr").on("mouseover", dragReorder.trMouseOver );
         $("#imgTbl").find("tr").on("mouseleave", dragReorder.trMouseLeave );
         $("#imgTbl").find("tr").each( function (i, row) {
             // save the original y positions of each row
             //if (row.id in dragReorder.originalHeights === false) {
                 dragReorder.originalHeights[row.id] = row.getBoundingClientRect().y + window.scrollY;
             //}
         });
 
 
         $(".area").each( function(t) {
                             this.onmouseover = dragReorder.mapItemMouseOver;
                             this.onmouseout = dragReorder.mapItemMouseOut;
                             this.onclick = posting.mapClk;
                         });
     }
 };
 
 function trackHubSkipHubName(name) {
     // Just like hg/lib/trackHub.c's...
     var matches;
     if (name && (matches = name.match(/^hub_[0-9]+_(.*)/)) !== null) {
         return matches[1];
     } else {
         return name;
     }
 }
 
 function replaceReserved(txt) {
     /* This should somehow be made more general so we can stop worrying about
      * user made tracks with whatever characters in it */
     if (!txt) {
         throw new Error("trying to replace null txt");
     }
     return txt.replace(/[^A-Za-z0-9_]/g, "_");
 }
 
 function boundingRect(refEl) {
     /* For regular HTML elements, this function wraps getBoundingClientRect(). For area
      * elements like on hgTracks, getBoundingClientRect() won't work and we have to figure
      * everything out from the .coords attribute along with taking into account dragReorder,
      * page scroll, etc */
     if (! (refEl instanceof Element)) {
         // not a map/area element, maybe from some other part of the UI
         console.log("trying to place a mouseover element next to an element that has not been created yet");
         throw new Error();
     }
 
     // obtain coordinates for placing the mouseover
     let refWidth, refHeight, refX, refY, y1;
     let refRight, refLeft, refTop, refBottom;
     let rect;
     let windowWidth = window.innerWidth;
     let windowHeight = window.innerHeight;
     if (refEl.coords !== undefined && refEl.coords.length > 0 && refEl.coords.split(",").length == 4) {
         // if we are dealing with an <area> element, the refEl width and height
         // are for the whole image and not for just the area, so
         // getBoundingClientRect() will return nothing, sad!
         let refImg = document.querySelector("[usemap='#" + refEl.parentNode.name + "']");
         if (refImg === null) {return;}
         let refImgRect = refImg.getBoundingClientRect();
         let refImgWidth = refImgRect.width;
         let label = document.querySelector("[id^=td_side]");
         let btn = document.querySelector("[id^=td_btn]");
         let labelWidth = 0, btnWidth = 0;
         if (label && btn) {
             labelWidth = label.getBoundingClientRect().width;
             btnWidth = label.getBoundingClientRect().width;
         }
         let imgWidth = refImgWidth;
         if (refEl.parentNode.name !== "ideoMap") {
             imgWidth -= labelWidth - btnWidth;
         }
         let refImgOffsetY = refImgRect.y; // distance from start of image to top of viewport, includes any scroll;
         [x1,y1,x2,y2] = refEl.coords.split(",").map(x => parseInt(x));
         refX = x1 + refImgRect.x;
         refY = y1 + refImgRect.y;
         refRight = x2 + refImgRect.left;
         refLeft = x1 + refImgRect.left;
         refTop = y1 + refImgOffsetY;
         refBottom = y2 + refImgOffsetY;
         refWidth = x2 - x1;
         refHeight = y2 - y1;
 
     } else {
         rect = refEl.getBoundingClientRect();
         refX = rect.x; refY = rect.y;
         refWidth = rect.width; refHeight = rect.height;
         refRight = rect.right; refLeft = rect.left;
         refTop = rect.top; refBottom = rect.bottom;
     }
     return {bottom: refBottom, height: refHeight,
             left: refLeft, right: refRight,
             top: refTop, width: refWidth,
             x: refX, y: refY};
 }
 
 function positionMouseover(ev, refEl, popUpEl, mouseX, mouseY) {
     /* The actual mouseover positioning function.
     * refEl is an already existing element with coords that we use to position popUpEl.
     * popUpEl will try to be as close to the right/above the refEl, except when:
     *     it would extend past the screen in which case it would go left/below appropriately.
     *     the refEl takes up the whole screen, in which case we can cover the refEl
     *     with no consequence */
     rect = boundingRect(refEl);
     refX = rect.x; refY = rect.y;
     refWidth = rect.width; refHeight = rect.height;
     refRight = rect.right; refLeft = rect.left;
     refTop = rect.top; refBottom = rect.bottom;
     let windowWidth = window.innerWidth;
     let windowHeight = window.innerHeight;
 
