Index: src/hg/js/hgTracks.js
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/js/hgTracks.js,v
retrieving revision 1.64
retrieving revision 1.65
diff -b -B -U 1000000 -r1.64 -r1.65
--- src/hg/js/hgTracks.js	8 Apr 2010 22:31:13 -0000	1.64
+++ src/hg/js/hgTracks.js	9 Apr 2010 07:48:47 -0000	1.65
@@ -1,1774 +1,1817 @@
 // Javascript for use in hgTracks CGI
 // $Header$
 
 var debug = false;
 var originalPosition;
 var originalSize;
 var originalCursor;
 var clickClipHeight;
 var revCmplDisp;
 var insideX;
 var startDragZoom = null;
 var newWinWidth;
 var imageV2 = false;
 var imgBoxPortal = false;
 var blockUseMap = false;
 var mapItems;
 var trackImg;               // jQuery element for the track image
 var trackImgTbl;            // jQuery element used for image table under imageV2
 var imgAreaSelect;          // jQuery element used for imgAreaSelect
 var originalImgTitle;
 var autoHideSetting = true; // Current state of imgAreaSelect autoHide setting
 var selectedMenuItem;       // currently choosen context menu item (via context menu).
 var browser;                // browser ("msie", "safari" etc.)
 
 function initVars(img)
 {
 // There are various entry points, so we call initVars in several places to make sure this variables get updated.
     if(!originalPosition) {
         // remember initial position and size so we can restore it if user cancels
         originalPosition = getOriginalPosition();
         originalSize = $('#size').text();
         originalCursor = jQuery('body').css('cursor');
     }
 }
 
 function selectStart(img, selection)
 {
     initVars();
     var now = new Date();
     startDragZoom = now.getTime();
     blockUseMap = true;
     // vvvvvvv Should be obsolete since maps items are ignored when startDragZoom is set
 //    if(imageV2 == false) {
 //        jQuery.each(jQuery.browser, function(i, val) {
 //            if(i=="msie" && val) {
 //                // Very hacky way to solve following probem specif to IE:
 //                // If the user ends selection with the mouse in a map box item, the map item
 //                // is choosen instead of the selection; to fix this, we remove map box items
 //                // during the mouse selection process.
 //                mapHtml = $('#map').html();
 //                $('#map').empty();
 //            }
 //        });
 //    }
     // ^^^^^^^^ Should be obsolete since maps items are ignored when startDragZoom is set
 }
 
 function setPositionByCoordinates(chrom, start, end)
 {
     var newPosition = chrom + ":" + commify(start) + "-" + commify(end);
     setPosition(newPosition, commify(end - start + 1));
     return newPosition;
 }
 
 function getPositionElement()
 {
 // 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;
 }
 
 function getPosition()
 {
 // Return current value of position box
     var ele = getPositionElement();
     if(ele != null) {
 	return ele.value;
     }
     return null;
 }
 
 function getOriginalPosition()
 {
     return originalPosition || getPosition();
 }
 
 function setPosition(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.
     if(position) {
         // XXXX There are multiple tags with name == "position":^(
 	var tags = document.getElementsByName("position");
 	for (var i = 0; i < tags.length; i++) {
 	    var ele = tags[i];
 	    ele.value = position;
 	}
     }
     if(size) {
         $('#size').text(size);
     }
 }
 
 function getDb()
 {
     var db = document.getElementsByName("db");
     if(db == undefined || db.length == 0)
         return undefined;
     return db[0].value;
 }
 
 function checkPosition(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 = revCmplDisp ? imgOfs.left - slop : imgOfs.left + insideX - slop;
     var rightX = revCmplDisp ? imgOfs.left + imgWidth - 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));
 }
 
+
+function selectionPixelsToBases(img, selection)
+// Convert selection x1/x2 coordinates to chromStart/chromEnd.
+{
+var insideX = parseInt(document.getElementById("hgt.insideX").value);
+var imgWidth = jQuery(img).width() - insideX;
+var winStart = parseInt(document.getElementById("hgt.winStart").value);
+var winEnd = parseInt(document.getElementById("hgt.winEnd").value);
+var width = winEnd - winStart;
+var mult = width / imgWidth;   // mult is bp/pixel multiplier
+var startDelta;                // startDelta is how many bp's to the right/left
+if(revCmplDisp) {
+    var x1 = Math.min(imgWidth, selection.x1);
+    startDelta = Math.floor(mult * (imgWidth - x1));
+} else {
+    var x1 = Math.max(insideX, selection.x1);
+    startDelta = Math.floor(mult * (x1 - insideX));
+}
+var endDelta;
+if(revCmplDisp) {
+    endDelta = startDelta;
+    var x2 = Math.min(imgWidth, selection.x2);
+    startDelta = Math.floor(mult * (imgWidth - x2));
+} else {
+    var x2 = Math.max(insideX, selection.x2);
+    endDelta = Math.floor(mult * (x2 - insideX));
+}
+var newStart = winStart + startDelta;
+var newEnd = winStart + 1 + endDelta;
+if(newEnd > winEnd) {
+    ewEnd = winEnd;
+}
+return {chromStart : newStart, chromEnd : newEnd};
+}
+
+
 function updatePosition(img, selection, singleClick)
 {
     // singleClick is true when the mouse hasn't moved (or has only moved a small amount).
     var chromName = document.getElementById("hgt.chromName").value;
     var winStart = parseInt(document.getElementById("hgt.winStart").value);
     var winEnd = parseInt(document.getElementById("hgt.winEnd").value);
     if(typeof imgBoxPortalStart != "undefined" && imgBoxPortalStart) {
         winStart = imgBoxPortalStart;
         winEnd = imgBoxPortalEnd;
     }
     var imgWidth = jQuery(img).width() - insideX;
     var width = winEnd - winStart;
     var newPos = null;
     var newSize = null;
     var mult = width / imgWidth;			    // mult is bp/pixel multiplier
     var startDelta;                                     // startDelta is how many bp's to the right/left
     if(revCmplDisp) {
         var x1 = Math.min(imgWidth, selection.x1);
         startDelta = Math.floor(mult * (imgWidth - x1));
     } else {
         var x1 = Math.max(insideX, selection.x1);
         startDelta = Math.floor(mult * (x1 - insideX));
     }
     if(singleClick) {
 	var newStart = (winStart + 1) + (startDelta - Math.floor(newWinWidth / 2));
         if(newStart < 1) {
             newStart = 1;
             newEnd = newWinWidth;
         } else {
             // hgTracks gracefully handles overflow past the end of the chrom, so don't worry about that.
             newEnd = (winStart + 1) + (startDelta + Math.floor(newWinWidth / 2));
         }
 	newPos = chromName + ":" + commify(newStart) + "-" + commify(newEnd);
 	newSize = newEnd - newStart + 1;
     } else {
         var endDelta;
         if(revCmplDisp) {
             endDelta = startDelta;
             var x2 = Math.min(imgWidth, selection.x2);
 	    startDelta = Math.floor(mult * (imgWidth - x2));
         } else {
             var x2 = Math.max(insideX, selection.x2);
 	    endDelta = Math.floor(mult * (x2 - insideX));
         }
         var newStart = winStart + 1 + startDelta;
         var newEnd = winStart + 1 + endDelta;
         if(newEnd > winEnd) {
             newEnd = winEnd;
         }
         newPos = chromName + ":" + commify(newStart) + "-" + commify(newEnd);
         newSize = newEnd - newStart + 1;
     }
 
