48269a38f1e536f3d25924bf96c09ac48284dd9a
larrym
  Thu May 26 11:32:57 2011 -0700
fix an encoding related bug (see redmine 4051)
diff --git src/hg/js/utils.js src/hg/js/utils.js
index fb4102e..876b7a6 100644
--- src/hg/js/utils.js
+++ src/hg/js/utils.js
@@ -1,2345 +1,2345 @@
 // Utility JavaScript
 // $Header: /projects/compbio/cvsroot/kent/src/hg/js/utils.js,v 1.31 2010/06/02 19:11:53 tdreszer Exp $
 
 var debug = false;
 
 function clickIt(obj,state,force)
 {
 // calls click() for an object, and click();click() if force
     if(obj.checked != state) {
         obj.click();
     } else if (force) {
         obj.click();
         obj.click();    //force onclick event
     }
 }
 function setCheckBoxesWithPrefix(obj, prefix, state)
 {
 // Set all checkboxes with given prefix to state boolean
     var list = inputArrayThatMatches("checkbox","id",prefix,"");
     for (var i=0;i<list.length;i++) {
         var ele = list[i];
             if(ele.checked != state)
                 ele.click();  // Forces onclick() javascript to run
     }
 }
 
 function setCheckBoxesThatContain(nameOrId, state, force, sub1)
 {
 // Set all checkboxes which contain 1 or more given substrings in NAME or ID to state boolean
 // First substring: must begin with it; 2 subs: beg and end; 3: begin, middle and end.
 // This can force the 'onclick() js of the checkbox, even if it is already in the state
     if(debug)
         alert("setCheckBoxesContains is about to set the checkBoxes to "+state);
     var list;
     if(arguments.length == 4)
         list = inputArrayThatMatches("checkbox",nameOrId,sub1,"");
     else if(arguments.length == 5)
         list = inputArrayThatMatches("checkbox",nameOrId,sub1,arguments[4]);
     else if(arguments.length == 6)
         list = inputArrayThatMatches("checkbox",nameOrId,sub1,arguments[4],arguments[5]);
     for (var ix=0;ix<list.length;ix++) {
         clickIt(list[ix],state,force);
     }
     return true;
 }
 
 function inputArrayThatMatches(inpType,nameOrId,prefix,suffix)
 {
     // returns an array of input controls that match the criteria
     var found = new Array();
     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 showSubTrackCheckBoxes(onlySelected)
 {
 // If a Subtrack configuration page has show "only selected subtracks" option,
 // This can show/hide tablerows that contain the checkboxes
 // Containing <tr>'s must be id'd with 'tr_' + the checkbox id,
 // while checkbox id must have 'cb_' prefix (ie: 'tr_cb_checkThis' & 'cb_checkThis')
     var trs = $('table.subtracks').children('tbody').children('tr');
     if(!onlySelected)
         $(trs).show();
     else {
         $(trs).each(function (ix) {
             var subCB = $(this).find('input.subCB');
             if (subCB.length > 0 && subCB[0].checked && subCB[0].disabled == false)
                 $(this).show();
             else
                 $(this).hide();
         });
     }
 }
 
 function hideOrShowSubtrack(obj)
 {
 // This can show/hide a tablerow that contains a specific object
 // Containing <tr>'s must be id'd with 'tr_' + obj.id
 // Also, this relies upon the "displaySubtracks" radio button control
     var tblRow = document.getElementById("tr_"+obj.id);
 
     if(!obj.checked || obj.disabled)
     {
         var list = document.getElementsByName("displaySubtracks");
         for (var ix=0;ix<list.length;ix++) {
             if(list[ix].value == "selected") {
                 if(list[ix].checked)
                     tblRow.style.display = 'none';  // hides
                 else
                     tblRow.style.display = ''; //'table-row' doesn't work in some browsers (ie: IE)
                 break;
             }
         }
     }
     else
         tblRow.style.display = '';
 }
 
 function waitCursor(obj)
 {
     //document.body.style.cursor="wait"
     obj.style.cursor="wait";
 }
 
 function endWaitCursor(obj)
 {
     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 = $(theForm).find("input[name='"+aName+"']:last");
     if(inp != undefined && inp.length > 0) {
         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 = $(theForm).find("input[name='"+aName+"']:last");
     if(inp != undefined && inp.length > 0)
         inp.disabled = true;
 }
 
 function parseUrlAndUpdateVars(theForm,href)
 {   // 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=$("form[name='"+formName+"']");
     if(goodForm.length == 1) {
         if(href != undefined && href.length > 0) {
             $(goodForm).attr('action',href); // just attach the straight href
         }
         $(goodForm).attr('method','POST');
 
         $(goodForm).submit();
     }
     return false; // Meaning do not continue with anything else
 }
 function setVarAndPostForm(aName,aValue,formName)
 {   // Sets a specific variable then posts
     var goodForm=$("form[name='"+formName+"']");
     if(goodForm.length == 1) {
         updateOrMakeNamedVariable(goodForm,aName,aValue);
     }
     return postTheForm(formName,window.location.href);
 }
 
 // json help routines
 function tdbGetJsonRecord(trackName)  { return trackDbJson[trackName]; }
 function tdbIsFolder(tdb)             { return (tdb.kindOfParent == 1); } // NOTE: These must jive with tdbKindOfParent() and tdbKindOfChild() in trackDb.h
 function tdbIsComposite(tdb)          { return (tdb.kindOfParent == 2); }
 function tdbIsMultiTrack(tdb)         { return (tdb.kindOfParent == 3); }
 function tdbIsView(tdb)               { return (tdb.kindOfParent == 4); } // Don't expect to use
 function tdbIsContainer(tdb)          { return (tdb.kindOfParent == 2 || tdb.kindOfParent == 3); }
 function tdbIsLeaf(tdb)               { return (tdb.kindOfParent == 0); }
 function tdbIsFolderContent(tdb)      { return (tdb.kindOfChild  == 1); }
 function tdbIsCompositeSubtrack(tdb)  { return (tdb.kindOfChild  == 2); }
 function tdbIsMultiTrackSubtrack(tdb) { return (tdb.kindOfChild  == 3); }
 function tdbIsSubtrack(tdb)           { return (tdb.kindOfChild  == 2 || tdb.kindOfChild == 3); }
 function tdbHasParent(tdb)            { return (tdb.kindOfChild  != 0 && tdb.parentTrack); }
 
 function aryFind(ary,val)
 {// returns the index of a value on the array or -1;
     for(var ix=0;ix<ary.length;ix++) {
         if(ary[ix] == val) {
             return ix;
         }
     }
     return -1;
 }
 
 function aryRemoveVals(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 aryRemove(ary,val)
 { // removes one or more variables that are found in the array
     for(var vIx=1;vIx<arguments.length;vIx++) {
         var ix = aryFind(ary,arguments[vIx]);
         if(ix != -1)
             ary.splice(ix,1);
     }
     return ary;
 }
 
