- " +
- "
- Hold Shift+drag to show this dialog" + - "
- Hold Alt+drag (Windows) or Option+drag (Mac) to add a highlight" + - "
- Hold Ctrl+drag (Windows) or Cmd+drag (Mac) to zoom" + - "
- To cancel, press Esc anytime during the drag" + - "
- Using the keyboard, highlight the current position with h then m" + - "
- Clear all highlights with View - Clear Highlights or h then c" + - "
- Clear specific highlights with right click > Remove highlight" + - "
- To merely save the color for the next keyboard or right-click > Highlight operations, click 'Save Color' below" + - "
" +
+ "
\n"; @@ -1212,7 +1212,7 @@ var dragSelect = { var start = pos.start - 1; var end = pos.end; var selectedRegions = 0; - for (i = 0, len = hgTracks.windows.length; i < len; ++i) { + 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) { @@ -1220,7 +1220,7 @@ var dragSelect = { var e = Math.min(end, w.virtEnd); var cs = s - w.virtStart + w.winStart; var ce = e - w.virtStart + w.winStart; - str2 += "" + w.chromName + ":" + (cs + 1) + "-" + ce + " \n";
+ str2 += "" + w.chromName + ":" + (cs+1) + "-" + ce + " \n";
selectedRegions += 1;
}
}
@@ -1233,81 +1233,81 @@ var dragSelect = {
$("#dragSelectPosition").html(newPosition);
}
$(dragSelectDialog).dialog({
- modal: true,
- title: "Drag-and-select",
- closeOnEscape: true,
- resizable: false,
- autoOpen: false,
- revertToOriginalPos: true,
- minWidth: 550,
- buttons: {
- "Zoom In": function () {
- // Zoom to selection
- $(this).dialog("option", "revertToOriginalPos", false);
- if ($("#disableDragHighlight").prop('checked'))
- hgTracks.enableHighlightingDialog = false;
- if (imageV2.inPlaceUpdate) {
- if (hgTracks.virtualSingleChrom && (newPosition.search("multi:") === 0)) {
- newPosition = genomePos.disguisePosition(newPosition); // DISGUISE
+ modal: true,
+ title: "Drag-and-select",
+ closeOnEscape: true,
+ resizable: false,
+ autoOpen: false,
+ revertToOriginalPos: true,
+ minWidth: 550,
+ buttons: {
+ "Zoom In": function() {
+ // Zoom to selection
+ $(this).dialog("option", "revertToOriginalPos", false);
+ if ($("#disableDragHighlight").prop('checked'))
+ hgTracks.enableHighlightingDialog = false;
+ if (imageV2.inPlaceUpdate) {
+ if (hgTracks.virtualSingleChrom && (newPosition.search("multi:")===0)) {
+ newPosition = genomePos.disguisePosition(newPosition); // DISGUISE
+ }
+ var params = "db=" + getDb() + "&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();
}
- var params = "db=" + getDb() + "&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");
+ },
+ "Single Highlight": function() {
+ // Clear old highlight and Highlight selection
+ $(imageV2.imgTbl).imgAreaSelect({hide:true});
+ if ($("#disableDragHighlight").prop('checked'))
+ hgTracks.enableHighlightingDialog = false;
+ var hlColor = $("#hlColorInput").val();
+ dragSelect.highlightThisRegion(newPosition, false, hlColor);
+ $(this).dialog("close");
+ },
+ "Add Highlight": function() {
+ // Highlight selection
+ if ($("#disableDragHighlight").prop('checked'))
+ hgTracks.enableHighlightingDialog = false;
+ var hlColor = $("#hlColorInput").val();
+ dragSelect.highlightThisRegion(newPosition, true, hlColor);
+ $(this).dialog("close");
+ },
+ "Save Color": function() {
+ var hlColor = $("#hlColorInput").val();
+ dragSelect.saveHlColor( hlColor );
+ $(this).dialog("close");
+ },
+ "Cancel": function() {
+ $(this).dialog("close");
}
- $(this).dialog("close");
},
- "Single Highlight": function () {
- // Clear old highlight and Highlight selection
- $(imageV2.imgTbl).imgAreaSelect({hide: true});
- if ($("#disableDragHighlight").prop('checked'))
- hgTracks.enableHighlightingDialog = false;
- var hlColor = $("#hlColorInput").val();
- dragSelect.highlightThisRegion(newPosition, false, hlColor);
- $(this).dialog("close");
+
+ open: function () { // Make zoom the focus/default action
+ $(this).parents('.ui-dialog-buttonpane button:eq(0)').trigger("focus");
},
- "Add Highlight": function () {
- // Highlight selection
+
+ close: function() {
+ // All exits to dialog should go through this
+ $(imageV2.imgTbl).imgAreaSelect({hide:true});
+ if ($(this).dialog("option", "revertToOriginalPos"))
+ genomePos.revertToOriginalPos();
if ($("#disableDragHighlight").prop('checked'))
- hgTracks.enableHighlightingDialog = false;
- var hlColor = $("#hlColorInput").val();
- dragSelect.highlightThisRegion(newPosition, true, hlColor);
- $(this).dialog("close");
- },
- "Save Color": function () {
- var hlColor = $("#hlColorInput").val();
- dragSelect.saveHlColor(hlColor);
- $(this).dialog("close");
- },
- "Cancel": function () {
- $(this).dialog("close");
+ $(this).remove();
+ else
+ $(this).hide();
+ $('body').css('cursor', ''); // Occasionally wait cursor got left behind
+ $("#hlColorPicker").spectrum("hide");
}
- },
-
- open: function () { // Make zoom the focus/default action
- $(this).parents('.ui-dialog-buttonpane button:eq(0)').trigger("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").prop('checked'))
- $(this).remove();
- else
- $(this).hide();
- $('body').css('cursor', ''); // Occasionally wait cursor got left behind
- $("#hlColorPicker").spectrum("hide");
- }
});
$(dragSelectDialog).dialog('open');
-
+
},
selectEnd: function (img, selection, event)
@@ -1329,25 +1329,25 @@ var dragSelect = {
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 singleClick = ( (selection.x2 === selection.x1)
+ || dragSelect.startTime === null
+ || (now.getTime() - dragSelect.startTime) < 100);
var newPosition = genomePos.update(img, selection, singleClick);
newPosition.replace("virt:", "multi:");
if (newPosition) {
if (event.altKey) {
// with the alt-key, only highlight the region, do not zoom
dragSelect.highlightThisRegion(newPosition, true);
- $(imageV2.imgTbl).imgAreaSelect({hide: true});
+ $(imageV2.imgTbl).imgAreaSelect({hide:true});
} else {
if (hgTracks.enableHighlightingDialog && !(event.metaKey || event.ctrlKey))
// don't show the dialog if: clicked on ruler, if dialog deactivated or meta/ctrl was pressed
dragSelect.selectionEndDialog(newPosition);
else {
// in every other case, show the dialog
- $(imageV2.imgTbl).imgAreaSelect({hide: true});
+ $(imageV2.imgTbl).imgAreaSelect({hide:true});
if (imageV2.inPlaceUpdate) {
- if (hgTracks.virtualSingleChrom && (newPosition.search("multi:") === 0)) {
+ if (hgTracks.virtualSingleChrom && (newPosition.search("multi:")===0)) {
newPosition = genomePos.disguisePosition(newPosition); // DISGUISE
}
imageV2.navigateInPlace("db=" + getDb() + "&position=" + newPosition, null, true);
@@ -1358,12 +1358,12 @@ var dragSelect = {
}
}
} else {
- $(imageV2.imgTbl).imgAreaSelect({hide: true});
+ $(imageV2.imgTbl).imgAreaSelect({hide:true});
genomePos.revertToOriginalPos();
}
dragSelect.startTime = null;
// blockMapClicks/allowMapClicks() is necessary if selectEnd was over a map item.