     if(newPos != null) {
         setPosition(newPos, commify(newSize));
 	return true;
     }
 }
 
 function selectChange(img, selection)
 {
     initVars();
     if(selection.x1 != selection.x2) { // TODO: Larry could you examine this?
         if(checkPosition(img, selection)) {
             updatePosition(img, selection, false);
             jQuery('body').css('cursor', originalCursor);
         } else {
             jQuery('body').css('cursor', 'not-allowed');
         }
     }
     return true;
 }
 
 function selectEnd(img, selection)
 {
     var now = new Date();
     var doIt = false;
     if(originalCursor != null)
         jQuery('body').css('cursor', originalCursor);
     // ignore releases outside of the image rectangle (allowing a 10 pixel slop)
     if(autoHideSetting && checkPosition(img, selection)) {
        // ignore single clicks that aren't in the top of the image (this happens b/c the clickClipHeight test in selectStart
        // doesn't occur when the user single clicks).
        doIt = startDragZoom != null || selection.y1 <= clickClipHeight;
     }
     if(doIt) {
         // startDragZoom is null if mouse has never been moved
 	if(updatePosition(img, selection, (selection.x2 == selection.x1) || startDragZoom == null || (now.getTime() - startDragZoom) < 100)) {
             jQuery('body').css('cursor', 'wait');
 	    document.TrackHeaderForm.submit();
 	}
     } else {
         setPosition(originalPosition, originalSize);
         originalPosition = originalSize = null;
 //        if(mapHtml) {
 //            $('#map').append(mapHtml);
 //        }
     }
 //    mapHtml = null;
     startDragZoom = null;
     setTimeout('blockUseMap=false;',50); // Necessary incase the selectEnd was over a map item. select takes precedence.
     return true;
 }
 
 $(window).load(function () {
     jQuery.each(jQuery.browser, function(i, val) {
         if(val) {
             browser = i;
         }
         });
     // jQuery load function with stuff to support drag selection in track img
     if(browser == "safari" && navigator.userAgent.indexOf("Chrome") != -1) {
         // Handle the fact that (as of 1.3.1), jQuery.browser reports "safari" when the browser is in fact Chrome.
         browser = "chrome";
     }
     loadImgAreaSelect(true);
     hgTracksInitTracks();
     if($('#hgTrackUiDialog'))
         $('#hgTrackUiDialog').hide();
 
     // Don't load contextMenu if jquery.contextmenu.js hasn't been loaded
     if(trackImg && jQuery.fn.contextMenu) {
         $('#hgTrackUiDialog').hide();
         if(imageV2) {
             $("map[name!=ideoMap]").each( function(t) { parseMap($(this,false));});
         } else {
             // XXXX still under debate whether we have to remove the map
             parseMap($('#map'),true);
             $('#map').empty();
         }
 
         originalImgTitle = trackImg.attr("title");
         if(imageV2) {
             loadContextMenu(trackImgTbl);
             $(".trDraggable,.nodrop").each( function(t) { loadContextMenu($(this)); });
         } else {
             loadContextMenu(trackImg);
             trackImg.mousemove(
                 function (e) {
                     mapEvent(e);
                 }
             );
             trackImg.mousedown(
                 function (e) {
                     mapMouseDown(e);
                 }
             );
         }
     }
     });
 
 function loadImgAreaSelect(firstTime)
 {
     var rulerEle = document.getElementById("hgt.rulerClickHeight");
     var dragSelectionEle = document.getElementById("hgt.dragSelection");
 
     // disable if ruler is not visible.
     if((dragSelectionEle != null) && (dragSelectionEle.value == '1') && (rulerEle != null)) {
         var imgHeight = 0;
         trackImg = $('#img_data_ruler');
 
         if(trackImg == undefined || trackImg.length == 0) {  // Revert to old imageV1
             trackImg = $('#trackMap');
             imgHeight = jQuery(trackImg).height();
         } else {
             imageV2   = true;
             trackImgTbl = $('#imgTbl');
             imgHeight = trackImg.height();
             // XXXX Tim, I think we should get height from trackImgTbl, b/c it automatically adjusts as we add/delete items.
             imgHeight = trackImgTbl.height();
         }
 
         clickClipHeight = parseInt(rulerEle.value);
         newWinWidth = parseInt(document.getElementById("hgt.newWinWidth").value);
         revCmplDisp = parseInt(document.getElementById("hgt.revCmplDisp").value) == 0 ? false : true;
         insideX = parseInt(document.getElementById("hgt.insideX").value);
 
         imgAreaSelect = jQuery((trackImgTbl || trackImg).imgAreaSelect({ selectionColor: 'blue', outerColor: '',
             minHeight: imgHeight, maxHeight: imgHeight,
             onSelectStart: selectStart, onSelectChange: selectChange, onSelectEnd: selectEnd,
             autoHide: autoHideSetting, movable: false,
             clickClipHeight: clickClipHeight}));
     }
 }
 
 function makeItemsEnd(img, selection)
 {
-alert("dragged out x1=" + selection.x1 + " x2=" + selection.x2);
+var image = $(img);
+var imageId = image.attr('id');
+var trackName = imageId.substring('img_data_'.length);
+var chrom = document.getElementById("hgt.chromName").value;
+var pos = selectionPixelsToBases(image, selection);
+var command = document.getElementById('hgt_doJsCommand');
+command.value = "makeItems " + trackName + " " + chrom + " " + pos.chromStart + " " + pos.chromEnd;
+document.TrackHeaderForm.submit();
 return true;
 }
 
 function setUpMakeItemsDrag(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 != undefined && img.length != 0) {
     var trackImgTbl = $('#imgTbl');
     var imgHeight = trackImgTbl.height();
     jQuery(img.imgAreaSelect( { selectionColor: 'green', outerColor: '',
 	minHeight: imgHeight, maxHeight: imgHeight, onSelectEnd: makeItemsEnd,
 	autoHide: true, movable: false}));
     }
 }
 
 function toggleTrackGroupVisibility(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.
     var retval = true;
     var hidden = $("input[name='hgtgroup_"+prefix+"_close']");
     var newVal=1; // we're going - => +
     if($(button) != undefined && $(hidden) != undefined && $(hidden).length > 0) {
         var oldSrc = $(button).attr("src");
         if(arguments.length > 2)
             newVal = arguments[2] ? 0 : 1;
         else
             newVal = oldSrc.indexOf("/remove") > 0 ? 1 : 0;
 
         var newSrc;
         if(newVal == 1) {
             newSrc = oldSrc.replace("/remove", "/add");
             $("tr[id^='"+prefix+"-']").hide();
         } else {
             newSrc = oldSrc.replace("/add", "/remove");
             $("tr[id^='"+prefix+"-']").show();
         }
         $(button).attr("src",newSrc);
         $(hidden).val(newVal);
         // setCartVar("hgtgroup_" + prefix + "_close", newVal);
         retval = false;
     }
     return retval;
 }
 
 function setAllTrackGroupVisibility(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.
     $("img[id$='_button']").each( function (i) {
         if(this.src.indexOf("/remove") > 0 || this.src.indexOf("/add") > 0)
             toggleTrackGroupVisibility(this,this.id.substring(0,this.id.length - 7),newState); // clip '_button' suffix
     });
     return false;
 }
 
