genoverse 3.2.0 → 4.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.eslintrc.js +93 -162
- package/.github/workflows/test.yml +9 -10
- package/.github/workflows/update-gh-pages.yml +33 -0
- package/LICENSE.TXT +2 -2
- package/README.md +174 -3
- package/{i → assets}/sort_handle.png +0 -0
- package/babel.config.js +19 -0
- package/dist/129.css +334 -0
- package/dist/129.css.map +1 -0
- package/dist/129.genoverse.js +2 -0
- package/dist/129.genoverse.js.map +1 -0
- package/dist/15d98c18221c8bcb2334.ttf +0 -0
- package/dist/166.css +2 -0
- package/dist/166.genoverse.js +1 -0
- package/dist/216.css +20 -0
- package/dist/216.css.map +1 -0
- package/dist/232.css +114 -0
- package/dist/232.css.map +1 -0
- package/dist/232.genoverse.js +2 -0
- package/dist/232.genoverse.js.map +1 -0
- package/dist/2e659e443f3e98569e9f.png +0 -0
- package/dist/394.css +114 -0
- package/dist/394.css.map +1 -0
- package/dist/394.genoverse.js +2 -0
- package/dist/394.genoverse.js.map +1 -0
- package/dist/469.css +24 -0
- package/dist/469.css.map +1 -0
- package/dist/469.genoverse.js +2 -0
- package/dist/469.genoverse.js.map +1 -0
- package/dist/4896d4b04430cc3dfb06.woff2 +0 -0
- package/dist/530.css +39 -0
- package/dist/530.css.map +1 -0
- package/dist/530.genoverse.js +2 -0
- package/dist/530.genoverse.js.map +1 -0
- package/dist/547.css +469 -0
- package/dist/547.css.map +1 -0
- package/dist/547.genoverse.js +1 -0
- package/dist/729.css +315 -0
- package/dist/729.css.map +1 -0
- package/dist/79da213423ac0def2058.ttf +0 -0
- package/dist/804.genoverse.js +2 -0
- package/dist/804.genoverse.js.map +1 -0
- package/dist/842.genoverse.js +2 -0
- package/dist/842.genoverse.js.map +1 -0
- package/dist/893.genoverse.js +2 -0
- package/dist/893.genoverse.js.map +1 -0
- package/dist/949.css +315 -0
- package/dist/949.css.map +1 -0
- package/dist/949.genoverse.js +2 -0
- package/dist/949.genoverse.js.map +1 -0
- package/dist/952.css +315 -0
- package/dist/952.css.map +1 -0
- package/dist/952.genoverse.js +2 -0
- package/dist/952.genoverse.js.map +1 -0
- package/dist/d79c2ec96ab9ff1161a2.woff2 +0 -0
- package/dist/genoverse.js +2 -0
- package/dist/genoverse.js.map +1 -0
- package/index.html +13 -14
- package/jest.config.js +5 -0
- package/jest.setup.js +13 -0
- package/package.json +29 -12
- package/{css → src/css}/controlPanel.css +0 -0
- package/{css → src/css}/fileDrop.css +0 -0
- package/src/css/fontawesome.css +3 -0
- package/{css → src/css}/fullscreen.css +0 -0
- package/{css → src/css}/genoverse.css +1 -1
- package/{css → src/css}/karyotype.css +2 -0
- package/{css → src/css}/resizer.css +0 -0
- package/{css → src/css}/tooltips.css +0 -0
- package/{css → src/css}/trackControls.css +0 -0
- package/src/js/Genoverse.js +1747 -0
- package/{js → src/js}/Track/Controller/Sequence.js +6 -4
- package/src/js/Track/Controller/Stranded.js +83 -0
- package/{js → src/js}/Track/Controller.js +201 -160
- package/src/js/Track/Model/File/BAM.js +47 -0
- package/src/js/Track/Model/File/BED.js +122 -0
- package/src/js/Track/Model/File/GFF.js +42 -0
- package/src/js/Track/Model/File/VCF.js +109 -0
- package/src/js/Track/Model/File/WIG.js +82 -0
- package/src/js/Track/Model/File.js +36 -0
- package/src/js/Track/Model/Gene/Ensembl.js +24 -0
- package/{js → src/js}/Track/Model/Gene.js +3 -1
- package/src/js/Track/Model/Sequence/Ensembl.js +6 -0
- package/{js → src/js}/Track/Model/Sequence/Fasta.js +24 -17
- package/{js → src/js}/Track/Model/Sequence.js +10 -7
- package/{js → src/js}/Track/Model/SequenceVariation.js +17 -11
- package/{js → src/js}/Track/Model/Stranded.js +11 -8
- package/src/js/Track/Model/Transcript/Ensembl.js +73 -0
- package/{js → src/js}/Track/Model/Transcript.js +3 -1
- package/{js → src/js}/Track/Model.js +125 -93
- package/{js → src/js}/Track/View/Gene/Ensembl.js +6 -4
- package/src/js/Track/View/Gene.js +8 -0
- package/{js → src/js}/Track/View/Sequence.js +18 -22
- package/src/js/Track/View/SequenceVariation.js +117 -0
- package/src/js/Track/View/Transcript/Ensembl.js +17 -0
- package/src/js/Track/View/Transcript.js +32 -0
- package/{js → src/js}/Track/View.js +200 -159
- package/{js → src/js}/Track/library/Chromosome.js +18 -13
- package/src/js/Track/library/File/BAM.js +34 -0
- package/src/js/Track/library/File/BED.js +27 -0
- package/src/js/Track/library/File/BIGBED.js +51 -0
- package/src/js/Track/library/File/BIGWIG.js +54 -0
- package/src/js/Track/library/File/GFF.js +10 -0
- package/{js → src/js}/Track/library/File/VCF.js +29 -22
- package/src/js/Track/library/File/WIG.js +8 -0
- package/{js → src/js}/Track/library/File.js +4 -2
- package/src/js/Track/library/Gene.js +44 -0
- package/src/js/Track/library/Graph/Bar.js +263 -0
- package/src/js/Track/library/Graph/Line.js +335 -0
- package/{js → src/js}/Track/library/Graph.js +137 -114
- package/{js → src/js}/Track/library/HighlightRegion.js +118 -93
- package/src/js/Track/library/Legend.js +258 -0
- package/{js → src/js}/Track/library/Scalebar.js +69 -49
- package/{js → src/js}/Track/library/Scaleline.js +29 -27
- package/src/js/Track/library/Static.js +82 -0
- package/{js → src/js}/Track/library/dbSNP.js +47 -50
- package/src/js/Track.js +651 -0
- package/{js → src/js}/genomes/grch37.js +52 -52
- package/{js → src/js}/genomes/grch38.js +52 -52
- package/src/js/lib/BWReader.js +562 -0
- package/src/js/lib/VCFReader.js +296 -0
- package/src/js/lib/dalliance/bam.js +517 -0
- package/src/js/lib/dalliance/bin.js +317 -0
- package/src/js/lib/dalliance/jszlib-inflate.js +2159 -0
- package/src/js/lib/dalliance/lh3utils.js +105 -0
- package/src/js/lib/dalliance/sha1.js +334 -0
- package/src/js/lib/import-tracks.js +42 -0
- package/{js/lib → src/js/lib/jquery-plugins}/jquery.mousehold.js +0 -0
- package/{js/lib → src/js/lib/jquery-plugins}/jquery.mousewheel.js +0 -0
- package/{js/lib → src/js/lib/jquery-plugins}/jquery.tipsy.js +0 -0
- package/src/js/lib/jquery.js +26 -0
- package/src/js/lib/polyfills.js +11 -0