- setTimeout(posting.allowMapClicks, 50);
+ setTimeout(posting.allowMapClicks,50);
return true;
}
},
@@ -1373,10 +1373,10 @@ var dragSelect = {
var imgHeight = 0;
if (imageV2.enabled)
imgHeight = imageV2.imgTbl.innerHeight() - 1; // last little bit makes border look ok
-
+
// No longer disable without ruler, because shift-drag still works
- if (typeof (hgTracks) !== "undefined") {
+ if (typeof(hgTracks) !== "undefined") {
if (hgTracks.rulerClickHeight === undefined || hgTracks.rulerClickHeight === null)
hgTracks.rulerClickHeight = 0; // will be zero if no ruler track
@@ -1385,32 +1385,32 @@ var dragSelect = {
var xLimits = genomePos.getXLimits($(imageV2.imgTbl), 0);
dragSelect.areaSelector = jQuery((imageV2.imgTbl).imgAreaSelect({
- minX: xLimits[0],
- maxX: xLimits[1],
- 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,
+ minX : xLimits[0],
+ maxX : xLimits[1],
+ 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
}));
// remove any ongoing drag-selects when the esc key is pressed anywhere for this document
// This allows to abort zooming / highlighting
- $(document).on("keyup", function (e) {
- if (e.keyCode === 27) {
- $(imageV2.imgTbl).imgAreaSelect({hide: true});
+ $(document).on("keyup", function(e){
+ if(e.keyCode === 27) {
+ $(imageV2.imgTbl).imgAreaSelect({hide:true});
dragSelect.escPressed = true;
}
});
// hide and redraw all current highlights when the browser window is resized
- $(window).on("resize", function () {
- $(imageV2.imgTbl).imgAreaSelect({hide: true});
+ $(window).on("resize", function() {
+ $(imageV2.imgTbl).imgAreaSelect({hide:true});
imageV2.drawHighlights();
});
@@ -1418,525 +1418,525 @@ var dragSelect = {
}
};
+ /////////////////////////////////////
+ //// Chrom Drag/Zoom/Expand code ////
/////////////////////////////////////
-//// 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').off('mousedown'); // Make sure this is only bound once
- $('area.cytoBand').on("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).on('mousemove', chromMove);
- $(document).on('mouseup', chromUp);
- hiliteShow(pxDown, pxDown);
- return false;
- }
- });
- }
- }
+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();
- 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);
+ $('area.cytoBand').off('mousedown'); // Make sure this is only bound once
+ $('area.cytoBand').on("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).on('mousemove',chromMove);
+ $(document).on( '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).off('mousemove', chromMove);
- $(document).off('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);
- }
+ }
+ function chromUp(e)
+ { // If mouse was down, handle final selection
+ $(document).off('mousemove',chromMove);
+ $(document).off('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;
+ }
+ 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)) {
+ if ( isWithin(chr.left,pxUp,chr.right+1) ) {
- selRange.beg = convertToBases(pxDown);
- selRange.end = convertToBases(pxUp);
+ 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 (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
+ }
+ 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;
+ 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 > -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').on("mousedown", function(e) { return false; });
- if (imageV2.backSupport) {
- imageV2.navigateInPlace("db=" + getDb() + "&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.
- }
+ //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').on("mousedown", function(e) { return false; });
+ if (imageV2.backSupport) {
+ imageV2.navigateInPlace("db=" + getDb() + "&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;
+ 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 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]);
- }
+ 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) {
+ 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]);
- //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", "");
+ 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
+
}
- });
- chr.size = (chr.end - chr.beg);
- chr.width = (chr.right - chr.left);
- }
+ $(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]));
- }
+ 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]));
- }
+ }
+ 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("");
- $(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 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 img;
}
- });
+ 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("");
+ $(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 = $(chrImg).width();
+ }
+ return img;
+ }
+});
};
+ //////////////////////////
+ //// Drag Scroll code ////
//////////////////////////
-//// Drag Scroll code ////
-//////////////////////////
-jQuery.fn.panImages = function () {
+jQuery.fn.panImages = function(){
// globals across all panImages
genomePos.original = genomePos.getOriginalPos(); // redundant but makes certain original is set.
- var leftLimit = hgTracks.imgBoxLeftLabel * -1;
- var rightLimit = (hgTracks.imgBoxPortalWidth - hgTracks.imgBoxWidth + leftLimit);
+ var leftLimit = hgTracks.imgBoxLeftLabel * -1;
+ var rightLimit = (hgTracks.imgBoxPortalWidth - hgTracks.imgBoxWidth + leftLimit);
var only1xScrolling = ((hgTracks.imgBoxWidth - hgTracks.imgBoxPortalWidth) === 0);
- var prevX = (hgTracks.imgBoxPortalOffsetX + hgTracks.imgBoxLeftLabel) * -1;
+ var prevX = (hgTracks.imgBoxPortalOffsetX + hgTracks.imgBoxLeftLabel) * -1;
var portalWidth = 0;
var portalAbsoluteX = 0;
var savedPosition;
- var highlightAreas = null; // Used to ensure dragSelect highlight will scroll.
+ var highlightAreas = null; // Used to ensure dragSelect highlight will scroll.
- this.each(function () {
+ this.each(function(){
- var pic;
- var pan;
+ var pic;
+ var pan;
- if ($(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();
+ 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
+ }
- function initialize() {
+ if (!pan || !pic) {
+ throw "Not a div with child image! 'panImages' can only be used with divs contain images.";
+ }
- $(pan).parents('td.tdData').on("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
- });
+ // 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').on("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);
+ panAdjustHeight(prevX);
- pan.on("mousedown", function (e) {
- if (e.which > 1 || e.button > 1 || e.shiftKey || e.metaKey || e.altKey || e.ctrlKey)
- return true;
- if (mouseIsDown === false) {
- if (rightClick.menu) {
- rightClick.menu.hide();
- }
- mouseIsDown = true;
- mouseDownX = e.clientX;
- highlightAreas = $('.highlightItem');
- atEdge = (!beyondImage && (prevX >= leftLimit || prevX <= rightLimit));
- $(document).on('mousemove', panner);
- $(document).on('mouseup', panMouseUp); // Will exec only once
- return false;
+ pan.on("mousedown", function(e){
+ if (e.which > 1 || e.button > 1 || e.shiftKey || e.metaKey || e.altKey || e.ctrlKey)
+ return true;
+ if (mouseIsDown === false) {
+ if (rightClick.menu) {
+ rightClick.menu.hide();
}
- });
- }
-
- function panner(e) {
- //if (!e) e = window.event;
- if (mouseIsDown) {
- var relativeX = (e.clientX - mouseDownX);
+ mouseIsDown = true;
+ mouseDownX = e.clientX;
+ highlightAreas = $('.highlightItem');
+ atEdge = (!beyondImage && (prevX >= leftLimit || prevX <= rightLimit));
+ $(document).on('mousemove',panner);
+ $(document).on('mouseup', panMouseUp); // Will exec only once
+ return false;
+ }
+ });
+ }
- 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
-
- posStatus = panUpdatePosition(newX, true);
- newX = posStatus.newX;
- // do not update highlights if we are at the end of a chromsome
- if (!posStatus.isOutsideChrom)
- scrollHighlight(relativeX);
-
- var nowPos = newX.toString() + "px";
- $(".panImg").css({'left': nowPos});
- $('.tdData').css({'backgroundPosition': nowPos});
- if (!only1xScrolling)
- panAdjustHeight(newX); // Will dynamically resize image while scrolling.
+ 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
+
+ posStatus = panUpdatePosition(newX,true);
+ newX = posStatus.newX;
+ // do not update highlights if we are at the end of a chromsome
+ if (!posStatus.isOutsideChrom)
+ scrollHighlight(relativeX);
+
+ var nowPos = newX.toString() + "px";
+ $(".panImg").css( {'left': nowPos });
+ $('.tdData').css( {'backgroundPosition': nowPos } );
+ 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).off('mousemove', panner);
- $(document).off('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 (highlightAreas)
- imageV2.drawHighlights();
- return true;
- }
+ }
+ function panMouseUp(e) { // Must be a separate function instead of pan.mouseup event.
+ //if (!e) e = window.event;
+ if (mouseIsDown) {
- // Do we need to fetch anything?
- if (beyondImage) {
- if (imageV2.inPlaceUpdate) {
- var pos = parsePosition(genomePos.get());
- imageV2.navigateInPlace("db=" + getDb() + "&position=" +
+ dragMaskClear();
+ $(document).off('mousemove',panner);
+ $(document).off('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 (highlightAreas)
+ imageV2.drawHighlights();
+ return true;
+ }
+
+ // Do we need to fetch anything?
+ if (beyondImage) {
+ if (imageV2.inPlaceUpdate) {
+ var pos = parsePosition(genomePos.get());
+ imageV2.navigateInPlace("db=" + getDb() + "&position=" +
encodeURIComponent(pos.chrom + ":" + pos.start + "-" + pos.end),
null, true);
- } else {
- document.TrackHeaderForm.submit();
- }
- return true; // Make sure the setTimeout below is not called.
+ } 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";
- }
+ // 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)
@@ -1944,16 +1944,16 @@ jQuery.fn.panImages = function () {
// 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 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);
+ Math.round(portalScrolledX*hgTracks.imgBoxBasesPerPixel);
else
newPortalStart = closedPortalStart - // As offset goes down, bases seen goes up!
