245532054096d60355181d660ccd1bfe4405526e larrym Thu Mar 22 23:11:26 2012 -0700 trim really long titles in right click menu items diff --git src/hg/js/hgTracks.js src/hg/js/hgTracks.js index 4085830..26504e3 100644 --- src/hg/js/hgTracks.js +++ src/hg/js/hgTracks.js @@ -1,3197 +1,3200 @@ // Javascript for use in hgTracks CGI // "use strict"; var debug = false; var browser; // browser ("msie", "safari" etc.) // move to utils.js? /* Data passed in from CGI via the hgTracks object: * * string cgiVersion // CGI_VERSION * string chromName // current chromosome * int winStart // genomic start coordinate (0-based, half-open) * int winEnd // genomic end coordinate * int newWinWidth // new width (in bps) if user clicks on the top ruler * boolean revCmplDisp // true if we are in reverse display * int insideX // width of side-bar (in pixels) * int rulerClickHeight // height of ruler (in pixels) - zero if ruler is hidden * boolean inPlaceUpdate // true if in-place-update is turned on * int imgBox* // various drag-scroll values * boolean measureTiming // true if measureTiming is on * Object trackDb // hash of trackDb entries for tracks which are visible on current page */ function initVars() { // There are various entry points, so we call initVars in several places to make sure all is well if (!genomePos.original) { // remember initial position and size so we can restore it if user cancels genomePos.original = genomePos.getOriginalPos(); genomePos.originalSize = $('#size').text(); dragSelect.originalCursor = jQuery('body').css('cursor'); imageV2.imgTbl = $('#imgTbl'); // imageV2.enabled == true unless: advancedJavascript==false, or trackSearch, or config pg imageV2.enabled = (imageV2.imgTbl != undefined && imageV2.imgTbl.length > 0); jQuery.each(jQuery.browser, function(i, val) { if(val) { browser = i; } }); // jQuery load function with stuff to support drag selection in track img if(browser == "safari") { if(navigator.userAgent.indexOf("Chrome") != -1) { // Handle the fact that (as of 1.3.1), jQuery.browser reports "safari" when the browser is in fact Chrome. browser = "chrome"; } else { // Safari has the following bug: if we update the hgTracks map dynamically, the browser ignores the changes (even // though if you look in the DOM the changes are there). So we have to do a full form submission when the // user changes visibility settings or track configuration. // As of 5.0.4 (7533.20.27) this is problem still exists in safari. // As of 5.1 (7534.50) this problem appears to have been fixed - unfortunately, logs for 7/2011 show vast majority of safari users // are pre-5.1 (5.0.5 is by far the most common). // // Early versions of Chrome had this problem too, but this problem went away as of Chrome 5.0.335.1 (or possibly earlier). imageV2.mapIsUpdateable = false; var reg = new RegExp("Version\/(\[0-9]+\.\[0-9]+) Safari"); var a = reg.exec(navigator.userAgent); if(a && a[1]) { var version = Number(a[1]); if(version >= 5.1) { imageV2.mapIsUpdateable = true; } } } } imageV2.inPlaceUpdate = hgTracks.inPlaceUpdate && imageV2.mapIsUpdateable; } } ///////////////////////////////////// ////////// Genomic position ///////// ///////////////////////////////////// var genomePos = { original: null, originalSize: 0, linkFixup: function (pos, id, reg, endParamName) { // fixup external links (e.g. ensembl) var ele = $(document.getElementById(id)); if(ele.length) { var link = ele.attr('href'); var a = reg.exec(link); if(a && a[1]) { ele.attr('href', a[1] + pos.start + "&" + endParamName + "=" + pos.end); } } }, setByCoordinates: function (chrom, start, end) { var newPosition = chrom + ":" + commify(start) + "-" + commify(end); genomePos.set(newPosition, commify(end - start + 1)); return newPosition; }, getElement: function () { // Return position box object var tags = document.getElementsByName("position"); // There are multiple tags with name == "position" (the visible position text input // and a hidden with id='positionHidden'); we return value of visible element. for (var i = 0; i < tags.length; i++) { var ele = tags[i]; if(ele.id != "positionHidden") { return ele; } } return null; }, get: function () { // Return current value of position box var ele = genomePos.getElement(); if(ele != null) { return ele.value; } return null; }, getOriginalPos: function () { return genomePos.original || genomePos.get(); }, set: function (position, size) { // Set value of position and size (in hiddens and input elements). // We assume size has already been commified. // Either position or size may be null. if(position) { // There are multiple tags with name == "position" // (one in TrackHeaderForm and another in TrackForm). var tags = document.getElementsByName("position"); for (var i = 0; i < tags.length; i++) { var ele = tags[i]; ele.value = position; } } if($('#positionDisplay').length) { $('#positionDisplay').text(position); } if(size) { $('#size').text(size); } var pos = parsePosition(position); if(pos) { // fixup external static links on page' // Example ensembl link: http://www.ensembl.org/Homo_sapiens/contigview?chr=21&start=33031934&end=33041241 genomePos.linkFixup(pos, "ensemblLink", new RegExp("(.+start=)[0-9]+"), "end"); // Example NCBI link: http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=21&BEG=33031934&END=33041241 genomePos.linkFixup(pos, "ncbiLink", new RegExp("(.+BEG=)[0-9]+"), "END"); // Example medaka link: http://utgenome.org/medakabrowser_ens_jump.php?revision=version1.0&chr=chromosome18&start=14435198&end=14444829 genomePos.linkFixup(pos, "medakaLink", new RegExp("(.+start=)[0-9]+"), "end"); if($('#wormbaseLink').length) { // e.g. http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=II:14646301-14667800 var link = $('#wormbaseLink').attr('href'); var reg = new RegExp("(.+:)[0-9]+"); var a = reg.exec(link); if(a && a[1]) { $('#wormbaseLink').attr('href', a[1] + pos.start + "-" + pos.end); } } // Fixup DNA link; e.g.: hgc?hgsid=2999470&o=114385768&g=getDna&i=mixed&c=chr7&l=114385768&r=114651696&db=panTro2&hgsid=2999470 if($('#dnaLink').length) { var link = $('#dnaLink').attr('href'); var reg = new RegExp("(.+&o=)[0-9]+.+&db=[^&]+(.*)"); var a = reg.exec(link); if(a && a[1]) { var url = a[1] + (pos.start - 1) + "&g=getDna&i=mixed&c=" + pos.chrom; url += "&l=" + (pos.start - 1) + "&r=" + pos.end + "&db=" + getDb() + a[2]; $('#dnaLink').attr('href', url); } } } imageV2.markAsDirtyPage(); }, check: function (img, selection) { // return true if user's selection is still w/n the img (including some slop). var imgWidth = jQuery(img).width(); var imgHeight = jQuery(img).height(); var imgOfs = jQuery(img).offset(); var slop = 10; // We ignore clicks in the gray tab and track title column // (we really should suppress all drag activity there, // but I don't know how to do that with imgAreaSelect). var leftX = hgTracks.revCmplDisp ? imgOfs.left - slop : imgOfs.left + hgTracks.insideX - slop; var rightX = hgTracks.revCmplDisp ? imgOfs.left + imgWidth - hgTracks.insideX + slop : imgOfs.left + imgWidth + slop; return ( (selection.event.pageX >= leftX) && (selection.event.pageX < rightX) && (selection.event.pageY >= (imgOfs.top - slop)) && (selection.event.pageY < (imgOfs.top + imgHeight + slop))); }, pixelsToBases: function (img, selStart, selEnd, winStart, winEnd) { // Convert image coordinates to chromosome coordinates var imgWidth = jQuery(img).width() - hgTracks.insideX; var width = hgTracks.winEnd - hgTracks.winStart; var mult = width / imgWidth; // mult is bp/pixel multiplier var startDelta; // startDelta is how many bp's to the right/left if(hgTracks.revCmplDisp) { var x1 = Math.min(imgWidth, selStart); startDelta = Math.floor(mult * (imgWidth - x1)); } else { var x1 = Math.max(hgTracks.insideX, selStart); startDelta = Math.floor(mult * (x1 - hgTracks.insideX)); } var endDelta; if(hgTracks.revCmplDisp) { endDelta = startDelta; var x2 = Math.min(imgWidth, selEnd); startDelta = Math.floor(mult * (imgWidth - x2)); } else { var x2 = Math.max(hgTracks.insideX, selEnd); endDelta = Math.floor(mult * (x2 - hgTracks.insideX)); } var newStart = hgTracks.winStart + startDelta; var newEnd = hgTracks.winStart + 1 + endDelta; if(newEnd > winEnd) { newEnd = winEnd; } return {chromStart : newStart, chromEnd : newEnd}; }, selectionPixelsToBases: function (img, selection) { // Convert selection x1/x2 coordinates to chromStart/chromEnd. return genomePos.pixelsToBases(img, selection.x1, selection.x2, hgTracks.winStart, hgTracks.winEnd); }, update: function (img, selection, singleClick) { var pos = genomePos.pixelsToBases(img, selection.x1, selection.x2, hgTracks.winStart, hgTracks.winEnd); // singleClick is true when the mouse hasn't moved (or has only moved a small amount). if(singleClick) { var center = (pos.chromStart + pos.chromEnd)/2; pos.chromStart = Math.floor(center - hgTracks.newWinWidth/2); pos.chromEnd = pos.chromStart + hgTracks.newWinWidth; } var newPosition = genomePos.setByCoordinates(hgTracks.chromName, pos.chromStart+1, pos.chromEnd); return newPosition; }, handleChange: function (response, status) { var json = eval("(" + response + ")"); genomePos.set(json.pos); }, changeAssemblies: function (ele) // UNUSED? Larry's experimental code { // code to update page when user changes assembly select list. $.ajax({ type: "GET", url: "../cgi-bin/hgApi", data: "cmd=defaultPos&db=" + getDb(), dataType: "html", trueSuccess: genomePos.handleChange, success: catchErrorOrDispatch, error: errorHandler, cache: true }); return false; } } ///////////////////////////////////// //// Creating items by dragging ///// ///////////////////////////////////// var makeItemsByDrag = { end: function (img, selection) { var image = $(img); var imageId = image.attr('id'); var trackName = imageId.substring('img_data_'.length); var pos = genomePos.selectionPixelsToBases(image, selection); var command = document.getElementById('hgt_doJsCommand'); command.value = "makeItems " + trackName + " " + hgTracks.chromName; command.value += " " + pos.chromStart + " " + pos.chromEnd; document.TrackHeaderForm.submit(); return true; }, init: function (trackName) { // Set up so that they can drag out to define a new item on a makeItems track. var img = $("#img_data_" + trackName); if(img != undefined && img.length != 0) { var imgHeight = imageV2.imgTbl.height(); jQuery(img.imgAreaSelect( { selectionColor: 'green', outerColor: '', minHeight: imgHeight, maxHeight: imgHeight, onSelectEnd: makeItemsByDrag.end, autoHide: true, movable: false})); } }, load: function () { for (var id in hgTracks.trackDb) { var rec = hgTracks.trackDb[id]; if(rec.type != null && rec.type.indexOf("makeItems") == 0) { this.init(id); } } } } /////////////////// ///// mouse ///// /////////////////// var mouse = { savedOffset: {x:0, y:0}, saveOffset: function (ev) { // Save the mouse offset associated with this event mouse.savedOffset = {x: ev.clientX, y: ev.clientY}; }, hasMoved: function (ev) { // return true if mouse has moved a significant amount var minPixels = 10; var movedX = ev.clientX - mouse.savedOffset.x; var movedY = ev.clientY - mouse.savedOffset.y; if (arguments.length == 2) { var num = Number(arguments[1]); if(isNaN(num)) { if ( arguments[1].toLowerCase() == "x" ) return (movedX > minPixels || movedX < (minPixels * -1)); if ( arguments[1].toLowerCase() == "y" ) return (movedY > minPixels || movedY < (minPixels * -1)); } else minPixels = num; } return ( movedX > minPixels || movedX < (minPixels * -1) || movedY > minPixels || movedY < (minPixels * -1)); } } ///////////////// //// posting //// ///////////////// var posting = { blockUseMap: false, blockMapClicks: function () { posting.blockUseMap=true; }, allowMapClicks: function () { posting.blockUseMap=false; }, mapClicksAllowed: function () { return (posting.blockUseMap == false); }, blockTheMapOnMouseMove: function (ev) { if (!posting.blockUseMap && mouse.hasMoved(ev)) { posting.blockUseMap=true; } }, mapClk: function () { var done = false; if(false && imageV2.inPlaceUpdate) { // XXXX experimental and only turned on in larrym's tree. // Use in-place update if the map item just modifies the current position (this is nice because it's faster // and it preserves the users current relative position in the track image). // // First test handles next/prev item. var str = "/cgi-bin/hgTracks\\?position=([^:]+):(.