- package/src/js/lib/wrap-functions.js +88 -0
- package/src/js/plugins/controlPanel.js +388 -0
- package/src/js/plugins/fileDrop.js +81 -0
- package/src/js/plugins/focusRegion.js +13 -0
- package/{js → src/js}/plugins/fullscreen.js +18 -14
- package/{js → src/js}/plugins/karyotype.js +51 -45
- package/src/js/plugins/resizer.js +52 -0
- package/{js → src/js}/plugins/tooltips.js +31 -29
- package/src/js/plugins/trackControls.js +159 -0
- package/test/View/render-legends.test.js +1 -1
- package/test/change-width.test.js +71 -0
- package/test/create-and-destroy.test.js +2 -2
- package/test/track-ordering.test.js +3 -2
- package/test/track_config/config-settings.test.js +1 -1
- package/test/utils.js +4 -2
- package/webpack.config.js +103 -34
- package/css/font-awesome.css +0 -3
- package/expanded.html +0 -120
- package/fontawesome/css/fontawesome.min.css +0 -5
- package/fontawesome/css/regular.min.css +0 -5
- package/fontawesome/css/solid.min.css +0 -5
- package/fontawesome/webfonts/fa-brands-400.ttf +0 -0
- package/fontawesome/webfonts/fa-brands-400.woff +0 -0
- package/fontawesome/webfonts/fa-brands-400.woff2 +0 -0
- package/fontawesome/webfonts/fa-regular-400.ttf +0 -0
- package/fontawesome/webfonts/fa-regular-400.woff +0 -0
- package/fontawesome/webfonts/fa-regular-400.woff2 +0 -0
- package/fontawesome/webfonts/fa-solid-900.ttf +0 -0
- package/fontawesome/webfonts/fa-solid-900.woff +0 -0
- package/fontawesome/webfonts/fa-solid-900.woff2 +0 -0
- package/help.pdf +0 -0
- package/index.js +0 -83
- package/js/Genoverse.js +0 -1681
- package/js/Track/Controller/Stranded.js +0 -73
- package/js/Track/Model/File/BAM.js +0 -44
- package/js/Track/Model/File/BED.js +0 -116
- package/js/Track/Model/File/GFF.js +0 -40
- package/js/Track/Model/File/VCF.js +0 -101
- package/js/Track/Model/File/WIG.js +0 -67
- package/js/Track/Model/File.js +0 -36
- package/js/Track/Model/Gene/Ensembl.js +0 -22
- package/js/Track/Model/Sequence/Ensembl.js +0 -4
- package/js/Track/Model/Transcript/Ensembl.js +0 -67
- package/js/Track/View/Gene.js +0 -6
- package/js/Track/View/Sequence/Variation.js +0 -115
- package/js/Track/View/Transcript/Ensembl.js +0 -12
- package/js/Track/View/Transcript.js +0 -28
- package/js/Track/library/File/BAM.js +0 -30
- package/js/Track/library/File/BED.js +0 -24
- package/js/Track/library/File/BIGBED.js +0 -47
- package/js/Track/library/File/BIGWIG.js +0 -52
- package/js/Track/library/File/GFF.js +0 -9
- package/js/Track/library/File/WIG.js +0 -5
- package/js/Track/library/Gene.js +0 -37
- package/js/Track/library/Graph/Bar.js +0 -235
- package/js/Track/library/Graph/Line.js +0 -296
- package/js/Track/library/Legend.js +0 -224
- package/js/Track/library/Static.js +0 -78
- package/js/Track.js +0 -632
- package/js/genoverse.min.js +0 -2
- package/js/genoverse.min.js.map +0 -1
- package/js/lib/BWReader.js +0 -578
- package/js/lib/Base.js +0 -145
- package/js/lib/VCFReader.js +0 -286
- package/js/lib/dalliance/js/bam.js +0 -494
- package/js/lib/dalliance/js/bin.js +0 -185
- package/js/lib/dalliance/js/das.js +0 -749
- package/js/lib/dalliance/js/utils.js +0 -370
- package/js/lib/dalliance-lib.js +0 -3594
- package/js/lib/dalliance-lib.min.js +0 -68
- package/js/lib/jDataView.js +0 -2
- package/js/lib/jParser.js +0 -192
- package/js/lib/jquery-ui.js +0 -8
- package/js/lib/jquery.js +0 -2
- package/js/lib/rtree.js +0 -1
- package/js/plugins/controlPanel.js +0 -395
- package/js/plugins/fileDrop.js +0 -62
- package/js/plugins/focusRegion.js +0 -12
- package/js/plugins/resizer.js +0 -45
- package/js/plugins/trackControls.js +0 -143
- package/utils/expandedTemplate.html +0 -46
- package/utils/git-hooks/post-commit +0 -9
- package/utils/git-hooks/pre-commit +0 -7
- package/utils/git-hooks/setup +0 -6
- package/utils/makeExpanded.js +0 -19
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import Base from 'basejs';
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import _get from 'lodash/get';
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import Track from './Track';
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import HighlightRegionTrack from './Track/library/HighlightRegion';
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import LegendTrack from './Track/library/Legend';
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import importTracks from './lib/import-tracks';
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import $ from './lib/jquery';
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import wrapFunctions from './lib/wrap-functions';
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const Genoverse = Base.extend({
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// Defaults
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baseURL : undefined, // If multiple instances of Genoverse exist on a page at once, specifying different baseURL values allows some/all to ignore external URL changes
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urlParamTemplate : 'r=__CHR__:__START__-__END__', // Overwrite this for your URL style
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width : 1000,
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longestLabel : 30,
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defaultLength : 5000,
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defaultScrollDelta : 100,
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tracks : [],
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highlights : [],
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plugins : [],
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dragAction : 'scroll', // Options are: scroll, select, off
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wheelAction : 'off', // Options are: zoom, off
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isStatic : false, // If true, will stop drag, select and zoom actions occurring