- Math.round(portalScrolledX * hgTracks.imgBoxBasesPerPixel);
+ Math.round(portalScrolledX*hgTracks.imgBoxBasesPerPixel);
if (newPortalStart < hgTracks.chromStart && bounded) { // Stay within bounds
newPortalStart = hgTracks.chromStart;
recalculate = true;
@@ -1968,16 +1968,17 @@ jQuery.fn.panImages = function () {
var newPos = hgTracks.chromName + ":" + newPortalStart + "-" + newPortalEnd;
genomePos.set(newPos); // no need to change the size
}
- if (recalculate && hgTracks.imgBoxBasesPerPixel > 0) {
+ if (recalculate && hgTracks.imgBoxBasesPerPixel > 0) {
// Need to recalculate X for bounding drag
portalScrolledX = (closedPortalStart - newPortalStart) / hgTracks.imgBoxBasesPerPixel;
- newOffsetX = portalScrolledX - (hgTracks.imgBoxPortalOffsetX + hgTracks.imgBoxLeftLabel);
+ newOffsetX = portalScrolledX - (hgTracks.imgBoxPortalOffsetX+hgTracks.imgBoxLeftLabel);
}
if (typeof (igv) !== "undefined") {
- igv.updateIgvStartPosition(newPortalStart);
+ igv.updateIgvStartPosition(newPortalStart);
}
+
ret = {};
ret.newX = newOffsetX;
ret.isOutsideChrom = recalculate;
@@ -1985,24 +1986,24 @@ jQuery.fn.panImages = function () {
}
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) {
+ // 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]);
+ var aleft = parseInt(loc[0]);
+ var aright = parseInt(loc[2]);
if (aleft < west && aright >= east) {
- var atop = parseInt(loc[1]);
+ var atop = parseInt(loc[1]);
var abottom = parseInt(loc[3]);
- if (mapPortal.top < 0) {
- mapPortal.top = atop;
+ if (mapPortal.top < 0 ) {
+ mapPortal.top = atop;
mapPortal.bottom = abottom;
} else if (mapPortal.top > atop) {
- mapPortal.top = atop;
+ mapPortal.top = atop;
} else if (mapPortal.bottom < abottom) {
- mapPortal.bottom = abottom;
+ mapPortal.bottom = abottom;
}
}
});
@@ -2019,42 +2020,42 @@ jQuery.fn.panImages = function () {
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();
+ $(".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);
+ 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);
+ $(hDiv).height( mapPortal.bottom - mapPortal.top );
north = mapPortal.top * -1;
- $(this).css({'top': north.toString() + "px"});
+ $(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]);
+ var center = $("#img_center_"+imgId[2]);
if (center.length > 0) {
titlePx = $(center).parent().height();
north += titlePx;
}
- var side = $("#img_side_" + imgId[2]);
+ var side = $("#img_side_"+imgId[2]);
if (side.length > 0) {
- $(side).parent().height(mapPortal.bottom - mapPortal.top + titlePx);
- $(side).css({'top': north.toString() + "px"});
+ $(side).parent().height( mapPortal.bottom - mapPortal.top + titlePx);
+ $(side).css( {'top': north.toString() + "px" });
}
- var btn = $("#p_btn_" + imgId[2]);
+ var btn = $("#p_btn_"+imgId[2]);
if (btn.length > 0) {
- $(btn).height(mapPortal.bottom - mapPortal.top + titlePx);
+ $(btn).height( mapPortal.bottom - mapPortal.top + titlePx);
} else {
- btn = $("#img_btn_" + imgId[2]);
+ btn = $("#img_btn_"+imgId[2]);
if (btn.length > 0) {
- $(btn).parent().height(mapPortal.bottom - mapPortal.top + titlePx);
- $(btn).css({'top': top.toString() + "px"});
+ $(btn).parent().height( mapPortal.bottom - mapPortal.top + titlePx);
+ $(btn).css( {'top': top.toString() + "px" });
}
}
}
@@ -2063,7 +2064,7 @@ jQuery.fn.panImages = function () {
dragMaskResize(); // Resizes the dragMask to match current image size
}
- function dragMaskShow()
+ function dragMaskShow()
{ // Sets up the dragMask to show grabbing cursor within image
// and not allowed north and south of image
var imgTbl = $('#imgTbl');
@@ -2074,45 +2075,45 @@ jQuery.fn.panImages = function () {
dragMask = $('div#dragMask');
}
- $('body').css('cursor', 'not-allowed');
- $(dragMask).css('cursor', "url(../images/grabbing.cur),w-resize");
+ $('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' });
+ top: $(imgTbl).position().top.toString() + 'px',
+ height: $(imgTbl).height().toString() + 'px' });
}
- function dragMaskResize()
+ 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());
+ $(dragMask).height( $(imgTbl).height() );
}
}
function dragMaskClear() { // Clears the dragMask
- $('body').css('cursor', 'auto');
- var dragMask = normed($('#dragMask'));
+ $('body').css('cursor','auto');
+ var dragMask = normed($('#dragMask'));
if (dragMask)
$(dragMask).hide();
}
- function scrollHighlight(relativeX)
+ function scrollHighlight(relativeX)
// Scrolls the highlight region if one exists
- {
+ {
if (highlightAreas) {
- for (i = 0; i < highlightAreas.length; i++) {
+ for (i=0; i
- "+
+ "
- Hold Shift+drag to show this dialog" + + "
- Hold Alt+drag (Windows) or Option+drag (Mac) to add a highlight" + + "
- Hold Ctrl+drag (Windows) or Cmd+drag (Mac) to zoom" + + "
- To cancel, press Esc anytime during the drag" + + "
- Using the keyboard, highlight the current position with h then m" + + "
- Clear all highlights with View - Clear Highlights or h then c" + + "
- Clear specific highlights with right click > Remove highlight" + + "
- To merely save the color for the next keyboard or right-click > Highlight operations, click 'Save Color' below" + + "
" +
- "Don't show this again and always zoom with shift.
" + - "Re-enable via 'View - Configure Browser' (c then f)
" +
- "Selected chromosome position: ");
+ $("#dragSelectDialog").append("" + - "Re-enable via 'View - Configure Browser' (c then f)
" +
+ "Don't show this again and always zoom with shift.
" + + "Re-enable via 'View - Configure Browser' (c then f)
"+
+ "Selected chromosome position: ");
dragSelectDialog = $("#dragSelectDialog")[0];
// reset value
// allow to click checkbox by clicking on the label
$('#hlNotShowAgainMsg').on("click", function() { $('#disableDragHighlight').trigger("click");});
// click "add highlight" when enter is pressed in color input box
- $("#hlColorInput").on("keyup", function (event) {
- if (event.keyCode == 13) {
+ $("#hlColorInput").on("keyup", function(event){
+ if(event.keyCode == 13){
$(".ui-dialog-buttonset button:nth-child(3)").trigger("click");
}
});
}
if (hgTracks.windows) {
- var i, len;
+ var i,len;
var newerPosition = newPosition;
- if (hgTracks.virtualSingleChrom && (newPosition.search("multi:") === 0)) {
+ if (hgTracks.virtualSingleChrom && (newPosition.search("multi:")===0)) {
newerPosition = genomePos.disguisePosition(newPosition);
}
var str = newerPosition + "" + + "Re-enable via 'View - Configure Browser' (c then f)
\n"; @@ -1212,7 +1212,7 @@ var dragSelect = { var start = pos.start - 1; var end = pos.end; var selectedRegions = 0; - for (i = 0, len = hgTracks.windows.length; i < len; ++i) { + 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) { @@ -1220,7 +1220,7 @@ var dragSelect = { var e = Math.min(end, w.virtEnd); var cs = s - w.virtStart + w.winStart; var ce = e - w.virtStart + w.winStart; - str2 += "
");
- $('#myPromptText').on('keypress', function (e) {
+ msg + "");
+ $('#myPromptText').on('keypress', function(e) {
if (e.which === 13) { // listens for return key
e.preventDefault(); // prevents return from also submitting whole form
$("#myPrompt").dialog("close");
@@ -2315,22 +2316,22 @@ var rightClick = {
}
});
$("#myPrompt").dialog({
- modal: true,
- closeOnEscape: true,
- buttons: { "OK": function() {
- var myPromptText = $("#myPromptText").val();
- $(this).dialog("close");
- callback(myPromptText);
- }
- }
- });
+ 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);
+ setTimeout( function() {
+ rightClick.hitFinish(menuItemClicked, menuObject, cmd, args);
+ }, 1);
},
hitFinish: function (menuItemClicked, menuObject, cmd, args)
@@ -2342,126 +2343,126 @@ var rightClick = {
var row = null;
var rows = null;
var selectUpdated = null;
- function mySuccess() {}
+ function mySuccess() {}
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));
+ // 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));
+ 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, true);
- }
+ if (result.chromStart != -1)
+ {
+ var newPos2 = hgTracks.chromName+":"+(result.chromStart+1)+"-"+result.chromEnd;
+ dragSelect.highlightThisRegion(newPos2, true);
+ }
- } else {
- var newChrom = hgTracks.chromName;
- if (hgTracks.windows && hgTracks.virtualSingleChrom) {
- newChrom = hgTracks.windows[0].chromName;
+ } 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, true);
}
- var newPos3 = newChrom + ":" + (parseInt(chromStart)) + "-" + parseInt(chromEnd);
- dragSelect.highlightThisRegion(newPos3, true);
- }
- } 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);
+ 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() + "&db=" + getDb();
+ 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)
+ // Add or update form input with gene to highlight