 /////////////////////////////////////////////////////
 // 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)
     var img = { top: -1, scrolledTop: -1, height: -1, left: -1, scrolledLeft: -1, width: -1 };  // Image dimensions all in pix
     var chr = { name: "", reverse: false, beg: -1, end: -1, size: -1, top: -1, bottom: -1, left: -1, right: -1, width: -1 };   // chrom Dimenaions beg,end,size in bases, rest in pix
     var pxDown = 0;     // pix X location of mouseDown
     var chrImg = $(this);
     var mouseIsDown   = false;
     var mouseHasMoved = false;
     var hilite = jQuery('<div></div>');
 
     initialize();
 
     function initialize(){
 
         findDimensions();
 
         if(chr.top == -1)
             warn("chromIdeo(): failed to register "+this.id);
         else {
             hiliteSetup();
 
             $('.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;
             //warn("chromIdeo("+chr.name+") selected range (pix):"+pxDown+"-"+pxUp+" chrom range (pix):"+chr.left+"-"+chr.right+" chrom range (bp):"+chr.name+":"+chr.beg+"-"+chr.end);
             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) {
                     if( isWithin(-20,pxUp,chr.left) ) // bounded by chrom dimensions: but must remain within image!
                         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;
                     }
                     //else warn("chromIdeo("+chr.name+") NOT WITHIN HORIZONTAL RANGE\n selected range (pix):"+pxDown+"-"+pxUp+" chrom range (pix):"+chr.left+"-"+chr.right);
                 }
                 if(mouseHasMoved == false) { // Not else because small drag turns this off
 
                     hiliteShow(pxUp,pxUp);
                     var curBeg = parseInt($("#hgt\\.winStart").val());  // Note the escaped '.'
                     var curEnd = parseInt($("#hgt\\.winEnd").val());
                     var curWidth = curEnd - curBeg;
                     selRange.beg = convertToBases(pxUp) - Math.round(curWidth/2); // Notice that beg is based upon up position
                     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)) ) {
                         setPositionByCoordinates(chr.name, selRange.beg, selRange.end)
                         $('.cytoBand').mousedown( function(e) { return false; }); // Stop the presses :0)
                         document.TrackHeaderForm.submit();
                         return true; // Make sure the setTimeout below is not called.
                     }
                 }
             }
             //else warn("chromIdeo("+chr.name+") NOT WITHIN VERTICAL RANGE\n selected range (pix):"+pxDown+"-"+pxUp+" chrom range (pix):"+chr.left+"-"+chr.right+"\n cytoTop-Bottom:"+chr.top +"-"+chr.bottom);
             hiliteCancel();
             setTimeout('blockUseMap=false;',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;
         $('.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, both in pix and bases
         var cyto = { left: -1, right: -1, beg: -1, end: -1 };
         $('.cytoBand').each(function(ix) {
             var loc = this.coords.split(",");
             if(loc.length == 4) {
                 var myLeft  = parseInt(loc[0]);
                 var myRight = parseInt(loc[2]);
                 if(cyto.left == -1 || cyto.left > myLeft) {
                     if( isWithin(myLeft,pxDown,myRight) || isWithin(myLeft,pxUp,myRight) ) {
                         cyto.left  = myLeft;
                         var range = this.title.substr(this.title.lastIndexOf(':')+1)
                         var 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;
                         var range = this.title.substr(this.title.lastIndexOf(':')+1)
                         var 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)
         $(hilite).css({ backgroundColor: 'green', opacity: 0.4, borderStyle: 'solid', borderWidth: '1px', bordercolor: '#0000FF' });
         $p = $(chrImg);
 
         $(hilite).css({ display: 'none', position: 'absolute', overflow: 'hidden', zIndex: 1 });
         jQuery($(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 - $("body").scrollLeft();
         if($.browser.msie) {
             img.height = $(chrImg).outerHeight();
             img.width  = $(chrImg).outerWidth();
         } else {
             img.height = $(chrImg).height();
             img.width  = $(chrImg).width();
         }
         return img;
     }
 });
 }
 /////////////////////////////////////////////////////
 // Drag Reorder Code
 function imgTblSetOrder(table)
 {
 // Sets the 'order' value for the image table after a drag reorder
     $("input[name$='_imgOrd']").each(function (i) {
         var tr = $(this).parents('tr');
         if($(this).val() != $(tr).attr('rowIndex')) {
             //warn('Reordered '+$(this).val() + " to "+$(tr).attr('rowIndex'));
             $(this).val($(tr).attr('rowIndex'));
         }
     });
 }
 
 function imgTblZipButtons(table)
 {
 // Goes through the image and binds composite track buttons when adjacent
     var rows = $(table).find('tr');
     var lastClass="";
     var lastBtn;
     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");
         if( btn.length == 0)
             continue;
         var classList = $( btn ).attr("class").split(" ");
         var curMatchesLast=(classList[0] == lastClass);
         if(lastBtn != undefined) {
             $( lastBtn ).removeClass('btnN btnU btnL btnD');
             if(curMatchesLast && lastMatchLast) {
                 $( lastBtn ).addClass('btnL');
             } else if(lastMatchLast) {
                 $( lastBtn ).addClass('btnU');
             } else if(curMatchesLast) {
                 $( lastBtn ).addClass('btnD');
             } else {
                 $( lastBtn ).addClass('btnN');
                 countN++;
             }
             count++;
             if(altColors) {
                 lastBlue = (lastMatchLast == lastBlue); // lastMatch and lastBlue or not lastMatch and notLastBlue
                 if(lastBlue)    // Too  smart by 1/3rd
                     $( lastBtn ).addClass(    'btnBlue' );
                 else
                     $( lastBtn ).removeClass( 'btnBlue' );
             }
         }
         lastMatchLast = curMatchesLast;
         lastClass = classList[0];
         lastBtn = btn;
     }
     if(lastBtn != undefined) {
         $( lastBtn ).removeClass('btnN btnU btnL btnD');
         if(lastMatchLast) {
             $( btn).addClass('btnU');
         } else {
             $( lastBtn ).addClass('btnN');
             countN++;
         }
         if(altColors) {
                 lastBlue = (lastMatchLast == lastBlue); // lastMatch and lastBlue or not lastMatch and notLastBlue
                 if(lastBlue)    // Too  smart by 1/3rd
                     $( lastBtn ).addClass(    'btnBlue' );
                 else
                     $( lastBtn ).removeClass( 'btnBlue' );
         }
         count++;
     }
     //warn("Zipped "+count+" buttons "+countN+" are independent.");
 }
 
