a53b9958fa734f73aeffb9ddfe2fbad1ca65f90c galt Mon Jan 30 16:18:41 2017 -0800 Check-in of CSP2 Content-Security-Policy work. All C-language CGIs should now support CSP2 in browser to stop major forms of XSS javascript injection. Javascript on pages is gathered together, and then emitted in a single script block at the end with a nonce that tells the browser, this is js that we generated instead of being injected by a hacker. Both inline script from script blocks and inline js event handlers had to be pulled out and separated. You will not see js sprinkled through-out the page now. Older browsers that support CSP1 or that do not understand CSP at all will still work, just without protection. External js libraries loaded at runtime need to be added to the CSP policy header in src/lib/htmshell.c. diff --git src/hg/js/hgTracks.js src/hg/js/hgTracks.js index 54a5607..951d9f7 100644 --- src/hg/js/hgTracks.js +++ src/hg/js/hgTracks.js @@ -1,4597 +1,4667 @@ // Javascript for use in hgTracks CGI // "use strict"; // Don't complain about line break before '||' etc: /* jshint -W014 */ var debug = false; /* Data passed in from CGI via the hgTracks object: * * string cgiVersion // CGI_VERSION * string chromName // current chromosome * int winStart // genomic start coordinate (0-based, half-open) * int winEnd // genomic end coordinate * int newWinWidth // new width (in bps) if user clicks on the top ruler * boolean revCmplDisp // true if we are in reverse display * int insideX // width of side-bar (in pixels) * int rulerClickHeight // height of ruler (in pixels) - zero if ruler is hidden * boolean inPlaceUpdate // true if in-place-update is turned on * int imgBox* // various drag-scroll values * boolean measureTiming // true if measureTiming is on * Object trackDb // hash of trackDb entries for tracks which are visible on current page */ function initVars() { // There are various entry points, so we call initVars in several places to make sure all is well if (typeof(hgTracks) !== "undefined" && !genomePos.original) { // remember initial position and size so we can restore it if user cancels genomePos.original = genomePos.getOriginalPos(); genomePos.originalSize = $('#size').text().replace(/,/g, ""); // strip out any commas dragSelect.originalCursor = jQuery('body').css('cursor'); imageV2.imgTbl = $('#imgTbl'); // imageV2.enabled === true unless: advancedJavascript===false, or trackSearch, or config pg imageV2.enabled = (imageV2.imgTbl && imageV2.imgTbl.length > 0); // jQuery load function with stuff to support drag selection in track img if (theClient.isSafari()) { // Safari has the following bug: if we update the hgTracks map dynamically, // the browser ignores the changes (even though if you look in the DOM the changes // are there). So we have to do a full form submission when the user changes // visibility settings or track configuration. // As of 5.0.4 (7533.20.27) this is problem still exists in safari. // As of 5.1 (7534.50) this problem appears to have been fixed - unfortunately, // logs for 7/2011 show vast majority of safari users are pre-5.1 (5.0.5 is by far // the most common). // // Early versions of Chrome had this problem too, but this problem went away // as of Chrome 5.0.335.1 (or possibly earlier). // // KRR/JAT 2/2016: // This Safari issue is likely resolved in all current versions. However the test // for version had been failing, likely for some time now. // (As of 9.0.9, possibly earlier, the 3rd part of the version is included in the // user agent string, so must be accounted for in string match) // Consequences were that page refresh was used instead of img update (e.g. // for drag-zoom). And UI dialog was unable to update (e.g. via Apply button). imageV2.mapIsUpdateable = false; var reg = new RegExp("Version\/([0-9]+.[0-9]+)(.[0-9]+)? Safari"); var a = reg.exec(navigator.userAgent); if (a && a[1]) { var version = Number(a[1]); if (version >= 5.1) { imageV2.mapIsUpdateable = true; } } } imageV2.inPlaceUpdate = hgTracks.inPlaceUpdate && imageV2.mapIsUpdateable; } } ///////////////////////////////////// ////////// Genomic position ///////// ///////////////////////////////////// var genomePos = { original: null, originalSize: 0, linkFixup: function (pos, id, reg, endParamName) { // fixup external links (e.g. ensembl) var ele = $(document.getElementById(id)); if (ele.length) { var link = ele.attr('href'); var a = reg.exec(link); if (a && a[1]) { ele.attr('href', a[1] + pos.start + "&" + endParamName + "=" + pos.end); } } }, setByCoordinates: function (chrom, start, end) { var newPosition = chrom + ":" + start + "-" + end; genomePos.set(newPosition, end - start + 1); return newPosition; }, getElement: function () { // Return position box object var tags = document.getElementsByName("position"); // There are multiple tags with name === "position" (the visible position text input // and a hidden with id='positionHidden'); we return value of visible element. for (var i = 0; i < tags.length; i++) { var ele = tags[i]; if (ele.id !== "positionHidden") { return ele; } } return null; }, get: function () { // Return current value of position box var ele = genomePos.getElement(); if (ele) { return ele.value; } return null; }, getOriginalPos: function () { return genomePos.original || genomePos.get(); }, revertToOriginalPos: function () { // undo changes to position (i.e. after user aborts a drag-and-select). this.set(this.original, this.originalSize); this.original = this.originalSize = null; // not sure if this is necessary. }, undisguisePosition: function(position) // UN-DISGUISE VMODE { // find the virt position // position should be real chrom span var pos = parsePosition(position); if (!pos) return position; // some parsing error, return original var start = pos.start - 1; var end = pos.end; var chromName = hgTracks.windows[0].chromName; if (pos.chrom !== chromName) return position; // return original var newStart = -1; var newEnd = -1; var lastW = null; var windows = null; for (j=0; j < 3; ++j) { if (j === 0) windows = hgTracks.windowsBefore; if (j === 1) windows = hgTracks.windows; if (j === 2) windows = hgTracks.windowsAfter; for (i=0,len=windows.length; i < len; ++i) { var w = windows[i]; // double check chrom is same thoughout all windows, otherwise warning, return original value if (w.chromName != chromName) { return position; // return original } // check that the regions are ascending and non-overlapping if (lastW && w.winStart < lastW.winEnd) { return position; // return original } // overlap with position? // if intersection, if (w.winEnd > start && end > w.winStart) { var s = Math.max(start, w.winStart); var e = Math.min(end, w.winEnd); var cs = s - w.winStart + w.virtStart; var ce = e - w.winStart + w.virtStart; if (newStart === -1) newStart = cs; newEnd = ce; } lastW = w; } } // return new virt undisguised position as a string var newPos = "virt:" + (newStart+1) + "-" + newEnd; return newPos; }, disguiseSize: function(position) // DISGUISE VMODE { // find the real size of the windows spanned // position should be a real chrom span var pos = parsePosition(position); if (!pos) return 0; var start = pos.start - 1; var end = pos.end; var newSize = 0; var windows = null; for (j=0; j < 3; ++j) { if (j === 0) windows = hgTracks.windowsBefore; if (j === 1) windows = hgTracks.windows; if (j === 2) windows = hgTracks.windowsAfter; for (i=0,len=windows.length; i < len; ++i) { var w = windows[i]; // overlap with position? // if intersection, if (w.winEnd > start && end > w.winStart) { var s = Math.max(start, w.winStart); var e = Math.min(end, w.winEnd); newSize += (e - s); } } } // return real size of the disguised position return newSize; }, disguisePosition: function(position) // DISGUISE VMODE { // find the single-chrom range spanned // position should be virt var pos = parsePosition(position); if (!pos) return position; // some parsing error, return original var start = pos.start - 1; var end = pos.end; var chromName = hgTracks.windows[0].chromName; var newStart = -1; var newEnd = -1; var lastW = null; var windows = null; for (j=0; j < 3; ++j) { if (j === 0) windows = hgTracks.windowsBefore; if (j === 1) windows = hgTracks.windows; if (j === 2) windows = hgTracks.windowsAfter; for (i=0,len=windows.length; i < len; ++i) { var w = windows[i]; // double check chrom is same thoughout all windows, otherwise warning, return original value if (w.chromName != chromName) { return position; // return undisguised original } // check that the regions are ascending and non-overlapping if (lastW && w.winStart < lastW.winEnd) { return position; // return undisguised original } // overlap with position? // if intersection, if (w.virtEnd > start && end > w.virtStart) { var s = Math.max(start, w.virtStart); var e = Math.min(end, w.virtEnd); var cs = s - w.virtStart + w.winStart; var ce = e - w.virtStart + w.winStart; if (newStart === -1) newStart = cs; newEnd = ce; } lastW = w; } } // return new non-virt disguised position as a string var newPos = chromName + ":" + (newStart+1) + "-" + newEnd; return newPos; }, set: function (position, size) { // Set value of position and size (in hiddens and input elements). // We assume size has already been commified. // Either position or size may be null. // stack dump // DEBUG //console.trace(); // NOT work on safari //var obj = {}; //Error.captureStackTrace(obj); //warn("genomePos.set() called "+obj.stack); position = position.replace(/,/g, ""); // strip out any commas if (position) { // DISGUISE VMODE //warn("genomePos.set() called, position = "+position); if (hgTracks.virtualSingleChrom && (position.search("virt:")===0)) { var newPosition = genomePos.disguisePosition(position); //warn("genomePos.set() position = "+position+", newPosition = "+newPosition); position = newPosition; } } if (position) { // There are multiple tags with name === "position" // (one in TrackHeaderForm and another in TrackForm). var tags = document.getElementsByName("position"); for (var i = 0; i < tags.length; i++) { var ele = tags[i]; ele.value = position; } } var pos = parsePosition(position); if ($('#positionDisplay').length) { // add commas to positionDisplay var commaPosition = position; if (pos) commaPosition = pos.chrom+":"+commify(pos.start)+"-"+commify(pos.end); $('#positionDisplay').text(commaPosition); } if (size) { if (hgTracks.virtualSingleChrom && (position.search("virt:")!==0)) { var newSize = genomePos.disguiseSize(position); //warn("genomePos.set() position = "+position+", newSize = "+newSize); if (newSize > 0) size = newSize; } $('#size').text(commify(size)); // add commas } if (pos) { // fixup external static links on page' // Example ensembl link: // http://www.ensembl.org/Homo_sapiens/contigview?chr=21&start=33031934&end=33041241 genomePos.linkFixup(pos, "ensemblLink", new RegExp("(.+start=)[0-9]+"), "end"); // Example NCBI link: // http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=21&BEG=33031934&END=33041241 genomePos.linkFixup(pos, "ncbiLink", new RegExp("(.+BEG=)[0-9]+"), "END"); // Example medaka link: // http://utgenome.org/medakabrowser_ens_jump.php?revision=version1.0&chr=chromosome18&start=14435198&end=14444829 genomePos.linkFixup(pos, "medakaLink", new RegExp("(.+start=)[0-9]+"), "end"); var link; var reg; var a; if ($('#wormbaseLink').length) { // e.g. http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=II:14646301-14667800 link = $('#wormbaseLink').attr('href'); reg = new RegExp("(.+:)[0-9]+"); a = reg.exec(link); if (a && a[1]) { $('#wormbaseLink').attr('href', a[1] + pos.start + "-" + pos.end); } } // Fixup DNA link; e.g.: // hgc?hgsid=2999470&o=114385768&g=getDna&i=mixed&c=chr7&l=114385768&r=114651696&db=panTro2&hgsid=2999470 if ($('#dnaLink').length) { link = $('#dnaLink').attr('href'); reg = new RegExp("(.+&o=)[0-9]+.+&db=[^&]+(.