be1a77e1e634b439617d8c04195a5ce90ae93e0d galt Wed Feb 24 13:15:15 2016 -0800 Removing DEBUG warnings from hgTracks.js multi-region code. diff --git src/hg/js/hgTracks.js src/hg/js/hgTracks.js index 6a746cd..4d4d39e 100644 --- src/hg/js/hgTracks.js +++ src/hg/js/hgTracks.js @@ -125,159 +125,147 @@ 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 - //warn("undisguisePosition position="+position); // DEBUG REMOVE 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; - //warn("start="+start+" end="+end); // DEBUG REMOVE 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; - //warn("cs="+cs+" ce="+ce); // DEBUG REMOVE if (newStart === -1) newStart = cs; newEnd = ce; } lastW = w; } } // return new virt undisguised position as a string var newPos = "virt:" + (newStart+1) + "-" + newEnd; - //warn("undisguisePosition newPos="+newPos); // DEBUG REMOVE return newPos; }, disguiseSize: function(position) // DISGUISE VMODE { // find the real size of the windows spanned // position should be a real chrom span - //warn("disguisePosition position="+position); // DEBUG REMOVE var pos = parsePosition(position); if (!pos) return 0; var start = pos.start - 1; var end = pos.end; var newSize = 0; var windows = null; - //warn("start="+start+" end="+end); // DEBUG REMOVE 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); - //warn("s="+s+" e="+e); // DEBUG REMOVE newSize += (e - s); } } } // return real size of the disguised position - //warn("disguiseSize newSize="+newSize); // DEBUG REMOVE return newSize; }, disguisePosition: function(position) // DISGUISE VMODE { // find the single-chrom range spanned // position should be virt - //warn("disguisePosition position="+position); // DEBUG REMOVE 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; - //warn("start="+start+" end="+end); // DEBUG REMOVE 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; - //warn("cs="+cs+" ce="+ce); // DEBUG REMOVE if (newStart === -1) newStart = cs; newEnd = ce; } lastW = w; } } // return new non-virt disguised position as a string var newPos = chromName + ":" + (newStart+1) + "-" + newEnd; - //warn("disguisePosition newPos="+newPos); // DEBUG REMOVE 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); @@ -410,53 +398,49 @@ 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; - //warn("length of hgTracks.windows = "+hgTracks.windows.length); // DEBUG REMOVE 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); - //warn("w.chromName="+w.chromName+" w.winStart="+w.winStart+" w.winEnd="+w.winEnd+" overlap?="+overlap+" virtStart="+virtStart); // DEBUG REMOVE 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); - //warn("s="+s+" e="+e+" virtStart="+virtStart+" virtEnd="+virtEnd); // DEBUG REMOVE } 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); - //warn("extend virtEnd="+virtEnd); // DEBUG REMOVE } 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); }, @@ -531,31 +515,30 @@ 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(); - //warn("positionDisplayDialog position="+position); // DEBUG REMOVE var positionDialog = $("#positionDialog")[0]; if (!positionDialog) { $("body").append("<div id='positionDialog'><span id='positionDisplayPosition'></span>"); positionDialog = $("#positionDialog")[0]; } if (hgTracks.windows) { var i,len; var str = position; if (!(hgTracks.virtualSingleChrom && (hgTracks.windows.length === 1))) { str += "<br>\n"; str += "<br>\n"; str += "<ul style='list-style-type:none; max-height:200px; padding:0; width:80%; overflow:hidden; overflow-y:scroll;'>\n"; for (i=0,len=hgTracks.windows.length; i < len; ++i) { var w = hgTracks.windows[i]; str += "<li>" + w.chromName + ":" + (w.winStart+1) + "-" + w.winEnd + "</li>\n"; @@ -1007,31 +990,30 @@ 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; - //warn("highlightThisRegion: newPosition="+newPosition); // DEBUG REMOVE 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); @@ -2442,37 +2424,35 @@ 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) { - //warn("hitFinish highlightItem chrom="+chrom+" chromStart="+chromStart+" chromEnd="+chromEnd); // DEBUG REMOVE // 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)); - //warn("result.chromStart="+result.chromStart+" result.chromEnd="+result.chromEnd); // DEBUG REMOVE 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 { @@ -3213,32 +3193,30 @@ }, uiDialog: function (response, status) { // Take html from hgTracks and put it up as a modal dialog. // make sure all links (e.g. help links) open up in