 function initImgTblButtons()
 {
 // Make side buttons visible (must also be called when updating rows in the imgTbl).
     var btns = $("p.btn");
     if(btns.length > 0) {
         imgTblZipButtons($('#imgTbl'));
         $(btns).mouseover( imgTblButtonMouseOver );
         $(btns).mouseout(  imgTblButtonMouseOut  );
         $(btns).show();
     }
 }
 
 function imgTblButtonMouseOver()
 {
 // Highlights a composite set of buttons, regarless of whether tracks are adjacent
     var classList = $( this ).attr("class").split(" ");
     var btns = $( "p." + classList[0] )
     $( btns ).removeClass('btnGrey');
     $( btns ).addClass('btnBlue');
 }
 
 function imgTblButtonMouseOut()
 {
 // Ends compositre highlighting by mouse over
     var classList = $( this ).attr("class").split(" ");
     var btns = $( "p." + classList[0] )
     $( btns ).removeClass('btnBlue');
     $( btns ).addClass('btnGrey');
 }
 
 
 /////////////////////////////////////////////////////
 // Drag Scroll code
 jQuery.fn.panImages = function(imgOffset,imgBoxLeftOffset){
     // globals across all panImages
     var leftLimit   = imgBoxLeftOffset*-1;
     var rightLimit  = (imgBoxPortalWidth - imgBoxWidth + leftLimit);
     var prevX       = (imgOffset + imgBoxLeftOffset)*-1;
     var portalWidth = 0;
     panAdjustHeight(prevX);
 
 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 == undefined || pic == undefined) {
         throw "Not a div with a child image! 'panImages' can only be used with divs contain images.";
     }
 
     // globals across all panImages
     portalWidth     = $(pan).width();
     // globals to one panImage
     var newX        = 0;
     var mouseDownX  = 0;
     var mouseIsDown = false;
     var beyondImage = false;
     var atEdge      = false;
 
     initialize();
 
     function initialize(){
 
         pan.css( 'cursor', 'w-resize');
 
         pan.mousedown(function(e){
             if(mouseIsDown == false) {
                 mouseIsDown = true;
 
                 mouseDownX = e.clientX;
                 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) {
                 blockUseMap = true;
                 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
 
                 var nowPos = newX.toString() + "px";
                 $(".panImg").css( {'left': nowPos });
                 $('.tdData').css( {'backgroundPosition': nowPos } );
                 panUpdatePosition(newX,false);
             }
         }
     }
     function panMouseUp(e) {  // Must be a separate function instead of pan.mouseup event.
         //if(!e) e = window.event;
         if(mouseIsDown) {
 
             $(document).unbind('mousemove',panner);
             $(document).unbind('mouseup',panMouseUp);
             mouseIsDown = false;
 
             // Talk to tim about this.
             if(beyondImage) {
                 // FIXME:
                 // 1) When dragging beyondImage, side label is seen. Only solution may be 2 images!
                 //    NOTE: tried clip:rect() but this only works with position:absolute!
                 // 2) Would be nice to support drag within AND beyond image:
                 //    a) Within stops at border, and then second drag needed to go beyond
                 //    b) Within needs support for next/prev arrows
                 // 3) AJAX does not work on full image.  Larry's callback routine needs extension beyond songle track
                 //$.ajax({type: "GET", url: "../cgi-bin/hgTracks",
                 //    data: "hgt.trackImgOnly=1&hgsid=" + getHgsid(), dataType: "html",
                 //    trueSuccess: handleUpdateTrackMap, success: catchErrorOrDispatch,
                 //    cmd: "wholeImage",  cache: false });
                 document.TrackHeaderForm.submit();
                 return true; // Make sure the setTimeout below is not called.
             }
             if(prevX != newX) {
                 panAdjustHeight(newX);
                 prevX = newX;
             }
             setTimeout('blockUseMap=false;',50); // Necessary incase the selectEnd was over a map item. select takes precedence.
         }
     }
 });
 
     function panUpdatePosition(newOffsetX,bounded)
     {
         // Updates the 'position/search" display with change due to panning
         var portalWidthBases = imgBoxPortalEnd - imgBoxPortalStart;
         var portalScrolledX  = (imgBoxPortalOffsetX+imgBoxLeftLabel) + newOffsetX;
 
         var newPortalStart = imgBoxPortalStart - Math.round(portalScrolledX*imgBoxBasesPerPixel); // As offset goes down, bases seen goes up!
         if( newPortalStart < imgBoxChromStart && bounded)     // Stay within bounds
             newPortalStart = imgBoxChromStart;
         var newPortalEnd = newPortalStart + portalWidthBases;
         if( newPortalEnd > imgBoxChromEnd && bounded) {
             newPortalEnd = imgBoxChromEnd;
             newPortalStart = newPortalEnd - portalWidthBases;
         }
         if(newPortalStart > 0) {
             // XXXX ? imgBoxPortalStart = newPortalStart;
             // XXXX ? imgBoxPortalEnd = newPortalEnd;
             var newPos = document.getElementById("hgt.chromName").value + ":" + commify(newPortalStart) + "-" + commify(newPortalEnd);
             setPosition(newPos, (newPortalEnd - newPortalStart + 1));
         }
         return true;
     }
     function mapTopAndBottom(mapName,left,right)
     {
     // Find the top and bottom px given left and right boundaries
         var span = { 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 < right && aright >= left) {
                     var atop    = parseInt(loc[1]);
                     var abottom = parseInt(loc[3]);
                     if( span.top    < 0 ) {
                         span.top    = atop;
                         span.bottom = abottom;
                     } else if(span.top > atop) {
                             span.top = atop;
                     } else if(span.bottom < abottom) {
                             span.bottom = abottom;
                     }
                 }
             });
         }
         return span;
     }
     function panAdjustHeight(newOffsetX) {
         // Adjust the height of the track data images so that bed items scrolled off screen
         // do not waste vertical real estate
         var left = newOffsetX * -1;
         var right = left + portalWidth;
         $(".panImg").each(function(t) {
             var mapid  = "map_" + this.id.substring(4);
             var hDiv   = $(this).parent();
             var top    = parseInt($(this).css("top")) * -1;
             var bottom = top + $(hDiv).height();
 
             var span = mapTopAndBottom(mapid,left,right);
             if(span.top > 0) {
                 var topdif = Math.abs(span.top - top);
                 var botdif = Math.abs(span.bottom - bottom);
                 if(topdif > 2 || botdif > 2) {
                     $(hDiv).height( span.bottom - span.top );
                     top = span.top * -1;
                     $(this).css( {'top': top.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();
                         top += titlePx;
                     }
                     var side = $("#img_side_"+imgId[2]);
                     if( side.length > 0) {
                         $(side).parent().height( span.bottom - span.top + titlePx);
                         $(side).css( {'top': top.toString() + "px" });
                     }
                     var btn = $("#p_btn_"+imgId[2]);
                     if( btn.length > 0) {
                         $(btn).height( span.bottom - span.top + titlePx);
                     } else {
                         btn = $("#img_btn_"+imgId[2]);
                         if( btn.length > 0) {
                             $(btn).parent().height( span.bottom - span.top + titlePx);
                             $(btn).css( {'top': top.toString() + "px" });
                         }
                     }
                 }
             }
         });
     }
 