 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=( $.browser.msie == false );
     for(;;) {
         if((obj.value == undefined || 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."); // try a prompt box!
                 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=( $.browser.msie == false );
     for(;;) {
         if((obj.value == undefined || 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 metadataShowHide(trackName,showLonglabel,showShortLabel)
 {
 // Will show subtrack specific configuration controls
 // Config controls not matching name will be hidden
     var divit = $("#div_"+trackName+"_meta");
     if($(divit).css('display') == 'none') {
         $("#div_"+trackName+"_cfg").hide();  // Hide any configuration when opening metadata
 
         if($(divit).find('table').length == 0) {
             lookupMetadata(trackName,showLonglabel,showShortLabel);
             return false;
         }
     }
     var tr = $(divit).parents('tr');
     if (tr.length > 0) {
         if ($(tr).hasClass("bgLevel2")) {
             $(divit).children('table').removeClass('bgLevel1');
             $(divit).children('table').addClass('bgLevel2');
         } else {
             $(divit).children('table').removeClass('bgLevel2');
             $(divit).children('table').addClass('bgLevel1');
         }
     }
     $(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 = $("input[name='"+hiddenPrefix+"_"+prefix+"_close']");
     if($(button) != undefined && $(hidden) != undefined && $(hidden).length > 0) {
         var oldSrc = $(button).attr("src");
 	var newVal;
         if(arguments.length > 5)
             newVal = arguments[5] ? 0 : 1;
         else
             newVal = oldSrc.indexOf("/remove") > 0 ? 1 : 0;
         var newSrc;
         if(newVal == 1) {
             newSrc = oldSrc.replace("/remove", "/add");
             $(button).attr('title', 'Expand this '+titleDesc);
             $("tr[id^='"+prefix+"-']").hide();
         } else {
             newSrc = oldSrc.replace("/add", "/remove");
             $(button).attr('title', 'Collapse this '+titleDesc);
             $("tr[id^='"+prefix+"-']").show();
         }
         $(button).attr("src", newSrc);
         $(hidden).val(newVal);
 	if (doAjax) {
 	    setCartVar(hiddenPrefix+"_"+prefix+"_close", newVal);
 	}
         retval = false;
     }
     return retval;
 }
 
 function warnBoxJsSetup()
 {   // Sets up warnBox if not already established.  This is duplicated from htmshell.c
     var html = "";
     html += "<center>";
     html += "<div id='warnBox' style='display:none; background-color:Beige; ";
     html += "border: 3px ridge DarkRed; width:640px; padding:10px; margin:10px; ";
     html += "text-align:left;'>";
     html += "<CENTER><B id='warnHead' style='color:DarkRed;'></B></CENTER>";
     html += "<UL id='warnList'></UL>";
     html += "<CENTER><button id='warnOK' onclick='hideWarnBox();return false;'></button></CENTER>";
     html += "</div></center>";
 
     html += "<script type='text/javascript'>";
     html += "function showWarnBox() {";
     html += "document.getElementById('warnOK').innerHTML='&nbsp;OK&nbsp;';";
     html += "var warnBox=document.getElementById('warnBox');";
     html += "warnBox.style.display=''; warnBox.style.width='65%%';";
     html += "document.getElementById('warnHead').innerHTML='Error(s):';";
     html += "}";
     html += "function hideWarnBox() {";
     html += "var warnBox=document.getElementById('warnBox');";
     html += "warnBox.style.display='none';warnBox.innerHTML='';";
     html += "var endOfPage = document.body.innerHTML.substr(document.body.innerHTML.length-20);";
     html += "if(endOfPage.lastIndexOf('-- ERROR --') > 0) { history.back(); }";
     html += "}";
     html += "</script>";
 
     $('body').prepend(html);
 }
 
 function warn(msg)
 { // adds warnings to the warnBox
     var warnList = $('#warnList'); // warnBox contains warnList
     if( warnList == undefined || $(warnList).length == 0 ) {
         warnBoxJsSetup();
         warnList = $('#warnList');
     }
     if( $(warnList).length == 0 )
         alert(msg);
     else {
         $( warnList ).append('<li>'+msg+'</li>');
         if(showWarnBox != undefined)
             showWarnBox();
         else
             alert(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 = new Object();
     if($(obj) == undefined)
         obj = $('document');
     var inp = $(obj).find('input');
     var sel = $(obj).find('select');
     //warn("obj:"+$(obj).attr('id') + " inputs:"+$(inp).length+ " selects:"+$(sel).length);
     $(inp).filter('[name]:enabled').each(function (i) {
         var name  = $(this).attr('name');
         var val = $(this).val();
         if($(this).attr('type') == 'checkbox') {
             name = cgiBooleanShadowPrefix() + name;
             val = $(this).attr('checked') ? 1 : 0;
         } else if($(this).attr('type') == 'radio') {
             if(!$(this).attr('checked')) {
                 name = undefined;
             }
         }
         if(name != undefined && name != "Submit" && val != undefined) {
             urlData[name] = val;
         }
     });
     $(sel).filter('[name]:enabled').each(function (i) {
         var name  = $(this).attr('name');
         var val = $(this).val();
         if(name != undefined && val != undefined) {
             if(subtrackName != undefined && name == subtrackName) {
                 if(val == 'hide') {
                    urlData[name+"_sel"] = 0;    // Can't delete "_sel" because default takes over
                    urlData[name]        = "[]";  // can delete vis because subtrack vis should be inherited.
                 } else {
                     urlData[name+"_sel"] = 1;
                     urlData[name]        = val;
                 }
             } else {
                 if ($.isArray( val ) && val.length > 1) {
                     urlData[name] = "[" + val.toString() + "]";
                 } else
                     urlData[name] = val;
             }
         }
     });
     return urlData;
 }
 
 function setIdRemoveName(obj)
 { // This function removes the name of an obj and sets it as the id.  This is very useful
   // to override forms submitting named inputs and instead setCartVarFromObjId() can be used selectively
     var id = $(obj).attr('name');
     if(id != undefined) {
         $(obj).attr('id',id);
         $(obj).removeAttr('name');
     }
     //warn($(obj).attr('id')+'='+$(obj).val()+" name:"+$(obj).attr('name'));
 }
 