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saveable : false, // If true, track configuration and ordering will be saved in sessionStorage/localStorage
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saveKey : '', // Default key for sessionStorage/localStorage configuration is 'genoverse'. saveKey will be appended to this if it is set
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storageType : 'sessionStorage', // Set to localStorage for permanence
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autoHideMessages : true, // Determines whether to collapse track messages by default
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trackAutoHeight : false, // Determines whether to automatically resize tracks to show all their features (can be overridden by track.autoHeight)
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hideEmptyTracks : true, // Determines whether to hide an automatically resized tracks if it has no features, or to show it empty (can be overridden by track.hideEmpty)
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genome : undefined, // The genome used in the browser - can be an object or a string, which will be used to obtain a javascript file
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useHash : undefined, // If true, window.location.hash is changed on navigation. If false, window.history.pushState is used. If undefined, pushState will be used if present in the browser
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// Default coordinates for initial view, overwrite in your config
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chr : 1,
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start : 1,
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end : 1000000,
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constructor: function (config = {}) {
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const jQuery = $;
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this.jQuery = jQuery;
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if (!this.supported()) {
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return this.die('Your browser does not support this functionality');
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}
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Genoverse.configure();
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let container = jQuery(config.container); // Make sure container is a jquery object, jquery recognises itself automatically
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if (!container?.length) {
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container = jQuery('<div>').appendTo('body');
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}
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container.addClass('genoverse').data('genoverse', this);
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Object.entries(config).forEach(
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([ key, val ]) => {
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if (typeof val !== 'undefined') {
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this[key] = val;
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}
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}
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);
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this.container = container;
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this.eventNamespace = `.genoverse.${++Genoverse.id}`;
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this.events = { browser: {}, tracks: {} };
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jQuery.when(
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this.loadCSS(),
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this.loadGenome(),
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this.loadPlugins()
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).always(() => {
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wrapFunctions(this, 'Genoverse');
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this.init();
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});
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},
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loadCSS: function () {
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const jQuery = this.jQuery;
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return jQuery.when(
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Genoverse.importCSS ? import('../css/genoverse.css') : jQuery.Deferred().resolve(),
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Genoverse.importFontAwesome ? import('../css/fontawesome.css') : jQuery.Deferred().resolve()
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);
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},
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loadGenome: function () {
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if (typeof this.genome === 'string') {
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const genomeName = this.genome.toLowerCase();
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return import(`./genomes/${genomeName}`).then((imported) => {
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this.genomeName = this.genome;
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this.genome = imported.default;
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if (!this.genome) {
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this.die(`Unable to load genome ${genomeName}`);
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}
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});
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}
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loadPlugins: function (plugins) {
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const pluginsByName = (plugins || this.plugins).map(plugin => (