+)&hgsid=(\\d+)&(hgt\.(next|prev)Item=[^&]+)"; var reg = new RegExp(str); var a = reg.exec(this.href); if(a && a[1] && a[1] == hgTracks.chromName) { imageV2.navigateInPlace("position=" + encodeURIComponent(a[1] + ":" + a[2]) + "&" + a[4], null, true); done = true; } else { // handle next/prev exon str = "/cgi-bin/hgTracks\\?position=([^:]+):(.+)&hgsid=(\\d+)$"; reg = new RegExp(str); a = reg.exec(this.href); if(a && a[1]) { imageV2.navigateInPlace("position=" + encodeURIComponent(a[1] + ":" + a[2]), null, true); done = true; } else { // handle toggle visibility. Request may include a track set, so we cannot use requestImgUpdate. str = "/cgi-bin/hgTracks\\?(position=[^:]+:.+&hgsid=\\d+&([^=]+)=([^&]+))$"; reg = new RegExp(str); a = reg.exec(this.href); if(a && a[1]) { imageV2.navigateInPlace(a[1], null, true); // imageV2.requestImgUpdate(a[1], a[1] + "=" + a[2], "", a[2]); done = true; } } } } if(done) return false; else return posting.saveSettings(this); }, saveSettings: function (obj) { if(posting.blockUseMap==true) { return false; } if(obj == undefined || obj.href == undefined) // called directly with obj obj = this; // and from callback without obj if ($(obj).hasClass('noLink')) // TITLE_BUT_NO_LINK return false; if (obj.href.match('#') || obj.target.length > 0) { //alert("Matched # ["+obj.href+"] or has target:"+obj.target); return true; } var thisForm=$(obj).parents('form'); if(thisForm == undefined || $(thisForm).length == 0) thisForm=$("FORM"); if($(thisForm).length > 1 ) thisForm=$(thisForm)[0]; if(thisForm != undefined && $(thisForm).length == 1) { //alert("posting form:"+$(thisForm).attr('name')); return postTheForm($(thisForm).attr('name'),obj.href); } return true; } } /////////////////////////////////////////////// //// visibility (mixed with group toggle) ///// /////////////////////////////////////////////// var vis = { enumOrder: new Array("hide", "dense", "full", "pack", "squish"), // map cgi enum visibility codes to strings update: function (track, visibility) { // Updates visibility state in hgTracks.trackDb and any visible elements on the page. // returns true if we modify at least one select in the group list var rec = hgTracks.trackDb[track]; var selectUpdated = false; $("select[name=" + escapeJQuerySelectorChars(track) + "]").each(function(t) { $(this).attr('class', visibility == 'hide' ? 'hiddenText' : 'normalText'); $(this).val(visibility); selectUpdated = true; }); if(rec) { rec.localVisibility = visibility; } return selectUpdated; }, get: function (track) { // return current visibility for given track var rec = hgTracks.trackDb[track]; if(rec) { if(rec.localVisibility) { return rec.localVisibility; } else { return vis.enumOrder[rec.visibility]; } } else { return null; } }, makeTrackVisible: function (track) { if(track != null && vis.get(track) != "full") { vis.update(track, 'pack'); $("<input type='hidden' name='" + track + "'value='pack'>").appendTo( $(document.TrackHeaderForm)); } }, toggleForGroup: function (button, prefix) { // toggle visibility of a track group; prefix is the prefix of all the id's of tr's in the // relevant group. This code also modifies the corresponding hidden fields and the gif of the +/- img tag. imageV2.markAsDirtyPage(); if(arguments.length > 2) return setTableRowVisibility(button, prefix, "hgtgroup", "group",false,arguments[2]); else return setTableRowVisibility(button, prefix, "hgtgroup", "group",false); }, expandAllGroups: function (newState) { // Set visibility of all track groups to newState (true means expanded). // This code also modifies the corresponding hidden fields and the gif's of the +/- img tag. imageV2.markAsDirtyPage(); $(".toggleButton[id$='_button']").each( function (i) { // works for old img type AND new BUTTONS_BY_CSS vis.toggleForGroup(this,this.id.substring(0,this.id.length - 7),newState); // clip '_button' suffix }); return false; } } //////////////////////////////////////////////////////////// // dragSelect is also known as dragZoom or shift-dragZoom // //////////////////////////////////////////////////////////// var dragSelect = { areaSelector: null, // formerly "imgAreaSelect". jQuery element used for imgAreaSelect autoHideSetting: true, // Current state of imgAreaSelect autoHide setting originalCursor: null, startTime: null, rulerModeToggle: function (ele) // UNUSED? { dragSelect.autoHideSetting = !ele.checked; var obj = dragSelect.areaSelector.data('imgAreaSelect'); obj.setOptions({autoHide : dragSelect.autoHideSetting}); }, selectStart: function (img, selection) { initVars(); if(rightClick.menu) { rightClick.menu.hide(); } var now = new Date(); dragSelect.startTime = now.getTime(); posting.blockMapClicks(); }, selectChange: function (img, selection) { if(selection.x1 != selection.x2) { if (genomePos.check(img, selection)) { genomePos.update(img, selection, false); jQuery('body').css('cursor', dragSelect.originalCursor); } else { jQuery('body').css('cursor', 'not-allowed'); } } return true; }, selectEnd: function (img, selection) { var now = new Date(); var doIt = false; if(dragSelect.originalCursor != null) jQuery('body').css('cursor', dragSelect.originalCursor); // ignore releases outside of the image rectangle (allowing a 10 pixel slop) if(dragSelect.autoHideSetting && genomePos.check(img, selection)) { // ignore single clicks that aren't in the top of the image (this happens b/c the clickClipHeight test in dragSelect.selectStart // doesn't occur when the user single clicks). doIt = dragSelect.startTime != null || selection.y1 <= hgTracks.rulerClickHeight; } if(doIt) { // dragSelect.startTime is null if mouse has never been moved var singleClick = ( (selection.x2 == selection.x1) || dragSelect.startTime == null || (now.getTime() - dragSelect.startTime) < 100); var newPosition = genomePos.update(img, selection, singleClick); if(newPosition != undefined) { if(imageV2.inPlaceUpdate) { imageV2.navigateInPlace("position=" + newPosition, null, true); } else { jQuery('body').css('cursor', 'wait'); document.TrackHeaderForm.submit(); } } } else { // what is this doing? genomePos.set(genomePos.original, genomePos.originalSize); genomePos.original = genomePos.originalSize = null; // <- XXXX I think this is unnecessary. } dragSelect.startTime = null; setTimeout('posting.allowMapClicks();',50); // Necessary incase the dragSelect.selectEnd was over a map item. select takes precedence. return true; }, load: function (firstTime) { var imgHeight = 0; if (imageV2.enabled) imgHeight = imageV2.imgTbl.height(); // No longer disable without ruler, because shift-drag still works if(typeof(hgTracks) != "undefined") { if (hgTracks.rulerClickHeight == undefined || hgTracks.rulerClickHeight == null) hgTracks.rulerClickHeight = 0; // will be zero if no ruler track var heights = hgTracks.rulerClickHeight; dragSelect.areaSelector = jQuery((imageV2.imgTbl).imgAreaSelect({ selectionColor: 'blue', outerColor: '', minHeight: imgHeight, maxHeight: imgHeight, onSelectStart: dragSelect.selectStart, onSelectChange: dragSelect.selectChange, onSelectEnd: dragSelect.selectEnd, autoHide: dragSelect.autoHideSetting, movable: false, clickClipHeight: heights })); } } } ///////////////////////////////////// //// Chrom Drag/Zoom/Expand code //// ///////////////////////////////////// jQuery.fn.chromDrag = function(){ this.each(function(){ // Plan: // mouseDown: determine where in map: convert to img location: pxDown // mouseMove: flag drag // mouseUp: if no drag, then create href centered on bpDown loc with current span // if drag, then create href from bpDown to bpUp // if ctrlKey then expand selection to containing cytoBand(s) var img = { top: -1, scrolledTop: -1, height: -1, left: -1, scrolledLeft: -1, width: -1 }; // Image dimensions all in pix var chr = { name: "", reverse: false, beg: -1, end: -1, size: -1, top: -1, bottom: -1, left: -1, right: -1, width: -1 }; // chrom Dimenaions beg,end,size in bases, rest in pix var pxDown = 0; // pix X location of mouseDown var chrImg = $(this); var mouseIsDown = false; var mouseHasMoved = false; var hilite = jQuery('<div></div>'); initialize(); function initialize(){ findDimensions(); if(chr.top == -1) warn("chromIdeo(): failed to register "+this.id); else { hiliteSetup(); $('area.cytoBand').mousedown( function(e) { // mousedown on chrom portion of image only (map items) updateImgOffsets(); pxDown = e.clientX - img.scrolledLeft; var pxY = e.clientY - img.scrolledTop; if(mouseIsDown == false && isWithin(chr.left,pxDown,chr.right) && isWithin(chr.top,pxY,chr.bottom)) { mouseIsDown = true; mouseHasMoved = false; $(document).bind('mousemove',chromMove); $(document).bind( 'mouseup', chromUp); hiliteShow(pxDown,pxDown); return false; } }); } } function chromMove(e) { // If mouse was down, determine if dragged, then show hilite if ( mouseIsDown ) { var pxX = e.clientX - img.scrolledLeft; var relativeX = (pxX - pxDown); if(mouseHasMoved || (mouseHasMoved == false && Math.abs(relativeX) > 2)) { mouseHasMoved = true; if(isWithin(chr.left,pxX,chr.right)) hiliteShow(pxDown,pxX); else if(pxX < chr.left) hiliteShow(pxDown,chr.left); else hiliteShow(pxDown,chr.right); } } } function chromUp(e) { // If mouse was down, handle final selection $(document).unbind('mousemove',chromMove); $(document).unbind('mouseup',chromUp); chromMove(e); // Just in case if(mouseIsDown) { updateImgOffsets(); var bands; var pxUp = e.clientX - img.scrolledLeft; var pxY = e.clientY - img.scrolledTop; //warn("chromIdeo("+chr.name+") selected range (pix):"+pxDown+"-"+pxUp+" chrom range (pix):"+chr.left+"-"+chr.right+" chrom range (bp):"+chr.name+":"+chr.beg+"-"+chr.end); if(isWithin(0,pxY,img.height)) { // within vertical range or else cancel var selRange = { beg: -1, end: -1, width: -1 }; var dontAsk = true; if(e.ctrlKey) { bands = findCytoBand(pxDown,pxUp); if(bands.end > -1) { pxDown = bands.left; pxUp = bands.right; mouseHasMoved = true; dontAsk = false; selRange.beg = bands.beg; selRange.end = bands.end; hiliteShow(pxDown,pxUp); } } else if(mouseHasMoved) { if ( isWithin(-20,pxUp,chr.left) ) // bounded by chrom dimensions: but must remain within image! pxUp = chr.left; if ( isWithin(chr.right,pxUp,img.width + 20) ) pxUp = chr.right; if ( isWithin(chr.left,pxUp,chr.right+1) ) { selRange.beg = convertToBases(pxDown); selRange.end = convertToBases(pxUp); if(Math.abs(selRange.end - selRange.beg) < 20) mouseHasMoved = false; // Drag so small: treat as simple click else dontAsk = false; } //else warn("chromIdeo("+chr.name+") NOT WITHIN HORIZONTAL RANGE\n selected range (pix):"+pxDown+"-"+pxUp+" chrom range (pix):"+chr.left+"-"+chr.right); } if(mouseHasMoved == false) { // Not else because small drag turns this off hiliteShow(pxUp,pxUp); var curWidth = hgTracks.winEnd - hgTracks.winStart; selRange.beg = convertToBases(pxUp) - Math.round(curWidth/2); // Notice that beg is based upon up position selRange.end = selRange.beg + curWidth; } if(selRange.end > -1) { // prompt, then submit for new position selRange = rangeNormalizeToChrom(selRange,chr); if(mouseHasMoved == false) { // Update highlight by converting bp back to pix pxDown = convertFromBases(selRange.beg) pxUp = convertFromBases(selRange.end) hiliteShow(pxDown,pxUp); } //if ((selRange.end - selRange.beg) < 50000) // dontAsk = true; if (dontAsk || confirm("Jump to new position:\n\n"+chr.name+":"+commify(selRange.beg)+ "-"+commify(selRange.end)+" size:"+commify(selRange.width)) ) { genomePos.setByCoordinates(chr.name, selRange.beg, selRange.end) $('area.cytoBand').mousedown( function(e) { return false; }); // Stop the presses :0) document.TrackHeaderForm.submit(); return true; // Make sure the setTimeout below is not called. } } } //else