 
 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 = new Object();
     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];
-        // XXXX encode var=val ?
         if (typeof(val) == 'string'
         && val.length >= 2
         && val.indexOf('[') == 0
         && val.lastIndexOf(']') == (val.length - 1)) {
             var vals = val.substr(1,val.length - 2).split(',');
             $(vals).each(function (ix) {
                 if (ix > 0)
                     retVal += "&";
-                retVal += aVar + "=" + this;
+                retVal += aVar + "=" + encodeURIComponent(this);
             });
-        } else
-            retVal += aVar + "=" + val;
+        } else {
+            retVal += aVar + "=" + encodeURIComponent(val);
+        }
     }
     return retVal;
 }
 
 function getAllVarsAsUrlData(obj)
 {
 // 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 == undefined) {
         popit = $('#popit');
 
         if(popit == undefined) {
             $('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 problems caused by duplicate html elements
                                    $(popDiv).empty();
                                }
                            });
     // Apparently the options above to dialog take only once, so we set title explicitly.
     if(popTitle != undefined && 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) // 4 extra STRING Params: boxWidth, boxTitle, applyFunc, applyName
 {
 // 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
 
     // 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 == undefined) {
         boxit = $('div#boxit');
 
         if (boxit == undefined) {
             $('body').prepend("<div id='boxit'></div>");
             //$('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 + "'>&nbsp;";
         buildHtml += "</div>";
 
         $(boxit).html("<div class='blueBox' style='width:" + boxWidth + "; background-color:#FFF9D2;'>" + buildHtml + "</div>");  // Make it boxed
     }
 
     if ($(boxit).html() == null || $(boxit).html().length == 0)
         warn("embedHtmlBox() called without content");
     else
         $(boxit).show();
 }
 
 function embedBoxClose(boxit, reenterable) // 4 extra STRING Params: boxWidth, boxTitle, applyFunc, applyName
 {
 // Close an embedded box
     if (boxit != undefined) {
         $(boxit).hide();
         if(!reenterable)
             $(boxit).empty();
     }
 }
 
 function startTiming()
 {
     var now = new Date();
     return now.getTime();
 }
 
 function showTiming(start,whatTookSoLong)
 {
     var now = new Date();
     var end = (now.getTime() - start);
     warn(whatTookSoLong+" took "+end+" msecs.");
     return end;
 }
 
 function getHgsid()
 {
 // return current session id
     var hgsid;
     var list = document.getElementsByName("hgsid");
     if(list.length) {
         var ele = list[0];
         hgsid = ele.value;
     }
     if(!hgsid) {
         hgsid = getURLParam(window.location.href, "hgsid");
     }
     return hgsid;
 }
 
 function getDb()
 {
     var db = document.getElementsByName("db");
     if(db == undefined || db.length == 0)
         {
         db = $("#db");
         if(db == undefined || db.length == 0)
             return ""; // default?
         }
     return db[0].value;
 }
 
 function getTrack()
 {
     var track = $("#track");
     if(track == undefined || track.length == 0)
         return ""; // default?
     return track[0].value;
 }
 
 function Rectangle()
 {
 // 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)
 {
 // 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);
 	var pre = commify(pre);
 	return pre + "," + post;
     }
 }
 
 function parsePosition(position)
 {
 // Parse chr:start-end string into a chrom, start, end object
     position = position.replace(/,/g, "");
     var a = /(\S+):(\d+)-(\d+)/.exec(position);
     if(a != null && a.length == 4) {
         var o = new Object();
         o.chrom = a[1];
         o.start = parseInt(a[2])
         o.end = parseInt(a[3]);
         return o;
     }
     return null;
 }
 
 function getSizeFromCoordinates(position)
 {
 // Parse size out of a chr:start-end string
     var o = parsePosition(position);
     if(o != null) {
         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 = $('#waitMask');
     if( waitMask != undefined )
         $(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 = $('#waitMask');
     if( waitMask == undefined || waitMask.length != 1) {
         // create the waitMask
         $("body").append("<div id='waitMask' class='waitMask');'></div>");
         waitMask = $('#waitMask');
         // Special for IE
         if ($.browser.msie)
             $(waitMask).css('filter','alpha(opacity= 0)');
     }
     $(waitMask).css('display','block');
 
     // Things could fail, so always have a timeout.
     if(timeOutInMs == undefined || timeOutInMs <=0)
         timeOutInMs = 5000; // Don't ever leave this as infinite
     setTimeout('waitMaskClear();',timeOutInMs); // Just in case
 }
 
 function _launchWaitOnFunction()
 { // should ONLY be called by waitOnFunction()
   // Launches the saved function
     var func = gWaitFunc;
     gWaitFunc = null;
     var funcArgs = gWaitFuncArgs;
     gWaitFuncArgs = [];
 
     if(func == undefined || !jQuery.isFunction(func))
         warn("_launchWaitOnFunction called without a function");
     else {
         if(funcArgs.length == 0)
             func();
         else if (funcArgs.length == 1)
             func(funcArgs[0]);
         else if (funcArgs.length == 2)
             func(funcArgs[0],funcArgs[1]);
         else if (funcArgs.length == 3)
             func(funcArgs[0],funcArgs[1],funcArgs[2]);
         else if (funcArgs.length == 4)
             func(funcArgs[0],funcArgs[1],funcArgs[2],funcArgs[3]);
         else if (funcArgs.length == 5)
             func(funcArgs[0],funcArgs[1],funcArgs[2],funcArgs[3],funcArgs[4]);
         else
             warn("_launchWaitOnFunction called with " + funcArgs.length + " arguments.  Only 5 are supported.");
     }
     // Special if the first var is a button that can visually be inset
     if(funcArgs.length > 0 && funcArgs[0].type != undefined) {
         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(arguments.length > 6) {
         warn("waitOnFunction called with " + arguments.length - 1 + " arguments.  Only 5 are supported.");
         return false;
     }
 
     waitMaskSetup(5000);  // Find or create the waitMask (which masks the 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 != undefined) {
         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();',50);
 
 }
 
 function showLoadingImage(id)
 {
 // Show a loading image above the given id; return's id of div added (so it can be removed when loading is finished).
 // This code was mostly directly copied from hgHeatmap.js, except I also added the "overlay.appendTo("body");"
     var loadingId = id + "LoadingOverlay";
     var overlay = $("<div></div>").attr("id", loadingId).css("position", "absolute");
     overlay.appendTo("body");
     overlay.css("top", $('#'+ id).position().top);
     var divLeft = $('#'+ id).position().left + 2;
     overlay.css("left",divLeft);
     var width = $('#'+ id).width() - 5;
     var height = $('#'+ id).height();
     overlay.width(width);
     overlay.height(height);
     overlay.css("background", "white");
     overlay.css("opacity", 0.75);
     var imgLeft = (width / 2) - 110;
     var imgTop = (height / 2 ) - 10;
     $("<img src='../images/loading.gif'/>").css("position", "relative").css('left', imgLeft).css('top', imgTop).appendTo(overlay);
     return loadingId;
 }
 
 function hideLoadingImage(id)
 {
     $('#' + 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");
 }
 