 };
 
 /////////////////////////////////////////////////////
 
 function blockTheMap(e)
 {
     blockUseMap=true;
 }
 
 // wait for jStore to prepare the storage engine (this token reload code is experimental and currently dead).
 jQuery.jStore && jQuery.jStore.ready(function(engine) {
     // alert(engine.jri);
     // wait for the storage engine to be ready.
     engine.ready(function(){
         var engine = this;
         var newToken = document.getElementById("hgt.token").value;
         if(newToken) {
             var oldToken = engine.get("token");
             if(oldToken && oldToken == newToken) {
                 // user has hit the back button.
                 jQuery('body').css('cursor', 'wait');
                 window.location = "../cgi-bin/hgTracks?hgsid=" + getHgsid();
             }
         }
         engine.set("token", newToken);
     });
 });
 
 function mapClk(obj)
 {
     return postToSaveSettings(obj);
 }
 
 function postToSaveSettings(obj)
 {
     if(blockUseMap==true) {
         return false;
     }
     if(obj.href == undefined) // called directly with obj and from callback without obj
         obj = this;
     if( obj.href.match('#') || obj.target.length > 0) {
         //alert("Matched # ["+obj.href+"] or has target:"+obj.target);
         return true;
     }
     var thisForm=$(obj).parents('form');
     if(thisForm == undefined || $(thisForm).length == 0)
         thisForm=$("FORM");
     if($(thisForm).length > 1 )
         thisForm=$(thisForm)[0];
     if(thisForm != undefined && $(thisForm).length == 1) {
         //alert("posting form:"+$(thisForm).attr('name'));
         return postTheForm($(thisForm).attr('name'),obj.href);
     }
     return true;
 }
 
 $(document).ready(function()
 {
     var db = getDb();
     if(jQuery.fn.autocomplete && $('input#suggest') && db) {
         $('input#suggest').autocomplete({
                                             delay: 500,
                                             minchars: 2,
                                             ajax_get: ajaxGet(function () {return db;}, new Object),
                                             callback: function (obj) {
                                                 setPosition(obj.id, commify(getSizeFromCoordinates(obj.id)));
                                                 // jQuery('body').css('cursor', 'wait');
                                                 // document.TrackHeaderForm.submit();
                                             }
                                         });
 
         // I want to set focus to the suggest element, but unforunately that prevents PgUp/PgDn from
         // working, which is a major annoyance.
         // $('input#suggest').focus();
     }
     initVars();
 
     if(jQuery.jStore) {
         // Experimental (currently dead) code to handle "user hits back button" problem.
         if(false) {
             jQuery.extend(jQuery.jStore.defaults, {
                               project: 'hgTracks',
                               engine: 'flash',
                               flash: '/jStore.Flash.html'
                           });
         }
         jQuery.jStore.load();
     }
 
     // Convert map AREA gets to post the form, ensuring that cart variables are kept up to date
     if($("FORM").length > 0) {
         var allLinks = $('a');
         $( allLinks ).unbind('click');
         $( allLinks ).click( postToSaveSettings );
     }
     if($('#pdfLink').length == 1) {
         $('#pdfLink').click(function(i) {
             var thisForm=$('#TrackForm');
             if(thisForm != undefined && $(thisForm).length == 1) {
                 //alert("posting form:"+$(thisForm).attr('name'));
                 updateOrMakeNamedVariable($(thisForm),'hgt.psOutput','on');
                 return postTheForm($(thisForm).attr('name'),this.href);
             }
             return true;
         });
     }
     if($('#imgTbl').length == 1) {
         imageV2   = true;
         initImgTblButtons();
         // Make imgTbl allow draw reorder of imgTrack rows
         var imgTable = $(".tableWithDragAndDrop");
         if($(imgTable).length > 0) {
             $(imgTable).tableDnD({
                 onDragClass: "trDrag",
                 dragHandle: "dragHandle",
                 onDragStart: function(table, row) {
                     $(document).bind('mousemove',blockTheMap);
                 },
                 onDrop: function(table, row, dragStartIndex) {
                     if($(row).attr('rowIndex') != dragStartIndex) {
                         if(imgTblSetOrder) {
                             imgTblSetOrder(table);
                         }
                         imgTblZipButtons( table );
                     }
                     $(document).unbind('mousemove',blockTheMap);
                     setTimeout('blockUseMap=false;',50); // Necessary incase the selectEnd was over a map item. select takes precedence.
                 }
             });
         }
         if(imgBoxPortal) {
             //warn("imgBox("+imgBoxChromStart+"-"+imgBoxChromEnd+","+imgBoxWidth+") bases/pix:"+imgBoxBasesPerPixel+"\nportal("+imgBoxPortalStart+"-"+imgBoxPortalEnd+","+imgBoxPortalWidth+") offset:"+imgBoxPortalOffsetX);
 
             // Turn on drag scrolling.
             $("div.scroller").panImages(imgBoxPortalOffsetX,imgBoxLeftLabel);
         }
         //$("#zoomSlider").slider({ min: -4, max: 3, step: 1 });//, handle: '.ui-slider-handle' });
 
         // Temporary warning while new imageV2 code is being worked through
         if($('#map').children("AREA").length > 0) {
             warn('Using imageV2, but old map is not empty!');
         }
     }
     if($('img#chrom').length == 1) {
         if($('.cytoBand').length > 1) {
             $('img#chrom').chromDrag();
         }
     }
 