*)"); a = reg.exec(link); if (a && a[1]) { var url = a[1] + (pos.start - 1) + "&g=getDna&i=mixed&c=" + pos.chrom; url += "&l=" + (pos.start - 1) + "&r=" + pos.end + "&db=" + getDb() + a[2]; $('#dnaLink').attr('href', url); } } } if (!imageV2.backSupport) imageV2.markAsDirtyPage(); }, check: function (img, selection) { // return true if user's selection is still w/n the img (including some slop). var imgWidth = jQuery(img).width(); var imgHeight = jQuery(img).height(); var imgOfs = jQuery(img).offset(); var slop = 10; // We ignore clicks in the gray tab and track title column // (we really should suppress all drag activity there, // but I don't know how to do that with imgAreaSelect). var leftX = hgTracks.revCmplDisp ? imgOfs.left - slop : imgOfs.left + hgTracks.insideX - slop; var rightX = hgTracks.revCmplDisp ? imgOfs.left + imgWidth - hgTracks.insideX + slop : imgOfs.left + imgWidth + slop; return ( (selection.event.pageX >= leftX) && (selection.event.pageX < rightX) && (selection.event.pageY >= (imgOfs.top - slop)) && (selection.event.pageY < (imgOfs.top + imgHeight + slop))); }, pixelsToBases: function (img, selStart, selEnd, winStart, winEnd) { // Convert image coordinates to chromosome coordinates var imgWidth = jQuery(img).width() - hgTracks.insideX; var width = hgTracks.winEnd - hgTracks.winStart; var mult = width / imgWidth; // mult is bp/pixel multiplier var startDelta; // startDelta is how many bp's to the right/left var x1; if (hgTracks.revCmplDisp) { x1 = Math.min(imgWidth, selStart); startDelta = Math.floor(mult * (imgWidth - x1)); } else { x1 = Math.max(hgTracks.insideX, selStart); startDelta = Math.floor(mult * (x1 - hgTracks.insideX)); } var endDelta; var x2; if (hgTracks.revCmplDisp) { endDelta = startDelta; x2 = Math.min(imgWidth, selEnd); startDelta = Math.floor(mult * (imgWidth - x2)); } else { x2 = Math.max(hgTracks.insideX, selEnd); endDelta = Math.floor(mult * (x2 - hgTracks.insideX)); } var newStart = hgTracks.winStart + startDelta; var newEnd = hgTracks.winStart + 1 + endDelta; if (newEnd > winEnd) { newEnd = winEnd; } return {chromStart : newStart, chromEnd : newEnd}; }, chromToVirtChrom: function (chrom, chromStart, chromEnd) { // Convert regular chromosome position to virtual chrom coordinates using hgTracks.windows list // Consider the first contiguous set of overlapping regions to define the match (for now). // only works for regions covered by the current hgTracks.windows var virtStart = -1, virtEnd = -1; var s,e; var i, len; for (i = 0, len = hgTracks.windows.length; i < len; ++i) { var w = hgTracks.windows[i]; var overlap = (chrom == w.chromName && chromEnd > w.winStart && w.winEnd > chromStart); if (virtStart == -1) { if (overlap) { // when they overlap the first time s = Math.max(chromStart, w.winStart); e = Math.min(chromEnd, w.winEnd); virtStart = w.virtStart + (s - w.winStart); virtEnd = w.virtStart + (e - w.winStart); } else { // until they overlap // do nothing } } else { if (overlap) { // while they continue to overlap, extend e = Math.min(chromEnd, w.winEnd); virtEnd = w.virtStart + (e - w.winStart); } else { // when they do not overlap anymore, stop break; } } } return {chromStart : virtStart, chromEnd : virtEnd}; }, selectionPixelsToBases: function (img, selection) { // Convert selection x1/x2 coordinates to chromStart/chromEnd. return genomePos.pixelsToBases(img, selection.x1, selection.x2, hgTracks.winStart, hgTracks.winEnd); }, update: function (img, selection, singleClick) { var pos = genomePos.pixelsToBases(img, selection.x1, selection.x2, hgTracks.winStart, hgTracks.winEnd); // singleClick is true when the mouse hasn't moved (or has only moved a small amount). if (singleClick) { var center = (pos.chromStart + pos.chromEnd)/2; pos.chromStart = Math.floor(center - hgTracks.newWinWidth/2); pos.chromEnd = pos.chromStart + hgTracks.newWinWidth; // clip if (pos.chromStart < hgTracks.chromStart) pos.chromStart = hgTracks.chromStart; // usually 1 if (pos.chromEnd > hgTracks.chromEnd) pos.chromEnd = hgTracks.chromEnd; // usually virt chrom size // save current position so that that it may be restored after highlight or cancel. genomePos.original = genomePos.getOriginalPos(); genomePos.originalSize = $('#size').text().replace(/,/g, ""); // strip out any commas } var newPosition = genomePos.setByCoordinates(hgTracks.chromName, pos.chromStart+1, pos.chromEnd); return newPosition; }, handleChange: function (response, status) { var json = JSON.parse(response); genomePos.set(json.pos); }, changeAssemblies: function (ele) // UNUSED? Larry's experimental code { // code to update page when user changes assembly select list. $.ajax({ type: "GET", url: "../cgi-bin/hgApi", data: cart.varsToUrlData({ 'cmd': 'defaultPos', 'db': getDb() }), dataType: "html", trueSuccess: genomePos.handleChange, success: catchErrorOrDispatch, error: errorHandler, cache: true }); return false; }, + + inlineJs : "", + + getInlineJs: function (response, status) + { + //alert("genomePos.getInlineJs called!"); // DEBUG REMOVE + genomePos.inlineJs = response; + }, + + fetchInlineJs: function (url) + { // code to fetch temp file with inline js in it. // OBSOLETE CSP1 + $.ajax({ + type: "GET", + async: false, // wait for result + url: url, + dataType: "html", + trueSuccess: genomePos.getInlineJs, + success: catchErrorOrDispatch, + error: errorHandler, + cache: false + }); + return genomePos.inlineJs; + }, + + convertedVirtCoords : {chromStart : -1, chromEnd : -1}, handleConvertChromPosToVirtCoords: function (response, status) { var virtStart = -1, virtEnd = -1; var newJson = scrapeVariable(response, "convertChromToVirtChrom"); if (!newJson) { warn("convertChromToVirtChrom object is missing from the response"); } else { virtStart = newJson.virtWinStart; virtEnd = newJson.virtWinEnd; } genomePos.convertedVirtCoords = {chromStart : virtStart, chromEnd : virtEnd}; }, convertChromPosToVirtCoords: function (chrom, chromStart, chromEnd) { // code to convert chrom position to virt coords genomePos.convertedVirtCoords = {chromStart : -1, chromEnd : -1}; // reset var pos = chrom+":"+(chromStart+1)+"-"+chromEnd; // easier to pass 1 parameter than 3 $.ajax({ type: "GET", async: false, // wait for result url: "../cgi-bin/hgTracks", data: cart.varsToUrlData({ 'hgt.convertChromToVirtChrom': pos, 'hgt.trackImgOnly' : 1, 'hgsid': getHgsid() }), dataType: "html", trueSuccess: genomePos.handleConvertChromPosToVirtCoords, success: catchErrorOrDispatch, error: errorHandler, cache: false }); return genomePos.convertedVirtCoords; }, positionDisplayDialog: function () // Show the virtual and real positions of the windows { var position = genomePos.get(); var positionDialog = $("#positionDialog")[0]; if (!positionDialog) { $("body").append("
"); positionDialog = $("#positionDialog")[0]; } if (hgTracks.windows) { var i,len; var str = position; if (!(hgTracks.virtualSingleChrom && (hgTracks.windows.length === 1))) { str += "
\n"; str += "
\n"; str += "\n"; } $("#positionDisplayPosition").html(str); } else { $("#positionDisplayPosition").html(position); } $(positionDialog).dialog({ modal: true, title: "Window-Positions", closeOnEscape: true, resizable: false, autoOpen: false, minWidth: 400, minHeight: 40, buttons: { "OK": function() { $(this).dialog("close"); } }, open: function () { // Make OK the focus/default action $(this).parents('.ui-dialog-buttonpane button:eq(0)').focus(); }, close: function() { // All exits to dialog should go through this $(imageV2.imgTbl).imgAreaSelect({hide:true}); $(this).hide(); $('body').css('cursor', ''); // Occasionally wait cursor got left behind } }); $(positionDialog).dialog('open'); } }; ///////////////////////////////////// //// Creating items by dragging ///// ///////////////////////////////////// var makeItemsByDrag = { end: function (img, selection) { var image = $(img); var imageId = image.attr('id'); var trackName = imageId.substring('img_data_'.length); var pos = genomePos.selectionPixelsToBases(image, selection); var command = document.getElementById('hgt_doJsCommand'); command.value = "makeItems " + trackName + " " + hgTracks.chromName; command.value += " " + pos.chromStart + " " + pos.chromEnd; document.TrackHeaderForm.submit(); return true; }, init: function (trackName) { // Set up so that they can drag out to define a new item on a makeItems track. var img = $("#img_data_" + trackName); if (img && img.length !== 0) { var imgHeight = imageV2.imgTbl.height(); jQuery(img.imgAreaSelect( { selectionColor: 'green', outerColor: '', minHeight: imgHeight, maxHeight: imgHeight, onSelectEnd: makeItemsByDrag.end, autoHide: true, movable: false})); } }, load: function () { for (var id in hgTracks.trackDb) { var rec = hgTracks.trackDb[id]; if (rec && rec.type && rec.type.indexOf("makeItems") === 0) { this.init(id); } } } }; /////////////////// ///// mouse ///// /////////////////// var mouse = { savedOffset: {x:0, y:0}, saveOffset: function (ev) { // Save the mouse offset associated with this event mouse.savedOffset = {x: ev.clientX, y: ev.clientY}; }, hasMoved: function (ev) { // return true if mouse has moved a significant amount var minPixels = 10; var movedX = ev.clientX - mouse.savedOffset.x; var movedY = ev.clientY - mouse.savedOffset.y; if (arguments.length === 2) { var num = Number(arguments[1]); if (isNaN(num)) { if ( arguments[1].toLowerCase() === "x" ) return (movedX > minPixels || movedX < (minPixels * -1)); if ( arguments[1].toLowerCase() === "y" ) return (movedY > minPixels || movedY < (minPixels * -1)); } else minPixels = num; } return ( movedX > minPixels || movedX < (minPixels * -1) || movedY > minPixels || movedY < (minPixels * -1)); } }; ///////////////// //// posting //// ///////////////// var posting = { blockUseMap: false, blockMapClicks: function () // Blocks clicking on map items when in effect. Drag opperations frequently call this. { posting.blockUseMap=true; }, allowMapClicks:function () // reallows map clicks. Called after operations that compete with clicks (e.g. dragging) { $('body').css('cursor', ''); // Explicitly remove wait cursor. posting.blockUseMap=false; }, mapClicksAllowed: function () // Verify that click-competing operation (e.g. dragging) isn't currently occurring. { return (posting.blockUseMap === false); }, blockTheMapOnMouseMove: function (ev) { if (!posting.blockUseMap && mouse.hasMoved(ev)) { posting.blockUseMap=true; } }, mapClk: function () { var done = false; if (false && imageV2.inPlaceUpdate) { // XXXX experimental and only turned on in larrym's tree. // Use in-place update if the map item just modifies the current position (this is nice // because it's faster and preserves the users relative position in the track image). // // First test handles next/prev item. var str = "/cgi-bin/hgTracks\\?position=([^:]+):(.+)&hgsid=(\\d+)" + "&(hgt.(next|prev)Item=[^&]+)"; var reg = new RegExp(str); var a = reg.exec(this.href); if (a && a[1] && a[1] === hgTracks.chromName) { imageV2.navigateInPlace("position=" + encodeURIComponent(a[1] + ":" + a[2]) + "&" + a[4], null, true); done = true; } else { // handle next/prev exon str = "/cgi-bin/hgTracks\\?position=([^:]+):(.+)&hgsid=(\\d+)$"; reg = new RegExp(str); a = reg.exec(this.href); if (a && a[1]) { imageV2.navigateInPlace("position=" + encodeURIComponent(a[1] + ":" + a[2]), null, true); done = true; } else { // handle toggle visibility. // Request may include a track set, so we cannot use requestImgUpdate. str = "/cgi-bin/hgTracks\\?(position=[^:]+:.+&hgsid=\\d+&([^=]+)=([^&]+))$"; reg = new RegExp(str); a = reg.exec(this.href); if (a && a[1]) { imageV2.navigateInPlace(a[1], null, true); // imageV2.requestImgUpdate(a[1], a[1] + "=" + a[2], "", a[2]); done = true; } } } } if (done) return false; else return posting.saveSettings(this); }, saveSettings: function (obj) { if (posting.blockUseMap === true) { return false; } if (!obj || !obj.href) // called directly with obj obj = this; // and from callback without obj if ($(obj).hasClass('noLink')) // TITLE_BUT_NO_LINK return false; if (obj.href.match('#') || obj.target.length > 0) { //alert("Matched # ["+obj.href+"] or has target:"+obj.target); return true; } var thisForm = normed($(obj).parents('form').first()); if (!thisForm) thisForm = normed($("FORM").first()); if (thisForm) { //alert("posting form:"+$(thisForm).attr('name')); return postTheForm($(thisForm).attr('name'),cart.addUpdatesToUrl(obj.href)); } return true; } }; ///////////////////////// //// cart updating ///// /////////////////////// var cart = { // Controls queuing and ultimately updating cart variables vis ajax or submit. Queued vars // are held in an object with unique keys preventing duplicate updates and ensuring last update // takes precedence. WARNING: be careful creating an object with variables on the fly: // cart.setVarsObj({track: vis}) is invalid but cart.setVarsObj({'knownGene': vis}) is ok! updateQueue: {}, updatesWaiting: function () { // returns TRUE if updates are waiting. return objNotEmpty(cart.updateQueue); }, addUpdatesToUrl: function (url) { // adds any outstanding cart updates to the url, then clears the queue if (cart.updatesWaiting()) { //console.log('cart.addUpdatesToUrl: '+objKeyCount(cart.updateQueue)+' vars'); var updates = cart.varsToUrlData(); // clears the queue if (!url || url.length === 0) return updates; if (updates.length > 0) { var dataOnly = (url.indexOf("cgi-bin") === -1); // all urls should be to our cgis if (!dataOnly && url.lastIndexOf("?") === -1) url += "?" + updates; else url += '&' + updates; } } return url; }, beforeUnload: function () { // named function that can be bound and unbound to beforeunload event // Makes sure any outstanding queued updates are sent before leaving the page. //console.log('cart.beforeUnload: '+objKeyCount(cart.updateQueue)+' vars'); cart.setVarsObj( {}, null, false ); // synchronous }, varsToUrlData: function (varsObj) { // creates a url data (var1=val1&var2=val2...) string from vars object and queue // The queue will be emptied by this call. cart.queueVarsObj(varsObj); // lay ontop of queue, to give new values precedence // Now convert to url data and clear queue var urlData = ''; if (cart.updatesWaiting()) { //console.log('cart.varsToUrlData: '+objKeyCount(cart.updateQueue)+' vars'); urlData = varHashToQueryString(cart.updateQueue); cart.updateQueue = {}; } return urlData; }, setVarsObj: function (varsObj, errFunc, async) { // Set all vars in a var hash, appending any queued updates //console.log('cart.setVarsObj: were:'+objKeyCount(cart.updateQueue) + // ' new:'+objKeyCount(varsObj); cart.queueVarsObj(varsObj); // lay ontop of queue, to give new values precedence // Now ajax update all in queue and clear queue if (cart.updatesWaiting()) { setVarsFromHash(cart.updateQueue, errFunc, async); cart.updateQueue = {}; } }, setVars: function (names, values, errFunc, async) { // ajax updates the cart, and includes any queued updates. cart.setVarsObj(arysToObj(names, values), errFunc, async); }, queueVarsObj: function (varsObj) { // Add object worth of cart updates to the 'to be updated' queue, so they can be sent to // the server later. Note: hash allows overwriting previous updates to the same variable. if (typeof varsObj !== 'undefined' && objNotEmpty(varsObj)) { //console.log('cart.queueVarsObj: were:'+objKeyCount(cart.updateQueue) + // ' new:'+objKeyCount(varsObj)); for (var name in varsObj) { cart.updateQueue[name] = varsObj[name]; // Could update in background, however, failing to hit "refresh" is user choice // first in queue, schedule background update if (objKeyCount(cart.updateQueue) === 1) { // By unbind/bind, we assure that there is only one instance bound $(window).unbind('beforeunload', cart.beforeUnload); $(window).bind( 'beforeunload', cart.beforeUnload); } } } }, addVarsToQueue: function (names,values) { // creates a string of updates to save for ajax batch or a submit cart.queueVarsObj(arysToObj(names,values)); } }; /////////////////////////////////////////////// //// visibility (mixed with group toggle) ///// /////////////////////////////////////////////// var vis = { // map cgi enum visibility codes to strings enumOrder: new Array("hide", "dense", "full", "pack", "squish"), update: function (track, visibility) { // Updates visibility state in hgTracks.trackDb and any visible elements on the page. // returns true if we modify at least one select in the group list var rec = hgTracks.trackDb[track]; var selectUpdated = false; $("select[name=" + escapeJQuerySelectorChars(track) + "]").each(function(t) { $(this).attr('class', visibility === 'hide' ? 