warn("chromIdeo("+chr.name+") NOT WITHIN VERTICAL RANGE\n selected range (pix):"+pxDown+"-"+pxUp+" chrom range (pix):"+chr.left+"-"+chr.right+"\n cytoTop-Bottom:"+chr.top +"-"+chr.bottom); hiliteCancel(); setTimeout('posting.allowMapClicks();',50); } mouseIsDown = false; mouseHasMoved = false; } function isWithin(beg,here,end) { // Simple utility return ( beg <= here && here < end ); } function convertToBases(pxX) { // Simple utility to convert pix to bases var offset = (pxX - chr.left)/chr.width; if(chr.reverse) offset = 1 - offset; return Math.round(offset * chr.size); } function convertFromBases(bases) { // Simple utility to convert bases to pix var offset = bases/chr.size; if(chr.reverse) offset = 1 - offset; return Math.round(offset * chr.width) + chr.left; } function findDimensions() { // Called at init: determine the dimensions of chrom from 'cytoband' map items var lastX = -1; $('area.cytoBand').each(function(ix) { var loc = this.coords.split(","); if(loc.length == 4) { var myLeft = parseInt(loc[0]); var myRight = parseInt(loc[2]); if (chr.top == -1) { chr.left = myLeft; chr.right = myRight; chr.top = parseInt(loc[1]); chr.bottom = parseInt(loc[3]); } else { if (chr.left > myLeft) chr.left = myLeft; if (chr.right < parseInt(loc[2])) chr.right = parseInt(loc[2]); } var range = this.title.substr(this.title.lastIndexOf(':')+1) var pos = range.split('-'); if(pos.length == 2) { if (chr.name.length == 0) { chr.beg = parseInt(pos[0]); //chr.end = parseInt(pos[1]); chr.name = this.title.substring(this.title.lastIndexOf(' ')+1, this.title.lastIndexOf(':')) } else { if (chr.beg > parseInt(pos[0])) chr.beg = parseInt(pos[0]); } if (chr.end < parseInt(pos[1])) { chr.end = parseInt(pos[1]); if(lastX == -1) lastX = myRight; else if(lastX > myRight) chr.reverse = true; // end is advancing, but X is not, so reverse } else if(lastX != -1 && lastX < myRight) chr.reverse = true; // end is not advancing, but X is, so reverse } $(this).css( 'cursor', 'text'); $(this).attr("href",""); } }); chr.size = (chr.end - chr.beg ); chr.width = (chr.right - chr.left); } function findCytoBand(pxDown,pxUp) { // Called when mouseup and ctrl: Find the bounding cytoband dimensions, both 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]); if(cyto.left == -1 || cyto.left > myLeft) { if ( isWithin(myLeft,pxDown,myRight) || isWithin(myLeft,pxUp,myRight) ) { cyto.left = myLeft; var range = this.title.substr(this.title.lastIndexOf(':')+1) var pos = range.split('-'); if(pos.length == 2) { cyto.beg = (chr.reverse ? parseInt(pos[1]) : parseInt(pos[0])); } } } if(cyto.right == -1 || cyto.right < myRight) { if ( isWithin(myLeft,pxDown,myRight) || isWithin(myLeft,pxUp,myRight) ) { cyto.right = myRight; var range = this.title.substr(this.title.lastIndexOf(':')+1) var pos = range.split('-'); if(pos.length == 2) { cyto.end = (chr.reverse ? parseInt(pos[0]) : parseInt(pos[1])); } } } } }); return cyto; } function rangeNormalizeToChrom(selection,chrom) { // Called before presenting or using base range: make sure chrom selection is within chrom range if(selection.end < selection.beg) { var tmp = selection.end; selection.end = selection.beg; selection.beg = tmp; } selection.width = (selection.end - selection.beg); selection.beg += 1; if (selection.beg < chrom.beg) { selection.beg = chrom.beg; selection.end = chrom.beg + selection.width; } if (selection.end > chrom.end) { selection.end = chrom.end; selection.beg = chrom.end - selection.width; if (selection.beg < chrom.beg) { // spans whole chrom selection.width = (selection.end - chrom.beg); selection.beg = chrom.beg + 1; } } return selection; } function hiliteShow(down,cur) { // Called on mousemove, mouseup: set drag hilite dimensions var topY = img.top; var high = img.height; var begX = -1; var wide = -1; if(cur < down) { begX = cur + img.left; wide = (down - cur); } else { begX = down + img.left; wide = (cur - down); } $(hilite).css({ left: begX + 'px', width: wide + 'px', top: topY + 'px', height: high + 'px', display:'' }); $(hilite).show(); } function hiliteCancel(left,width,top,height) { // Called on mouseup: Make green drag hilite disappear when no longer wanted $(hilite).hide(); $(hilite).css({ left: '0px', width: '0px', top: '0px', height: '0px' }); } function hiliteSetup() { // Called on init: setup of drag region hilite (but don't show yet) $(hilite).css({ backgroundColor: 'green', opacity: 0.4, borderStyle: 'solid', borderWidth: '1px', bordercolor: '#0000FF' }); $(hilite).css({ display: 'none', position: 'absolute', overflow: 'hidden', zIndex: 1 }); jQuery($(chrImg).parents('body')).append($(hilite)); return hilite; } function updateImgOffsets() { // Called on mousedown: Gets the current offsets var offs = $(chrImg).offset(); img.top = Math.round(offs.top ); img.left = Math.round(offs.left); img.scrolledTop = img.top - $("body").scrollTop(); img.scrolledLeft = img.left - $("body").scrollLeft(); if($.browser.msie) { img.height = $(chrImg).outerHeight(); img.width = $(chrImg).outerWidth(); } else { img.height = $(chrImg).height(); img.width = $(chrImg).width(); } return img; } }); } /////////////////////////// //// Drag Reorder Code //// /////////////////////////// var dragReorder = { setOrder: function (table) { // Sets the 'order' value for the image table after a drag reorder var names = []; var values = []; $("tr.imgOrd").each(function (i) { if ($(this).attr('abbr') != $(this).attr('rowIndex').toString()) { $(this).attr('abbr',$(this).attr('rowIndex').toString()); var name = this.id.substring('tr_'.length) + '_imgOrd'; names.push(name); values.push($(this).attr('abbr')); } }); if(names.length > 0) { setCartVars(names,values); imageV2.markAsDirtyPage(); } }, showCenterLabel: function (tr, show) { // Will show or hide centerlabel as requested // adjust button, sideLabel height, sideLabelOffset and centerlabel display if (!$(tr).hasClass('clOpt')) return; var center = $(tr).find(".sliceDiv.cntrLab"); if($(center) == undefined) return; seen = ($(center).css('display') != 'none'); if(show == seen) return; var centerHeight = $(center).height(); var btn = $(tr).find("p.btn"); var side = $(tr).find(".sliceDiv.sideLab"); if($(btn) != undefined && $(side) != undefined) { var sideImg = $(side).find("img"); if($(sideImg) != undefined) { var top = parseInt($(sideImg).css('top')); if(show) { $(btn).css('height',$(btn).height() + centerHeight); $(side).css('height',$(side).height() + centerHeight); top += centerHeight; // top is a negative number $(sideImg).css( {'top': top.toString() + "px" }); $( center ).show(); } else if (!show) { $(btn).css('height',$(btn).height() - centerHeight); $(side).css('height',$(side).height() - centerHeight); top -= centerHeight; // top is a negative number $(sideImg).css( {'top': top.toString() + "px" }); $( center ).hide(); } } } }, getContiguousRowSet: function (row) { // Returns the set of rows that are of the same class and contiguous if(row == null) return null; var btn = $( row ).find("p.btn"); if (btn.length == 0) return null; var classList = $( btn ).attr("class").split(" "); var matchClass = classList[0]; var table = $(row).parents('table#imgTbl')[0]; var rows = $(table).find('tr'); // Find start index var startIndex = $(row).attr('rowIndex'); var endIndex = startIndex; for(var ix=startIndex-1;ix>=0;ix--) { btn = $( rows[ix] ).find("p.btn"); if (btn.length == 0) break; classList = $( btn ).attr("class").split(" "); if (classList[0] != matchClass) break; startIndex = ix; } // Find end index for(var ix=endIndex;ix<rows.length;ix++) { btn = $( rows[ix] ).find("p.btn"); if (btn.length == 0) break; classList = $( btn ).attr("class").split(" "); if (classList[0] != matchClass) break; endIndex = ix; } return rows.slice(startIndex,endIndex+1); // endIndex is 1 based! }, getCompositeSet: function (row) { // Returns the set of rows that are of the same class and contiguous if(row == null) return null; var rowId = $(row).attr('id').substring('tr_'.length); var rec = hgTracks.trackDb[rowId]; if (tdbIsSubtrack(rec) == false) return null; var rows = $('tr.trDraggable:has(p.' + rec.parentTrack+')'); return rows; }, zipButtons: function (table) { // Goes through the image and binds composite track buttons when adjacent var rows = $(table).find('tr'); var lastClass=""; var lastBtn; var lastMatchesLast=false; var lastBlue=true; var altColors=false; var count=0; var countN=0; for(var ix=0;ix<rows.length;ix++) { // Need to have buttons in order var btn = $( rows[ix] ).find("p.btn"); if (btn.length == 0) continue; var classList = $( btn ).attr("class").split(" "); var curMatchesLast=(classList[0] == lastClass); // centerLabels may be conditionally seen if($( rows[ix] ).hasClass('clOpt')) { if(curMatchesLast && $( rows[ix - 1] ).hasClass('clOpt')) dragReorder.showCenterLabel(rows[ix],false); // if same composite and previous is also centerLabel optional then hide center label else dragReorder.showCenterLabel(rows[ix],true); } // On with buttons if(lastBtn != undefined) { $( lastBtn ).removeClass('btnN btnU btnL btnD'); if(curMatchesLast && lastMatchesLast) { $( lastBtn ).addClass('btnL'); } else if(lastMatchesLast) { $( lastBtn ).addClass('btnU'); } else if(curMatchesLast) { $( lastBtn ).addClass('btnD'); } else { $( lastBtn ).addClass('btnN'); countN++; } count++; if(altColors) { lastBlue = (lastMatchesLast == lastBlue); // lastMatch and lastBlue or not lastMatch and notLastBlue if(lastBlue) // Too smart by 1/3rd $( lastBtn ).addClass( 'btnBlue' ); else $( lastBtn ).removeClass( 'btnBlue' ); } } lastMatchesLast = curMatchesLast; lastClass = classList[0]; lastBtn = btn; } if(lastBtn != undefined) { $( lastBtn ).removeClass('btnN btnU btnL btnD'); if(lastMatchesLast) { $( btn).addClass('btnU'); } else { $( lastBtn ).addClass('btnN'); countN++; } if(altColors) { lastBlue = (lastMatchesLast == lastBlue); // lastMatch and lastBlue or not lastMatch and notLastBlue if(lastBlue) // Too smart by 1/3rd $( lastBtn ).addClass( 'btnBlue' ); else $( lastBtn ).removeClass( 'btnBlue' ); } count++; } //warn("Zipped "+count+" buttons "+countN+" are independent."); }, dragHandleMouseOver: function () { // Highlights a single row when mouse over a dragHandle column (sideLabel and buttons) if(jQuery.tableDnD == undefined) { //var handle = $("td.dragHandle"); //$(handle) // .unbind('mouseenter')//, jQuery.tableDnD.mousemove); // .unbind('mouseleave');//, jQuery.tableDnD.mouseup); return; } if (jQuery.tableDnD.dragObject == null) { $( this ).parents("tr.trDraggable").addClass("trDrag"); } }, dragHandleMouseOut: function () { // Ends row highlighting by mouse over $( this ).parents("tr.trDraggable").removeClass("trDrag"); }, buttonMouseOver: function () { // Highlights a composite set of buttons, regarless of whether tracks are adjacent if(jQuery.tableDnD == undefined || jQuery.tableDnD.dragObject == null) { var classList = $( this ).attr("class").split(" "); var btns = $( "p." + classList[0] ); $( btns ).removeClass('btnGrey'); $( btns ).addClass('btnBlue'); if (jQuery.tableDnD != undefined) { var rows = dragReorder.getContiguousRowSet($(this).parents('tr.trDraggable')[0]); if (rows) $( rows ).addClass("trDrag"); } } }, buttonMouseOut: function () { // Ends composite highlighting by mouse over var classList = $( this ).attr("class").split(" "); var btns = $( "p." + classList[0] ); $( btns ).removeClass('btnBlue'); $( btns ).addClass('btnGrey'); if (jQuery.tableDnD != undefined) { var rows = dragReorder.getContiguousRowSet($(this).parents('tr.trDraggable')[0]); if (rows) $( rows ).removeClass("trDrag"); } }, trMouseOver: function (e) // LARRY: is this the right thing? { // Trying to make sure there is always a imageV2.lastTrack so that we know where we are var id = ''; var a = /tr_(.