diff --git a/example.html b/example.html index d08be29..4a393a8 100644 --- a/example.html +++ b/example.html @@ -2,10 +2,45 @@ -
+ + +

Fixed width

+
+ For fixed width, the PV containing div needs to have a set width. +
+
+ +

Dynamic size

+
+ Without set width, a DIV elemebt takes 100% of width of the parent element (window in this case). + Because ProtVista plugin is listening to its embedded iframe window resize event, it scales accordingly. +
+
+ +

Dynamic size with minimal width

+
+ It is possible to set a minimal width which the ProtVista plugin can take (600px here). +
+
+ + diff --git a/gulpfile.js b/gulpfile.js index feab5e2..3f5579d 100644 --- a/gulpfile.js +++ b/gulpfile.js @@ -162,7 +162,9 @@ gulp.task('build-browser-min',['copy-resources'], function() { return b.bundle() .pipe(source(outputFile + ".min.js")) .pipe(chmod(644)) - .pipe(streamify(uglify())) + .pipe(streamify(uglify().on('error', function(e){ + console.log(e); + }))) .pipe(gulp.dest(buildDir)); }); diff --git a/npm-shrinkwrap.json b/npm-shrinkwrap.json new file mode 100644 index 0000000..8fc57cb --- /dev/null +++ b/npm-shrinkwrap.json @@ -0,0 +1,9193 @@ +{ + "name": "ProtVista", + "version": "2.0.6", + "lockfileVersion": 1, + "requires": true, + "dependencies": { + "Base64": { + "version": "0.2.1", + "resolved": "https://registry.npmjs.org/Base64/-/Base64-0.2.1.tgz", + "integrity": "sha1-ujpCMHCOGGcFBl5mur3Uw1z2ACg=", + "dev": true + }, + "JSONStream": { + "version": "1.3.5", + "resolved": "https://registry.npmjs.org/JSONStream/-/JSONStream-1.3.5.tgz", + "integrity": 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"window-size": "0.1.0" + }, + "dependencies": { + "camelcase": { + "version": "1.2.1", + "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-1.2.1.tgz", + "integrity": "sha1-m7UwTS4LVmmLLHWLCKPqqdqlijk=", + "dev": true + } + } + }, + "yauzl": { + "version": "2.4.1", + "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.4.1.tgz", + "integrity": "sha1-lSj0QtqxsihOWLQ3m7GU4i4MQAU=", + "dev": true, + "requires": { + "fd-slicer": "~1.0.1" + } + } + } +} diff --git a/package.json b/package.json index 9b1aa49..a9bf0c6 100644 --- a/package.json +++ b/package.json @@ -4,7 +4,8 @@ "version": "2.0.6", "homepage": "https://github.com/ebi-uniprot/ProtVista", "author": "UniProt", - "contributors": [{ + "contributors": [ + { "name": "Leyla Jael Garcia Castro", "email": "ljgarcia@ebi.ac.uk" }, @@ -20,10 +21,12 @@ "bugs": { "url": "https://github.com/ebi-uniprot/ProtVista/issues" }, - "licenses": [{ - "type": "Apache 2", - "url": "https://github.com/ebi-uniprot/ProtVista/blob/master/LICENSE" - }], + "licenses": [ + { + "type": "Apache 2", + "url": "https://github.com/ebi-uniprot/ProtVista/blob/master/LICENSE" + } + ], "main": "src/FeaturesViewer", "config": { "classname": "FeaturesViewerTest", @@ -59,7 +62,7 @@ "gulp-jshint": "^1.8.4", "gulp-minify-css": "^1.2.0", "gulp-mocha": "^1.0.0", - "gulp-mocha-phantomjs": "^0.5.0", + "gulp-mocha-phantomjs": "^0.12.2", "gulp-rename": "^1.2.0", "gulp-sass": "^1.3.2", "gulp-streamify": "0.0.5", @@ -69,13 +72,16 @@ "mkdirp": "^0.5.0", "mocha": "~1.20.1", "mocha-sonar-reporter": "^0.1.2", - "phantomjs": "^1.9.1", + "phantomjs-prebuilt": "^2.1.4", "sinon": "^1.17.3", "sniper": "^0.2.16", "vinyl-source-stream": "^1.0.0", "watchify": "^3.2.3", "xunit-file": "0.0.6" }, + "overrides": { + "graceful-fs": "^4.2.9" + }, "shields": { "test": { "img": "https://travis-ci.org/ebi-uniprot/ProtVista.svg?branch=master", @@ -105,4 +111,4 @@ "domains", "protein" ] -} \ No newline at end of file +} diff --git a/src/CategoryFactory.js b/src/CategoryFactory.js index 3ddef37..79a6f6c 100644 --- a/src/CategoryFactory.js +++ b/src/CategoryFactory.js @@ -25,7 +25,13 @@ var Category = function(name, data, catInfo, fv, container) { category.categoryContainer = container.append('div') .attr('class', 'up_pftv_category'); - category.header = category.categoryContainer.append('a') + var headerRow = category.categoryContainer.append('div') + .style('display', 'table-caption') + .append('div') + .style('display', 'table') + .style('width', '100%'); + + category.header = headerRow.append('a') .attr('class', 'up_pftv_category-name up_pftv_arrow-right') .attr('title', category.name) .text(catInfo.label) @@ -34,12 +40,14 @@ var Category = function(name, data, catInfo, fv, container) { category.propagateSelection(); }); - category.viewerContainer = category.categoryContainer.append('div') + category.viewerContainer = headerRow.append('div') .attr('class', 'up_pftv_category-viewer'); category.tracksContainer = category.categoryContainer.append('div') - .attr('class', 'up_pftv_category-tracks') - .style('display','none'); + .style('display','table-row') + .append('div') + .attr('class', 'up_pftv_category-tracks') + .style('display','none'); }; Category.prototype.reset = function() { diff --git a/src/Constants.js b/src/Constants.js index 6586bdd..8a9b32f 100644 --- a/src/Constants.js +++ b/src/Constants.js @@ -34,118 +34,124 @@ var uniprotSources = [ ]; var allSources = uniprotSources.slice(0); var externalSource; -var allCategories = Config.categories; +var allCategories = Config.categories.slice(0); var allTrackNames = Config.trackNames; var downloadFormats = [{text: 'JSON', type: 'json', all: true}, {text: 'XML', type: 'xml', all: false}, {text: 'GFF', type: 'gff', all: false}]; var consequenceTypes = []; var Constants = function() { - return { - getBlastURL: function() { - return 'http://www.uniprot.org/blast/?about='; - }, - getNoBlastTypes: function() { - return ['helix', 'strand', 'turn', 'disulfid', 'crosslnk', 'variant']; - }, - getVisualizationTypes: function() { - return visualizationTypes; - }, - getDownloadFormats: function() { - return downloadFormats; - }, - getDataSources: function() { - return allSources; - }, - getUniProtDataSources: function() { - return uniprotSources; - }, - getExternalDataSource: function() { - return externalSource; - }, - getUniProtSource: function() { - return uniprotSource; - }, - addSource: function(source) { - allSources.push(source); - externalSource = source; - }, - addConsequenceType: function(consequence) { - consequenceTypes.push(consequence); - }, - getConsequenceTypes: function() { - return _.uniq(consequenceTypes); - }, - clearDataSources: function() { - allSources = []; - }, - getCategoryNamesInOrder: function() { - return allCategories; - }, - setCategoryNamesInOrder: function(categories) { - allCategories = categories; - }, - setOrderForCategoryNames: function(categoryNames) { - var orderedCategories = []; - _.each(categoryNames, function(name) { - var position = 0; - var category = _.find(allCategories, function(cat, index) { - position = index; - return cat.name.toUpperCase() === name.toUpperCase(); + return { + getBlastURL: function() { + return 'http://www.uniprot.org/blast/?about='; + }, + getNoBlastTypes: function() { + return ['helix', 'strand', 'turn', 'disulfid', 'crosslnk', 'variant']; + }, + getVisualizationTypes: function() { + return visualizationTypes; + }, + getDownloadFormats: function() { + return downloadFormats; + }, + getDataSources: function() { + return allSources; + }, + getUniProtDataSources: function() { + return uniprotSources; + }, + getExternalDataSource: function() { + return externalSource; + }, + getUniProtSource: function() { + return uniprotSource; + }, + addSource: function(source) { + allSources.push(source); + externalSource = source; + }, + initSources: function(){ + allSources = uniprotSources.slice(0); + allCategories = Config.categories.slice(0); + consequenceTypes = []; + externalSource = undefined; + }, + addConsequenceType: function(consequence) { + consequenceTypes.push(consequence); + }, + getConsequenceTypes: function() { + return _.uniq(consequenceTypes); + }, + clearDataSources: function() { + allSources = []; + }, + getCategoryNamesInOrder: function() { + return allCategories; + }, + setCategoryNamesInOrder: function(categories) { + allCategories = categories; + }, + setOrderForCategoryNames: function(categoryNames) { + var orderedCategories = []; + _.each(categoryNames, function(name) { + var position = 0; + var category = _.find(allCategories, function(cat, index) { + position = index; + return cat.name.toUpperCase() === name.toUpperCase(); + }); + if (category) { + orderedCategories.push(category); + allCategories.splice(position, 1); + } }); - if (category) { - orderedCategories.push(category); - allCategories.splice(position, 1); - } - }); - allCategories = orderedCategories.concat(allCategories); - }, - convertNameToLabel: function(name) { - var label = name.replace(/_/g, ' '); - label = label.charAt(0).toUpperCase() + label.slice(1).toLowerCase(); - return label; - }, - getCategoryInfo: function(categoryName) { - var exist = _.find(allCategories, function(cat) { - return cat.name === categoryName; - }); - return exist ? exist - : {name: categoryName, label: Constants.convertNameToLabel(categoryName), - visualizationType: Constants.getVisualizationTypes().basic}; - }, - addCategories: function(categories) { - var index = 0; - _.each(categories, function (newCat) { + allCategories = orderedCategories.concat(allCategories); + }, + convertNameToLabel: function(name) { + var label = name.replace(/_/g, ' '); + label = label.charAt(0).toUpperCase() + label.slice(1).toLowerCase(); + return label; + }, + getCategoryInfo: function(categoryName) { var exist = _.find(allCategories, function(cat) { - return cat.name === newCat.name; + return cat.name === categoryName; }); - if (exist) { - exist.label = newCat.label; - exist.visualizationType = newCat.visualizationType; - } else { - allCategories.splice(index, 0, newCat); - index++; - } - }); - }, - getTrackNames: function() { - return allTrackNames; - }, - setTrackNames: function(trackNames) { - allTrackNames = trackNames; - }, - addTrackTypes: function(tracksToAdd) { - _.each(tracksToAdd, function(elem, key) { - key = key.toLowerCase(); - allTrackNames[key] = elem; - }); - }, - getTrackInfo: function(trackName) { - var name = trackName.toLowerCase(); - return this.getTrackNames()[name] ? this.getTrackNames()[name] - : {label: Constants.convertNameToLabel(name), tooltip:''}; - } - }; + return exist ? exist + : {name: categoryName, label: Constants.convertNameToLabel(categoryName), + visualizationType: Constants.getVisualizationTypes().basic}; + }, + addCategories: function(categories) { + var index = 0; + _.each(categories, function (newCat) { + var exist = _.find(allCategories, function(cat) { + return cat.name === newCat.name; + }); + if (exist) { + exist.label = newCat.label; + exist.visualizationType = newCat.visualizationType; + } else { + allCategories.splice(index, 0, newCat); + index++; + } + }); + }, + getTrackNames: function() { + return allTrackNames; + }, + setTrackNames: function(trackNames) { + allTrackNames = trackNames; + }, + addTrackTypes: function(tracksToAdd) { + _.each(tracksToAdd, function(elem, key) { + key = key.toLowerCase(); + allTrackNames[key] = elem; + }); + }, + getTrackInfo: function(trackName) { + var name = trackName.toLowerCase(); + return this.getTrackNames()[name] ? this.getTrackNames()[name] + : {label: Constants.convertNameToLabel(name), tooltip:''}; + } + }; }(); module.exports = Constants; diff --git a/src/DataLoader.js b/src/DataLoader.js index 9bd6d0f..acd0f2e 100644 --- a/src/DataLoader.js +++ b/src/DataLoader.js @@ -47,10 +47,55 @@ var setVariantData = function(source, d) { return datum; }; +/*** + * Sometimes in October 2020, the variation API changed. The purpose of this method is to reformat + * the variants in such a way that the rest of the applications gets the data in the expected format. + * @param variants + */ +var fixVariants = function(variants) +{ + variants.forEach(function(v){ + if (v.predictions) { + v.predictions.forEach(function(p){ + if (p.predAlgorithmNameType == 'PolyPhen'){ + v.polyphenPrediction = p.predictionValType; + v.polyphenScore = p.score; + } else if (p.predAlgorithmNameType == 'SIFT') { + v.siftPrediction = p.predictionValType; + v.siftScore = p.score; + } + }) + } + + if (v.alternativeSequence === undefined) { + v.alternativeSequence = "*"; + console.warn("Variant alternative sequence changed to * as no alternative sequence provided by the API", v); + } + }) +} + var DataLoader = function() { return { get: function(url) { - return $.getJSON(url); + //IE does not support data URI, therefore such data sources need to be parsed directly + return url.indexOf("data:") == 0 ? $.Deferred().resolve(JSON.parse(decodeURI(url).replace(/[^,]*,/, ''))) : $.getJSON(url); + // return $.getJSON(url); + }, + post: function(url, data, contentType, unpack) { + var settings = { + url: url, + data: data + }; + if (contentType !== undefined){ + settings.contentType = contentType; + } + return $.post(settings).then(function (data) { + if (unpack === undefined){ + return $.Deferred().resolve(data); + } else { + return unpack(data); + } + }); }, groupFeaturesByCategory: function(features, sequence, source, includeVariants) { features = groupEvidencesByCode(features); @@ -117,6 +162,7 @@ var DataLoader = function() { ]; }, processVariants: function(variants, sequence, source, evidenceAlreadyGrouped) { + fixVariants(variants); if (source && (source !