     // figure out how large the mouseover will be
     let popUpRect = popUpEl.getBoundingClientRect();
     // position the popUp to the right and above the cursor by default
     // tricky: when the mouse enters the element from the top, we want the tooltip
     // relatively close to the element itself, because the mouse will already be
     // on top of it, leaving it clickable or interactable. But if we are entering
     // the element from the bottom, if we position the tooltip close to the mouse,
     // we obscure the element itself, so we need to leave a bit of extra room
     let topOffset;
     if (Math.abs(mouseY - refBottom) < Math.abs(mouseY - refTop)) {
         // just use the mouseY position for placement, the -15 accounts for enough room
         topOffset = mouseY - window.scrollY - popUpRect.height - 15;
     } else {
         // just use the mouseY position for placement, the -5 accounts for cursor size
         topOffset = mouseY - window.scrollY - popUpRect.height - 5;
     }
     let leftOffset = mouseX; // add 15 for large cursor sizes
 
     // first case, refEl takes the whole width of the image, so not a big deal to cover some of it
     // this is most common for the track labels
     if (mouseX + popUpRect.width >= (windowWidth - 25)) {
         // move to the left
         leftOffset = mouseX - popUpRect.width;
     }
     // or the mouse is on the right third of the screen
     if (mouseX > (windowWidth* 0.66)) {
         // move to the left
         leftOffset = mouseX - popUpRect.width;
     }
 
     // the page is scrolled or otherwise off the screen
     if (topOffset <= 0) {
         topOffset = mouseY - window.scrollY;
     }
 
     if (leftOffset < 0) {
         throw new Error("trying to position off of screen to left");
     }
     popUpEl.style.left = leftOffset + "px";
     popUpEl.style.top = topOffset + "px";
 }
 
 // The div that moves around the users screen with the visible mouseover text
 let  mouseoverContainer;
 // Global needed for contextmenu to disable tooltips
 var suppressTooltips = false;
 
 function addMouseover(ele1, text = null, ele2 = null) {
     /* Adds wrapper elements to control various mouseover events using mouseenter/mouseleave. */
     if (!mouseoverContainer) {
         mouseoverContainer = document.createElement("div");
         mouseoverContainer.className = "tooltip";
         mouseoverContainer.style.position = "fixed";
         mouseoverContainer.style.display = "inline-block";
         mouseoverContainer.style.visibility = "hidden";
         mouseoverContainer.style.opacity = "0";
         mouseoverContainer.id = "mouseoverContainer";
         let tooltipTextSize = localStorage.getItem("tooltipTextSize");
         if (tooltipTextSize === null) {tooltipTextSize = window.browserTextSize !== null ? window.browserTextSize : 12;}
         mouseoverContainer.style.fontSize =  tooltipTextSize + "px";
         document.body.append(mouseoverContainer);
 
         // Tooltip mouseenter/mouseleave
         mouseoverContainer.addEventListener("mouseenter", function() {
             mouseoverContainer._isMouseOver = true;
             // Clear any hide timeout when entering tooltip
             if (mouseoverContainer._hideTimeout) {
                 clearTimeout(mouseoverContainer._hideTimeout);
                 mouseoverContainer._hideTimeout = null;
             }
         });
         mouseoverContainer.addEventListener("mouseleave", function() {
             mouseoverContainer._isMouseOver = false;
             // Hide after a short delay to allow for quick mouse movements
             mouseoverContainer._hideTimeout = setTimeout(function() {
                 hideMouseoverText(mouseoverContainer);
             }, 100);
         });
     }
 
     if (ele1) {
         ele1.setAttribute("mouseoverText", text);
         // Remove title attribute to prevent default browser tooltip
         if (ele1.title || ele1.dataset.tooltip) {
             ele1.title = "";
         }
         // Remove previous listeners if any
         ele1.removeEventListener("mouseenter", ele1._mouseenterHandler);
         ele1.removeEventListener("mouseleave", ele1._mouseleaveHandler);
         // Show tooltip on mouseenter with delay
         ele1._mouseenterHandler = function(e) {
             // Clear any existing hide timeout
             if (ele1._tooltipHideTimeout) {
                 clearTimeout(ele1._tooltipHideTimeout);
                 ele1._tooltipHideTimeout = null;
             }
             // Determine delay based on tooltip type
             let isDelayedTooltip = ele1.getAttribute("tooltipDelay") === "delayed";
             let delay = isDelayedTooltip ? 1500 : 500;
             ele1._tooltipShowTimeout = setTimeout(function() {
                 showTooltipForElement(ele1, e);
             }, delay);
         };
         ele1._mouseleaveHandler = function(e) {
             // Clear show timeout if mouse leaves before delay
             if (ele1._tooltipShowTimeout) {
                 clearTimeout(ele1._tooltipShowTimeout);
                 ele1._tooltipShowTimeout = null;
             }
             // Use a grace period to allow moving to the tooltip itself
             ele1._tooltipHideTimeout = setTimeout(function() {
                 if (!mouseoverContainer._isMouseOver) {
                     hideMouseoverText(mouseoverContainer);
                 }
             }, 500); // 500ms grace period
         };
         ele1.addEventListener("mouseenter", ele1._mouseenterHandler);
         ele1.addEventListener("mouseleave", ele1._mouseleaveHandler);
     }
 }
 