*)/.exec($(this).attr('id')); // voodoo if(a && a[1]) { id = a[1]; } if (id.length > 0) { if (imageV2.lastTrack == null || imageV2.lastTrack.id != id) imageV2.lastTrack = rightClick.makeMapItem(id); // currentMapItem gets set by mapItemMapOver } // This is just backup }, mapItemMouseOver: function () { // Record data for current map area item var id = this.id; if (id == undefined || id == null || id.length == 0) { id = ''; var tr = $( this ).parents('tr.imgOrd'); if ( $(tr).length == 1 ) { var a = /tr_(.*)/.exec($(tr).attr('id')); // voodoo if(a && a[1]) { id = a[1]; } } } if (id.length > 0) { rightClick.currentMapItem = rightClick.makeMapItem(id); if(rightClick.currentMapItem != null) { rightClick.currentMapItem.href = this.href; rightClick.currentMapItem.title = this.title; } } }, mapItemMouseOut: function () { imageV2.lastTrack = rightClick.currentMapItem; // Just a backup rightClick.currentMapItem = null; }, init: function () { // Make side buttons visible (must also be called when updating rows in the imgTbl). var btns = $("p.btn"); if(btns.length > 0) { dragReorder.zipButtons($('#imgTbl')); $(btns).mouseenter( dragReorder.buttonMouseOver ); $(btns).mouseleave( dragReorder.buttonMouseOut ); $(btns).show(); } var handle = $("td.dragHandle"); if(handle.length > 0) { $(handle).mouseenter( dragReorder.dragHandleMouseOver ); $(handle).mouseleave( dragReorder.dragHandleMouseOut ); } // setup mouse callbacks for the area tags $(imageV2.imgTbl).find("tr").mouseover( dragReorder.trMouseOver ); $(".area").each( function(t) { this.onmouseover = dragReorder.mapItemMouseOver; this.onmouseout = dragReorder.mapItemMouseOut; this.onclick = posting.mapClk; }); } } ////////////////////////// //// Drag Scroll code //// ////////////////////////// jQuery.fn.panImages = function(){ // globals across all panImages genomePos.original = genomePos.getOriginalPos(); // XXXX what is this for? (this already happened in initVars). var leftLimit = hgTracks.imgBoxLeftLabel * -1; var rightLimit = (hgTracks.imgBoxPortalWidth - hgTracks.imgBoxWidth + leftLimit); var only1xScrolling = ((hgTracks.imgBoxWidth - hgTracks.imgBoxPortalWidth) == 0);//< hgTracks.imgBoxLeftLabel); var prevX = (hgTracks.imgBoxPortalOffsetX + hgTracks.imgBoxLeftLabel) * -1; var portalWidth = 0; var savedPosition; this.each(function(){ var pic; var pan; if ( $(this).is("img") ) { pan = $(this).parent("div"); pic = $(this); } else if ( $(this).is("div.scroller") ) { pan = $(this); pic = $(this).children("img#panImg"); // Get the real pic } if(pan == undefined || pic == undefined) { throw "Not a div with a child image! 'panImages' can only be used with divs contain images."; } // globals across all panImages portalWidth = $(pan).width(); // globals to one panImage var newX = 0; var mouseDownX = 0; var mouseIsDown = false; var beyondImage = false; var atEdge = false; initialize(); function initialize(){ $(pan).parents('td.tdData').mousemove(function(e) { if (e.shiftKey) $(this).css('cursor',"crosshair"); // shift-dragZoom else if ( $.browser.msie ) // IE will override map item cursors if this gets set $(this).css('cursor',""); // normal pointer when not over clickable item //else // NOTE: Open hand cursor is being removed because it makes vis toggling less obvious // $(this).css('cursor',"url(../images/grabber.cur),w-resize"); // dragScroll }); panAdjustHeight(prevX); pan.mousedown(function(e){ if (e.which > 1 || e.button > 1 || e.shiftKey) return true; if(mouseIsDown == false) { if(rightClick.menu) { rightClick.menu.hide(); } mouseIsDown = true; mouseDownX = e.clientX; atEdge = (!beyondImage && (prevX >= leftLimit || prevX <= rightLimit)); $(document).bind('mousemove',panner); $(document).bind( 'mouseup', panMouseUp); // Will exec only once return false; } }); } function panner(e) { //if (!e) e = window.event; if ( mouseIsDown ) { var relativeX = (e.clientX - mouseDownX); if(relativeX != 0) { if (posting.mapClicksAllowed()) { // need to throw up a z-index div. Wait mask? savedPosition = genomePos.get(); dragMaskShow(); posting.blockMapClicks(); } var decelerator = 1; //var wingSize = 1000; // 0 stops the scroll at the edges. // Remeber that offsetX (prevX) is negative newX = prevX + relativeX; if ( newX >= leftLimit ) { // scrolled all the way to the left if(atEdge) { // Do not drag straight off edge. Force second drag beyondImage = true; newX = leftLimit + (newX - leftLimit)/decelerator;// slower //if (newX >= leftLimit + wingSize) // Don't go too far over the edge! // newX = leftLimit + wingSize; } else newX = leftLimit; } else if ( newX < rightLimit ) { // scrolled all the way to the right if(atEdge) { // Do not drag straight off edge. Force second drag beyondImage = true; newX = rightLimit - (rightLimit - newX)/decelerator;// slower //if (newX < rightLimit - wingSize) // Don't go too far over the edge! // newX = rightLimit - wingSize; } else newX = rightLimit; } else if(newX >= rightLimit && newX < leftLimit) beyondImage = false; // could have scrolled back without mouse up newX = panUpdatePosition(newX,true); var nowPos = newX.toString() + "px"; $(".panImg").css( {'left': nowPos }); $('.tdData').css( {'backgroundPosition': nowPos } ); if (!only1xScrolling) panAdjustHeight(newX); // NOTE: This will dynamically resize image while scrolling. Do we want to? } } } function panMouseUp(e) { // Must be a separate function instead of pan.mouseup event. //if (!e) e = window.event; if(mouseIsDown) { dragMaskClear(); $(document).unbind('mousemove',panner); $(document).unbind('mouseup',panMouseUp); mouseIsDown = false; setTimeout('posting.allowMapClicks();',50); // Necessary incase the dragSelect.selectEnd was over a map item. select takes precedence. // 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 != undefined) genomePos.set(savedPosition,null); var oldPos = prevX.toString() + "px"; $(".panImg").css( {'left': oldPos }); $('.tdData').css( {'backgroundPosition': oldPos } ); return true; } // Do we need to fetch anything? if(beyondImage) { if(imageV2.inPlaceUpdate) { var pos = parsePosition(genomePos.get()); imageV2.navigateInPlace("position=" + encodeURIComponent(pos.chrom + ":" + pos.start + "-" + pos.end), null, true); } else { document.TrackHeaderForm.submit(); } return true; // Make sure the setTimeout below is not called. } // Just a normal scroll within a >1X image if(prevX != newX) { prevX = newX; if (!only1xScrolling) { //panAdjustHeight(newX); // NOTE: This will resize image after scrolling. Do we want to while scrolling? // This is important, since AJAX could lead to reinit after this within bounds scroll hgTracks.imgBoxPortalOffsetX = (prevX * -1) - hgTracks.imgBoxLeftLabel; hgTracks.imgBoxPortalLeft = newX.toString() + "px"; } } } } }); // end of this.each(function(){ function panUpdatePosition(newOffsetX,bounded) { // Updates the 'position/search" display with change due to panning var closedPortalStart = hgTracks.imgBoxPortalStart + 1; // Correction for half open portal coords var portalWidthBases = hgTracks.imgBoxPortalEnd - closedPortalStart; var portalScrolledX = hgTracks.imgBoxPortalOffsetX+hgTracks.imgBoxLeftLabel + newOffsetX; var recalculate = false; var newPortalStart = 0; if (hgTracks.revCmplDisp) newPortalStart = closedPortalStart + Math.round(portalScrolledX*hgTracks.imgBoxBasesPerPixel); // As offset goes down, so do bases seen. else newPortalStart = closedPortalStart - Math.round(portalScrolledX*hgTracks.imgBoxBasesPerPixel); // As offset goes down, bases seen goes up! if (newPortalStart < hgTracks.chromStart && bounded) { // Stay within bounds newPortalStart = hgTracks.chromStart; recalculate = true; } var newPortalEnd = newPortalStart + portalWidthBases; if (newPortalEnd > hgTracks.chromEnd && bounded) { newPortalEnd = hgTracks.chromEnd; newPortalStart = newPortalEnd - portalWidthBases; recalculate = true; } if(newPortalStart > 0) { var newPos = hgTracks.chromName + ":" + commify(newPortalStart) + "-" + commify(newPortalEnd); genomePos.set(newPos, 0); // 0 means no need to change the size } if (recalculate && hgTracks.imgBoxBasesPerPixel > 0) { // Need to recalculate X for bounding drag portalScrolledX = (closedPortalStart - newPortalStart) / hgTracks.imgBoxBasesPerPixel; newOffsetX = portalScrolledX - (hgTracks.imgBoxPortalOffsetX+hgTracks.imgBoxLeftLabel); } return newOffsetX; } function mapTopAndBottom(mapName,east,west) { // Find the top and bottom px given left and right boundaries var mapPortal = { top: -10, bottom: -10 }; var items = $("map[name='"+mapName+"']").children(); if ($(items).length>0) { $(items).each(function(t) { var loc = this.coords.split(","); var aleft = parseInt(loc[0]); var aright = parseInt(loc[2]); if(aleft < west && aright >= east) { var atop = parseInt(loc[1]); var abottom = parseInt(loc[3]); if (mapPortal.top < 0 ) { mapPortal.top = atop; mapPortal.bottom = abottom; } else if(mapPortal.top > atop) { mapPortal.top = atop; } else if(mapPortal.bottom < abottom) { mapPortal.bottom = abottom; } } }); } return mapPortal; } function panAdjustHeight(newOffsetX) { // Adjust the height of the track data images so that bed items scrolled off screen // do not waste vertical real estate // Is the > 1x? if (only1xScrolling) return; var east = newOffsetX * -1; var west = east + portalWidth; $(".panImg").each(function(t) { var mapid = this.id.replace('img_','map_'); var hDiv = $(this).parent(); var north = parseInt($(this).css("top")) * -1; var south = north + $(hDiv).height(); var mapPortal = mapTopAndBottom(mapid,east,west); if(mapPortal.top > 0) { var topdif = Math.abs(mapPortal.top - north); var botdif = Math.abs(mapPortal.bottom - south); if(topdif > 2 || botdif > 2) { $(hDiv).height( mapPortal.bottom - mapPortal.top ); north = mapPortal.top * -1; $(this).css( {'top': north.toString() + "px" }); // Need to adjust side label height as well! var imgId = this.id.split("_"); var titlePx = 0; var center = $("#img_center_"+imgId[2]); if(center.length > 0) { titlePx = $(center).parent().height(); north += titlePx; } var side = $("#img_side_"+imgId[2]); if (side.length > 0) { $(side).parent().height( mapPortal.bottom - mapPortal.top + titlePx); $(side).css( {'top': north.toString() + "px" }); } var btn = $("#p_btn_"+imgId[2]); if (btn.length > 0) { $(btn).height( mapPortal.bottom - mapPortal.top + titlePx); } else { btn = $("#img_btn_"+imgId[2]); if (btn.length > 0) { $(btn).parent().height( mapPortal.bottom - mapPortal.top + titlePx); $(btn).css( {'top': top.toString() + "px" }); } } } } }); dragMaskResize(); // Resizes the dragMask to match current image size } function dragMaskShow() { // Sets up the dragMask to show grabbing cursor within image and not allowed north and south of image var imgTbl = $('#imgTbl'); // Find or create the waitMask (which masks the whole page) var dragMask = $('div#dragMask'); if (dragMask == undefined || dragMask.length == 0) { $("body").prepend("<div id='dragMask' class='waitMask'></div>"); dragMask = $('div#dragMask'); } $('body').css('cursor','not-allowed'); $(dragMask).css('cursor',"url(../images/grabbing.cur),w-resize"); $(dragMask).css({opacity:0.0,display:'block', top: $(imgTbl).position().top.toString() + 'px', height: $(imgTbl).height().toString() + 'px' }); //$(dragMask).css({opacity:0.4,backgroundColor:'gray',zIndex:999}); // temporarily so I can see it } 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 = $('div#dragMask'); if (dragMask != undefined && dragMask.length >= 1) { $(dragMask).height( $(imgTbl).height() ); } } function dragMaskClear() { // Clears the dragMask $('body').css('cursor','auto') var dragMask = $('#dragMask'); if (dragMask != undefined ) $(dragMask).hide(); } }; /////////////////////////////////////// //// rightClick (aka context menu) //// /////////////////////////////////////// var rightClick = { menu: null, selectedMenuItem: null, // currently choosen context menu item (via context menu). floatingMenuItem: null, currentMapItem: null, supportZoomCodon: false, // turn on experimental zoom-to-codon functionality (currently only on in larry's tree). makeMapItem: function (id) { // Create a dummy mapItem on the fly (for objects that don't have corresponding entry in the map). if(id && id.length > 0 && typeof(hgTracks.trackDb) != "undefined" && hgTracks.trackDb != null) { var title; var rec = hgTracks.trackDb[id]; if(rec) { title = rec.shortLabel; } else { title = id; } return {id: id, title: "configure " + title}; } else { return null; } }, findMapItem: function (e) { // Find mapItem for given event; returns item object or null if none found. if(rightClick.currentMapItem) { return rightClick.currentMapItem; } // rightClick for non-map items that can be resolved to their parent tr and then trackName (e.g. items in gray bar) var tr = $( e.target ).parents('tr.imgOrd'); if ( $(tr).length == 1 ) { var a = /tr_(.