== Constants.getUniProtSource())) { _.each(variants, function(variant) { delete variant.category; diff --git a/src/FeaturesViewer.js b/src/FeaturesViewer.js index 51f13b4..c56cf50 100644 --- a/src/FeaturesViewer.js +++ b/src/FeaturesViewer.js @@ -134,23 +134,27 @@ var createNavRuler = function(fv, container) { var navXScale = d3.scale.linear() .domain([1,fv.maxPos]) - .range([fv.padding.left, fv.width - fv.padding.right]); + .range(getFvXScaleRange(fv, true)); var svg = container .append('div') .attr('class', 'up_pftv_navruler') .append('svg') .attr('id','up_pftv_svg-navruler') - .attr('width', fv.width) + .attr('width', "100%") .attr('height', (navWithTrapezoid)); + // .attr('viewBox', function(){return "0,0," + fv.width + "," + navWithTrapezoid;}); var navXAxis = d3.svg.axis() - .scale(fv.xScale) + .scale(d3.scale.linear() + .domain(fv.xScale.domain()) + .range(getFvXScaleRange(fv, true))) .orient('bottom'); - svg.append('g') - .attr('class', 'x axis') - .call(navXAxis); + var xAxis = svg.append('g') + .attr('class', 'x axis'); + + xAxis.call(navXAxis); var viewport = d3.svg.brush() .x(navXScale) @@ -164,6 +168,10 @@ var createNavRuler = function(fv, container) { update(fv); viewport.updateTrapezoid(); }); + + viewport.xAxis = xAxis; + viewport.navXAxis = navXAxis; + viewport.on("brushstart", function () { closeTooltipAndPopup(fv); }); @@ -211,7 +219,7 @@ var createNavRuler = function(fv, container) { var begin = fv.globalContainer.select(".up_pftv_navruler .extent").attr("x"); var tWidth = fv.globalContainer.select(".up_pftv_navruler .extent").attr("width"); var end = (+begin) + (+tWidth); - var path = "M0," + (navWithTrapezoid) + "L0" + "," + (navWithTrapezoid-2) + var path = "M0," + (navWithTrapezoid) + "L0" + "," + (navWithTrapezoid) + "L" + begin + "," + (navHeight-12) + "L" + begin + "," + navHeight + "L" + end + "," + navHeight + "L" + end + "," + (navHeight-12) + "L" + fv.width + "," + (navWithTrapezoid-2) + "L" + fv.width + "," + (navWithTrapezoid) + "Z"; @@ -281,8 +289,9 @@ var createAAViewer = function(fv, container, sequence) { .append('div') .attr('class','up_pftv_aaviewer') .append('svg') - .attr('width', aaViewWidth) + .attr('width', "100%") .attr('height',aaViewHeight); + // .attr('viewBox', function(){return "0,0," + aaViewWidth + "," + aaViewHeight;}); //amino acids selector var aaSelectorPlot = function(){ @@ -401,21 +410,37 @@ var findFeature = function(fv, selection) { }; var initSources = function (opts) { + Constants.initSources(); if (opts.defaultSources === false) { Constants.clearDataSources(); } if (opts.customDataSource) { Constants.addSource(opts.customDataSource); } + + if (opts.customDataSources) { + _.each(opts.customDataSources, function(source) { + Constants.addSource(source); + }); + } + }; var loadSources = function(opts, dataSources, loaders, delegates, fv) { fv.initLayout(opts); _.each(dataSources, function(source, index) { if (!_.contains(opts.exclusions, source.category)) { - var url = source.url + opts.uniprotacc; - url = source.useExtension === true ? url + '.json' : url; - var dataLoader = DataLoader.get(url); + var url = source.url; + var dataLoader; + if (source.payload == undefined) { + if (url.indexOf("data:") != 0) + url += opts.uniprotacc; + url = source.useExtension === true ? url + '.json' : url; + dataLoader = DataLoader.get(url); + } else { + dataLoader = DataLoader.post(source.url, source.payload, source.contentType, source.unpack); + } + loaders.push(dataLoader); dataLoader.done(function (d) { if (d instanceof Array) //Workaround to be removed @@ -424,6 +449,8 @@ var loadSources = function(opts, dataSources, loaders, delegates, fv) { if (!fv.sequence) { fv.loadZoom(d); } + // If data of the first promise did not have accession field, it would not be set + if (!fv.accession && d.accession) fv.accession = d.accession; var features = d.features; // group by categories if (features.length > 0 && _.has(features[0], 'category')) { @@ -463,12 +490,55 @@ var loadSources = function(opts, dataSources, loaders, delegates, fv) { }); }; +var catNameWidth = 0; +var getFvWidth = function(fv){ + + if (fv.fixedWidth) return fv.fixedWidth; + + if (catNameWidth === 0){ + //TODO: fix the following which currently results in catNameWidth. If the divCatName is appended + // to jQuery("body") the size differs in Chrome and FF in cases when the category is created before + // the rest of the components are ready. This can happen when user provides, her own custom category + // which does not need to be retrieved from an external resource, but is passed as an object + // var divCatName = jQuery('