 function showTooltipForElement(ele, ev) {
     // Show the tooltip for the given element
     if (suppressTooltips) {return;}
     // wiggle mouseovers have special code, don't use these tooltips for those:
     if (typeof mouseOver !== "undefined" && mouseOver.visible) {return;}
     let text = ele.getAttribute("mouseoverText");
     if (!text) return;
     mouseoverContainer.replaceChildren();
     let newEl = document.createElement("span");
     newEl.style = "max-width: 400px";
     newEl.innerHTML = text;
     mouseoverContainer.appendChild(newEl);
     positionMouseover(ev, ele, mouseoverContainer, ev.pageX, ev.pageY);
     mouseoverContainer.classList.add("isShown");
     mouseoverContainer.style.opacity = "1";
     mouseoverContainer.style.visibility = "visible";
 }
 
 function hideMouseoverText(ele) {
     /* Actually hides the tooltip text */
     ele.classList.remove("isShown");
     ele.style.opacity = "0";
     ele.style.visibility = "hidden";
 }
 
 function titleTagToMouseover(mapEl) {
     /* for a given area tag, extract the title text into a div that can be positioned
     * like a standard tooltip mouseover next to the item */
     if (mapEl.dataset.tooltip)
         addMouseover(mapEl, mapEl.dataset.tooltip);
     else
         addMouseover(mapEl, mapEl.title);
 }
 
 function htmlEncode(s) {
     /* HTML-escape a value (&, <, >, ", ') so it is safe to insert as text or into an attribute
      * value in a string of HTML.  Shared helper: prefer this over rolling a per-file escaper.
-     * Uses the browser's own text->markup conversion via a detached element (jQuery required). */
-    return $('<div>').text(s === null || s === undefined ? '' : String(s)).html();
+     * Uses the browser's own text->markup conversion via a detached element (jQuery required).
+     * That conversion only escapes &, < and > - quotes need no escaping in text, so it leaves them
+     * alone - hence the explicit quote handling below.  Without it this function silently failed
+     * the "safe in an attribute" half of its contract: a value containing a double quote closed the
+     * attribute early, truncating it (and worse, allowing markup injection). */
+    return $('<div>').text(s === null || s === undefined ? '' : String(s)).html()
+        .replace(/"/g, '&quot;')
+        .replace(/'/g, '&#39;');
 }
 
 function convertTitleTagsToMouseovers() {
     /* make all the title tags in the document have mouseovers */
     document.querySelectorAll("[title],[data-tooltip]").forEach(function(a, i) {
         if (a.id !== "" && (a.id === "hotkeyHelp" || a.id.endsWith("Dialog") || a.id.endsWith("Popup"))) {
             // these divs are populated by ui-dialog, they should not have tooltips
             return;
         }
         if (a.title !== undefined &&
                 (a.title.startsWith("click & drag to scroll") || a.title.startsWith("drag select or click to zoom")))
             a.title = "";
         else if ((a.title !== undefined && a.title.length > 0) || a.getAttribute("data-tooltip") !== null) {
             if (a.title && a.title.startsWith("Click to alter the display density")) {
                 // these tooltips have a longer delay:
                 a.setAttribute("tooltipDelay", "delayed");
             }
             titleTagToMouseover(a);
         }
     });
 
     /* Mouseover should clear if you leave the document window altogether */
     document.body.addEventListener("mouseleave", (ev) => {
         if (mouseoverContainer) {
             hideMouseoverText(mouseoverContainer);
         }
     });
 
     /* Mouseover should clear on scroll */
     document.addEventListener("scroll", (ev) => {
         if (mouseoverContainer) {
             hideMouseoverText(mouseoverContainer);
         }
     });
 
     function hideTooltips() {
         if (mouseoverContainer) {
             hideMouseoverText(mouseoverContainer);
         }
     }
 
     /* make the mouseovers go away if we are in an input */
     const inps = document.getElementsByTagName("input");
     for (let inp of inps) {
         if (!(inp.type == "hidden" || inp.type == "HIDDEN")) {
             if (inp.type !== "submit") {
                 inp.addEventListener("focus", hideTooltips);
             } else {
                 // the buttons are inputs that don't blur right away (or ever? I can't tell), so
                 // be sure to restore the tooltips when they are clicked
                 inp.addEventListener("click", hideTooltips);
             }
         }
     }
     /* on a select, we can hide the tooltip on focus, but don't disable them
      * altogether, because it's easy to click out of a select without actually
      * losing focus, and we can't detect that because the web browser handles
      * that click separately */
     const sels = document.getElementsByTagName("select");
     for (let sel of sels) {
         sel.addEventListener("focus", hideTooltips);
         for (let opt of sel.options) {
             opt.addEventListener("click", hideTooltips);
         }
     }
 
     /* Make the ESC key hide tooltips */
     document.body.addEventListener("keyup", (ev) => {
         if (ev.keyCode === 27) {
             if (mouseoverContainer) {
                 hideMouseoverText(mouseoverContainer);
             }
         }
     });
 