'hiddenText' : 'normalText'); $(this).val(visibility); selectUpdated = true; }); if (rec) { rec.localVisibility = visibility; } return selectUpdated; }, get: function (track) { // return current visibility for given track var rec = hgTracks.trackDb[track]; if (rec) { if (rec.localVisibility) { return rec.localVisibility; } else { return vis.enumOrder[rec.visibility]; } } else { return null; } }, makeTrackVisible: function (track) { // Sets the vis box to visible, and ques a cart update, but does not update the image if (track && vis.get(track) !== "full") { vis.update(track, 'pack'); cart.addVarsToQueue([track], ['pack']); } }, toggleForGroup: function (button, prefix) { // toggle visibility of a track group; prefix is the prefix of all the id's of tr's in the // relevant group. This code also modifies the corresponding hidden fields and the gif // of the +/- img tag. imageV2.markAsDirtyPage(); if (arguments.length > 2) return setTableRowVisibility(button, prefix, "hgtgroup", "group",false,arguments[2]); else return setTableRowVisibility(button, prefix, "hgtgroup", "group",false); }, expandAllGroups: function (newState) { // Set visibility of all track groups to newState (true means expanded). // This code also modifies the corresponding hidden fields and the gif's of the +/- img tag. imageV2.markAsDirtyPage(); $(".toggleButton[id$='_button']").each( function (i) { // works for old img type AND new BUTTONS_BY_CSS // - 7: clip '_button' suffix vis.toggleForGroup(this,this.id.substring(0,this.id.length - 7),newState); }); return false; }, initForAjax: function() { // To better support the back-button, it is good to eliminate extraneous form puts // Towards that end, we support visBoxes making ajax calls to update cart. var sels = $('select.normalText,select.hiddenText'); $(sels).change(function() { var track = $(this).attr('name'); if ($(this).val() === 'hide') { var rec = hgTracks.trackDb[track]; if (rec) rec.visibility = 0; // else Would be nice to hide subtracks as well but that may be overkill $(document.getElementById('tr_' + track)).remove(); imageV2.highlightRegion(); $(this).attr('class', 'hiddenText'); } else $(this).attr('class', 'normalText'); cart.addVarsToQueue([track], [$(this).val()]); imageV2.markAsDirtyPage(); return false; }); // Now we can rid the submt of the burden of all those vis boxes var form = $('form#TrackForm'); $(form).submit(function () { $('select.normalText,select.hiddenText').attr('disabled',true); }); $(form).attr('method','get'); }, restoreFromBackButton: function() // Re-enabling vis dropdowns is necessary because initForAjax() disables them on submit. { $('select.normalText,select.hiddenText').attr('disabled',false); } }; //////////////////////////////////////////////////////////// // dragSelect is also known as dragZoom or shift-dragZoom // //////////////////////////////////////////////////////////// var dragSelect = { areaSelector: null, // formerly "imgAreaSelect". jQuery element used for imgAreaSelect originalCursor: null, startTime: null, selectStart: function (img, selection) { initVars(); if (rightClick.menu) { rightClick.menu.hide(); } var now = new Date(); dragSelect.startTime = now.getTime(); posting.blockMapClicks(); }, selectChange: function (img, selection) { if (selection.x1 !== selection.x2) { if (genomePos.check(img, selection)) { genomePos.update(img, selection, false); jQuery('body').css('cursor', dragSelect.originalCursor); } else { jQuery('body').css('cursor', 'not-allowed'); } } return true; }, highlightThisRegion: function(newPosition) // set highlighting newPosition in server-side cart and apply the highlighting in local UI. { var pos = parsePosition(newPosition); var start = pos.start; var end = pos.end; hgTracks.highlight = getDb() + "." + pos.chrom + ":" + start + "-" + end + '#AAFFFF'; hgTracks.highlight = imageV2.disguiseHighlight(hgTracks.highlight); // we include enableHighlightingDialog because it may have been changed by the dialog var cartSettings = { 'highlight': hgTracks.highlight, 'enableHighlightingDialog': hgTracks.enableHighlightingDialog ? 1 : 0 }; if (hgTracks.windows && !hgTracks.virtualSingleChrom) { var nonVirtChrom = ""; var nonVirtStart = -1; var nonVirtEnd = -1; for (i=0,len=hgTracks.windows.length; i < len; ++i) { var w = hgTracks.windows[i]; // overlap with new position? if (w.virtEnd > start && end > w.virtStart) { var s = Math.max(start, w.virtStart); var e = Math.min(end, w.virtEnd); var cs = s - w.virtStart + w.winStart; var ce = e - w.virtStart + w.winStart; if (nonVirtChrom === "") { nonVirtChrom = w.chromName; nonVirtStart = cs; nonVirtEnd = ce; } else { if (w.chromName === nonVirtChrom) { nonVirtEnd = Math.max(ce, nonVirtEnd); } else { break; } } } } if (nonVirtChrom !== "") cartSettings.nonVirtHighlight = getDb() + '.' + nonVirtChrom + ':' + nonVirtStart + '-' + (nonVirtEnd+1) + '#AAFFFF'; } else if (hgTracks.windows && hgTracks.virtualSingleChrom) { cartSettings.nonVirtHighlight = hgTracks.highlight; } // TODO if not virt, do we need to erase cart nonVirtHighlight ? cart.setVarsObj(cartSettings); imageV2.highlightRegion(); }, selectionEndDialog: function (newPosition) // Let user choose between zoom-in and highlighting. { var dragSelectDialog = $("#dragSelectDialog")[0]; if (!dragSelectDialog) { $("body").append("
" + "

" + "Don't show this dialog again and always zoom.
" + "(Re-enable highlight via the 'configure' menu at any time.)

"); dragSelectDialog = $("#dragSelectDialog")[0]; } if (hgTracks.windows) { var i,len; var newerPosition = newPosition; if (hgTracks.virtualSingleChrom && (newPosition.search("virt:")===0)) { newerPosition = genomePos.disguisePosition(newPosition); } var str = newerPosition + "
\n"; var str2 = "
\n"; str2 += "\n"; if (!(hgTracks.virtualSingleChrom && (selectedRegions === 1))) { str += str2; } $("#dragSelectPosition").html(str); } else { $("#dragSelectPosition").html(newPosition); } $(dragSelectDialog).dialog({ modal: true, title: "Drag-and-select", closeOnEscape: true, resizable: false, autoOpen: false, revertToOriginalPos: true, minWidth: 400, buttons: { "Zoom In": function() { // Zoom to selection $(this).dialog("option", "revertToOriginalPos", false); if ($("#disableDragHighlight").attr('checked')) hgTracks.enableHighlightingDialog = false; if (imageV2.inPlaceUpdate) { if (hgTracks.virtualSingleChrom && (newPosition.search("virt:")===0)) { newPosition = genomePos.disguisePosition(newPosition); // DISGUISE } var params = "position=" + newPosition; if (!hgTracks.enableHighlightingDialog) params += "&enableHighlightingDialog=0"; imageV2.navigateInPlace(params, null, true); } else { $('body').css('cursor', 'wait'); if (!hgTracks.enableHighlightingDialog) cart.setVarsObj({'enableHighlightingDialog': 0 },null,false); // async=false document.TrackHeaderForm.submit(); } $(this).dialog("close"); }, "Highlight": function() { // Highlight selection $(imageV2.imgTbl).imgAreaSelect({hide:true}); if ($("#disableDragHighlight").attr('checked')) hgTracks.enableHighlightingDialog = false; dragSelect.highlightThisRegion(newPosition); $(this).dialog("close"); }, "Cancel": function() { $(this).dialog("close"); } }, open: function () { // Make zoom the focus/default action $(this).parents('.ui-dialog-buttonpane button:eq(0)').focus(); }, close: function() { // All exits to dialog should go through this $(imageV2.imgTbl).imgAreaSelect({hide:true}); if ($(this).dialog("option", "revertToOriginalPos")) genomePos.revertToOriginalPos(); if ($("#disableDragHighlight").attr('checked')) $(this).remove(); else $(this).hide(); $('body').css('cursor', ''); // Occasionally wait cursor got left behind } }); $(dragSelectDialog).dialog('open'); }, selectEnd: function (img, selection) { var now = new Date(); var doIt = false; if (dragSelect.originalCursor) jQuery('body').css('cursor', dragSelect.originalCursor); // ignore releases outside of the image rectangle (allowing a 10 pixel slop) if (genomePos.check(img, selection)) { // ignore single clicks that aren't in the top of the image // (this happens b/c the clickClipHeight test in dragSelect.selectStart // doesn't occur when the user single clicks). doIt = dragSelect.startTime !== null || selection.y1 <= hgTracks.rulerClickHeight; } if (doIt) { // dragSelect.startTime is null if mouse has never been moved var singleClick = ( (selection.x2 === selection.x1) || dragSelect.startTime === null || (now.getTime() - dragSelect.startTime) < 100); var newPosition = genomePos.update(img, selection, singleClick); if (newPosition) { if (hgTracks.enableHighlightingDialog) dragSelect.selectionEndDialog(newPosition); else { $(imageV2.imgTbl).imgAreaSelect({hide:true}); if (imageV2.inPlaceUpdate) { if (hgTracks.virtualSingleChrom && (newPosition.search("virt:")===0)) { newPosition = genomePos.disguisePosition(newPosition); // DISGUISE } imageV2.navigateInPlace("position=" + newPosition, null, true); } else { jQuery('body').css('cursor', 'wait'); document.TrackHeaderForm.submit(); } } } } else { $(imageV2.imgTbl).imgAreaSelect({hide:true}); genomePos.revertToOriginalPos(); } dragSelect.startTime = null; // blockMapClicks/allowMapClicks() is necessary if selectEnd was over a map item. setTimeout(posting.allowMapClicks,50); return true; }, load: function (firstTime) { var imgHeight = 0; if (imageV2.enabled) imgHeight = imageV2.imgTbl.innerHeight() - 1; // last little bit makes border look ok // No longer disable without ruler, because shift-drag still works if (typeof(hgTracks) !== "undefined") { if (hgTracks.rulerClickHeight === undefined || hgTracks.rulerClickHeight === null) hgTracks.rulerClickHeight = 0; // will be zero if no ruler track var heights = hgTracks.rulerClickHeight; dragSelect.areaSelector = jQuery((imageV2.imgTbl).imgAreaSelect({ selectionColor: 'blue', outerColor: '', minHeight: imgHeight, maxHeight: imgHeight, onSelectStart: dragSelect.selectStart, onSelectChange: dragSelect.selectChange, onSelectEnd: dragSelect.selectEnd, autoHide: false, // gets hidden after possible dialog movable: false, clickClipHeight: heights })); } } }; ///////////////////////////////////// //// Chrom Drag/Zoom/Expand code //// ///////////////////////////////////// jQuery.fn.chromDrag = function(){ this.each(function(){ // Plan: // mouseDown: determine where in map: convert to img location: pxDown // mouseMove: flag drag // mouseUp: if no drag, then create href centered on bpDown loc with current span // if drag, then create href from bpDown to bpUp // if ctrlKey then expand selection to containing cytoBand(s) // Image dimensions all in pix var img = { top: -1, scrolledTop: -1, height: -1, left: -1, scrolledLeft: -1, width: -1 }; // chrom Dimensions beg,end,size in bases, rest in pix var chr = { name: "", reverse: false, beg: -1, end: -1, size: -1, top: -1, bottom: -1, left: -1, right: -1, width: -1 }; var pxDown = 0; // pix X location of mouseDown var chrImg = $(this); var mouseIsDown = false; var mouseHasMoved = false; var hilite = null; initialize(); function initialize(){ findDimensions(); if (chr.top === -1) warn("chromIdeo(): failed to register "+this.id); else { hiliteSetup(); $('area.cytoBand').unbind('mousedown'); // Make sure this is only bound once $('area.cytoBand').mousedown( function(e) { // mousedown on chrom portion of image only (map items) updateImgOffsets(); pxDown = e.clientX - img.scrolledLeft; var pxY = e.clientY - img.scrolledTop; if (mouseIsDown === false && isWithin(chr.left,pxDown,chr.right) && isWithin(chr.top,pxY,chr.bottom)) { mouseIsDown = true; mouseHasMoved = false; $(document).bind('mousemove',chromMove); $(document).bind( 'mouseup', chromUp); hiliteShow(pxDown,pxDown); return false; } }); } } function chromMove(e) { // If mouse was down, determine if dragged, then show hilite if ( mouseIsDown ) { var pxX = e.clientX - img.scrolledLeft; var relativeX = (pxX - pxDown); if (mouseHasMoved || (mouseHasMoved === false && Math.abs(relativeX) > 2)) { mouseHasMoved = true; if (isWithin(chr.left,pxX,chr.right)) hiliteShow(pxDown,pxX); else if (pxX < chr.left) hiliteShow(pxDown,chr.left); else hiliteShow(pxDown,chr.right); } } } function chromUp(e) { // If mouse was down, handle final selection $(document).unbind('mousemove',chromMove); $(document).unbind('mouseup',chromUp); chromMove(e); // Just in case if (mouseIsDown) { updateImgOffsets(); var bands; var pxUp = e.clientX - img.scrolledLeft; var pxY = e.clientY - img.scrolledTop; if (isWithin(0,pxY,img.height)) { // within vertical range or else cancel var selRange = { beg: -1, end: -1, width: -1 }; var dontAsk = true; if (e.ctrlKey) { bands = findCytoBand(pxDown,pxUp); if (bands.end > -1) { pxDown = bands.left; pxUp = bands.right; mouseHasMoved = true; dontAsk = false; selRange.beg = bands.beg; selRange.end = bands.end; hiliteShow(pxDown,pxUp); } } else if (mouseHasMoved) { // bounded by chrom dimensions: but must remain within image! if (isWithin(-20,pxUp,chr.left)) pxUp = chr.left; if (isWithin(chr.right,pxUp,img.width + 20)) pxUp = chr.right; if ( isWithin(chr.left,pxUp,chr.right+1) ) { selRange.beg = convertToBases(pxDown); selRange.end = convertToBases(pxUp); if (Math.abs(selRange.end - selRange.beg) < 20) mouseHasMoved = false; // Drag so small: treat as simple click else dontAsk = false; } } if (mouseHasMoved === false) { // Not else because small drag turns this off hiliteShow(pxUp,pxUp); var curWidth = hgTracks.winEnd - hgTracks.winStart; // Notice that beg is based upon up position selRange.beg = convertToBases(pxUp) - Math.round(curWidth/2); selRange.end = selRange.beg + curWidth; } if (selRange.end > -1) { // prompt, then submit for new position selRange = rangeNormalizeToChrom(selRange,chr); if (mouseHasMoved === false) { // Update highlight by converting bp back to pix pxDown = convertFromBases(selRange.beg); pxUp = convertFromBases(selRange.end); hiliteShow(pxDown,pxUp); } //if ((selRange.end - selRange.beg) < 50000) // dontAsk = true; if (dontAsk || confirm("Jump to new position:\n\n"+chr.name+":"+commify(selRange.beg)+ "-"+commify(selRange.end)+" size:"+commify(selRange.width)) ) { genomePos.setByCoordinates(chr.name, selRange.beg, selRange.end); // Stop the presses :0) $('area.cytoBand').mousedown( function(e) { return false; }); if (imageV2.backSupport) { imageV2.navigateInPlace("position=" + encodeURIComponent(genomePos.get().replace(/,/g,'')) + "&findNearest=1",null,true); hiliteCancel(); } else document.TrackHeaderForm.submit(); return true; // Make sure the setTimeout below is not called. } } } hiliteCancel(); setTimeout(posting.allowMapClicks,50); } mouseIsDown = false; mouseHasMoved = false; } function isWithin(beg,here,end) { // Simple utility return ( beg <= here && here < end ); } function convertToBases(pxX) { // Simple utility to convert pix to bases var offset = (pxX - chr.left)/chr.width; if (chr.reverse) offset = 1 - offset; return Math.round(offset * chr.size); } function convertFromBases(bases) { // Simple utility to convert bases to pix var offset = bases/chr.size; if (chr.reverse) offset = 1 - offset; return Math.round(offset * chr.width) + chr.left; } function findDimensions() { // Called at init: determine the dimensions of chrom from 'cytoband' map items var lastX = -1; $('area.cytoBand').each(function(ix) { var loc = this.coords.split(","); if (loc.length === 4) { var myLeft = parseInt(loc[0]); var myRight = parseInt(loc[2]); if (chr.top === -1) { chr.left = myLeft; chr.right = myRight; chr.top = parseInt(loc[1]); chr.bottom = parseInt(loc[3]); } else { if (chr.left > myLeft) chr.left = myLeft; if (chr.right < parseInt(loc[2])) chr.right = parseInt(loc[2]); } var range = this.title.substr(this.title.lastIndexOf(':')+1); var pos = range.split('-'); if (pos.length === 2) { if (chr.name.length === 0) { chr.beg = parseInt(pos[0]); //chr.end = parseInt(pos[1]); chr.name = this.title.substring(this.title.lastIndexOf(' ')+1, this.title.lastIndexOf(':')); } else { if (chr.beg > parseInt(pos[0])) chr.beg = parseInt(pos[0]); } if (chr.end < parseInt(pos[1])) { chr.end = parseInt(pos[1]); if (lastX === -1) lastX = myRight; else if (lastX > myRight) chr.reverse = true; // end is advancing, but X is not, so reverse } else if (lastX !== -1 && lastX < myRight) chr.reverse = true; // end is not advancing, but X is, so reverse } $(this).css( 'cursor', 'text'); $(this).attr("href",""); } }); chr.size = (chr.end - chr.beg ); chr.width = (chr.right - chr.left); } function findCytoBand(pxDown,pxUp) { // Called when mouseup and ctrl: Find the bounding cytoband dimensions (in pix and bases) var cyto = { left: -1, right: -1, beg: -1, end: -1 }; $('area.cytoBand').each(function(ix) { var loc = this.coords.split(","); if (loc.length === 4) { var myLeft = parseInt(loc[0]); var myRight = parseInt(loc[2]); var range; var pos; if (cyto.left === -1 || cyto.left > myLeft) { if ( isWithin(myLeft,pxDown,myRight) || isWithin(myLeft,pxUp,myRight) ) { cyto.left = myLeft; range = this.title.substr(this.title.lastIndexOf(':')+1); pos = range.split('-'); if (pos.length === 2) { cyto.beg = (chr.reverse ? parseInt(pos[1]) : parseInt(pos[0])); } } } if (cyto.right === -1 || cyto.right < myRight) { if ( isWithin(myLeft,pxDown,myRight) || isWithin(myLeft,pxUp,myRight) ) { cyto.right = myRight; range = this.title.substr(this.title.lastIndexOf(':')+1); pos = range.split('-'); if (pos.length === 2) { cyto.end = (chr.reverse ? parseInt(pos[0]) : parseInt(pos[1])); } } } } }); return cyto; } function rangeNormalizeToChrom(selection,chrom) { // Called before presenting or using base range: make sure chrom selection // is within chrom range if (selection.end < selection.beg) { var tmp = selection.end; selection.end = selection.beg; selection.beg = tmp; } selection.width = (selection.end - selection.beg); selection.beg += 1; if (selection.beg < chrom.beg) { selection.beg = chrom.beg; selection.end = chrom.beg + selection.width; } if (selection.end > chrom.end) { selection.end = chrom.end; selection.beg = chrom.end - selection.width; if (selection.beg < chrom.beg) { // spans whole chrom selection.width = (selection.end - chrom.beg); selection.beg = chrom.beg + 1; } } return selection; } function hiliteShow(down,cur) { // Called on mousemove, mouseup: set drag hilite dimensions var topY = img.top; var high = img.height; var begX = -1; var wide = -1; if (cur < down) { begX = cur + img.left; wide = (down - cur); } else { begX = down + img.left; wide = (cur - down); } $(hilite).css({ left: begX + 'px', width: wide + 'px', top: topY + 'px', height: high + 'px', display:'' }); $(hilite).show(); } function hiliteCancel(left,width,top,height) { // Called on mouseup: Make green drag hilite disappear when no longer wanted $(hilite).hide(); $(hilite).css({ left: '0px', width: '0px', top: '0px', height: '0px' }); } function hiliteSetup() { // Called on init: setup of drag region hilite (but don't show yet) if (hilite === null) { // setup only once hilite = jQuery("
"); $(hilite).css({ backgroundColor: 'green', opacity: 0.4, borderStyle: 'solid', borderWidth: '1px', bordercolor: '#0000FF' }); $(hilite).css({ display: 'none', position: 'absolute', overflow: 'hidden', zIndex: 1 }); jQuery($(chrImg).parents('body')).append($(hilite)); } return hilite; } function updateImgOffsets() { // Called on mousedown: Gets the current offsets var offs = $(chrImg).offset(); img.top = Math.round(offs.top ); img.left = Math.round(offs.left); img.scrolledTop = img.top - $("body").scrollTop(); img.scrolledLeft = img.left - $("body").scrollLeft(); if (theClient.isIePre11()) { img.height = $(chrImg).outerHeight(); img.width = $(chrImg).outerWidth(); } else { img.height = $(chrImg).height(); img.width = $(chrImg).width(); } return img; } }); }; /////////////////////////// //// Drag Reorder Code //// /////////////////////////// var dragReorder = { setOrder: function (table) { // Sets the 'order' value for the image table after a drag reorder var varsToUpdate = {}; $("tr.imgOrd").each(function (i) { if ($(this).attr('abbr') !== $(this).attr('rowIndex').toString()) { $(this).attr('abbr',$(this).attr('rowIndex').toString()); var name = this.id.substring('tr_'.length) + '_imgOrd'; varsToUpdate[name] = $(this).attr('abbr'); } }); if (objNotEmpty(varsToUpdate)) { cart.setVarsObj(varsToUpdate); imageV2.markAsDirtyPage(); } }, sort: function (table) { // Sets the table row order to match the order of the abbr attribute. // This is needed for back-button, and for visBox changes combined with refresh. var tbody = $(table).find('tbody')[0]; if (!tbody) tbody = table; // Do we need to sort? var trs = tbody.rows; var needToSort = false; $(trs).each(function(ix) { if ($(this).attr('abbr') !== $(this).attr('rowIndex').toString()) { needToSort = true; return false; // break for each() loops } }); if (!needToSort) return false; // Create array of tr holders to sort var ary = []; $(trs).each(function(ix) { // using sortTable found in utils.js ary.push(new sortTable.field(parseInt($(this).attr('abbr')),false,this)); }); // Sort the array ary.sort(sortTable.fieldCmp); // most efficient reload of sorted rows I have found var sortedRows = jQuery.map(ary, function(ary, i) { return ary.row; }); $(tbody).append( sortedRows ); // removes tr from current position and adds to end. return true; }, showCenterLabel: function (tr, show) { // Will show or hide centerlabel as requested // adjust button, sideLabel height, sideLabelOffset and centerlabel display if (!$(tr).hasClass('clOpt')) return; var center = normed($(tr).find(".sliceDiv.cntrLab")); if (!center) return; var seen = ($(center).css('display') !== 'none'); if (show === seen) return; var centerHeight = $(center).height(); var btn = normed($(tr).find("p.btn")); var side = normed($(tr).find(".sliceDiv.sideLab")); if (btn && side) { var sideImg = normed($(side).find("img")); if (sideImg) { var top = parseInt($(sideImg).css('top')); if (show) { $(btn).css('height',$(btn).height() + centerHeight); $(side).css('height',$(side).height() + centerHeight); top += centerHeight; // top is a negative number $(sideImg).css( {'top': top.toString() + "px" }); $( center ).show(); } else if (!show) { $(btn).css('height',$(btn).height() - centerHeight); $(side).css('height',$(side).height() - centerHeight); top -= centerHeight; // top is a negative number $(sideImg).css( {'top': top.toString() + "px" }); $( center ).hide(); } } } }, getContiguousRowSet: function (row) { // Returns the set of rows that are of the same class and contiguous if (!row) return null; var btn = $( row ).find("p.btn"); if (btn.length === 0) return null; var classList = $( btn ).attr("class").split(" "); var matchClass = classList[0]; var table = $(row).parents('table#imgTbl')[0]; var rows = $(table).find('tr'); // Find start index var startIndex = $(row).attr('rowIndex'); var endIndex = startIndex; for (var ix=startIndex-1; ix >= 0; ix--) { btn = $( rows[ix] ).find("p.btn"); if (btn.length === 0) break; classList = $( btn ).attr("class").split(" "); if (classList[0] !== matchClass) break; startIndex = ix; } // Find end index for (var rIx=endIndex; rIx 0) { if ( ! imageV2.lastTrack || imageV2.lastTrack.id !== id) imageV2.lastTrack = rightClick.makeMapItem(id); // currentMapItem gets set by mapItemMapOver. This is just backup } }, mapItemMouseOver: function () { // Record data for current map area item var id = this.id; if (!id || id.length === 0) { id = ''; var tr = $( this ).parents('tr.imgOrd'); if ( $(tr).length === 1 ) { var a = /tr_(.*)/.exec($(tr).attr('id')); // voodoo if (a && a[1]) { id = a[1]; } } } if (id.length > 0) { rightClick.currentMapItem = rightClick.makeMapItem(id); if (rightClick.currentMapItem) { rightClick.currentMapItem.href = this.href; rightClick.currentMapItem.title = this.title; // Handle linked features with separate clickmaps for each exon/intron if ((this.title.indexOf('Exon ') === 0) || (this.title.indexOf('Intron ') === 0)) { // if the title is Exon ... or Intron ... // then search for the sibling with the same href // that has the real title item label var elem = this.parentNode.firstChild; while (elem) { if ((elem.href === this.href) && !((elem.title.indexOf('Exon ') === 0) || (elem.title.indexOf('Intron ') === 0))) { rightClick.currentMapItem.title = elem.title; break; } elem = elem.nextSibling; } } } } }, mapItemMouseOut: function () { imageV2.lastTrack = rightClick.currentMapItem; // Just a backup rightClick.currentMapItem = null; }, init: function () { // Make side buttons visible (must also be called when updating rows in the imgTbl). var btns = $("p.btn"); if (btns.length > 0) { dragReorder.zipButtons($('#imgTbl')); $(btns).mouseenter( dragReorder.buttonMouseOver ); $(btns).mouseleave( dragReorder.buttonMouseOut ); $(btns).show(); } var handle = $("td.dragHandle"); if (handle.length > 0) { $(handle).mouseenter( dragReorder.dragHandleMouseOver ); $(handle).mouseleave( dragReorder.dragHandleMouseOut ); } // setup mouse callbacks for the area tags $(imageV2.imgTbl).find("tr").mouseover( dragReorder.trMouseOver ); $(".area").each( function(t) { this.onmouseover = dragReorder.mapItemMouseOver; this.onmouseout = dragReorder.mapItemMouseOut; this.onclick = posting.mapClk; }); } }; ////////////////////////// //// Drag Scroll code //// ////////////////////////// jQuery.fn.panImages = function(){ // globals across all panImages genomePos.original = genomePos.getOriginalPos(); // redundant but makes certain original is set. var leftLimit = hgTracks.imgBoxLeftLabel * -1; var rightLimit = (hgTracks.imgBoxPortalWidth - hgTracks.imgBoxWidth + leftLimit); var only1xScrolling = ((hgTracks.imgBoxWidth - hgTracks.imgBoxPortalWidth) === 0); var prevX = (hgTracks.imgBoxPortalOffsetX + hgTracks.imgBoxLeftLabel) * -1; var portalWidth = 0; var portalAbsoluteX = 0; var savedPosition; var highlightArea = null; // Used to ensure dragSelect highlight will scroll. this.each(function(){ var pic; var pan; if ( $(this).is("img") ) { pan = $(this).parent("div"); pic = $(this); } else if ( $(this).is("div.scroller") ) { pan = $(this); pic = $(this).children("img#panImg"); // Get the real pic } if (!pan || !pic) { throw "Not a div with child image! 'panImages' can only be used with divs contain images."; } // globals across all panImages portalWidth = $(pan).width(); portalAbsoluteX = $(pan).offset().left; // globals to one panImage var newX = 0; var mouseDownX = 0; var mouseIsDown = false; var beyondImage = false; var atEdge = false; initialize(); function initialize(){ $(pan).parents('td.tdData').mousemove(function(e) { if (e.shiftKey) $(this).css('cursor',"crosshair"); // shift-dragZoom else if ( theClient.isIePre11() ) // IE will override map item cursors if this gets set $(this).css('cursor',""); // normal pointer when not over clickable item }); panAdjustHeight(prevX); pan.mousedown(function(e){ if (e.which > 1 || e.button > 1 || e.shiftKey) return true; if (mouseIsDown === false) { if (rightClick.menu) { rightClick.menu.hide(); } mouseIsDown = true; mouseDownX = e.clientX; highlightArea = $('#highlightItem')[0]; atEdge = (!beyondImage && (prevX >= leftLimit || prevX <= rightLimit)); $(document).bind('mousemove',panner); $(document).bind( 'mouseup', panMouseUp); // Will exec only once return false; } }); } function panner(e) { //if (!e) e = window.event; if ( mouseIsDown ) { var relativeX = (e.clientX - mouseDownX); if (relativeX !