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? { name: plugin[0], conf: plugin[1] }
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: { name: plugin, conf: undefined }
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)).reduce(
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{}
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initializePlugin({
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conf : (pluginsByName[pluginName] || {}).conf,
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pluginFn.call(this, plugin.conf || {});
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this.container.addClass(`gv-${plugin.name.replace(/([A-Z])/g, '-$1').toLowerCase()}-plugin`);
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initializePlugin({
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exports : imported.default,
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});
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}
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));
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+
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159
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return this.jQuery.when(...pluginImports);
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},
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init: function () {
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const width = this.width;
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this.addDomElements(width);
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this.addUserEventHandlers();
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if (this.isStatic) {
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this.dragAction = this.wheelAction = 'off';
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this.urlParamTemplate = false;
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}
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+
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this.tracksById = {};
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this.prev = {};
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this.legends = {};
|
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this.initialLocation = { chr: this.chr, start: this.start, end: this.end };
|
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this.saveKey = this.saveKey ? `genoverse-${this.saveKey}` : 'genoverse';
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this.urlParamTemplate = this.urlParamTemplate || '';
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this.useHash = typeof this.useHash === 'boolean' ? this.useHash : typeof window.history.pushState !== 'function';
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this.textWidth = document.createElement('canvas').getContext('2d').measureText('W').width;
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this.labelWidth = this.labelContainer.outerWidth(true) || 0;
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this.width = Math.min(this.width - this.labelWidth, this.wrapper.width() || Infinity); // Recalculate the width to ignore the affect of borders
|
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this.paramRegex = (
|
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this.urlParamTemplate
|
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? new RegExp(
|
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186
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`([?&;])${
|
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this.urlParamTemplate
|
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.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')
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.replace(/(\b(\w+=)?__CHR__(.)?)/, '$2([\\w\\.]+)$3')
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.replace(/(\b(\w+=)?__START__(.)?)/, '$2(\\d+)$3')
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.replace(/(\b(\w+=)?__END__(.)?)/, '$2(\\d+)$3')
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}([;&])`
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)
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: ''
|
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);
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+
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const coords = this.getCoords();
|
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+
|
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+
this.chr = coords.chr;
|
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|
+
|
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201
|
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if (this.genome) {
|
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|
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this.chromosomeSize = this.genome[this.chr].size;
|
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|
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}
|
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+
|
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this.canChangeChr = !!this.genome;
|
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|
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if (this.saveable) {
|
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this.loadConfig();
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} else {
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this.addTracks();
|
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}
|
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|
+
|
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|
+
if (this.width > 0) {
|
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|
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this.setRange(coords.start, coords.end);
|
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215
|
+
}
|
|
216
|
+
|
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217
|
+