+ suggestBox.updateFindMatches(name);
+ ele.submit();
}
- }
- 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() + "&db=" + getDb();
- 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)
- // Add or update form input with gene to highlight
- suggestBox.updateFindMatches(name);
- ele.submit();
}
}
- }
} else if (cmd === 'zoomCodon' || cmd === 'zoomExon') {
var num, ajaxCmd, msg;
if (cmd === 'zoomCodon') {
@@ -2471,27 +2472,27 @@ var rightClick = {
msg = "Please enter the exon number to zoom to:";
ajaxCmd = 'exonToPos';
}
- rightClick.myPrompt(msg, function (results) {
+ rightClick.myPrompt(msg, function(results) {
$.ajax({
- type: "GET",
- url: "../cgi-bin/hgApi",
- data: cart.varsToUrlData({ 'hgsid': getHgsid(), 'db': getDb(), 'cmd': ajaxCmd, 'num': results,
- 'table': args.table, 'name': args.name, 'chrom': hgTracks.chromName}),
- trueSuccess: rightClick.handleZoomCodon,
- success: catchErrorOrDispatch,
- error: errorHandler,
- cache: true
- });
- });
+ type: "GET",
+ url: "../cgi-bin/hgApi",
+ data: cart.varsToUrlData({ 'hgsid': getHgsid(), 'db': getDb(), 'cmd': ajaxCmd, 'num': results,
+ 'table': args.table, 'name': args.name, 'chrom': hgTracks.chromName}),
+ trueSuccess: rightClick.handleZoomCodon,
+ success: catchErrorOrDispatch,
+ error: errorHandler,
+ cache: true
+ });
+ });
} else if (cmd === 'hgTrackUi_popup') {
// Launches the popup but shields the ajax with a waitOnFunction
- popUp.hgTrackUi(rightClick.selectedMenuItem.id, false);
+ popUp.hgTrackUi( rightClick.selectedMenuItem.id, false );
} else if (cmd === 'hgTrackUi_popup_description') {
// Launches the popup but shields the ajax with a waitOnFunction
- popUp.hgTrackUi(rightClick.selectedMenuItem.id, true);
+ popUp.hgTrackUi( rightClick.selectedMenuItem.id, true );
} else if (cmd === 'hgTrackUi_follow') {
@@ -2501,7 +2502,7 @@ var rightClick = {
url += rec.parentTrack;
else {
// The button already has the ref
- var link = normed($('td#td_btn_' + rightClick.selectedMenuItem.id).children('a'));
+ var link = normed($( 'td#td_btn_'+ rightClick.selectedMenuItem.id ).children('a'));
if (link)
url = $(link).attr('href');
else
@@ -2514,7 +2515,7 @@ var rightClick = {
type: "PUT",
async: false,
url: "../cgi-bin/hgCollection",
- data: "cmd=newCollection&track=" + id + "&hgsid=" + getHgsid(),
+ data: "cmd=newCollection&track=" + id + "&hgsid=" + getHgsid(),
trueSuccess: mySuccess,
success: catchErrorOrDispatch,
error: errorHandler,
@@ -2522,11 +2523,11 @@ var rightClick = {
imageV2.fullReload();
} else if (cmd === 'addCollection') {
- var shortLabel = $(menuItemClicked).text().substring(9).slice(0, -1);
+ var shortLabel = $(menuItemClicked).text().substring(9).slice(0,-1);
var ii;
var collectionName;
- for (ii = 0; ii < hgTracks.collections.length; ii++) {
- if (hgTracks.collections[ii].shortLabel === shortLabel) {
+ for(ii=0; ii < hgTracks.collections.length; ii++) {
+ if ( hgTracks.collections[ii].shortLabel === shortLabel) {
collectionName = hgTracks.collections[ii].track;
break;
}
@@ -2556,7 +2557,7 @@ var rightClick = {
url += rec.parentTrack;
else {
// The button already has the ref
- var link2 = normed($('td#td_btn_' + rightClick.selectedMenuItem.id).children('a'));
+ var link2 = normed($( 'td#td_btn_'+ rightClick.selectedMenuItem.id ).children('a'));
if (link2)
url = $(link2).attr('href');
else
@@ -2569,17 +2570,17 @@ var rightClick = {
// 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(), 'db': getDb() }),
- dataType: "html",
- trueSuccess: rightClick.handleViewImg,
- success: catchErrorOrDispatch,
- error: errorHandler,
- cmd: cmd,
- cache: false
- });
+ type: "GET",
+ url: "../cgi-bin/hgTracks",
+ data: cart.varsToUrlData({ 'hgt.imageV1': '1','hgt.trackImgOnly': '1',
+ 'hgsid': getHgsid(), 'db': getDb() }),
+ 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");
@@ -2596,9 +2597,9 @@ var rightClick = {
val = hgTracks[valNames[i]];
}
if (val
- && id !== "wikiTrack"
- && (href.indexOf("?" + v + "=") === -1)
- && (href.indexOf("&" + v + "=") === -1)) {
+ && id !== "wikiTrack"
+ && (href.indexOf("?" + v + "=") === -1)
+ && (href.indexOf("&" + v + "=") === -1)) {
href = href + "&" + v + "=" + val;
}
}
@@ -2607,7 +2608,7 @@ var rightClick = {
} else {
// XXXX This is blocked by Safari's popup blocker (without any warning message).
href = removeHgsid(href);
- if (!window.open(href)) {
+ if ( ! window.open(href) ) {
rightClick.windowOpenFailedMsg();
}
}
@@ -2627,16 +2628,16 @@ var rightClick = {
imageV2.requestImgUpdate(id, "hgt.transparentImage=0", "");
}
} else if (cmd === 'hideSet') {
- row = $('tr#tr_' + id);
+ 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--) {
+ 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;
+ varsToUpdate[rowId] = '[]';
+ varsToUpdate[rowId+'_sel'] = 0;
$(rows[ix]).remove();
}
if (objNotEmpty(varsToUpdate)) {
@@ -2647,33 +2648,33 @@ var rightClick = {
} else if (cmd === 'hideComposite') {
rec = hgTracks.trackDb[id];
if (tdbIsSubtrack(rec)) {
- let trid = id.replaceAll(".", "\\.");
- row = $('tr#tr_' + trid);
+ let trid = id.replaceAll(".","\\.");
+ row = $( 'tr#tr_' + trid );
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--) {
+ for (var rIx=rows.length - 1; rIx >= 0; rIx--) {
$(rows[rIx]).remove();
}
- selectUpdated = vis.update(rec.parentTrack, 'hide');
- cart.setVars([rec.parentTrack], ['hide']);
- imageV2.afterImgChange(true);
+ selectUpdated = vis.update(rec.parentTrack, 'hide');
+ cart.setVars( [rec.parentTrack], ['hide']);
+ imageV2.afterImgChange(true);
}
}
} else if (cmd === 'jumpToHighlight') { // If highlight exists for this assembly, jump to it
- if (hgTracks.highlight && rightClick.clickedHighlightIdx !== null) {
+ if (hgTracks.highlight && rightClick.clickedHighlightIdx!==null) {
var newPos = getHighlight(hgTracks.highlight, rightClick.clickedHighlightIdx);
if (newPos && newPos.db === getDb()) {
- if ($('#highlightItem').length === 0) { // not visible? jump to it
+ 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);
+ newPos.start = Math.max( Math.floor(newPos.start - (diff/2) ), 0 );
+ newPos.end = newPos.start + (curPos.end - curPos.start);
}
}
if (imageV2.inPlaceUpdate) {
- var params = "db=" + getDb() + "&position=" + newPos.chrom + ':' + newPos.start + '-' + newPos.end;
+ var params = "db=" + getDb() + "&position=" + newPos.chrom+':'+newPos.start+'-'+newPos.end;
imageV2.navigateInPlace(params, null, true);
} else {
genomePos.setByCoordinates(newPos.chrom, newPos.start, newPos.end);
@@ -2688,7 +2689,7 @@ var rightClick = {
var highlights = hgTracks.highlight.split("|");
highlights.splice(rightClick.clickedHighlightIdx, 1); // splice = remove element from array
hgTracks.highlight = highlights.join("|");
- cart.setVarsObj({'highlight': hgTracks.highlight});
+ cart.setVarsObj({'highlight' : hgTracks.highlight});
imageV2.drawHighlights();
} else if (cmd === 'toggleMerge') {
// toggle both the cart (if the user goes to trackUi)
@@ -2698,12 +2699,12 @@ var rightClick = {
if (args[key] === 1) {
args[key] = 0;
updateObj[key] = 0;
- cart.setVarsObj(updateObj, null, false);
+ cart.setVarsObj(updateObj,null,false);
imageV2.requestImgUpdate(id, id + ".doMergeItems=0");
} else {
args[key] = 1;
updateObj[key] = 1;
- cart.setVarsObj(updateObj, null, false);
+ cart.setVarsObj(updateObj,null,false);
imageV2.requestImgUpdate(id, id + ".doMergeItems=1");
}
} else { // if ( cmd in 'hide','dense','squish','pack','full','show' )
@@ -2724,9 +2725,9 @@ var rightClick = {
// assert(document.TrackForm);
document.TrackForm.submit();
} else {
- // Add vis update to queue then submit
- cart.setVars([id], [cmd], null, false); // synchronous
- document.TrackHeaderForm.submit();
+ // Add vis update to queue then submit
+ cart.setVars([id], [cmd], null, false); // synchronous
+ document.TrackHeaderForm.submit();
}
} else {
imageV2.requestImgUpdate(id, id + "=" + cmd, "", cmd);
@@ -2736,7 +2737,7 @@ var rightClick = {
makeHitCallback: function (title)
{ // stub to avoid problem with a function closure w/n a loop
- return function (menuItemClicked, menuObject) {
+ return function(menuItemClicked, menuObject) {
rightClick.hit(menuItemClicked, menuObject, title); return true;
};
},
@@ -2745,7 +2746,7 @@ var rightClick = {
{ // currently dead (experimental code)
if (rightClick.floatingMenuItem) {
$('#img_data_' + rightClick.floatingMenuItem).parent().makeFloat(
- {x: "current", y: "current", speed: 'fast', alwaysVisible: true, alwaysTop: true});
+ {x:"current",y:"current", speed: 'fast', alwaysVisible: true, alwaysTop: true});
}
},
@@ -2755,7 +2756,7 @@ var rightClick = {
// seen in FireFox 3.X, which occurred b/c FF doesn't actually fetch the image until
// the menu is being shown.