 
 //////////// 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(tableSetPositions) {
                     tableSetPositions(table);
                 }
             }
     });
     $(thisTable).find("td.dragHandle").hover(
         function(){ $(this).closest('tr').addClass('trDrag'); },
         function(){ $(this).closest('tr').removeClass('trDrag'); }
     );
 }
 
 //////////// Sorting ////////////
 // Sorting a table by columns relies upon the sortColumns structure
 
 // The sortColumns structure looks like:
 //{
 //    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 innerHtml?
 //}
 // These 2 globals are used by setTimeout, so that rows can be hidden while sorting and javascript timeout is less likely
 var gSortColumns;
 var gTbody
 
 function sortField(value,index)
 {
 this.value=value;
 this.index=index;
 }
 
 function sortRow(tr,sortColumns,row)  // UNUSED: sortField works fine
 {
     this.fields  = new Array();
     this.reverse = new Array();
     this.row     = row;
     for(var ix=0;ix<sortColumns.cellIxs.length;ix++)
         {
         var th = tr.cells[sortColumns.cellIxs[ix]];
         this.fields[ix]  = (sortColumns.useAbbr[ix] ? th.abbr : $(th).text()).toLowerCase(); // case insensitive sorts
         this.reverse[ix] = sortColumns.reverse[ix];
         }
 }
 
 function sortRowCmp(a,b)  // UNUSED: sortField works fine
 {
     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;
 }
 
 function sortField(value,reverse,row)
 {
     this.value   = value.toLowerCase(); // case insensitive sorts NOTE: Do not need to define every field
     this.reverse = reverse;
     this.row     = row;
 }
 function sortFieldCmp(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;
 }
 
 function tableSort(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 array of the primary sort column's text
     var cols = new Array();
     var trs = tbody.rows;
     $(trs).each(function(ix) {
         //cols.push(new sortRow(this,sortColumns,$(this).clone()));
         var th = this.cells[sortColumns.cellIxs[0]];
         if(sortColumns.useAbbr[0])
             cols.push(new sortField(th.abbr,sortColumns.reverse[0],$(this).clone())); // When jQuery >= v1.4, use detach() insterad of clone()
         else
             cols.push(new sortField($(th).text(),sortColumns.reverse[0],$(this).clone()));
     });
 
     // Sort the array
     //cols.sort(sortRowCmp);
     cols.sort(sortFieldCmp);
 
     // Now reorder the table
     for(var cIx=0;cIx<cols.length;cIx++) {
         $(tbody.rows[cIx]).replaceWith(cols[cIx].row);
     }
 
     gTbody=tbody;
     gSortColumns=sortColumns;
     setTimeout('tableSortFinish(gTbody,gSortColumns)',5); // Avoid javascript timeouts!
 }
 
 function tableSortFinish(tbody,sortColumns)
 {// Additional sort cleanup.
  // This is in a separate function to allow calling with setTimeout() which will prevent javascript timeouts (I hope)
     tableSetPositions(tbody);
     if ($(tbody).hasClass('altColors'))
         sortedTableAlternateColors(tbody,sortColumns);
     $(tbody).parents("table.tableWithDragAndDrop").each(function (ix) {
         tableDragAndDropRegister(this);
     });
     //$(tbody).show();
     $(tbody).removeClass('sorting');
 }
 
 function tableSortByColumns(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
     //$(tbody).hide();
     $(tbody).addClass('sorting');
     gTbody=tbody;
     gSortColumns=sortColumns;
     setTimeout('tableSort(gTbody,gSortColumns)',50); // This allows hiding the rows while sorting!
 }
 
 function trAlternateColors(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 == undefined || 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 = new Array();
         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");
             }
         });
     }
 }
 
 function sortedTableAlternateColors(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 sortColumnsGetFromTable(table);
     }
 
     if (sortColumns) {
         if (sortColumns.cellIxs.length==1)
             trAlternateColors(tbody,0,sortColumns.cellIxs[0]);
         else if (sortColumns.cellIxs.length==2)
             trAlternateColors(tbody,0,sortColumns.cellIxs[0],sortColumns.cellIxs[1]);
         else // Three columns is plenty
             trAlternateColors(tbody,0,sortColumns.cellIxs[0],sortColumns.cellIxs[1],sortColumns.cellIxs[2]);
     } else {
         trAlternateColors(tbody,5); // alternates every 5th row
     }
 }
 
 function sortOrderFromColumns(sortColumns)
 {// Creates the trackDB setting entry sortOrder subGroup1=+ ... from a sortColumns structure
     fields = new Array();
     for(var ix=0;ix < sortColumns.cellIxs.length;ix++) {
         if (sortColumns.tags[ix] != undefined && 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(' ');
     //warn("sortOrderFromColumns("+sortColumns.cellIxs.length+"):["+sortOrder+"]");
     return sortOrder;
 }
 
 function sortOrderUpdate(table,sortColumns,addSuperscript)
 {// Updates the sortOrder in a sortable table
     if (addSuperscript == undefined)
         addSuperscript = false;
     if ($(table).is('tbody'))
         table = $(table).parent();
     var tr = $(table).find('tr.sortable')[0];
     if (tr) {
         //warn("sortOrderUpdate("+sortColumns.cellIxs.length+")");
         for(cIx=0;cIx<sortColumns.cellIxs.length;cIx++) {
             var th = tr.cells[sortColumns.cellIxs[cIx]];
             $(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(sortOrderFromColumns(sortColumns));
     }
 }
 
 function sortOrderFromTr(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 = new Array();
         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 (ix != NaN) {
                             sortIx = ix;
                         }
                     }
                 }
             }
             if (sortIx >= 0) {
                 if (this.id != undefined && this.id.length > 0)
                     fields[sortIx] = this.id + "=" + (reverse ? "-":"+");
                 else
                     fields[sortIx] = this.cellIndex + "=" + (reverse ? "-":"+");
             }
         });
         if (fields.length > 0) {
             if (fields[0] == undefined)
                 fields.shift();  // 1 based sort ix and 0 based fields ix
             return fields.join(' ');
         }
     }
     return "";
 }
 function sortColumnsGetFromSortOrder(sortOrder)
 {// Creates sortColumns struct (without cellIxs[]) from a trackDB.sortOrder setting string
     this.tags = new Array();
     this.reverse = new Array();
     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] != '+');
         }
     }
 }
 function sortColumnsGetFromTr(tr,silent)
 {// Creates a sortColumns struct from the entries in the 'tr.sortable' heading row of a sortable table
     this.inheritFrom = sortColumnsGetFromSortOrder;
     var sortOrder = sortOrderFromTr(tr);
     if (sortOrder.length == 0 && silent == undefined) {
         warn("Unable to obtain sortOrder from sortable table.");   // developer needs to know something is wrong
         return;
     }
 
