a53b9958fa734f73aeffb9ddfe2fbad1ca65f90c
galt
  Mon Jan 30 16:18:41 2017 -0800
Check-in of CSP2 Content-Security-Policy work. All C-language CGIs should now support CSP2 in browser to stop major forms of XSS javascript injection. Javascript on pages is gathered together, and then emitted in a single script block at the end with a nonce that tells the browser, this is js that we generated instead of being injected by a hacker. Both inline script from script blocks and inline js event handlers had to be pulled out and separated. You will not see js sprinkled through-out the page now. Older browsers that support CSP1 or that do not understand CSP at all will still work, just without protection. External js libraries loaded at runtime need to be added to the CSP policy header in src/lib/htmshell.c.

diff --git src/hg/js/hgTracks.js src/hg/js/hgTracks.js
index 54a5607..951d9f7 100644
--- src/hg/js/hgTracks.js
+++ src/hg/js/hgTracks.js
@@ -1,4597 +1,4667 @@
 // Javascript for use in hgTracks CGI
 
 // "use strict";
 // Don't complain about line break before '||' etc:
 /* jshint -W014 */
 
 
 var debug = false;
 
 /* Data passed in from CGI via the hgTracks object:
  *
  * string cgiVersion      // CGI_VERSION
  * string chromName       // current chromosome
  * int winStart           // genomic start coordinate (0-based, half-open)
  * int winEnd             // genomic end coordinate
  * int newWinWidth        // new width (in bps) if user clicks on the top ruler
  * boolean revCmplDisp    // true if we are in reverse display
  * int insideX            // width of side-bar (in pixels)
  * int rulerClickHeight   // height of ruler (in pixels) - zero if ruler is hidden
  * boolean inPlaceUpdate  // true if in-place-update is turned on
  * int imgBox*            // various drag-scroll values
  * boolean measureTiming  // true if measureTiming is on
  * Object trackDb         // hash of trackDb entries for tracks which are visible on current page
  */
 
 function initVars()
 {  // There are various entry points, so we call initVars in several places to make sure all is well
     if (typeof(hgTracks) !== "undefined" && !genomePos.original) {
         // remember initial position and size so we can restore it if user cancels
         genomePos.original = genomePos.getOriginalPos();
         genomePos.originalSize = $('#size').text().replace(/,/g, ""); // strip out any commas
         dragSelect.originalCursor = jQuery('body').css('cursor');
 
         imageV2.imgTbl = $('#imgTbl');
         // imageV2.enabled === true unless: advancedJavascript===false, or trackSearch, or config pg
         imageV2.enabled = (imageV2.imgTbl && imageV2.imgTbl.length > 0);
 
         // jQuery load function with stuff to support drag selection in track img
         if (theClient.isSafari()) {
             // Safari has the following bug: if we update the hgTracks map dynamically,
             // the browser ignores the changes (even though if you look in the DOM the changes
             // are there). So we have to do a full form submission when the user changes
             // visibility settings or track configuration.
             // As of 5.0.4 (7533.20.27) this is problem still exists in safari.
             // As of 5.1 (7534.50) this problem appears to have been fixed - unfortunately,
             // logs for 7/2011 show vast majority of safari users are pre-5.1 (5.0.5 is by far
             // the most common).
             //
             // Early versions of Chrome had this problem too, but this problem went away
             // as of Chrome 5.0.335.1 (or possibly earlier).
             //
             // KRR/JAT 2/2016:
             // This Safari issue is likely resolved in all current versions.  However the test
             // for version had been failing, likely for some time now.
             // (As of 9.0.9, possibly earlier, the 3rd part of the version is included in the
             // user agent string, so must be accounted for in string match)
             // Consequences were that page refresh was used instead of img update (e.g. 
             // for drag-zoom).  And UI dialog was unable to update (e.g. via Apply button).
             imageV2.mapIsUpdateable = false;
             var reg = new RegExp("Version\/([0-9]+.[0-9]+)(.[0-9]+)? Safari");
             var a = reg.exec(navigator.userAgent);
             if (a && a[1]) {
                 var version = Number(a[1]);
                 if (version >= 5.1) {
                     imageV2.mapIsUpdateable = true;
                 }
             }
         }
         imageV2.inPlaceUpdate = hgTracks.inPlaceUpdate && imageV2.mapIsUpdateable;
     }
 }
 
   /////////////////////////////////////
  ////////// Genomic position /////////
 /////////////////////////////////////
 var genomePos = {
 
     original: null,
     originalSize: 0,
 
     linkFixup: function (pos, id, reg, endParamName)
     {   // fixup external links (e.g. ensembl)
         var ele = $(document.getElementById(id));
         if (ele.length) {
             var link = ele.attr('href');
             var a = reg.exec(link);
             if (a && a[1]) {
                 ele.attr('href', a[1] + pos.start + "&" + endParamName + "=" + pos.end);
             }
         }
     },
 
     setByCoordinates: function (chrom, start, end)
     {
         var newPosition = chrom + ":" + start + "-" + end;
         genomePos.set(newPosition, end - start + 1);
         return newPosition;
     },
 
     getElement: function ()
     {
     // Return position box object
         var tags = document.getElementsByName("position");
         // There are multiple tags with name === "position" (the visible position text input
         // and a hidden with id='positionHidden'); we return value of visible element.
         for (var i = 0; i < tags.length; i++) {
                 var ele = tags[i];
                 if (ele.id !== "positionHidden") {
                     return ele;
                 }
         }
         return null;
     },
 
     get: function ()
     {
     // Return current value of position box
         var ele = genomePos.getElement();
         if (ele) {
             return ele.value;
         }
         return null;
     },
 
     getOriginalPos: function ()
     {
         return genomePos.original || genomePos.get();
     },
 
     revertToOriginalPos: function ()
     {
     // undo changes to position (i.e. after user aborts a drag-and-select).
         this.set(this.original, this.originalSize);
         this.original = this.originalSize = null;         // not sure if this is necessary.
     },
 
     undisguisePosition: function(position) // UN-DISGUISE VMODE
     {   // find the virt position
         //  position should be real chrom span
         var pos = parsePosition(position);
         if (!pos)
             return position; // some parsing error, return original
         var start = pos.start - 1;
         var end = pos.end;
         var chromName = hgTracks.windows[0].chromName;
         if (pos.chrom !== chromName)
             return position; // return original
         var newStart = -1;
         var newEnd = -1;
         var lastW = null;
         var windows = null;
         for (j=0; j < 3; ++j) {
             if (j === 0) windows = hgTracks.windowsBefore;
             if (j === 1) windows = hgTracks.windows;
             if (j === 2) windows = hgTracks.windowsAfter;
             for (i=0,len=windows.length; i < len; ++i) {
                 var w = windows[i];
                 //  double check chrom is same thoughout all windows, otherwise warning, return original value
                 if (w.chromName != chromName) {
                     return position; // return original
                 }
                 // check that the regions are ascending and non-overlapping
                 if (lastW && w.winStart < lastW.winEnd) {
                     return position; // return original
                 }
                 // overlap with position?
                 //  if intersection, 
                 if (w.winEnd > start && end > w.winStart) {
                     var s = Math.max(start, w.winStart);
                     var e = Math.min(end, w.winEnd);
                     var cs = s - w.winStart + w.virtStart;
                     var ce = e - w.winStart + w.virtStart;
                     if (newStart === -1)
                         newStart = cs;
                     newEnd = ce;
                 }
                 lastW = w;
             }
         }
         //  return new virt undisguised position as a string
         var newPos = "virt:" + (newStart+1) + "-" + newEnd;
         return newPos;
     },
 
     disguiseSize: function(position) // DISGUISE VMODE
     {   // find the real size of the windows spanned
         //  position should be a real chrom span
         var pos = parsePosition(position);
         if (!pos)
             return 0;
         var start = pos.start - 1;
         var end = pos.end;
         var newSize = 0;
         var windows = null;
         for (j=0; j < 3; ++j) {
             if (j === 0) windows = hgTracks.windowsBefore;
             if (j === 1) windows = hgTracks.windows;
             if (j === 2) windows = hgTracks.windowsAfter;
             for (i=0,len=windows.length; i < len; ++i) {
                 var w = windows[i];
                 // overlap with position?
                 //  if intersection, 
                 if (w.winEnd > start && end > w.winStart) {
                     var s = Math.max(start, w.winStart);
                     var e = Math.min(end, w.winEnd);
                     newSize += (e - s);
                 }
             }
         }
         //  return real size of the disguised position 
         return newSize;
     },
 
     disguisePosition: function(position) // DISGUISE VMODE
     {   // find the single-chrom range spanned
         //  position should be virt
         var pos = parsePosition(position);
         if (!pos)
             return position; // some parsing error, return original
         var start = pos.start - 1;
         var end = pos.end;
         var chromName = hgTracks.windows[0].chromName;
         var newStart = -1;
         var newEnd = -1;
         var lastW = null;
         var windows = null;
         for (j=0; j < 3; ++j) {
             if (j === 0) windows = hgTracks.windowsBefore;
             if (j === 1) windows = hgTracks.windows;
             if (j === 2) windows = hgTracks.windowsAfter;
             for (i=0,len=windows.length; i < len; ++i) {
                 var w = windows[i];
                 //  double check chrom is same thoughout all windows, otherwise warning, return original value
                 if (w.chromName != chromName) {
                     return position; // return undisguised original
                 }
                 // check that the regions are ascending and non-overlapping
                 if (lastW && w.winStart < lastW.winEnd) {
                     return position; // return undisguised original
                 }
                 // overlap with position?
                 //  if intersection, 
                 if (w.virtEnd > start && end > w.virtStart) {
                     var s = Math.max(start, w.virtStart);
                     var e = Math.min(end, w.virtEnd);
                     var cs = s - w.virtStart + w.winStart;
                     var ce = e - w.virtStart + w.winStart;
                     if (newStart === -1)
                         newStart = cs;
                     newEnd = ce;
                 }
                 lastW = w;
             }
         }
         //  return new non-virt disguised position as a string
         var newPos = chromName + ":" + (newStart+1) + "-" + newEnd;
         return newPos;
     },
 
     set: function (position, size)
     {   // Set value of position and size (in hiddens and input elements).
         // We assume size has already been commified.
         // Either position or size may be null.
 
         // stack dump  // DEBUG
         //console.trace();
         // NOT work on safari
         //var obj = {};
         //Error.captureStackTrace(obj);
         //warn("genomePos.set() called "+obj.stack);
 
         position = position.replace(/,/g, ""); // strip out any commas
 
         if (position) {
             // DISGUISE VMODE
             //warn("genomePos.set() called, position = "+position);
             if (hgTracks.virtualSingleChrom && (position.search("virt:")===0)) {
                 var newPosition = genomePos.disguisePosition(position);
                 //warn("genomePos.set() position = "+position+", newPosition = "+newPosition);
                 position = newPosition;
             }
         }
         if (position) {
             // There are multiple tags with name === "position"
             // (one in TrackHeaderForm and another in TrackForm).
             var tags = document.getElementsByName("position");
             for (var i = 0; i < tags.length; i++) {
                 var ele = tags[i];
                 ele.value = position;
             }
         }
         var pos = parsePosition(position);
         if ($('#positionDisplay').length) {
             // add commas to positionDisplay
             var commaPosition = position;
             if (pos)
                 commaPosition = pos.chrom+":"+commify(pos.start)+"-"+commify(pos.end);  
             $('#positionDisplay').text(commaPosition);
         }
         if (size) {
             if (hgTracks.virtualSingleChrom && (position.search("virt:")!==0)) {
                 var newSize = genomePos.disguiseSize(position);
                 //warn("genomePos.set() position = "+position+", newSize = "+newSize);
                 if (newSize > 0)
                     size = newSize;
             }
             $('#size').text(commify(size)); // add commas
         }
         if (pos) {
             // fixup external static links on page'
 
             // Example ensembl link:
             // http://www.ensembl.org/Homo_sapiens/contigview?chr=21&start=33031934&end=33041241
             genomePos.linkFixup(pos, "ensemblLink", new RegExp("(.+start=)[0-9]+"), "end");
 
             // Example NCBI link:
             // http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=21&BEG=33031934&END=33041241
             genomePos.linkFixup(pos, "ncbiLink", new RegExp("(.+BEG=)[0-9]+"), "END");
 
             // Example medaka link: 
             // http://utgenome.org/medakabrowser_ens_jump.php?revision=version1.0&chr=chromosome18&start=14435198&end=14444829
             genomePos.linkFixup(pos, "medakaLink", new RegExp("(.+start=)[0-9]+"), "end");
 
             var link;
             var reg;
             var a;
             if ($('#wormbaseLink').length) {
                 // e.g. http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=II:14646301-14667800
                 link = $('#wormbaseLink').attr('href');
                 reg = new RegExp("(.+:)[0-9]+");
                 a = reg.exec(link);
                 if (a && a[1]) {
                     $('#wormbaseLink').attr('href', a[1] + pos.start + "-" + pos.end);
                 }
             }
             // Fixup DNA link; e.g.: 
             // hgc?hgsid=2999470&o=114385768&g=getDna&i=mixed&c=chr7&l=114385768&r=114651696&db=panTro2&hgsid=2999470
             if ($('#dnaLink').length) {
                 link = $('#dnaLink').attr('href');
                 reg = new RegExp("(.+&o=)[0-9]+.+&db=[^&]+(.*)");
                 a = reg.exec(link);
                 if (a && a[1]) {
                     var url = a[1] + (pos.start - 1) + "&g=getDna&i=mixed&c=" + pos.chrom;
                     url += "&l=" + (pos.start - 1) + "&r=" + pos.end + "&db=" + getDb() + a[2];
                     $('#dnaLink').attr('href', url);
                 }
             }
         }
         if (!imageV2.backSupport)
             imageV2.markAsDirtyPage();
     },
 
     check: function (img, selection)
     {   // return true if user's selection is still w/n the img (including some slop).
         var imgWidth = jQuery(img).width();
         var imgHeight = jQuery(img).height();
         var imgOfs = jQuery(img).offset();
         var slop = 10;
 
         // We ignore clicks in the gray tab and track title column
         // (we really should suppress all drag activity there,
         // but I don't know how to do that with imgAreaSelect).
         var leftX = hgTracks.revCmplDisp ?  imgOfs.left - slop :
                                             imgOfs.left + hgTracks.insideX - slop;
         var rightX = hgTracks.revCmplDisp ? imgOfs.left + imgWidth - hgTracks.insideX + slop :
                                             imgOfs.left + imgWidth + slop;
 
         return (   (selection.event.pageX >= leftX)
                 && (selection.event.pageX < rightX)
                 && (selection.event.pageY >= (imgOfs.top - slop))
                 && (selection.event.pageY <  (imgOfs.top + imgHeight + slop)));
     },
 
     pixelsToBases: function (img, selStart, selEnd, winStart, winEnd)
     {   // Convert image coordinates to chromosome coordinates
         var imgWidth = jQuery(img).width() - hgTracks.insideX;
         var width = hgTracks.winEnd - hgTracks.winStart;
         var mult = width / imgWidth;   // mult is bp/pixel multiplier
         var startDelta;   // startDelta is how many bp's to the right/left
         var x1;
         if (hgTracks.revCmplDisp) {
             x1 = Math.min(imgWidth, selStart);
             startDelta = Math.floor(mult * (imgWidth - x1));
         } else {
             x1 = Math.max(hgTracks.insideX, selStart);
             startDelta = Math.floor(mult * (x1 - hgTracks.insideX));
         }
         var endDelta;
         var x2;
         if (hgTracks.revCmplDisp) {
             endDelta = startDelta;
             x2 = Math.min(imgWidth, selEnd);
             startDelta = Math.floor(mult * (imgWidth - x2));
         } else {
             x2 = Math.max(hgTracks.insideX, selEnd);
             endDelta = Math.floor(mult * (x2 - hgTracks.insideX));
         }
         var newStart = hgTracks.winStart + startDelta;
         var newEnd = hgTracks.winStart + 1 + endDelta;
         if (newEnd > winEnd) {
             newEnd = winEnd;
         }
         return {chromStart : newStart, chromEnd : newEnd};
     },
 
     chromToVirtChrom: function (chrom, chromStart, chromEnd)
     {   // Convert regular chromosome position to virtual chrom coordinates using hgTracks.windows list
         // Consider the first contiguous set of overlapping regions to define the match (for now).
         // only works for regions covered by the current hgTracks.windows
         var virtStart = -1, virtEnd = -1;
         var s,e;
         var i, len;
         for (i = 0, len = hgTracks.windows.length; i < len; ++i) {
             var w = hgTracks.windows[i];
             var overlap = (chrom == w.chromName && chromEnd > w.winStart && w.winEnd > chromStart);
             if (virtStart == -1) {
                 if (overlap) {
                     // when they overlap the first time
                     s = Math.max(chromStart, w.winStart);
                     e = Math.min(chromEnd, w.winEnd);
                     virtStart = w.virtStart + (s - w.winStart);
                     virtEnd   = w.virtStart + (e - w.winStart);
                 } else {
                     // until they overlap
                     // do nothing
                 }
             } else {
                 if (overlap) {
                     // while they continue to overlap, extend
                     e = Math.min(chromEnd, w.winEnd);
                     virtEnd   = w.virtStart + (e - w.winStart);
                 } else {
                     // when they do not overlap anymore, stop
                     break;
                 }
             }
         }
         return {chromStart : virtStart, chromEnd : virtEnd};
     },
 
     selectionPixelsToBases: function (img, selection)
     {   // Convert selection x1/x2 coordinates to chromStart/chromEnd.
         return genomePos.pixelsToBases(img, selection.x1, selection.x2,
                                         hgTracks.winStart, hgTracks.winEnd);
     },
 
     update: function (img, selection, singleClick)
     {
         var pos = genomePos.pixelsToBases(img, selection.x1, selection.x2,
                                             hgTracks.winStart, hgTracks.winEnd);
         // singleClick is true when the mouse hasn't moved (or has only moved a small amount).
         if (singleClick) {
             var center = (pos.chromStart + pos.chromEnd)/2;
             pos.chromStart = Math.floor(center - hgTracks.newWinWidth/2);
             pos.chromEnd = pos.chromStart + hgTracks.newWinWidth;
             // clip
             if (pos.chromStart < hgTracks.chromStart)
                 pos.chromStart = hgTracks.chromStart; // usually  1
             if (pos.chromEnd > hgTracks.chromEnd)
                 pos.chromEnd = hgTracks.chromEnd; // usually virt chrom size
 
             // save current position so that that it may be restored after highlight or cancel.
             genomePos.original = genomePos.getOriginalPos();
             genomePos.originalSize = $('#size').text().replace(/,/g, ""); // strip out any commas
 
         }
         var newPosition = genomePos.setByCoordinates(hgTracks.chromName,
                                                             pos.chromStart+1, pos.chromEnd);
         return newPosition;
     },
 
     handleChange: function (response, status)
     {
         var json = JSON.parse(response);
         genomePos.set(json.pos);
     },
 
     changeAssemblies: function (ele)  // UNUSED?  Larry's experimental code
     {   // code to update page when user changes assembly select list.
         $.ajax({
                 type: "GET",
                 url: "../cgi-bin/hgApi",
                 data: cart.varsToUrlData({ 'cmd': 'defaultPos', 'db': getDb() }),
                 dataType: "html",
                 trueSuccess: genomePos.handleChange,
                 success: catchErrorOrDispatch,
                 error: errorHandler,
                 cache: true
             });
         return false;
     },
 
+
+    inlineJs : "",
+
+    getInlineJs: function (response, status)
+    {
+	//alert("genomePos.getInlineJs called!"); // DEBUG REMOVE
+        genomePos.inlineJs = response;
+    },
+
+    fetchInlineJs: function (url)
+    {   // code to fetch temp file with inline js in it.  // OBSOLETE CSP1
+        $.ajax({
+                type: "GET",
+                async: false, // wait for result
+                url: url,
+                dataType: "html",
+                trueSuccess: genomePos.getInlineJs,
+                success: catchErrorOrDispatch,
+                error: errorHandler,
+                cache: false
+            });
+        return genomePos.inlineJs;
+    },
+
+
     convertedVirtCoords : {chromStart : -1, chromEnd : -1},
 
     handleConvertChromPosToVirtCoords: function (response, status)
     {
         var virtStart = -1, virtEnd = -1;
         var newJson = scrapeVariable(response, "convertChromToVirtChrom");
         if (!newJson) {
             warn("convertChromToVirtChrom object is missing from the response");
         } else {
             virtStart = newJson.virtWinStart;
             virtEnd   = newJson.virtWinEnd;
         }
         genomePos.convertedVirtCoords = {chromStart : virtStart, chromEnd : virtEnd};
     },
 
     convertChromPosToVirtCoords: function (chrom, chromStart, chromEnd)
     {   // code to convert chrom position to virt coords
         genomePos.convertedVirtCoords = {chromStart : -1, chromEnd : -1};  // reset
         var pos = chrom+":"+(chromStart+1)+"-"+chromEnd; // easier to pass 1 parameter than 3
         $.ajax({
                 type: "GET",
                 async: false, // wait for result
                 url: "../cgi-bin/hgTracks",
                 data: cart.varsToUrlData({ 'hgt.convertChromToVirtChrom': pos, 'hgt.trackImgOnly' : 1, 'hgsid': getHgsid() }),
                 dataType: "html",
                 trueSuccess: genomePos.handleConvertChromPosToVirtCoords,
                 success: catchErrorOrDispatch,
                 error: errorHandler,
                 cache: false
             });
         return genomePos.convertedVirtCoords;
     },
 
     positionDisplayDialog: function ()
     // Show the virtual and real positions of the windows
     {   
         var position = genomePos.get();
         var positionDialog = $("#positionDialog")[0];
         if (!positionDialog) {
             $("body").append("<div id='positionDialog'><span id='positionDisplayPosition'></span>");
             positionDialog = $("#positionDialog")[0];
         }
         if (hgTracks.windows) {
             var i,len;
             var str = position;
             if (!(hgTracks.virtualSingleChrom && (hgTracks.windows.length === 1))) {
                 str += "<br>\n";
                 str += "<br>\n";
                 str += "<ul style='list-style-type:none; max-height:200px; padding:0; width:80%; overflow:hidden; overflow-y:scroll;'>\n";
                 for (i=0,len=hgTracks.windows.length; i < len; ++i) {
                     var w = hgTracks.windows[i];
                     str += "<li>" + w.chromName + ":" + (w.winStart+1) + "-" + w.winEnd + "</li>\n";
                 }
                 str += "</ul>\n";
             }
             $("#positionDisplayPosition").html(str);
         } else {
             $("#positionDisplayPosition").html(position);
         }
         $(positionDialog).dialog({
                 modal: true,
                 title: "Window-Positions",
                 closeOnEscape: true,
                 resizable: false,
                 autoOpen: false,
                 minWidth: 400,
                 minHeight: 40,
                 buttons: {  
                     "OK": function() {
                         $(this).dialog("close");
                     }
                 },
 
                 open: function () { // Make OK the focus/default action
                    $(this).parents('.ui-dialog-buttonpane button:eq(0)').focus(); 
                 },
 
                 close: function() {
                     // All exits to dialog should go through this
                     $(imageV2.imgTbl).imgAreaSelect({hide:true});
                     $(this).hide();
                     $('body').css('cursor', ''); // Occasionally wait cursor got left behind
                 }
         });
         $(positionDialog).dialog('open');
     }
 