if (this.highlights.length) {
|
|
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|
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this.addHighlights(this.highlights);
|
|
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|
+
}
|
|
220
|
+
},
|
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|
+
|
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|
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loadConfig: function () {
|
|
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|
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let config;
|
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|
+
|
|
225
|
+
this.defaultTracks = this.jQuery.extend(true, [], this.tracks);
|
|
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|
+
|
|
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|
+
try {
|
|
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|
+
config = window[this.storageType].getItem(this.saveKey);
|
|
229
|
+
} catch (e) {
|
|
230
|
+
// do nothing
|
|
231
|
+
}
|
|
232
|
+
|
|
233
|
+
if (config) {
|
|
234
|
+
config = JSON.parse(config);
|
|
235
|
+
} else {
|
|
236
|
+
this.addTracks();
|
|
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|
+
|
|
238
|
+
return;
|
|
239
|
+
}
|
|
240
|
+
|
|
241
|
+
const tracksByNamespace = Genoverse.getAllTrackTypes();
|
|
242
|
+
const tracks = [];
|
|
243
|
+
const tracksById = {};
|
|
244
|
+
const savedConfig = {};
|
|
245
|
+
|
|
246
|
+
function setConfig(track, conf) {
|
|
247
|
+
Object.keys(conf).forEach(
|
|
248
|
+
(prop) => {
|
|
249
|
+
if (prop === 'config') {
|
|
250
|
+
savedConfig[conf.id] = conf[prop];
|
|
251
|
+
} else {
|
|
252
|
+
if (prop === 'height') {
|
|
253
|
+
conf[prop] = parseInt(conf[prop], 10);
|
|
254
|
+
|
|
255
|
+
if (isNaN(conf[prop])) {
|
|
256
|
+
return;
|
|
257
|
+
}
|
|
258
|
+
}
|
|
259
|
+
|
|
260
|
+
track.prototype[prop] = conf[prop];
|
|
261
|
+
}
|
|
262
|
+
}
|
|
263
|
+
);
|
|
264
|
+
}
|
|
265
|
+
|
|
266
|
+
this.tracks.forEach(
|
|
267
|
+
(track) => {
|
|
268
|
+
const TrackClass = this.normaliseTrackDefinition(track);
|
|
269
|
+
|
|
270
|
+
if (TrackClass.prototype.id) {
|
|
271
|
+
tracksById[TrackClass.prototype.id] = TrackClass;
|
|
272
|
+
}
|
|
273
|
+
}
|
|
274
|
+
);
|
|
275
|
+
|
|
276
|
+
config.forEach(
|
|
277
|
+
(conf) => {
|
|
278
|
+
let track = tracksById[conf.id];
|
|
279
|
+
|
|
280
|
+
if (track) {
|
|
281
|
+
setConfig(track, conf);
|
|
282
|
+
track._fromStorage = true;
|
|
283
|
+
} else if (tracksByNamespace[conf.namespace]) {
|
|
284
|
+
track = tracksByNamespace[conf.namespace];
|
|
285
|
+
|
|
286
|
+
const trackId = track.prototype.id;
|
|
287
|
+
|
|
288
|
+
this.trackIds = this.trackIds || {};
|
|
289
|
+
this.trackIds[trackId] = this.trackIds[trackId] || 1;
|
|
290
|
+
|
|
291
|
+
if (tracksById[trackId]) {
|
|
292
|
+
track = tracksById[trackId];
|
|
293
|
+
}
|
|
294
|
+
|
|
295
|
+
setConfig(track, conf);
|
|
296
|
+
tracks.push(track);
|
|
297
|
+
}
|
|
298
|
+
}
|
|
299
|
+
);
|
|
300
|
+
|
|
301
|
+
this.tracks.forEach(
|
|
302
|
+
(track) => {
|
|
303
|
+
const TrackClass = this.normaliseTrackDefinition(track);
|
|
304
|
+
|
|
305
|
+
if (TrackClass.prototype.id && !tracksById[TrackClass.prototype.id]?._fromStorage) {
|
|
306
|
+
return;
|
|
307
|
+
}
|
|
308
|
+
|
|
309
|
+
tracks.push(TrackClass);
|
|
310
|
+
}
|
|
311
|
+
);
|
|
312
|
+
|
|
313
|
+
this.tracks = tracks;
|
|
314
|
+
this.savedConfig = savedConfig;
|
|
315
|
+
|
|
316
|
+
this.addTracks();
|
|
317
|
+
},
|
|
318
|
+
|
|
319
|
+
saveConfig: function () {
|
|
320
|
+
if (this._constructing || !this.saveable) {
|
|
321
|
+
return;
|
|
322
|
+
}
|
|
323
|
+
|
|
324
|
+
const config = [];
|
|
325
|
+
|
|
326
|
+
this.tracks.forEach(
|
|
327
|
+
(track) => {
|
|
328
|
+
if (track.id && !(track instanceof LegendTrack) && !(track instanceof HighlightRegionTrack)) {
|
|
329
|
+
// when saving height, initialHeight is the height of the track once margins have been added, while defaultHeight is the DEFINED height of the track.
|
|
330
|
+
// Subtracting the difference between them gives you back the correct height to input back into the track when loading configuration
|
|
331
|
+
const conf = {
|
|
332
|
+
id : track.id,
|
|
333
|
+
namespace : track.namespace,
|
|
334
|
+
order : track.order,
|
|
335
|
+
autoHeight : track.autoHeight,
|
|
336
|
+
height : track.height - (track.initialHeight - track.defaultHeight),
|
|
337
|
+
};
|
|
338
|
+
|
|
339
|
+
if (track.config) {
|
|
340
|
+
conf.config = Object.assign(conf.config || {}, track.config);
|
|
341
|
+
}
|
|
342
|
+
|
|
343
|
+
config.push(conf);
|
|
344
|
+
}
|
|
345
|
+
}
|
|
346
|
+
);
|
|
347
|
+
|
|
348
|
+
// Safari in private browsing mode does not allow writes to storage, so wrap in a try/catch to stop errors occuring
|
|
349
|
+
try {
|
|
350
|
+
window[this.storageType].setItem(this.saveKey, JSON.stringify(config));
|
|
351
|
+
} catch (e) {
|
|
352
|
+
// do nothing
|
|
353
|
+
}
|
|
354
|
+
},
|
|
355
|
+
|
|
356
|
+
resetConfig: function () {
|
|
357
|
+
// Non removable highlights should be re-added after reset
|
|
358
|
+
let unremovableHighlights = [];
|
|
359
|
+
|
|
360
|
+
if (this.tracksById.highlights) {
|
|
361
|
+
this.tracksById.highlights.removeHighlights();
|
|
362
|
+
unremovableHighlights = Object.values(this.tracksById.highlights.prop('featuresById'));
|
|
363
|
+
}
|
|
364
|
+
|
|
365
|
+
try {
|
|
366
|
+
window[this.storageType].removeItem(this.saveKey);
|
|
367
|
+
} catch (e) {
|
|
368
|
+
// do nothing
|
|
369
|
+
}
|
|
370
|
+
|
|
371
|
+
this._constructing = true;
|
|
372
|
+
this.savedConfig = {};
|
|
373
|
+
|
|
374
|
+
this.removeTracks([ ...this.tracks ]); // Shallow clone to ensure that removeTracks doesn't hit problems when splicing this.tracks
|
|
375
|
+
this.addTracks(this.jQuery.extend(true, [], this.defaultTracks));
|
|
376
|
+
|
|
377
|
+
if (unremovableHighlights.length) {
|
|
378
|
+