     {
         var pos = $("input[name='position']");
         if( pos != undefined)
             $( pos ).focus();
     }
 });
 
 function rulerModeToggle (ele)
 {
     autoHideSetting = !ele.checked;
     var obj = imgAreaSelect.data('imgAreaSelect');
     obj.setOptions({autoHide : autoHideSetting});
 }
 
 function makeMapItem(id)
 {
     // Create a dummy mapItem on the fly (for objects that don't have corresponding entry in the map).
     var title;
     var rec = trackDbJson[id];
     if(rec) {
         title = rec.shortLabel;
     } else {
         title = id;
     }
     return {id: id, title: "configure " + title};
 }
 
 function findMapItem(e)
 {
 // Find mapItem for given event; returns item object or null if none found.
     var x,y;
     if(imageV2) {
         // It IS appropriate to use coordinates relative to the img WHEN we have a hit in the right-hand side, but NOT
         // when we have a hit in the left hand elements (which do not have relative coordinates).
         // XXXX still trying to figure this out.
         var pos = $(e.target).position();
         if(e.target.tagName == "IMG") {
             // msie
             // warn("img: x: " + x + ", y:" + y);
             // warn("pageX: " + e.pageX + "; offsetLeft: " + pos.left);
             x = e.pageX - pos.left;
             y = e.pageY - pos.top;
             // warn("x: " + x + "; y: " + y);
         } else {
             x = e.pageX - trackImg.attr("offsetLeft");
             y = e.pageY - trackImg.attr("offsetTop");
         }
         // console.log(trackImg.attr("offsetLeft"), trackImg.attr("offsetTop"));
         // console.log("findMapItem:", x, y);
         // console.dir(mapItems);
     } else {
         x = e.pageX - e.target.offsetLeft;
         y = e.pageY - e.target.offsetTop;
     }
 
     if(e.target.tagName.toUpperCase() == "P") {
         // This occurs in the left buttons when IMAGEv2_DRAG_REORDER is true.
         var a = /p_btn_(.*)/.exec(e.target.id);
         if(a && a[1]) {
             var id = a[1];
             return makeMapItem(id);
         } else {
             return null;
         }
     } else if(e.target.tagName.toUpperCase() == "IMG") {
         // This occurs in the left buttons when IMAGEv2_DRAG_REORDER is false.
         var a = /img_btn_(.*)/.exec(e.target.id);
         if(a && a[1]) {
             var id = a[1];
             return makeMapItem(id);
         }
         // else fall-through (under msie).
     }
 
     var retval = -1;
     // console.log(e.target.tagName + "; " + e.target.id);
     for(var i=0;i<mapItems.length;i++)
     {
         if(mapItems[i].obj && e.target === mapItems[i].obj) {
             // e.target is AREA tag under FF and Safari;
             // This never occurs under IE
             // console.log("Found match by objects comparison");
             retval = i;
             break;
         } else if (!imageV2 || browser == "msie") {
             // Under IE, target is the IMG tag for the map's img and y is relative to the top of that,
             // so we must use the target's src to make sure we are looking at the right map.
             // We start falling through to here under safari under imageV2 once something has been modified
             // (that's a bug I still haven't figured out how to fix).
             if(mapItems[i].r.contains(x, y) && mapItems[i].src == $(e.target).attr('src')) {
                 retval = i;
                 break;
             }
         }
     }
     // showWarning(x + " " + y + " " + retval + " " + e.target.tagName + " " + $(e.target).attr('src'));
     // console.log("findMapItem:", e.clientX, e.clientY, x, y, pos.left, pos.top, retval, mapItems.length, e.target.tagName);
     // console.log(e.clientX, pos);
     if(retval >= 0) {
         return mapItems[retval];
     } else {
         return null;
     }
 }
 
 function mapEvent(e)
 {
     var o = findMapItem(e);
     if(o) {
         e.target.title = o.title;
     } else {
         // XXXX this doesn't work.
         // $('#myMenu').html("<ul id='myMenu' class='contextMenu'><li class='edit'><a href='#img'>Get Image</a></li></ul>");
         e.target.title = originalImgTitle;
     }
 }
 
 function mapMouseDown(e)
 {
     // XXXX Is rightclick logic necessary?
     var rightclick = e.which ? (e.which == 3) : (e.button == 2);
     if(rightclick)
     {
         return false;
     } else {
         var o = findMapItem(e);
         if(o) {
             // XXXX Why does href get changed to "about://" on IE?
             window.location = o.href;
         }
         return true;
     }
 }
 
 function contextMenuHit(menuItemClicked, menuObject, cmd)
 {
     setTimeout(function() { contextMenuHitFinish(menuItemClicked, menuObject, cmd); }, 1);
 }
 
 function contextMenuHitFinish(menuItemClicked, menuObject, cmd)
 {
 // dispatcher for context menu hits
     if(menuObject.shown) {
         // showWarning("Spinning: menu is still shown");
         setTimeout(function() { contextMenuHitFinish(menuItemClicked, menuObject, cmd); }, 10);
         return;
     }
     if(cmd == 'selectWholeGene' || cmd == 'getDna') {
             // bring whole gene into view or redirect to DNA screen.
             var href = selectedMenuItem.href;
             var chromStart, chromEnd;
             var a = /hgg_chrom=(\w+)&/.exec(href);
             // Many links leave out the chrom (b/c it's in the server side cart as "c")
             var chrom = document.getElementById("hgt.chromName").value;
             if(a) {
                 if(a && a[1])
                     chrom = a[1];
                 a = /hgg_start=(\d+)/.exec(href);
                 if(a && a[1])
                     // XXXX does chromStart have to be incremented by 1?
                     chromStart = a[1];
                 a = /hgg_end=(\d+)/.exec(href);
                 if(a && a[1])
                     chromEnd = 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 == null || chromStart == null || chromEnd == null) {
                 showWarning("couldn't parse out genomic coordinates");
             } else {
                 if(cmd == 'getDna')
                 {
                     // start coordinate seems to be off by one (+1).
                     window.open("../cgi-bin/hgc?hgsid=" + getHgsid() + "&g=getDna&i=mixed&c=" + chrom + "&l=" + chromStart + "&r=" + chromEnd);
                 } else {
                     var newPosition = setPositionByCoordinates(chrom, chromStart, chromEnd);
                     if(browser == "safari" || imageV2) {
                         // We need to parse out more stuff to support resetting the position under imageV2 via ajax, but it's probably possible.
                         // See comments below on safari problems.
                         jQuery('body').css('cursor', 'wait');
                         document.TrackForm.submit();
                     } else {
                         jQuery('body').css('cursor', '');
                         $.ajax({
                                    type: "GET",
                                    url: "../cgi-bin/hgTracks",
                                    data: "hgt.trackImgOnly=1&hgt.ideogramToo=1&position=" + newPosition + "&hgsid=" + getHgsid(),
                                    dataType: "html",
                                    trueSuccess: handleUpdateTrackMap,
                                    success: catchErrorOrDispatch,
                                    cmd: cmd,
                                    cache: false
                                });
                     }
                 }
             }
     } else if (cmd == 'hgTrackUi') {
         // data: ?
         jQuery('body').css('cursor', 'wait');
         $.ajax({
                    type: "GET",
                    url: "../cgi-bin/hgTrackUi?ajax=1&g=" + selectedMenuItem.id + "&hgsid=" + getHgsid(),
                    dataType: "html",
                    trueSuccess: handleTrackUi,
                    success: catchErrorOrDispatch,
                    cmd: selectedMenuItem,
                    cache: false
                });
     } else if (cmd == 'dragZoomMode') {
         autoHideSetting = true;
         var obj = imgAreaSelect.data('imgAreaSelect');
         obj.setOptions({autoHide : true, movable: false});
     } else if (cmd == 'hilightMode') {
         autoHideSetting = false;
         var obj = imgAreaSelect.data('imgAreaSelect');
         obj.setOptions({autoHide : false, movable: true});
     } 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).
         var data = "hgt.trackImgOnly=1&hgsid=" + getHgsid();
         jQuery('body').css('cursor', 'wait');
         $.ajax({
                    type: "GET",
                    url: "../cgi-bin/hgTracks",
                    data: data,
                    dataType: "html",
                    trueSuccess: handleViewImg,
                    success: catchErrorOrDispatch,
                    cmd: cmd,
                    cache: false
                });
     } else if (cmd == 'openLink') {
         // XXXX This is blocked by Safari's popup blocker (without any warning message).
         window.open(selectedMenuItem.href);
     } else {
         // Change visibility settings:
         //
         // First change the select on our form:
 