     /* Make jquery-ui dialogs hide tooltips */
     $(document).on("dialogopen", (ev) => {
         hideMouseoverText(mouseoverContainer);
     });
 }
 
 function parseUrl(url) {
     // turn a url into some of it's components like server, query-string, etc
     let protocol, serverName, pathInfo, queryString, queryArgs = {};
     let temp;
     temp = url.split("?");
     if (temp.length > 1)
         queryString = temp.slice(1).join("?");
     temp = temp[0].split("/");
     protocol = temp[0]; // "https:"
     serverName = temp[2]; // "genome-test.gi.ucsc.edu"
     pathInfo = temp.slice(3).join("/"); // "cgi-bin/hgTracks"
     cgi = pathInfo.startsWith("cgi-bin") ? pathInfo.split('/')[1] : "";
     let i, s = queryString ? queryString.split('&') : []; // Fix for when there is no query string in the URL
     for (i = 0; i < s.length; i++) {
         argVal = s[i].split('=');
         queryArgs[argVal[0]] = argVal[1];
     }
     return {protocol: protocol, serverName: serverName, pathInfo: pathInfo, queryString: queryString, cgi: cgi, queryArgs: queryArgs};
 }
 
 function dumpCart(seconds, skipNotification) {
     // dump current cart
     let currUrl = parseUrl(window.location.href);
     logUrl = currUrl.protocol + "//" + currUrl.serverName + "/" + currUrl.pathInfo + "?hgsid=" + getHgsid() + "&_dumpCart=" + encodeURIComponent(seconds) + "&skipNotif=" + skipNotification;
     let xmlhttp = new XMLHttpRequest();
     xmlhttp.open("GET", logUrl, true);
     xmlhttp.send();  // sends request and exits this function
 }
 
 function writeToApacheLog(msg) {
     // send msg to web servers error_log
     // first need to figure out what server and CGI we are requesting:
     let currUrl = parseUrl(window.location.href);
     logUrl = currUrl.protocol + "//" + currUrl.serverName + "/" + currUrl.pathInfo + "?_dumpToLog=" + encodeURIComponent(msg);
     let xmlhttp = new XMLHttpRequest();
     xmlhttp.open("GET", logUrl, true);
     xmlhttp.send();  // sends request and exits this function
 }
 
 function addRecentGenome(item) {
     // Save a genome selection to localStorage for showing recent selections in species search.
     // item is the autocomplete selection object with genome, label, commonName, category, etc.
     // Keeps the 10 most recently selected genomes, ordered by recency.
     const MAX_RECENT = 10;
     let stored = window.localStorage.getItem("recentGenomes");
     let recentObj = stored ? JSON.parse(stored) : {stack: [], results: {}};
 
     let stack = recentObj.stack;
     // Use db as the primary key so hg38 and hg19 don't overwrite each other (both have genome="Human")
     // Fall back to genome for GenArk results which may not have a db field
     let key = item.db || item.genome;
     if (!key) return; // Can't save without an identifier
 
     // Check if this key already exists
     let existingItem = recentObj.results[key];
 
     // Remove if already exists (will re-add at front)
     if (stack.includes(key)) {
         stack.splice(stack.indexOf(key), 1);
     } else if (stack.length >= MAX_RECENT) {
         // Remove oldest
         let toDelete = stack.pop();
         delete recentObj.results[toDelete];
     }
 
     // Create a clean copy of the item with HTML stripped from labels
     // Start with the new item, then selectively preserve better data from existing item
     let cleanItem = Object.assign({}, item);
     if (cleanItem.label) {
         cleanItem.label = cleanItem.label.replace(/<[^>]*>/g, '');
     }
     if (cleanItem.value) {
         cleanItem.value = cleanItem.value.replace(/<[^>]*>/g, '');
     }
 
     // If this key already exists, preserve the more descriptive label and other important fields
     // A label with parentheses or longer length is considered more descriptive
     // (e.g., "Gorilla gorilla gorilla (gorGor3)" vs just "Gorilla")
     if (existingItem) {
         let existingLabel = existingItem.label || '';
         let newLabel = cleanItem.label || '';
         // Preserve the existing label if it's more descriptive
         if (existingLabel.includes('(') || existingLabel.length > newLabel.length) {
             cleanItem.label = existingLabel;
         }
         // Preserve category if not present in new item
         if (!cleanItem.category && existingItem.category) {
             cleanItem.category = existingItem.category;
         }
         // Preserve hubUrl if not present in new item
         if (!cleanItem.hubUrl && existingItem.hubUrl) {
             cleanItem.hubUrl = existingItem.hubUrl;
         }
         // Preserve hubName if not present in new item
         if (!cleanItem.hubName && existingItem.hubName) {
             cleanItem.hubName = existingItem.hubName;
         }
     }
 