this.addHighlights(unremovableHighlights);
|
|
379
|
+
}
|
|
380
|
+
|
|
381
|
+
this._constructing = false;
|
|
382
|
+
},
|
|
383
|
+
|
|
384
|
+
addDomElements: function (width) {
|
|
385
|
+
const jQuery = this.jQuery;
|
|
386
|
+
|
|
387
|
+
this.menus = jQuery();
|
|
388
|
+
this.labelContainer = jQuery('<ul class="gv-label-container">').appendTo(this.container).sortable({
|
|
389
|
+
items : 'li:not(.gv-unsortable)',
|
|
390
|
+
handle : '.gv-handle',
|
|
391
|
+
axis : 'y',
|
|
392
|
+
helper : 'clone',
|
|
393
|
+
cursor : 'move',
|
|
394
|
+
update : this.updateTrackOrder.bind(this),
|
|
395
|
+
start : function (e, ui) {
|
|
396
|
+
ui.placeholder.css({ height: ui.item.height(), visibility: 'visible' }).html(ui.item.html());
|
|
397
|
+
ui.helper.hide();
|
|
398
|
+
},
|
|
399
|
+
});
|
|
400
|
+
|
|
401
|
+
this.wrapper = this.jQuery('<div class="gv-wrapper">').appendTo(this.container);
|
|
402
|
+
this.selector = this.jQuery('<div class="gv-selector gv-crosshair">').appendTo(this.wrapper);
|
|
403
|
+
|
|
404
|
+
this.selectorControls = this.zoomInHighlight = this.zoomOutHighlight = jQuery();
|
|
405
|
+
|
|
406
|
+
this.container.addClass('gv-canvas-container').width(width);
|
|
407
|
+
|
|
408
|
+
if (!this.isStatic) {
|
|
409
|
+
this.selectorControls = jQuery(`
|
|
410
|
+
<div class="gv-selector-controls gv-panel">
|
|
411
|
+
<div class="gv-button-set">
|
|
412
|
+
<div class="gv-position">
|
|
413
|
+
<div class="gv-chr"></div>
|
|
414
|
+
<div class="gv-start-end">
|
|
415
|
+
<div class="gv-start"></div>
|
|
416
|
+
<div class="gv-end"></div>
|
|
417
|
+
</div>
|
|
418
|
+
</div>
|
|
419
|
+
</div>
|
|
420
|
+
<div class="gv-button-set">
|
|
421
|
+
<button class="gv-zoom-here">Zoom here</butto
|
|
422
|
+
</div>
|
|
423
|
+
<div class="gv-button-set">
|
|
424
|
+
<button class="gv-center">Center</button>
|
|
425
|
+
</div>
|
|
426
|
+
<div class="gv-button-set">
|
|
427
|
+
<button class="gv-highlight">Highlight</butto
|
|
428
|
+
</div>
|
|
429
|
+
<div class="gv-button-set">
|
|
430
|
+
<button class="gv-cancel">Cancel</button>
|
|
431
|
+
</div>
|
|
432
|
+
</div>'
|
|
433
|
+
`).appendTo(this.selector);
|
|
434
|
+
|
|
435
|
+
this.zoomInHighlight = jQuery(`
|
|
436
|
+
<div class="gv-canvas-zoom gv-i">
|
|
437
|
+
<div class="gv-t gv-l gv-h"></div>
|
|
438
|
+
<div class="gv-t gv-r gv-h"></div>
|
|
439
|
+
<div class="gv-t gv-l gv-v"></div>
|
|
440
|
+
<div class="gv-t gv-r gv-v"></div>
|
|
441
|
+
<div class="gv-b gv-l gv-h"></div>
|
|
442
|
+
<div class="gv-b gv-r gv-h"></div>
|
|
443
|
+
<div class="gv-b gv-l gv-v"></div>
|
|
444
|
+
<div class="gv-b gv-r gv-v"></div>
|
|
445
|
+
</div>
|
|
446
|
+
`).appendTo('body');
|
|
447
|
+
|
|
448
|
+
this.zoomOutHighlight = this.zoomInHighlight.clone().toggleClass('gv-i gv-o').appendTo('body');
|
|
449
|
+
}
|
|
450
|
+
},
|
|
451
|
+
|
|
452
|
+
addUserEventHandlers: function () {
|
|
453
|
+
const jQuery = this.jQuery;
|
|
454
|
+
const eventNamespace = this.eventNamespace;
|
|
455
|
+
const documentEvents = {};
|
|
456
|
+
const events = {};
|
|
457
|
+
|
|
458
|
+
events[`mousedown${eventNamespace}`] = (e) => {
|
|
459
|
+
this.hideMessages();
|
|
460
|
+
|
|
461
|
+
// Only scroll on left click, and do nothing if clicking on a button in selectorControls
|
|
462
|
+
if ((!e.which || e.which === 1) && !(e.currentTarget === this.selector[0] && e.target !== e.currentTarget)) {
|
|
463
|
+
this.mousedown(e);
|
|
464
|
+
}
|
|
465
|
+
|
|
466
|
+
return false;
|
|
467
|
+
};
|
|
468
|
+
|
|
469
|
+
events[`mousewheel${eventNamespace}`] = (e, delta, deltaX, deltaY) => {
|
|
470
|
+
if (this.noWheelZoom) {
|
|
471
|
+
return true;
|
|
472
|
+
}
|
|
473
|
+
|
|
474
|
+
this.hideMessages();
|
|
475
|
+
|
|
476
|
+
if (this.wheelAction === 'zoom') {
|
|
477
|
+
return this.mousewheelZoom(e, delta);
|
|
478
|
+
}
|
|
479
|
+
|
|
480
|
+
// Support horizontal wheel/2-finger scroll on trackpads
|
|
481
|
+
if (deltaY === 0 && deltaX !== 0) {
|
|
482
|
+
this.startDragScroll(e);
|
|
483
|
+
this.move(-deltaX * 10);
|
|
484
|
+
this.stopDragScroll(false);
|
|
485
|
+
|
|
486
|
+
return false;
|
|
487
|
+
}
|
|
488
|
+
};
|
|
489
|
+
|
|
490
|
+
events[`dblclick${eventNamespace}`] = (e) => {
|
|
491
|
+
if (this.isStatic) {
|
|
492
|
+
return true;
|
|
493
|
+
}
|
|
494
|
+
|
|
495
|
+
this.hideMessages();
|
|
496
|
+
this.mousewheelZoom(e, 1);
|
|
497
|
+
};
|
|
498
|
+
|
|
499
|
+
this.container.on(events, '.gv-image-container, .gv-selector');
|
|
500
|
+
|
|
501
|
+
this.selectorControls.on('click', (e) => {
|
|
502
|
+
const pos = this.getSelectorPosition();
|
|
503
|
+
|
|
504
|
+
switch (e.target.className) {
|
|
505
|
+
case 'gv-zoom-here':
|
|
506
|
+
this.setRange(pos.start, pos.end, true);
|
|
507
|
+
|
|
508
|
+
break;
|
|
509
|
+
case 'gv-center':
|
|
510
|
+
this.moveTo(this.chr, pos.start, pos.end, true, true);
|
|
511
|
+
this.cancelSelect();
|
|
512
|
+
|
|
513
|
+
break;
|
|
514
|
+
case 'gv-highlight':
|
|
515
|
+
this.addHighlight({ chr: this.chr, start: pos.start, end: pos.end });
|
|
516
|
+
case 'gv-cancel':
|
|
517
|
+
this.cancelSelect();
|
|
518
|
+
|
|
519
|
+
break;
|
|
520
|
+
default: break;
|
|
521
|
+
}
|
|
522
|
+
});
|
|
523
|
+
|
|
524
|
+
documentEvents[`mouseup${this.eventNamespace}`] = this.mouseup.bind(this);
|
|
525
|
+
documentEvents[`mousemove${this.eventNamespace}`] = this.mousemove.bind(this);
|
|
526
|
+
documentEvents[`keydown${this.eventNamespace}`] = this.keydown.bind(this);
|
|
527
|
+
documentEvents[`keyup${this.eventNamespace}`] = this.keyup.bind(this);
|
|
528
|
+
documentEvents[`mousewheel${this.eventNamespace}`] = (e) => {
|
|
529
|
+
if (this.wheelAction === 'zoom') {
|
|
530
|
+
if (this.wheelTimeout) {
|
|
531
|
+
clearTimeout(this.wheelTimeout);
|
|
532
|
+
}
|
|
533
|
+
|
|
534
|
+
this.noWheelZoom = this.noWheelZoom || e.target !== this.container[0];
|
|
535
|
+
this.wheelTimeout = setTimeout(() => { this.noWheelZoom = false; }, 300);