 };
 
   /////////////////////////////////////
  //// Creating items by dragging /////
 /////////////////////////////////////
 var makeItemsByDrag = {
 
     end: function (img, selection)
     {
         var image = $(img);
         var imageId = image.attr('id');
         var trackName = imageId.substring('img_data_'.length);
         var pos = genomePos.selectionPixelsToBases(image, selection);
         var command = document.getElementById('hgt_doJsCommand');
         command.value  = "makeItems " + trackName + " " + hgTracks.chromName;
         command.value +=  " " + pos.chromStart + " " + pos.chromEnd;
         document.TrackHeaderForm.submit();
         return true;
     },
 
     init: function (trackName)
     {
     // Set up so that they can drag out to define a new item on a makeItems track.
     var img = $("#img_data_" + trackName);
     if (img && img.length !== 0) {
         var imgHeight = imageV2.imgTbl.height();
         jQuery(img.imgAreaSelect( { selectionColor: 'green', outerColor: '',
             minHeight: imgHeight, maxHeight: imgHeight, onSelectEnd: makeItemsByDrag.end,
             autoHide: true, movable: false}));
         }
     },
 
     load: function ()
     {
         for (var id in hgTracks.trackDb) {
             var rec = hgTracks.trackDb[id];
             if (rec && rec.type && rec.type.indexOf("makeItems") === 0) {
                 this.init(id);
             }
         }
     }
 };
 
   ///////////////////
  /////  mouse  /////
 ///////////////////
 var mouse = {
 
     savedOffset: {x:0, y:0},
 
     saveOffset: function (ev)
     {   // Save the mouse offset associated with this event
         mouse.savedOffset = {x: ev.clientX, y: ev.clientY};
     },
 
     hasMoved: function (ev)
     {   // return true if mouse has moved a significant amount
         var minPixels = 10;
         var movedX = ev.clientX - mouse.savedOffset.x;
         var movedY = ev.clientY - mouse.savedOffset.y;
         if (arguments.length === 2) {
             var num = Number(arguments[1]);
             if (isNaN(num)) {
                 if ( arguments[1].toLowerCase() === "x" )
                     return (movedX > minPixels || movedX < (minPixels * -1));
                 if ( arguments[1].toLowerCase() === "y" )
                     return (movedY > minPixels || movedY < (minPixels * -1));
             }
             else
                 minPixels = num;
         }
         return (   movedX > minPixels || movedX < (minPixels * -1)
                 || movedY > minPixels || movedY < (minPixels * -1));
     }
 };
 
   /////////////////
  //// posting ////
 /////////////////
 var posting = {
 
     blockUseMap: false,
 
     blockMapClicks: function () 
     // Blocks clicking on map items when in effect. Drag opperations frequently call this.
     { 
         posting.blockUseMap=true;  
     },
     
     allowMapClicks:function ()  
     // reallows map clicks.  Called after operations that compete with clicks (e.g. dragging) 
     { 
         $('body').css('cursor', ''); // Explicitly remove wait cursor.
         posting.blockUseMap=false; 
     },
 
     mapClicksAllowed: function () 
     // Verify that click-competing operation (e.g. dragging) isn't currently occurring.
     { 
         return (posting.blockUseMap === false); 
     },
 
     blockTheMapOnMouseMove: function (ev)
     {
         if (!posting.blockUseMap && mouse.hasMoved(ev)) {
             posting.blockUseMap=true;
         }
     },
 
     mapClk: function ()
     {
         var done = false;
         if (false && imageV2.inPlaceUpdate) {
             // XXXX experimental and only turned on in larrym's tree.
             // Use in-place update if the map item just modifies the current position (this is nice
             // because it's faster and preserves the users relative position in the track image).
             //
             // First test handles next/prev item.
             var str = "/cgi-bin/hgTracks\\?position=([^:]+):(.+)&hgsid=(\\d+)" +
                                                                     "&(hgt.(next|prev)Item=[^&]+)";
             var reg = new RegExp(str);
             var a = reg.exec(this.href);
             if (a && a[1] && a[1] === hgTracks.chromName) {
                 imageV2.navigateInPlace("position=" + encodeURIComponent(a[1] + ":" + a[2]) + 
                                                                             "&" + a[4], null, true);
                 done = true;
             } else {
                 // handle next/prev exon
                 str = "/cgi-bin/hgTracks\\?position=([^:]+):(.+)&hgsid=(\\d+)$";
                 reg = new RegExp(str);
                 a = reg.exec(this.href);
                 if (a && a[1]) {
                     imageV2.navigateInPlace("position=" + encodeURIComponent(a[1] + ":" + a[2]), 
                                                                                         null, true);
                     done = true;
                 } else {
                     // handle toggle visibility.
                     // Request may include a track set, so we cannot use requestImgUpdate.
                     str = "/cgi-bin/hgTracks\\?(position=[^:]+:.+&hgsid=\\d+&([^=]+)=([^&]+))$";
                     reg = new RegExp(str);
                     a = reg.exec(this.href);
                     if (a && a[1]) {
                         imageV2.navigateInPlace(a[1], null, true);
                         // imageV2.requestImgUpdate(a[1], a[1] + "=" + a[2], "", a[2]);
                         done = true;
                     }
                 }
             }
         }
         if (done)
             return false;
         else
             return posting.saveSettings(this);
     },
 
     saveSettings: function (obj)
     {
         if (posting.blockUseMap === true) {
             return false;
         }
         if (!obj || !obj.href) // called directly with obj
             obj = this;                               // and from callback without obj
 
         if ($(obj).hasClass('noLink'))  // TITLE_BUT_NO_LINK
             return false;
 
         if (obj.href.match('#') || obj.target.length > 0) {
             //alert("Matched # ["+obj.href+"] or has target:"+obj.target);
             return true;
         }
         var thisForm = normed($(obj).parents('form').first());
         if (!thisForm)
             thisForm = normed($("FORM").first());
         if (thisForm) {
             //alert("posting form:"+$(thisForm).attr('name'));
             return postTheForm($(thisForm).attr('name'),cart.addUpdatesToUrl(obj.href));
         }
         return true;
     }
 };
 
 /////////////////////////
 //// cart updating /////
 ///////////////////////
 var cart = {
     // Controls queuing and ultimately updating cart variables vis ajax or submit. Queued vars
     // are held in an object with unique keys preventing duplicate updates and ensuring last update 
     // takes precedence.  WARNING: be careful creating an object with variables on the fly:
     // cart.setVarsObj({track: vis}) is invalid but cart.setVarsObj({'knownGene': vis}) is ok! 
 
     updateQueue: {},
     
     updatesWaiting: function ()
     {   // returns TRUE if updates are waiting.
         return objNotEmpty(cart.updateQueue);
     },
     
     addUpdatesToUrl: function (url)
     {   // adds any outstanding cart updates to the url, then clears the queue
         if (cart.updatesWaiting()) {
             //console.log('cart.addUpdatesToUrl: '+objKeyCount(cart.updateQueue)+' vars');
             var updates = cart.varsToUrlData(); // clears the queue
             if (!url || url.length === 0)
                 return updates;
 
             if (updates.length > 0) {
                 var dataOnly = (url.indexOf("cgi-bin") === -1); // all urls should be to our cgis
                 if (!dataOnly && url.lastIndexOf("?") === -1)
                     url += "?" + updates;
                 else
                     url += '&' + updates;
             }
         }
         return url;
     },
     
     beforeUnload: function ()
     {   // named function that can be bound and unbound to beforeunload event
         // Makes sure any outstanding queued updates are sent before leaving the page.
         //console.log('cart.beforeUnload: '+objKeyCount(cart.updateQueue)+' vars');
         cart.setVarsObj( {}, null, false ); // synchronous
     },
     
     varsToUrlData: function (varsObj)
     {   // creates a url data (var1=val1&var2=val2...) string from vars object and queue
         // The queue will be emptied by this call.
         cart.queueVarsObj(varsObj); // lay ontop of queue, to give new values precedence
         
         // Now convert to url data and clear queue
         var urlData = '';
         if (cart.updatesWaiting()) {
             //console.log('cart.varsToUrlData: '+objKeyCount(cart.updateQueue)+' vars');
             urlData = varHashToQueryString(cart.updateQueue);
             cart.updateQueue = {};
         }
         return urlData;
     },
     
     setVarsObj: function (varsObj, errFunc, async)
     {   // Set all vars in a var hash, appending any queued updates
         //console.log('cart.setVarsObj: were:'+objKeyCount(cart.updateQueue) + 
         //            ' new:'+objKeyCount(varsObj);
         cart.queueVarsObj(varsObj); // lay ontop of queue, to give new values precedence
         
         // Now ajax update all in queue and clear queue
         if (cart.updatesWaiting()) {
             setVarsFromHash(cart.updateQueue, errFunc, async);
             cart.updateQueue = {};
         }
     },
     
     setVars: function (names, values, errFunc, async)
     {   // ajax updates the cart, and includes any queued updates.
         cart.setVarsObj(arysToObj(names, values), errFunc, async);
     },
 
     queueVarsObj: function (varsObj)
     {   // Add object worth of cart updates to the 'to be updated' queue, so they can be sent to
         // the server later. Note: hash allows overwriting previous updates to the same variable.
         if (typeof varsObj !== 'undefined' && objNotEmpty(varsObj)) {
             //console.log('cart.queueVarsObj: were:'+objKeyCount(cart.updateQueue) + 
             //            ' new:'+objKeyCount(varsObj));
             for (var name in varsObj) {
                 cart.updateQueue[name] = varsObj[name];
                 
                 // Could update in background, however, failing to hit "refresh" is user choice
                 // first in queue, schedule background update
                 if (objKeyCount(cart.updateQueue) === 1) {
                     // By unbind/bind, we assure that there is only one instance bound
                     $(window).unbind('beforeunload', cart.beforeUnload); 
                     $(window).bind(  'beforeunload', cart.beforeUnload); 
                 }
             }
         }
     },
     
     addVarsToQueue: function (names,values)
     {   // creates a string of updates to save for ajax batch or a submit
         cart.queueVarsObj(arysToObj(names,values));
     }
 };
 
   ///////////////////////////////////////////////
  //// visibility (mixed with group toggle) /////
 ///////////////////////////////////////////////
 var vis = {
 
     // map cgi enum visibility codes to strings
     enumOrder: new Array("hide", "dense", "full", "pack", "squish"),  
 
     update: function (track, visibility)
     {   // Updates visibility state in hgTracks.trackDb and any visible elements on the page.
         // returns true if we modify at least one select in the group list
         var rec = hgTracks.trackDb[track];
         var selectUpdated = false;
         $("select[name=" + escapeJQuerySelectorChars(track) + "]").each(function(t) {
             $(this).attr('class', visibility === 'hide' ? 'hiddenText' : 'normalText');
             $(this).val(visibility);
             selectUpdated = true;
         });
         if (rec) {
             rec.localVisibility = visibility;
         }
         return selectUpdated;
     },
 
     get: function (track)
     {   // return current visibility for given track
         var rec = hgTracks.trackDb[track];
         if (rec) {
             if (rec.localVisibility) {
                 return rec.localVisibility;
             } else {
                 return vis.enumOrder[rec.visibility];
             }
         } else {
             return null;
         }
     },
 
     makeTrackVisible: function (track)
     {   // Sets the vis box to visible, and ques a cart update, but does not update the image
         if (track && vis.get(track) !== "full") {
             vis.update(track, 'pack');
             cart.addVarsToQueue([track], ['pack']);
         }
     },
 
     toggleForGroup: function (button, prefix)
     {   // toggle visibility of a track group; prefix is the prefix of all the id's of tr's in the
         // relevant group. This code also modifies the corresponding hidden fields and the gif
         // of the +/- img tag.
         imageV2.markAsDirtyPage();
         if (arguments.length > 2)
             return setTableRowVisibility(button, prefix, "hgtgroup", "group",false,arguments[2]);
         else
             return setTableRowVisibility(button, prefix, "hgtgroup", "group",false);
     },
 
     expandAllGroups: function (newState)
     {   // Set visibility of all track groups to newState (true means expanded).
         // This code also modifies the corresponding hidden fields and the gif's of the +/- img tag.
         imageV2.markAsDirtyPage();
         $(".toggleButton[id$='_button']").each( function (i) {  
             // works for old img type AND new BUTTONS_BY_CSS      // - 7: clip '_button' suffix
             vis.toggleForGroup(this,this.id.substring(0,this.id.length - 7),newState);
         });
         return false;
     },
     
     initForAjax: function()
     {   // To better support the back-button, it is good to eliminate extraneous form puts
         // Towards that end, we support visBoxes making ajax calls to update cart.
         var sels = $('select.normalText,select.hiddenText');
         $(sels).change(function() {
             var track = $(this).attr('name');
             if ($(this).val() === 'hide') {
                 var rec = hgTracks.trackDb[track];
                 if (rec)
                     rec.visibility = 0;
                 // else Would be nice to hide subtracks as well but that may be overkill
                 $(document.getElementById('tr_' + track)).remove();
                 imageV2.highlightRegion();
                 $(this).attr('class', 'hiddenText');
             } else
                 $(this).attr('class', 'normalText');
             
             cart.addVarsToQueue([track], [$(this).val()]);
             imageV2.markAsDirtyPage();
             return false;
         });
         // Now we can rid the submt of the burden of all those vis boxes
         var form = $('form#TrackForm');
         $(form).submit(function () {
             $('select.normalText,select.hiddenText').attr('disabled',true);
         });
         $(form).attr('method','get');
     },
 
     restoreFromBackButton: function()
     // Re-enabling vis dropdowns is necessary because initForAjax() disables them on submit.
     {
         $('select.normalText,select.hiddenText').attr('disabled',false);
     }
 };
 
   ////////////////////////////////////////////////////////////
  // dragSelect is also known as dragZoom or shift-dragZoom //
 ////////////////////////////////////////////////////////////
 var dragSelect = {
 
     areaSelector:    null, // formerly "imgAreaSelect". jQuery element used for imgAreaSelect
     originalCursor:  null,
     startTime:       null,
 
     selectStart: function (img, selection)
     {
         initVars();
         if (rightClick.menu) {
             rightClick.menu.hide();
         }
         var now = new Date();
         dragSelect.startTime = now.getTime();
         posting.blockMapClicks();
     },
 
     selectChange: function (img, selection)
     {
         if (selection.x1 !== selection.x2) {
             if (genomePos.check(img, selection)) {
                 genomePos.update(img, selection, false);
                 jQuery('body').css('cursor', dragSelect.originalCursor);
             } else {
                 jQuery('body').css('cursor', 'not-allowed');
             }
         }
         return true;
     },
 
     highlightThisRegion: function(newPosition)
     // set highlighting newPosition in server-side cart and apply the highlighting in local UI.
     {
         var pos = parsePosition(newPosition);
         var start = pos.start;
         var end = pos.end;
         hgTracks.highlight = getDb() + "." + pos.chrom + ":" + start + "-" + end + '#AAFFFF';
         hgTracks.highlight = imageV2.disguiseHighlight(hgTracks.highlight);
         // we include enableHighlightingDialog because it may have been changed by the dialog
         var cartSettings = {             'highlight': hgTracks.highlight, 
                           'enableHighlightingDialog': hgTracks.enableHighlightingDialog ? 1 : 0 };
 
         if (hgTracks.windows && !hgTracks.virtualSingleChrom) {
             var nonVirtChrom = "";
             var nonVirtStart = -1; 
             var nonVirtEnd   = -1; 
             for (i=0,len=hgTracks.windows.length; i < len; ++i) {
                 var w = hgTracks.windows[i];
                 // overlap with new position?
                 if (w.virtEnd > start && end > w.virtStart) {
                     var s = Math.max(start, w.virtStart);
                     var e = Math.min(end, w.virtEnd);
                     var cs = s - w.virtStart + w.winStart;
                     var ce = e - w.virtStart + w.winStart;
                     if (nonVirtChrom === "") {
                         nonVirtChrom = w.chromName;
                         nonVirtStart = cs; 
                         nonVirtEnd   = ce;
                     } else {
                         if (w.chromName === nonVirtChrom) {
                             nonVirtEnd = Math.max(ce, nonVirtEnd);
                         } else {
                             break;
                         }
                     }
                 }
             }
             if (nonVirtChrom !== "")
                 cartSettings.nonVirtHighlight = getDb() + '.' + nonVirtChrom + ':' + nonVirtStart + '-' + (nonVirtEnd+1) + '#AAFFFF';
         } else if (hgTracks.windows && hgTracks.virtualSingleChrom) {
                 cartSettings.nonVirtHighlight = hgTracks.highlight;
         }
         // TODO if not virt, do we need to erase cart nonVirtHighlight ?
         cart.setVarsObj(cartSettings);
         imageV2.highlightRegion();
     },
 
     selectionEndDialog: function (newPosition)
     // Let user choose between zoom-in and highlighting.
     {   
         var dragSelectDialog = $("#dragSelectDialog")[0];
         if (!dragSelectDialog) {
             $("body").append("<div id='dragSelectDialog'><span id='dragSelectPosition'></span>" + 
                              "<p><input type='checkbox' id='disableDragHighlight'>" + 
                              "Don't show this dialog again and always zoom.<BR>" + 
                              "(Re-enable highlight via the 'configure' menu at any time.)</p>");
             dragSelectDialog = $("#dragSelectDialog")[0];
         }
         if (hgTracks.windows) {
             var i,len;
             var newerPosition = newPosition;
             if (hgTracks.virtualSingleChrom && (newPosition.search("virt:")===0)) {
                 newerPosition = genomePos.disguisePosition(newPosition);
             }
             var str = newerPosition + "<br>\n";
             var str2 = "<br>\n";
             str2 += "<ul style='list-style-type:none; max-height:200px; padding:0; width:80%; overflow:hidden; overflow-y:scroll;'>\n";
             var pos = parsePosition(newPosition);
             var start = pos.start - 1;
             var end = pos.end;
             var selectedRegions = 0;
             for (i=0,len=hgTracks.windows.length; i < len; ++i) {
                 var w = hgTracks.windows[i];
                 // overlap with new position?
                 if (w.virtEnd > start && end > w.virtStart) {
                     var s = Math.max(start, w.virtStart);
                     var e = Math.min(end, w.virtEnd);
                     var cs = s - w.virtStart + w.winStart;
                     var ce = e - w.virtStart + w.winStart;
                     str2 += "<li>" + w.chromName + ":" + (cs+1) + "-" + ce + "</li>\n";
                     selectedRegions += 1;
                 }
             }
             str2 += "</ul>\n";
             if (!(hgTracks.virtualSingleChrom && (selectedRegions === 1))) {
                 str += str2;
             }
             $("#dragSelectPosition").html(str);
         } else {
             $("#dragSelectPosition").html(newPosition);
         }
         $(dragSelectDialog).dialog({
                 modal: true,
                 title: "Drag-and-select",
                 closeOnEscape: true,
                 resizable: false,
                 autoOpen: false,
                 revertToOriginalPos: true,
                 minWidth: 400,
                 buttons: {  
                     "Zoom In": function() {
                         // Zoom to selection
                         $(this).dialog("option", "revertToOriginalPos", false);
                         if ($("#disableDragHighlight").attr('checked'))
                             hgTracks.enableHighlightingDialog = false;
                         if (imageV2.inPlaceUpdate) {
                             if (hgTracks.virtualSingleChrom && (newPosition.search("virt:")===0)) {
                                 newPosition = genomePos.disguisePosition(newPosition); // DISGUISE
                             }
                             var params = "position=" + newPosition;
                             if (!hgTracks.enableHighlightingDialog)
                                 params += "&enableHighlightingDialog=0";
                             imageV2.navigateInPlace(params, null, true);
                         } else {
                             $('body').css('cursor', 'wait');
                             if (!hgTracks.enableHighlightingDialog)
                                 cart.setVarsObj({'enableHighlightingDialog': 0 },null,false); // async=false
                             document.TrackHeaderForm.submit();
                         }
                         $(this).dialog("close");
                     },
                     "Highlight": function() {
                         // Highlight selection
                         $(imageV2.imgTbl).imgAreaSelect({hide:true});
                         if ($("#disableDragHighlight").attr('checked'))
                             hgTracks.enableHighlightingDialog = false;
                         dragSelect.highlightThisRegion(newPosition);
                         $(this).dialog("close");
                     },
                     "Cancel": function() {
                         $(this).dialog("close");
                     }
                 },
 
                 open: function () { // Make zoom the focus/default action
                    $(this).parents('.ui-dialog-buttonpane button:eq(0)').focus(); 
                 },
 
                 close: function() {
                     // All exits to dialog should go through this
                     $(imageV2.imgTbl).imgAreaSelect({hide:true});
                     if ($(this).dialog("option", "revertToOriginalPos"))
                         genomePos.revertToOriginalPos();
                     if ($("#disableDragHighlight").attr('checked'))
                         $(this).remove();
                     else
                         $(this).hide();
                     $('body').css('cursor', ''); // Occasionally wait cursor got left behind
                 }
         });
         $(dragSelectDialog).dialog('open');
     },
 
     selectEnd: function (img, selection)
     {
         var now = new Date();
         var doIt = false;
         if (dragSelect.originalCursor)
             jQuery('body').css('cursor', dragSelect.originalCursor);
         // ignore releases outside of the image rectangle (allowing a 10 pixel slop)
         if (genomePos.check(img, selection)) {
             // ignore single clicks that aren't in the top of the image
             // (this happens b/c the clickClipHeight test in dragSelect.selectStart
             // doesn't occur when the user single clicks).
             doIt = dragSelect.startTime !== null || selection.y1 <= hgTracks.rulerClickHeight;
         }
         if (doIt) {
             // dragSelect.startTime is null if mouse has never been moved
             var singleClick = (  (selection.x2 === selection.x1)
                               || dragSelect.startTime === null
                               || (now.getTime() - dragSelect.startTime) < 100);
             var newPosition = genomePos.update(img, selection, singleClick);
             if (newPosition) {
                 if (hgTracks.enableHighlightingDialog)
                     dragSelect.selectionEndDialog(newPosition);
                 else {
                     $(imageV2.imgTbl).imgAreaSelect({hide:true});
                     if (imageV2.inPlaceUpdate) {
                         if (hgTracks.virtualSingleChrom && (newPosition.search("virt:")===0)) {
                             newPosition = genomePos.disguisePosition(newPosition); // DISGUISE
                         }
                         imageV2.navigateInPlace("position=" + newPosition, null, true);
                     } else {
                         jQuery('body').css('cursor', 'wait');
                         document.TrackHeaderForm.submit();
                     }
                 }
             }
         } else {
             $(imageV2.imgTbl).imgAreaSelect({hide:true});
             genomePos.revertToOriginalPos();
         }
         dragSelect.startTime = null;
         // blockMapClicks/allowMapClicks() is necessary if selectEnd was over a map item.
         setTimeout(posting.allowMapClicks,50);
         return true;
     },
 
     load: function (firstTime)
     {
         var imgHeight = 0;
         if (imageV2.enabled)
             imgHeight = imageV2.imgTbl.innerHeight() - 1; // last little bit makes border look ok
 