     // Add to front
     stack.unshift(key);
     recentObj.results[key] = cleanItem;
 
     window.localStorage.setItem("recentGenomes", JSON.stringify(recentObj));
 }
 
 function getRecentGenomes() {
     // Retrieve recent genome selections from localStorage, formatted for autocomplete display.
     // Preserves original category for re-selection logic, adds displayCategory for UI.
     let stored = window.localStorage.getItem("recentGenomes");
     if (!stored) return [];
 
     let recentObj = JSON.parse(stored);
     let results = [];
     for (let genome of recentObj.stack) {
         if (recentObj.results[genome]) {
             let item = Object.assign({}, recentObj.results[genome]);
             // Preserve original category for setDbFromAutocomplete to detect GenArk/hubs
             item.originalCategory = item.category;
             // Set category for autocomplete grouping header
             item.category = "Recent";
             item.displayCategory = "Recent";
             results.push(item);
         }
     }
     return results;
 }
 
 function getPopularGenomes($inputEl) {
     // Parse the popular assemblies JSON embedded in the page by printGenomeSearchBar().
     // Returns an array of autocomplete-formatted items with category "Popular".
     // Items already present in recents are excluded to avoid duplicates.
     let inputId = $inputEl.attr('id');
     let dataEl = document.getElementById(inputId + 'PopularData');
     if (!dataEl) return [];
     let popularData;
     try {
         popularData = JSON.parse(dataEl.textContent);
     } catch (e) {
         return [];
     }
     // Build a set of db names already in recents to avoid duplicates
     let recentDbs = new Set();
     let recents = getRecentGenomes();
     for (let r of recents) {
         recentDbs.add(r.db || r.genome);
     }
     let results = [];
     for (let p of popularData) {
         if (recentDbs.has(p.db)) continue;
         results.push({
             genome: p.db,
             db: p.db,
             label: p.label,
             commonName: p.commonName,
             category: "Popular",
             displayCategory: "Popular"
         });
     }
     return results;
 }
 
 function removeRecentGenomesByHubUrl(hubUrl) {
     // Remove all recent genome entries whose hubUrl matches the given URL.
     // Used when a hub is disconnected to clean up stale entries.
     let stored = window.localStorage.getItem("recentGenomes");
     if (!stored) return;
     let recentObj = JSON.parse(stored);
     let newStack = [];
     for (let key of recentObj.stack) {
         let item = recentObj.results[key];
         if (item && item.hubUrl === hubUrl) {
             delete recentObj.results[key];
         } else {
             newStack.push(key);
         }
     }
     recentObj.stack = newStack;
     window.localStorage.setItem("recentGenomes", JSON.stringify(recentObj));
 }
 
 function dbFromRecentItem(item) {
     let db = item.db || item.genome;
     if (item.hubName && item.category && item.category.startsWith('Assembly Hub'))
         db = item.hubName + "_" + db;
     return db;
 }
 
 function recentGenomeHref(res) {
     // Build an hgTracks URL for a recent genome entry. GenArk assemblies are
     // handled transparently by fixUpDb() in cartNew() when given just db= with
     // the accession. UCSC native databases also just need db=.
     let db = dbFromRecentItem(res);
     let url = new URL("../cgi-bin/hgTracks", window.location.href);
     url.searchParams.set("hgsid", getHgsid());
     if (res.hubUrl) {
         if (res.category && res.category.startsWith("Assembly Hub")) {
             url.searchParams.set("hubUrl", res.hubUrl);
         } else if (!res.category) {
             // in practice this shouldn't happen, but just in case:
             let msg = "recentGenomeHref: item has hubUrl but no category: " + JSON.stringify(res);
             console.warn(msg);
             writeToApacheLog(msg);
         }
     }
     url.searchParams.set("db", db);
     url.searchParams.set("position", "lastDbPos");
     return url.toString();
 }
 
 function addRecentGenomesToMenuBar() {
     // Retrieve recent genome selections from localStorage and add them to the "Genomes" menu heading
     // Tries not add duplicate genomes
     let stored = window.localStorage.getItem("recentGenomes");
     if (!stored) return;
 
     let recentObj = JSON.parse(stored);
     let results = [];
     for (let genome of recentObj.stack) {
         if (recentObj.results[genome]) {
             let item = document.createElement("li");
             let link = document.createElement("a");
             link.href = recentGenomeHref(recentObj.results[genome]);
             link.textContent = recentObj.results[genome].label;
             item.appendChild(link);
             results.push(item);
         }
     }
 
     // construct the current list of labels
     const labelList = [];
     document.querySelectorAll("#tools1 > ul > li > a").forEach( (a) => {
         if (a.textContent.includes("/")) {
             // try to extract just the 'hg38' or 'mm10' part
             let splitLabel = a.textContent.split("/");
             if (splitLabel[1].length > 0)
                 labelList.push(splitLabel[1]);
         } else {
             labelList.push(a.textContent);
         }
     });
 
     // filter our list of recents against the list of "Genomes"
     let finalResult = results.filter( (result) => {
         return !labelList.some( (l) => {
             return result.firstChild.textContent.includes(l);
         });
     });
 
     // Only add separators and items if we have recents to add
     if (finalResult.length === 0) return;
 
     let lastLink = document.querySelector("#tools1 > ul > .last");
     let parent = lastLink.parentNode;
 
     // Add a separator after the default entries to separate from recents
     let defaultLinks = parent.querySelectorAll("li.defaultDropdownLink");
     if (defaultLinks.length > 0) {
         let lastDefault = defaultLinks[defaultLinks.length - 1];
         let separator = document.createElement("li");
         separator.className = "horizSep noHighlight";
         lastDefault.after(separator);
     }
 