return "![](../images/" +
- img + ")
";
+ img + "' />";
},
@@ -2783,572 +2784,572 @@ var rightClick = {
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;
- let trid = id.replaceAll(".", "\\.");
- var row = $('tr#tr_' + trid);
- 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
- }
+ 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;
+ let trid = id.replaceAll(".","\\.");
+ var row = $( 'tr#tr_' + trid );
+ 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;
+ $( subSet ).addClass("greenRows"); // green persists
}
}
}
}
+ }
- // First option is hide sets
- if (offerHideComposite) {
- if (offerHideSubset) {
- o = {};
- o[blankImg + " hide track subset (green)"] = {
- onclick: rightClick.makeHitCallback('hideSet')};
- menu.push(o);
- }
-
+ // First option is hide sets
+ if (offerHideComposite) {
+ if (offerHideSubset) {
o = {};
- str = blankImg + " hide track set";
- if (offerHideSubset)
- str += " (blue)";
- o[str] = {onclick: rightClick.makeHitCallback('hideComposite')};
+ o[blankImg + " hide track subset (green)"] = {
+ onclick: rightClick.makeHitCallback('hideSet')};
menu.push(o);
}
- // Second set of options: visibility for single track
- if (offerSingles) {
- if (offerHideComposite)
- menu.push($.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 = $(this).val();
- str = blankImg + " " + title;
- if (title === cur)
- str = selectedImg + " " + title;
- o = {};
- o[str] = {onclick: function (menuItemClicked, menuObject) {
+ o = {};
+ str = blankImg + " hide track set";
+ if (offerHideSubset)
+ str += " (blue)";
+ o[str] = {onclick: rightClick.makeHitCallback('hideComposite')};
+ menu.push(o);
+ }
+
+ // Second set of options: visibility for single track
+ if (offerSingles) {
+ if (offerHideComposite)
+ menu.push($.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]) {
+ 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];
}
- o[str] = { onclick:
- rightClick.makeHitCallback(visStrings[i])
- };
- menu.push(o);
+ } else if (visStrings[i] === vis.enumOrder[rec.visibility]) {
+ str = selectedImg + " " + visStrings[i];
}
+ o[str] = { onclick:
+ rightClick.makeHitCallback(visStrings[i])
+ };
+ menu.push(o);
}
- done = true;
}
+ done = true;
}
}
+ }
- if (done) {
- o = {};
- var any = false;
- var title = rightClick.selectedMenuItem.title || "feature";
- var maxLength = 60;
-
- if ((isGene || isHgc || id === "wikiTrack") && href.indexOf("i=mergedItem") === -1) {
- // 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;
- }
- // For barChart mouseovers, replace title (which may be a category
- // name+value) with item name
- if (rec.type.indexOf("barChart") === 0
- || rec.type.indexOf("bigBarChart") === 0) {
- let a = /i=([^&]+)/.exec(href);
- if (a && a[1]) {
- title = a[1];
- }
+ if (done) {
+ o = {};
+ var any = false;
+ var title = rightClick.selectedMenuItem.title || "feature";
+ var maxLength = 60;
+
+ if ((isGene || isHgc || id === "wikiTrack") && href.indexOf("i=mergedItem") === -1) {
+ // 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;
+ }
+ // For barChart mouseovers, replace title (which may be a category
+ // name+value) with item name
+ if (rec.type.indexOf("barChart") === 0
+ || rec.type.indexOf("bigBarChart") === 0) {
+ let a = /i=([^&]+)/.exec(href);
+ if (a && a[1]) {
+ title = a[1];
}
}
+ }
- // pick out the exon number from the mouseover text
- // Probably should be a data-exonNum tag on the DOM element
- var exonNum = rightClick.mouseOverToExon(title);
+ // pick out the exon number from the mouseover text
+ // Probably should be a data-exonNum tag on the DOM element
+ var exonNum = rightClick.mouseOverToExon(title);
- // remove special genePred exon mouseover html text
- // CGIs now use HTML tags, e.g. "Transcript: ENST00000297261.7
Strand:" - title = rightClick.mouseOverToLabel(title); + // remove special genePred exon mouseover html text + // CGIs now use HTML tags, e.g. "Transcript: ENST00000297261.7
Strand:" + title = rightClick.mouseOverToLabel(title); - if (title.length > maxLength) { - title = title.substring(0, maxLength) + "..."; - } + if (title.length > maxLength) { + title = title.substring(0, maxLength) + "..."; + } - if (isHgc && (href.indexOf('g=gtexGene') !== -1 - || href.indexOf('g=unip') !== -1 - || href.indexOf('g=knownGene') !== -1)) { - // For GTEx gene and UniProt mouseovers, replace title (which may be a tissue name) with - // item (gene) name. Also need to unescape the urlencoded characters and the + sign. - let a = /i=([^&]+)/.exec(href); - if (a && a[1]) { - title = decodeURIComponent(a[1].replace(/\+/g, " ")); - } + if (isHgc && ( href.indexOf('g=gtexGene')!== -1 + || href.indexOf('g=unip') !== -1 + || href.indexOf('g=knownGene') !== -1 )) { + // For GTEx gene and UniProt mouseovers, replace title (which may be a tissue name) with + // item (gene) name. Also need to unescape the urlencoded characters and the + sign. + let a = /i=([^&]+)/.exec(href); + if (a && a[1]) { + title = decodeURIComponent(a[1].replace(/\+/g, " ")); } + } - if (displayItemFunctions) { - o[rightClick.makeImgTag("magnify.png") + " Zoom to " + title] = { - onclick: function (menuItemClicked, menuObject) { + 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, - "selectWholeGene"); return true; + "highlightItem"); + return true; } }; - o[rightClick.makeImgTag("highlight.png") + " Highlight " + title] = - { onclick: function(menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, - "highlightItem"); - return true; - } - }; - if (rightClick.supportZoomCodon && + if (rightClick.supportZoomCodon && (rec.type.indexOf("genePred") !== -1 || rec.type.indexOf("bigGenePred") !== -1)) { - // http://hgwdev-larrym.gi.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=([^&]+)"); - let a = reg.exec(href); + // http://hgwdev-larrym.gi.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=([^&]+)"); + let 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.gi.ucsc.edu/cgi-bin/hgc?o=55086724&t=55275031&g=refGene&i=NM_005228&c=chr7 + // http://hgwdev-larrym.gi.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("hgg_type=([^&]+)"); + reg = new RegExp("g=([^&]+)"); a = reg.exec(href); if (a && a[1]) { table = a[1]; } - } else { - // http://hgwdev-larrym.gi.ucsc.edu/cgi-bin/hgc?o=55086724&t=55275031&g=refGene&i=NM_005228&c=chr7 - // http://hgwdev-larrym.gi.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) { - if (exonNum > 0) { - o[rightClick.makeImgTag("magnify.png") + " Zoom to this exon"] = { - onclick: function (menuItemClicked, menuObject) { - $.ajax({ + } + if (name && table) { + if (exonNum > 0) { + o[rightClick.makeImgTag("magnify.png")+" Zoom to this exon"] = { + onclick: function(menuItemClicked, menuObject) { + $.ajax({ type: "GET", url: "../cgi-bin/hgApi", data: cart.varsToUrlData({ 'hgsid': getHgsid(), 'db': getDb(), - 'cmd': "exonToPos", 'num': exonNum, - 'table': table, 'name': name, 'chrom': hgTracks.chromName}), + 'cmd': "exonToPos", 'num': exonNum, + 'table': table, 'name': name, 'chrom': hgTracks.chromName}), trueSuccess: rightClick.handleZoomCodon, success: catchErrorOrDispatch, error: errorHandler, cache: true }); - return true; } - }; - o[rightClick.makeImgTag("magnify.png") + " Enter codon to zoom to..."] = - { onclick: function(menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, - "zoomCodon", - {name: name, table: table, 'chrom': hgTracks.chromName}); - return true;} - }; - o[rightClick.makeImgTag("magnify.png") + " Enter exon to zoom to..."] = - { onclick: function(menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, + return true; } + }; + o[rightClick.makeImgTag("magnify.png")+" Enter codon to zoom to..."] = + { onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, + "zoomCodon", + {name: name, table: table, 'chrom': hgTracks.chromName}); + return true;} + }; + o[rightClick.makeImgTag("magnify.png")+" Enter exon to zoom to..."] = + { onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "zoomExon", {name: name, table: table, 'chrom': hgTracks.chromName}); - return true;} - }; - } + 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"); + o[rightClick.makeImgTag("dnaIcon.png")+" Get DNA for "+title] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "getDna"); return true; } }; - any = true; } - if (href && href.length > 0 && href.indexOf("i=mergedItem") === -1) { - // 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); + 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 && href.indexOf("i=mergedItem") === -1) { + // 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($.contextMenu.separator); + menu.push(o); + } } + } - menu.push($.contextMenu.separator); - o = {}; - o[rightClick.makeImgTag("hiddenIcon.png") + " Hide all other tracks "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "hideOthers"); - return true; } - }; - menu.push(o); + menu.push($.contextMenu.separator); + o = {}; + o[rightClick.makeImgTag("hiddenIcon.png") + " Hide all other tracks "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "hideOthers"); + return true; } + }; + menu.push(o); - //o = {}; - //o[" Float "] = { + //o = {}; + //o[" Float "] = { //onclick: function(menuItemClicked, menuObject) { - //rightClick.hit(menuItemClicked, menuObject, "float"); - //return true; } - //}; - //menu.push(o); - - o = {}; - o[rightClick.makeImgTag("ab_up.gif") + " Move to top "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "moveTop"); - return true; } - }; - menu.push(o); - - o = {}; - o[rightClick.makeImgTag("ab_down.gif") + " Move to bottom "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "moveBottom"); - return true; } - }; - 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"); + //rightClick.hit(menuItemClicked, menuObject, "float"); + //return true; } + //}; + //menu.push(o); + + o = {}; + o[rightClick.makeImgTag("ab_up.gif") + " Move to top "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "moveTop"); + return true; } + }; + menu.push(o); + + o = {}; + o[rightClick.makeImgTag("ab_down.gif") + " Move to bottom "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "moveBottom"); + return true; } + }; + 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; } }; + } - // add a toggle to hide/show the merged item(s) - mergeTrack = rightClick.selectedMenuItem.id + ".doMergeItems"; - if (rec.hasOwnProperty(mergeTrack)) { - var hasMergedItems = rec[mergeTrack] === 1; - titleStr = rightClick.makeImgTag("wrench.png") + " "; - if (hasMergedItems) { - titleStr += "Show merged items"; - } else { - titleStr += "Merge items that span the current region"; - } - o[titleStr] = {onclick: function(menuItemClick, menuObject) { - rightClick.hit(menuItemClick, menuObject, "toggleMerge", rec); + 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("book.png") + " Track Description " + rec.shortLabel] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_popup_description"); + 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); + } + // add a toggle to hide/show the merged item(s) + mergeTrack = rightClick.selectedMenuItem.id + ".doMergeItems"; + if (rec.hasOwnProperty(mergeTrack)) { + var hasMergedItems = rec[mergeTrack] === 1; + titleStr = rightClick.makeImgTag("wrench.png") + " "; + if (hasMergedItems) { + titleStr += "Show merged items"; + } else { + titleStr += "Merge items that span the current region"; + } + o[titleStr] = {onclick: function(menuItemClick, menuObject) { + rightClick.hit(menuItemClick, menuObject, "toggleMerge", rec); + return true; } + }; } + o[rightClick.makeImgTag("book.png")+" Track Description "+rec.shortLabel] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_popup_description"); + return true; } + }; + menu.push($.contextMenu.separator); - if (hgTracks.highlight && rightClick.clickedHighlightIdx !== null) { - var currentlySeen = ($('#highlightItem').length > 0); - o = {}; - // Jumps to highlight when not currently seen in image - var text = (currentlySeen ? " Zoom" : " Jump") + " to highlight"; - o[rightClick.makeImgTag("highlightZoom.png") + text] = { - onclick: rightClick.makeHitCallback('jumpToHighlight') - }; + menu.push(o); + } - if (currentlySeen) { // Remove only when seen - o[rightClick.makeImgTag("highlightRemove.png") + - " Remove highlight"] = { - onclick: rightClick.makeHitCallback('removeHighlight') - }; - } - menu.push(o); + menu.push($.contextMenu.separator); + if (hgTracks.highlight && rightClick.clickedHighlightIdx!==null) { + var currentlySeen = ($('#highlightItem').length > 0); + o = {}; + // Jumps to highlight when not currently seen in image + var text = (currentlySeen ? " Zoom" : " Jump") + " to highlight"; + o[rightClick.makeImgTag("highlightZoom.png") + text] = { + onclick: rightClick.makeHitCallback('jumpToHighlight') + }; + + if ( currentlySeen ) { // Remove only when seen + o[rightClick.makeImgTag("highlightRemove.png") + + " Remove highlight"] = { + onclick: rightClick.makeHitCallback('removeHighlight') + }; } + menu.push(o); + } - if (rec.isCustomComposite) + if (rec.isCustomComposite) { - // add delete from composite + // add delete from composite } - else if ((!rec.type.startsWith("wigMaf")) && - (rec.type.startsWith("bigWig") || rec.type.startsWith("multiWig") || rec.type.startsWith("wig") || rec.type.startsWith("bedGraph"))) { - o = {}; - o[" Make a New Collection with \"" + rec.shortLabel + "\""] = { - onclick: rightClick.makeHitCallback("newCollection") - }; - menu.push(o); + else if ((!rec.type.startsWith("wigMaf")) && + (rec.type.startsWith("bigWig") || rec.type.startsWith("multiWig") || rec.type.startsWith("wig") || rec.type.startsWith("bedGraph"))) { + o = {}; + o[" Make a New Collection with \"" + rec.shortLabel + "\""] = { + onclick: rightClick.makeHitCallback("newCollection") + }; + menu.push(o); - if (hgTracks.collections) { - var ii; - for (ii = 0; ii < hgTracks.collections.length; ii++) { - o = {}; - o[" Add to \"" + hgTracks.collections[ii].shortLabel + "\""] = { - onclick: rightClick.makeHitCallback("addCollection") - }; - menu.push(o); - } + if (hgTracks.collections) { + var ii; + for(ii=0; ii < hgTracks.collections.length; ii++) { + o = {}; + o[" Add to \"" + hgTracks.collections[ii].shortLabel + "\""] = { + onclick: rightClick.makeHitCallback("addCollection") + }; + menu.push(o); } - menu.push($.contextMenu.separator); } + menu.push($.contextMenu.separator); + } - // add sort options if this is a custom composite - if (rec.isCustomComposite && tdbHasParent(rec) && tdbIsLeaf(rec)) { - - o = {}; - o[" Sort by Magnitude "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "sortExp"); - return true; } - }; - menu.push(o); - - o = {}; - o[" Sort by Similarity "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "sortSim"); - return true; } - }; - menu.push(o); + // add sort options if this is a custom composite + if (rec.isCustomComposite && tdbHasParent(rec) && tdbIsLeaf(rec)) { - menu.push($.contextMenu.separator); - } + o = {}; + o[" Sort by Magnitude "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "sortExp"); + return true; } + }; + menu.push(o); - // Add view image at end o = {}; - o[rightClick.makeImgTag("eye.png") + " View image"] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "viewImg"); + o[" Sort by Similarity "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "sortSim"); return true; } - }; + }; menu.push(o); - return menu; + menu.push($.contextMenu.separator); + } + + // 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); + + // find the highlight that was clicked + var imageX = (imageV2.imgTbl[0].getBoundingClientRect().left) + imageV2.LEFTADD; + var xDiff = (e.clientX) - imageX; + var clickPos = genomePos.pixelsToBases(img, xDiff, xDiff+1, hgTracks.winStart, hgTracks.winEnd, false); + rightClick.clickedHighlightIdx = dragSelect.findHighlightIdxForPos(clickPos); + + // XXXX? posting.blockUseMap = true; + return true; }, - { - beforeShow: function (e) { - // console.log(mapItems[rightClick.selectedMenuItem]); - rightClick.selectedMenuItem = rightClick.findMapItem(e); - - // find the highlight that was clicked - var imageX = (imageV2.imgTbl[0].getBoundingClientRect().left) + imageV2.LEFTADD; - var xDiff = (e.clientX) - imageX; - var clickPos = genomePos.pixelsToBases(img, xDiff, xDiff + 1, hgTracks.winStart, hgTracks.winEnd, false); - rightClick.clickedHighlightIdx = dragSelect.findHighlightIdxForPos(clickPos); - - // 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'); - } - }); + 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 //// + ////////////////////////////////// + //// 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
";
+ img + "' />";
},