*)/.exec($(tr).attr('id')); // voodoo if(a && a[1]) { var id = a[1]; return rightClick.makeMapItem(id); } } return null; }, windowOpenFailedMsg: function () { warn("Your web browser prevented us from opening a new window.\n\nPlease change your browser settings to allow pop-up windows from " + document.domain + "."); }, handleZoomCodon: function (response, status) { var json = eval("(" + response + ")"); if(json.pos) { genomePos.set(json.pos, 3); if(document.TrackForm) document.TrackForm.submit(); else document.TrackHeaderForm.submit(); } else { alert(json.error); } }, handleViewImg: function (response, status) { // handles view image response, which must get new image without imageV2 gimmickery jQuery('body').css('cursor', ''); var str = "<IMG[^>]*SRC='([^']+)'"; var reg = new RegExp(str); a = reg.exec(response); if(a && a[1]) { if(window.open(a[1]) == null) { rightClick.windowOpenFailedMsg(); } return; } warn("Couldn't parse out img src"); }, myPrompt: function (msg, callback) { // replacement for prompt; avoids misleading/confusing security warnings which are caused by prompt in IE 7+ // callback is called if user presses "OK". $("body").append("<div id = 'myPrompt'><div id='dialog' title='Basic dialog'><form>" + msg + "<input id='myPromptText' value=''></form>"); $("#myPrompt").dialog({ modal: true, closeOnEscape: true, buttons: { "OK": function() { var myPromptText = $("#myPromptText").val(); $(this).dialog("close"); callback(myPromptText); } } }); }, hit: function (menuItemClicked, menuObject, cmd, args) { setTimeout( function() { rightClick.hitFinish(menuItemClicked, menuObject, cmd, args); }, 1); }, hitFinish: function (menuItemClicked, menuObject, cmd, args) { // dispatcher for context menu hits var id = rightClick.selectedMenuItem.id; if(menuObject.shown) { // warn("Spinning: menu is still shown"); setTimeout(function() { rightClick.hitFinish(menuItemClicked, menuObject, cmd); }, 10); return; } if(cmd == 'selectWholeGene' || cmd == 'getDna') { // bring whole gene into view or redirect to DNA screen. var href = rightClick.selectedMenuItem.href; var chromStart, chromEnd; var a = /hgg_chrom=(\w+)&/.exec(href); // Many links leave out the chrom (b/c it's in the server side cart as "c") var chrom = hgTracks.chromName; if(a) { if(a && a[1]) chrom = a[1]; a = /hgg_start=(\d+)/.exec(href); if(a && a[1]) // XXXX does chromStart have to be incremented by 1? chromStart = a[1]; a = /hgg_end=(\d+)/.exec(href); if(a && a[1]) chromEnd = a[1]; } else { // a = /hgc.*\W+c=(\w+)/.exec(href); a = /hgc.*\W+c=(\w+)/.exec(href); if(a && a[1]) chrom = a[1]; a = /o=(\d+)/.exec(href); if(a && a[1]) chromStart = parseInt(a[1]) + 1; a = /t=(\d+)/.exec(href); if(a && a[1]) chromEnd = parseInt(a[1]); } if(chrom == null || chromStart == null || chromEnd == null) { warn("couldn't parse out genomic coordinates"); } else { if(cmd == 'getDna') { if(window.open("../cgi-bin/hgc?g=getDna&i=mixed&c=" + chrom + "&l=" + (chromStart - 1) + "&r=" + chromEnd ) == null) { rightClick.windowOpenFailedMsg(); } } else { var newPosition = genomePos.setByCoordinates(chrom, chromStart, chromEnd); var reg = new RegExp("hgg_gene=([^&]+)"); var a = reg.exec(href); var name; // pull item name out of the url so we can set hgFind.matches (redmine 3062) if(a && a[1]) { name = a[1]; } else { reg = new RegExp("[&?]i=([^&]+)"); a = reg.exec(href); if(a && a[1]) { name = a[1]; } } if(imageV2.inPlaceUpdate) { // XXXX This attempt to "update whole track image in place" didn't work for a variety of reasons // (e.g. safari doesn't parse map when we update on the client side), so this is currently dead code. // However, this now works in all other browsers, so we may turn this on for non-safari browsers // (see redmine #4667). jQuery('body').css('cursor', ''); var data = "hgt.trackImgOnly=1&hgt.ideogramToo=1&position=" + newPosition + "&hgsid=" + getHgsid(); if(name) data += "&hgFind.matches=" + name; $.ajax({ type: "GET", url: "../cgi-bin/hgTracks", data: 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) $(ele).append("<input type='hidden' name='hgFind.matches' " + "value='" + name + "'>"); ele.submit(); } } } } else if (cmd == 'zoomCodon' || cmd == 'zoomExon') { var num, ajaxCmd, msg; if(cmd == 'zoomCodon') { msg = "Please enter the codon number to jump to:"; ajaxCmd = 'codonToPos'; } else { msg = "Please enter the exon number to jump to:"; ajaxCmd = 'exonToPos'; } rightClick.myPrompt(msg, function(results) { $.ajax({ type: "GET", url: "../cgi-bin/hgApi", data: "db=" + getDb() + "&cmd=" + ajaxCmd + "&num=" + results + "&table=" + args.table + "&name=" + args.name, trueSuccess: rightClick.handleZoomCodon, success: catchErrorOrDispatch, error: errorHandler, cache: true }); }); } else if (cmd == 'hgTrackUi_popup') { popUp.hgTrackUi( rightClick.selectedMenuItem.id, false ); // Launches the popup but shields the ajax with a waitOnFunction } else if (cmd == 'hgTrackUi_follow') { var url = "hgTrackUi?hgsid=" + getHgsid() + "&g="; var rec = hgTracks.trackDb[id]; if (tdbHasParent(rec) && tdbIsLeaf(rec)) url += rec.parentTrack else { var link = $( 'td#td_btn_'+ rightClick.selectedMenuItem.id ).children('a'); // The button already has the ref if ($(link) != undefined) url = $(link).attr('href'); else url += rightClick.selectedMenuItem.id; } location.assign(url); } else if (cmd == 'dragZoomMode') { dragSelect.autoHideSetting = true; var obj = dragSelect.areaSelector.data('imgAreaSelect'); obj.setOptions({autoHide : true, movable: false}); } else if (cmd == 'hilightMode') { dragSelect.autoHideSetting = false; var obj = dragSelect.areaSelector.data('imgAreaSelect'); obj.setOptions({autoHide : false, movable: true}); } else if (cmd == 'viewImg') { // Fetch a new copy of track img and show it to the user in another window. This code assume we have updated // remote cart with all relevant chages (e.g. drag-reorder). /* Here's how to do this more directly with hgRenderTracks: if(window.open("../cgi-bin/hgRenderTracks?hgt.internal=1&hgsid=" + getHgsid()) == null) { rightClick.windowOpenFailedMsg(); } return; */ var data = "hgt.imageV1=1&hgt.trackImgOnly=1&hgsid=" + getHgsid(); jQuery('body').css('cursor', 'wait'); $.ajax({ type: "GET", url: "../cgi-bin/hgTracks", data: data, dataType: "html", trueSuccess: rightClick.handleViewImg, success: catchErrorOrDispatch, error: errorHandler, cmd: cmd, cache: false }); } else if (cmd == 'openLink' || cmd == 'followLink') { var href = rightClick.selectedMenuItem.href; var vars = new Array("c", "l", "r", "db"); var valNames = new Array("chromName", "winStart", "winEnd"); for (var i in vars) { // make sure the link contains chrom and window width info (necessary b/c we are stripping hgsid and/or the cart may be empty); // but don't add chrom to wikiTrack links (see redmine #2476). var v = vars[i]; var val; if(v == "db") { val = getDb(); } else { val = hgTracks[valNames[i]]; } if (val && id != "wikiTrack" && (href.indexOf("?" + v + "=") == -1) && (href.indexOf("&" + v + "=") == -1)) { href = href + "&" + v + "=" + val; } } if(cmd == 'followLink') { // XXXX This is blocked by Safari's popup blocker (without any warning message). location.assign(href); } else { // Remove hgsid to force a new session (see redmine ticket 1333). href = removeHgsid(href); if(window.open(href) == null) { rightClick.windowOpenFailedMsg(); } } } else if (cmd == 'float') { if(rightClick.floatingMenuItem && rightClick.floatingMenuItem == id) { $.floatMgr.FOArray = new Array(); rightClick.floatingMenuItem = null; } else { if(rightClick.floatingMenuItem) { // This doesn't work. $('#img_data_' + rightClick.floatingMenuItem).parent().restartFloat(); // This does work $.floatMgr.FOArray = new Array(); } rightClick.floatingMenuItem = id; rightClick.reloadFloatingItem(); imageV2.requestImgUpdate(id, "hgt.transparentImage=0", ""); } } else if (cmd == 'hideSet') { var row = $( 'tr#tr_' + id ); var rows = dragReorder.getContiguousRowSet(row); if (rows && rows.length > 0) { var vars = new Array(); var vals = new Array(); for (var ix=rows.length - 1; ix >= 0; ix--) { // from bottom, just in case remove screws with us var rowId = $(rows[ix]).attr('id').substring('tr_'.length); //if (tdbIsSubtrack(hgTracks.trackDb[rowId]) == false) // warn('What went wrong?'); vars.push(rowId, rowId+'_sel'); // Remove subtrack level vis and explicitly uncheck. vals.push('[]', 0); $(rows[ix]).remove(); } if (vars.length > 0) { setCartVars( vars, vals ); dragReorder.init(); dragSelect.load(false); } imageV2.markAsDirtyPage(); } } else if (cmd == 'hideComposite') { var rec = hgTracks.trackDb[id]; if (tdbIsSubtrack(rec)) { var row = $( 'tr#tr_' + id ); var rows = dragReorder.getCompositeSet(row); if (rows && rows.length > 0) { for (var ix=rows.length - 1; ix >= 0; ix--) { // from bottom, just in case remove screws with us $(rows[ix]).remove(); } var selectUpdated = vis.update(rec.parentTrack, 'hide'); setCartVar(rec.parentTrack, 'hide' ); dragReorder.init(); dragSelect.load(false); imageV2.markAsDirtyPage(); } } //else // warn('What went wrong?'); } else { // if ( cmd in 'hide','dense','squish','pack','full','show' ) // Change visibility settings: // // First change the select on our form: var rec = hgTracks.trackDb[id]; var selectUpdated = vis.update(id, cmd); // Now change the track image if(imageV2.enabled && cmd == 'hide') { // Hide local display of this track and update server side cart. // Subtracks controlled by 2 settings so del vis and set sel=0. Others, just set vis hide. if(tdbIsSubtrack(rec)) setCartVars( [ id, id+"_sel" ], [ '[]', 0 ] ); // Remove subtrack level vis and explicitly uncheck. else if(tdbIsFolderContent(rec)) setCartVars( [ id, id+"_sel" ], [ 'hide', 0 ] ); // supertrack children need to have _sel set to trigger superttrack reshaping else setCartVar(id, 'hide' ); $(document.getElementById('tr_' + id)).remove(); dragReorder.init(); dragSelect.load(false); imageV2.markAsDirtyPage(); } else if (!imageV2.mapIsUpdateable) { jQuery('body').css('cursor', 'wait'); if(selectUpdated) { // assert(document.TrackForm); document.TrackForm.submit(); } else { // add a hidden with new visibility value var form = $(document.TrackHeaderForm); $("<input type='hidden' name='"+id+"'value='"+cmd+"'>").appendTo(form); document.TrackHeaderForm.submit(); } } else { imageV2.requestImgUpdate(id, id + "=" + cmd, "", cmd); } } }, makeHitCallback: function (title) { // stub to avoid problem with a function closure w/n a loop return function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, title); return true; }; }, reloadFloatingItem: function () { // currently dead (experimental code) if(rightClick.floatingMenuItem) { $('#img_data_' + rightClick.floatingMenuItem).parent().makeFloat( {x:"current",y:"current", speed: 'fast', alwaysVisible: true, alwaysTop: true}); } }, makeImgTag: function (img) { // Return img tag with explicit dimensions for img (dimensions are currently hardwired). // This fixes the "weird shadow problem when first loading the right-click menu" seen in FireFox 3.X, // which occurred b/c FF doesn't actually fetch the image until the menu is being shown. return "<img style='width:16px; height:16px; border-style:none;' src='../images/" + img + "' />"; }, load: function (img) { rightClick.menu = img.contextMenu( function() { popUp.cleanup(); // Popup box is not getting closed properly so must do it here if (rightClick.selectedMenuItem == null) // This is literally an edge case so ignore return; var menu = []; var selectedImg = rightClick.makeImgTag("greenChecksm.png"); var blankImg = rightClick.makeImgTag("invisible16.png"); var done = false; if(rightClick.selectedMenuItem && rightClick.selectedMenuItem.id != null) { var href = rightClick.selectedMenuItem.href; var isHgc, isGene; if(href) { isGene = href.match("hgGene"); isHgc = href.match("hgc"); } var id = rightClick.selectedMenuItem.id; var rec = hgTracks.trackDb[id]; var offerHideSubset = false; var offerHideComposite = false; var offerSingles = true; var row = $( 'tr#tr_' + id ); if (row) { var btn = $(row).find('p.btnBlue'); // btnBlue means cursor over left button if (btn.length == 1) { var compositeSet = dragReorder.getCompositeSet(row); if (compositeSet && compositeSet.length > 0) { // There is a 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; $( subSet ).addClass("greenRows"); // green persists } } } } } // First option is hide sets if (offerHideComposite) { if (offerHideSubset) { var o = new Object(); o[blankImg + " hide track subset (green)"] = { onclick: rightClick.makeHitCallback('hideSet')}; //o[rightClick.makeImgTag("highliteGreenX.png") + " hide track subset"] = {onclick: rightClick.makeHitCallback('hideSet')}; menu.push(o); } var o = new Object(); var str = blankImg + " hide track set"; if (offerHideSubset) str += " (blue)"; o[str] = {onclick: rightClick.makeHitCallback('hideComposite')}; //o[rightClick.makeImgTag("btnBlueX.png") + " hide track set"] = {onclick: rightClick.makeHitCallback('hideComposite')}; menu.push(o); } // Second set of options: visibility for single track if (offerSingles) { if (offerHideComposite) menu.push($.