a new window response = response.replace(/<a /ig, "<a target='_blank' "); var cleanHtml = response; cleanHtml = stripJsFiles(cleanHtml,false); // DEBUG msg with true cleanHtml = stripCssFiles(cleanHtml,false); // DEBUG msg with true cleanHtml = stripJsEmbedded(cleanHtml,false);// DEBUG msg with true cleanHtml = stripMainMenu(cleanHtml,false); // DEBUG msg with true - //alert(cleanHtml); // DEBUG REMOVE - $('#hgTracksDialog').html("<div id='pop' style='font-size:.9em;'>"+ cleanHtml +"</div>"); // Strategy for popups with js: // - jsFiles and CSS should not be included in html. Here they are shluped out. // - The resulting files ought to be loadable dynamically (with getScript()), // but this was not working nicely with the modal dialog // Therefore include files must be included with hgTracks CGI ! // - embedded js should not be in the popup box. // - Somethings should be in a popup.ready() function, and this is emulated below, // as soon as the cleanHtml is added // Since there are many possible popup cfg dialogs, the ready should be all inclusive. // -- popup.ready() -- Here is the place to do things that might otherwise go // into a $('#pop').ready() routine! @@ -3384,31 +3362,31 @@ var allVars = getAllVars($('#hgTrackUiDialog'), subtrack ); // Since 2010, when Tim changed this to only report changed vars instead of all form vars, // it no longer matches the behavior of hgTrackUi when called the non-popup way. // A few places in the hgTracks C code have been patched to explicitly set the cart vars // for some default checkboxes. So now this still means that QA must explicitly test // both paths through the code: as a separate full hgTracksUi page, and as a popup config window. // hgTrackUi always sends in its form all variables causing them to be explicitly set in the cart. // The popup only sends things that have changed, causing those changes to appear explicitly // and even then it skips over disabled form items. // There is some C code that was written before the popup config, // and it expects all the variables are set or none are. // If just some are set, and not the default ones, it gets confused. // I fixed just such a bug in the code that handles refSeq. // See commit daf92c0f9eb331ea60740e6802aabd241d4be363. var changedVars = varHashChanges(allVars,popUp.saveAllVars); - // DEBUG REMOVE + // DEBUG Examples: //debugDumpFormCollection("saveAllVars", popUp.saveAllVars); //debugDumpFormCollection("allVars", allVars); //debugDumpFormCollection("changedVars", changedVars); var newVis = changedVars[trackName]; // subtracks do not have "hide", thus '[]' var hide = (newVis && (newVis === 'hide' || newVis === '[]')); if ( ! normed($('#imgTbl')) ) { // On findTracks or config page if (objNotEmpty(changedVars)) cart.setVarsObj(changedVars); } else { // On image page if (hide) { if (objNotEmpty(changedVars)) cart.setVarsObj(changedVars); $(document.getElementById('tr_' + trackName)).remove(); @@ -3861,39 +3839,35 @@ else url += '&' + extraData; } window.location.assign(url); return false; } document.TrackHeaderForm.submit(); }, updateImgAndMap: function (response, status) { // Handle ajax response with an updated trackMap image, map and optional ideogram. // and maybe the redLines background too. // this.cmd can be used to figure out which menu item triggered this. // this.id === appropriate track if we are retrieving just a single track. - //warn("updateImgAndMap got here 0"); // DEBUG REMOVE GALT - // update local hgTracks.trackDb to reflect possible side-effects of ajax request. - //alert(response); //DEBUG REMOVE GALT - var newJson = scrapeVariable(response, "hgTracks"); - //alert(JSON.stringify(newJson)); // DEBUG REMOVE GALT + //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]; @@ -4142,54 +4116,50 @@ 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 - //console.warn("undisguiseHighlight: got here 0"); // DEBUG REMOVE if (hgTracks.virtualSingleChrom && (pos.chrom.search("virt") !== 0)) { var position = pos.chrom+":"+pos.start+"-"+pos.end; var newPosition = genomePos.undisguisePosition(position); - //console.warn("undisguiseHighlight: newPosition="+newPosition); // DEBUG REMOVE 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) { - //console.warn("highlightRegion: hgTracks.highlight="+hgTracks.highlight); // DEBUG REMOVE pos = parsePositionWithDb(hgTracks.highlight); - //console.warn("highlightRegion: pos.chrom="+pos.chrom); // DEBUG REMOVE // 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);