         // No longer disable without ruler, because shift-drag still works
         if (typeof(hgTracks) !== "undefined") {
 
             if (hgTracks.rulerClickHeight === undefined || hgTracks.rulerClickHeight === null)
                 hgTracks.rulerClickHeight = 0; // will be zero if no ruler track
             var heights = hgTracks.rulerClickHeight;
 
             dragSelect.areaSelector = jQuery((imageV2.imgTbl).imgAreaSelect({
                 selectionColor:  'blue',
                 outerColor:      '',
                 minHeight:       imgHeight,
                 maxHeight:       imgHeight,
                 onSelectStart:   dragSelect.selectStart,
                 onSelectChange:  dragSelect.selectChange,
                 onSelectEnd:     dragSelect.selectEnd,
                 autoHide:        false, // gets hidden after possible dialog
                 movable:         false,
                 clickClipHeight: heights
             }));
         }
     }
 };
 
   /////////////////////////////////////
  //// Chrom Drag/Zoom/Expand code ////
 /////////////////////////////////////
 jQuery.fn.chromDrag = function(){
 this.each(function(){
     // Plan:
     // mouseDown: determine where in map: convert to img location: pxDown
     // mouseMove: flag drag
     // mouseUp: if no drag, then create href centered on bpDown loc with current span
     //          if drag, then create href from bpDown to bpUp
     //          if ctrlKey then expand selection to containing cytoBand(s)
 
     // Image dimensions all in pix
     var img = { top: -1, scrolledTop: -1, height: -1, left: -1, scrolledLeft: -1, width: -1 };  
     // chrom Dimensions beg,end,size in bases, rest in pix
     var chr = { name: "", reverse: false, beg: -1, end: -1, size: -1,
                 top: -1, bottom: -1, left: -1, right: -1, width: -1 };   
     var pxDown = 0;     // pix X location of mouseDown
     var chrImg = $(this);
     var mouseIsDown   = false;
     var mouseHasMoved = false;
     var hilite = null;
 
     initialize();
 
     function initialize(){
 
         findDimensions();
 
         if (chr.top === -1)
             warn("chromIdeo(): failed to register "+this.id);
         else {
             hiliteSetup();
 
             $('area.cytoBand').unbind('mousedown');  // Make sure this is only bound once
             $('area.cytoBand').mousedown( function(e)
             {   // mousedown on chrom portion of image only (map items)
                 updateImgOffsets();
                 pxDown = e.clientX - img.scrolledLeft;
                 var pxY = e.clientY - img.scrolledTop;
                 if (mouseIsDown === false
                 && isWithin(chr.left,pxDown,chr.right) && isWithin(chr.top,pxY,chr.bottom)) {
                     mouseIsDown = true;
                     mouseHasMoved = false;
 
                     $(document).bind('mousemove',chromMove);
                     $(document).bind( 'mouseup', chromUp);
                     hiliteShow(pxDown,pxDown);
                     return false;
                 }
             });
         }
     }
 
     function chromMove(e)
     {   // If mouse was down, determine if dragged, then show hilite
         if ( mouseIsDown ) {
             var pxX = e.clientX - img.scrolledLeft;
             var relativeX = (pxX - pxDown);
             if (mouseHasMoved || (mouseHasMoved === false && Math.abs(relativeX) > 2)) {
                 mouseHasMoved = true;
                 if (isWithin(chr.left,pxX,chr.right))
                     hiliteShow(pxDown,pxX);
                 else if (pxX < chr.left)
                     hiliteShow(pxDown,chr.left);
                 else
                     hiliteShow(pxDown,chr.right);
             }
         }
     }
     function chromUp(e)
     {   // If mouse was down, handle final selection
         $(document).unbind('mousemove',chromMove);
         $(document).unbind('mouseup',chromUp);
         chromMove(e); // Just in case
         if (mouseIsDown) {
             updateImgOffsets();
             var bands;
             var pxUp = e.clientX - img.scrolledLeft;
             var pxY  = e.clientY - img.scrolledTop;
             if (isWithin(0,pxY,img.height)) {  // within vertical range or else cancel
                 var selRange = { beg: -1, end: -1, width: -1 };
                 var dontAsk = true;
 
                 if (e.ctrlKey) {
                     bands = findCytoBand(pxDown,pxUp);
                     if (bands.end > -1) {
                         pxDown = bands.left;
                         pxUp   = bands.right;
                         mouseHasMoved = true;
                         dontAsk = false;
                         selRange.beg = bands.beg;
                         selRange.end = bands.end;
                         hiliteShow(pxDown,pxUp);
                     }
                 }
                 else if (mouseHasMoved) {
                     // bounded by chrom dimensions: but must remain within image!
                     if (isWithin(-20,pxUp,chr.left)) 
                         pxUp = chr.left;
                     if (isWithin(chr.right,pxUp,img.width + 20))
                         pxUp = chr.right;
 
                     if ( isWithin(chr.left,pxUp,chr.right+1) ) {
 
                         selRange.beg = convertToBases(pxDown);
                         selRange.end = convertToBases(pxUp);
 
                         if (Math.abs(selRange.end - selRange.beg) < 20)
                             mouseHasMoved = false; // Drag so small: treat as simple click
                         else
                             dontAsk = false;
                     }
                 }
                 if (mouseHasMoved === false) { // Not else because small drag turns this off
 
                     hiliteShow(pxUp,pxUp);
                     var curWidth = hgTracks.winEnd - hgTracks.winStart;
                     // Notice that beg is based upon up position
                     selRange.beg = convertToBases(pxUp) - Math.round(curWidth/2); 
                     selRange.end  = selRange.beg + curWidth;
                 }
                 if (selRange.end > -1) {
                     // prompt, then submit for new position
                     selRange = rangeNormalizeToChrom(selRange,chr);
                     if (mouseHasMoved === false) { // Update highlight by converting bp back to pix
                         pxDown = convertFromBases(selRange.beg);
                         pxUp = convertFromBases(selRange.end);
                         hiliteShow(pxDown,pxUp);
                     }
                     //if ((selRange.end - selRange.beg) < 50000)
                     //    dontAsk = true;
                     if (dontAsk
                     || confirm("Jump to new position:\n\n"+chr.name+":"+commify(selRange.beg)+
                                "-"+commify(selRange.end)+" size:"+commify(selRange.width)) ) {
                         genomePos.setByCoordinates(chr.name, selRange.beg, selRange.end);
                         // Stop the presses :0)
                         $('area.cytoBand').mousedown( function(e) { return false; });
                         if (imageV2.backSupport) {
                             imageV2.navigateInPlace("position=" +  
                                     encodeURIComponent(genomePos.get().replace(/,/g,'')) + 
                                     "&findNearest=1",null,true);
                             hiliteCancel();
                         } else
                             document.TrackHeaderForm.submit();
                         return true; // Make sure the setTimeout below is not called.
                     }
                 }
             }
             hiliteCancel();
             setTimeout(posting.allowMapClicks,50);
         }
         mouseIsDown = false;
         mouseHasMoved = false;
     }
 
     function isWithin(beg,here,end)
     {   // Simple utility
         return ( beg <= here && here < end );
     }
     function convertToBases(pxX)
     {   // Simple utility to convert pix to bases
         var offset = (pxX - chr.left)/chr.width;
         if (chr.reverse)
             offset = 1 - offset;
         return Math.round(offset * chr.size);
     }
     function convertFromBases(bases)
     {   // Simple utility to convert bases to pix
         var offset = bases/chr.size;
         if (chr.reverse)
             offset = 1 - offset;
         return Math.round(offset * chr.width) + chr.left;
     }
 
     function findDimensions()
     {   // Called at init: determine the dimensions of chrom from 'cytoband' map items
         var lastX = -1;
         $('area.cytoBand').each(function(ix) {
             var loc = this.coords.split(",");
             if (loc.length === 4) {
                 var myLeft  = parseInt(loc[0]);
                 var myRight = parseInt(loc[2]);
                 if (chr.top === -1) {
                     chr.left   = myLeft;
                     chr.right  = myRight;
                     chr.top    = parseInt(loc[1]);
                     chr.bottom = parseInt(loc[3]);
                 } else {
                     if (chr.left  > myLeft)
                         chr.left  = myLeft;
                     if (chr.right < parseInt(loc[2]))
                         chr.right = parseInt(loc[2]);
                 }
 
                 var range = this.title.substr(this.title.lastIndexOf(':')+1);
                 var pos = range.split('-');
                 if (pos.length === 2) {
                     if (chr.name.length === 0) {
                         chr.beg = parseInt(pos[0]);
                         //chr.end = parseInt(pos[1]);
                         chr.name = this.title.substring(this.title.lastIndexOf(' ')+1,
                                                         this.title.lastIndexOf(':'));
                     } else {
                         if (chr.beg > parseInt(pos[0]))
                             chr.beg = parseInt(pos[0]);
                     }
                     if (chr.end < parseInt(pos[1])) {
                         chr.end = parseInt(pos[1]);
                         if (lastX === -1)
                             lastX = myRight;
                         else if (lastX > myRight)
                             chr.reverse = true;  // end is advancing, but X is not, so reverse
                     } else if (lastX !== -1 && lastX < myRight)
                         chr.reverse = true;      // end is not advancing, but X is, so reverse
 
                 }
                 $(this).css( 'cursor', 'text');
                 $(this).attr("href","");
             }
         });
         chr.size  = (chr.end   - chr.beg );
         chr.width = (chr.right - chr.left);
     }
 
     function findCytoBand(pxDown,pxUp)
     {   // Called when mouseup and ctrl: Find the bounding cytoband dimensions (in pix and bases)
         var cyto = { left: -1, right: -1, beg: -1, end: -1 };
         $('area.cytoBand').each(function(ix) {
             var loc = this.coords.split(",");
             if (loc.length === 4) {
                 var myLeft  = parseInt(loc[0]);
                 var myRight = parseInt(loc[2]);
                 var range;
                 var pos;
                 if (cyto.left === -1 || cyto.left > myLeft) {
                     if ( isWithin(myLeft,pxDown,myRight) || isWithin(myLeft,pxUp,myRight) ) {
                         cyto.left  = myLeft;
                         range = this.title.substr(this.title.lastIndexOf(':')+1);
                         pos = range.split('-');
                         if (pos.length === 2) {
                             cyto.beg  = (chr.reverse ? parseInt(pos[1]) : parseInt(pos[0]));
                         }
                     }
                 }
                 if (cyto.right === -1 || cyto.right < myRight) {
                     if ( isWithin(myLeft,pxDown,myRight) || isWithin(myLeft,pxUp,myRight) ) {
                         cyto.right = myRight;
                         range = this.title.substr(this.title.lastIndexOf(':')+1);
                         pos = range.split('-');
                         if (pos.length === 2) {
                             cyto.end  = (chr.reverse ? parseInt(pos[0]) : parseInt(pos[1]));
                         }
                     }
                 }
             }
         });
         return cyto;
     }
     function rangeNormalizeToChrom(selection,chrom)
     {   // Called before presenting or using base range: make sure chrom selection
         // is within chrom range
         if (selection.end < selection.beg) {
             var tmp = selection.end;
             selection.end = selection.beg;
             selection.beg = tmp;
         }
         selection.width = (selection.end - selection.beg);
         selection.beg += 1;
         if (selection.beg < chrom.beg) {
             selection.beg = chrom.beg;
             selection.end = chrom.beg + selection.width;
         }
         if (selection.end > chrom.end) {
             selection.end = chrom.end;
             selection.beg = chrom.end - selection.width;
             if (selection.beg < chrom.beg) { // spans whole chrom
                 selection.width = (selection.end - chrom.beg);
                 selection.beg = chrom.beg + 1;
             }
         }
         return selection;
     }
 
     function hiliteShow(down,cur)
     {   // Called on mousemove, mouseup: set drag hilite dimensions
         var topY = img.top;
         var high = img.height;
         var begX = -1;
         var wide = -1;
         if (cur < down) {
             begX = cur + img.left;
             wide = (down - cur);
         } else {
             begX = down + img.left;
             wide = (cur - down);
         }
         $(hilite).css({ left: begX + 'px', width: wide + 'px', top: topY + 'px',
                         height: high + 'px', display:'' });
         $(hilite).show();
     }
     function hiliteCancel(left,width,top,height)
     {   // Called on mouseup: Make green drag hilite disappear when no longer wanted
         $(hilite).hide();
         $(hilite).css({ left: '0px', width: '0px', top: '0px', height: '0px' });
     }
 
     function hiliteSetup()
     {   // Called on init: setup of drag region hilite (but don't show yet)
         if (hilite === null) {  // setup only once
             hilite = jQuery("<div id='chrHi'></div>");
             $(hilite).css({ backgroundColor: 'green', opacity: 0.4, borderStyle: 'solid',
                             borderWidth: '1px', bordercolor: '#0000FF' });
             $(hilite).css({ display: 'none', position: 'absolute', overflow: 'hidden', zIndex: 1 });
             jQuery($(chrImg).parents('body')).append($(hilite));
         }
         return hilite;
     }
 
     function updateImgOffsets()
     {   // Called on mousedown: Gets the current offsets
         var offs = $(chrImg).offset();
         img.top  = Math.round(offs.top );
         img.left = Math.round(offs.left);
         img.scrolledTop  = img.top  - $("body").scrollTop();
         img.scrolledLeft = img.left - $("body").scrollLeft();
         if (theClient.isIePre11()) {
             img.height = $(chrImg).outerHeight();
             img.width  = $(chrImg).outerWidth();
         } else {
             img.height = $(chrImg).height();
             img.width  = $(chrImg).width();
         }
         return img;
     }
 });
 };
 
   ///////////////////////////
  //// Drag Reorder Code ////
 ///////////////////////////
 var dragReorder = {
 
     setOrder: function (table)
     {   // Sets the 'order' value for the image table after a drag reorder
         var varsToUpdate = {};
         $("tr.imgOrd").each(function (i) {
             if ($(this).attr('abbr') !== $(this).attr('rowIndex').toString()) {
                 $(this).attr('abbr',$(this).attr('rowIndex').toString());
                 var name = this.id.substring('tr_'.length) + '_imgOrd';
                 varsToUpdate[name] = $(this).attr('abbr');
             }
         });
         if (objNotEmpty(varsToUpdate)) {
             cart.setVarsObj(varsToUpdate);
             imageV2.markAsDirtyPage();
         }
     },
 
     sort: function (table)
     {   // Sets the table row order to match the order of the abbr attribute.
         // This is needed for back-button, and for visBox changes combined with refresh.
         var tbody = $(table).find('tbody')[0];
         if (!tbody)
             tbody = table;
         
         // Do we need to sort?
         var trs = tbody.rows;
         var needToSort = false;
         $(trs).each(function(ix) {
             if ($(this).attr('abbr') !== $(this).attr('rowIndex').toString()) {
                 needToSort = true;
                 return false;  // break for each() loops
             }
         });
         if (!needToSort)
             return false;
             
         // Create array of tr holders to sort
         var ary = [];
         $(trs).each(function(ix) {  // using sortTable found in utils.js
             ary.push(new sortTable.field(parseInt($(this).attr('abbr')),false,this));
         });
 
         // Sort the array
         ary.sort(sortTable.fieldCmp);
 
         // most efficient reload of sorted rows I have found
         var sortedRows = jQuery.map(ary, function(ary, i) { return ary.row; });
         $(tbody).append( sortedRows ); // removes tr from current position and adds to end.
         return true;
     },
 
     showCenterLabel: function (tr, show)
     {   // Will show or hide centerlabel as requested
         // adjust button, sideLabel height, sideLabelOffset and centerlabel display
 
         if (!$(tr).hasClass('clOpt'))
             return;
         var center = normed($(tr).find(".sliceDiv.cntrLab"));
         if (!center)
             return;
         var seen = ($(center).css('display') !== 'none');
         if (show === seen)
             return;
 
         var centerHeight = $(center).height();
 
         var btn = normed($(tr).find("p.btn"));
         var side = normed($(tr).find(".sliceDiv.sideLab"));
         if (btn && side) {
             var sideImg = normed($(side).find("img"));
             if (sideImg) {
                 var top = parseInt($(sideImg).css('top'));
                 if (show) {
                     $(btn).css('height',$(btn).height() + centerHeight);
                     $(side).css('height',$(side).height() + centerHeight);
                     top += centerHeight; // top is a negative number
                     $(sideImg).css( {'top': top.toString() + "px" });
                     $( center ).show();
                 } else if (!show) {
                     $(btn).css('height',$(btn).height() - centerHeight);
                     $(side).css('height',$(side).height() - centerHeight);
                     top -= centerHeight; // top is a negative number
                     $(sideImg).css( {'top': top.toString() + "px" });
                     $( center ).hide();
                 }
             }
         }
     },
 
     getContiguousRowSet: function (row)
     {   // Returns the set of rows that are of the same class and contiguous
         if (!row)
             return null;
         var btn = $( row ).find("p.btn");
         if (btn.length === 0)
             return null;
         var classList = $( btn ).attr("class").split(" ");
         var matchClass = classList[0];
         var table = $(row).parents('table#imgTbl')[0];
         var rows = $(table).find('tr');
 
         // Find start index
         var startIndex = $(row).attr('rowIndex');
         var endIndex = startIndex;
         for (var ix=startIndex-1; ix >= 0; ix--) {
             btn = $( rows[ix] ).find("p.btn");
             if (btn.length === 0)
                 break;
             classList = $( btn ).attr("class").split(" ");
             if (classList[0] !== matchClass)
                 break;
             startIndex = ix;
         }
 
         // Find end index
         for (var rIx=endIndex; rIx<rows.length; rIx++) {
             btn = $( rows[rIx] ).find("p.btn");
             if (btn.length === 0)
                 break;
             classList = $( btn ).attr("class").split(" ");
             if (classList[0] !== matchClass)
                 break;
             endIndex = rIx;
         }
         return rows.slice(startIndex,endIndex+1); // endIndex is 1 based!
     },
 
     getCompositeSet: function (row)
     {   // Returns the set of rows that are of the same class and contiguous
         if (!row)
             return null;
         var rowId = $(row).attr('id').substring('tr_'.length);
         var rec = hgTracks.trackDb[rowId];
         if (tdbIsSubtrack(rec) === false)
             return null;
 
         var rows = $('tr.trDraggable:has(p.' + rec.parentTrack+')');
         return rows;
     },
 
     zipButtons: function (table)
     {   // Goes through the image and binds composite track buttons when adjacent
         var rows = $(table).find('tr');
         var lastClass="";
         var lastBtn = null;
         var lastSide = null;
         var lastMatchesLast=false;
         var lastBlue=true;
         var altColors=false;
         var count=0;
         var countN=0;
         for (var ix=0; ix<rows.length; ix++) {    // Need to have buttons in order
             var btn = $( rows[ix] ).find("p.btn");
             var side = $( rows[ix] ).find(".sliceDiv.sideLab"); // added by GALT
             if (btn.length === 0)
                 continue;
             var classList = $( btn ).attr("class").split(" ");
             var curMatchesLast=(classList[0] === lastClass);
 
             // centerLabels may be conditionally seen
             if ($( rows[ix] ).hasClass('clOpt')) {
                 // if same composite and previous also centerLabel optional then hide center label
                 if (curMatchesLast && $( rows[ix - 1] ).hasClass('clOpt'))
                     dragReorder.showCenterLabel(rows[ix],false);
                 else
                     dragReorder.showCenterLabel(rows[ix],true);
             }
 