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(); var str = blankImg + " " + title; if(title == cur) str = selectedImg + " " + title; var o = new Object(); 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) { // XXXX use maxVisibility and change hgTracks so it can hide subtracks var o = new Object(); var str = blankImg + " " + visStrings[i]; if (rec.canPack || (visStrings[i] != "pack" && visStrings[i] != "squish")) { if(rec.localVisibility) { if(visStrings[i] == rec.localVisibility) { str = selectedImg + " " + visStrings[i]; } } else if(visStrings[i] == vis.enumOrder[rec.visibility]) { str = selectedImg + " " + visStrings[i]; } o[str] = { onclick: rightClick.makeHitCallback(visStrings[i]) }; menu.push(o); } } done = true; } } } if(done) { var o = new Object(); var any = false; var title = rightClick.selectedMenuItem.title || "feature"; + if(title.length > 60) { + title = title.substring(0, 50) + "..."; + } if(isGene || isHgc || id == "wikiTrack") { // Add "Open details..." item var displayItemFunctions = false; if(rec) { if(rec.type.indexOf("wig") == 0 || rec.type.indexOf("bigWig") == 0 || id == "wikiTrack") { displayItemFunctions = false; } else if(rec.type.indexOf("expRatio") == 0) { displayItemFunctions = title != "zoomInMore"; } else { displayItemFunctions = true; } } if(displayItemFunctions) { o[rightClick.makeImgTag("magnify.png") + " Zoom to " + title] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "selectWholeGene"); return true; } }; if(rightClick.supportZoomCodon && rec.type.indexOf("genePred") != -1) { // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc003tqk.2&hgg_prot=P00533&hgg_chrom=chr7&hgg_start=55086724&hgg_end=55275030&hgg_type=knownGene&db=hg19&c=chr7 var name, table; var reg = new RegExp("hgg_gene=([^&]+)"); var a = reg.exec(href); if(a && a[1]) { name = a[1]; reg = new RegExp("hgg_type=([^&]+)"); a = reg.exec(href); if(a && a[1]) { table = a[1]; } } else { // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgc?o=55086724&t=55275031&g=refGene&i=NM_005228&c=chr7 // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgc?o=55086713&t=55270769&g=wgEncodeGencodeManualV4&i=ENST00000455089&c=chr7 var reg = new RegExp("i=([^&]+)"); var a = reg.exec(href); if(a && a[1]) { name = a[1]; reg = new RegExp("g=([^&]+)"); a = reg.exec(href); if(a && a[1]) { table = a[1]; } } } if(name && table) { o[rightClick.makeImgTag("magnify.png")+" Zoom to codon"] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "zoomCodon", {name: name, table: table}); return true;} }; o[rightClick.makeImgTag("magnify.png")+" Zoom to exon"] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "zoomExon", {name: name, table: table}); return true; } }; } } o[rightClick.makeImgTag("dnaIcon.png")+" Get DNA for "+title] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "getDna"); return true; } }; } o[rightClick.makeImgTag("bookOut.png")+ " Open details page in new window..."] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "openLink"); return true; } }; any = true; } if(href != undefined && href.length > 0) { // Add "Show details..." item if(title.indexOf("Click to alter ") == 0) { ; // suppress the "Click to alter..." items } else if(rightClick.selectedMenuItem.href.indexOf("cgi-bin/hgTracks") != -1) { ; // suppress menu items for hgTracks links (e.g. Next/Prev map items). } else { var item; if(title == "zoomInMore") // avoid showing menu item that says "Show details for zoomInMore..." (redmine 2447) item = rightClick.makeImgTag("book.png") + " Show details..."; else item = rightClick.makeImgTag("book.png")+" Show details for "+ title + "..."; o[item] = {onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked,menuObject,"followLink"); return true; } }; any = true; } } if(any) { menu.push($.contextMenu.separator); menu.push(o); } } } if (!done) { if(false) { // Currently toggling b/n drag-and-zoom mode and hilite mode is disabled b/c we don't know how to keep hilite mode from disabling the // context menus. var o = new Object(); var str = "drag-and-zoom mode"; if(dragSelect.autoHideSetting) { str += selectedImg; // menu[str].className = 'context-menu-checked-item'; } o[str] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "dragZoomMode"); return true; } }; menu.push(o); o = new Object(); // console.dir(ele); str = "hilight mode"; if (!dragSelect.autoHideSetting) { str += selectedImg; } o[str] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "hilightMode"); return true; } }; menu.push(o); } //menu.push({"view image": {onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "viewImg"); return true; }}}); } if(rightClick.selectedMenuItem && rec && rec["configureBy"] != 'none') { // Add cfg options at just shy of end... var o = new Object(); if(tdbIsLeaf(rec) && (!tdbIsCompositeSubtrack(rec) || rec["configureBy"] != 'clickThrough')) { // Note that subtracks never do clickThrough because composite 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 != undefined) o[rightClick.makeImgTag("folderWrench.png")+" Configure "+ rec.parentLabel + " track set..."] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked,menuObject,"hgTrackUi_follow"); return true; } }; } else o[rightClick.makeImgTag("folderWrench.png")+" Configure "+rec.shortLabel + " track set..."] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_follow"); return true; } }; if(jQuery.floatMgr) { o[(rightClick.selectedMenuItem.id == rightClick.floatingMenuItem ? selectedImg : blankImg) + " float"] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "float"); return true; } }; } menu.push($.contextMenu.separator); menu.push(o); } // Add view image at end var o = new Object(); o[rightClick.makeImgTag("eye.png") + " View image"] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "viewImg"); return true; } }; menu.push($.contextMenu.separator); menu.push(o); return menu; }, { beforeShow: function(e) { // console.log(mapItems[rightClick.selectedMenuItem]); rightClick.selectedMenuItem = rightClick.findMapItem(e); // XXXX? posting.blockUseMap = true; return true; }, hideTransition:'hide', // hideCallback fails if these are not defined. hideSpeed:10, hideCallback: function() { $('p.btn.blueButtons').removeClass('blueButtons'); $('tr.trDraggable.greenRows').removeClass('greenRows'); } }); return; } } ////////////////////////////////// //// popup (aka modal dialog) //// ////////////////////////////////// var popUp = { trackName: "", trackDescriptionOnly: false, saveAllVars: null, cleanup: function () { // Clean out the popup box on close if ($('#hgTrackUiDialog').html().length > 0 ) { $('#hgTrackUiDialog').html(""); // clear out html after close to prevent problems caused by duplicate html elements popUp.trackName = ""; //set to defaults popUp.trackDescriptionOnly = false; popUp.saveAllVars = null; } }, _uiDialigRequest: function (trackName,descriptionOnly) { // popup cfg dialog popUp.trackName = trackName; var myLink = "../cgi-bin/hgTrackUi?g=" + trackName + "&hgsid=" + getHgsid() + "&db=" + getDb(); popUp.trackDescriptionOnly = descriptionOnly; if(popUp.trackDescriptionOnly) myLink += "&descriptionOnly=1"; var rec = hgTracks.trackDb[trackName]; if (!descriptionOnly && rec != null && rec["configureBy"] != null) { if (rec["configureBy"] == 'none') return; else if (rec["configureBy"] == 'clickThrough') { jQuery('body').css('cursor', 'wait'); window.location = myLink; return; } // default falls through to configureBy popup } myLink += "&ajax=1"; $.ajax({ type: "GET", url: myLink, dataType: "html", trueSuccess: popUp.uiDialog, success: catchErrorOrDispatch, error: errorHandler, cmd: rightClick.selectedMenuItem, cache: false }); }, hgTrackUi: function (trackName,descriptionOnly) { waitOnFunction( popUp._uiDialigRequest, trackName, descriptionOnly ); // Launches the popup but shields the ajax with a waitOnFunction }, uiDialogOk: function (popObj, trackName) { // When hgTrackUi Cfg popup closes with ok, then update cart and refresh parts of page var rec = hgTracks.trackDb[trackName]; var subtrack = tdbIsSubtrack(rec) ? trackName :undefined; // If subtrack then vis rules differ var allVars = getAllVars($('#hgTrackUiDialog'), subtrack );// For unknown reasons IE8 fails to find $('#pop'), occasionally var changedVars = varHashChanges(allVars,popUp.saveAllVars); //warn("cfgVars:"+varHashToQueryString(changedVars)); var newVis = changedVars[trackName]; var hide = (newVis != null && (newVis == 'hide' || newVis == '[]')); // subtracks do not have "hide", thus '[]' if($('#imgTbl') == undefined) { // On findTracks or config page setVarsFromHash(changedVars); //if(hide) // TODO: When findTracks or config page has cfg popup, then vis change needs to be handled in page here } else { // On image page if(hide) { setVarsFromHash(changedVars); $(document.getElementById('tr_' + trackName)).remove(); dragReorder.init(); dragSelect.load(false); } else { // Keep local state in sync if user changed visibility if(newVis != null) { vis.update(trackName, newVis); } var urlData = varHashToQueryString(changedVars); if(urlData.length > 0) { if(imageV2.mapIsUpdateable) { imageV2.requestImgUpdate(trackName,urlData,""); } else { window.location = "../cgi-bin/hgTracks?" + urlData + "&hgsid=" + getHgsid(); } } } } }, uiDialog: function (response, status) { // Take html from hgTrackUi and put it up as a modal dialog. // make sure all links (e.g. help links) open up in a new window response = response.replace(/<a /ig, "<a target='_blank' "); var cleanHtml = response; cleanHtml = stripJsFiles(cleanHtml,true); // DEBUG msg with true cleanHtml = stripCssFiles(cleanHtml,true); // DEBUG msg with true cleanHtml = stripJsEmbedded(cleanHtml,true);// DEBUG msg with true $('#hgTrackUiDialog').html("<div id='pop' style='font-size:.9em;'>"+ cleanHtml +"</div>"); // Strategy for poups with js: // - jsFiles and CSS should not be included in html. Here they are shluped out. // - The resulting files ought to be loadable dynamically (with getScript()), but this was not working nicely with the modal dialog // Therefore include files must be included with hgTracks CGI ! // - embedded js should not be in the popup box. // - Somethings should be in a popup.ready() function, and this is emulated below, as soon as the cleanHtml is added // Since there are many possible popup cfg dialogs, the ready should be