'); + // catNameWidth = divCatName.outerWidth(false); + catNameWidth = 198; + } + + var parent = jQuery(fv.parentElement); + var container = parent.children('.up_pftv_container'); + + return container.length > 0 ? container.width() - catNameWidth : parent.width() - catNameWidth; +}; + +var getFvXScaleRange = function(fv, padding) { + return padding ? [fv.padding.left, fv.width - fv.padding.right] : [0, fv.width]; + +}; + +var addIframe = function (opts, fv) { + var iframe = document.createElement('iframe'); + iframe.class = "pv-resize-listener"; + iframe.style.cssText = 'height: 0; background-color: transparent; margin: 0; padding: 0; overflow: hidden; border-width: 0; position: absolute; width: 100%;'; + iframe.onload = function() { + iframe.contentWindow.addEventListener('resize', function() { + fv.resize(); + }); + }; + // opts.el.appendChild(iframe); + jQuery(opts.el).children('.up_pftv_container').append(iframe); //child of up_pftv_container so that it can respond to scrollbar (dis)appearance + fv.resize(); //sometimes needed after adding iframe +}; + var FeaturesViewer = function(opts) { + var fv = this; fv.dispatcher = d3.dispatch("featureSelected", "featureDeselected", "ready", "noDataAvailable", "noDataRetrieved", - "notFound", "notConfigRetrieved", "regionHighlighted"); + "notFound", "notConfigRetrieved", "regionHighlighted", "variantDataUpdated"); - fv.width = 760; + fv.parentElement = opts.el; + fv.minWidth = opts.minWidth ? opts.minWidth : 0; + fv.width = getFvWidth(fv); fv.maxZoomSize = 30; fv.selectedFeature = undefined; fv.selectedFeatureElement = undefined; @@ -480,6 +550,7 @@ var FeaturesViewer = function(opts) { fv.uniprotacc = opts.uniprotacc; fv.overwritePredictions = opts.overwritePredictions; fv.defaultSource = opts.defaultSources !== undefined ? opts.defaultSources : true; + fv.variantFilterDefaultBehavior = opts.variantFilterDefaultBehavior === undefined ? true : opts.variantFilterDefaultBehavior; fv.load = function() { initSources(opts); @@ -526,7 +597,12 @@ var FeaturesViewer = function(opts) { } else if (opts.selectedFeature){ fv.selectFeature(opts.selectedFeature); } + + addIframe(opts, fv); + + return fv; }); + }; fv.load(); @@ -557,6 +633,11 @@ FeaturesViewer.prototype.deselectFeature = function() { ViewerHelper.deselectFeature(fv); }; +FeaturesViewer.prototype.resetHighlight = function() { + var fv = this; + ViewerHelper.resetHighlight(fv); +}; + FeaturesViewer.prototype.selectFeature = function(selection) { var fv = this; selection.type = selection.type.toUpperCase(); @@ -606,7 +687,7 @@ FeaturesViewer.prototype.selectFeature = function(selection) { } }; -FeaturesViewer.prototype.highlightRegion = function(begin, end) { +FeaturesViewer.prototype.highlightRegion = function(begin, end, zoomout) { var fv = this; begin = begin < 1 ? 1: begin; end = end @@ -615,8 +696,10 @@ FeaturesViewer.prototype.highlightRegion = function(begin, end) { if ((1 <= begin) && (begin <= end) && (end <= fv.sequence.length)) { fv.deselectFeature(); fv.highlight = {begin: begin, end: end, type:'continuous'}; - if ((fv.xScale(fv.xScale.domain()[0]) > fv.xScale(begin)) || - (fv.xScale(end) > fv.xScale(fv.xScale.domain()[1]))) { + if (zoomout && ( + (fv.xScale(fv.xScale.domain()[0]) > fv.xScale(begin)) || + (fv.xScale(end) > fv.xScale(fv.xScale.domain()[1])) + )) { zoomOut(fv); } ViewerHelper.updateHighlight(fv); @@ -658,9 +741,14 @@ FeaturesViewer.prototype.loadZoom = function(d) { fv.xScale = d3.scale.linear() .domain([1, d.sequence.length + 1]) - .range([fv.padding.left, fv.width - fv.padding.right]); + .range(getFvXScaleRange(fv, true)); fv.viewport = createNavRuler(fv, fv.header); + fv.header = fv.header.append('div') + .style('display', 'table') + .style('width', '100%') + .append('div') + .style('display', 'table-row'); createButtons(fv, d, fv.header); fv.aaViewer = createAAViewer(fv, fv.header, d.sequence); fv.zoom = createZoom(fv); @@ -691,4 +779,29 @@ FeaturesViewer.prototype.drawCategories = function(data, fv) { }); }; +FeaturesViewer.prototype.zoomIn = function() { + zoomIn(this) +}; + +FeaturesViewer.prototype.resize = function() { + var fv = this; + + var widthAux = fv.width; + fv.width = Math.max(getFvWidth(fv), fv.minWidth); + + if (fv.width <= fv.minWidth || widthAux === fv.width) return; + + fv.xScale.range(getFvXScaleRange(fv, true)); + + fv.viewport.x().range(getFvXScaleRange(fv, true)); + fv.viewport.domainEndLabel.attr('x',fv.width); + fv.viewport.xAxis.selectAll("*").remove(); + fv.viewport.navXAxis.scale().range(getFvXScaleRange(fv, true)); + fv.viewport.xAxis.call(fv.viewport.navXAxis); + + update(fv); + updateZoomFromChart(fv); + updateViewportFromChart(fv); +}; + module.exports = FeaturesViewer; diff --git a/src/TrackFactory.js b/src/TrackFactory.js index 9bccf09..4ac7e24 100644 --- a/src/TrackFactory.js +++ b/src/TrackFactory.js @@ -19,10 +19,18 @@ var Track = function(typeFeatures, category) { track.category = category; track.id = track.type + '_track'; - track.titleContainer = category.tracksContainer.append('div').style('display', 'inline-block'); + var tab = category.tracksContainer.append('div').style("display", "table").style("width", "100%"); + var row = tab.append('div').style("display", "table-row"); - track.trackContainer = category.tracksContainer.append('div') + track.titleContainer = row.append('div').style('display', 'table-cell'); + + track.trackContainer = row.append('div') .attr('class', 'up_pftv_track'); + + // category.tracksContainer.append('div').attr("class", "up_pftv-clear"); + + + }; Track.prototype.update = function() { @@ -38,7 +46,7 @@ var BasicTrackViewer = function(track) { var VariantTrackViewer = function(track) { return new VariantViewer( - track.category.name, track.data, track.trackContainer, track.category.fv, track.variantHeight + track.category.name, track.data, track.trackContainer, track.category.fv, track.category, track.variantHeight , track.titleContainer ); }; diff --git a/src/VariantCategoryViewer.js b/src/VariantCategoryViewer.js index b4e1422..8dbf260 100644 --- a/src/VariantCategoryViewer.js +++ b/src/VariantCategoryViewer.js @@ -23,21 +23,31 @@ var VariantCategoryViewer = function(category) { return d.variants.length; }); - var varYScale = d3.scale.linear() - .domain([0,d3.max(varCatViewer.variationCountArray)]) + + varCatViewer.yScale = d3.scale.linear() .range([height, 0]); + this.updateYScaleDomain = function() { + varCatViewer = this; + + varCatViewer.yScale.domain([0,d3.max(varCatViewer.variationCountArray)]); + }; + this.updateYScaleDomain(); + var line = d3.svg.line() .x(function(d,i) { return xScale(i); }) .y(function(d) { - return varYScale(d); + return varCatViewer.yScale(d); }) .interpolate('linear'); this.init = function () { var varCatViewer = this; + + varCatViewer.updateYScaleDomain(); + varCatViewer.varChart.append("path") .data(varCatViewer.features) .attr("class","up_pftv_block-area") diff --git a/src/VariantFilterDialog.js b/src/VariantFilterDialog.js index 2adae10..17f6d45 100644 --- a/src/VariantFilterDialog.js +++ b/src/VariantFilterDialog.js @@ -66,6 +66,21 @@ var defaultFilterCaseOthers = { }, color: LegendDialog.othersColor }; +var defaultFilterCaseUnknown = { + label: 'Unknown', + on: true, + properties: { + 'type': function (variant) { + //this is rather a hack as I need to test that some properties are not present in the object + return variant.siftPrediction === undefined && + variant.polyphenPrediction === undefined && + variant.association === undefined; + }, + 'alternativeSequence': /[^*]/, + 'sourceType': Evidence.variantSourceType.lss + }, + color: LegendDialog.unknownColor +}; var defaultFilterConsequence = { label: 'Filter consequence', cases: [] @@ -107,6 +122,7 @@ var populateFilters = function(fv) { defaultFilterConsequence.cases.push(defaultFilterCasePrediction); defaultFilterConsequence.cases.push(defaultFilterCaseNonDisease); defaultFilterConsequence.cases.push(defaultFilterCaseOthers); + defaultFilterConsequence.cases.push(defaultFilterCaseUnknown); filters.push(defaultFilterConsequence); defaultFilterSource.cases.push(defaultFilterCaseUP); defaultFilterSource.cases.push(defaultFilterCaseLSS); @@ -204,7 +220,7 @@ var VariantFilterDialog = function(fv, container, variantViewer) { var anchor = li.append('a') .on('click', function(filter) { if (filter.on === true) { - clearOthers(filterSet, filter); + fv.variantFilterDefaultBehavior ? clearOthers(filterSet, filter) : filter.on = false; container.select('.up_pftv_inner-icon-container') .style('visibility', 'visible'); } else { diff --git a/src/VariantLegendDialog.js b/src/VariantLegendDialog.js index 1978164..4d7be15 100644 --- a/src/VariantLegendDialog.js +++ b/src/VariantLegendDialog.js @@ -35,6 +35,7 @@ var LegendDialog = function() { createLegendRow(self, self.getPredictionColor(1), 'Benign (Large scale studies)'); createLegendRow(self, self.UPNonDiseaseColor, 'Non-disease (UniProt)'); createLegendRow(self, self.othersColor, 'Init codon, stop lost & gained'); + createLegendRow(self, self.unknownColor, 'Unknown'); }; return { @@ -43,6 +44,7 @@ var LegendDialog = function() { benignColor: '#8FE3FF', UPNonDiseaseColor: '#99cc00', othersColor: '#FFCC00', + unknownColor: '#808080', consequenceColors: ["#66c2a5","#8da0cb","#e78ac3","#e5c494","#fc8d62","#ffd92f","#a6d854","#b3b3b3"], getPredictionColor: d3.scale.linear() .domain([0,1]) diff --git a/src/VariantViewer.js b/src/VariantViewer.js index ef46542..c17780c 100644 --- a/src/VariantViewer.js +++ b/src/VariantViewer.js @@ -82,6 +82,8 @@ var variantsFill = function(d, fv) { } else { return LegendDialog.UPNonDiseaseColor; } + } else if (d.sourceType === Evidence.variantSourceType.lss && Evidence.existAssociation(d.association)){ + return LegendDialog.UPDiseaseColor; } else { var externalPrediction, extDatum = {}; if (d.externalData) { @@ -95,6 +97,10 @@ var variantsFill = function(d, fv) { var predictionScore = getPredictionColorScore(d.siftScore, d.siftPrediction, d.polyphenScore, d.polyphenPrediction); + if (d.sourceType === Evidence.variantSourceType.lss && predictionScore === undefined) { + return LegendDialog.unknownColor; + } + return getVariantsFillColor(fv, d, extDatum, externalPrediction, predictionScore); } }; @@ -152,9 +158,29 @@ var drawVariants = function(variantViewer, bars, frequency, fv, container, catTi variantCircle.exit().remove(); }; -var createDataSeries = function(fv, variantViewer, svg, features, series) { - var mainChart = svg.append('g') - .attr('transform', 'translate(0,' + variantViewer.margin.top + ')'); +var updateChartArea = function(variantViewer){ + variantViewer.svg.select('#plotAreaClip rect') + .attr("width", function(){return getClipPathWidth(variantViewer);}); + + variantViewer.svg.selectAll('.variation-y.axis.left line') + .attr('x2', getAxisLength(variantViewer)); + + variantViewer.svg.selectAll('.variation-y.axis.right') + .attr('transform','translate(' + getAxisLength(variantViewer) + ', 0)'); + +}; + +var getClipPathWidth = function(variantViewer) { + return variantViewer.width - 20; +}; + +var getAxisLength = function(variantViewer) { + return variantViewer.width - 18; +}; + +var createDataSeries = function(fv, variantViewer, features, series) { + var mainChart = variantViewer.svg.append('g') + .attr('transform','translate(0,' + variantViewer.margin.top + ')'); var chartArea = mainChart.append('g') .attr('clip-path', 'url(#plotAreaClip)'); @@ -162,8 +188,8 @@ var createDataSeries = function(fv, variantViewer, svg, features, series) { mainChart.append('clipPath') .attr('id', 'plotAreaClip') .append('rect') - .attr({ width: (variantViewer.width - 20), height: variantViewer.height }) - .attr('transform', 'translate(10, -10)'); + .attr({ width: (getClipPathWidth(variantViewer)) , height: variantViewer.height}) + .attr('transform','translate(10, -10)'); var dataSeries = chartArea .datum(features) @@ -179,13 +205,13 @@ var createDataSeries = function(fv, variantViewer, svg, features, series) { .orient('right'); mainChart.append('g') - .attr('transform', 'translate(12 ,0)') - .attr('class', 'variation-y axis') + .attr('transform','translate(12 ,0)') + .attr('class','variation-y axis left') .call(yAxis); mainChart.append('g') - .attr('transform', 'translate(' + (variantViewer.width - 18) + ', 0)') - .attr('class', 'variation-y axis') + .attr('transform','translate(' + getAxisLength(variantViewer) + ', 0)') + .attr('class','variation-y axis right') .call(yAxis2); fv.globalContainer.selectAll('g.variation-y g.tick').attr('class', function(d) { @@ -195,7 +221,7 @@ var createDataSeries = function(fv, variantViewer, svg, features, series) { return dataSeries; }; -var VariantViewer = function(catTitle, features, container, fv, variantHeight, titleContainer) { +var