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": "sha512-E+iruNOY8VV9s4JEbe1aNEm6MiszPRr/UfcHMz0TQh1BXSxHK+ASV1R6W4HpjBhSeS+54PIsAMCBmwD06LLsqQ==",
+ "dev": true,
+ "requires": {
+ "jsonparse": "^1.2.0",
+ "through": ">=2.2.7 <3"
+ }
+ },
+ "abbrev": {
+ "version": "1.0.9",
+ "resolved": "https://registry.npmjs.org/abbrev/-/abbrev-1.0.9.tgz",
+ "integrity": "sha1-kbR5JYinc4wl813W9jdSovh3YTU=",
+ "dev": true
+ },
+ "acorn": {
+ "version": "4.0.13",
+ "resolved": "https://registry.npmjs.org/acorn/-/acorn-4.0.13.tgz",
+ "integrity": "sha1-EFSVrlNh1pe9GVyCUZLhrX8lN4c=",
+ "dev": true
+ },
+ "acorn-node": {
+ "version": "1.8.2",
+ "resolved": "https://registry.npmjs.org/acorn-node/-/acorn-node-1.8.2.tgz",
+ "integrity": "sha512-8mt+fslDufLYntIoPAaIMUe/lrbrehIiwmR3t2k9LljIzoigEPF27eLk2hy8zSGzmR/ogr7zbRKINMo1u0yh5A==",
+ "dev": true,
+ "requires": {
+ "acorn": "^7.0.0",
+ "acorn-walk": "^7.0.0",
+ "xtend": "^4.0.2"
+ },
+ "dependencies": {
+ "acorn": {
+ "version": "7.4.1",
+ "resolved": "https://registry.npmjs.org/acorn/-/acorn-7.4.1.tgz",
+ "integrity": "sha512-nQyp0o1/mNdbTO1PO6kHkwSrmgZ0MT/jCCpNiwbUjGoRN4dlBhqJtoQuCnEOKzgTVwg0ZWiCoQy6SxMebQVh8A==",
+ "dev": true
+ }
+ }
+ },
+ "acorn-walk": {
+ "version": "7.2.0",
+ "resolved": "https://registry.npmjs.org/acorn-walk/-/acorn-walk-7.2.0.tgz",
+ "integrity": "sha512-OPdCF6GsMIP+Az+aWfAAOEt2/+iVDKE7oy6lJ098aoe59oAmK76qV6Gw60SbZ8jHuG2wH058GF4pLFbYamYrVA==",
+ "dev": true
+ },
+ "align-text": {
+ "version": "0.1.4",
+ "resolved": "https://registry.npmjs.org/align-text/-/align-text-0.1.4.tgz",
+ "integrity": "sha1-DNkKVhCT810KmSVsIrcGlDP60Rc=",
+ "dev": true,
+ "requires": {
+ "kind-of": "^3.0.2",
+ "longest": "^1.0.1",
+ "repeat-string": "^1.5.2"
+ },
+ "dependencies": {
+ "kind-of": {
+ "version": "3.2.2",
+ "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-3.2.2.tgz",
+ "integrity": "sha1-MeohpzS6ubuw8yRm2JOupR5KPGQ=",
+ "dev": true,
+ "requires": {
+ "is-buffer": "^1.1.5"
+ }
+ }
+ }
+ },
+ "amdefine": {
+ "version": "1.0.1",
+ "resolved": "https://registry.npmjs.org/amdefine/-/amdefine-1.0.1.tgz",
+ "integrity": "sha1-SlKCrBZHKek2Gbz9OtFR+BfOkfU=",
+ "dev": true
+ },
+ "ansi": {
+ "version": "0.3.1",
+ "resolved": "https://registry.npmjs.org/ansi/-/ansi-0.3.1.tgz",
+ "integrity": "sha1-DELU+xcWDVqa8eSEus4cZpIsGyE=",
+ "dev": true
+ },
+ "ansi-gray": {
+ "version": "0.1.1",
+ "resolved": "https://registry.npmjs.org/ansi-gray/-/ansi-gray-0.1.1.tgz",
+ "integrity": "sha1-KWLPVOyXksSFEKPetSRDaGHvclE=",
+ "dev": true,
+ "requires": {
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+ }
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+ "ansi-regex": {
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+ "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-2.1.1.tgz",
+ "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8=",
+ "dev": true
+ },
+ "ansi-styles": {
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+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-2.2.1.tgz",
+ "integrity": "sha1-tDLdM1i2NM914eRmQ2gkBTPB3b4=",
+ "dev": true
+ },
+ "ansi-wrap": {
+ "version": "0.1.0",
+ "resolved": "https://registry.npmjs.org/ansi-wrap/-/ansi-wrap-0.1.0.tgz",
+ "integrity": "sha1-qCJQ3bABXponyoLoLqYDu/pF768=",
+ "dev": true
+ },