== 0) { if (posting.mapClicksAllowed()) { // need to throw up a z-index div. Wait mask? savedPosition = genomePos.get(); dragMaskShow(); posting.blockMapClicks(); } var decelerator = 1; //var wingSize = 1000; // 0 stops the scroll at the edges. // Remeber that offsetX (prevX) is negative newX = prevX + relativeX; if ( newX >= leftLimit ) { // scrolled all the way to the left if (atEdge) { // Do not drag straight off edge. Force second drag beyondImage = true; newX = leftLimit + (newX - leftLimit)/decelerator;// slower //if (newX >= leftLimit + wingSize) // Don't go too far over the edge! // newX = leftLimit + wingSize; } else newX = leftLimit; } else if ( newX < rightLimit ) { // scrolled all the way to the right if (atEdge) { // Do not drag straight off edge. Force second drag beyondImage = true; newX = rightLimit - (rightLimit - newX)/decelerator;// slower //if (newX < rightLimit - wingSize) // Don't go too far over the edge! // newX = rightLimit - wingSize; } else newX = rightLimit; } else if (newX >= rightLimit && newX < leftLimit) beyondImage = false; // could have scrolled back without mouse up newX = panUpdatePosition(newX,true); var nowPos = newX.toString() + "px"; $(".panImg").css( {'left': nowPos }); $('.tdData').css( {'backgroundPosition': nowPos } ); scrollHighlight(relativeX); if (!only1xScrolling) panAdjustHeight(newX); // Will dynamically resize image while scrolling. } } } function panMouseUp(e) { // Must be a separate function instead of pan.mouseup event. //if (!e) e = window.event; if (mouseIsDown) { dragMaskClear(); $(document).unbind('mousemove',panner); $(document).unbind('mouseup',panMouseUp); mouseIsDown = false; // timeout incase the dragSelect.selectEnd was over a map item. select takes precedence. setTimeout(posting.allowMapClicks,50); // Outside image? Then abandon. var curY = e.pageY; var imgTbl = $('#imgTbl'); var north = $(imgTbl).offset().top; var south = north + $(imgTbl).height(); if (curY < north || curY > south) { atEdge = false; beyondImage = false; if (savedPosition) genomePos.set(savedPosition); var oldPos = prevX.toString() + "px"; $(".panImg").css( {'left': oldPos }); $('.tdData').css( {'backgroundPosition': oldPos } ); if (highlightArea) imageV2.highlightRegion(); return true; } // Do we need to fetch anything? if (beyondImage) { if (imageV2.inPlaceUpdate) { var pos = parsePosition(genomePos.get()); imageV2.navigateInPlace("position=" + encodeURIComponent(pos.chrom + ":" + pos.start + "-" + pos.end), null, true); } else { document.TrackHeaderForm.submit(); } return true; // Make sure the setTimeout below is not called. } // Just a normal scroll within a >1X image if (prevX !== newX) { prevX = newX; if (!only1xScrolling) { //panAdjustHeight(newX); // Will resize image AFTER scrolling. // Important, since AJAX could lead to reinit after this within bounds scroll hgTracks.imgBoxPortalOffsetX = (prevX * -1) - hgTracks.imgBoxLeftLabel; hgTracks.imgBoxPortalLeft = newX.toString() + "px"; } } } } }); // end of this.each(function(){ function panUpdatePosition(newOffsetX,bounded) { // Updates the 'position/search" display with change due to panning var closedPortalStart = hgTracks.imgBoxPortalStart + 1; // Correction for half open var portalWidthBases = hgTracks.imgBoxPortalEnd - closedPortalStart; var portalScrolledX = hgTracks.imgBoxPortalOffsetX+hgTracks.imgBoxLeftLabel + newOffsetX; var recalculate = false; var newPortalStart = 0; if (hgTracks.revCmplDisp) newPortalStart = closedPortalStart + // As offset goes down, so do bases seen. Math.round(portalScrolledX*hgTracks.imgBoxBasesPerPixel); else newPortalStart = closedPortalStart - // As offset goes down, bases seen goes up! Math.round(portalScrolledX*hgTracks.imgBoxBasesPerPixel); if (newPortalStart < hgTracks.chromStart && bounded) { // Stay within bounds newPortalStart = hgTracks.chromStart; recalculate = true; } var newPortalEnd = newPortalStart + portalWidthBases; if (newPortalEnd > hgTracks.chromEnd && bounded) { newPortalEnd = hgTracks.chromEnd; newPortalStart = newPortalEnd - portalWidthBases; recalculate = true; } if (newPortalStart > 0) { var newPos = hgTracks.chromName + ":" + newPortalStart + "-" + newPortalEnd; genomePos.set(newPos); // no need to change the size } if (recalculate && hgTracks.imgBoxBasesPerPixel > 0) { // Need to recalculate X for bounding drag portalScrolledX = (closedPortalStart - newPortalStart) / hgTracks.imgBoxBasesPerPixel; newOffsetX = portalScrolledX - (hgTracks.imgBoxPortalOffsetX+hgTracks.imgBoxLeftLabel); } return newOffsetX; } function mapTopAndBottom(mapName,east,west) { // Find the top and bottom px given left and right boundaries var mapPortal = { top: -10, bottom: -10 }; var items = $("map[name='"+mapName+"']").children(); if ($(items).length>0) { $(items).each(function(t) { var loc = this.coords.split(","); var aleft = parseInt(loc[0]); var aright = parseInt(loc[2]); if (aleft < west && aright >= east) { var atop = parseInt(loc[1]); var abottom = parseInt(loc[3]); if (mapPortal.top < 0 ) { mapPortal.top = atop; mapPortal.bottom = abottom; } else if (mapPortal.top > atop) { mapPortal.top = atop; } else if (mapPortal.bottom < abottom) { mapPortal.bottom = abottom; } } }); } return mapPortal; } function panAdjustHeight(newOffsetX) { // Adjust the height of the track data images so that bed items scrolled off screen // do not waste vertical real estate // Is the > 1x? if (only1xScrolling) return; var east = newOffsetX * -1; var west = east + portalWidth; $(".panImg").each(function(t) { var mapid = this.id.replace('img_','map_'); var hDiv = $(this).parent(); var north = parseInt($(this).css("top")) * -1; var south = north + $(hDiv).height(); var mapPortal = mapTopAndBottom(mapid,east,west); if (mapPortal.top > 0) { var topdif = Math.abs(mapPortal.top - north); var botdif = Math.abs(mapPortal.bottom - south); if (topdif > 2 || botdif > 2) { $(hDiv).height( mapPortal.bottom - mapPortal.top ); north = mapPortal.top * -1; $(this).css( {'top': north.toString() + "px" }); // Need to adjust side label height as well! var imgId = this.id.split("_"); var titlePx = 0; var center = $("#img_center_"+imgId[2]); if (center.length > 0) { titlePx = $(center).parent().height(); north += titlePx; } var side = $("#img_side_"+imgId[2]); if (side.length > 0) { $(side).parent().height( mapPortal.bottom - mapPortal.top + titlePx); $(side).css( {'top': north.toString() + "px" }); } var btn = $("#p_btn_"+imgId[2]); if (btn.length > 0) { $(btn).height( mapPortal.bottom - mapPortal.top + titlePx); } else { btn = $("#img_btn_"+imgId[2]); if (btn.length > 0) { $(btn).parent().height( mapPortal.bottom - mapPortal.top + titlePx); $(btn).css( {'top': top.toString() + "px" }); } } } } }); dragMaskResize(); // Resizes the dragMask to match current image size } function dragMaskShow() { // Sets up the dragMask to show grabbing cursor within image // and not allowed north and south of image var imgTbl = $('#imgTbl'); // Find or create the waitMask (which masks the whole page) var dragMask = normed($('div#dragMask')); if (!dragMask) { $("body").prepend("
"); dragMask = $('div#dragMask'); } $('body').css('cursor','not-allowed'); $(dragMask).css('cursor',"url(../images/grabbing.cur),w-resize"); $(dragMask).css({opacity:0.0,display:'block', top: $(imgTbl).position().top.toString() + 'px', height: $(imgTbl).height().toString() + 'px' }); } function dragMaskResize() { // Resizes dragMask (called when image is dynamically resized in >1x scrolling) var imgTbl = $('#imgTbl'); // Find or create the waitMask (which masks the whole page) var dragMask = normed($('div#dragMask')); if (dragMask) { $(dragMask).height( $(imgTbl).height() ); } } function dragMaskClear() { // Clears the dragMask $('body').css('cursor','auto'); var dragMask = normed($('#dragMask')); if (dragMask) $(dragMask).hide(); } function scrollHighlight(relativeX) // Scrolls the highlight region if one exists { if (highlightArea) { // Best to have a left and right, then min/max the edges, then set width var hiOffset = $(highlightArea).offset(); var hiDefinedLeft = $(highlightArea).data('leftPixels'); var hiDefinedWidth = $(highlightArea).data('widthPixels'); hiOffset.left = Math.max(hiDefinedLeft + relativeX, portalAbsoluteX); var right = Math.min(hiDefinedLeft + hiDefinedWidth + relativeX, portalAbsoluteX + portalWidth); var newWidth = Math.max(right - hiOffset.left,0); if (hiDefinedWidth !== newWidth) $(highlightArea).width(newWidth); $(highlightArea).offset(hiOffset); } } }; /////////////////////////////////////// //// rightClick (aka context menu) //// /////////////////////////////////////// var rightClick = { menu: null, selectedMenuItem: null, // currently choosen context menu item (via context menu). floatingMenuItem: null, currentMapItem: null, supportZoomCodon: false, // turns on experimental feature (currently only in larry's tree). makeMapItem: function (id) { // Create a dummy mapItem on the fly // (for objects that don't have corresponding entry in the map). if (id && id.length > 0 && hgTracks.trackDb) { var title; var rec = hgTracks.trackDb[id]; if (rec) { title = rec.shortLabel; } else { title = id; } return {id: id, title: "configure " + title}; } else { return null; } }, findMapItem: function (e) { // Find mapItem for given event; returns item object or null if none found. if (rightClick.currentMapItem) { return rightClick.currentMapItem; } // rightClick for non-map items that can be resolved to their parent tr and // then trackName (e.g. items in gray bar) var tr = $( e.target ).parents('tr.imgOrd'); if ($(tr).length === 1) { var a = /tr_(.*)/.exec($(tr).attr('id')); // voodoo if (a && a[1]) { var id = a[1]; return rightClick.makeMapItem(id); } } return null; }, windowOpenFailedMsg: function () { warn("Your web browser prevented us from opening a new window.\n\n" + "Please change your browser settings to allow pop-up windows from " + document.domain + "."); }, handleZoomCodon: function (response, status) { var json = JSON.parse(response); if (json.pos) { genomePos.set(json.pos, 3); if (document.TrackForm) document.TrackForm.submit(); else document.TrackHeaderForm.submit(); } else { alert(json.error); } }, handleViewImg: function (response, status) { // handles view image response, which must get new image without imageV2 gimmickery jQuery('body').css('cursor', ''); var str = "]*SRC='([^']+)'"; var reg = new RegExp(str); var a = reg.exec(response); if (a && a[1]) { if ( ! window.open(a[1]) ) { rightClick.windowOpenFailedMsg(); } return; } warn("Couldn't parse out img src"); }, myPrompt: function (msg, callback) { // replacement for prompt; avoids misleading/confusing security warnings which are caused // by prompt in IE 7+. Callback is called if user presses "OK". $("body").append("
" + msg + "
"); $("#myPrompt").dialog({ modal: true, closeOnEscape: true, buttons: { "OK": function() { var myPromptText = $("#myPromptText").val(); $(this).dialog("close"); callback(myPromptText); } } }); }, hit: function (menuItemClicked, menuObject, cmd, args) { setTimeout( function() { rightClick.hitFinish(menuItemClicked, menuObject, cmd, args); }, 1); }, hitFinish: function (menuItemClicked, menuObject, cmd, args) { // dispatcher for context menu hits var id = rightClick.selectedMenuItem.id; var url = null; // TODO: Break this giant routine with shared vars into some sub-functions var href = null; var rec = null; var row = null; var rows = null; var selectUpdated = null; if (menuObject.shown) { // warn("Spinning: menu is still shown"); setTimeout(function() { rightClick.hitFinish(menuItemClicked, menuObject, cmd); }, 10); return; } if (cmd === 'selectWholeGene' || cmd === 'getDna' || cmd === 'highlightItem') { // bring whole gene into view or redirect to DNA screen. href = rightClick.selectedMenuItem.href; var chrom, chromStart, chromEnd; // Many links leave out the chrom (b/c it's in the server side cart as "c") // var chrom = hgTracks.chromName; // This is no longer acceptable // with multi-window capability drawing multiple positions on multiple chroms. var a = /hgg_chrom=(\w+)&/.exec(href); if (a) { if (a && a[1]) chrom = a[1]; a = /hgg_start=(\d+)/.exec(href); if (a && a[1]) chromStart = parseInt(a[1]) + 1; a = /hgg_end=(\d+)/.exec(href); if (a && a[1]) chromEnd = parseInt(a[1]); } else { // a = /hgc.*\W+c=(\w+)/.exec(href); a = /hgc.