     this.inheritFrom(sortOrder);
     // Add two additional arrays
     this.cellIxs = new Array();
     this.useAbbr = new Array();
     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 != undefined && ths[ix].id == this.tags[tIx])
             ||  (ths[ix].cellIndex == this.tags[tIx]))
             {
                 this.cellIxs[tIx] = ths[ix].cellIndex;
                 this.useAbbr[tIx] = (ths[ix].abbr.length > 0);
             }
         }
     }
     if (this.cellIxs.length == 0 && silent == undefined) {
         warn("Unable to find any sortOrder.cells for sortable table.  ths.length:"+ths.length + " tags.length:"+this.tags.length + " sortOrder:["+sortOrder+"]");
         return;
     }
 }
 
 function sortColumnsGetFromTable(table)
 {// Creates a sortColumns struct from the contents of a 'table.sortable'
     this.inheritNow = sortColumnsGetFromTr;
     var tr = $(table).find('tr.sortable')[0];
     //if (tr == undefined && debug) warn("Couldn't find 'tr.sortable' rows:"+table.rows.length);
     this.inheritNow(tr);
 }
 
 
 function _tableSortOnButtonPressEncapsulated(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 sortColumnsGetFromTr(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) {
         warn("Failure to find '"+th.id+"' in sort columns."); // Developer must be warned that something is wrong with sortable table setup
         return;
     }
     // assert(th.id == theOrder.tags[oIx] || th.id == undefined);
     if (oIx > 0) { // Need to reorder
         var newOrder = new sortColumnsGetFromTr(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
         sortOrderUpdate(table,theOrder);  // Must update sortOrder first!
         var tbody = $(table).find("tbody.sortable")[0];
         //if (tbody == undefined && debug) warn("Couldn't find 'tbody.sortable' 5");
         tableSortByColumns(tbody,theOrder);
     }
     return;
 
 }
 
 function tableSortOnButtonPress(anchor,tagId)
 {
     var table = $( anchor ).closest("table.sortable")[0];
     if (table) {
         waitOnFunction( _tableSortOnButtonPressEncapsulated, anchor, tagId);
     }
     return false;  // called by link so return false means don't try to go anywhere
 }
 
 function tableSortUsingSortColumns(table) // NOT USED
 {// Sorts a table body based upon the marked columns
     var columns = new sortColumnsGetFromTable(table);
     tbody = $(table).find("tbody.sortable")[0];
     if (tbody)
         tableSortByColumns(tbody,columns);
 }
 
 function hintOverSortableColumnHeader(th) // NOT USED
 {// Upodates the sortColumns struct and sorts the table when a column headder has been pressed
     //th.title = "Click to make this the primary sort column, or toggle direction";
     //var tr=th.parentNode;
     //th.title = "Current Sort Order: " + sortOrderFromTr(tr);
 }
 
 function tableSetPositions(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];
         $( this ).val( $(tr).attr('rowIndex') );
     });
 }
 
 ///// Following functions are for Sorting by priority
 function trFindPosition(tr)
 {
 // returns the position (*.priority) of a sortable table row
     var inp = $(tr).find('input.trPos')[0];
     if (inp)
         return $(inp).val();
     return 999999;
 }
 
 function trComparePriority(tr1,tr2)  // UNUSED FUNCTION
 {
 // Compare routine for sorting by *.priority
     var priority1 = trFindPosition(tr1);
     var priority2 = trFindPosition(tr2);
     return priority2 - priority1;
 }
 
 function tablesSortAtStartup()
 {// 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) {
         sortTableInitialize(this,true); // Will initialize superscripts
         tableSortUsingSortColumns(this);
     });
 }
 
 function sortTableInitialize(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) The 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 tableSortOnButtonPress(this) directly or indirectly in the onclick event :
  //       e.g. <TH id='factor' class='sortable sortRev sort3' nowrap title='Sort list on this column' onclick="return tableSortOnButtonPress(this);">
  //       (NOTE: If no onclick function is found in a TH.sortable, then it will automatically be added.)
  //     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 (e.g. ZCTRL vs Control forcing controls to bottom)
  //          e.g. <TD id='wgEncodeBroadHistoneGm12878ControlSig_factor' 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
  //
  // 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:
  //   e.g.: <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 ther cart is if the order will affect other cgis.  For instance: sort subtracks and see that order in the hgTracks image.
 
     if ($(table).hasClass('sortable') == false) {
         warn('Table is not sortable');
         return;
     }
     var tr = $(table).find('tr.sortable')[0];
     if(tr == undefined) {
         tr = $(table).find('tr')[0];
         if(tr == undefined) {
             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 == undefined) {
         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 != undefined && $(tbody).hasClass('altColors') == false) {
         $(tbody).addClass('altColors');
         //warn('Added altColors class to tbody.sortable');
     }
     $(tbody).hide();
 
     // If not THEAD is found, then create, wrapping first row.
     thead = $(table).find('thead')[0];
     if(thead == undefined) {
         $(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 sortColumnsGetFromTr(tr,"silent");
     if (sortColumns == undefined || 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 sortColumnsGetFromTr(tr,"silent");
         if (sortColumns == undefined || 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).queue('click').length == 0 ) {
         if ( $(this).attr('onclick') == undefined ) {
             $(this).click( function () { tableSortOnButtonPress(this);} );
         }
         if ($.browser.msie) { // Special case for IE since CSS :hover doesn't work (note pointer and hand because older IE calls it hand)
             $(this).hover(
                 function () { $(this).css( { backgroundColor: '#CCFFCC', cursor: 'pointer', cursor: 'hand' } ); },
                 function () { $(this).css( { backgroundColor: '#FCECC0', cursor: '' } ); }
             );
         }
         if ( $(this).attr('title').length == 0) {
             var title = $(this).text().replace(/[^a-z0-9 ]/ig,'');
             if (title.length > 0 && $(this).find('sup'))
                 title = title.replace(/[0-9]$/g,'');
             if (title.length > 0)
                 $(this).attr('title',"Sort list on '" + title + "'." );
             else
                 $(this).attr('title',"Sort list on column." );
         }
     })
     // Now update all of those cells
     sortOrderUpdate(table,sortColumns,addSuperscript);
 
     // Alternate colors if requested
     if(altColors != undefined)
         sortedTableAlternateColors(tbody);
 
     // Highlight rows?  But on subtrack list, this will mess up the "..." 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'); },      // Will highlight the rows, including '...'
             function(){ $(this).removeClass('bgLevel3');
                         $(this).find('table').removeClass('bgLevel3'); }
         );
     }
 