     // Add a "Recent Genomes" title after the separator
     let title = document.createElement("li");
     title.className = "noHighlight";
     let titleSpan = document.createElement("span");
     titleSpan.textContent = "Recent Genomes";
     titleSpan.style.cssText = "color: #888; font-size: 11px; padding: 4px 8px; display: block;";
     title.appendChild(titleSpan);
     parent.insertBefore(title, lastLink);
 
     // Add a separator before the "Other" link to separate recents from it
     let separatorBeforeOther = document.createElement("li");
     separatorBeforeOther.className = "horizSep noHighlight";
     parent.insertBefore(separatorBeforeOther, lastLink);
 
     // Append the recent genomes above the "other" link (and its separator)
     finalResult.forEach( (res) => {
         parent.insertBefore(res, separatorBeforeOther);
     });
 }
 
 function addRecentSearch(db, searchTerm, extra={}) {
     // Push a searchTerm onto a stack in localStorage to show users their most recent
     // search terms. If an optional extra argument is supplied (ex: the response from hgSuggest),
     // save that as well
     // The searchStack object (note: saved as a string via JSON.stringify in localStorage) keeps
     // a per database stack of the 5 most recently searched terms, as well as their "result",
     // which can be an autocomplete object from hgSuggest, something from hgSearch, or just nothing
     // Example:
     // var searchStack = {
     //  hg38: {
     //   "stack": ["foxp", "flag", "fla"],
     //   "results: {
     //     "foxp": {
     //       "value": "FOXP1 (Homo sap...",
     //       "id": "chr3:70954708-71583728",
     //       ...
     //     },
     //     "flag": {}, // NOTE: empty object
     //     "fla": {
     //       "value": ...,
     //       "id": ...,
     //     },
     //   }
     // },
     // mm10: {
     //  "stack": [...],
     //  "results": {},
     // }
     let searchStack = window.localStorage.getItem("searchStack");
     let searchObj = {};
     if (searchStack === null) {
         searchObj[db] = {"stack": [searchTerm], "results": {}};
         searchObj[db].results[searchTerm] = extra;
         window.localStorage.setItem("searchStack", JSON.stringify(searchObj));
     } else {
         searchObj = JSON.parse(searchStack);
         if (db in searchObj) {
             let searchList = searchObj[db].stack;
             if (searchList.includes(searchTerm)) {
                 // remove it from wherever it is cause it's going to the front
                 searchList.splice(searchList.indexOf(searchTerm), 1);
             } else {
                 if (searchList.length >= 5) {
                     let toDelete = searchList.pop();
                     delete searchObj[db].results[toDelete];
                 }
             }
             // always update results in case the extra data has changed
             searchObj[db].results[searchTerm] = extra;
             searchList.unshift(searchTerm);
         } else {
             searchObj[db] = {"stack": [searchTerm], "results": {}};
             searchObj[db].results[searchTerm] = extra;
         }
         window.localStorage.setItem("searchStack", JSON.stringify(searchObj));
     }
 }
 
 // variables to parse url arguments correctly
 var digitTest = /^\d+$/,
     keyBreaker = /([^\[\]]+)|(\[\])/g,
     plus = /\+/g,
     paramTest = /([^?#]*)(#.*)?$/;
 
 function deparam(params) {
     /* From https://github.com/jupiterjs/jquerymx/blob/master/lang/string/deparam/deparam.js
      * Used by the cell browser */
     if(! params || ! paramTest.test(params) ) {
         return {};
     }
 
     var data = {},
         pairs = params.split('&'),
         current;
 
     for (var i=0; i < pairs.length; i++){
         current = data;
         var pair = pairs[i].split('=');
 
         // if we find foo=1+1=2
         if(pair.length !== 2) {
             pair = [pair[0], pair.slice(1).join("=")];
         }
 
         var key = decodeURIComponent(pair[0].replace(plus, " ")),
         value = decodeURIComponent(pair[1].replace(plus, " ")),
         parts = key.match(keyBreaker);
 
         for ( var j = 0; j < parts.length - 1; j++ ) {
             var part = parts[j];
             if (!current[part] ) {
                 //if what we are pointing to looks like an array
                 current[part] = digitTest.test(parts[j+1]) || parts[j+1] === "[]" ? [] : {};
             }
             current = current[part];
             }
         var lastPart = parts[parts.length - 1];
         if (lastPart === "[]"){
             current.push(value);
         } else{
             current[lastPart] = value;
         }
     }
     return data;
 }
 
 function changeUrl(vars, oldVars) {
     /* Save the users search string to the url so web browser can easily
      * cache search results into the browser history
      * vars: object of new key: val pairs like CGI arguments
      * oldVars: arguments we want to keep between calls */
     var myUrl = window.location.href;
     myUrl = myUrl.replace('#','');
     var urlParts = myUrl.split("?");
     var baseUrl;
     if (urlParts.length > 1)
         baseUrl = urlParts[0];
     else
         baseUrl = myUrl;
 
     var urlVars;
     if (oldVars === undefined) {
         var queryStr = urlParts[1];
         urlVars = deparam(queryStr);
     } else {
         urlVars = oldVars;
     }
 