*\W+c=(\w+)/.exec(href); if (a && a[1]) chrom = a[1]; a = /o=(\d+)/.exec(href); if (a && a[1]) chromStart = parseInt(a[1]) + 1; a = /t=(\d+)/.exec(href); if (a && a[1]) chromEnd = parseInt(a[1]); } if (!chrom || chrom.length === 0 || !chromStart || !chromEnd) {// 1-based chromStart warn("couldn't parse out genomic coordinates"); } else { if (cmd === 'getDna') { // NOTE: this should be shared with URL generation for getDna blue bar menu url = "../cgi-bin/hgc?g=getDna&i=mixed&c=" + chrom; url += "&l=" + (chromStart - 1) + "&r=" + chromEnd; url += "&db=" + getDb() + "&hgsid=" + getHgsid(); if ( ! window.open(url) ) { rightClick.windowOpenFailedMsg(); } } else if (cmd === 'highlightItem') { if (hgTracks.windows && !hgTracks.virtualSingleChrom) { // orig way only worked if the entire item was visible in the windows. //var result = genomePos.chromToVirtChrom(chrom, parseInt(chromStart-1), parseInt(chromEnd)); var result = genomePos.convertChromPosToVirtCoords(chrom, parseInt(chromStart-1), parseInt(chromEnd)); if (result.chromStart != -1) { var newPos2 = hgTracks.chromName+":"+(result.chromStart+1)+"-"+result.chromEnd; dragSelect.highlightThisRegion(newPos2); } } else { var newChrom = hgTracks.chromName; if (hgTracks.windows && hgTracks.virtualSingleChrom) { newChrom = hgTracks.windows[0].chromName; } var newPos3 = newChrom+":"+(parseInt(chromStart))+"-"+parseInt(chromEnd); dragSelect.highlightThisRegion(newPos3); } } else { var newPosition = genomePos.setByCoordinates(chrom, chromStart, chromEnd); var reg = new RegExp("hgg_gene=([^&]+)"); var b = reg.exec(href); var name; // pull item name out of the url so we can set hgFind.matches (redmine 3062) if (b && b[1]) { name = b[1]; } else { reg = new RegExp("[&?]i=([^&]+)"); b = reg.exec(href); if (b && b[1]) { name = b[1]; } } if (imageV2.inPlaceUpdate) { // XXXX This attempt to "update whole track image in place" didn't work // for a variety of reasons (e.g. safari doesn't parse map when we // update on the client side), so this is currently dead code. // However, this now works in all other browsers, so we may turn this // on for non-safari browsers (see redmine #4667). jQuery('body').css('cursor', ''); var data = "hgt.trackImgOnly=1&hgt.ideogramToo=1&position=" + newPosition + "&hgsid=" + getHgsid(); if (name) data += "&hgFind.matches=" + name; $.ajax({ type: "GET", url: "../cgi-bin/hgTracks", data: cart.addUpdatesToUrl(data), dataType: "html", trueSuccess: imageV2.updateImgAndMap, success: catchErrorOrDispatch, error: errorHandler, cmd: cmd, loadingId: showLoadingImage("imgTbl"), cache: false }); } else { // do a full page refresh to update hgTracks image jQuery('body').css('cursor', 'wait'); var ele; if (document.TrackForm) ele = document.TrackForm; else ele = document.TrackHeaderForm; if (name) cart.addVarsToQueue(['hgFind.matches'], [name]); ele.submit(); } } } } else if (cmd === 'zoomCodon' || cmd === 'zoomExon') { var num, ajaxCmd, msg; if (cmd === 'zoomCodon') { msg = "Please enter the codon number to jump to:"; ajaxCmd = 'codonToPos'; } else { msg = "Please enter the exon number to jump to:"; ajaxCmd = 'exonToPos'; } rightClick.myPrompt(msg, function(results) { $.ajax({ type: "GET", url: "../cgi-bin/hgApi", data: cart.varsToUrlData({ 'db': getDb(), 'cmd': ajaxCmd, 'num': results, 'table': args.table, 'name': args.name }), trueSuccess: rightClick.handleZoomCodon, success: catchErrorOrDispatch, error: errorHandler, cache: true }); }); } else if (cmd === 'hgTrackUi_popup') { // Launches the popup but shields the ajax with a waitOnFunction popUp.hgTrackUi( rightClick.selectedMenuItem.id, false ); } else if (cmd === 'hgTrackUi_follow') { url = "hgTrackUi?hgsid=" + getHgsid() + "&g="; rec = hgTracks.trackDb[id]; if (tdbHasParent(rec) && tdbIsLeaf(rec)) url += rec.parentTrack; else { // The button already has the ref var link = normed($( 'td#td_btn_'+ rightClick.selectedMenuItem.id ).children('a')); if (link) url = $(link).attr('href'); else url += rightClick.selectedMenuItem.id; } location.assign(url); } else if (cmd === 'viewImg') { // Fetch a new copy of track img and show it to the user in another window. This code // assume we have updated remote cart with all relevant chages (e.g. drag-reorder). jQuery('body').css('cursor', 'wait'); $.ajax({ type: "GET", url: "../cgi-bin/hgTracks", data: cart.varsToUrlData({ 'hgt.imageV1': '1','hgt.trackImgOnly': '1', 'hgsid': getHgsid() }), dataType: "html", trueSuccess: rightClick.handleViewImg, success: catchErrorOrDispatch, error: errorHandler, cmd: cmd, cache: false }); } else if (cmd === 'openLink' || cmd === 'followLink') { href = rightClick.selectedMenuItem.href; var vars = new Array("c", "l", "r", "db"); var valNames = new Array("chromName", "winStart", "winEnd"); for (var i in vars) { // make sure the link contains chrom and window width info // (necessary b/c we are stripping hgsid and/or the cart may be empty); // but don't add chrom to wikiTrack links (see redmine #2476). var v = vars[i]; var val; if (v === "db") { val = getDb(); } else { val = hgTracks[valNames[i]]; } if (val && id !== "wikiTrack" && (href.indexOf("?" + v + "=") === -1) && (href.indexOf("&" + v + "=") === -1)) { href = href + "&" + v + "=" + val; } } if (cmd === 'followLink') { // XXXX This is blocked by Safari's popup blocker (without any warning message). location.assign(href); } else { // Remove hgsid to force a new session (see redmine ticket 1333). href = removeHgsid(href); if ( ! window.open(href) ) { rightClick.windowOpenFailedMsg(); } } } else if (cmd === 'float') { if (rightClick.floatingMenuItem && rightClick.floatingMenuItem === id) { $.floatMgr.FOArray = []; rightClick.floatingMenuItem = null; } else { if (rightClick.floatingMenuItem) { // This doesn't work. $('#img_data_' + rightClick.floatingMenuItem).parent().restartFloat(); // This does work $.floatMgr.FOArray = []; } rightClick.floatingMenuItem = id; rightClick.reloadFloatingItem(); imageV2.requestImgUpdate(id, "hgt.transparentImage=0", ""); } } else if (cmd === 'hideSet') { row = $( 'tr#tr_' + id ); rows = dragReorder.getContiguousRowSet(row); if (rows && rows.length > 0) { var varsToUpdate = {}; // from bottom up, just in case remove screws with us for (var ix=rows.length - 1; ix >= 0; ix--) { var rowId = $(rows[ix]).attr('id').substring('tr_'.length); // Remove subtrack level vis and explicitly uncheck. varsToUpdate[rowId] = '[]'; varsToUpdate[rowId+'_sel'] = 0; $(rows[ix]).remove(); } if (objNotEmpty(varsToUpdate)) { cart.setVarsObj(varsToUpdate); } imageV2.afterImgChange(true); } } else if (cmd === 'hideComposite') { rec = hgTracks.trackDb[id]; if (tdbIsSubtrack(rec)) { row = $( 'tr#tr_' + id ); rows = dragReorder.getCompositeSet(row); // from bottom up, just in case remove screws with us if (rows && rows.length > 0) { for (var rIx=rows.length - 1; rIx >= 0; rIx--) { $(rows[rIx]).remove(); } selectUpdated = vis.update(rec.parentTrack, 'hide'); cart.setVars( [rec.parentTrack], ['hide']); imageV2.afterImgChange(true); } } } else if (cmd === 'jumpToHighlight') { // If highlight exists for this assembly, jump to it if (hgTracks.highlight) { var newPos = parsePositionWithDb(hgTracks.highlight); if (newPos && newPos.db === getDb()) { if ( $('#highlightItem').length === 0) { // not visible? jump to it var curPos = parsePosition(genomePos.get()); var diff = ((curPos.end - curPos.start) - (newPos.end - newPos.start)); if (diff > 0) { // new position is smaller then current, then center it newPos.start = Math.max( Math.floor(newPos.start - (diff/2) ), 0 ); newPos.end = newPos.start + (curPos.end - curPos.start); } } if (imageV2.inPlaceUpdate) { var params = "position=" + newPos.chrom+':'+newPos.start+'-'+newPos.end; imageV2.navigateInPlace(params, null, true); } else { genomePos.setByCoordinates(newPos.chrom, newPos.start, newPos.end); jQuery('body').css('cursor', 'wait'); document.TrackHeaderForm.submit(); } } } } else if (cmd === 'removeHighlight') { hgTracks.highlight = null; cart.setVarsObj({ 'highlight': '[]' }); imageV2.highlightRegion(); } else { // if ( cmd in 'hide','dense','squish','pack','full','show' ) // Change visibility settings: // // First change the select on our form: rec = hgTracks.trackDb[id]; selectUpdated = vis.update(id, cmd); // Now change the track image if (imageV2.enabled && cmd === 'hide') { // Hide local display of this track and update server side cart. // Subtracks controlled by 2 settings so del vis and set sel=0. if (tdbIsSubtrack(rec)) { // Remove subtrack level vis and explicitly uncheck. cart.setVars( [ id, id+"_sel" ], [ '[]', 0 ] ); } else if (tdbIsFolderContent(rec)) { // supertrack children need to have _sel set to trigger superttrack reshaping cart.setVars( [ id, id+"_sel" ], [ 'hide', 0 ] ); } else { cart.setVars([id], ['hide']); // Others, just set vis hide. } $(document.getElementById('tr_' + id)).remove(); imageV2.afterImgChange(true); } else if (!imageV2.mapIsUpdateable) { jQuery('body').css('cursor', 'wait'); if (selectUpdated) { // assert(document.TrackForm); document.TrackForm.submit(); } else { // Add vis update to queue then submit cart.addVarsToQueue([id], [cmd]); document.TrackHeaderForm.submit(); } } else { imageV2.requestImgUpdate(id, id + "=" + cmd, "", cmd); } } }, makeHitCallback: function (title) { // stub to avoid problem with a function closure w/n a loop return function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, title); return true; }; }, reloadFloatingItem: function () { // currently dead (experimental code) if (rightClick.floatingMenuItem) { $('#img_data_' + rightClick.floatingMenuItem).parent().makeFloat( {x:"current",y:"current", speed: 'fast', alwaysVisible: true, alwaysTop: true}); } }, makeImgTag: function (img) { // Return img tag with explicit dimensions for img (dimensions are currently hardwired). // This fixes the "weird shadow problem when first loading the right-click menu" // seen in FireFox 3.X, which occurred b/c FF doesn't actually fetch the image until // the menu is being shown. return ""; }, load: function (img) { rightClick.menu = img.contextMenu(function() { popUp.cleanup(); // Popup box is not getting closed properly so must do it here if ( ! rightClick.selectedMenuItem ) // This is literally an edge case so ignore return; var o; // TODO: Break this giant routine with shared vars into some sub-functions var str; var rec = null; var menu = []; var selectedImg = rightClick.makeImgTag("greenChecksm.png"); var blankImg = rightClick.makeImgTag("invisible16.png"); var done = false; if (rightClick.selectedMenuItem && rightClick.selectedMenuItem.id) { var href = rightClick.selectedMenuItem.href; var isHgc, isGene; if (href) { isGene = href.match("hgGene"); isHgc = href.match("hgc"); } var id = rightClick.selectedMenuItem.id; rec = hgTracks.trackDb[id]; var offerHideSubset = false; var offerHideComposite = false; var offerSingles = true; var row = $( 'tr#tr_' + id ); if (row) { var btn = $(row).find('p.btnBlue'); // btnBlue means cursor over left button if (btn.length === 1) { var compositeSet = dragReorder.getCompositeSet(row); if (compositeSet && compositeSet.length > 0) { // There is composite set offerHideComposite = true; $( compositeSet ).find('p.btn').addClass('blueButtons');// blue persists var subSet = dragReorder.getContiguousRowSet(row); if (subSet && subSet.length > 1) { offerSingles = false; if (subSet.length < compositeSet.length) { offerHideSubset = true; $( subSet ).addClass("greenRows"); // green persists } } } } } // First option is hide sets if (offerHideComposite) { if (offerHideSubset) { o = {}; o[blankImg + " hide track subset (green)"] = { onclick: rightClick.makeHitCallback('hideSet')}; menu.push(o); } o = {}; str = blankImg + " hide track set"; if (offerHideSubset) str += " (blue)"; o[str] = {onclick: rightClick.makeHitCallback('hideComposite')}; menu.push(o); } // Second set of options: visibility for single track if (offerSingles) { if (offerHideComposite) menu.push($.contextMenu.separator); // XXXX what if select is not available (b/c trackControlsOnMain is off)? // Move functionality to a hidden variable? var select = $("select[name=" + escapeJQuerySelectorChars(id) + "]"); if (select.length > 1) // Not really needed if $('#hgTrackUiDialog').html(""); has worked select = [ $(select)[0] ]; var cur = $(select).val(); if (cur) { $(select).children().each(function(index, o) { var title = $(this).val(); str = blankImg + " " + title; if (title === cur) str = selectedImg + " " + title; o = {}; o[str] = {onclick: function (menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, title); return true;}}; menu.push(o); }); done = true; } else { if (rec) { // XXXX check current state from a hidden variable. var visStrings = new Array("hide","dense","squish","pack","full"); for (var i in visStrings) { // use maxVisibility and change hgTracks so it can hide subtracks o = {}; str = blankImg + " " + visStrings[i]; if (rec.canPack || (visStrings[i] !== "pack" && visStrings[i] !== "squish")) { if (rec.localVisibility) { if (visStrings[i] === rec.localVisibility) { str = selectedImg + " " + visStrings[i]; } } else if (visStrings[i] === vis.enumOrder[rec.visibility]) { str = selectedImg + " " + visStrings[i]; } o[str] = { onclick: rightClick.makeHitCallback(visStrings[i]) }; menu.push(o); } } done = true; } } } if (done) { o = {}; var any = false; var title = rightClick.selectedMenuItem.title || "feature"; var maxLength = 60; if (title.length > maxLength) { title = title.substring(0, maxLength) + "..."; } if (isGene || isHgc || id === "wikiTrack") { // Add "Open details..." item var displayItemFunctions = false; if (rec) { if (rec.type.indexOf("wig") === 0 || rec.type.indexOf("bigWig") === 0 || id === "wikiTrack") { displayItemFunctions = false; } else if (rec.type.indexOf("expRatio") === 0) { displayItemFunctions = title !== "zoomInMore"; } else { displayItemFunctions = true; } } if (isHgc && href.indexOf('g=gtexGene') !== -1) { // For GTEx gene mouseovers, replace title (which may be a tissue name) with // item (gene) name a = /i=([^&]+)/.exec(href); if (a && a[1]) { title = a[1]; } } if (displayItemFunctions) { o[rightClick.makeImgTag("magnify.png") + " Zoom to " + title] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "selectWholeGene"); return true; } }; o[rightClick.makeImgTag("highlight.png") + " Highlight " + title] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "highlightItem"); return true; } }; if (rightClick.supportZoomCodon && rec.type.indexOf("genePred") !