         var id = selectedMenuItem.id;
         var rec = trackDbJson[id];
         if(rec && rec.parentTrack) {
             // currently we fall back to the parentTrack
             id = rec.parentTrack;
         }
         $("select[name=" + id + "]").each(function(t) {
             $(this).val(cmd);
                 });
 
         // Now change the track image
         if(imageV2 && cmd == 'hide')
         {
             // Hide local display of this track and update server side cart.
             setCartVar(id, cmd);
             $('#tr_' + id).remove();
             loadImgAreaSelect(false);
         } else if (false && browser == "safari") {
             // This problem seems to have gone away (I don't see it in Safari AppleWebKit 531.9.1 or
             // Chrome 5.0.335.1.); I'm leaving this dead code here for now in case this problem re-appears.
             //
             // Safari has the following bug: if we update the local 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.
             jQuery('body').css('cursor', 'wait');
             document.TrackForm.submit();
         } else {
             var data = "hgt.trackImgOnly=1&" + id + "=" + cmd + "&hgsid=" + getHgsid();
             if(imageV2) {
 	        data += "&hgt.trackNameFilter=" + id;
             }
             jQuery('body').css('cursor', 'wait');
             $.ajax({
                        type: "GET",
                        url: "../cgi-bin/hgTracks",
                        data: data,
                        dataType: "html",
                        trueSuccess: handleUpdateTrackMap,
                        success: catchErrorOrDispatch,
                        cmd: cmd,
                        cache: false
                    });
         }
     }
 }
 
 function loadContextMenu(img)
 {
     var menu = img.contextMenu(
         function() {
             var menu = [];
             var selectedImg = " <img src='../images/Green_check.png' height='10' width='10' />";
             var done = false;
             if(selectedMenuItem) {
                 var href = selectedMenuItem.href;
                 var isHgc, isGene;
                 if(href) {
                     isGene = href.match("hgGene");
                     isHgc = href.match("hgc");
                 }
                 var rec = trackDbJson[id];
                 var id = selectedMenuItem.id;
                 var rec = trackDbJson[id];
                 if(rec && rec.parentTrack) {
                     // currently we fall back to the parentTrack
                     id = rec.parentTrack;
                 }
                 // XXXX what if select is not available (b/c trackControlsOnMain is off)?
                 // Move functionality to a hidden variable?
                 var select = $("select[name=" + id + "]");
                 var cur = select.val();
                 if(cur) {
                     select.children().each(function(index, o) {
                                                var title = $(this).val();
                                                var str = title;
                                                if(title == cur) {
                                                    str += selectedImg;
                                                }
                                                var o = new Object();
                                                o[str] = {onclick: function (menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, title); return true;}};
                                                menu.push(o);
                                            });
                     done = true;
                 } else {
                     // XXXX currently dead code (unless JSON is enabled in hgTracks.c)
                     if(rec) {
                         // XXXX check current state from a hidden variable.
                         var visibilityStrsOrder = new Array("hide", "dense", "full", "pack", "squish");
                         var visibilityStrs = new Array("hide", "dense", "squish", "pack", "full");
                         for (i in visibilityStrs) {
                             // XXXX use maxVisibility and change hgTracks so it can hide subtracks
                             var o = new Object();
                             var str = visibilityStrs[i];
                             if(rec.canPack || (str != "pack" && str != "squish")) {
                                 if(str == visibilityStrsOrder[rec.visibility]) {
                                     str += selectedImg;
                                 }
                                 o[str] = {onclick: function(menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, visibilityStrs[i]); return true; }};
                                 menu.push(o);
                             }
                         }
                         done = true;
                     }
                 }
                 if(done) {
                     menu.push($.contextMenu.separator);
                     var o = new Object();
                     if(isGene || isHgc) {
                         var title = selectedMenuItem.title || "feature";
                         o["Zoom to " +  title] = {onclick: function(menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, "selectWholeGene"); return true; }};
                         o["Get DNA for " +  title] = {onclick: function(menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, "getDna"); return true; }};
                         o["Open details page in new window"] = {onclick: function(menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, "openLink"); return true; }};
                     } else {
                         o[selectedMenuItem.title] = {onclick: function(menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, "hgTrackUi"); return true; }};
                     }
                     menu.push(o);
                 }
             }
             if(!done) {
                 if(false) {
                     // Currently toggling b/n drag-and-zoom mode and hilite mode is disabled b/c we don't know how to keep hilite mode from disabling the
                     // context menus.
                     var o = new Object();
                     var str = "drag-and-zoom mode";
                     if(autoHideSetting) {
                         str += selectedImg;
                         // menu[str].className = 'context-menu-checked-item';
                     }
                     o[str] = { onclick: function(menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, "dragZoomMode"); return true; }};
                     menu.push(o);
                     o = new Object();
                     // console.dir(ele);
                     str = "hilight mode";
                     if(!autoHideSetting) {
                         str += selectedImg;
                     }
                     o[str] = { onclick: function(menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, "hilightMode"); return true; }};
                     menu.push(o);
                 }
                 menu.push({"view image": {onclick: function(menuItemClicked, menuObject) { contextMenuHit(menuItemClicked, menuObject, "viewImg"); return true; }}});
             }
             return menu;
         },
         {
             beforeShow: function(e) {
                 // console.log(mapItems[selectedMenuItem]);
                 selectedMenuItem = findMapItem(e);
                 // XXXX? blockUseMap = true;
             },
             hideCallback: function() {
                 // this doesn't work
                 warn("hideCallback");
             }
         });
     return;
 }
 
 function parseMap(ele, reset)
 {
 // Parse the jQuery <map> object into returned mapItems array (ele needn't be the element attached to current document).
         if(reset || !mapItems) {
             mapItems = new Array();
         }
         if(ele) {
                 var i = mapItems.length;
                 // src is necessary under msie
                 var src = ele.next().attr('src');
                 ele.children().each(function() {
                                       mapItems[i++] = {
                                           r : new Rectangle(this.coords),
                                           href : this.href,
                                           title : this.title,
                                           id : this.id,
                                           src : src,
                                           obj : this
                                       };
                                   });
     }
     return mapItems;
 }
 
 function handleTrackUi(response, status)
 {
 // Take html from hgTrackUi and put it up as a modal dialog.
 