             // On with buttons
             if (lastBtn) {
                 $( lastBtn ).removeClass('btnN btnU btnL btnD');
                 if (curMatchesLast && lastMatchesLast) {
                     $( lastBtn ).addClass('btnL');
                     $( lastBtn ).css('height', $( lastSide ).height() - 0);  // added by GALT
                 } else if (lastMatchesLast) {
                     $( lastBtn ).addClass('btnU');
                     $( lastBtn ).css('height', $( lastSide ).height() - 1);  // added by GALT
                 } else if (curMatchesLast) {
                     $( lastBtn ).addClass('btnD');
                     $( lastBtn ).css('height', $( lastSide ).height() - 2);  // added by GALT
                 } else {
                     $( lastBtn ).addClass('btnN');
                     $( lastBtn ).css('height', $( lastSide ).height() - 3);  // added by GALT
                     countN++;
                 }
                 count++;
                 if (altColors) {
                     // lastMatch and lastBlue or not lastMatch and notLastBlue
                     lastBlue = (lastMatchesLast === lastBlue);
                     if (lastBlue)    // Too  smart by 1/3rd
                         $( lastBtn ).addClass(    'btnBlue' );
                     else
                         $( lastBtn ).removeClass( 'btnBlue' );
                 }
             }
             lastMatchesLast = curMatchesLast;
             lastClass = classList[0];
             lastBtn = btn;
             lastSide = side;
         }
         if (lastBtn) {
             $( lastBtn ).removeClass('btnN btnU btnL btnD');
             if (lastMatchesLast) {
                 $( lastBtn ).addClass('btnU');
                 $( lastBtn ).css('height', $( lastSide ).height() - 1);  // added by GALT
             } else {
                 $( lastBtn ).addClass('btnN');
                 $( lastBtn ).css('height', $( lastSide ).height() - 3);  // added by GALT
                 countN++;
             }
             if (altColors) {
                 // lastMatch and lastBlue or not lastMatch and notLastBlue
                 lastBlue = (lastMatchesLast === lastBlue); 
                 if (lastBlue)    // Too  smart by 1/3rd
                     $( lastBtn ).addClass(    'btnBlue' );
                 else
                     $( lastBtn ).removeClass( 'btnBlue' );
             }
             count++;
         }
         //warn("Zipped "+count+" buttons "+countN+" are independent.");
     },
 
     dragHandleMouseOver: function ()
     {   // Highlights a single row when mouse over a dragHandle column (sideLabel and buttons)
         if ( ! jQuery.tableDnD ) {
             //var handle = $("td.dragHandle");
             //$(handle)
             //    .unbind('mouseenter')//, jQuery.tableDnD.mousemove);
             //    .unbind('mouseleave');//, jQuery.tableDnD.mouseup);
             return;
         }
         if ( ! jQuery.tableDnD.dragObject ) {
             $( this ).parents("tr.trDraggable").addClass("trDrag");
         }
     },
 
     dragHandleMouseOut: function ()
     {   // Ends row highlighting by mouse over
         $( this ).parents("tr.trDraggable").removeClass("trDrag");
     },
 
     buttonMouseOver: function ()
     {   // Highlights a composite set of buttons, regarless of whether tracks are adjacent
         if ( ! jQuery.tableDnD || ! jQuery.tableDnD.dragObject ) {
             var classList = $( this ).attr("class").split(" ");
             var btns = $( "p." + classList[0] );
             $( btns ).removeClass('btnGrey');
             $( btns ).addClass('btnBlue');
             if (jQuery.tableDnD) {
                 var rows = dragReorder.getContiguousRowSet($(this).parents('tr.trDraggable')[0]);
                 if (rows)
                     $( rows ).addClass("trDrag");
             }
         }
     },
 
     buttonMouseOut: function ()
     {   // Ends composite highlighting by mouse over
         var classList = $( this ).attr("class").split(" ");
         var btns = $( "p." + classList[0] );
         $( btns ).removeClass('btnBlue');
         $( btns ).addClass('btnGrey');
         if (jQuery.tableDnD) {
             var rows = dragReorder.getContiguousRowSet($(this).parents('tr.trDraggable')[0]);
             if (rows)
             $( rows ).removeClass("trDrag");
         }
     },
 
     trMouseOver: function (e)
     {   // Trying to make sure there is always a imageV2.lastTrack so that we know where we are
         var id = '';
         var a = /tr_(.*)/.exec($(this).attr('id'));  // voodoo
         if (a && a[1]) {
             id = a[1];
         }
         if (id.length > 0) {
             if ( ! imageV2.lastTrack || imageV2.lastTrack.id !== id)
                 imageV2.lastTrack = rightClick.makeMapItem(id); 
                 // currentMapItem gets set by mapItemMapOver.   This is just backup
         }
     },
 
     mapItemMouseOver: function ()
     {
         // Record data for current map area item
         var id = this.id;
         if (!id || id.length === 0) {
             id = '';
             var tr = $( this ).parents('tr.imgOrd');
             if ( $(tr).length === 1 ) {
                 var a = /tr_(.*)/.exec($(tr).attr('id'));  // voodoo
                 if (a && a[1]) {
                     id = a[1];
                 }
             }
         }
         if (id.length > 0) {
             rightClick.currentMapItem = rightClick.makeMapItem(id);
             if (rightClick.currentMapItem) {
                 rightClick.currentMapItem.href = this.href;
                 rightClick.currentMapItem.title = this.title;
 
                 // Handle linked features with separate clickmaps for each exon/intron 
                 if ((this.title.indexOf('Exon ') === 0) || (this.title.indexOf('Intron ') === 0)) {
                     // if the title is Exon ... or Intron ... 
                     // then search for the sibling with the same href
                     // that has the real title item label
                     var elem = this.parentNode.firstChild;
                     while (elem) {
                         if ((elem.href === this.href)
                             && !((elem.title.indexOf('Exon ') === 0) || (elem.title.indexOf('Intron ') === 0))) {
                             rightClick.currentMapItem.title = elem.title;
                             break;
                         }
                         elem = elem.nextSibling;
                     }
                 }
 
             }
         }
     },
 
     mapItemMouseOut: function ()
     {
         imageV2.lastTrack = rightClick.currentMapItem; // Just a backup
         rightClick.currentMapItem = null;
     },
 
     init: function ()
     {   // Make side buttons visible (must also be called when updating rows in the imgTbl).
         var btns = $("p.btn");
         if (btns.length > 0) {
             dragReorder.zipButtons($('#imgTbl'));
             $(btns).mouseenter( dragReorder.buttonMouseOver );
             $(btns).mouseleave( dragReorder.buttonMouseOut  );
             $(btns).show();
         }
         var handle = $("td.dragHandle");
         if (handle.length > 0) {
             $(handle).mouseenter( dragReorder.dragHandleMouseOver );
             $(handle).mouseleave( dragReorder.dragHandleMouseOut  );
         }
 
         // setup mouse callbacks for the area tags
         $(imageV2.imgTbl).find("tr").mouseover( dragReorder.trMouseOver );
 
         $(".area").each( function(t) {
                             this.onmouseover = dragReorder.mapItemMouseOver;
                             this.onmouseout = dragReorder.mapItemMouseOut;
                             this.onclick = posting.mapClk;
                         });
     }
 };
 
 
   //////////////////////////
  //// Drag Scroll code ////
 //////////////////////////
 jQuery.fn.panImages = function(){
     // globals across all panImages
     genomePos.original = genomePos.getOriginalPos(); // redundant but makes certain original is set.
     var leftLimit   = hgTracks.imgBoxLeftLabel * -1;
     var rightLimit  = (hgTracks.imgBoxPortalWidth - hgTracks.imgBoxWidth + leftLimit);
     var only1xScrolling = ((hgTracks.imgBoxWidth - hgTracks.imgBoxPortalWidth) === 0);
     var prevX       = (hgTracks.imgBoxPortalOffsetX + hgTracks.imgBoxLeftLabel) * -1;
     var portalWidth = 0;
     var portalAbsoluteX = 0;
     var savedPosition;
     var highlightArea  = null; // Used to ensure dragSelect highlight will scroll. 
 
     this.each(function(){
 
     var pic;
     var pan;
 
     if ( $(this).is("img") ) {
         pan = $(this).parent("div");
         pic = $(this);
     }
     else if ( $(this).is("div.scroller")  ) {
         pan = $(this);
         pic = $(this).children("img#panImg"); // Get the real pic
     }
 
     if (!pan || !pic) {
         throw "Not a div with child image! 'panImages' can only be used with divs contain images.";
     }
 
     // globals across all panImages
     portalWidth     = $(pan).width();
     portalAbsoluteX = $(pan).offset().left;
     // globals to one panImage
     var newX        = 0;
     var mouseDownX  = 0;
     var mouseIsDown = false;
     var beyondImage = false;
     var atEdge      = false;
 
     initialize();
 
     function initialize(){
 
         $(pan).parents('td.tdData').mousemove(function(e) {
             if (e.shiftKey)
                 $(this).css('cursor',"crosshair");  // shift-dragZoom
             else if ( theClient.isIePre11() )     // IE will override map item cursors if this gets set
                 $(this).css('cursor',"");  // normal pointer when not over clickable item
         });
 
         panAdjustHeight(prevX);
 
         pan.mousedown(function(e){
              if (e.which > 1 || e.button > 1 || e.shiftKey)
                  return true;
             if (mouseIsDown === false) {
                 if (rightClick.menu) {
                     rightClick.menu.hide();
                 }
                 mouseIsDown = true;
                 mouseDownX = e.clientX;
                 highlightArea = $('#highlightItem')[0];
                 atEdge = (!beyondImage && (prevX >= leftLimit || prevX <= rightLimit));
                 $(document).bind('mousemove',panner);
                 $(document).bind( 'mouseup', panMouseUp);  // Will exec only once
                 return false;
             }
         });
     }
 
     function panner(e) {
         //if (!e) e = window.event;
         if ( mouseIsDown ) {
             var relativeX = (e.clientX - mouseDownX);
 
             if (relativeX !== 0) {
                 if (posting.mapClicksAllowed()) {
                     // need to throw up a z-index div.  Wait mask?
                     savedPosition = genomePos.get();
                     dragMaskShow();
                     posting.blockMapClicks();
                 }
                 var decelerator = 1;
                 //var wingSize    = 1000; // 0 stops the scroll at the edges.
                 // Remeber that offsetX (prevX) is negative
                 newX = prevX + relativeX;
                 if ( newX >= leftLimit ) { // scrolled all the way to the left
                     if (atEdge) {  // Do not drag straight off edge.  Force second drag
                         beyondImage = true;
                         newX = leftLimit + (newX - leftLimit)/decelerator;// slower
                         //if (newX >= leftLimit + wingSize) // Don't go too far over the edge!
                         //    newX =  leftLimit + wingSize;
                     } else
                         newX = leftLimit;
 
                 } else if ( newX < rightLimit ) { // scrolled all the way to the right
                     if (atEdge) {  // Do not drag straight off edge.  Force second drag
                         beyondImage = true;
                         newX = rightLimit - (rightLimit - newX)/decelerator;// slower
                         //if (newX < rightLimit - wingSize) // Don't go too far over the edge!
                         //    newX = rightLimit - wingSize;
                     } else
                         newX = rightLimit;
 
                 } else if (newX >= rightLimit && newX < leftLimit)
                     beyondImage = false; // could have scrolled back without mouse up
 
                 newX = panUpdatePosition(newX,true);
                 var nowPos = newX.toString() + "px";
                 $(".panImg").css( {'left': nowPos });
                 $('.tdData').css( {'backgroundPosition': nowPos } );
                 scrollHighlight(relativeX);
                 if (!only1xScrolling)
                     panAdjustHeight(newX);  // Will dynamically resize image while scrolling.
             }
         }
     }
     function panMouseUp(e) {  // Must be a separate function instead of pan.mouseup event.
         //if (!e) e = window.event;
         if (mouseIsDown) {
 
             dragMaskClear();
             $(document).unbind('mousemove',panner);
             $(document).unbind('mouseup',panMouseUp);
             mouseIsDown = false;
             // timeout incase the dragSelect.selectEnd was over a map item. select takes precedence.
             setTimeout(posting.allowMapClicks,50); 
 
             // Outside image?  Then abandon.
             var curY = e.pageY;
             var imgTbl = $('#imgTbl');
             var north = $(imgTbl).offset().top;
             var south = north + $(imgTbl).height();
             if (curY < north || curY > south) {
                 atEdge = false;
                 beyondImage = false;
                 if (savedPosition)
                     genomePos.set(savedPosition);
                 var oldPos = prevX.toString() + "px";
                 $(".panImg").css( {'left': oldPos });
                 $('.tdData').css( {'backgroundPosition': oldPos } );
                 if (highlightArea)
                     imageV2.highlightRegion();
                 return true;
             }
 
             // Do we need to fetch anything?
             if (beyondImage) {
                 if (imageV2.inPlaceUpdate) {
                     var pos = parsePosition(genomePos.get());
                     imageV2.navigateInPlace("position=" +
                             encodeURIComponent(pos.chrom + ":" + pos.start + "-" + pos.end),
                             null, true);
                 } else {
                     document.TrackHeaderForm.submit();
                 }
                 return true; // Make sure the setTimeout below is not called.
             }
 
             // Just a normal scroll within a >1X image
             if (prevX !== newX) {
                 prevX = newX;
                 if (!only1xScrolling) {
                     //panAdjustHeight(newX); // Will resize image AFTER scrolling.
                     // Important, since AJAX could lead to reinit after this within bounds scroll
                     hgTracks.imgBoxPortalOffsetX = (prevX * -1) - hgTracks.imgBoxLeftLabel;
                     hgTracks.imgBoxPortalLeft = newX.toString() + "px";
                 }
             }
         }
     }
     });  // end of this.each(function(){
 
     function panUpdatePosition(newOffsetX,bounded)
     {
         // Updates the 'position/search" display with change due to panning
         var closedPortalStart = hgTracks.imgBoxPortalStart + 1;   // Correction for half open
         var portalWidthBases = hgTracks.imgBoxPortalEnd - closedPortalStart;
         var portalScrolledX  = hgTracks.imgBoxPortalOffsetX+hgTracks.imgBoxLeftLabel + newOffsetX;
         var recalculate = false;
 
         var newPortalStart = 0;
         if (hgTracks.revCmplDisp)
             newPortalStart = closedPortalStart +     // As offset goes down, so do bases seen.
                                 Math.round(portalScrolledX*hgTracks.imgBoxBasesPerPixel);
         else
             newPortalStart = closedPortalStart -     // As offset goes down, bases seen goes up!
                                 Math.round(portalScrolledX*hgTracks.imgBoxBasesPerPixel);
         if (newPortalStart < hgTracks.chromStart && bounded) {     // Stay within bounds
             newPortalStart = hgTracks.chromStart;
             recalculate = true;
         }
         var newPortalEnd = newPortalStart + portalWidthBases;
         if (newPortalEnd > hgTracks.chromEnd && bounded) {
             newPortalEnd = hgTracks.chromEnd;
             newPortalStart = newPortalEnd - portalWidthBases;
             recalculate = true;
         }
         if (newPortalStart > 0) {
             var newPos = hgTracks.chromName + ":" + newPortalStart + "-" + newPortalEnd;
             genomePos.set(newPos); // no need to change the size
         }
         if (recalculate && hgTracks.imgBoxBasesPerPixel > 0) { 
             // Need to recalculate X for bounding drag
             portalScrolledX = (closedPortalStart - newPortalStart) / hgTracks.imgBoxBasesPerPixel;
             newOffsetX = portalScrolledX - (hgTracks.imgBoxPortalOffsetX+hgTracks.imgBoxLeftLabel);
         }
         return newOffsetX;
     }
     function mapTopAndBottom(mapName,east,west)
     {
     // Find the top and bottom px given left and right boundaries
         var mapPortal = { top: -10, bottom: -10 };
         var items = $("map[name='"+mapName+"']").children();
         if ($(items).length>0) {
             $(items).each(function(t) {
                 var loc = this.coords.split(",");
                 var aleft   = parseInt(loc[0]);
                 var aright  = parseInt(loc[2]);
                 if (aleft < west && aright >= east) {
                     var atop    = parseInt(loc[1]);
                     var abottom = parseInt(loc[3]);
                     if (mapPortal.top    < 0 ) {
                         mapPortal.top    = atop;
                         mapPortal.bottom = abottom;
                     } else if (mapPortal.top > atop) {
                             mapPortal.top = atop;
                     } else if (mapPortal.bottom < abottom) {
                             mapPortal.bottom = abottom;
                     }
                 }
             });
         }
         return mapPortal;
     }
     function panAdjustHeight(newOffsetX) {
         // Adjust the height of the track data images so that bed items scrolled off screen
         // do not waste vertical real estate
 
         // Is the > 1x?
         if (only1xScrolling)
             return;
 
         var east = newOffsetX * -1;
         var west = east + portalWidth;
         $(".panImg").each(function(t) {
             var mapid  = this.id.replace('img_','map_');
             var hDiv   = $(this).parent();
             var north  = parseInt($(this).css("top")) * -1;
             var south  = north + $(hDiv).height();
 
             var mapPortal = mapTopAndBottom(mapid,east,west);
             if (mapPortal.top > 0) {
                 var topdif = Math.abs(mapPortal.top - north);
                 var botdif = Math.abs(mapPortal.bottom - south);
                 if (topdif > 2 || botdif > 2) {
                     $(hDiv).height( mapPortal.bottom - mapPortal.top );
                     north = mapPortal.top * -1;
                     $(this).css( {'top': north.toString() + "px" });
 
                     // Need to adjust side label height as well!
                     var imgId = this.id.split("_");
                     var titlePx = 0;
                     var center = $("#img_center_"+imgId[2]);
                     if (center.length > 0) {
                         titlePx = $(center).parent().height();
                         north += titlePx;
                     }
                     var side = $("#img_side_"+imgId[2]);
                     if (side.length > 0) {
                         $(side).parent().height( mapPortal.bottom - mapPortal.top + titlePx);
                         $(side).css( {'top': north.toString() + "px" });
                     }
                     var btn = $("#p_btn_"+imgId[2]);
                     if (btn.length > 0) {
                         $(btn).height( mapPortal.bottom - mapPortal.top + titlePx);
                     } else {
                         btn = $("#img_btn_"+imgId[2]);
                         if (btn.length > 0) {
                             $(btn).parent().height( mapPortal.bottom - mapPortal.top + titlePx);
                             $(btn).css( {'top': top.toString() + "px" });
                         }
                     }
                 }
             }
         });
         dragMaskResize();  // Resizes the dragMask to match current image size
     }
 
     function dragMaskShow() 
     {   // Sets up the dragMask to show grabbing cursor within image
         // and not allowed north and south of image
         var imgTbl = $('#imgTbl');
         // Find or create the waitMask (which masks the whole page)
         var dragMask = normed($('div#dragMask'));
         if (!dragMask) {
             $("body").prepend("<div id='dragMask' class='waitMask'></div>");
             dragMask = $('div#dragMask');
         }
 
         $('body').css('cursor','not-allowed');
         $(dragMask).css('cursor',"url(../images/grabbing.cur),w-resize");
         $(dragMask).css({opacity:0.0,display:'block',
                         top: $(imgTbl).position().top.toString() + 'px',
                         height: $(imgTbl).height().toString() + 'px' });
     }
 
     function dragMaskResize() 
     {   // Resizes dragMask (called when image is dynamically resized in >1x scrolling)
         var imgTbl = $('#imgTbl');
         // Find or create the waitMask (which masks the whole page)
         var dragMask = normed($('div#dragMask'));
         if (dragMask) {
             $(dragMask).height( $(imgTbl).height() );
         }
     }
 
     function dragMaskClear() {        // Clears the dragMask
         $('body').css('cursor','auto');
         var  dragMask = normed($('#dragMask'));
         if (dragMask)
             $(dragMask).hide();
     }
 
     function scrollHighlight(relativeX) 
     // Scrolls the highlight region if one exists
     {        
         if (highlightArea) {
             // Best to have a left and right, then min/max the edges, then set width
             var hiOffset = $(highlightArea).offset();
             var hiDefinedLeft  = $(highlightArea).data('leftPixels');
             var hiDefinedWidth = $(highlightArea).data('widthPixels');
             hiOffset.left = Math.max(hiDefinedLeft + relativeX,
                                      portalAbsoluteX);
             var right     = Math.min(hiDefinedLeft + hiDefinedWidth + relativeX,
                                      portalAbsoluteX + portalWidth);
             var newWidth = Math.max(right - hiOffset.left,0);
             if (hiDefinedWidth !== newWidth)
                 $(highlightArea).width(newWidth);
             $(highlightArea).offset(hiOffset);
         }
     }
 
 
 };
 
   ///////////////////////////////////////
  //// rightClick (aka context menu) ////
 ///////////////////////////////////////
 var rightClick = {
 
     menu: null,
     selectedMenuItem: null,   // currently choosen context menu item (via context menu).
     floatingMenuItem: null,
     currentMapItem:   null,
     supportZoomCodon: false,  // turns on experimental feature (currently only in larry's tree).
 
     makeMapItem: function (id)
     {   // Create a dummy mapItem on the fly
         // (for objects that don't have corresponding entry in the map).
         if (id && id.length > 0 && hgTracks.trackDb) {
             var title;
             var rec = hgTracks.trackDb[id];
             if (rec) {
                 title = rec.shortLabel;
             } else {
                 title = id;
             }
             return {id: id, title: "configure " + title};
         } else {
             return null;
         }
     },
 
     findMapItem: function (e)
     {   // Find mapItem for given event; returns item object or null if none found.
 
         if (rightClick.currentMapItem) {
             return rightClick.currentMapItem;
         }
 
         // rightClick for non-map items that can be resolved to their parent tr and
         // then trackName (e.g. items in gray bar)
         var tr = $( e.target ).parents('tr.imgOrd');
         if ($(tr).length === 1) {
             var a = /tr_(.*)/.exec($(tr).attr('id'));  // voodoo
             if (a && a[1]) {
                 var id = a[1];
                 return rightClick.makeMapItem(id);
             }
         }
         return null;
     },
 
     windowOpenFailedMsg: function ()
     {
         warn("Your web browser prevented us from opening a new window.\n\n" +
              "Please change your browser settings to allow pop-up windows from " +
              document.domain + ".");
     },
 
     handleZoomCodon: function (response, status)
     {
         var json = JSON.parse(response);
         if (json.pos) {
             genomePos.set(json.pos, 3);
             if (document.TrackForm)
                 document.TrackForm.submit();
             else
                 document.TrackHeaderForm.submit();
         } else {
             alert(json.error);
         }
     },
 
     handleViewImg: function (response, status)
     {   // handles view image response, which must get new image without imageV2 gimmickery
         jQuery('body').css('cursor', '');
         var str = "<IMG[^>]*SRC='([^']+)'";
         var reg = new RegExp(str);
         var a = reg.exec(response);
         if (a && a[1]) {
             if ( ! window.open(a[1]) ) {
                 rightClick.windowOpenFailedMsg();
             }
             return;
         }
         warn("Couldn't parse out img src");
     },
 
     myPrompt: function (msg, callback)
     {   // replacement for prompt; avoids misleading/confusing security warnings which are caused
         // by prompt in IE 7+.   Callback is called if user presses "OK".
         $("body").append("<div id = 'myPrompt'><div id='dialog' title='Basic dialog'><form>" +
                             msg + "<input id='myPromptText' value=''></form>");
         $("#myPrompt").dialog({
                                 modal: true,
                                 closeOnEscape: true,
                                 buttons: { "OK": function() {
                                                     var myPromptText = $("#myPromptText").val();
                                                     $(this).dialog("close");
                                                     callback(myPromptText);
                                                 }
                                         }
                             });
     },
 
     hit: function (menuItemClicked, menuObject, cmd, args)
     {
         setTimeout( function() {
                         rightClick.hitFinish(menuItemClicked, menuObject, cmd, args);
                     }, 1);
     },
 
     hitFinish: function (menuItemClicked, menuObject, cmd, args)
     {   // dispatcher for context menu hits
         var id = rightClick.selectedMenuItem.id;
         var url = null;  // TODO: Break this giant routine with shared vars into some sub-functions
         var href = null;
         var rec = null;
         var row = null;
         var rows = null;
         var selectUpdated = null;
         if (menuObject.shown) {
             // warn("Spinning: menu is still shown");
             setTimeout(function() { rightClick.hitFinish(menuItemClicked, menuObject, cmd); }, 10);
             return;
         }
         if (cmd === 'selectWholeGene' || cmd === 'getDna' || cmd === 'highlightItem') {
                 // bring whole gene into view or redirect to DNA screen.
                 href = rightClick.selectedMenuItem.href;
                 var chrom, chromStart, chromEnd;
                 // Many links leave out the chrom (b/c it's in the server side cart as "c")
                 // var chrom = hgTracks.chromName; // This is no longer acceptable
                 // with multi-window capability drawing multiple positions on multiple chroms.
                 var a = /hgg_chrom=(\w+)&/.exec(href);
                 if (a) {
                     if (a && a[1])
                         chrom = a[1];
                     a = /hgg_start=(\d+)/.exec(href);
                     if (a && a[1])
                         chromStart = parseInt(a[1]) + 1;
                     a = /hgg_end=(\d+)/.exec(href);
                     if (a && a[1])
                         chromEnd = parseInt(a[1]);
                 } else {
                     // a = /hgc.*\W+c=(\w+)/.exec(href);
                     a = /hgc.*\W+c=(\w+)/.exec(href);
                     if (a && a[1])
                         chrom = a[1];
                     a = /o=(\d+)/.exec(href);
                     if (a && a[1])
                         chromStart = parseInt(a[1]) + 1;
                     a = /t=(\d+)/.exec(href);
                     if (a && a[1])
                         chromEnd = parseInt(a[1]);
                 }
                 if (!chrom || chrom.length === 0 || !chromStart || !chromEnd) {// 1-based chromStart
                     warn("couldn't parse out genomic coordinates");
                 } else {
                     if (cmd === 'getDna') {
                         // NOTE: this should be shared with URL generation for getDna blue bar menu
                         url = "../cgi-bin/hgc?g=getDna&i=mixed&c=" + chrom;
                         url += "&l=" + (chromStart - 1) + "&r=" + chromEnd;
                         url += "&db=" + getDb() + "&hgsid=" + getHgsid();
                         if ( ! window.open(url) ) {
                             rightClick.windowOpenFailedMsg();
                         }
                     } else if (cmd === 'highlightItem') {
                         if (hgTracks.windows && !hgTracks.virtualSingleChrom) {
                             // orig way only worked if the entire item was visible in the windows.
                             //var result = genomePos.chromToVirtChrom(chrom, parseInt(chromStart-1), parseInt(chromEnd));
 