== -1) { // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc003tqk.2&hgg_prot=P00533&hgg_chrom=chr7&hgg_start=55086724&hgg_end=55275030&hgg_type=knownGene&db=hg19&c=chr7 var name, table; var reg = new RegExp("hgg_gene=([^&]+)"); var a = reg.exec(href); if (a && a[1]) { name = a[1]; reg = new RegExp("hgg_type=([^&]+)"); a = reg.exec(href); if (a && a[1]) { table = a[1]; } } else { // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgc?o=55086724&t=55275031&g=refGene&i=NM_005228&c=chr7 // http://hgwdev-larrym.cse.ucsc.edu/cgi-bin/hgc?o=55086713&t=55270769&g=wgEncodeGencodeManualV4&i=ENST00000455089&c=chr7 reg = new RegExp("i=([^&]+)"); a = reg.exec(href); if (a && a[1]) { name = a[1]; reg = new RegExp("g=([^&]+)"); a = reg.exec(href); if (a && a[1]) { table = a[1]; } } } if (name && table) { o[rightClick.makeImgTag("magnify.png")+" Zoom to codon"] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "zoomCodon", {name: name, table: table}); return true;} }; o[rightClick.makeImgTag("magnify.png")+" Zoom to exon"] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "zoomExon", {name: name, table: table}); return true; } }; } } o[rightClick.makeImgTag("dnaIcon.png")+" Get DNA for "+title] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "getDna"); return true; } }; } o[rightClick.makeImgTag("bookOut.png")+ " Open details page in new window..."] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "openLink"); return true; } }; any = true; } if (href && href.length > 0) { // Add "Show details..." item if (title.indexOf("Click to alter ") === 0) { // suppress the "Click to alter..." items } else if (rightClick.selectedMenuItem.href.indexOf("cgi-bin/hgTracks") !== -1) { // suppress menu items for hgTracks links (e.g. Next/Prev map items). } else { var item; if (title === "zoomInMore") // avoid showing menu item that says // "Show details for zoomInMore..." (redmine 2447) item = rightClick.makeImgTag("book.png") + " Show details..."; else item = rightClick.makeImgTag("book.png")+" Show details for "+ title + "..."; o[item] = {onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked,menuObject,"followLink"); return true; } }; any = true; } } if (any) { menu.push($.contextMenu.separator); menu.push(o); } } } if (rightClick.selectedMenuItem && rec) { // Add cfg options at just shy of end... o = {}; if (tdbIsLeaf(rec)) { if (rec.configureBy !== 'none' && (!tdbIsCompositeSubtrack(rec) || rec.configureBy !== 'clickThrough')) { // Note that subtracks never do clickThrough because // parentTrack cfg is the desired clickThrough o[rightClick.makeImgTag("wrench.png")+" Configure "+rec.shortLabel] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_popup"); return true; } }; } if (rec.parentTrack) { o[rightClick.makeImgTag("folderWrench.png")+" Configure "+ rec.parentLabel + " track set..."] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked,menuObject,"hgTrackUi_follow"); return true; } }; } } else { o[rightClick.makeImgTag("folderWrench.png")+" Configure "+rec.shortLabel + " track set..."] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "hgTrackUi_follow"); return true; } }; } if (jQuery.floatMgr) { o[(rightClick.selectedMenuItem.id === rightClick.floatingMenuItem ? selectedImg : blankImg) + " float"] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "float"); return true; } }; } menu.push($.contextMenu.separator); menu.push(o); } menu.push($.contextMenu.separator); if (hgTracks.highlight) { if (hgTracks.highlight.search(getDb() + '.') === 0) { var currentlySeen = ($('#highlightItem').length > 0); o = {}; // Jumps to highlight when not currently seen in image var text = (currentlySeen ? " Zoom" : " Jump") + " to highlighted region"; o[rightClick.makeImgTag("highlightZoom.png") + text] = { onclick: rightClick.makeHitCallback('jumpToHighlight') }; if ( currentlySeen ) { // Remove only when seen o[rightClick.makeImgTag("highlightRemove.png") + " Remove highlighting"] = { onclick: rightClick.makeHitCallback('removeHighlight') }; } menu.push(o); } } // Add view image at end o = {}; o[rightClick.makeImgTag("eye.png") + " View image"] = { onclick: function(menuItemClicked, menuObject) { rightClick.hit(menuItemClicked, menuObject, "viewImg"); return true; } }; menu.push(o); return menu; }, { beforeShow: function(e) { // console.log(mapItems[rightClick.selectedMenuItem]); rightClick.selectedMenuItem = rightClick.findMapItem(e); // XXXX? posting.blockUseMap = true; return true; }, hideTransition:'hide', // hideCallback fails if these are not defined. hideSpeed:10, hideCallback: function() { $('p.btn.blueButtons').removeClass('blueButtons'); $('tr.trDraggable.greenRows').removeClass('greenRows'); } }); return; } }; ////////////////////////////////// //// external tools //// ////////////////////////////////// function showExtToolDialog() { /* show the 'send to external tool' dialog */ // information about external tools is stored in the extTools global list // defined by a "; + var reg = new RegExp(srcPattern); + var a = reg.exec(strippedJsFiles.jsFiles[i]); + if (a && a[1]) { + if (a[1].match("inline")) { + inlinePath = a[1]; + //alert("SRC found: "+a[1]); // DEBUG REMOVE + } + } + } + } + if (inlinePath !== "") { + //alert("inlinePath found: "+inlinePath); // DEBUG REMOVE + var js = genomePos.fetchInlineJs(inlinePath); + //alert(js); // DEBUG REMOVE + response += (""); + newJson = scrapeVariable(response, "hgTracks"); + } + } + //alert(JSON.stringify(newJson)); // DEBUG Example var oldJson = hgTracks; var valid = false; if (!newJson) { var stripped = {}; stripJsEmbedded(response, true, stripped); if ( ! stripped.warnMsg ) warn("hgTracks object is missing from the response"); } else { if (this.id) { if (newJson.trackDb[this.id]) { var visibility = vis.enumOrder[newJson.trackDb[this.id].visibility]; var limitedVis; if (newJson.trackDb[this.id].limitedVis) limitedVis = vis.enumOrder[newJson.trackDb[this.id].limitedVis]; if (this.newVisibility && limitedVis && this.newVisibility !== limitedVis) // see redmine 1333#note-9 alert("There are too many items to display the track in " + this.newVisibility + " mode."); var rec = oldJson.trackDb[this.id]; rec.limitedVis = newJson.trackDb[this.id].limitedVis; vis.update(this.id, visibility); valid = true; } else { warn("Invalid hgTracks.trackDb received from the server"); } } else { valid = true; } } if (valid) { if (imageV2.enabled && this.id && this.cmd && this.cmd !== 'wholeImage' && this.cmd !== 'selectWholeGene' && !newJson.virtChromChanged) { // Extract ... and update appropriate row in imgTbl; // this updates src in img_left_ID, img_center_ID and img_data_ID // and map in map_data_ID var id = this.id; if (imageV2.updateImgForId(response, id, false)) { imageV2.afterReload(id); imageV2.updateBackground(response); // Added by galt to update window separators } else { warn("Couldn't parse out new image for id: " + id); // Very helpful when debugging and alert doesn't render the html: //alert("Couldn't parse out new image for id: " + id+"BR"+response); } } else { if (imageV2.enabled) { // Implement in-place updating of hgTracks image // GALT delaying this until after newJson updated in hgTracks so disguising works //genomePos.setByCoordinates(newJson.chromName, newJson.winStart + 1, newJson.winEnd); $("input[name='c']").val(newJson.chromName); $("input[name='l']").val(newJson.winStart); $("input[name='r']").val(newJson.winEnd); if (newJson.cgiVersion !== oldJson.cgiVersion || newJson.virtChromChanged) { // Must reload whole page because of a new version on the server; // this should happen very rarely. Note that we have already updated // position based on the user's action. imageV2.fullReload(); } else { // Will rebuild image adding new, removing old and resorting tracks imageV2.updateImgForAllIds(response,oldJson,newJson); imageV2.updateChromImg(response); imageV2.updateBackground(response); // Added by galt to update window separators hgTracks = newJson; genomePos.original = undefined; genomePos.setByCoordinates(hgTracks.chromName, hgTracks.winStart + 1, hgTracks.winEnd); // MOVED HERE GALT initVars(); imageV2.afterReload(); } } else { warn("ASSERT: Attempt to update track without advanced javascript features."); } } if (hgTracks.measureTiming) { imageV2.updateTiming(response); } } if (this.disabledEle) { this.disabledEle.removeAttr('disabled'); } if (this.loadingId) { hideLoadingImage(this.loadingId); } jQuery('body').css('cursor', ''); if (valid && this.currentId) { var top = $(document.getElementById("tr_" + this.currentId)).position().top; $(window).scrollTop(top - this.currentIdYOffset); } }, loadRemoteTracks: function () { if (hgTracks.trackDb) { for (var id in hgTracks.trackDb) { var rec = hgTracks.trackDb[id]; if (rec.type === "remote") { if ($("#img_data_" + id).length > 0) { // load the remote track renderer via jsonp rec.loadingId = showLoadingImage("tr_" + id); var script = document.createElement('script'); var pos = parsePosition(genomePos.get()); var name = rec.remoteTrack || id; script.setAttribute('src', rec.url + "?track=" + name + "&jsonp=imageV2.remoteTrackCallback&position=" + encodeURIComponent(pos.chrom + ":" + pos.start + "-" + pos.end) + "&pix=" + $('#imgTbl').width() ); document.getElementsByTagName('head')[0].appendChild(script); } } } } }, remoteTrackCallback: function (rec) // jsonp callback to load a remote track. { if (rec.error) { alert("retrieval from remote site failed with error: " + rec.error); } else { var remoteTrack = rec.track; for (var track in hgTracks.trackDb) { if (hgTracks.trackDb[track].remoteTrack === remoteTrack) { $('#img_data_' + track).attr('style', "left:-116px; top: -23px;"); $('#img_data_' + track).attr('height', rec.height); // XXXX use width in some way? // $('#img_data_' + track).attr('width', rec.width); $('#img_data_' + track).attr('width', $('#img_data_ruler').width()); $('#img_data_' + track).attr('src', rec.img); /* jshint loopfunc: true */// function inside loop works and replacement is awkward. $('#td_data_' + track + ' > div').each(function(index) { if (index === 1) { var style = $(this).attr('style'); style = style.replace(/height:\s*\d+/i, "height:" + rec.height); $(this).attr('style', style); } }); var style = $('#p_btn_' + track).attr('style'); style = style.replace(/height:\s*\d+/i, "height:" + rec.height); $('#p_btn_' + track).attr('style', style); if (hgTracks.trackDb[track].loadingId) { hideLoadingImage(hgTracks.trackDb[track].loadingId); } } } } }, navigateButtonClick: function (ele) // called from hgTracks.c { // code to update just the imgTbl in response to navigation buttons (zoom-out etc.). if (imageV2.inPlaceUpdate) { var params = ele.name + "=" + ele.value; $(ele).attr('disabled', 'disabled'); // dinking navigation needs additional data if (ele.name === "hgt.dinkLL" || ele.name === "hgt.dinkLR") { params += "&dinkL=" + $("input[name='dinkL']").val(); } else if (ele.name === "hgt.dinkRL" || ele.name === "hgt.dinkRR") { params += "&dinkR=" + $("input[name='dinkR']").val(); } imageV2.navigateInPlace(params, $(ele), false); return false; } else { return true; } }, updateButtonClick: function (ele) // UNUSED? { // code to update the imgTbl based on changes in the track controls. // This is currently experimental code and is dead in the main branch. if (imageV2.mapIsUpdateable) { var data = ""; $("select").each(function(index, o) { var cmd = $(this).val(); if (cmd === "hide") { if (hgTracks.trackDb[this.name]) { alert("Need to implement hide"); } } else { if ( ! hgTracks.trackDb[this.name] || cmd !== vis.enumOrder[hgTracks.trackDb[this.name].visibility]) { if (data.length > 0) { data = data + "&"; } data = data + this.name + "=" + cmd; } } }); if (data.length > 0) { imageV2.navigateInPlace(data, null, false); } return false; } else { return true; } }, navigateInPlace: function (params, disabledEle, keepCurrentTrackVisible) { // request an hgTracks image, using params // disabledEle is optional; this element will be enabled when update is complete // If keepCurrentTrackVisible is true, we try to maintain relative position of the item // under the mouse after the in-place update. // Tim thinks we should consider disabling all UI input while we are doing in-place update. // TODO: waitOnFuction? // No ajax image update if there are too many tracks! if (imageV2.manyTracks()) { imageV2.fullReload(params); return false; // Shouldn't return from fullReload but I have seen it in FF } // If UCSC Genes (or any suggestion) is supposed to be made visible, then do so if ($("#suggestTrack").length && $('#hgFindMatches').length) vis.makeTrackVisible($("#suggestTrack").val()); jQuery('body').css('cursor', 'wait'); var currentId, currentIdYOffset; if (keepCurrentTrackVisible) { var item = rightClick.currentMapItem || imageV2.lastTrack; if (item) { var top = $(document.getElementById("tr_" + item.id)).position().top; if (top >= $(window).scrollTop() || top < $(window).scrollTop() + $(window).height()) { // don't bother if the item is not currently visible. currentId = item.id; currentIdYOffset = top - $(window).scrollTop(); } } } $.ajax({ type: "GET", url: "../cgi-bin/hgTracks", data: cart.addUpdatesToUrl(params + "&hgt.trackImgOnly=1&hgt.ideogramToo=1&hgsid=" + getHgsid()), dataType: "html", trueSuccess: imageV2.updateImgAndMap, success: catchErrorOrDispatch, error: errorHandler, cmd: 'wholeImage', loadingId: showLoadingImage("imgTbl"), disabledEle: disabledEle, currentId: currentId, currentIdYOffset: currentIdYOffset, cache: false }); }, disguiseHighlight: function(position) // disguise highlight position { pos = parsePositionWithDb(position); // DISGUISE if (hgTracks.virtualSingleChrom && (pos.chrom.search("virt") === 0)) { var positionStr = pos.chrom+":"+pos.start+"-"+pos.end; var newPosition = genomePos.disguisePosition(positionStr); var newPos = parsePosition(newPosition); pos.chrom = newPos.chrom; pos.start = newPos.start; pos.end = newPos.end; } return pos.db+"."+pos.chrom+":"+pos.start+"-"+pos.end+pos.color; }, undisguiseHighlight: function(pos) // undisguise highlight pos { // UN-DISGUISE if (hgTracks.virtualSingleChrom && (pos.chrom.search("virt") !== 0)) { var position = pos.chrom+":"+pos.start+"-"+pos.end; var newPosition = genomePos.undisguisePosition(position); var newPos = parsePosition(newPosition); if (newPos) { pos.chrom = newPos.chrom; pos.start = newPos.start; pos.end = newPos.end; } } }, highlightRegion: function() // highlight vertical region in imgTbl based on hgTracks.highlight (#709). { var pos; var hexColor = '#FFAAAA'; $('.highlightItem').remove(); if (hgTracks.highlight) { var hlArray = hgTracks.highlight.split("|"); // support multiple highlight items for (var i = 0; i < hlArray.length; i++) { hlString = hlArray[i]; pos = parsePositionWithDb(hlString); // UN-DISGUISE imageV2.undisguiseHighlight(pos); if (pos) { pos.start--; // make start 0-based to match hgTracks.winStart if (pos.color) hexColor = pos.color; } if (pos && pos.chrom === hgTracks.chromName && pos.db === getDb() && pos.start <= hgTracks.imgBoxPortalEnd && pos.end >= hgTracks.imgBoxPortalStart) { var portalWidthBases = hgTracks.imgBoxPortalEnd - hgTracks.imgBoxPortalStart; var portal = $('#imgTbl td.tdData')[0]; var leftPixels = $(portal).offset().left + 3; // 3 for borders and cgi item calcs ?? var pixelsPerBase = ($(portal).width() - 2) / portalWidthBases; var clippedStartBases = Math.max(pos.start, hgTracks.imgBoxPortalStart); var clippedEndBases = Math.min(pos.end, hgTracks.imgBoxPortalEnd); var widthPixels = (clippedEndBases - clippedStartBases) * pixelsPerBase; if (hgTracks.revCmplDisp) leftPixels += (hgTracks.imgBoxPortalEnd - clippedEndBases) * pixelsPerBase - 1; else leftPixels += (clippedStartBases - hgTracks.imgBoxPortalStart) * pixelsPerBase; // Impossible to get perfect... Okay to overrun by a pixel on each side leftPixels = Math.floor(leftPixels); widthPixels = Math.ceil(widthPixels); if (widthPixels < 2) { widthPixels = 3; leftPixels -= 1; } var area = jQuery("