@@ -2783,572 +2784,572 @@ var rightClick = {
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;
- let trid = id.replaceAll(".", "\\.");
- var row = $('tr#tr_' + trid);
- 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
- }
+ 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;
+ let trid = id.replaceAll(".","\\.");
+ var row = $( 'tr#tr_' + trid );
+ 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;
+ $( subSet ).addClass("greenRows"); // green persists
}
}
}
}
+ }
- // First option is hide sets
- if (offerHideComposite) {
- if (offerHideSubset) {
- o = {};
- o[blankImg + " hide track subset (green)"] = {
- onclick: rightClick.makeHitCallback('hideSet')};
- menu.push(o);
- }
-
+ // First option is hide sets
+ if (offerHideComposite) {
+ if (offerHideSubset) {
o = {};
- str = blankImg + " hide track set";
- if (offerHideSubset)
- str += " (blue)";
- o[str] = {onclick: rightClick.makeHitCallback('hideComposite')};
+ o[blankImg + " hide track subset (green)"] = {
+ onclick: rightClick.makeHitCallback('hideSet')};
menu.push(o);
}
- // Second set of options: visibility for single track
- if (offerSingles) {
- if (offerHideComposite)
- menu.push($.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 = $(this).val();
- str = blankImg + " " + title;
- if (title === cur)
- str = selectedImg + " " + title;
- o = {};
- o[str] = {onclick: function (menuItemClicked, menuObject) {
+ o = {};
+ str = blankImg + " hide track set";
+ if (offerHideSubset)
+ str += " (blue)";
+ o[str] = {onclick: rightClick.makeHitCallback('hideComposite')};
+ menu.push(o);
+ }
+
+ // Second set of options: visibility for single track
+ if (offerSingles) {
+ if (offerHideComposite)
+ menu.push($.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]) {
+ 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];
}
- o[str] = { onclick:
- rightClick.makeHitCallback(visStrings[i])
- };
- menu.push(o);
+ } else if (visStrings[i] === vis.enumOrder[rec.visibility]) {
+ str = selectedImg + " " + visStrings[i];
}
+ o[str] = { onclick:
+ rightClick.makeHitCallback(visStrings[i])
+ };
+ menu.push(o);
}
- done = true;
}
+ done = true;
}
}
+ }
- if (done) {
- o = {};
- var any = false;
- var title = rightClick.selectedMenuItem.title || "feature";
- var maxLength = 60;
-
- if ((isGene || isHgc || id === "wikiTrack") && href.indexOf("i=mergedItem") === -1) {
- // 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;
- }
- // For barChart mouseovers, replace title (which may be a category
- // name+value) with item name
- if (rec.type.indexOf("barChart") === 0
- || rec.type.indexOf("bigBarChart") === 0) {
- let a = /i=([^&]+)/.exec(href);
- if (a && a[1]) {
- title = a[1];
- }
+ if (done) {
+ o = {};
+ var any = false;
+ var title = rightClick.selectedMenuItem.title || "feature";
+ var maxLength = 60;
+
+ if ((isGene || isHgc || id === "wikiTrack") && href.indexOf("i=mergedItem") === -1) {
+ // 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;
+ }
+ // For barChart mouseovers, replace title (which may be a category
+ // name+value) with item name
+ if (rec.type.indexOf("barChart") === 0
+ || rec.type.indexOf("bigBarChart") === 0) {
+ let a = /i=([^&]+)/.exec(href);
+ if (a && a[1]) {
+ title = a[1];
}
}
+ }
- // pick out the exon number from the mouseover text
- // Probably should be a data-exonNum tag on the DOM element
- var exonNum = rightClick.mouseOverToExon(title);
+ // pick out the exon number from the mouseover text
+ // Probably should be a data-exonNum tag on the DOM element
+ var exonNum = rightClick.mouseOverToExon(title);
- // remove special genePred exon mouseover html text
- // CGIs now use HTML tags, e.g. "Transcript: ENST00000297261.7Strand:" - title = rightClick.mouseOverToLabel(title); + // remove special genePred exon mouseover html text + // CGIs now use HTML tags, e.g. "Transcript: ENST00000297261.7
Strand:" + title = rightClick.mouseOverToLabel(title); - if (title.length > maxLength) { - title = title.substring(0, maxLength) + "..."; - } + if (title.length > maxLength) { + title = title.substring(0, maxLength) + "..."; + } - if (isHgc && (href.indexOf('g=gtexGene') !== -1 - || href.indexOf('g=unip') !== -1 - || href.indexOf('g=knownGene') !== -1)) { - // For GTEx gene and UniProt mouseovers, replace title (which may be a tissue name) with - // item (gene) name. Also need to unescape the urlencoded characters and the + sign. - let a = /i=([^&]+)/.exec(href); - if (a && a[1]) { - title = decodeURIComponent(a[1].replace(/\+/g, " ")); - } + if (isHgc && ( href.indexOf('g=gtexGene')!== -1 + || href.indexOf('g=unip') !== -1 + || href.indexOf('g=knownGene') !== -1 )) { + // For GTEx gene and UniProt mouseovers, replace title (which may be a tissue name) with + // item (gene) name. Also need to unescape the urlencoded characters and the + sign. + let a = /i=([^&]+)/.exec(href); + if (a && a[1]) { + title = decodeURIComponent(a[1].replace(/\+/g, " ")); } + } - if (displayItemFunctions) { - o[rightClick.makeImgTag("magnify.png") + " Zoom to " + title] = { - onclick: function (menuItemClicked, menuObject) { + 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, - "selectWholeGene"); return true; + "highlightItem"); + return true; } }; - o[rightClick.makeImgTag("highlight.png") + " Highlight " + title] = - { onclick: function(menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, - "highlightItem"); - return true; - } - }; - if (rightClick.supportZoomCodon && + if (rightClick.supportZoomCodon && (rec.type.indexOf("genePred") !== -1 || rec.type.indexOf("bigGenePred") !== -1)) { - // http://hgwdev-larrym.gi.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=([^&]+)"); - let a = reg.exec(href); + // http://hgwdev-larrym.gi.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=([^&]+)"); + let 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.gi.ucsc.edu/cgi-bin/hgc?o=55086724&t=55275031&g=refGene&i=NM_005228&c=chr7 + // http://hgwdev-larrym.gi.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("hgg_type=([^&]+)"); + reg = new RegExp("g=([^&]+)"); a = reg.exec(href); if (a && a[1]) { table = a[1]; } - } else { - // http://hgwdev-larrym.gi.ucsc.edu/cgi-bin/hgc?o=55086724&t=55275031&g=refGene&i=NM_005228&c=chr7 - // http://hgwdev-larrym.gi.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) { - if (exonNum > 0) { - o[rightClick.makeImgTag("magnify.png") + " Zoom to this exon"] = { - onclick: function (menuItemClicked, menuObject) { - $.ajax({ + } + if (name && table) { + if (exonNum > 0) { + o[rightClick.makeImgTag("magnify.png")+" Zoom to this exon"] = { + onclick: function(menuItemClicked, menuObject) { + $.ajax({ type: "GET", url: "../cgi-bin/hgApi", data: cart.varsToUrlData({ 'hgsid': getHgsid(), 'db': getDb(), - 'cmd': "exonToPos", 'num': exonNum, - 'table': table, 'name': name, 'chrom': hgTracks.chromName}), + 'cmd': "exonToPos", 'num': exonNum, + 'table': table, 'name': name, 'chrom': hgTracks.chromName}), trueSuccess: rightClick.handleZoomCodon, success: catchErrorOrDispatch, error: errorHandler, cache: true }); - return true; } - }; - o[rightClick.makeImgTag("magnify.png") + " Enter codon to zoom to..."] = - { onclick: function(menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, - "zoomCodon", - {name: name, table: table, 'chrom': hgTracks.chromName}); - return true;} - }; - o[rightClick.makeImgTag("magnify.png") + " Enter exon to zoom to..."] = - { onclick: function(menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, + return true; } + }; + o[rightClick.makeImgTag("magnify.png")+" Enter codon to zoom to..."] = + { onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, + "zoomCodon", + {name: name, table: table, 'chrom': hgTracks.chromName}); + return true;} + }; + o[rightClick.makeImgTag("magnify.png")+" Enter exon to zoom to..."] = + { onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "zoomExon", {name: name, table: table, 'chrom': hgTracks.chromName}); - return true;} - }; - } + 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"); + o[rightClick.makeImgTag("dnaIcon.png")+" Get DNA for "+title] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "getDna"); return true; } }; - any = true; } - if (href && href.length > 0 && href.indexOf("i=mergedItem") === -1) { - // 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); + 