                             var result = genomePos.convertChromPosToVirtCoords(chrom, parseInt(chromStart-1), parseInt(chromEnd));
 
                             if (result.chromStart != -1)
                                 {
                                 var newPos2 = hgTracks.chromName+":"+(result.chromStart+1)+"-"+result.chromEnd;
                                 dragSelect.highlightThisRegion(newPos2);
                                 }
 
                         } else {
                             var newChrom = hgTracks.chromName;
                             if (hgTracks.windows && hgTracks.virtualSingleChrom) {
                                 newChrom = hgTracks.windows[0].chromName;
                             }
                             var newPos3 = newChrom+":"+(parseInt(chromStart))+"-"+parseInt(chromEnd);
                             dragSelect.highlightThisRegion(newPos3);
                         }
                     } else {
                         var newPosition = genomePos.setByCoordinates(chrom, chromStart, chromEnd);
                         var reg = new RegExp("hgg_gene=([^&]+)");
                         var b = reg.exec(href);
                         var name;
                         // pull item name out of the url so we can set hgFind.matches (redmine 3062)
                         if (b && b[1]) {
                             name = b[1];
                         } else {
                             reg = new RegExp("[&?]i=([^&]+)");
                             b = reg.exec(href);
                             if (b && b[1]) {
                                 name = b[1];
                             }
                         }
                         if (imageV2.inPlaceUpdate) {
                             // XXXX This attempt to "update whole track image in place" didn't work
                             // for a variety of reasons (e.g. safari doesn't parse map when we
                             // update on the client side), so this is currently dead code.
                             // However, this now works in all other browsers, so we may turn this
                             // on for non-safari browsers (see redmine #4667).
                             jQuery('body').css('cursor', '');
                             var data = "hgt.trackImgOnly=1&hgt.ideogramToo=1&position=" +
                                        newPosition + "&hgsid=" + getHgsid();
                             if (name)
                                 data += "&hgFind.matches=" + name;
                             $.ajax({
                                     type: "GET",
                                     url: "../cgi-bin/hgTracks",
                                     data: cart.addUpdatesToUrl(data),
                                     dataType: "html",
                                     trueSuccess: imageV2.updateImgAndMap,
                                     success: catchErrorOrDispatch,
                                     error: errorHandler,
                                     cmd: cmd,
                                     loadingId: showLoadingImage("imgTbl"),
                                     cache: false
                                 });
                         } else {
                             // do a full page refresh to update hgTracks image
                             jQuery('body').css('cursor', 'wait');
                             var ele;
                             if (document.TrackForm)
                                 ele = document.TrackForm;
                             else
                                 ele = document.TrackHeaderForm;
                             if (name)
                                 cart.addVarsToQueue(['hgFind.matches'], [name]);
                             ele.submit();
                         }
                     }
                 }
         } else if (cmd === 'zoomCodon' || cmd === 'zoomExon') {
             var num, ajaxCmd, msg;
             if (cmd === 'zoomCodon') {
                 msg = "Please enter the codon number to jump to:";
                 ajaxCmd = 'codonToPos';
             } else {
                 msg = "Please enter the exon number to jump to:";
                 ajaxCmd = 'exonToPos';
             }
             rightClick.myPrompt(msg, function(results) {
                 $.ajax({
                         type: "GET",
                         url: "../cgi-bin/hgApi",
                         data: cart.varsToUrlData({ 'db': getDb(), 'cmd': ajaxCmd, 'num': results,
                               'table': args.table, 'name': args.name }),
                         trueSuccess: rightClick.handleZoomCodon,
                         success: catchErrorOrDispatch,
                         error: errorHandler,
                         cache: true
                     });
                     });
         } else if (cmd === 'hgTrackUi_popup') {
 
             // Launches the popup but shields the ajax with a waitOnFunction
             popUp.hgTrackUi( rightClick.selectedMenuItem.id, false );  
 
         } else if (cmd === 'hgTrackUi_follow') {
 
             url = "hgTrackUi?hgsid=" + getHgsid() + "&g=";
             rec = hgTracks.trackDb[id];
             if (tdbHasParent(rec) && tdbIsLeaf(rec))
                 url += rec.parentTrack;
             else {
                 // The button already has the ref
                 var link = normed($( 'td#td_btn_'+ rightClick.selectedMenuItem.id ).children('a')); 
                 if (link)
                     url = $(link).attr('href');
                 else
                     url += rightClick.selectedMenuItem.id;
             }
             location.assign(url);
 
         } else if (cmd === 'viewImg') {
             // Fetch a new copy of track img and show it to the user in another window. This code
             // assume we have updated remote cart with all relevant chages (e.g. drag-reorder).
             jQuery('body').css('cursor', 'wait');
             $.ajax({
                     type: "GET",
                     url: "../cgi-bin/hgTracks",
                     data: cart.varsToUrlData({ 'hgt.imageV1': '1','hgt.trackImgOnly': '1', 
                                                'hgsid': getHgsid() }),
                     dataType: "html",
                     trueSuccess: rightClick.handleViewImg,
                     success: catchErrorOrDispatch,
                     error: errorHandler,
                     cmd: cmd,
                     cache: false
                 });
         } else if (cmd === 'openLink' || cmd === 'followLink') {
             href = rightClick.selectedMenuItem.href;
             var vars = new Array("c", "l", "r", "db");
             var valNames = new Array("chromName", "winStart", "winEnd");
             for (var i in vars) {
                 // make sure the link contains chrom and window width info
                 // (necessary b/c we are stripping hgsid and/or the cart may be empty);
                 // but don't add chrom to wikiTrack links (see redmine #2476).
                 var v = vars[i];
                 var val;
                 if (v === "db") {
                     val = getDb();
                 } else {
                     val = hgTracks[valNames[i]];
                 }
                 if (val
                 && id !== "wikiTrack"
                 && (href.indexOf("?" + v + "=") === -1)
                 && (href.indexOf("&" + v + "=") === -1)) {
                     href = href + "&" + v + "=" + val;
                 }
             }
             if (cmd === 'followLink') {
                 // XXXX This is blocked by Safari's popup blocker (without any warning message).
                 location.assign(href);
             } else {
                 // Remove hgsid to force a new session (see redmine ticket 1333).
                 href = removeHgsid(href);
                 if ( ! window.open(href) ) {
                     rightClick.windowOpenFailedMsg();
                 }
             }
         } else if (cmd === 'float') {
             if (rightClick.floatingMenuItem && rightClick.floatingMenuItem === id) {
                 $.floatMgr.FOArray = [];
                 rightClick.floatingMenuItem = null;
             } else {
                 if (rightClick.floatingMenuItem) {
                     // This doesn't work.
                     $('#img_data_' + rightClick.floatingMenuItem).parent().restartFloat();
                     // This does work
                     $.floatMgr.FOArray = [];
                 }
                 rightClick.floatingMenuItem = id;
                 rightClick.reloadFloatingItem();
                 imageV2.requestImgUpdate(id, "hgt.transparentImage=0", "");
             }
         } else if (cmd === 'hideSet') {
             row = $( 'tr#tr_' + id );
             rows = dragReorder.getContiguousRowSet(row);
             if (rows && rows.length > 0) {
                 var varsToUpdate = {};
                 // from bottom up, just in case remove screws with us
                 for (var ix=rows.length - 1; ix >= 0; ix--) { 
                     var rowId = $(rows[ix]).attr('id').substring('tr_'.length);
                     // Remove subtrack level vis and explicitly uncheck.
                     varsToUpdate[rowId]        = '[]';
                     varsToUpdate[rowId+'_sel'] = 0;
                     $(rows[ix]).remove();
                 }
                 if (objNotEmpty(varsToUpdate)) {
                     cart.setVarsObj(varsToUpdate);
                 }
                 imageV2.afterImgChange(true);
             }
         } else if (cmd === 'hideComposite') {
             rec = hgTracks.trackDb[id];
             if (tdbIsSubtrack(rec)) {
                 row = $( 'tr#tr_' + id );
                 rows = dragReorder.getCompositeSet(row);
                 // from bottom up, just in case remove screws with us
                 if (rows && rows.length > 0) {
                     for (var rIx=rows.length - 1; rIx >= 0; rIx--) {
                         $(rows[rIx]).remove();
                     }
                 selectUpdated = vis.update(rec.parentTrack, 'hide');
                 cart.setVars( [rec.parentTrack], ['hide']);
                 imageV2.afterImgChange(true);
                 }
             }
         } else if (cmd === 'jumpToHighlight') { // If highlight exists for this assembly, jump to it
             if (hgTracks.highlight) {
                 var newPos = parsePositionWithDb(hgTracks.highlight);
                 if (newPos && newPos.db === getDb()) {
                     if ( $('#highlightItem').length === 0) { // not visible? jump to it
                         var curPos = parsePosition(genomePos.get());
                         var diff = ((curPos.end - curPos.start) - (newPos.end - newPos.start));
                         if (diff > 0) { // new position is smaller then current, then center it
                             newPos.start = Math.max( Math.floor(newPos.start - (diff/2) ), 0 );
                             newPos.end   = newPos.start + (curPos.end - curPos.start);
                         }
                     }
                     if (imageV2.inPlaceUpdate) {
                         var params = "position=" + newPos.chrom+':'+newPos.start+'-'+newPos.end;
                         imageV2.navigateInPlace(params, null, true);
                     } else {
                         genomePos.setByCoordinates(newPos.chrom, newPos.start, newPos.end);
                         jQuery('body').css('cursor', 'wait');
                         document.TrackHeaderForm.submit();
                     }
                 }
             }
         } else if (cmd === 'removeHighlight') {
             hgTracks.highlight = null;
             cart.setVarsObj({ 'highlight': '[]' });
             imageV2.highlightRegion();
         } else {   // if ( cmd in 'hide','dense','squish','pack','full','show' )
             // Change visibility settings:
             //
             // First change the select on our form:
             rec = hgTracks.trackDb[id];
             selectUpdated = vis.update(id, cmd);
 
             // Now change the track image
             if (imageV2.enabled && cmd === 'hide') {
                 // Hide local display of this track and update server side cart.
                 // Subtracks controlled by 2 settings so del vis and set sel=0.
                 if (tdbIsSubtrack(rec)) {
                     // Remove subtrack level vis and explicitly uncheck.
                     cart.setVars( [ id, id+"_sel" ], [ '[]', 0 ] ); 
                 } else if (tdbIsFolderContent(rec)) {
                     // supertrack children need to have _sel set to trigger superttrack reshaping
                     cart.setVars( [ id, id+"_sel" ], [ 'hide', 0 ] ); 
                 } else {
                     cart.setVars([id], ['hide']);  // Others, just set vis hide.
                 }
                 $(document.getElementById('tr_' + id)).remove();
                 imageV2.afterImgChange(true);
             } else if (!imageV2.mapIsUpdateable) {
                 jQuery('body').css('cursor', 'wait');
                 if (selectUpdated) {
                     // assert(document.TrackForm);
                     document.TrackForm.submit();
                 } else {
                         // Add vis update to queue then submit
                         cart.addVarsToQueue([id], [cmd]);
                         document.TrackHeaderForm.submit();
                 }
             } else {
                 imageV2.requestImgUpdate(id, id + "=" + cmd, "", cmd);
             }
         }
     },
 
     makeHitCallback: function (title)
     {   // stub to avoid problem with a function closure w/n a loop
         return function(menuItemClicked, menuObject) {
             rightClick.hit(menuItemClicked, menuObject, title); return true;
         };
     },
 
     reloadFloatingItem: function ()
     {   // currently dead (experimental code)
         if (rightClick.floatingMenuItem) {
             $('#img_data_' + rightClick.floatingMenuItem).parent().makeFloat(
                 {x:"current",y:"current", speed: 'fast', alwaysVisible: true, alwaysTop: true});
         }
     },
 
     makeImgTag: function (img)
     {   // Return img tag with explicit dimensions for img (dimensions are currently hardwired).
         // This fixes the "weird shadow problem when first loading the right-click menu"
         // seen in FireFox 3.X, which occurred b/c FF doesn't actually fetch the image until
         // the menu is being shown.
         return "<img style='width:16px; height:16px; border-style:none;' src='../images/" +
                 img + "' />";
     },
 
 
     load: function (img)
     {
         rightClick.menu = img.contextMenu(function() {
             popUp.cleanup();   // Popup box is not getting closed properly so must do it here
             if ( ! rightClick.selectedMenuItem )  // This is literally an edge case so ignore
                 return;
 
             var o; // TODO: Break this giant routine with shared vars into some sub-functions
             var str;
             var rec = null;
             var menu = [];
             var selectedImg = rightClick.makeImgTag("greenChecksm.png");
             var blankImg    = rightClick.makeImgTag("invisible16.png");
             var done = false;
             if (rightClick.selectedMenuItem && rightClick.selectedMenuItem.id) {
                 var href = rightClick.selectedMenuItem.href;
                 var isHgc, isGene;
                 if (href) {
                     isGene = href.match("hgGene");
                     isHgc = href.match("hgc");
                 }
                 var id = rightClick.selectedMenuItem.id;
                 rec = hgTracks.trackDb[id];
                 var offerHideSubset    = false;
                 var offerHideComposite = false;
                 var offerSingles       = true;
                 var row = $( 'tr#tr_' + id );
                 if (row) {
                     var btn = $(row).find('p.btnBlue'); // btnBlue means cursor over left button
                     if (btn.length === 1) {
                         var compositeSet = dragReorder.getCompositeSet(row);
                         if (compositeSet && compositeSet.length > 0) {  // There is composite set
                             offerHideComposite = true;
                             $( compositeSet ).find('p.btn').addClass('blueButtons');// blue persists
 
                             var subSet = dragReorder.getContiguousRowSet(row);
                             if (subSet && subSet.length > 1) {
                                 offerSingles = false;
                                 if (subSet.length < compositeSet.length) {
                                     offerHideSubset = true;
                                     $( subSet ).addClass("greenRows"); // green persists
                                 }
                             }
                         }
                     }
                 }
 
                 // First option is hide sets
                 if (offerHideComposite) {
                     if (offerHideSubset) {
                         o = {};
                         o[blankImg + " hide track subset (green)"] = {
                                             onclick: rightClick.makeHitCallback('hideSet')};
                         menu.push(o);
                     }
 
                     o = {};
                     str = blankImg + " hide track set";
                     if (offerHideSubset)
                         str += " (blue)";
                     o[str] = {onclick: rightClick.makeHitCallback('hideComposite')};
                     menu.push(o);
                 }
 
                 // Second set of options: visibility for single track
                 if (offerSingles) {
                     if (offerHideComposite)
                         menu.push($.contextMenu.separator);
 
                     // XXXX what if select is not available (b/c trackControlsOnMain is off)?
                     // Move functionality to a hidden variable?
                     var select = $("select[name=" + escapeJQuerySelectorChars(id) + "]");
                     if (select.length > 1)  
                         // Not really needed if $('#hgTrackUiDialog').html(""); has worked
                         select =  [ $(select)[0] ];
                     var cur = $(select).val();
                     if (cur) {
                         $(select).children().each(function(index, o) {
                             var title = $(this).val();
                             str = blankImg + " " + title;
                             if (title === cur)
                                 str = selectedImg + " " + title;
                             o = {};
                             o[str] = {onclick: function (menuItemClicked, menuObject) {
                                         rightClick.hit(menuItemClicked, menuObject, title);
                                         return true;}};
                             menu.push(o);
                         });
                         done = true;
                     } else {
                         if (rec) {
                             // XXXX check current state from a hidden variable.
                             var visStrings = new Array("hide","dense","squish","pack","full");
                             for (var i in visStrings) {
                                 // use maxVisibility and change hgTracks so it can hide subtracks
                                 o = {};
                                 str = blankImg + " " + visStrings[i];
                                 if (rec.canPack
                                 || (visStrings[i] !== "pack" && visStrings[i] !== "squish")) {
                                     if (rec.localVisibility) {
                                         if (visStrings[i] === rec.localVisibility) {
                                             str = selectedImg + " " + visStrings[i];
                                         }
                                     } else if (visStrings[i] === vis.enumOrder[rec.visibility]) {
                                         str = selectedImg + " " + visStrings[i];
                                     }
                                     o[str] = { onclick:
                                                 rightClick.makeHitCallback(visStrings[i])
                                              };
                                     menu.push(o);
                                 }
                             }
                             done = true;
                         }
                     }
                 }
 
                 if (done) {
                     o = {};
                     var any = false;
                     var title = rightClick.selectedMenuItem.title || "feature";
                     var maxLength = 60;
                     if (title.length > maxLength) {
                         title = title.substring(0, maxLength) + "...";
                     }
                     if (isGene || isHgc || id === "wikiTrack") {
                         // Add "Open details..." item
                         var displayItemFunctions = false;
                         if (rec) {
                             if (rec.type.indexOf("wig") === 0
                             ||  rec.type.indexOf("bigWig") === 0
                             ||  id === "wikiTrack") {
                                 displayItemFunctions = false;
                             } else if (rec.type.indexOf("expRatio") === 0) {
                                 displayItemFunctions = title !== "zoomInMore";
                             } else {
                                 displayItemFunctions = true;
                             }
                         }
                         if (isHgc && href.indexOf('g=gtexGene') !== -1) {
                             // For GTEx gene mouseovers, replace title (which may be a tissue name) with 
                             // item (gene) name
                             a = /i=([^&]+)/.exec(href);
                             if (a && a[1]) {
                                 title = a[1];
                             }
                         }
                         if (displayItemFunctions) {
                             o[rightClick.makeImgTag("magnify.png") + " Zoom to " +  title] = {
                                 onclick: function(menuItemClicked, menuObject) {
                                             rightClick.hit(menuItemClicked, menuObject,
                                                     "selectWholeGene"); return true;
                                           }
                                 };
                             o[rightClick.makeImgTag("highlight.png") + " Highlight " + title] = 
                                 {   onclick: function(menuItemClicked, menuObject) {
                                         rightClick.hit(menuItemClicked, menuObject,
                                                        "highlightItem"); 
                                         return true;
                                     }
                                 };
                             if (rightClick.supportZoomCodon && rec.type.indexOf("genePred") !== -1) {
                                 // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc003tqk.2&hgg_prot=P00533&hgg_chrom=chr7&hgg_start=55086724&hgg_end=55275030&hgg_type=knownGene&db=hg19&c=chr7
                                 var name, table;
                                 var reg = new RegExp("hgg_gene=([^&]+)");
                                 var a = reg.exec(href);
                                 if (a && a[1]) {
                                     name = a[1];
                                     reg = new RegExp("hgg_type=([^&]+)");
                                     a = reg.exec(href);
                                     if (a && a[1]) {
                                         table = a[1];
                                     }
                                 } else {
                                     // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgc?o=55086724&t=55275031&g=refGene&i=NM_005228&c=chr7
                                     // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgc?o=55086713&t=55270769&g=wgEncodeGencodeManualV4&i=ENST00000455089&c=chr7
                                     reg = new RegExp("i=([^&]+)");
                                     a = reg.exec(href);
                                     if (a && a[1]) {
                                         name = a[1];
                                         reg = new RegExp("g=([^&]+)");
                                         a = reg.exec(href);
                                         if (a && a[1]) {
                                             table = a[1];
                                         }
                                     }
                                 }
                                 if (name && table) {
                                     o[rightClick.makeImgTag("magnify.png")+" Zoom to codon"] =
                                     {   onclick: function(menuItemClicked, menuObject) {
                                             rightClick.hit(menuItemClicked, menuObject,
                                                         "zoomCodon",
                                                         {name: name, table: table});
                                             return true;}
                                     };
                                     o[rightClick.makeImgTag("magnify.png")+" Zoom to exon"] = {
                                         onclick: function(menuItemClicked, menuObject) {
                                             rightClick.hit(menuItemClicked, menuObject,
                                                           "zoomExon",
                                                           {name: name, table: table});
                                             return true; }
                                     };
                                 }
                             }
                             o[rightClick.makeImgTag("dnaIcon.png")+" Get DNA for "+title] = {
                                 onclick: function(menuItemClicked, menuObject) {
                                     rightClick.hit(menuItemClicked, menuObject, "getDna");
                                     return true; }
                             };
                         }
                         o[rightClick.makeImgTag("bookOut.png")+
                                                 " Open details page in new window..."] = {
                             onclick: function(menuItemClicked, menuObject) {
                                 rightClick.hit(menuItemClicked, menuObject, "openLink");
                                 return true; }
                         };
                         any = true;
                     }
                     if (href && href.length  > 0) {
                         // Add "Show details..." item
                         if (title.indexOf("Click to alter ") === 0) {
                             // suppress the "Click to alter..." items
                         } else if (rightClick.selectedMenuItem.href.indexOf("cgi-bin/hgTracks")
                                                                                         !== -1) {
                             // suppress menu items for hgTracks links (e.g. Next/Prev map items).
                         } else {
                             var item;
                             if (title === "zoomInMore")
                                 // avoid showing menu item that says
                                 // "Show details for zoomInMore..." (redmine 2447)
                                 item = rightClick.makeImgTag("book.png") + " Show details...";
                             else
                                 item = rightClick.makeImgTag("book.png")+" Show details for "+
                                        title + "...";
                             o[item] = {onclick: function(menuItemClicked, menuObject) {
                                        rightClick.hit(menuItemClicked,menuObject,"followLink");
                                        return true; }
                             };
                             any = true;
                         }
                     }
                     if (any) {
                         menu.push($.contextMenu.separator);
                         menu.push(o);
                     }
                 }
             }
 