"); $(area).css({ backgroundColor: hexColor, // display: 'none' left: leftPixels + 'px', top: $('#imgTbl').offset().top + 1 + 'px', width: widthPixels + 'px', height: $('#imgTbl').css('height') }); $(area).data({leftPixels: leftPixels, widthPixels: widthPixels});// needed by dragScroll // Larry originally appended to imgTbl, but discovered that doesn't work on IE 8 and 9. $('body').append($(area)); // z-index is done in css class, so highlight is beneath transparent data images. // NOTE: ideally highlight would be below transparent blue-lines, but THAT is a // background-image so z-index can't get below it! PS/PDF looks better for blue-lines! } } } }, backSupport: (window.History.enabled !== undefined), // support of our back button via: history: null, // jquery.history.js and HTML5 history API setupHistory: function () { // Support for back-button using jquery.history.js. // Sets up the history and initializes a state. // Since ajax updates leave the browser cached pages different from the server state, // simple back-button fails. Using a 'dirty flag' we had forced an update from server, // whenever the back button was hit, meaning there was no going back from server-state! // NOW using the history API, the back-button triggers a 'statechange' event which can // contain data. We save the position in the data and ajax update the image when the // back-button is pressed. This works great for going back through ajax-updated position // changes, but is a bit messier when going back past a full-page retrieved state (as // described below). // NOTE: many things besides position could be ajax updated (e.g. track visibility). We are // using the back-button to keep track of position only. Since the image should be updated // every-time the back button is pressed, all track settings should persist (not go back). // What will occasionally fail is vis box state and group expansion state. This is because // the back-button goes to a browser cached page and then the image alone is updated. imageV2.history = window.History; // The 'statechange' function triggerd by the back-button. // Whenever the position changes, then use ajax-update to refetch the position imageV2.history.Adapter.bind(window,'statechange',function(){ var prevDbPos = imageV2.history.getState().data.lastDbPos; var prevPos = imageV2.history.getState().data.position; var curDbPos = hgTracks.lastDbPos; if (prevDbPos && prevDbPos !== curDbPos) { // NOTE: this function is NOT called when backing past a full retrieval boundary genomePos.set(decodeURIComponent(prevPos)); imageV2.navigateInPlace("" + prevDbPos, null, false); } }); // With history support it is best that most position changes will ajax-update the image // This ensures that the 'go' and 'refresh' button will do so unless the chrom changes. $("input[value='go'],input[value='refresh']").click(function () { var newPos = genomePos.get().replace(/,/g,''); if (newPos.length > 2000) { alert("Sorry, you cannot paste identifiers or sequences with more than 2000 characters into this box."); $('input[name="hgt.positionInput"]').val(""); return false; } var newDbPos = hgTracks.lastDbPos; if ( ! imageV2.manyTracks() ) { var newChrom = newPos.split(':')[0]; var oldChrom = genomePos.getOriginalPos().split(':')[0]; if (newChrom === oldChrom) { imageV2.markAsDirtyPage(); imageV2.navigateInPlace("position=" + newPos, null, false); window.scrollTo(0,0); return false; } } // If not just image update AND there are vis updates waiting... if (cart.updatesWaiting()) { var url = "../cgi-bin/hgTracks?position=" + newPos + "&" + cart.varsToUrlData({ 'db': getDb(), 'hgsid': getHgsid() }); window.location.assign(url); return false; } // redirect to hgBlat if the input looks like a DNA sequence // minimum length=19 so we do not accidentally redirect to hgBlat for a gene identifier // like ATG5 var dnaRe = new RegExp("^(>[^\n\r ]+[\n\r ]+)?(\\s*[actgnACTGN \n\r]{19,}\\s*)$"); if (dnaRe.test(newPos)) { var blatUrl = "hgBlat?type=BLAT%27s+guess&userSeq="+newPos; window.location.href = blatUrl; return false; } return true; }); // Have vis box changes update cart through ajax. This helps keep page/cart in sync. vis.initForAjax(); // We reach here from these possible paths: // A) Forward: Full page retrieval: hgTracks is first navigated to (or chrom change) // B) Back-button past a full retrieval (B in: ->A,->b,->c(full page),->d,<-c,<-B(again)) // B1) Dirty page: at least one non-position change (e.g. 1 track vis changed in b) // B2) Clean page: only position changes from A->b->| var curPos = encodeURIComponent(genomePos.get().replace(/,/g,'')); var curDbPos = hgTracks.lastDbPos; var cachedPos = imageV2.history.getState().data.position; var cachedDbPos = imageV2.history.getState().data.lastDbPos; // A) Forward: Full page retrieval: hgTracks is first navigated to (or chrom change) if (!cachedDbPos) { // Not a back-button operation // set the current position into history outright (will replace). No img update needed imageV2.setInHistory(true); } else { // B) Back-button past a full retrieval genomePos.set(decodeURIComponent(cachedPos)); // B1) Dirty page: at least one non-position change if (imageV2.isDirtyPage()) { imageV2.markAsCleanPage(); // Only forcing a full page refresh if chrom changes var cachedChrom = decodeURIComponent(cachedPos).split(':')[0]; var curChrom = decodeURIComponent( curPos).split(':')[0]; if (cachedChrom === curChrom) { imageV2.navigateInPlace("db="+getDb()+"&"+cachedDbPos, null, false); } else { imageV2.fullReload(); } } else { // B2) Clean page: only position changes from a->b if (cachedDbPos !== curDbPos) { imageV2.navigateInPlace("db="+getDb()+"&"+cachedDbPos, null, false); } } // Special because FF is leaving vis drop-downs disabled vis.restoreFromBackButton(); } }, setInHistory: function (fullPageLoad) { // Keep a position history and allow the back-button to work (sort of) // replaceState on initial page load, pushState on each advance // When call triggered by back button, the lastPos===newPos, so no action. var lastDbPos = imageV2.history.getState().data.lastDbPos; var newPos = encodeURIComponent(genomePos.get().replace(/,/g,'')); // no commas var newDbPos = hgTracks.lastDbPos; // A full page load could be triggered by back-button, but then there will be a lastPos // if this is the case then don't set the position in history again! if (fullPageLoad && lastDbPos) return; if (!lastDbPos || lastDbPos !== newDbPos) { // Swap the position into the title var title = $('TITLE')[0].text; var ttlWords = title.split(' '); if (ttlWords.length >= 2) { for (var i=1; i < ttlWords.length; i++) { if (ttlWords[i].indexOf(':') >= 0) { ttlWords[i] = genomePos.get(); } } title = ttlWords.join(' '); } else title = genomePos.get(); var sid = getHgsid(); if (fullPageLoad) { // Should only be on initial set-up: first navigation to page imageV2.history.replaceState({lastDbPos: newDbPos, position: newPos, hgsid: + sid },title, "hgTracks?db="+getDb()+"&"+newDbPos+"&hgsid="+sid); } else { // Should be when advancing (not-back-button) imageV2.history.pushState({lastDbPos: newDbPos, position: newPos, hgsid: + sid },title, "hgTracks?db="+getDb()+"&"+newDbPos+"&hgsid="+sid); } } } }; ////////////////////// //// track search //// ////////////////////// var trackSearch = { searchKeydown: function (event) { if (event.which === 13) { // Required to fix problem on IE and Safari where value of hgt_tSearch is "-" // (i.e. not "Search"). // NOTE: must match TRACK_SEARCH_PAGER in hg/inc/searchTracks.h $("input[name=hgt_tsPage]").val(0); $('#trackSearch').submit(); // This doesn't work with IE or Safari. // $('#searchSubmit').click(); } }, init: function () { // Track search uses tabs if ($("#tabs").length > 0) { // Search page specific code var val = $('#currentTab').val(); $("#tabs").tabs({ show: function(event, ui) { $('#currentTab').val(ui.panel.id); }, select: function(event, ui) { findTracks.switchTabs(ui); } }); $('#tabs').show(); $("#tabs").tabs('option', 'selected', '#' + val); if (val === 'simpleTab' && $('div#found').length < 1) { $('input#simpleSearch').focus(); } $("#tabs").css('font-family', jQuery('body').css('font-family')); $("#tabs").css('font-size', jQuery('body').css('font-size')); $('.submitOnEnter').keydown(trackSearch.searchKeydown); findTracks.normalize(); findTracks.updateMdbHelp(0); } } }; /////////////// //// READY //// /////////////// $(document).ready(function() { // The page may be reached via browser history (back button) // If so, then this code should detect if the image has been changed via js/ajax // and will reload the image if necessary. // NOTE: this is needed for IE but other browsers can detect the dirty page much earlier if (!imageV2.backSupport) { if (imageV2.isDirtyPage()) { // mark as non dirty to avoid infinite loop in chrome. imageV2.markAsCleanPage(); jQuery('body').css('cursor', 'wait'); window.location = "../cgi-bin/hgTracks?hgsid=" + getHgsid(); return false; } } initVars(); imageV2.loadSuggestBox(); if ($('#pdfLink').length === 1) { $('#pdfLink').click(function(i) { var thisForm = normed($('#TrackForm')); if (thisForm) { //alert("posting form:"+$(thisForm).attr('name')); updateOrMakeNamedVariable($(thisForm),'hgt.psOutput','on'); return postTheForm($(thisForm).attr('name'),this.href); } return true; }); } if (imageV2.enabled) { // Make imgTbl allow drag reorder of imgTrack rows dragReorder.init(); var imgTable = $(".tableWithDragAndDrop"); if ($(imgTable).length > 0) { $(imgTable).tableDnD({ onDragClass: "trDrag", dragHandle: "dragHandle", scrollAmount: 40, onDragStart: function(ev, table, row) { mouse.saveOffset(ev); $(document).bind('mousemove',posting.blockTheMapOnMouseMove); // Can drag a contiguous set of rows if dragging blue button table.tableDnDConfig.dragObjects = [ row ]; // defaults to just the one var btn = $( row ).find('p.btnBlue'); // btnBlue means cursor over left button if (btn.length === 1) { table.tableDnDConfig.dragObjects = dragReorder.getContiguousRowSet(row); var compositeSet = dragReorder.getCompositeSet(row); if (compositeSet && compositeSet.length > 0) $( compositeSet ).find('p.btn').addClass('blueButtons');// blue persists } }, onDrop: function(table, row, dragStartIndex) { var compositeSet = dragReorder.getCompositeSet(row); if (compositeSet && compositeSet.length > 0) $( compositeSet ).find('p.btn').removeClass('blueButtons');// blue persists if ($(row).attr('rowIndex') !== dragStartIndex) { // NOTE Even if dragging a contiguous set of rows, // still only need to check the one under the cursor. if (dragReorder.setOrder) { dragReorder.setOrder(table); } dragReorder.zipButtons( table ); } $(document).unbind('mousemove',posting.blockTheMapOnMouseMove); // Timeout necessary incase the onDrop over map item. onDrop takes precedence. setTimeout(posting.allowMapClicks,100); } }); } // Drag scroll init if (hgTracks.imgBoxPortal) { // Turn on drag scrolling. $("div.scroller").panImages(); } // Retrieve tracks via AJAX that may take too long to draw initialliy (i.e. a remote bigWig) var retrievables = $('#imgTbl').find("tr.mustRetrieve"); if ($(retrievables).length > 0) { $(retrievables).each( function (i) { var trackName = $(this).attr('id').substring(3); imageV2.requestImgUpdate(trackName,"",""); }); } imageV2.loadRemoteTracks(); makeItemsByDrag.load(); // Any highlighted region must be shown and warnBox must play nice with it. imageV2.highlightRegion(); // When warnBox is dismissed, any image highlight needs to be redrawn. $('#warnOK').click(function (e) { imageV2.highlightRegion();}); // Also extend the function that shows the warn box so that it too redraws the highlight. showWarnBox = (function (oldShowWarnBox) { function newShowWarnBox() { oldShowWarnBox.apply(); imageV2.highlightRegion(); } return newShowWarnBox; })(showWarnBox); } // Drag select in chromIdeogram if ($('img#chrom').length === 1) { if ($('area.cytoBand').length >= 1) { $('img#chrom').chromDrag(); } } // Track search uses tabs trackSearch.init(); // Drag select initialize if (imageV2.enabled) { // moved from window.load(). dragSelect.load(true); if ($('#hgTrackUiDialog')) $('#hgTrackUiDialog').hide(); // Don't load contextMenu if jquery.contextmenu.js hasn't been loaded if (jQuery.fn.contextMenu) { rightClick.load(imageV2.imgTbl); } } // jquery.history.js Back-button support if (imageV2.enabled && imageV2.backSupport) { imageV2.setupHistory(); } });