|
|
536
|
+
}
|
|
537
|
+
};
|
|
538
|
+
|
|
539
|
+
jQuery(document).on(documentEvents);
|
|
540
|
+
jQuery(window).on(`${this.useHash ? 'hashchange' : 'popstate'}${this.eventNamespace}`, this.popState.bind(this));
|
|
541
|
+
},
|
|
542
|
+
|
|
543
|
+
onTracks: function (func, ...args) {
|
|
544
|
+
this.tracks.forEach(
|
|
545
|
+
(track) => {
|
|
546
|
+
if (track.disabled) {
|
|
547
|
+
return;
|
|
548
|
+
}
|
|
549
|
+
|
|
550
|
+
const mvc = track._interface[func];
|
|
551
|
+
|
|
552
|
+
if (mvc) {
|
|
553
|
+
track[mvc][func](...args);
|
|
554
|
+
} else if (track[func]) {
|
|
555
|
+
track[func](...args);
|
|
556
|
+
}
|
|
557
|
+
}
|
|
558
|
+
);
|
|
559
|
+
},
|
|
560
|
+
|
|
561
|
+
reset: function (...args) {
|
|
562
|
+
this.onTracks('reset', ...args);
|
|
563
|
+
this.prev = {};
|
|
564
|
+
this.scale = 9e99; // arbitrary value so that setScale resets track scales as well
|
|
565
|
+
this.setRange(this.start, this.end);
|
|
566
|
+
},
|
|
567
|
+
|
|
568
|
+
setWidth: function (width) {
|
|
569
|
+
this.width = width;
|
|
570
|
+
this.width -= this.labelWidth;
|
|
571
|
+
|
|
572
|
+
if (this.controlPanel) {
|
|
573
|
+
this.width -= this.controlPanel.outerWidth(true);
|
|
574
|
+
}
|
|
575
|
+
|
|
576
|
+
if (this.superContainer) {
|
|
577
|
+
this.superContainer.width(width);
|
|
578
|
+
this.container.width(this.width);
|
|
579
|
+
} else {
|
|
580
|
+
this.container.width(width);
|
|
581
|
+
}
|
|
582
|
+
|
|
583
|
+
setTimeout(
|
|
584
|
+
() => {
|
|
585
|
+
this.onTracks('setWidth', Math.min(this.width, this.container.width())); // If this.container has borders, this.container.width() could be less than this.width
|
|
586
|
+
this.reset('resizing');
|
|
587
|
+
},
|
|
588
|
+
1
|
|
589
|
+
);
|
|
590
|
+
},
|
|
591
|
+
|
|
592
|
+
mousewheelZoom: function (e, delta) {
|
|
593
|
+
const jQuery = this.jQuery;
|
|
594
|
+
|
|
595
|
+
clearTimeout(this.zoomDeltaTimeout);
|
|
596
|
+
clearTimeout(this.zoomTimeout);
|
|
597
|
+
|
|
598
|
+
this.zoomDeltaTimeout = setTimeout(
|
|
599
|
+
() => {
|
|
600
|
+
if (delta > 0) {
|
|
601
|
+
this.zoomInHighlight.css({ left: e.pageX - 20, top: e.pageY - 20, display: 'block' }).animate(
|
|
602
|
+
{
|
|
603
|
+
width : 80,
|
|
604
|
+
height : 80,
|
|
605
|
+
top : '-=20',
|
|
606
|
+
left : '-=20',
|
|
607
|
+
},
|
|
608
|
+
{
|
|
609
|
+
complete: function () {
|
|
610
|
+
jQuery(this).css({ width: 40, height: 40, display: 'none' });
|
|
611
|
+
},
|
|
612
|
+
}
|
|
613
|
+
);
|
|
614
|
+
} else {
|
|
615
|
+
this.zoomOutHighlight.css({ left: e.pageX - 40, top: e.pageY - 40, display: 'block' }).animate(
|
|
616
|
+
{
|
|
617
|
+
width : 40,
|
|
618
|
+
height : 40,
|
|
619
|
+
top : '+=20',
|
|
620
|
+
left : '+=20',
|
|
621
|
+
},
|
|
622
|
+
{
|
|
623
|
+
complete: function () {
|
|
624
|
+
jQuery(this).css({ width: 80, height: 80, display: 'none' });
|
|
625
|
+
},
|
|
626
|
+
}
|
|
627
|
+
);
|
|
628
|
+
}
|
|
629
|
+
},
|
|
630
|
+
100
|
|
631
|
+
);
|
|
632
|
+
|
|
633
|
+
this.zoomTimeout = setTimeout(
|
|
634
|
+
() => {
|
|
635
|
+
this[delta > 0 ? 'zoomIn' : 'zoomOut'](e.pageX - this.container.offset().left - this.labelWidth);
|
|
636
|
+
|
|
637
|
+
if (this.dragAction === 'select') {
|
|
638
|
+
this.moveSelector(e);
|
|
639
|
+
}
|
|
640
|
+
},
|
|
641
|
+
300
|
|
642
|
+
);
|
|
643
|
+
|
|
644
|
+
return false;
|
|
645
|
+
},
|
|
646
|
+
|
|
647
|
+
startDragScroll: function (e) {
|
|
648
|
+
this.dragging = 'scroll';
|
|
649
|
+
this.scrolling = !e;
|
|
650
|
+
this.dragOffset = e ? e.pageX - this.left : 0;
|
|
651
|
+
this.dragStart = this.start;
|
|
652
|
+
this.scrollDelta = Math.max(this.scale, this.defaultScrollDelta);
|
|
653
|
+
},
|
|
654
|
+
|
|
655
|
+
stopDragScroll: function (update) {
|
|
656
|
+
this.dragging = false;
|
|
657
|
+
this.scrolling = false;
|
|
658
|
+
|
|
659
|
+
if (update !== false) {
|
|
660
|
+
if (this.start !== this.dragStart) {
|
|
661
|
+
this.updateURL();
|
|
662
|
+
}
|
|
663
|
+
|
|
664
|
+
this.checkTrackHeights();
|
|
665
|
+
}
|
|
666
|
+
},
|
|
667
|
+
|
|
668
|
+
startDragSelect: function (e) {
|
|
669
|
+
if (!e) {
|
|
670
|
+
return false;
|
|
671
|
+
}
|
|
672
|
+
|
|
673
|
+
const x = Math.max(0, e.pageX - this.wrapper.offset().left - 2);
|
|
674
|
+
|
|
675
|
+
this.dragging = 'select';
|
|
676
|
+
this.selectorStalled = false;
|
|
677
|
+
this.selectorStart = x;
|
|
678
|
+
|
|
679
|
+
this.selector.css({ left: x, width: 0 }).removeClass('gv-crosshair');
|
|
680
|
+
this.selectorControls.hide();
|
|
681
|
+
},
|
|
682
|
+
|
|
683
|
+
stopDragSelect: function (e) {
|
|
684
|
+
if (!e) {
|
|
685
|
+
return false;
|
|
686
|
+
}
|
|
687
|
+
|
|
688
|
+
this.dragging = false;
|
|
689
|
+
this.selectorStalled = true;
|
|
690
|
+
|
|
691
|
+
if (this.selector.outerWidth(true) < 2) {
|
|
692
|
+
return this.cancelSelect();
|
|
693
|
+
}
|
|
694
|
+
|
|
695
|
+
// Calculate the position, so that selectorControls appear near the mouse cursor
|
|
696
|
+
const top = Math.min(e.pageY - this.wrapper.offset().top, this.wrapper.outerHeight(true) - 1.2 * this.selectorControls.outerHeight(true));
|
|
697
|
+
const pos = this.getSelectorPosition();
|
|
698
|
+
|
|
699
|
+
this.selectorControls.find('.gv-chr').html(this.chr);
|
|
700
|
+
this.selectorControls.find('.gv-start').html(pos.start);
|
|
701
|
+
this.selectorControls.find('.gv-end').html(pos.end);
|
|
702
|
+
|
|
703
|
+
this.selectorControls.find('.gv-selector-location').html(`${this.chr}:${pos.start}-${pos.end}`).end().css({
|
|
704
|
+
top : top,
|
|
705
|
+
left : this.selector.outerWidth(true) / 2 - this.selectorControls.outerWidth(true) / 2,
|
|
706
|
+
}).show();
|
|
707
|
+
},
|
|
708
|
+
|
|
709
|
+
cancelSelect: function (keepDragging) {
|
|
710
|
+
if (!keepDragging) {
|
|
711
|
+
this.dragging = false;
|
|
712
|
+
}
|
|
713
|
+
|
|
714
|
+
this.selectorStalled = false;
|
|
715
|
+
|
|
716
|
+
this.selector.addClass('gv-crosshair').width(0);
|
|
717
|
+