all inclusive. if ( ! popUp.trackDescriptionOnly ) { var subtrack = tdbIsSubtrack(hgTracks.trackDb[popUp.trackName]) ? popUp.trackName :""; // If subtrack then vis rules differ popUp.saveAllVars = getAllVars( $('#hgTrackUiDialog'), subtrack ); // Saves the vars that may get changed by the popup cfg. // -- popup.ready() -- Here is the place to do things that might otherwise go into a $('#pop').ready() routine! } // Searching for some selblance of size suitability var popMaxHeight = ($(window).height() - 40); var popMaxWidth = ($(window).width() - 40); var popWidth = 740; if (popWidth > popMaxWidth) popWidth > popMaxWidth; $('#hgTrackUiDialog').dialog({ ajaxOptions: { // This doesn't work cache: true }, resizable: true, height: (popUp.trackDescriptionOnly ? popMaxHeight : 'auto'), // Let description scroll vertically width: popWidth, minHeight: 200, minWidth: 700, maxHeight: popMaxHeight, maxWidth: popMaxWidth, modal: true, closeOnEscape: true, autoOpen: false, buttons: { "OK": function() { if ( ! popUp.trackDescriptionOnly ) popUp.uiDialogOk($('#pop'), popUp.trackName); $(this).dialog("close"); }}, // popup.ready() doesn't seem to work in open. So there is no need for open at this time. //open: function() { // var subtrack = tdbIsSubtrack(hgTracks.trackDb[popUp.trackName]) ? popUp.trackName :""; // If subtrack then vis rules differ // popUp.saveAllVars = getAllVars( $('#pop'), subtrack ); //}, open: function () { if ( ! popUp.trackDescriptionOnly ) { $('#hgTrackUiDialog').find('.filterBy,.filterComp').each( function(i) { if ($(this).hasClass('filterComp')) ddcl.setup(this); else ddcl.setup(this, 'noneIsAll'); } ); } }, close: function() { popUp.cleanup(); } }); // FIXME: Why are open and close no longer working!!! if(popUp.trackDescriptionOnly) { var myWidth = $(window).width() - 300; if(myWidth > 900) myWidth = 900; $('#hgTrackUiDialog').dialog("option", "maxWidth", myWidth); $('#hgTrackUiDialog').dialog("option", "width", myWidth); $('#hgTrackUiDialog').dialog('option' , 'title' , hgTracks.trackDb[popUp.trackName].shortLabel+" Track Description"); $('#hgTrackUiDialog').dialog('open'); var buttOk = $('button.ui-state-default'); if($(buttOk).length == 1) $(buttOk).focus(); } else { $('#hgTrackUiDialog').dialog('option' , 'title' , hgTracks.trackDb[popUp.trackName].shortLabel+" Track Settings"); $('#hgTrackUiDialog').dialog('open'); } } } /////////////////////////////// //// imageV2 (aka imgTbl) //// /////////////////////////////// var imageV2 = { enabled: false, // Will be set to true unless advancedJavascriptFeatures is turned off OR if track search of config page imgTbl: null, // formerly "trackImgTbl" The imgTbl or null if non-imageV2. inPlaceUpdate: false, // modified based on value of hgTracks.inPlaceUpdate and mapIsUpdateable mapIsUpdateable:true, lastTrack: null, // formerly (lastMapItem) this is used to try to keep what the last track the cursor passed. markAsDirtyPage: function () { // Page is marked as dirty so that the backbutton can be overridden var dirty = $('#dirty'); if (dirty != undefined && dirty.length != 0) $(dirty).val('true'); }, isDirtyPage: function () { // returns true if page was marked as dirty // This will allow the backbutton to be overridden var dirty = $('#dirty'); if (dirty != undefined && dirty.length > 0) { if ($(dirty).val() == 'true') return true; } return false; }, updateTiming: function (response) { // update measureTiming text on current page based on what's in the response var reg = new RegExp("(<span class='timing'>.+?</span>)", "g"); var strs = []; for(var a = reg.exec(response); a != null && a[1] != null; a = reg.exec(response)) { strs.push(a[1]); } if(strs.length > 0) { $('.timing').remove(); for(var i = strs.length; i > 0; i--) { $('body').prepend(strs[i - 1]); } } reg = new RegExp("(<span class='trackTiming'>[\\S\\s]+?</span>)"); a = reg.exec(response); if(a != null && a[1] != null) { $('.trackTiming').replaceWith(a[1]); } }, afterReload: function () { // Reload various UI widgets after updating imgTbl map. dragReorder.init(); dragSelect.load(false); // Do NOT reload context menu (otherwise we get the "context menu sticks" problem). // rightClick.load($('#tr_' + id)); if(imageV2.imgTbl.tableDnDUpdate) imageV2.imgTbl.tableDnDUpdate(); rightClick.reloadFloatingItem(); // Turn on drag scrolling. if(hgTracks.imgBoxPortal) { $("div.scroller").panImages(); } imageV2.loadRemoteTracks(); makeItemsByDrag.load(); imageV2.markAsDirtyPage(); }, updateImgForId: function (html, id) { // update row in imgTbl for given id. // return true if we successfully pull slice for id and update it in imgTrack. var str = "<TR id='tr_" + id + "'[^>]*>([\\s\\S]+?)</TR>"; var reg = new RegExp(str); var a = reg.exec(html); if(a && a[1]) { var tr = $(document.getElementById("tr_" + id)); if (tr.length > 0) { $(tr).html(a[1]); // Need to update tr class list too str = "<TR id='tr_" + id + "[^>]* class='(.*)'>"; reg = new RegExp(str); var classes = reg.exec(html); if(classes && classes[1] && classes[1].length > 0) { $(tr).removeClass(); $(tr).addClass(classes[1]); } // NOTE: Want to examine the png? Uncomment: //var img = $('#tr_' + id).find("img[id^='img_data_']").attr('src'); //warn("Just parsed image:<BR>"+img); // >1x dragScrolling needs some extra care. if(hgTracks.imgBoxPortal && (hgTracks.imgBoxWidth > hgTracks.imgBoxPortalWidth)) { if (hgTracks.imgBoxPortalLeft != undefined) { $(tr).find('.panImg').css({'left': hgTracks.imgBoxPortalLeft }); $(tr).find('.tdData').css( {'backgroundPosition': hgTracks.imgBoxPortalLeft}); } } return true; } } return false; }, requestImgUpdate: function (trackName,extraData,loadingId,newVisibility) { // extraData, loadingId and newVisibility are optional var data = "hgt.trackImgOnly=1&hgsid=" + getHgsid() + "&hgt.trackNameFilter=" + trackName; if(extraData != undefined && extraData != "") data += "&" + extraData; if(loadingId == undefined || loadingId == "") loadingId = showLoadingImage("tr_" + trackName); var getOrPost = "GET"; if ((data.length) > 2000) // extraData could contain a bunch of changes from the cfg dialog getOrPost = "POST"; $.ajax({ type: getOrPost, url: "../cgi-bin/hgTracks", data: data, dataType: "html", trueSuccess: imageV2.updateImgAndMap, success: catchErrorOrDispatch, error: errorHandler, cmd: 'refresh', loadingId: loadingId, id: trackName, newVisibility: newVisibility, cache: false }); }, fullReload: function() { // force reload of whole page via trackform submit // This function does not return jQuery('body').css('cursor', 'wait'); document.TrackHeaderForm.submit(); }, updateImgAndMap: function (response, status) { // Handle ajax response with an updated trackMap image, map and optional ideogram. // // this.cmd can be used to figure out which menu item triggered this. // this.id == appropriate track if we are retrieving just a single track. // update local hgTracks.trackDb to reflect possible side-effects of ajax request. var json = scrapeVariable(response, "hgTracks"); var oldTrackDb = hgTracks.trackDb; var valid = false; if(json == undefined) { var stripped = new Object(); stripJsEmbedded(response, true, stripped); if(stripped.warnMsg == null) warn("hgTracks object is missing from the response"); } else { if(this.id != null) { if(json.trackDb[this.id]) { var visibility = vis.enumOrder[json.trackDb[this.id].visibility]; var limitedVis; if(json.trackDb[this.id].limitedVis) limitedVis = vis.enumOrder[json.trackDb[this.id].limitedVis]; if(this.newVisibility && limitedVis && this.newVisibility != limitedVis) // see redmine 1333#note-9 alert("There are too many items to display the track in " + this.newVisibility + " mode."); var rec = hgTracks.trackDb[this.id]; rec.limitedVis = json.trackDb[this.id].limitedVis; vis.update(this.id, visibility); valid = true; } else { warn("Invalid hgTracks.trackDb received from the server"); } } else { valid = true; hgTracks.trackDb = json.trackDb; } } if(valid) { if(imageV2.enabled && this.id && this.cmd && this.cmd != 'wholeImage' && this.cmd != 'selectWholeGene') { // Extract <TR id='tr_ID'>...</TR> and update appropriate row in imgTbl; // this updates src in img_left_ID, img_center_ID and img_data_ID and map in map_data_ID var id = this.id; if(imageV2.updateImgForId(response, id)) { imageV2.afterReload(); } else { warn("Couldn't parse out new image for id: " + id); //alert("Couldn't parse out new image for id: " + id+"BR"+response); // Very helpful } } else { if(imageV2.enabled) { // Implement in-place updating of hgTracks image genomePos.setByCoordinates(json.chromName, json.winStart + 1, json.winEnd); $("input[name='c']").val(json.chromName); $("input[name='l']").val(json.winStart); $("input[name='r']").val(json.winEnd); if(json.cgiVersion != hgTracks.cgiVersion) { // Must reload whole page because of a new version on the server; this should happen very rarely. // Note that we have already updated position based on the user's action. imageV2.fullReload(); } else { // We update rows one at a time (b/c updating the whole imgTable at one time doesn't work in IE). for (var id in hgTracks.trackDb) { // handle case where invisible items may be in the trackDb list (see redmine #5670). if(hgTracks.trackDb[id].type != "remote" && hgTracks.trackDb[id].visibility > 0 // && $('#tr_' + id).length > 0 && !imageV2.updateImgForId(response, id)) { warn("Couldn't parse out new image for id: " + id); } } /* This (disabled) code handles dynamic addition of tracks: for (var id in hgTracks.trackDb) { if(oldTrackDb[id] == undefined) { // XXXX Tim, what s/d abbr attribute be? $('#imgTbl').append("<tr id='tr_" + id + "' class='imgOrd trDraggable'></tr>"); imageV2.updateImgForId(response, id); vis.update(id, vis.enumOrder[hgTracks.trackDb[id].visibility]); } } */ hgTracks = json; genomePos.original = undefined; initVars(); imageV2.afterReload(); } } else { warn("ASSERT: Attempt to update track without advanced javascript features."); } // now pull out and parse the map. //a = /<MAP id='map' Name=map>([\s\S]+)<\/MAP>/.exec(response); //if(!a[1]) // warn("Couldn't parse out map"); } // Parse out new ideoGram url (if available) // e.g.: <IMG SRC = "../trash/hgtIdeo/hgtIdeo_hgwdev_larrym_61d1_8b4a80.gif" BORDER=1 WIDTH=1039 HEIGHT=21 USEMAP=#ideoMap id='chrom'> // We do this last b/c it's least important. var a = /<IMG([^>]+SRC[^>]+id='chrom'[^>]*)>/.exec(response); if(a && a[1]) { var b = /SRC\s*=\s*"([^")]+)"/.exec(a[1]); if(b && b[1]) { $('#chrom').attr('src', b[1]); } } if(hgTracks.measureTiming) { imageV2.updateTiming(response); } } if(this.disabledEle) { this.disabledEle.removeAttr('disabled'); } if(this.loadingId) { hideLoadingImage(this.loadingId); } jQuery('body').css('cursor', ''); if(valid && this.currentId) { var top = $(document.getElementById("tr_" + this.currentId)).position().top; $(window).scrollTop(top - this.currentIdYOffset); } }, loadRemoteTracks: function () { if(typeof(hgTracks.trackDb) != "undefined" && hgTracks.trackDb != null) { for (var id in hgTracks.trackDb) { var rec = hgTracks.trackDb[id]; if(rec.type == "remote") { if($("#img_data_" + id).length > 0) { // load the remote track renderer via jsonp rec.loadingId = showLoadingImage("tr_" + id); var script = document.createElement('script'); var pos = parsePosition(genomePos.get()); var name = rec.remoteTrack || id; script.setAttribute('src', rec.url + "?track=" + name + "&jsonp=imageV2.remoteTrackCallback&position=" + encodeURIComponent(pos.chrom + ":" + pos.start + "-" + pos.end) + "&pix=" + $('#imgTbl').width() ); document.getElementsByTagName('head')[0].appendChild(script); } } } } }, remoteTrackCallback: function (rec) // jsonp callback to load a remote track. { if(rec.error) { alert("retrieval from remote site failed with error: " + rec.error) } else { var remoteTrack = rec.track; for (var track in hgTracks.trackDb) { if(hgTracks.trackDb[track].remoteTrack == remoteTrack) { $('#img_data_' + track).attr('style', "left:-116px; top: -23px;"); $('#img_data_' + track).attr('height', rec.height); // XXXX