+ "anymatch": {
+ "version": "1.3.2",
+ "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-1.3.2.tgz",
+ "integrity": "sha512-0XNayC8lTHQ2OI8aljNCN3sSx6hsr/1+rlcDAotXJR7C1oZZHCNsfpbKwMjRA3Uqb5tF1Rae2oloTr4xpq+WjA==",
+ "dev": true,
+ "requires": {
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+ "normalize-path": "^2.0.0"
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+ "dev": true,
+ "requires": {
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+ }
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+ "integrity": "sha1-odl8yvy8JiXMcPrc6zalDFiwGlM=",
+ "dev": true
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+ "integrity": "sha1-uneWLhLf+WnWt2cR6RS3N4V79qc=",
+ "dev": true,
+ "requires": {
+ "expand-range": "^1.8.1",
+ "preserve": "^0.2.0",
+ "repeat-element": "^1.1.2"
+ }
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+ "dev": true,
+ "requires": {
+ "is-posix-bracket": "^0.1.0"
+ }
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+ "dev": true,
+ "requires": {
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+ }
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+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/is-extglob/-/is-extglob-1.0.0.tgz",
+ "integrity": "sha1-rEaBd8SUNAWgkvyPKXYMb/xiBsA=",
+ "dev": true
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+ "resolved": "https://registry.npmjs.org/is-glob/-/is-glob-2.0.1.tgz",
+ "integrity": "sha1-0Jb5JqPe1WAPP9/ZEZjLCIjC2GM=",
+ "dev": true,
+ "requires": {
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+ }
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+ "kind-of": {
+ "version": "3.2.2",
+ "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-3.2.2.tgz",
+ "integrity": "sha1-MeohpzS6ubuw8yRm2JOupR5KPGQ=",
+ "dev": true,
+ "requires": {
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+ }
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+ "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-2.3.11.tgz",
+ "integrity": "sha1-hmd8l9FyCzY0MdBNDRUpO9OMFWU=",
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+ "object.omit": "^2.0.0",
+ "parse-glob": "^3.0.4",
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+ "resolved": "https://registry.npmjs.org/archy/-/archy-1.0.0.tgz",
+ "integrity": "sha1-+cjBN1fMHde8N5rHeyxipcKGjEA=",
+ "dev": true
+ },
+ "are-we-there-yet": {
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+ "resolved": "https://registry.npmjs.org/are-we-there-yet/-/are-we-there-yet-1.0.6.tgz",
+ "integrity": "sha1-otKMkxAqpsyWJFomy5VN4G7FPww=",
+ "dev": true,
+ "requires": {
+ "delegates": "^1.0.0",
+ "readable-stream": "^2.0.0 || ^1.1.13"
+ }
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+ "resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.10.tgz",
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+ "dev": true,
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+ }
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+ "resolved": "https://registry.npmjs.org/arr-diff/-/arr-diff-4.0.0.tgz",
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+ "resolved": "https://registry.npmjs.org/arr-union/-/arr-union-3.1.0.tgz",
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+}
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;
+}