             if (rightClick.selectedMenuItem && rec) {
                 // Add cfg options at just shy of end...
                 o = {};
                 if (tdbIsLeaf(rec)) {
 
                     if (rec.configureBy !== 'none'
                     && (!tdbIsCompositeSubtrack(rec) || rec.configureBy !== 'clickThrough')) {
                         // Note that subtracks never do clickThrough because
                         // parentTrack cfg is the desired clickThrough
                         o[rightClick.makeImgTag("wrench.png")+" Configure "+rec.shortLabel] = {
                             onclick: function(menuItemClicked, menuObject) {
                                 rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_popup");
                                 return true; }
                         };
                     }
                     if (rec.parentTrack) {
                         o[rightClick.makeImgTag("folderWrench.png")+" Configure "+
                           rec.parentLabel + " track set..."] = {
                             onclick: function(menuItemClicked, menuObject) {
                                 rightClick.hit(menuItemClicked,menuObject,"hgTrackUi_follow");
                                 return true; }
                           };
                     }
                 } else {
 
                     o[rightClick.makeImgTag("folderWrench.png")+" Configure "+rec.shortLabel +
                       " track set..."] = {
                         onclick: function(menuItemClicked, menuObject) {
                             rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_follow");
                             return true; }
                       };
                 }
                 if (jQuery.floatMgr) {
                     o[(rightClick.selectedMenuItem.id === rightClick.floatingMenuItem ?
                             selectedImg : blankImg) + " float"] = {
                         onclick: function(menuItemClicked, menuObject) {
                             rightClick.hit(menuItemClicked, menuObject, "float");
                             return true; }
                     };
                 }
                 menu.push($.contextMenu.separator);
                 menu.push(o);
             }
 
             menu.push($.contextMenu.separator);
             if (hgTracks.highlight) {
                 if (hgTracks.highlight.search(getDb() + '.') === 0) {
                     var currentlySeen = ($('#highlightItem').length > 0); 
                     o = {};
                     // Jumps to highlight when not currently seen in image
                     var text = (currentlySeen ? " Zoom" : " Jump") + " to highlighted region";
                     o[rightClick.makeImgTag("highlightZoom.png") + text] = {
                         onclick: rightClick.makeHitCallback('jumpToHighlight')
                     };
 
                     if ( currentlySeen ) {   // Remove only when seen
                         o[rightClick.makeImgTag("highlightRemove.png") + 
                                                                    " Remove highlighting"] = {
                             onclick: rightClick.makeHitCallback('removeHighlight')
                         };
                     }
                     menu.push(o);
                 }
             }
             // Add view image at end
             o = {};
             o[rightClick.makeImgTag("eye.png") + " View image"] = {
                 onclick: function(menuItemClicked, menuObject) {
                     rightClick.hit(menuItemClicked, menuObject, "viewImg");
                     return true; }
             };
             menu.push(o);
 
             return menu;
         },
         {
             beforeShow: function(e) {
                 // console.log(mapItems[rightClick.selectedMenuItem]);
                 rightClick.selectedMenuItem = rightClick.findMapItem(e);
                 // XXXX? posting.blockUseMap = true;
                 return true;
             },
             hideTransition:'hide', // hideCallback fails if these are not defined.
             hideSpeed:10,
             hideCallback: function() {
                 $('p.btn.blueButtons').removeClass('blueButtons');
                 $('tr.trDraggable.greenRows').removeClass('greenRows');
             }
         });
         return;
     }
 };
 
   //////////////////////////////////
  //// external tools           ////
 //////////////////////////////////
 
 function showExtToolDialog() {
         /* show the 'send to external tool' dialog */
         // information about external tools is stored in the extTools global list
         // defined by a <script> at the end of the body
 
         // remove an existing dialog box
         var extToolDialog = $("#extToolDialog").remove();
 
         // construct the contents
         var htmlLines = ["<ul class='indent'>"];
         var winSize = hgTracks.winEnd - hgTracks.winStart;
         for (i = 0; i < extTools.length; i++) {
             var tool = extTools[i];
             var toolId = tool[0];
             var shortLabel = tool[1];
             var longLabel = tool[2];
             var maxSize = tool[3];
             if ((maxSize===0) || (winSize < maxSize))
                 {
                 var url = "hgTracks?hgsid="+getHgsid()+"&hgt.redirectTool="+toolId;
-                var onclick = "$('#extToolDialog').dialog('close');";
-                htmlLines.push("<li><a onclick="+'"'+onclick+'"'+"id='extToolLink' target='_BLANK' href='"+url+"'>"+shortLabel+"</a>: <small>"+longLabel+"</small></li>");
+                //var onclick = "$('#extToolDialog').dialog('close');";
+                //htmlLines.push("<li><a onclick="+'"'+onclick+'"'+"id='extToolLink' target='_BLANK' href='"+url+"'>"+shortLabel+"</a>: <small>"+longLabel+"</small></li>");
+		// onclick js code moved to jsInline
+                htmlLines.push("<li><a class='extToolLink2' target='_BLANK' href='"+url+"'>"+shortLabel+"</a>: <small>"+longLabel+"</small></li>");
                 }
             else
                 {
                 note = "<br><b>Needs zoom to &lt; "+maxSize/1000+" kbp.</b></small></span></li>";
                 htmlLines.push('<li><span style="color:grey">'+shortLabel+": <small>"+longLabel+note);
                 }
         }
         htmlLines.push("</ul>");
         content = htmlLines.join("");
             
         var title = hgTracks.chromName + ":" + (hgTracks.winStart+1) + "-" + hgTracks.winEnd;
         if (hgTracks.nonVirtPosition)
             title = hgTracks.nonVirtPosition;
         title += " on another website";
         $("body").append("<div id='extToolDialog' title='"+title+"'><p>" + content + "</p>");
 
+	// GALT 
+	$('a.extToolLink2').click(function(){$('#extToolDialog').dialog('close');});
+
         // copied from the hgTrackUi function below
         var popMaxHeight = ($(window).height() - 40);
         var popMaxWidth  = ($(window).width() - 40);
         var popWidth     = 600;
         if (popWidth > popMaxWidth)
             popWidth = popMaxWidth;
 
         // also copied from the hgTrackUi code below
         $('#extToolDialog').dialog({
             resizable: true,               // Let description scroll vertically
             height: popMaxHeight,
             width: popWidth,
             minHeight: 200,
             minWidth: 600,
             maxHeight: popMaxHeight,
             maxWidth: popMaxWidth,
             modal: true,
             closeOnEscape: true,
             autoOpen: false,
             buttons: { "Close": function() {
                     $(this).dialog("close");
             }},
         });
         
         $('#extToolDialog').dialog('open');
 }
 
   /////////////////////////////////////////////////////////
  //// popupHgt popup for hgTracks  (aka modal dialog) ////
 /////////////////////////////////////////////////////////
 var popUpHgt = {
 
     whichHgTracksMethod: "",
     title: "",
 
     cleanup: function ()
     {  // Clean out the popup box on close
         if ($('#hgTracksDialog').html().length > 0 ) {
             // clear out html after close to prevent problems caused by duplicate html elements
             $('#hgTracksDialog').html("");
             popUpHgt.whichHgTracksMethod = "";
             popUpHgt.title = "";
         }
     },
 
     _uiDialogRequest: function (whichHgTracksMethod)
     { // popup cfg dialog
         popUpHgt.whichHgTracksMethod = whichHgTracksMethod;
         var myLink = "../cgi-bin/hgTracks?hgsid=" + getHgsid() + "&db=" + getDb();
         if (popUpHgt.whichHgTracksMethod === "multi-region config") {
             myLink += "&hgTracksConfigMultiRegionPage=multi-region";
             popUpHgt.title = "Configure Multi-Region View";
         }
 
         $.ajax({
                     type: "GET",
                     url: cart.addUpdatesToUrl(myLink),
                     dataType: "html",
                     trueSuccess: popUpHgt.uiDialog,
                     success: catchErrorOrDispatch,
                     error: errorHandler,
                     cache: false
                 });
     },
 
     hgTracks: function (whichHgTracksMethod)
     {   // Launches the popup but shields the ajax with a waitOnFunction
         waitOnFunction( popUpHgt._uiDialogRequest, whichHgTracksMethod);
     },
 
     uiDialogOk: function (popObj)
-    {   // When hgTracks Cfg popup closes with ok, then update cart and refresh parts of page
+    {   // When popup closes with ok
 
     },
 
     uiDialog: function (response, status)
     {
     // Take html from hgTracks and put it up as a modal dialog.
 
         // make sure all links (e.g. help links) open up in a new window
         response = response.replace(/<a /ig, "<a target='_blank' ");
 
         var cleanHtml = response;
+        cleanHtml = stripCspHeader(cleanHtml,false); // DEBUG msg with true
         cleanHtml = stripJsFiles(cleanHtml,false);   // DEBUG msg with true
         cleanHtml = stripCssFiles(cleanHtml,false);  // DEBUG msg with true
         cleanHtml = stripJsEmbedded(cleanHtml,false);// DEBUG msg with true
         cleanHtml = stripMainMenu(cleanHtml,false);  // DEBUG msg with true
 
         $('#hgTracksDialog').html("<div id='pop' style='font-size:.9em;'>"+ cleanHtml +"</div>");
 
+
         // Strategy for popups with js:
         // - jsFiles and CSS should not be included in html.  Here they are shluped out.
         // - The resulting files ought to be loadable dynamically (with getScript()), 
         //   but this was not working nicely with the modal dialog
         //   Therefore include files must be included with hgTracks CGI !
         // - embedded js should not be in the popup box.
         // - Somethings should be in a popup.ready() function, and this is emulated below, 
         //   as soon as the cleanHtml is added
         //   Since there are many possible popup cfg dialogs, the ready should be all inclusive.
 
         // -- popup.ready() -- Here is the place to do things that might otherwise go
         //                     into a $('#pop').ready() routine!
 
         // Searching for some semblance of size suitability
         var popMaxHeight = ($(window).height() - 40);
         var popMaxWidth  = ($(window).width() - 40);
         var popWidth     = 700;
         if (popWidth > popMaxWidth)
             popWidth = popMaxWidth;
 
         $('#hgTracksDialog').dialog({
             ajaxOptions: {
                 // This doesn't work
                 cache: true
             },
             resizable: true,               // Let scroll vertically
             height: 'auto',
             width: popWidth,
             minHeight: 200,
             minWidth: 400,
             maxHeight: popMaxHeight,
             maxWidth: popMaxWidth,
             modal: true,
             closeOnEscape: true,
             autoOpen: false,
             buttons: { 
                 /* NOT NOW
                 "OK": function() {
                     popUpHgt.uiDialogOk($('#pop'));
                     $(this).dialog("close");
                 }
                 */
             },
             // popup.ready() doesn't seem to work in open.
 
             //create: function () { 
                 //$(this).siblings().find(".ui-dialog-title").html('<span style="">Test </span>'); 
                 //$(this).siblings().find(".ui-dialog-title").html('<span style="       visibility: hidden;"></span>'); 
             //},
             
             open: function () {
                 $('#hgTracksDialog').find('.filterBy,.filterComp').each(
                     function(i) {  // ddcl.js is dropdown checklist lib support
                         if ($(this).hasClass('filterComp'))
                             ddcl.setup(this);
                         else
                             ddcl.setup(this, 'noneIsAll');
                     }
                 );
             },
 
             close: function() {
                 popUpHgt.cleanup();
             }
         });
         
     
         $('#hgTracksDialog').dialog('option' , 'title' , popUpHgt.title);
         $('#hgTracksDialog').dialog('open');
     
     }
 };
 
 // A function to show the keyboard help dialog box, bound to ? and called from the menu bar
 function showHotkeyHelp() {
     $("#hotkeyHelp").dialog({width:'600'});
 }
 
 // A function to add an entry for the keyboard help dialog box to the menubar 
 // and add text that indicates the shortcuts to many static menubar items as suggested by good old IBM CUA/SAA
 function addKeyboardHelpEntries() {
-    var html = '<li><a title="List all possible keyboard shortcuts" href="javascript:showHotkeyHelp()">Keyboard Shortcuts</a><span class="shortcut">?</span></li>';
+    var html = '<li><a id="keybShorts" title="List all possible keyboard shortcuts" href="#">Keyboard Shortcuts</a><span class="shortcut">?</span></li>';
     $('#help .last').before(html);
+    $("#keybShorts").onclick = function(){showHotKeyHelp(); return false;};
 
     html = '<span class="shortcut">s s</span>';
     $('#sessionsMenuLink').after(html);
 
     html = '<span class="shortcut">p s</span>';
     $('#publicSessionsMenuLink').after(html);
 
     html = '<span class="shortcut">c t</span>';
     $('#customTracksMenuLink').after(html);
 
     html = '<span class="shortcut">t h</span>';
     $('#trackHubsMenuLink').after(html);
 
     html = '<span class="shortcut">t b</span>';
     $('#blatMenuLink').after(html);
 
     html = '<span class="shortcut">t t</span>';
     $('#tableBrowserMenuLink').after(html);
 
     html = '<span class="shortcut">t i</span>';
     $('#ispMenuLink').after(html);
 
     html = '<span class="shortcut">t s</span>';
     $('#trackSearchMenuLink').after(html);
 
     html = '<span class="shortcut">c f</span>';
     $('#configureMenuLink').after(html);
 
     html = '<span class="shortcut">c r</span>';
     $('#cartResetMenuLink').after(html);
 }
 
 // A function for the keyboard shortcut:
 // View DNA
 function gotoGetDnaPage() {
     var position = hgTracks.chromName+":"+hgTracks.winStart+"-"+hgTracks.winEnd;
     if (hgTracks.virtualSingleChrom && (pos.chrom.search("virt") === 0)) {
         position = genomePos.get().replace(/,/g,'');
     } else if (hgTracks.windows && hgTracks.nonVirtPosition) {
         position = hgTracks.nonVirtPosition;
     }
     var pos = parsePosition(position);
     if (pos) {
         var url = "hgc?hgsid="+getHgsid()+"&g=getDna&i=mixed&c="+pos.chrom+"&l="+pos.start+"&r="+pos.end+"&db="+getDb();
         window.location.href = url;
     }
     return false;
 }
 
 // A function for the keyboard shortcuts "zoom to x bp"
 function zoomTo(zoomSize) {
     var flankSize = Math.floor(zoomSize/2);
     var pos = parsePosition(genomePos.get());
     var mid = pos.start+(Math.floor((pos.end-pos.start)/2));
     var newStart = Math.max(mid - flankSize, 0);
     var newEnd = mid + flankSize - 1;
     var newPos = genomePos.setByCoordinates(pos.chrom, newStart, newEnd);
     if (hgTracks.virtualSingleChrom && (newPos.search("virt:")===0))
         newPos = genomePos.disguisePosition(newPosition); // DISGUISE?
     imageV2.navigateInPlace("position="+newPos, null, true);
 }
 
   //////////////////////////////////
  //// popup (aka modal dialog) ////
 //////////////////////////////////
 var popUp = {
 
     trackName:            "",
     trackDescriptionOnly: false,
     saveAllVars:          null,
 
     cleanup: function ()
     {  // Clean out the popup box on close
         if ($('#hgTrackUiDialog').html().length > 0 ) {
             // clear out html after close to prevent problems caused by duplicate html elements
             $('#hgTrackUiDialog').html("");
             popUp.trackName = ""; //set to defaults
             popUp.trackDescriptionOnly = false;
             popUp.saveAllVars = null;
         }
     },
 
     _uiDialogRequest: function (trackName,descriptionOnly)
     { // popup cfg dialog
         popUp.trackName = trackName;
         var myLink = "../cgi-bin/hgTrackUi?g=" + trackName + "&hgsid=" + getHgsid() +
                      "&db=" + getDb();
         popUp.trackDescriptionOnly = descriptionOnly;
         if (popUp.trackDescriptionOnly)
             myLink += "&descriptionOnly=1";
 
         var rec = hgTracks.trackDb[trackName];
         if (!descriptionOnly && rec && rec.configureBy) {
             if (rec.configureBy === 'none')
                 return;
             else if (rec.configureBy === 'clickThrough') {
                 jQuery('body').css('cursor', 'wait');
                 window.location = cart.addUpdatesToUrl(myLink);
                 return;
             }  // default falls through to configureBy popup
         }
         myLink += "&ajax=1";
         $.ajax({
                     type: "GET",
                     url: cart.addUpdatesToUrl(myLink),
                     dataType: "html",
                     trueSuccess: popUp.uiDialog,
                     success: catchErrorOrDispatch,
                     error: errorHandler,
                     cmd: rightClick.selectedMenuItem,
                     cache: false
                 });
     },
 
     hgTrackUi: function (trackName,descriptionOnly)
     {   // Launches the popup but shields the ajax with a waitOnFunction
         waitOnFunction( popUp._uiDialogRequest, trackName, descriptionOnly );  
     },
 
     uiDialogOk: function (popObj, trackName)
     {   // When hgTrackUi Cfg popup closes with ok, then update cart and refresh parts of page
         var rec = hgTracks.trackDb[trackName];
         var subtrack = tdbIsSubtrack(rec) ? trackName : undefined;  // subtrack vis rules differ
         // For unknown reasons IE8 fails to find $('#pop'), occasionally
         var allVars = getAllVars($('#hgTrackUiDialog'), subtrack );
         //  Since 2010, when Tim changed this to only report changed vars instead of all form vars,
         // it no longer matches the behavior of hgTrackUi when called the non-popup way.
         // A few places in the hgTracks C code have been patched to explicitly set the cart vars
         // for some default checkboxes. So now this still means that QA must explicitly test
         // both paths through the code: as a separate full hgTracksUi page, and as a popup config window.
         // hgTrackUi always sends in its form all variables causing them to be explicitly set in the cart.  
         // The popup only sends things that have changed, causing those changes to appear explicitly
         // and even then it skips over disabled form items.
         // There is some C code that was written before the popup config, 
         // and it expects all the variables are set or none are.
         // If just some are set, and not the default ones, it gets confused.
         // I fixed just such a bug in the code that handles refSeq.
         // See commit daf92c0f9eb331ea60740e6802aabd241d4be363.
         var changedVars = varHashChanges(allVars,popUp.saveAllVars);
          // DEBUG Examples:
         //debugDumpFormCollection("saveAllVars", popUp.saveAllVars);
         //debugDumpFormCollection("allVars", allVars);
         //debugDumpFormCollection("changedVars", changedVars);
         var newVis = changedVars[trackName];
         // subtracks do not have "hide", thus '[]'
         var hide = (newVis && (newVis === 'hide' || newVis === '[]'));  
         if ( ! normed($('#imgTbl')) ) { // On findTracks or config page
             if (objNotEmpty(changedVars))
                 cart.setVarsObj(changedVars);
         }
         else {  // On image page
             if (hide) {
                 if (objNotEmpty(changedVars))
                     cart.setVarsObj(changedVars);
                 $(document.getElementById('tr_' + trackName)).remove();
                 imageV2.afterImgChange(true);
             } else {
                 // Keep local state in sync if user changed visibility
                 if (newVis) {
                     vis.update(trackName, newVis);
                 }
                 if (objNotEmpty(changedVars)) {
                     var urlData = cart.varsToUrlData(changedVars);
                     if (imageV2.mapIsUpdateable) {
                         imageV2.requestImgUpdate(trackName,urlData,"");
                     } else {
                         window.location = "../cgi-bin/hgTracks?" + urlData + "&hgsid=" + getHgsid();
                     }
                 }
             }
         }
     },
 
     uiDialog: function (response, status)
     {
     // Take html from hgTrackUi and put it up as a modal dialog.
 