VariantViewer = function(catTitle, features, container, fv, category, variantHeight, titleContainer) { var variantViewer = this; variantViewer.height = variantHeight; variantViewer.width = fv.width; @@ -266,16 +292,18 @@ var VariantViewer = function(catTitle, features, container, fv, variantHeight, t return variationPlot; }; - var svg = ViewerHelper.createSVG(container, variantViewer.width, variantViewer.height, fv, 'up_pftv_variants-svg'); + variantViewer.svg = ViewerHelper.createSVG(container, variantViewer.width, variantViewer.height, fv, 'up_pftv_variants-svg'); // Data series var series = variationPlot() .xScale(variantViewer.xScale) .yScale(variantViewer.yScale); - var dataSeries = createDataSeries(fv, variantViewer, svg, features, series); + var dataSeries = createDataSeries(fv, variantViewer, features, series); this.update = function() { + variantViewer.width = fv.width; + updateChartArea(variantViewer); dataSeries.call(series); if (fv.selectedFeature) { ViewerHelper.updateHighlight(fv); @@ -286,7 +314,9 @@ var VariantViewer = function(catTitle, features, container, fv, variantHeight, t this.updateData = function(data) { dataSeries.datum(data); + category.categoryViewer.updateData(data); this.update(); + fv.dispatcher.variantDataUpdated(); }; this.reset = function() { diff --git a/src/ViewerHelper.js b/src/ViewerHelper.js index 234ef87..2bb8a94 100644 --- a/src/ViewerHelper.js +++ b/src/ViewerHelper.js @@ -13,8 +13,10 @@ var ViewerHelper = function() { createSVG: function(container, width, height, fv, clazz) { var svg = container .append('svg') - .attr('width', width) + .attr('width', '100%') .attr('height', height) + // .attr('viewBox', function(){return "0,0," + width + "," + height;}) + // .attr('preserveAspectRatio', 'none') .on('mousedown', function() { mousedownXY = { x: d3.event.pageX, y: d3.event.pageY }; mouseupXY = { x: -2, y: -2 }; diff --git a/style/main.css b/style/main.css index db66eaa..126a10e 100644 --- a/style/main.css +++ b/style/main.css @@ -3,19 +3,26 @@ svg { } .up_pftv_buttons { - display: inline-block; + display: table-cell; padding: 0 .5em 0 .5em; - width: 180px; + width: 198px; text-align: right; vertical-align: bottom; position: relative; + box-sizing: border-box; +} + +.bottom-aa-container { + display: table; + width: 100%; } .up_pftv_credit_container { - display: inline-block; + display: table-cell; vertical-align: top; - width: 180px; + width: 198px; padding: 0 0.5em; + box-sizing: border-box; } .up_pftv_credit { @@ -45,7 +52,7 @@ svg { .up_pftv_container { position: relative; - width: 960px; + /*width: 960px;*/ color:#557071 !important; font-family: 'Helvetica neue', Helvetica, Arial, sans-serif !important; font-size: 13px !important; @@ -96,15 +103,17 @@ svg { .up_pftv_category { margin-bottom: .1em; border-bottom: .1em solid #b2f5ff; + display: table; + width: 100%; } .up_pftv_category-name, .up_pftv_track-header { font-weight: 400; line-height: 2.1em; - display: inline-block; - width: 180px; + width: 198px; + max-width: 198px; vertical-align: bottom; - padding: .485em; + padding: .5em; border: none; text-overflow: ellipsis; white-space: nowrap; @@ -113,6 +122,8 @@ svg { .up_pftv_category-name { background-color: #b2f5ff; + display: table-cell; + box-sizing: border-box; } .up_pftv_category a:hover { @@ -122,16 +133,28 @@ svg { } .up_pftv_track-header { + display: table-cell; background-color: #d9faff; + box-sizing: border-box; /*line-height: 1.6em; margin: .05em 0;*/ } .up_pftv_category-viewer, .up_pftv_track, .up_pftv_aaviewer { position: relative; - display: inline-block; vertical-align: bottom; - width: 760px; + /*width: 760px;*/ +} +.up_pftv_track { + display: table-cell; +} + +.up_pftv_aaviewer { + display: table-cell; +} + +.up_pftv_category-viewer { + display: table-cell; } .up_pftv_category-viewer svg, .up_pftv_track svg, .up_pftv_aaviewer svg { @@ -148,6 +171,10 @@ svg { background-color: #D9FAFF; } +.up_pftv_category-tracks { + display: table-row; +} + .up_pftv_track { border-top: 1px #b2f5ff solid; } @@ -189,6 +216,10 @@ svg { stroke: black; } +.up_pftv_aaviewer path { + display: no; +} + .up_pftv_navruler .up_pftv_viewport { fill: #D7DCE0; fill-opacity: 0.4; @@ -783,3 +814,7 @@ a.up_pftv_icon-button:hover { .up_pftv_icon-info { background: url(../SVG/info.svg); } + +.up_pftv-clear { + clear:both; +}