     // Finally, make visible
     $(tbody).removeClass('sorting');
     $(tbody).show();
 }
 
 function setCheckboxList(list, value)
 {
 // set value of all checkboxes in semicolon delimited list
     var names = list.split(";");
     for(var i=0;i<names.length;i++) {
         $("input[name='" + names[i] + "']").attr('checked', value);
     }
 }
 
 function calculateHgTracksWidth()
 {
 // return appropriate width for hgTracks image given users current window width
     return $(window).width() - 20;
 }
 
 function hgTracksSetWidth()
 {
     var winWidth = calculateHgTracksWidth();
     if($("#imgTbl").length == 0) {
         // XXXX what's this code for?
         $("#TrackForm").append('<input type="hidden" name="pix" value="' + winWidth + '"/>');
         //$("#TrackForm").submit();
     } else {
         $("input[name=pix]").val(winWidth);
     }
 }
 
 /////////////////////////////////////////////////////
 // findTracks functions
 
 function updateMetaDataHelpLinks(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, 'dataType':        1, 'dataVersion': 1, 'geoSample':    1, 'grant':     1,
         'lab':       1, 'labExpId':        1, 'labVersion':  1, 'origAssembly': 1, 'replicate': 1,
         'setType':   1, 'softwareVersion': 1, 'subId':       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) {
             var val = $("select[name='hgt_mdbVar" + ix + "']").val();  // NOTE must match METADATA_NAME_PREFIX in hg/hgTracks/searchTracks.c
             var text = $("select[name='hgt_mdbVar" + ix + "'] option:selected").text();
             helpLink.html("&nbsp;"); // Do not want this with length == 0 later!
             if (typeof(disabled[val]) == 'undefined') {
                 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("<a target='_blank' title='detailed descriptions of terms' href='" + str + "'>" + text + "</a>");
             }
         }
     }
 }
 
 function findTracksMdbVarChanged(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)
 
     findTracksClearFound();  // Changing values so abandon what has been found
 
     var newVar = $(obj).val();
     var a = /hgt_mdbVar(\d+)/.exec(obj.name); // NOTE must match METADATA_NAME_PREFIX in hg/hgTracks/searchTracks.c
     if(newVar != undefined && a && a[1]) {
         var num = a[1];
         if ($('#advancedTab').length == 1 && $('#filesTab').length == 1) {
             $("select.mdbVar[name='hgt_mdbVar"+num+"'][value!='"+newVar+"']").val(newVar);
         }
         var cgiVars = "db=" + getDb() +  "&cmd=hgt_mdbVal" + num + "&var=" + newVar;
         if (document.URL.search('hgFileSearch') != -1)
             cgiVars += "&fileSearch=1";
         else
             cgiVars += "&fileSearch=0";
 
         $.ajax({
                    type: "GET",
                    url: "../cgi-bin/hgApi",
                    data: cgiVars,
                    trueSuccess: findTracksHandleNewMdbVals,
                    success: catchErrorOrDispatch,
                    error: errorHandler,
                    cache: true,
                    cmd: "hgt_mdbVal" + num, // NOTE must match METADATA_VALUE_PREFIX in hg/hgTracks/searchTracks.c
                    num: num
                });
     }
     //findTracksSearchButtonsEnable(true);
 }
 
 function findTracksHandleNewMdbVals(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 = $('td#' + this.cmd );
     if (td != undefined) {
         var usesFilterBy = ($("select.mdbVar[name='hgt_mdbVar"+this.num+"']").hasClass('noMulti') == false);
         td.empty();
         td.append(response);
         var inp = $(td).find('.mdbVal');
         var tdIsLike = $('td#isLike'+this.num);
         if (inp != undefined && tdIsLike != undefined) {
             if ($(inp).hasClass('freeText')) {
                 $(tdIsLike).text('contains');
             } else if (usesFilterBy && $(inp).hasClass('filterBy')) {
                 $(tdIsLike).text('is among');
             } else {
                 $(tdIsLike).text('is');
             }
         }
         $(td).find('.filterBy').each( function(i) { // Do this by 'each' to set noneIsAll individually
             if (usesFilterBy) {
                 $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true, maxDropHeight: filterByMaxHeight(this) });
             } else {
                 $(this).attr("multiple",false);
                 $(this).removeClass('filterBy');
                 $(this).show();
             }
         });
     }
     updateMetaDataHelpLinks(this.num);
 }
 
 function findTracksMdbValChanged(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)
 
     findTracksClearFound();  // Changing values so abandon what has been found
 
     if ($('#advancedTab').length == 1 && $('#filesTab').length == 1) {
         var newVal = $(obj).val();
         var a = /hgt_mdbVal(\d+)/.exec(obj.name); // NOTE must match METADATA_NAME_PREFIX in hg/hgTracks/searchTracks.c
         if(newVal != undefined && 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("refresh");  // requires v1.1
                     $(this).dropdownchecklist("destroy");
                     $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true, maxDropHeight: filterByMaxHeight(this) });
                 }
             });
         }
     }
     //findTracksSearchButtonsEnable(true);
 }
 
 function findTracksChangeVis(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 it to [] because that means default setting is used.  However, we are explicitly hiding this!
         $(seenVis).attr('disabled',true);  // Can't set it to [] because that means default setting is used.  However, we are explicitly hiding this!
         var needSel = (tdb.parentTrack != undefined);
         if (needSel) {
             var hiddenSel = $("input[name='"+trackName+"_sel']");
             $(hiddenSel).val('0');  // Can't set it to [] because that means default setting is used.  However, we are explicitly hiding this!
             $(hiddenSel).attr('disabled',false);
         }
         if(tdbIsSubtrack(tdb))
             $(hiddenVis).val("[]");
         else
             $(hiddenVis).val("hide");
     }
     $(hiddenVis).attr('disabled',false);
 
     $('input.viewBtn').val('View in Browser');
     //warn("Changed "+trackName+" to "+$(hiddenVis).val())
 }
 
 function findTracksClickedOne(selCb,justClicked)
 { // called by on click of CB and findTracksCheckAll()
     var selName = $(selCb).attr('id');
     var trackName = selName.substring(0,selName.length - "_sel_id".length)
     var hiddenSel = $("input[name='"+trackName+"_sel']");
     var seenVis = $('select#' + trackName + "_id");
     var hiddenVis = $("input[name='"+trackName+"']");
     var tr = $(selCb).parents('tr.found');
     var tdb = tdbGetJsonRecord(trackName);
     var needSel = (tdb.parentTrack != undefined);
     var shouldPack = tdb.canPack && tdb.kindOfParent == 0; // If parent then not pack but full
     if (shouldPack && tdb.shouldPack != undefined && !tdb.shouldPack)
         shouldPack = false;
     var checked = $(selCb).attr('checked');
     //warn(trackName +" selName:"+selName +" justClicked:"+justClicked +" hiddenSel:"+$(hiddenSel).attr('name') +" seenVis:"+$(seenVis).attr('id') +" hiddenVis:"+$(hiddenVis).attr('name') +" needSel:"+needSel +" shouldPack:"+shouldPack);
 