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 && href.indexOf("i=mergedItem") === -1) { + // 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($.contextMenu.separator); + menu.push(o); + } } + } - menu.push($.contextMenu.separator); - o = {}; - o[rightClick.makeImgTag("hiddenIcon.png") + " Hide all other tracks "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "hideOthers"); - return true; } - }; - menu.push(o); + menu.push($.contextMenu.separator); + o = {}; + o[rightClick.makeImgTag("hiddenIcon.png") + " Hide all other tracks "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "hideOthers"); + return true; } + }; + menu.push(o); - //o = {}; - //o[" Float "] = { + //o = {}; + //o[" Float "] = { //onclick: function(menuItemClicked, menuObject) { - //rightClick.hit(menuItemClicked, menuObject, "float"); - //return true; } - //}; - //menu.push(o); - - o = {}; - o[rightClick.makeImgTag("ab_up.gif") + " Move to top "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "moveTop"); - return true; } - }; - menu.push(o); - - o = {}; - o[rightClick.makeImgTag("ab_down.gif") + " Move to bottom "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "moveBottom"); - return true; } - }; - 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"); + //rightClick.hit(menuItemClicked, menuObject, "float"); + //return true; } + //}; + //menu.push(o); + + o = {}; + o[rightClick.makeImgTag("ab_up.gif") + " Move to top "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "moveTop"); + return true; } + }; + menu.push(o); + + o = {}; + o[rightClick.makeImgTag("ab_down.gif") + " Move to bottom "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "moveBottom"); + return true; } + }; + 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; } }; + } - // add a toggle to hide/show the merged item(s) - mergeTrack = rightClick.selectedMenuItem.id + ".doMergeItems"; - if (rec.hasOwnProperty(mergeTrack)) { - var hasMergedItems = rec[mergeTrack] === 1; - titleStr = rightClick.makeImgTag("wrench.png") + " "; - if (hasMergedItems) { - titleStr += "Show merged items"; - } else { - titleStr += "Merge items that span the current region"; - } - o[titleStr] = {onclick: function(menuItemClick, menuObject) { - rightClick.hit(menuItemClick, menuObject, "toggleMerge", rec); + 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("book.png") + " Track Description " + rec.shortLabel] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_popup_description"); + 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); + } + // add a toggle to hide/show the merged item(s) + mergeTrack = rightClick.selectedMenuItem.id + ".doMergeItems"; + if (rec.hasOwnProperty(mergeTrack)) { + var hasMergedItems = rec[mergeTrack] === 1; + titleStr = rightClick.makeImgTag("wrench.png") + " "; + if (hasMergedItems) { + titleStr += "Show merged items"; + } else { + titleStr += "Merge items that span the current region"; + } + o[titleStr] = {onclick: function(menuItemClick, menuObject) { + rightClick.hit(menuItemClick, menuObject, "toggleMerge", rec); + return true; } + }; } + o[rightClick.makeImgTag("book.png")+" Track Description "+rec.shortLabel] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_popup_description"); + return true; } + }; + menu.push($.contextMenu.separator); - if (hgTracks.highlight && rightClick.clickedHighlightIdx !== null) { - var currentlySeen = ($('#highlightItem').length > 0); - o = {}; - // Jumps to highlight when not currently seen in image - var text = (currentlySeen ? " Zoom" : " Jump") + " to highlight"; - o[rightClick.makeImgTag("highlightZoom.png") + text] = { - onclick: rightClick.makeHitCallback('jumpToHighlight') - }; + menu.push(o); + } - if (currentlySeen) { // Remove only when seen - o[rightClick.makeImgTag("highlightRemove.png") + - " Remove highlight"] = { - onclick: rightClick.makeHitCallback('removeHighlight') - }; - } - menu.push(o); + menu.push($.contextMenu.separator); + if (hgTracks.highlight && rightClick.clickedHighlightIdx!==null) { + var currentlySeen = ($('#highlightItem').length > 0); + o = {}; + // Jumps to highlight when not currently seen in image + var text = (currentlySeen ? " Zoom" : " Jump") + " to highlight"; + o[rightClick.makeImgTag("highlightZoom.png") + text] = { + onclick: rightClick.makeHitCallback('jumpToHighlight') + }; + + if ( currentlySeen ) { // Remove only when seen + o[rightClick.makeImgTag("highlightRemove.png") + + " Remove highlight"] = { + onclick: rightClick.makeHitCallback('removeHighlight') + }; } + menu.push(o); + } - if (rec.isCustomComposite) + if (rec.isCustomComposite) { - // add delete from composite + // add delete from composite } - else if ((!rec.type.startsWith("wigMaf")) && - (rec.type.startsWith("bigWig") || rec.type.startsWith("multiWig") || rec.type.startsWith("wig") || rec.type.startsWith("bedGraph"))) { - o = {}; - o[" Make a New Collection with \"" + rec.shortLabel + "\""] = { - onclick: rightClick.makeHitCallback("newCollection") - }; - menu.push(o); + else if ((!rec.type.startsWith("wigMaf")) && + (rec.type.startsWith("bigWig") || rec.type.startsWith("multiWig") || rec.type.startsWith("wig") || rec.type.startsWith("bedGraph"))) { + o = {}; + o[" Make a New Collection with \"" + rec.shortLabel + "\""] = { + onclick: rightClick.makeHitCallback("newCollection") + }; + menu.push(o); - if (hgTracks.collections) { - var ii; - for (ii = 0; ii < hgTracks.collections.length; ii++) { - o = {}; - o[" Add to \"" + hgTracks.collections[ii].shortLabel + "\""] = { - onclick: rightClick.makeHitCallback("addCollection") - }; - menu.push(o); - } + if (hgTracks.collections) { + var ii; + for(ii=0; ii < hgTracks.collections.length; ii++) { + o = {}; + o[" Add to \"" + hgTracks.collections[ii].shortLabel + "\""] = { + onclick: rightClick.makeHitCallback("addCollection") + }; + menu.push(o); } - menu.push($.contextMenu.separator); } + menu.push($.contextMenu.separator); + } - // add sort options if this is a custom composite - if (rec.isCustomComposite && tdbHasParent(rec) && tdbIsLeaf(rec)) { - - o = {}; - o[" Sort by Magnitude "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "sortExp"); - return true; } - }; - menu.push(o); - - o = {}; - o[" Sort by Similarity "] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "sortSim"); - return true; } - }; - menu.push(o); + // add sort options if this is a custom composite + if (rec.isCustomComposite && tdbHasParent(rec) && tdbIsLeaf(rec)) { - menu.push($.contextMenu.separator); - } + o = {}; + o[" Sort by Magnitude "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "sortExp"); + return true; } + }; + menu.push(o); - // Add view image at end o = {}; - o[rightClick.makeImgTag("eye.png") + " View image"] = { - onclick: function (menuItemClicked, menuObject) { - rightClick.hit(menuItemClicked, menuObject, "viewImg"); + o[" Sort by Similarity "] = { + onclick: function(menuItemClicked, menuObject) { + rightClick.hit(menuItemClicked, menuObject, "sortSim"); return true; } - }; + }; menu.push(o); - return menu; + menu.push($.contextMenu.separator); + } + + // 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); + + // find the highlight that was clicked + var imageX = (imageV2.imgTbl[0].getBoundingClientRect().left) + imageV2.LEFTADD; + var xDiff = (e.clientX) - imageX; + var clickPos = genomePos.pixelsToBases(img, xDiff, xDiff+1, hgTracks.winStart, hgTracks.winEnd, false); + rightClick.clickedHighlightIdx = dragSelect.findHighlightIdxForPos(clickPos); + + // XXXX? posting.blockUseMap = true; + return true; }, - { - beforeShow: function (e) { - // console.log(mapItems[rightClick.selectedMenuItem]); - rightClick.selectedMenuItem = rightClick.findMapItem(e); - - // find the highlight that was clicked - var imageX = (imageV2.imgTbl[0].getBoundingClientRect().left) + imageV2.LEFTADD; - var xDiff = (e.clientX) - imageX; - var clickPos = genomePos.pixelsToBases(img, xDiff, xDiff + 1, hgTracks.winStart, hgTracks.winEnd, false); - rightClick.clickedHighlightIdx = dragSelect.findHighlightIdxForPos(clickPos); - - // 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'); - } - }); + 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 //// + ////////////////////////////////// + //// 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