+	//alert("Got here popUp.uiDialog"); // DEBUG REMOVE GALT
+
         // make sure all links (e.g. help links) open up in a new window
         response = response.replace(/<a /ig, "<a target='_blank' ");
 
         var cleanHtml = response;
-        cleanHtml = stripJsFiles(cleanHtml,true);   // DEBUG msg with true
-        cleanHtml = stripCssFiles(cleanHtml,true);  // DEBUG msg with true
-        cleanHtml = stripJsEmbedded(cleanHtml,true);// DEBUG msg with true
+        cleanHtml = stripJsFiles(cleanHtml,false);   // DEBUG msg with true
+        cleanHtml = stripCssFiles(cleanHtml,false);  // DEBUG msg with true
+        cleanHtml = stripJsEmbedded(cleanHtml,false);// DEBUG msg with true
+	//alert(cleanHtml);  // DEBUG REMOVE
         $('#hgTrackUiDialog').html("<div id='pop' style='font-size:.9em;'>"+ cleanHtml +"</div>");
 
         // Strategy for popups with js:
         // - jsFiles and CSS should not be included in html.  Here they are shluped out.
         // - The resulting files ought to be loadable dynamically (with getScript()), 
         //   but this was not working nicely with the modal dialog
         //   Therefore include files must be included with hgTracks CGI !
         // - embedded js should not be in the popup box.
         // - Somethings should be in a popup.ready() function, and this is emulated below, 
         //   as soon as the cleanHtml is added
         //   Since there are many possible popup cfg dialogs, the ready should be all inclusive.
 
         if ( ! popUp.trackDescriptionOnly ) {
             // If subtrack then vis rules differ
             var subtrack = tdbIsSubtrack(hgTracks.trackDb[popUp.trackName]) ? popUp.trackName :"";  
             // Saves the original vars (and vals) that may get changed by the popup cfg.
             popUp.saveAllVars = getAllVars( $('#hgTrackUiDialog'), subtrack ); 
 
             // -- popup.ready() -- Here is the place to do things that might otherwise go
             //                     into a $('#pop').ready() routine!
         }
 
         // Searching for some semblance of size suitability
         var popMaxHeight = ($(window).height() - 40);
         var popMaxWidth  = ($(window).width() - 40);
         var popWidth     = 640;
         if (popWidth > popMaxWidth)
             popWidth = popMaxWidth;
 
         // Create dialog buttons for UI popup
         var uiDialogButtons = {};
         if (popUp.trackDescriptionOnly) {
             uiDialogButtons.OK = function() {
                 $(this).dialog("close");
             };
         } else {
             uiDialogButtons.Apply = function() {
                  popUp.uiDialogOk($('#pop'), popUp.trackName);
                  // thanks to JAT for this cleverness to keep button functioning
                  popUp.saveAllVars = getAllVars( $('#hgTrackUiDialog'), popUp.trackName);
                  if (popUp.saveAllVars[popUp.trackName+"_sel"] === 0) {       // hide
                     // NOTE: once hidden, can't be unhidden by popup, so shut it down
                     $(this).dialog("close");
                 }
             };
             uiDialogButtons.OK = function() {
                 popUp.uiDialogOk($('#pop'), popUp.trackName);
                 $(this).dialog("close");
             };
         }
 
         $('#hgTrackUiDialog').dialog({
             ajaxOptions: {
                 // This doesn't work
                 cache: true
             },
             resizable: true,               // Let description scroll vertically
             height: (popUp.trackDescriptionOnly ? popMaxHeight : 'auto'),
             width: popWidth,
             minHeight: 200,
             minWidth: 400,
             maxHeight: popMaxHeight,
             maxWidth: popMaxWidth,
             modal: true,
             closeOnEscape: true,
             autoOpen: false,
             buttons: uiDialogButtons,
 
             // popup.ready() doesn't seem to work in open.
             
             open: function () {
                 if (!popUp.trackDescriptionOnly) {
                     $('#hgTrackUiDialog').find('.filterBy,.filterComp').each(
                         function(i) {
                             if ($(this).hasClass('filterComp'))
                                 ddcl.setup(this);
                             else
                                 ddcl.setup(this, 'noneIsAll');
                         }
                     );
                 }
             },
             close: function() {
                 popUp.cleanup();
             }
         });
         
         // FIXME: Why are open and close no longer working!!!
         if (popUp.trackDescriptionOnly) {
             var myWidth =  $(window).width() - 300;
             if (myWidth > 900)
                 myWidth = 900;
             $('#hgTrackUiDialog').dialog("option", "maxWidth", myWidth);
             $('#hgTrackUiDialog').dialog("option", "width", myWidth);
             $('#hgTrackUiDialog').dialog('option' , 'title' ,
                                hgTracks.trackDb[popUp.trackName].shortLabel+" Track Description");
             $('#hgTrackUiDialog').dialog('open');
         } else {
             $('#hgTrackUiDialog').dialog('option' , 'title' ,
                                   hgTracks.trackDb[popUp.trackName].shortLabel+" Track Settings");
             $('#hgTrackUiDialog').dialog('open');
         }
         var buttOk = $('button.ui-state-default');
         $(buttOk).focus();
     }
 };
 
   ///////////////////////////////
  //// imageV2  (aka imgTbl) ////
 ///////////////////////////////
 var imageV2 = {
 
     enabled:        false,  // Will be set to true unless advancedJavascriptFeatures
                             // is turned off OR if track search of config page
     imgTbl:         null,   // formerly "trackImgTbl"  The imgTbl or null if non-imageV2.
     inPlaceUpdate:  false,  // modified based on value of hgTracks.inPlaceUpdate & mapIsUpdateable
     mapIsUpdateable:true,
     lastTrack:      null,   // formerly (lastMapItem) this is used to try to keep what the
                             // last track the cursor passed.
 
     markAsDirtyPage: function ()
     {   // Page is marked as dirty so that the back-button knows page doesn't match cart
         var dirty = normed($('#dirty'));
         if (dirty)
             $(dirty).val('true');
     },
 
     markAsCleanPage: function ()
     {   // Clears signal that history may be out of sync with cart.
         var dirty = normed($('#dirty'));
         if (dirty)
             $(dirty).val('false');
     },
 
     isDirtyPage: function ()
     { // returns true if page was marked as dirty
     // This will allow the backbutton to be overridden
 
         var dirty = normed($('#dirty'));
         if (dirty && $(dirty).val() === 'true')
             return true;
         return false;
     },
     
     manyTracks: function ()
     {   // image-reload is slower than whole page reload when there are too many tracks
         if (!hgTracks || !hgTracks.trackDb || objKeyCount(hgTracks.trackDb) > 50)
             return true;
         return false;
     },
 
     updateTiming: function (response)
     {   // update measureTiming text on current page based on what's in the response
         var reg = new RegExp("(<span class='timing'>.+?</span>)", "g");
         var strs = [];
         for (var a = reg.exec(response); a && a[1]; a = reg.exec(response)) {
             strs.push(a[1]);
         }
         if (strs.length > 0) {
             $('.timing').remove();
             for (var ix = strs.length; ix > 0; ix--) {
                 $('body').prepend(strs[ix - 1]);
             }
         }
         reg = new RegExp("(<span class='trackTiming'>[\\S\\s]+?</span>)");
         a = reg.exec(response);
         if (a && a[1]) {
             $('.trackTiming').replaceWith(a[1]);
         }
     },
 
     loadSuggestBox: function ()
     {
         if ($('#positionInput').length) {
             if (!suggestBox.initialized) { // only call init once
                  suggestBox.init(getDb(), 
                             $("#suggestTrack").length > 0,
                             function (item) {
                                 genomePos.set(item.id, getSizeFromCoordinates(item.id));
                             },
                             function (position) {
                                 genomePos.set(position, getSizeFromCoordinates(position));
                             });
             }
             // Make sure suggestTrack is visible when user chooses via gene select (#3484).
             if ($("#suggestTrack").length) {
                 $(document.TrackForm || document.TrackHeaderForm).submit(function(event) {
                                                if ($('#hgFindMatches').length) {
                                                    vis.makeTrackVisible($("#suggestTrack").val());
                                                }
                                            });
             }
         }
     },
     
     afterImgChange: function (dirty)
     {   // Standard things to do when manipulations change image without ajax update.
         dragReorder.init();
         dragSelect.load(false);
         imageV2.highlightRegion();
         if (dirty)
             imageV2.markAsDirtyPage();
     },
     
     afterReload: function (id)
     {   // Reload various UI widgets after updating imgTbl map.
         dragReorder.init();
         dragSelect.load(false);
         // Do NOT reload context menu (otherwise we get the "context menu sticks" problem).
         // rightClick.load($('#tr_' + id));
         if (imageV2.imgTbl.tableDnDUpdate)
             imageV2.imgTbl.tableDnDUpdate();
         rightClick.reloadFloatingItem();
         // Turn on drag scrolling.
         if (hgTracks.imgBoxPortal) {
             $("div.scroller").panImages();
         }
         if (imageV2.backSupport) {
             if (id) { // The remainder is only needed for full reload
                 imageV2.markAsDirtyPage(); // vis of cfg change
                 imageV2.highlightRegion();
                 return;
             }
         }
         
         imageV2.loadRemoteTracks();
         makeItemsByDrag.load();
         imageV2.loadSuggestBox();
         imageV2.highlightRegion();
 
         if (imageV2.backSupport) {
             imageV2.setInHistory(false);    // Set this new position into History stack
         } else {
             imageV2.markAsDirtyPage();
         }
     },
 
     updateImgForId: function (html, id, fullImageReload, newJsonRec)
     {   // update row in imgTbl for given id.
         // return true if we successfully pull slice for id and update it in imgTrack.
         var newTr = $(html).find("tr[id='tr_" + id + "']");
         if (newTr.length > 0) {
             var tr = $(document.getElementById("tr_" + id));
             if (tr.length > 0) {
                 $(tr).html(newTr.children());
 
                 // Need to update tr class list too
                 var classes = $(html).find("tr[id='tr_"+ id + "']")[0].className;
                 if (classes && classes.length > 0) {
                     $(tr).removeClass();
                     $(tr).addClass(classes);
                 }
 
                 // NOTE: Want to examine the png? Uncomment:
                 //var img = $('#tr_' + id).find("img[id^='img_data_']").attr('src');
                 //warn("Just parsed image:<BR>"+img);
 
                 // >1x dragScrolling needs some extra care.
                 if (hgTracks.imgBoxPortal && (hgTracks.imgBoxWidth > hgTracks.imgBoxPortalWidth)) {
                     if (hgTracks.imgBoxPortalLeft !== undefined
                     &&  hgTracks.imgBoxPortalLeft !== null) {
                         $(tr).find('.panImg').css({'left': hgTracks.imgBoxPortalLeft });
                         $(tr).find('.tdData').css(
                                 {'backgroundPosition': hgTracks.imgBoxPortalLeft});
                     }
                 }
 
                 // Need to update vis box (in case this is reached via back-button)
                 if (imageV2.backSupport && fullImageReload) {
                     // Update abbr so that rows can be resorted properly
                     var abbr = $(newTr).attr('abbr');
 
                     if (abbr) {
                         $(tr).attr('abbr', abbr);
                     }
 
                     if (newJsonRec)
                         vis.update(id, vis.enumOrder[newJsonRec.visibility]);
                 }
 
                 return true;
             }
         }
         return false;
     },
 
     updateImgForAllIds: function (response, oldJson, newJson)
     {   // update all rows in imgTbl based upon navigateInPlace response.
         var imgTbl = $('#imgTbl');
 
         // We update rows one at a time 
         // (b/c updating the whole imgTbl at one time doesn't work in IE).
         var id;
         for (id in newJson.trackDb) {
             var newJsonRec = newJson.trackDb[id];
             var oldJsonRec = oldJson.trackDb[id];
             
             if (newJsonRec.visibility === 0)  // hidden 'ruler' is in newJson.trackDb!
                 continue;
             if (newJsonRec.type === "remote")
                 continue;
             if (oldJsonRec &&  oldJsonRec.visibility !== 0 && $('tr#tr_' + id).length === 1) {
                 // New track replacing old:
                 if (!imageV2.updateImgForId(response, id, true, newJsonRec))
                     warn("Couldn't parse out new image for id: " + id);
             } else { //if (!oldJsonRec || oldJsonRec.visibility === 0)
                 // New track seen for the first time
                 if (imageV2.backSupport) {
                     $(imgTbl).append("<tr id='tr_" + id + "' abbr='0'" + // abbr gets filled in
                                         " class='imgOrd trDraggable'></tr>");
                     if (!imageV2.updateImgForId(response, id, true, newJsonRec))
                         warn("Couldn't insert new image for id: " + id);
                 }
             }
         }
         if (imageV2.backSupport) {
             // Removes OLD: those in oldJson but not in newJson
             for (id in oldJson.trackDb) {
                 if ( ! newJson.trackDb[id] )
                     $(document.getElementById('tr_' + id)).remove();
             }
             
             // Need to reorder the rows based upon abbr
             dragReorder.sort($(imgTbl));
         }
     },
     
     updateChromImg: function (response)
     {   // Parse out new chrom 'ideoGram' (if available)
         // e.g.: <IMG SRC = "../trash/hgtIdeo/hgtIdeo_hgwdev_larrym_61d1_8b4a80.gif"
         //                BORDER=1 WIDTH=1039 HEIGHT=21 USEMAP=#ideoMap id='chrom' style='display: inline;'>
         // If the ideo is hidden or missing, we supply a place-holder for dynamic update later.
         // e.g.: <IMG SRC = ""
         //                BORDER=1 WIDTH=1039 HEIGHT=0 USEMAP=#ideoMap id='chrom' style='display: none'>
         // Larry's regex voodoo:
         var a = /<IMG([^>]+SRC[^>]+id='chrom'[^>]*)>/.exec(response);
         if (a && a[1]) {
             var b = /SRC\s*=\s*"([^")]*)"/.exec(a[1]);
             if (b) { // tolerate empty SRC= string when no ideo
                 $('#chrom').attr('src', b[1]);
                 var c = /style\s*=\s*'([^')]+)'/.exec(a[1]);
                 if (c && c[1]) {
                     $('#chrom').attr('style', c[1]);
                 }
                 var d = /HEIGHT\s*=\s*(\d*)/.exec(a[1]);
                 if (d && d[1]) {
                     $('#chrom').attr('HEIGHT', d[1]);
                 }
                 // Even if we're on the same chrom, ideoMap may change because the label
                 // on the left changes width depending on band name, and that changes px scaling.
                 var ideoMapMatch = /<MAP Name=ideoMap>[\s\S]+?<\/MAP>/.exec(response);
                 if (ideoMapMatch) {
                     var $oldMap = $("map[name='ideoMap']");
                     var $container = $oldMap.parent();
                     $oldMap.remove();
                     $container.append(ideoMapMatch[0]);
                 }
                 if (imageV2.backSupport) {
                     // Reinit chrom dragging.
                     if ($('area.cytoBand').length >= 1) {
                         $('img#chrom').chromDrag();
                     }
                 }
             }
         }
     },
 
     updateBackground: function (response)
     {
         // Added by galt to update window separators
         // Parse out background image url
         // background-image:url("../trash/hgt/blueLines1563-118-12_hgwdev_galt_9df9_e33b30.png")
         // background-image:url("../trash/hgt/winSeparators_hgwdev_galt_5bcb_baff60.png")
         // This will only need to update when multi-region is on and is using winSeparators.
 
         var a = /background-image:url\("(..\/trash\/hgt\/winSeparators[^"]+[.]png)"\)/.exec(response);
         if (a && a[1]) {
             $('td.tdData').css("background-image", "url("+a[1]+")");
         }
 
     },
 
         
     requestImgUpdate: function (trackName,extraData,loadingId,newVisibility)
     {
         // extraData, loadingId and newVisibility are optional
         var data = "hgt.trackImgOnly=1&hgsid=" + getHgsid() + "&hgt.trackNameFilter=" + trackName;
         if (extraData && extraData !== "")
             data += "&" + extraData;
         if (!loadingId || loadingId === "")
             loadingId = showLoadingImage("tr_" + trackName);
         var getOrPost = "GET";
         if ((data.length) > 2000) // extraData could contain a bunch of changes from the cfg dialog
             getOrPost = "POST";
         $.ajax({
                     type: getOrPost,
                     url: "../cgi-bin/hgTracks",
                     data: cart.addUpdatesToUrl(data),
                     dataType: "html",
                     trueSuccess: imageV2.updateImgAndMap,
                     success: catchErrorOrDispatch,
                     error: errorHandler,
                     cmd: 'refresh',
                     loadingId: loadingId,
                     id: trackName,
                     newVisibility: newVisibility,
                     cache: false
                 });
     },
 
     fullReload: function(extraData)
     {
         // force reload of whole page via trackform submit
         // This function does not return
         jQuery('body').css('cursor', 'wait');
         if (extraData || cart.updatesWaiting()) {
             var url = cart.addUpdatesToUrl(window.location.href);
             if (extraData) {
                 if ( url.lastIndexOf("?") === -1)
                     url += "?" + extraData;
                 else
                     url += '&' + extraData;
             }
             window.location.assign(url);
             return false;
         }
         document.TrackHeaderForm.submit();
     },
 
     updateImgAndMap: function (response, status)
     {   // Handle ajax response with an updated trackMap image, map and optional ideogram. 
         //    and maybe the redLines background too.
         // this.cmd can be used to figure out which menu item triggered this.
         // this.id === appropriate track if we are retrieving just a single track.
 
         // update local hgTracks.trackDb to reflect possible side-effects of ajax request.
 
+	// alert("response=["+response+"]");  // DEBUG GALT REMOVE
+
         var newJson = scrapeVariable(response, "hgTracks");
 
+	// added by GALT for CSP/XSS
+        if (!newJson) {
+	    // OLD CSP1 way not using now?
+            var strippedJsFiles = {};
+            stripJsFiles(response, false, strippedJsFiles);
+	    //alert(strippedJsFiles.toSource()); // DEBUG GALT FF ONLY
+	    //alert("strippedJsFiles.jsFiles="+strippedJsFiles.jsFiles+"");  // DEBUG GALT REMOVE
+	    var inlinePath = "";
+	    var i, len;
+	    if (strippedJsFiles.jsFiles) {		
+		for (i = 0, len = strippedJsFiles.jsFiles.length; i < len; ++i) {
+		    //alert(strippedJsFiles.jsFiles[i]); // DEBUG REMOVE
+		    var srcPattern="<script type='text/javascript' SRC='(.*)'></script>";
+		    var reg = new RegExp(srcPattern);
+		    var a = reg.exec(strippedJsFiles.jsFiles[i]);
+		    if (a && a[1]) {
+			if (a[1].match("inline")) {
+			    inlinePath = a[1];
+			    //alert("SRC found: "+a[1]);  // DEBUG REMOVE
+			}
+		    }
+		}
+	    }
+	    if (inlinePath !== "") {
+		//alert("inlinePath found: "+inlinePath); // DEBUG REMOVE
+		var js = genomePos.fetchInlineJs(inlinePath);
+		//alert(js); // DEBUG REMOVE
+		response += ("<script type='text/javascript'>"+js+"</script>");
+		newJson = scrapeVariable(response, "hgTracks");
+	    }
+	}
+
         //alert(JSON.stringify(newJson)); // DEBUG Example
 
         var oldJson = hgTracks;
         var valid = false;
         if (!newJson) {
             var stripped = {};
             stripJsEmbedded(response, true, stripped);
             if ( ! stripped.warnMsg )
                 warn("hgTracks object is missing from the response");
         } else {
             if (this.id) {
                 if (newJson.trackDb[this.id]) {
                     var visibility = vis.enumOrder[newJson.trackDb[this.id].visibility];
                     var limitedVis;
                     if (newJson.trackDb[this.id].limitedVis)
                         limitedVis = vis.enumOrder[newJson.trackDb[this.id].limitedVis];
                     if (this.newVisibility && limitedVis && this.newVisibility !== limitedVis)
                         // see redmine 1333#note-9
                         alert("There are too many items to display the track in " +
                                 this.newVisibility + " mode.");
                     var rec = oldJson.trackDb[this.id];
                     rec.limitedVis = newJson.trackDb[this.id].limitedVis;
                     vis.update(this.id, visibility);
                     valid = true;
                 } else {
                     warn("Invalid hgTracks.trackDb received from the server");
                 }
             } else {
                 valid = true;
             }
         }
         if (valid) {
             if (imageV2.enabled
             && this.id
             && this.cmd
             && this.cmd !== 'wholeImage'
             && this.cmd !== 'selectWholeGene'
             && !newJson.virtChromChanged) {
                 // Extract <TR id='tr_ID'>...</TR> and update appropriate row in imgTbl;
                 // this updates src in img_left_ID, img_center_ID and img_data_ID
                 // and map in map_data_ID
                 var id = this.id;
                 if (imageV2.updateImgForId(response, id, false)) {
                     imageV2.afterReload(id);
                     imageV2.updateBackground(response);  // Added by galt to update window separators
                 } else {
                     warn("Couldn't parse out new image for id: " + id);
                     // Very helpful when debugging and alert doesn't render the html:
                     //alert("Couldn't parse out new image for id: " + id+"BR"+response);
                 }
             } else {
                 if (imageV2.enabled) {
                     // Implement in-place updating of hgTracks image
                     // GALT delaying this until after newJson updated in hgTracks so disguising works
                     //genomePos.setByCoordinates(newJson.chromName, newJson.winStart + 1, newJson.winEnd);
                     $("input[name='c']").val(newJson.chromName);
                     $("input[name='l']").val(newJson.winStart);
                     $("input[name='r']").val(newJson.winEnd);
 
                     if (newJson.cgiVersion !== oldJson.cgiVersion || newJson.virtChromChanged) {
                         // Must reload whole page because of a new version on the server;
                         // this should happen very rarely. Note that we have already updated 
                         // position based on the user's action.
                         imageV2.fullReload();
                     } else {
                         // Will rebuild image adding new, removing old and resorting tracks
                         imageV2.updateImgForAllIds(response,oldJson,newJson);
                         imageV2.updateChromImg(response);
                         imageV2.updateBackground(response);  // Added by galt to update window separators
                         hgTracks = newJson;
                         genomePos.original = undefined;
                         genomePos.setByCoordinates(hgTracks.chromName, hgTracks.winStart + 1, hgTracks.winEnd); // MOVED HERE GALT
                         initVars();
                         imageV2.afterReload();
                     }
                 } else {
                     warn("ASSERT: Attempt to update track without advanced javascript features.");
                 }
             }
             if (hgTracks.measureTiming) {
                 imageV2.updateTiming(response);
             }
         }
         if (this.disabledEle) {
             this.disabledEle.removeAttr('disabled');
         }
         if (this.loadingId) {
             hideLoadingImage(this.loadingId);
         }
         jQuery('body').css('cursor', '');
         if (valid && this.currentId) {
             var top = $(document.getElementById("tr_" + this.currentId)).position().top;
             $(window).scrollTop(top - this.currentIdYOffset);
         }
     },
 
     loadRemoteTracks: function ()
     {
         if (hgTracks.trackDb) {
             for (var id in hgTracks.trackDb) {
                 var rec = hgTracks.trackDb[id];
                 if (rec.type === "remote") {
                     if ($("#img_data_" + id).length > 0) {
                         // load the remote track renderer via jsonp
                         rec.loadingId = showLoadingImage("tr_" + id);
                         var script = document.createElement('script');
                         var pos = parsePosition(genomePos.get());
                         var name = rec.remoteTrack || id;
                         script.setAttribute('src',
                                 rec.url + "?track=" + name +
                                 "&jsonp=imageV2.remoteTrackCallback&position=" +
                                 encodeURIComponent(pos.chrom + ":" + pos.start + "-" + pos.end) +
                                 "&pix=" + $('#imgTbl').width()
                         );
                         document.getElementsByTagName('head')[0].appendChild(script);
                     }
                 }
             }
         }
     },
 
     remoteTrackCallback: function (rec)
     // jsonp callback to load a remote track.
     {
         if (rec.error) {
             alert("retrieval from remote site failed with error: " + rec.error);
         } else {
             var remoteTrack = rec.track;
             for (var track in hgTracks.trackDb) {
                 if (hgTracks.trackDb[track].remoteTrack === remoteTrack) {
                     $('#img_data_' + track).attr('style', "left:-116px; top: -23px;");
                     $('#img_data_' + track).attr('height', rec.height);
                     // XXXX use width in some way?
            //       $('#img_data_' + track).attr('width', rec.width);
                     $('#img_data_' + track).attr('width', $('#img_data_ruler').width());
                     $('#img_data_' + track).attr('src', rec.img);
           /* jshint loopfunc: true */// function inside loop works and replacement is awkward.
                     $('#td_data_' + track + ' > div').each(function(index) {
                         if (index === 1) {
                             var style = $(this).attr('style');
                             style = style.replace(/height:\s*\d+/i, "height:" + rec.height);
                             $(this).attr('style', style);
                         }
                     });
                     var style = $('#p_btn_' + track).attr('style');
                     style = style.replace(/height:\s*\d+/i, "height:" + rec.height);
                     $('#p_btn_' + track).attr('style', style);
                     if (hgTracks.trackDb[track].loadingId) {
                         hideLoadingImage(hgTracks.trackDb[track].loadingId);
                     }
                 }
             }
         }
     },
 
     navigateButtonClick: function (ele) // called from hgTracks.c
     {   // code to update just the imgTbl in response to navigation buttons (zoom-out etc.).
         if (imageV2.inPlaceUpdate) {
             var params = ele.name + "=" + ele.value;
             $(ele).attr('disabled', 'disabled');
             // dinking navigation needs additional data
             if (ele.name === "hgt.dinkLL" || ele.name === "hgt.dinkLR") {
                 params += "&dinkL=" + $("input[name='dinkL']").val();
             } else if (ele.name === "hgt.dinkRL" || ele.name === "hgt.dinkRR") {
                 params += "&dinkR=" + $("input[name='dinkR']").val();
             }
             imageV2.navigateInPlace(params, $(ele), false);
             return false;
         } else {
             return true;
         }
     },
 
     updateButtonClick: function (ele) // UNUSED?
     {   // code to update the imgTbl based on changes in the track controls.
         // This is currently experimental code and is dead in the main branch.
         if (imageV2.mapIsUpdateable) {
             var data = "";
             $("select").each(function(index, o) {
                 var cmd = $(this).val();
                 if (cmd === "hide") {
                     if (hgTracks.trackDb[this.name]) {
                         alert("Need to implement hide");
                     }
                 } else {
                     if ( ! hgTracks.trackDb[this.name]
                     ||  cmd !== vis.enumOrder[hgTracks.trackDb[this.name].visibility]) {
                         if (data.length > 0) {
                             data = data + "&";
                         }
                         data = data + this.name + "=" + cmd;
                     }
             }
             });
             if (data.length > 0) {
                 imageV2.navigateInPlace(data, null, false);
             }
             return false;
         } else {
             return true;
         }
     },
 
     navigateInPlace: function (params, disabledEle, keepCurrentTrackVisible)
     {   // request an hgTracks image, using params
         // disabledEle is optional; this element will be enabled when update is complete
         // If keepCurrentTrackVisible is true, we try to maintain relative position of the item
         // under the mouse after the in-place update.
         // Tim thinks we should consider disabling all UI input while we are doing in-place update.
         // TODO: waitOnFuction?
     