     // 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 != ($(hiddenSel).val() == '1'));
         else if (checked)
             setHiddenInputs = ($(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 that means default setting is used.  However, we are explicitly hiding this!
             $(hiddenSel).attr('disabled',false);
         }
     }
 
     // The "view in browser" button should be enabled/disabled
     if(justClicked) {
         $('input.viewBtn').val('View in Browser');
         findTracksCounts();
     }
 }
 
 
 function findTracksNormalize()
 { // 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) { findTracksClickedOne(this,false); });
 
     findTracksCounts();
 }
 
 function findTracksNormalizeWaitOn()
 { // Put up wait mask then Normalize the page based upon current state of all found tracks
     waitOnFunction( findTracksNormalize );
 }
 
 function findTracksCheckAll(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) { findTracksClickedOne(this,false); });
 
     $('input.viewBtn').val('View in Browser');
     findTracksCounts();
     return false;  // Pressing button does nothing more
 }
 
 function findTracksCheckAllWithWait(check)
 {
     waitOnFunction( findTracksCheckAll, check);
 }
 
 function findTracksSearchButtonsEnable(enable)
 { // Displays visible and checked track count
     var searchButton = $('input[name="hgt_tSearch"]'); // NOTE: must match TRACK_SEARCH in hg/inc/searchTracks.h
     var clearButton  = $('input.clear');
     if(enable) {
         $(searchButton).attr('disabled',false);
         $(clearButton).attr('disabled',false);
     } else {
         $(searchButton).attr('disabled',true);
         $(clearButton).attr('disabled',true);
     }
 }
 
 function findTracksCounts()
 {// Displays visible and checked track count
     var counter = $('.selCbCount');
     if(counter != undefined) {
         var selCbs =  $("input.selCb");
         $(counter).text("("+$(selCbs).filter(":enabled:checked").length + " of " +$(selCbs).length+ " selected)");
     }
 }
 
 function findTracksClearFound()
 {// Clear found tracks and all input controls
     var found = $('div#found');
     if(found != undefined)
         $(found).remove();
     found = $('div#filesFound');
     if(found != undefined)
         $(found).remove();
     return false;
 }
 
 function filterByMaxHeight(multiSel)
 {   // Setting a max hieght 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 = $('input#currentTab');
     if (tabbed != undefined) {
         var tabDiv = $(multiSel).parents('div#'+ $(tabbed).attr('value'));
         if (tabDiv == null || tabDiv == undefined || $(tabDiv).length == 0) {
             pos = 360;
         }
     }
     var maxHeight = $(window).height() - pos;
     var selHeight = $(multiSel).children().length * 21;
     if (maxHeight > selHeight)
         maxHeight = null;
     return maxHeight;
 }
 
 function findTracksClear()
 {// Clear found tracks and all input controls
     findTracksClearFound();
     $('input[type="text"]').val(''); // This will always be found
     //$('select.mdbVar').attr('selectedIndex',0); // Do we want to set the first two to cell/antibody?
     $('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).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true, maxDropHeight: filterByMaxHeight(this) });
     });
 
     $('select.groupSearch').attr('selectedIndex',0);
     $('select.typeSearch').attr('selectedIndex',0);
     //findTracksSearchButtonsEnable(false);
     return false;
 }
 
 function findTracksSortNow(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');
         $('form#trackSearch').attr('method','POST'); // Must be post to avoid url too long  NOTE: probably needs to be post anyway
     }
 
     $('#searchSubmit').click();
     return true;
 }
 
 function findTracksPage(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');
         $('form#trackSearch').attr('method','POST'); // Must be post to avoid url too long  NOTE: probably needs to be post anyway
     }
 
     $('#searchSubmit').click();
     return false;
 }
 
 function findTracksConfigureSet(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();
 }
 
 function findTracksMdbSelectPlusMinus(obj, rowNum)
 { // 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 = $(obj).attr('id');
     rowNum = objId.substring(objId.length - 1);
     if ($(obj).val() == '+') {
         var buttons = $("input#plusButton"+rowNum);  // Two tabs may have the exact same buttons!
         if (buttons.length > 0) {
             $(buttons).each(function (i) {
                 var tr = $(this).parents('tr.mdbSelect')[0];
                 if (tr != undefined)
                     $(tr).after( $(tr).clone() );
                 findTracksMdbSelectRowsNormalize($(tr).parents('table')[0]); // magic is in this function
             });
             return false;
         }
     } else { // == '-'
         var buttons = $("input#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 != undefined)
                     $(tr).remove();
                 remaining = findTracksMdbSelectRowsNormalize(table);  // Must renormalize since 2nd of 3 rows may have been removed
             });
             if (remaining > 0) {
                 removeNum = remaining + 1;  // Got to remove the cart vars, though it doesn't matter which as count must not be too many.
                 setCartVars( [ "hgt_mdbVar"+removeNum, "hgt_mdbVal"+removeNum ], [ "[]","[]" ] );
             }
 
             findTracksClearFound();  // Changing values so abandon what has been found
             return false;
         }
     }
     return true;
 }
 
 function findTracksMdbSelectRowsNormalize(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 != undefined) {
         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("input[value='+']")[0];
             if (plusButton != undefined) {
                 $(plusButton).attr('id',"plusButton"+rowNum);
                 $(plusButton).unbind('click')
                 $(plusButton).click(function() { return findTracksMdbSelectPlusMinus($(plusButton), rowNum); });
                 var minusButton = $(this).find("input[value='-']")[0];
                 if (needMinus) {
                     if (minusButton == undefined) {
                         $(plusButton).before("<input type='button' id='minusButton"+rowNum+"' value='-' style='font-size:.7em;' title='delete this row' onclick='return findTracksMdbSelectPlusMinus(this,"+rowNum+");'>");
                         minusButton = $(this).find("input[value='-']")[0];
                     } else {
                         $(minusButton).attr('id',"minusButton"+rowNum);
                         $(minusButton).unbind('click');
                         $(minusButton).click(function() { return findTracksMdbSelectPlusMinus($(minusButton), rowNum); });
                     }
                 } else if (minusButton != undefined)
                     $(minusButton).remove();
             }
             // Now the mdb var=val pair of selects
             var element = $(this).find("select[name^='hgt_mdbVar']")[0];
             if (element != undefined)
                 $(element).attr('name','hgt_mdbVar' + rowNum);
 
             element = $(this).find("select[name^='hgt_mdbVal']")[0];
             if (element != undefined)
                 $(element).attr('name','hgt_mdbVal' + rowNum);
 