use width in some way? // $('#img_data_' + track).attr('width', rec.width); $('#img_data_' + track).attr('width', $('#img_data_ruler').width()); $('#img_data_' + track).attr('src', rec.img); $('#td_data_' + track + ' > div').each(function(index) { if(index == 1) { var style = $(this).attr('style'); style = style.replace(/height:\s*\d+/i, "height:" + rec.height); $(this).attr('style', style); } }); var style = $('#p_btn_' + track).attr('style'); style = style.replace(/height:\s*\d+/i, "height:" + rec.height); $('#p_btn_' + track).attr('style', style); if(hgTracks.trackDb[track].loadingId) { hideLoadingImage(hgTracks.trackDb[track].loadingId); } } } } }, navigateButtonClick: function (ele) // called from hgTracks.c { // code to update just the imgTbl in response to navigation buttons (zoom-out etc.). // This is currently experimental code (controlled by IN_PLACE_UPDATE in imageV2.h). if(imageV2.inPlaceUpdate) { var params = ele.name + "=" + ele.value; $(ele).attr('disabled', 'disabled'); // dinking navigation needs additional data if(ele.name == "hgt.dinkLL" || ele.name == "hgt.dinkLR") { params += "&dinkL=" + $("input[name='dinkL']").val(); } else if(ele.name == "hgt.dinkRL" || ele.name == "hgt.dinkRR") { params += "&dinkR=" + $("input[name='dinkR']").val(); } imageV2.navigateInPlace(params, $(ele), false); return false; } else { return true; } }, updateButtonClick: function (ele) // UNUSED? { // code to update the imgTbl based on changes in the track controls. // This is currently experimental code and is dead in the main branch. if(imageV2.mapIsUpdateable) { var data = ""; $("select").each(function(index, o) { var cmd = $(this).val(); if(cmd == "hide") { if(hgTracks.trackDb[this.name] != undefined) { alert("Need to implement hide"); } } else { if(hgTracks.trackDb[this.name] == undefined || cmd != vis.enumOrder[hgTracks.trackDb[this.name].visibility]) { if(data.length > 0) { data = data + "&"; } data = data + this.name + "=" + cmd; } } }); if(data.length > 0) { imageV2.navigateInPlace(data, null, false); } return false; } else { return true; } }, jumpButtonOnClick: function () // called from hgTracks.c { // onClick handler for the "jump" button. // Handles situation where user types a gene name into the gene box and immediately hits the jump button, // expecting the browser to jump to that gene. var gene = $('#suggest').val(); var db = getDb(); if(gene && gene.length > 0 && gene != "gene" && db && $('#positionDisplay').length == 0 && (genomePos.getOriginalPos() == genomePos.get() || genomePos.get().length == 0)) { var pos = lookupGene(db, gene); if(pos) { vis.makeTrackVisible($("#suggestTrack").val()); genomePos.set(pos, null); // Following doesn't work b/c we get the hugo symbol from the suggest list, not the known gene id. // $(document.TrackForm || document.TrackHeaderForm).append("<input type='hidden' name='hgFind.matches' " + "value='" + name + "'>"); } else { // turn this into a full text search. genomePos.set(gene, null); } } return true; }, navigateInPlace: function (params, disabledEle, keepCurrentTrackVisible) { // request an hgTracks image, using params // disabledEle is optional; this element will be enabled when update is complete // If keepCurrentTrackVisible is true, we try to maintain relative position of the item under the mouse after the in-place update. jQuery('body').css('cursor', ''); var currentId, currentIdYOffset; if(keepCurrentTrackVisible) { var item = rightClick.currentMapItem || imageV2.lastTrack; if(item) { var top = $(document.getElementById("tr_" + item.id)).position().top; if(top >= $(window).scrollTop() || top < $(window).scrollTop() + $(window).height()) { // don't bother if the item is not currently visible. currentId = item.id; currentIdYOffset = top - $(window).scrollTop(); } } } $.ajax({ type: "GET", url: "../cgi-bin/hgTracks", data: params + "&hgt.trackImgOnly=1&hgt.ideogramToo=1&hgsid=" + getHgsid(), dataType: "html", trueSuccess: imageV2.updateImgAndMap, success: catchErrorOrDispatch, error: errorHandler, cmd: 'wholeImage', loadingId: showLoadingImage("imgTbl"), disabledEle: disabledEle, currentId: currentId, currentIdYOffset: currentIdYOffset, cache: false }); } } //////////////////////////////////// //// suggest (aka gene search) //// //////////////////////////////////// var suggestBox = { lastEntered: null, init: function (db) { var ele = $('#positionInput'); if(!ele.length) { ele = $('input#suggest'); } if(jQuery.fn.autocomplete && ele.length && db) { if(jQuery.fn.Watermark) { var str; if(hgTracks.assemblySupportsGeneSuggest) { str = "enter new position, gene symbol or annotation search terms"; } else { str = "enter new position or annotation search terms"; } $('#positionInput').Watermark(str, '#686868'); } ele.autocomplete({ delay: 500, minLength: 2, source: ajaxGet(function () {return getDb();}, new Object, true), open: function(event, ui) { var pos = $(this).offset().top + $(this).height(); if (!isNaN(pos)) { var maxHeight = $(window).height() - pos - 30; // take off a little more because IE needs it var auto = $('.ui-autocomplete'); var curHeight = $(auto).children().length * 21; if (curHeight > maxHeight) $(auto).css({maxHeight: maxHeight+'px',overflow:'scroll'}); else $(auto).css({maxHeight: 'none',overflow:'hidden'}); } }, select: function (event, ui) { genomePos.set(ui.item.id, commify(getSizeFromCoordinates(ui.item.id))); vis.makeTrackVisible($("#suggestTrack").val()); suggestBox.lastEntered = ui.item.value; // jQuery('body').css('cursor', 'wait'); // document.TrackHeaderForm.submit(); } }); // I want to set focus to the suggest element, but unforunately that prevents PgUp/PgDn from // working, which is a major annoyance. // $('input#suggest').focus(); } } } ////////////////////// //// track search //// ////////////////////// var trackSearch = { searchKeydown: function (event) { if (event.which == 13) { // Required to fix problem on IE and Safari where value of hgt_tSearch is "-" (i.e. not "Search"). $("input[name=hgt_tsPage]").val(0); // NOTE: must match TRACK_SEARCH_PAGER in hg/inc/searchTracks.h $('#trackSearch').submit(); // This doesn't work with IE or Safari. // $('#searchSubmit').click(); } }, init: function () { // Track search uses tabs if($("#tabs").length > 0) { // Search page specific code var val = $('#currentTab').val(); $("#tabs").tabs({ show: function(event, ui) { $('#currentTab').val(ui.panel.id); }, select: function(event, ui) { findTracks.switchTabs(ui); } }); $('#tabs').show(); $("#tabs").tabs('option', 'selected', '#' + val); if(val =='simpleTab' && $('div#found').length < 1) { $('input#simpleSearch').focus(); } $("#tabs").css('font-family', jQuery('body').css('font-family')); $("#tabs").css('font-size', jQuery('body').css('font-size')); $('.submitOnEnter').keydown(trackSearch.searchKeydown); findTracks.normalize(); findTracks.updateMdbHelp(0); } } } /* // wait for jStore to prepare the storage engine (this token reload code is experimental and currently dead). jQuery.jStore && jQuery.jStore.ready(function(engine) { // alert(engine.jri); // wait for the storage engine to be ready. engine.ready(function(){ var engine = this; var newToken = hgTracks.time; if(newToken) { var oldToken = engine.get("token"); if(oldToken && oldToken == newToken) { // user has hit the back button. jQuery('body').css('cursor', 'wait'); window.location = "../cgi-bin/hgTracks?hgsid=" + getHgsid(); } } engine.set("token", newToken); }); }); */ /////////////// //// READY //// /////////////// $(document).ready(function() { // The page may be reached via browser history (back button) // If so, then this code should detect if the image has been changed via js/ajax // and will reload the image if necessary. // NOTE: this is needed for IE but other browsers can detect the dirty page much earlier if (imageV2.isDirtyPage()) { // mark as non dirty to avoid infinite loop in chrome. $('#dirty').val('false'); jQuery('body').css('cursor', 'wait'); window.location = "../cgi-bin/hgTracks?hgsid=" + getHgsid(); return false; } initVars(); var db = getDb(); suggestBox.init(db); if(jQuery.jStore) { // Experimental code to handle "user hits back button" problem by reloading the page based on the user's cart if(jQuery.browser.msie && jQuery.browser.version < 8) { // IE 7 requires flash to support jStore. jQuery.extend(jQuery.jStore.defaults, { project: 'hgTracks', engine: 'flash', flash: '/jStore.Flash.html' }); } jQuery.jStore.load(); } // Convert map AREA gets to post the form, ensuring that cart variables are kept up to date (but turn this off for search form). if($("FORM").length > 0 && $('#trackSearch').length == 0) { var allLinks = $('a'); $( allLinks ).unbind('click'); $( allLinks ).click( posting.saveSettings ); } if($('#pdfLink').length == 1) { $('#pdfLink').click(function(i) { var thisForm=$('#TrackForm'); if(thisForm != undefined && $(thisForm).length == 1) { //alert("posting form:"+$(thisForm).attr('name')); updateOrMakeNamedVariable($(thisForm),'hgt.psOutput','on'); return postTheForm($(thisForm).attr('name'),this.href); } return true; }); } if($("#positionInput").length) { $("#positionInput").change(function(event) { if(!suggestBox.lastEntered || suggestBox.lastEntered != $('#positionInput').val()) { $('#position').val($('#positionInput').val()); } }); $("#positionDisplay").click(function(event) { genomePos.set($(this).text()); $('#positionInput').val($(this).text()); }); } if(imageV2.enabled) { // Make imgTbl allow drag reorder of imgTrack rows dragReorder.init(); var imgTable = $(".tableWithDragAndDrop"); if($(imgTable).length > 0) { $(imgTable).tableDnD({ onDragClass: "trDrag", dragHandle: "dragHandle", scrollAmount: 40, onDragStart: function(ev, table, row) { mouse.saveOffset(ev); $(document).bind('mousemove',posting.blockTheMapOnMouseMove); // Can drag a contiguous set of rows if dragging blue button table.tableDnDConfig.dragObjects = [ row ]; // defaults to just the one var btn = $( row ).find('p.btnBlue'); // btnBlue means cursor over left button if (btn.length == 1) { table.tableDnDConfig.dragObjects = dragReorder.getContiguousRowSet(row); var compositeSet = dragReorder.getCompositeSet(row); if (compositeSet && compositeSet.length > 0) $( compositeSet ).find('p.btn').addClass('blueButtons'); // blue persists } }, onDrop: function(table, row, dragStartIndex) { var compositeSet = dragReorder.getCompositeSet(row); if (compositeSet && compositeSet.length > 0) $( compositeSet ).find('p.btn').removeClass('blueButtons'); // blue persists if($(row).attr('rowIndex') != dragStartIndex) { // NOTE Even if dragging a contiguous set of rows, // still only need to check the one under the cursor. if(dragReorder.setOrder) { dragReorder.setOrder(table); } dragReorder.zipButtons( table ); } $(document).unbind('mousemove',posting.blockTheMapOnMouseMove); setTimeout('posting.allowMapClicks();',50); // Necessary incase the onDrop was over a map item. onDrop takes precedence. } }); } // Drag scroll init if(hgTracks.imgBoxPortal) { // Turn on drag scrolling. $("div.scroller").panImages(); } //$("#zoomSlider").slider({ min: -4, max: 3, step: 1 });//, handle: '.ui-slider-handle' }); // Retrieve tracks via AJAX that may take too long to draw initialliy (i.e. a remote bigWig) var retrievables = $('#imgTbl').find("tr.mustRetrieve") if($(retrievables).length > 0) { $(retrievables).each( function (i) { var trackName = $(this).attr('id').substring(3); imageV2.requestImgUpdate(trackName,"",""); }); } imageV2.loadRemoteTracks(); makeItemsByDrag.load(); } // Drag select in chromIdeogram if($('img#chrom').length == 1) { if($('area.cytoBand').length > 1) { $('img#chrom').chromDrag(); } } // Track search uses tabs trackSearch.init(); // Drag select initialize if (imageV2.enabled) { // moved from window.load(). dragSelect.load(true); if($('#hgTrackUiDialog')) $('#hgTrackUiDialog').hide(); // Don't load contextMenu if jquery.contextmenu.js hasn't been loaded if (jQuery.fn.contextMenu) { rightClick.load(imageV2.imgTbl); } } });