         // No ajax image update if there are too many tracks!
         if (imageV2.manyTracks()) {
             imageV2.fullReload(params);
             return false;  // Shouldn't return from fullReload but I have seen it in FF
         }
     
         // If UCSC Genes (or any suggestion) is supposed to be made visible, then do so
         if ($("#suggestTrack").length && $('#hgFindMatches').length)
             vis.makeTrackVisible($("#suggestTrack").val());
 
         jQuery('body').css('cursor', 'wait');
         var currentId, currentIdYOffset;
         if (keepCurrentTrackVisible) {
             var item = rightClick.currentMapItem || imageV2.lastTrack;
             if (item) {
                 var top = $(document.getElementById("tr_" + item.id)).position().top;
                 if (top >= $(window).scrollTop()
                 || top < $(window).scrollTop() + $(window).height()) {
                     // don't bother if the item is not currently visible.
                     currentId = item.id;
                     currentIdYOffset = top - $(window).scrollTop();
                 }
             }
         }
         $.ajax({
                 type: "GET",
                 url: "../cgi-bin/hgTracks",
                 data: cart.addUpdatesToUrl(params + 
                                       "&hgt.trackImgOnly=1&hgt.ideogramToo=1&hgsid=" + getHgsid()),
                 dataType: "html",
                 trueSuccess: imageV2.updateImgAndMap,
                 success: catchErrorOrDispatch,
                 error: errorHandler,
                 cmd: 'wholeImage',
                 loadingId: showLoadingImage("imgTbl"),
                 disabledEle: disabledEle,
                 currentId: currentId,
                 currentIdYOffset: currentIdYOffset,
                 cache: false
             });
     },
 
     disguiseHighlight: function(position)
     // disguise highlight position
     {
         pos = parsePositionWithDb(position);
         // DISGUISE
         if (hgTracks.virtualSingleChrom && (pos.chrom.search("virt") === 0)) {
             var positionStr = pos.chrom+":"+pos.start+"-"+pos.end;
             var newPosition = genomePos.disguisePosition(positionStr);
             var newPos = parsePosition(newPosition);
             pos.chrom = newPos.chrom;
             pos.start = newPos.start;
             pos.end   = newPos.end;
         }
         return pos.db+"."+pos.chrom+":"+pos.start+"-"+pos.end+pos.color;
     },
 
     undisguiseHighlight: function(pos)
     // undisguise highlight pos
     {
         // UN-DISGUISE
         if (hgTracks.virtualSingleChrom && (pos.chrom.search("virt") !== 0)) {
             var position = pos.chrom+":"+pos.start+"-"+pos.end;
             var newPosition = genomePos.undisguisePosition(position);
             var newPos = parsePosition(newPosition);
             if (newPos) {
                 pos.chrom = newPos.chrom;
                 pos.start = newPos.start;
                 pos.end   = newPos.end;
             }
         }
     },
 
     highlightRegion: function()
     // highlight vertical region in imgTbl based on hgTracks.highlight (#709).
     {
         var pos;
         var hexColor = '#FFAAAA';
         $('.highlightItem').remove();
         if (hgTracks.highlight) {
             var hlArray = hgTracks.highlight.split("|"); // support multiple highlight items
             for (var i = 0; i < hlArray.length; i++) {
                 hlString = hlArray[i];
                 pos = parsePositionWithDb(hlString);
                 // UN-DISGUISE
                 imageV2.undisguiseHighlight(pos);
                 if (pos) {
                     pos.start--;  // make start 0-based to match hgTracks.winStart
                     if (pos.color)
                         hexColor = pos.color;
                 }
 
                 if (pos && pos.chrom === hgTracks.chromName && pos.db === getDb() 
                 &&  pos.start <= hgTracks.imgBoxPortalEnd && pos.end >= hgTracks.imgBoxPortalStart) {
                     var portalWidthBases = hgTracks.imgBoxPortalEnd - hgTracks.imgBoxPortalStart;
                     var portal = $('#imgTbl td.tdData')[0];
                     var leftPixels = $(portal).offset().left + 3; // 3 for borders and cgi item calcs ??
                     var pixelsPerBase = ($(portal).width() - 2) / portalWidthBases;
                     var clippedStartBases = Math.max(pos.start, hgTracks.imgBoxPortalStart);
                     var clippedEndBases = Math.min(pos.end, hgTracks.imgBoxPortalEnd);
                     var widthPixels = (clippedEndBases - clippedStartBases) * pixelsPerBase;
                     if (hgTracks.revCmplDisp)
                         leftPixels += (hgTracks.imgBoxPortalEnd - clippedEndBases) * pixelsPerBase - 1;
                     else
                         leftPixels += (clippedStartBases - hgTracks.imgBoxPortalStart) * pixelsPerBase;
                     // Impossible to get perfect... Okay to overrun by a pixel on each side
                     leftPixels  = Math.floor(leftPixels);
                     widthPixels = Math.ceil(widthPixels);
                     if (widthPixels < 2) {
                         widthPixels = 3;
                         leftPixels -= 1;
                     }
     
                     var area = jQuery("<div id='highlightItem' class='highlightItem'></div>");
                     $(area).css({ backgroundColor: hexColor, // display: 'none'
                                 left: leftPixels + 'px', top: $('#imgTbl').offset().top + 1 + 'px',
                                 width: widthPixels + 'px',
                                 height: $('#imgTbl').css('height') });
                     $(area).data({leftPixels: leftPixels, widthPixels: widthPixels});// needed by dragScroll
     
                     // Larry originally appended to imgTbl, but discovered that doesn't work on IE 8 and 9.
                     $('body').append($(area)); 
                     // z-index is done in css class, so highlight is beneath transparent data images.
                     // NOTE: ideally highlight would be below transparent blue-lines, but THAT is a  
                     // background-image so z-index can't get below it!  PS/PDF looks better for blue-lines!
                 }
             }
         }
     },
 
     backSupport: (window.History.enabled !== undefined), // support of our back button via: 
     history: null,                                     //  jquery.history.js and HTML5 history API
     
     setupHistory: function ()
     {   // Support for back-button using jquery.history.js.
         // Sets up the history and initializes a state.
     
         // Since ajax updates leave the browser cached pages different from the server state, 
         // simple back-button fails.  Using a 'dirty flag' we had forced an update from server,
         // whenever the back button was hit, meaning there was no going back from server-state!
         // NOW using the history API, the back-button triggers a 'statechange' event which can 
         // contain data.  We save the position in the data and ajax update the image when the
         // back-button is pressed.  This works great for going back through ajax-updated position
         // changes, but is a bit messier when going back past a full-page retrieved state (as
         // described below).
     
         // NOTE: many things besides position could be ajax updated (e.g. track visibility). We are
         // using the back-button to keep track of position only.  Since the image should be updated
         // every-time the back button is pressed, all track settings should persist (not go back).
         // What will occasionally fail is vis box state and group expansion state. This is because
         // the back-button goes to a browser cached page and then the image alone is updated.
     
         imageV2.history = window.History;
         
         // The 'statechange' function triggerd by the back-button.
         // Whenever the position changes, then use ajax-update to refetch the position
         imageV2.history.Adapter.bind(window,'statechange',function(){
             var prevDbPos = imageV2.history.getState().data.lastDbPos;
             var prevPos = imageV2.history.getState().data.position;
             var curDbPos = hgTracks.lastDbPos;
             if (prevDbPos && prevDbPos !== curDbPos) {
                 // NOTE: this function is NOT called when backing past a full retrieval boundary
                 genomePos.set(decodeURIComponent(prevPos));
                 imageV2.navigateInPlace("" + prevDbPos, null, false);
             }
         });
         
         // With history support it is best that most position changes will ajax-update the image
         // This ensures that the 'go' and 'refresh' button will do so unless the chrom changes.
         $("input[value='go'],input[value='refresh']").click(function () {
             var newPos = genomePos.get().replace(/,/g,'');
             if (newPos.length > 2000) {
                alert("Sorry, you cannot paste identifiers or sequences with more than 2000 characters into this box.");
                $('input[name="hgt.positionInput"]').val("");
                return false;
             }
 
             var newDbPos = hgTracks.lastDbPos;
             if ( ! imageV2.manyTracks() ) {
                 var newChrom = newPos.split(':')[0];
                 var oldChrom  = genomePos.getOriginalPos().split(':')[0];
                 if (newChrom === oldChrom) {
                     imageV2.markAsDirtyPage();
                     imageV2.navigateInPlace("position=" + newPos, null, false);
                     window.scrollTo(0,0);
                     return false;
                 }
             }
             
             // If not just image update AND there are vis updates waiting...
             if (cart.updatesWaiting()) {
                 var url = "../cgi-bin/hgTracks?position=" + newPos + "&" + cart.varsToUrlData({ 'db': getDb(), 'hgsid': getHgsid() });
                 window.location.assign(url);
                 return false;
             }
 
             // redirect to hgBlat if the input looks like a DNA sequence
             // minimum length=19 so we do not accidentally redirect to hgBlat for a gene identifier 
             // like ATG5
             var dnaRe = new RegExp("^(>[^\n\r ]+[\n\r ]+)?(\\s*[actgnACTGN \n\r]{19,}\\s*)$");
             if (dnaRe.test(newPos)) {
                 var blatUrl = "hgBlat?type=BLAT%27s+guess&userSeq="+newPos;
                 window.location.href = blatUrl;
                 return false;
             }
                 
             return true;
         });
         // Have vis box changes update cart through ajax.  This helps keep page/cart in sync.
         vis.initForAjax();
 
         // We reach here from these possible paths:
         // A) Forward: Full page retrieval: hgTracks is first navigated to (or chrom change)
         // B) Back-button past a full retrieval (B in: ->A,->b,->c(full page),->d,<-c,<-B(again))
         //    B1) Dirty page: at least one non-position change (e.g. 1 track vis changed in b)
         //    B2) Clean page: only position changes from A->b->| 
         var curPos = encodeURIComponent(genomePos.get().replace(/,/g,''));
         var curDbPos = hgTracks.lastDbPos;
         var cachedPos = imageV2.history.getState().data.position;
         var cachedDbPos = imageV2.history.getState().data.lastDbPos;
         // A) Forward: Full page retrieval: hgTracks is first navigated to (or chrom change)
         if (!cachedDbPos) { // Not a back-button operation
             // set the current position into history outright (will replace). No img update needed
             imageV2.setInHistory(true);
         } else { // B) Back-button past a full retrieval
             genomePos.set(decodeURIComponent(cachedPos));
             // B1) Dirty page: at least one non-position change 
             if (imageV2.isDirtyPage()) {
                 imageV2.markAsCleanPage();
                 // Only forcing a full page refresh if chrom changes
                 var cachedChrom = decodeURIComponent(cachedPos).split(':')[0];
                 var curChrom    = decodeURIComponent(   curPos).split(':')[0];
                 if (cachedChrom === curChrom) {
                     imageV2.navigateInPlace("db="+getDb()+"&"+cachedDbPos, null, false);
                 } else {
                     imageV2.fullReload();
                 }
             } else {
                 // B2) Clean page: only position changes from a->b 
                 if (cachedDbPos !== curDbPos) {
                     imageV2.navigateInPlace("db="+getDb()+"&"+cachedDbPos, null, false);
                 }
             }
             // Special because FF is leaving vis drop-downs disabled
             vis.restoreFromBackButton();
         }
     },
     
     setInHistory: function (fullPageLoad)
     {   // Keep a position history and allow the back-button to work (sort of)
         // replaceState on initial page load, pushState on each advance
         // When call triggered by back button, the lastPos===newPos, so no action.
         var lastDbPos = imageV2.history.getState().data.lastDbPos;
         var newPos  = encodeURIComponent(genomePos.get().replace(/,/g,''));  // no commas
         var newDbPos  = hgTracks.lastDbPos;
         
         // A full page load could be triggered by back-button, but then there will be a lastPos
         // if this is the case then don't set the position in history again!
         if (fullPageLoad && lastDbPos)
             return;
 
         if (!lastDbPos || lastDbPos !== newDbPos) {
             // Swap the position into the title
             var title = $('TITLE')[0].text;
             var ttlWords = title.split(' ');
             if (ttlWords.length >= 2) {
                 for (var i=1; i < ttlWords.length; i++) {
                     if (ttlWords[i].indexOf(':') >= 0) {
                         ttlWords[i] = genomePos.get();
                     }
                 }
                 title = ttlWords.join(' ');
             } else
                 title = genomePos.get();
 
             var sid = getHgsid();
             if (fullPageLoad) { 
                 // Should only be on initial set-up: first navigation to page
                 imageV2.history.replaceState({lastDbPos: newDbPos, position: newPos, hgsid: + sid },title,
                                  "hgTracks?db="+getDb()+"&"+newDbPos+"&hgsid="+sid);
             } else {  
                 // Should be when advancing (not-back-button)
                 imageV2.history.pushState({lastDbPos: newDbPos, position: newPos, hgsid: + sid },title,
                                  "hgTracks?db="+getDb()+"&"+newDbPos+"&hgsid="+sid);
             }
         }
     }
 };
 
   //////////////////////
  //// track search ////
 //////////////////////
 var trackSearch = {
 
     searchKeydown: function (event)
     {
         if (event.which === 13) {
             // Required to fix problem on IE and Safari where value of hgt_tSearch is "-"
             //    (i.e. not "Search").
             // NOTE: must match TRACK_SEARCH_PAGER in hg/inc/searchTracks.h
             $("input[name=hgt_tsPage]").val(0);  
             $('#trackSearch').submit();
             // This doesn't work with IE or Safari.
             // $('#searchSubmit').click();
         }
     },
 
     init: function ()
     {
         // Track search uses tabs
         if ($("#tabs").length > 0) {
             // Search page specific code
 
             var val = $('#currentTab').val();
             $("#tabs").tabs({
                                 show: function(event, ui) {
                                     $('#currentTab').val(ui.panel.id);
                                 },
                                 select: function(event, ui) { findTracks.switchTabs(ui); }
                             });
             $('#tabs').show();
             $("#tabs").tabs('option', 'selected', '#' + val);
             if (val === 'simpleTab' && $('div#found').length < 1) {
                 $('input#simpleSearch').focus();
             }
             $("#tabs").css('font-family', jQuery('body').css('font-family'));
             $("#tabs").css('font-size', jQuery('body').css('font-size'));
             $('.submitOnEnter').keydown(trackSearch.searchKeydown);
             findTracks.normalize();
             findTracks.updateMdbHelp(0);
         }
     }
 };
 
 
   ///////////////
  //// READY ////
 ///////////////
 $(document).ready(function()
 {
     // The page may be reached via browser history (back button)
     // If so, then this code should detect if the image has been changed via js/ajax
     // and will reload the image if necessary.
     // NOTE: this is needed for IE but other browsers can detect the dirty page much earlier
     if (!imageV2.backSupport) {
         if (imageV2.isDirtyPage()) {
             // mark as non dirty to avoid infinite loop in chrome.
             imageV2.markAsCleanPage();
             jQuery('body').css('cursor', 'wait');
             window.location = "../cgi-bin/hgTracks?hgsid=" + getHgsid();
             return false;
         }
     }
     initVars();
     imageV2.loadSuggestBox();
     if ($('#pdfLink').length === 1) {
         $('#pdfLink').click(function(i) {
             var thisForm = normed($('#TrackForm'));
             if (thisForm) {
                 //alert("posting form:"+$(thisForm).attr('name'));
                 updateOrMakeNamedVariable($(thisForm),'hgt.psOutput','on');
                 return postTheForm($(thisForm).attr('name'),this.href);
             }
             return true;
         });
     }
 
     if (imageV2.enabled) {
 
         // Make imgTbl allow drag reorder of imgTrack rows
         dragReorder.init();
         var imgTable = $(".tableWithDragAndDrop");
         if ($(imgTable).length > 0) {
             $(imgTable).tableDnD({
                 onDragClass: "trDrag",
                 dragHandle: "dragHandle",
                 scrollAmount: 40,
                 onDragStart: function(ev, table, row) {
                     mouse.saveOffset(ev);
                     $(document).bind('mousemove',posting.blockTheMapOnMouseMove);
 
                     // Can drag a contiguous set of rows if dragging blue button
                     table.tableDnDConfig.dragObjects = [ row ]; // defaults to just the one
                     var btn = $( row ).find('p.btnBlue');  // btnBlue means cursor over left button
                     if (btn.length === 1) {
                         table.tableDnDConfig.dragObjects = dragReorder.getContiguousRowSet(row);
                         var compositeSet = dragReorder.getCompositeSet(row);
                         if (compositeSet && compositeSet.length > 0)
                             $( compositeSet ).find('p.btn').addClass('blueButtons');// blue persists
                     }
                 },
                 onDrop: function(table, row, dragStartIndex) {
                     var compositeSet = dragReorder.getCompositeSet(row);
                     if (compositeSet && compositeSet.length > 0)
                         $( compositeSet ).find('p.btn').removeClass('blueButtons');// blue persists
                     if ($(row).attr('rowIndex') !== dragStartIndex) {
                         // NOTE Even if dragging a contiguous set of rows,
                         // still only need to check the one under the cursor.
                         if (dragReorder.setOrder) {
                             dragReorder.setOrder(table);
                         }
                         dragReorder.zipButtons( table );
                     }
                     $(document).unbind('mousemove',posting.blockTheMapOnMouseMove);
                     // Timeout necessary incase the onDrop over map item. onDrop takes precedence.
                     setTimeout(posting.allowMapClicks,100);
                 }
             });
         }
 
         // Drag scroll init
         if (hgTracks.imgBoxPortal) {
             // Turn on drag scrolling.
             $("div.scroller").panImages();
         }
 
         // Retrieve tracks via AJAX that may take too long to draw initialliy (i.e. a remote bigWig)
         var retrievables = $('#imgTbl').find("tr.mustRetrieve");
         if ($(retrievables).length > 0) {
             $(retrievables).each( function (i) {
                 var trackName = $(this).attr('id').substring(3);
                 imageV2.requestImgUpdate(trackName,"","");
             });
         }
         imageV2.loadRemoteTracks();
         makeItemsByDrag.load();
         
         // Any highlighted region must be shown and warnBox must play nice with it.
         imageV2.highlightRegion();
         // When warnBox is dismissed, any image highlight needs to be redrawn.
         $('#warnOK').click(function (e) { imageV2.highlightRegion();});
         // Also extend the function that shows the warn box so that it too redraws the highlight.
         showWarnBox = (function (oldShowWarnBox) {
             function newShowWarnBox() {
                 oldShowWarnBox.apply();
                 imageV2.highlightRegion();
             }
             return newShowWarnBox;
         })(showWarnBox);
     }
 
     // Drag select in chromIdeogram
     if ($('img#chrom').length === 1) {
         if ($('area.cytoBand').length >= 1) {
             $('img#chrom').chromDrag();
         }
     }
 
     // Track search uses tabs
     trackSearch.init();
 
     // Drag select initialize
     if (imageV2.enabled) {   // moved from window.load().
         dragSelect.load(true);
 
         if ($('#hgTrackUiDialog'))
             $('#hgTrackUiDialog').hide();
 
         // Don't load contextMenu if jquery.contextmenu.js hasn't been loaded
         if (jQuery.fn.contextMenu) {
             rightClick.load(imageV2.imgTbl);
         }
     }
 
     // jquery.history.js Back-button support
     if (imageV2.enabled && imageV2.backSupport) {
         imageV2.setupHistory();
     }
 
 });