             // A couple more things
             element = $(this).find("td[id^='isLike']")[0];
             if (element != undefined)
                 $(element).attr('id','isLike' + rowNum);
             element = $(this).find("td[id^='hgt_mdbVal']")[0];
             if (element != undefined)
                 $(element).attr('id','hgt_mdbVal' + rowNum);
         });
         return mdbSelectRows.length;
     }
     return 0;
 }
 
 function findTracksSwitchTabs(ui)
 { // switching tabs on findTracks page
 
     if( ui.panel.id == 'simpleTab' && $('div#found').length < 1) {
         setTimeout("$('input#simpleSearch').focus();",20); // delay necessary, since select event not afterSelect event
     }
     if( $('div#filesFound').length == 1) {
         if( ui.panel.id == 'filesTab')
             $('div#filesFound').show();
         else
             $('div#filesFound').hide();
     }
     if( $('div#found').length == 1) {
         if( ui.panel.id != 'filesTab')
             $('div#found').show();
         else
             $('div#found').hide();
     }
 }
 
 /////////////////////////////////////////////////////
 // filterTable functions
 
 function filterTableFilterVar(filter)
 { // returns the var associated with a fileFilter
 
     if($(filter).hasClass('filterBy') == false)
         return undefined;
     if($(filter).hasClass('filterTable') == false)
         return undefined;
 
     // Find the var for this filter
     var classes = $(filter).attr("class").split(' ');
     classes = aryRemove(classes,"filterBy","filterTable");
     if (classes.length > 1 ) {
         warn('Too many classes for filterBy: ' + classes);
         return undefined;
     }
     return classes.pop();
 }
 
 function filterTablesTrsSurviving(filterClass)
 // returns a list of trs that satisfy all filters
 // If defined, will exclude filter identified by filterClass
 {
     // find all filterable table rows
     var showTrs = $('tr.filterable'); // Default all
     if (showTrs.length == 0)
         return undefined;
 
     // Find all filters
     var filters = $("select.filterBy");
     if (filters.length == 0)
         return undefined;
 
     // Exclude one if requested.
     if (filterClass != undefined && filterClass.length > 0)
         filters = $(filters).not('.' + filterClass);
 
     // For each filter, filter the list of trs that matches that filter
     $(filters).each(function (i) {
         var val = $(this).val();
         if (val == null || val.length == 0)
             return;
         val = val.join();
         if(val.indexOf("All") == 0)
             return;
 
         // Get the filter variable
         var filterVar = filterTableFilterVar(this);
         if (filterVar == undefined)
             return;
 
         // Get the selected values for this filter
         var classes = $(this).val();
         if (classes.length == 0)
             return;
 
         var varTds = $(showTrs).children('td.' + filterVar);
         var filteredTrs = new Array;
         var ix =0;
         for(;ix<classes.length;ix++) {
             var tds = $(varTds).filter('.' + classes[ix]);
             if (tds.length > 0) {
                 if (filteredTrs.length == 0)
                     filteredTrs = $(tds).parent('tr').get();
                 else
                     filteredTrs = filteredTrs.concat( $(tds).parent('tr').get() );
             }
         }
         // The following tighter code may take too long
         //var filterVals = 'td.'+filterVar+'.' + classes.join(',td.'+filterVar+'.');   // "td.cell.GM12878,td.cell.K562,td.cell.H1-hESC"
         //var filteredTrs = $(showTrs).filter(":has(" + filterVals + ")");
 
         if (filteredTrs.length > 0)
             showTrs = filteredTrs;
     });
     return showTrs;
 }
 
 function _filterTable()
 { // Called by filter onchange event.  Will show/hide trs based upon all filters
     var showTrs = filterTablesTrsSurviving();
     if (showTrs == undefined)
         return;
     //$('tr.filterable').hide();  // <========= This is what is taking so long!
     $('tr.filterable').css('display', 'none')
 
     $(showTrs).show();
 
     // Update count
     var counter = $('.filesCount');
     if(counter != undefined)
         $(counter).text($(showTrs).length + " / ");
 
     var tbody = $( $('tr.filterable')[0] ).parent('tbody.sorting');
     if (tbody != undefined)
          $(tbody).removeClass('sorting');
 }
 
 function filterTableTrigger()
 { // Called by filter onchange event.  Will show/hide trs based upon all filters
     var tbody = $( $('tr.filterable')[0] ).parent('tbody');
     if (tbody != undefined)
          $(tbody).addClass('sorting');
 
     setTimeout('_filterTable();',10); // Just in case
 }
 
 function filterTable()
 { // Called by filter onchange event.  Will show/hide trs based upon all filters
     waitOnFunction(filterTableTrigger );
 }
 
 function filterTableExcludeOptions(filter)
 { // bound to 'click' event inside ui.dorpdownchecklist.js.
   // Will mark all options in one filterBy box that are inconsistent with the current
   // selections in other filterBy boxes.  Mark with class ".excluded"
 
     // Find the var for this filter
     var filterVar = filterTableFilterVar(filter);
     if (filterVar == undefined)
         return false;
 
     // Look at list of visible trs.
     var visibleTrs = filterTablesTrsSurviving(filterVar);
     if (visibleTrs == undefined)
         return false;
 
     // Compare to the list of all trs
     var allTrs = $('tr.filterable'); // Default all
     if (allTrs.length == 0)
         return false;
     if (allTrs.length == visibleTrs.length) {
         $(filter).children('option.excluded').removeClass('excluded');   // remove .excluded" from all
         return true;  // Nothing more to do.  All are already excluded
     }
 
     // Find the tds that belong to this var
     var tds = $(visibleTrs).find('td.'+filterVar);
     if (tds.length == 0) {
         $(filter).children('option').addClass('excluded');   // add .excluded" to all
         return true;
     }
 
     // Find the val classes
     var classes = new Array();
     $(tds).each(function (i) {
         var someClass = $(this).attr("class").split(' ');
         someClass = aryRemove(someClass,filterVar);
         var val = someClass.pop()
         if (aryFind(classes,val) == -1)
             classes.push(val);
     });
     if (classes.length == 0) {
         $(filter).children('option').addClass('excluded');   // add .excluded" to all
         return true;
     }
 
     // Find all options with those classes
     $(filter).children('option').each(function (i) {
         if (aryFind(classes,$(this).val()) != -1)
             $(this).removeClass('excluded'); // remove .excluded from matching
         else
             $(this).addClass('excluded');    // add .excluded" to non-matching
     });
     return true;
 }