     $('#hgTrackUiDialog').html("<div style='font-size:80%'>" + response + "</div>");
     $('#hgTrackUiDialog').dialog({
                                ajaxOptions: {
                                    // This doesn't work
                                    cache: true
                                },
                                resizable: true,
                                bgiframe: true,
                                height: 'auto',
                                width: 'auto',
                                minHeight: 200,
                                minWidth: 400,
                                modal: true,
                                closeOnEscape: true,
                                autoOpen: false,
                                close: function() {
                                    // clear out html after close to prevent problems caused by duplicate html elements
                                    $('#hgTrackUiDialog').html("");
                                }
                            });
     // Apparently the options above to dialog take only once, so we set title explicitly.
     $('#hgTrackUiDialog').dialog('option' , 'title' , trackDbJson[this.cmd.id].shortLabel + " Track Settings");
     jQuery('body').css('cursor', '');
     $('#hgTrackUiDialog').dialog('open');
 }
 
 function handleUpdateTrackMap(response, status)
 {
 // Handle ajax response with an updated trackMap image (gif or png) and map.
 //
 // this.cmd can be used to figure out which menu item triggered this.
 //
 // e.g.: <IMG SRC = "../trash/hgtIdeo/hgtIdeo_hgwdev_larrym_61d1_8b4a80.gif" BORDER=1 WIDTH=1039 HEIGHT=21 USEMAP=#ideoMap id='chrom'>
     // Parse out new ideoGram url (if available)
     var a = /<IMG([^>]+SRC[^>]+id='chrom'[^>]*)>/.exec(response);
     if(a && a[1]) {
         b = /SRC\s*=\s*"([^")]+)"/.exec(a[1]);
         if(b[1]) {
             $('#chrom').attr('src', b[1]);
         }
     }
     if(imageV2 && this.cmd && this.cmd != 'wholeImage' && this.cmd != 'selectWholeGene') {
           // 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 = selectedMenuItem.id;
           var rec = trackDbJson[id];
           if(rec && rec.parentTrack) {
               // currently we fall back to the parentTrack
               id = rec.parentTrack;
           }
           var str = "<TR id='tr_" + id + "'[^>]*>([\\s\\S]+?)</TR>";
           var reg = new RegExp(str);
           a = reg.exec(response);
           if(a && a[1]) {
 //               $('#tr_' + id).html();
 //               $('#tr_' + id).empty();
                $('#tr_' + id).html(a[1]);
                // XXXX move following to a shared method
                parseMap(null, true);
                $("map[name!=ideoMap]").each( function(t) { parseMap($(this, false));});
                initImgTblButtons();
                loadImgAreaSelect(false);
                // Do NOT reload context menu (otherwise we get the "context menu sticks" problem).
                // loadContextMenu($('#tr_' + id));
                if(trackImgTbl.tableDnDUpdate)
                    trackImgTbl.tableDnDUpdate();
           } else {
                showWarning("Couldn't parse out new image for id: " + id);
           }
     } else {
         if(imageV2) {
             a= /<TABLE id=\'imgTbl\'[^>]*>([\S\s]+?)<\/TABLE>/.exec(response);
             if(a[1]) {
                 // This doesn't work (much weirdness ensues).
                 $('#imgTbl').html(a[1]);
             } else {
                 showWarning("Couldn't parse out new image");
             }
         } else {
             a= /<IMG([^>]+SRC[^>]+id='trackMap[^>]*)>/.exec(response);
             // Deal with a is null
             if(a[1]) {
                     var b = /WIDTH\s*=\s*['"]?(\d+)['"]?/.exec(a[1]);
                     var width = b[1];
                     b = /HEIGHT\s*=\s*['"]?(\d+)['"]?/.exec(a[1]);
                     var height = b[1];
                     b = /SRC\s*=\s*"([^")]+)"/.exec(a[1]);
                     var src = b[1];
                     $('#trackMap').attr('src', src);
                     var obj = imgAreaSelect.data('imgAreaSelect');
                     if(width) {
                         trackImg.attr('width', width);
                     }
                     if(height) {
                         trackImg.attr('height', height);
 
                         // obj.setOptions({minHeight : height, maxHeight: height});
                         // obj.getOptions().minHeight = height;
         		// obj.getOptions().maxHeight = height;
                         // XXX doesn't work obj.options.maxHeight = height;
                         // This doesn't work: obj.windowResize();
                         // This works, but causes weird error IF we also change minHeight and maxHeight.
                         // jQuery(window).triggerHandler("resize");
 
                        // After much debugging, I found the best way to have imgAreaSelect continue to work
                        // was to reload it:
                        loadImgAreaSelect(false);
                        // XXX this doesn't work (i.e. does't make the re-sized row draggable under safari).
                        trackImgTbl.tableDnD();
                    }
             } else {
                 showWarning("Couldn't parse out new image");
             }
         }
         // now pull out and parse the map.
         a = /<MAP id='map' Name=map>([\s\S]+)<\/MAP>/.exec(response);
         if(a[1]) {
             var $map = $('<map>' + a[1] + '</map>');
             parseMap($map, true);
         } else {
             showWarning("Couldn't parse out map");
         }
     }
     jQuery('body').css('cursor', '');
 }
 
 function handleViewImg(response, status)
 {
     jQuery('body').css('cursor', '');
     for (var id in trackDbJson) {
         // Use an arbitrary id to pull out a src from the track image table;
         // e.g.: <IMG id='img_data_knownGene' src='../trash/hgt/hgt_hgwdev_larrym_479c_abde90.png' ...>
         var str = "<IMG[^>]*id='img_data_" + id + "'[^>]*src='([^']+)'";
         var reg = new RegExp(str);
         a = reg.exec(response);
         if(a && a[1]) {
             window.open(a[1]);
             return;
         }
     }
     showWarning("Couldn't parse out img src");
 }
 
 function jumpButtonOnClick()
 {
 // onClick handler for the "jump" button.
 // Handles situation where user types a gene name into the gene box and immediately hits the jump button,
 // expecting the browser to jump to that gene.
     var gene = $('#suggest').val();
     var db = getDb();
     if(gene && db && gene.length > 0 && (getOriginalPosition() == getPosition() || getPosition().length == 0)) {
         pos = lookupGene(db, gene);
         if(pos) {
             setPosition(pos, null);
         } else {
             // turn this into a full text search.
             setPosition(gene, null);
         }
     }
     return true;
 }