     for (var key in vars) {
         var val = vars[key];
         if (val === null || val === "") {
             if (key in urlVars) {
                 delete urlVars[key];
             }
         } else {
             urlVars[key] = val;
         }
     }
 
     var argStr = jQuery.param(urlVars);
     argStr = argStr.replace(/%20/g, "+");
 
     return {"baseUrl": baseUrl, "args": argStr, "urlVars": urlVars};
 }
 
 function saveHistory(obj, urlParts, replace) {
     /* Save an object to the web browser's history stack. When we visit the page for the
      * first time, we replace the basic state after we are done making the initial UI */
     if (replace) {
         history.replaceState(obj, "", urlParts.baseUrl + (urlParts.args.length !== 0 ? "?" + urlParts.args : ""));
     } else {
         history.pushState(obj, "", urlParts.baseUrl + (urlParts.args.length !== 0 ? "?" + urlParts.args : ""));
     }
 }
 
 function forceDisplayBedFile(url) {
     var w = window.open('');
     w.document.write('<a class="button" HREF="'+url+'" TARGET=_blank><button>Download File</button></a>&nbsp;');
     w.document.write('<button id="closeWindowLink" HREF="#">Close Tab</button>');
     w.onload = function(ev) {
       // Attach event listeners after the new window is loaded
       w.document.getElementById('closeWindowLink').addEventListener('click', function() { w.close(); } );
     };
     fetch(url).then(response => response.text()) // Read the response as text
     .then(function(text) {
        w.document.write('<pre>' + text + '</pre>'); // Display the content
        w.document.close(); // Close the document to finish rendering
     })
     .catch(error => console.error('Error fetching BED file:', error));
 }
 
 function processFindGenome(result, term) {
     // process the hubApi/findGenome?q= result set into somthing
     // jquery-ui autocomplete can use
     let data = [];
     let apiSkipList = new Set(["downloadTime", "downloadTimeStamp", "availableAssemblies", "browser", "elapsedTimeMs", "itemCount", "q", "totalMatchCount", "liftable"]);
     Object.keys(result).forEach((key) => {
         if (!(apiSkipList.has(key))) {
             let val = result[key];
             let d = {
                 "genome": key,
                 "label": `${val.commonName} (${key})`,
             };
 
             Object.keys(val).forEach((vkey) => {
                 d[vkey] = val[vkey];
             });
             // Set db to the key (database name or accession) so the autocomplete
             // select handler can save it to recent genomes
             d.db = key;
             if (val.hubUrl !== null) {
                 d.category = "UCSC GenArk - bulk annotated assemblies from NCBI GenBank / Refseq";
             } else {
                 d.category = "UCSC Genome Browser assemblies - annotation tracks curated by UCSC";
             }
             data.push(d);
         }
     });
     return data;
 }
 
 function initSpeciesAutoCompleteDropdown(inputId, selectFunction, baseUrl = null,
         watermark = null, onServerReply = null, onError = null, onFilterDropdown = null) {
 /* Generic function for turning an <input> element into a species search bar with an autocomplete
  * list separating results by category.
  * Required arguments:
  *     inputId: id of the input element itself, not created here
  *     selectFunction: the function to call when the user actually clicks on a result
  * Optional arguments:
  *     baseUrl: where we send requests to which will return json we can parse into a list
  *         of results, defaults to 'hubApi/findGenome?browser=mustExist&q='
  *     watermark: placeholder text in the input
  *     onServerReply: function to run after querying baseUrl, by default use processFindGenome()
  *         to standardize on hubApi, but can be something else
  *     onError: function to call when the server returns an error (e.g. HTTP 400)
  *         signature: onError(jqXHR, textStatus, errorThrown, searchTerm) => results array or null
  */
     let defaultSearchUrl = "hubApi/findGenome?browser=mustExist&q=";
     $.widget("custom.autocompleteCat",
         $.ui.autocomplete,
         {
             _renderMenu: function(ul, items) {
                 var that = this;
                 var currentCategory = "";
                 // There's no this._super as shown in the doc, so I can't override
                 // _create as shown in the doc -- just do this every time we render...
                 this.widget().menu("option", "items", "> :not(.ui-autocomplete-category)");
                 $(ul).css("z-index", "99999999");
                 // Check if all items are from recents (have displayCategory === "Recent")
                 // If so, skip category headers since they're all recent selections
                 var allRecent = items.length > 0 && items.every(function(item) {
                     return item.displayCategory === "Recent";
                 });
                 $.each(items, function(index, item) {
                     // Add a heading each time we see a new category (but not for recents)
                     if (!allRecent && item.category && item.category !== currentCategory) {
                         ul.append("<li class='ui-autocomplete-category'>" +
                                 item.category + "</li>" );
                         currentCategory = item.category;
                     }
                     that._renderItem( ul, item );
                 });
             },
             _renderItem: function(ul, item) {
                 // In order to use HTML markup in the autocomplete, one has to overwrite
                 // autocomplete's _renderItem method using .html instead of .text.
                 // http://forum.jquery.com/topic/using-html-in-autocomplete
                 // Hits to assembly hub top level (not individial db names) have no item label,
                 // so use the value instead
                 var searchTerm = this.term;
                 // remove special characters - the \W means remove anything
                 // that is not: [A-Za-z0-9_] which are 'word' == \w characters
                 // then eliminate runs of white space characters and trim any
                 // white space at the beginning or end of the string
                 var cleanTerm = searchTerm.replace(/\W/g, ' ')
                                   .replace(/\s+/g, ' ')
                                   .trim();
                 var label = item.label !== null ? item.label : item.value;
 
                 // Highlight matching search terms with bold tags
                 if (cleanTerm && cleanTerm.length > 0) {
                     // Split search term into individual words (by whitespace)
                     var words = cleanTerm.split(/\s+/).filter(function(word) {
                         return word.length > 0;  // Filter out empty strings
                     });
 
                     // Apply bolding for each word separately
                     words.forEach(function(word) {
                        // Escape special regex characters in each word
                        var escapedWord = word.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
 
                        // Create case-insensitive regex to find all occurrences
                        var regex = new RegExp('(' + escapedWord + ')', 'gi');
 
                        // Replace matches with bolded version (preserves original case)
                        label = label.replace(regex, '<b>$1</b>');
                    });
                 }
                 let $li = $("<li></li>")
                     .data("ui-autocomplete-item", item)
                     .append($("<a></a>").html(label))
                     .appendTo(ul);
                 if (item.disabled) {
                     $li.attr('title', item.disabledReason || 'Not available');
                     $li.css({'opacity': '0.5'});
                     $li.find('a').css({'pointer-events': 'none'});
                 }
                 return $li;
             }
         }
     );
     autocompleteCat.init($("[id='"+inputId+"']"), {
         baseUrl: baseUrl !== null ? baseUrl : defaultSearchUrl,
         watermark: watermark,
         onSelect: selectFunction,
         onServerReply: onServerReply !== null ? onServerReply : processFindGenome,
         onError: onError,
         onFilterDropdown: onFilterDropdown,
         showRecentGenomes: true,
         enterSelectsIdentical: false
     });
 }
 
 function setupGenomeSearchBar(config) {
 /* Higher-level wrapper for setting up a genome search bar with standard boilerplate.
  * This handles the common pattern used across CGIs: error handling, DOMContentLoaded,
  * element binding, search button handler, item validation, and label update.
  *
  * config object properties:
  *   inputId (required): ID of the search input element
  *   labelElementId: ID of the element to update with selected genome label (default: 'genomeLabel')
  *   onSelect: Callback function(item, labelElement) when genome is selected.
  *             Called AFTER standard validation and label update.
  *             item has: {genome, label, commonName, disabled, ...}
  *   apiUrl: Custom API URL (default: null uses standard hubApi/findGenome)
  *   onServerReply: Custom function to process API results (default: null uses processFindGenome)
  */
     function onSearchError(jqXHR, textStatus, errorThrown, term) {
         return [{label: 'No genomes found', value: '', genome: '', disabled: true}];
     }
 
     function wrappedSelect(labelElement, item) {
         // Standard validation - all CGIs check this
         if (item.disabled || !item.genome) return;
         // Standard label update - all CGIs do this
         if (labelElement)
             labelElement.innerHTML = item.label;
         // Call user's custom callback for CGI-specific logic
         if (typeof config.onSelect === 'function') {
             config.onSelect(item, labelElement);
         }
     }
 
     document.addEventListener("DOMContentLoaded", () => {
         let labelElementId = config.labelElementId || 'genomeLabel';
         let labelElement = document.getElementById(labelElementId);
         let boundSelect = wrappedSelect.bind(null, labelElement);
 
         initSpeciesAutoCompleteDropdown(config.inputId, boundSelect,
             config.apiUrl || null, null, config.onServerReply || null, onSearchError);
 
         // Standard search button handler
         let btn = document.getElementById(config.inputId + "Button");
         if (btn) {
             btn.addEventListener("click", () => {
                 let val = document.getElementById(config.inputId).value;
                 $("[id='" + config.inputId + "']").autocompleteCat("search", val);
             });
         }
 
         // Dropdown toggle button: opens/closes the autocomplete with recent+popular
         let toggle = document.getElementById(config.inputId + "Toggle");
         if (toggle) {
             let wasOpen = false;
             toggle.addEventListener("mousedown", () => {
                 let $input = $("[id='" + config.inputId + "']");
                 wasOpen = $input.autocompleteCat("widget").is(":visible");
             });
             toggle.addEventListener("click", () => {
                 let $input = $("[id='" + config.inputId + "']");
                 if (wasOpen) {
                     $input.autocompleteCat("close");
                 } else {
                     $input.val("");
                     $input.autocompleteCat("search", "");
                     $input.focus();
                 }
             });
         }
     });
 }
 
 function capitalizeFirstLetter(string) {
   return string.charAt(0).toUpperCase() + string.slice(1);
 }
 
 // check whether an autocomplete item is for a genark assembly
 function isGenarkItem(item) {
     return (typeof item.hubUrl !== "undefined" && item.hubUrl) &&
         (typeof item.genome !== "undefined" && item.genome) &&
         (item.genome.startsWith('GCA_') || item.genome.startsWith('GCF_'));
 }