this.selectorControls.hide();
|
|
718
|
+
|
|
719
|
+
if (this.dragAction === 'scroll') {
|
|
720
|
+
this.selector.hide();
|
|
721
|
+
}
|
|
722
|
+
},
|
|
723
|
+
|
|
724
|
+
dragSelect: function (e) {
|
|
725
|
+
const x = e.pageX - this.wrapper.offset().left;
|
|
726
|
+
|
|
727
|
+
if (x > this.selectorStart) {
|
|
728
|
+
this.selector.css({
|
|
729
|
+
left : this.selectorStart,
|
|
730
|
+
width : Math.min(x - this.selectorStart, this.width - this.selectorStart - 1),
|
|
731
|
+
});
|
|
732
|
+
} else {
|
|
733
|
+
this.selector.css({
|
|
734
|
+
left : Math.max(x, 1),
|
|
735
|
+
width : Math.min(this.selectorStart - x, this.selectorStart - 1),
|
|
736
|
+
});
|
|
737
|
+
}
|
|
738
|
+
},
|
|
739
|
+
|
|
740
|
+
setDragAction: function (action, keepSelect) {
|
|
741
|
+
this.dragAction = action;
|
|
742
|
+
|
|
743
|
+
if (this.dragAction === 'select') {
|
|
744
|
+
this.selector.addClass('gv-crosshair').width(0).show();
|
|
745
|
+
} else if (keepSelect && !this.selector.hasClass('gv-crosshair')) {
|
|
746
|
+
this.selectorStalled = false;
|
|
747
|
+
} else {
|
|
748
|
+
this.cancelSelect();
|
|
749
|
+
this.selector.hide();
|
|
750
|
+
}
|
|
751
|
+
},
|
|
752
|
+
|
|
753
|
+
toggleSelect: function (on) {
|
|
754
|
+
if (on) {
|
|
755
|
+
this.prev.dragAction = 'scroll';
|
|
756
|
+
this.setDragAction('select');
|
|
757
|
+
} else {
|
|
758
|
+
this.setDragAction(this.prev.dragAction, true);
|
|
759
|
+
delete this.prev.dragAction;
|
|
760
|
+
}
|
|
761
|
+
},
|
|
762
|
+
|
|
763
|
+
setWheelAction: function (action) {
|
|
764
|
+
this.wheelAction = action;
|
|
765
|
+
},
|
|
766
|
+
|
|
767
|
+
keydown: function (e) {
|
|
768
|
+
if (e.which === 16 && !this.prev.dragAction && this.dragAction === 'scroll') { // shift key
|
|
769
|
+
this.toggleSelect(true);
|
|
770
|
+
} else if (e.which === 27) { // escape key
|
|
771
|
+
this.cancelSelect();
|
|
772
|
+
this.closeMenus();
|
|
773
|
+
}
|
|
774
|
+
},
|
|
775
|
+
|
|
776
|
+
keyup: function (e) {
|
|
777
|
+
if (e.which === 16 && this.prev.dragAction) { // shift key
|
|
778
|
+
this.toggleSelect();
|
|
779
|
+
}
|
|
780
|
+
},
|
|
781
|
+
|
|
782
|
+
mousedown: function (e) {
|
|
783
|
+
if (e.shiftKey) {
|
|
784
|
+
if (this.dragAction === 'scroll') {
|
|
785
|
+
this.toggleSelect(true);
|
|
786
|
+
}
|
|
787
|
+
} else if (this.prev.dragAction) {
|
|
788
|
+
this.toggleSelect();
|
|
789
|
+
}
|
|
790
|
+
|
|
791
|
+
switch (this.dragAction) {
|
|
792
|
+
case 'select':
|
|
793
|
+
this.startDragSelect(e);
|
|
794
|
+
|
|
795
|
+
break;
|
|
796
|
+
case 'scroll':
|
|
797
|
+
this.startDragScroll(e);
|
|
798
|
+
|
|
799
|
+
break;
|
|
800
|
+
default: break;
|
|
801
|
+
}
|
|
802
|
+
},
|
|
803
|
+
|
|
804
|
+
mouseup: function (e) {
|
|
805
|
+
switch (this.dragging) {
|
|
806
|
+
case 'select':
|
|
807
|
+
this.stopDragSelect(e);
|
|
808
|
+
|
|
809
|
+
break;
|
|
810
|
+
case 'scroll':
|
|
811
|
+
this.stopDragScroll();
|
|
812
|
+
|
|
813
|
+
break;
|
|
814
|
+
default: break;
|
|
815
|
+
}
|
|
816
|
+
},
|
|
817
|
+
|
|
818
|
+
mousemove: function (e) {
|
|
819
|
+
if (this.dragging && !this.scrolling) {
|
|
820
|
+
switch (this.dragAction) {
|
|
821
|
+
case 'scroll':
|
|
822
|
+
this.move(e.pageX - this.dragOffset - this.left);
|
|
823
|
+
|
|
824
|
+
break;
|
|
825
|
+
case 'select':
|
|
826
|
+
this.dragSelect(e);
|
|
827
|
+
|
|
828
|
+
break;
|
|
829
|
+
default: break;
|
|
830
|
+
}
|
|
831
|
+
} else if (this.dragAction === 'select') {
|
|
832
|
+
this.moveSelector(e);
|
|
833
|
+
}
|
|
834
|
+
},
|
|
835
|
+
|
|
836
|
+
moveSelector: function (e) {
|
|
837
|
+
if (!this.selectorStalled) {
|
|
838
|
+
this.selector.css('left', e.pageX - this.wrapper.offset().left - 2);
|
|
839
|
+
}
|
|
840
|
+
},
|
|
841
|
+
|
|
842
|
+
move: function (delta) {
|
|
843
|
+
const scale = this.scale;
|
|
844
|
+
|
|
845
|
+
if (scale > 1) {
|
|
846
|
+
delta = Math.round(delta / scale) * scale; // Force stepping by base pair when in small regions
|
|
847
|
+
}
|
|
848
|
+
|
|
849
|
+
let left = this.left + delta;
|
|
850
|
+
|
|
851
|
+
if (left <= this.minLeft) {
|
|
852
|
+
left = this.minLeft;
|
|
853
|
+
delta = this.minLeft - this.left;
|
|
854
|
+
} else if (left >= this.maxLeft) {
|
|
855
|
+
left = this.maxLeft;
|
|
856
|
+
delta = this.maxLeft - this.left;
|
|
857
|
+
}
|
|
858
|
+
|
|
859
|
+
let start = Math.max(Math.round(this.start - delta / scale), 1);
|
|
860
|
+
let end = start + this.length - 1;
|
|
861
|
+
|
|
862
|
+
if (end > this.chromosomeSize) {
|
|
863
|
+
end = this.chromosomeSize;
|
|
864
|
+
start = end - this.length + 1;
|
|
865
|
+
}
|
|
866
|
+
|
|
867
|
+
this.left = left;
|
|
868
|
+
|
|
869
|
+
if (start !== this.dragStart) {
|
|
870
|
+
this.closeMenus();
|
|
871
|
+
this.cancelSelect(true);
|
|
872
|
+
}
|
|
873
|
+
|
|
874
|
+
this.onTracks('move', delta);
|
|
875
|
+
this.setRange(start, end);
|
|
876
|
+
},
|
|
877
|
+
|
|
878
|
+
moveTo: function (chr, start, end, update, keepLength) {
|
|
879
|
+
if (typeof chr !== 'undefined' && String(chr) !== String(this.chr)) {
|
|
880
|
+
if (this.canChangeChr) {
|
|
881
|
+
if (this.genome && this.genome[chr]) {
|
|
882
|
+
this.chr = chr;
|
|
883
|
+
this.chromosomeSize = this.genome[chr].size;
|
|
884
|
+
this.start = this.end = this.scale = -1;
|
|
885
|
+
} else {
|
|
886
|
+
this.die('Chromosome cannot be found in genome');
|
|
887
|
+
}
|
|
888
|
+
|
|
889
|
+
this.onTracks('changeChr');
|
|
890
|
+
} else {
|
|
891
|
+
this.die('Chromosome changing is not allowed');
|
|
892
|
+
}
|
|
893
|
+
}
|
|
894
|
+
|
|
895
|
+
this.setRange(start, end, update, keepLength);
|
|
896
|
+
|
|
897
|
+
if (this.prev.scale === this.scale) {
|
|
898
|
+
this.left = Math.max(Math.min(this.left + Math.round((this.prev.start - this.start) * this.scale), this.maxLeft), this.minLeft);
|
|
899
|
+
this.onTracks('moveTo', this.chr, this.start, this.end, (this.prev.start - this.start) * this.scale);
|
|
900
|
+
}
|
|
901
|
+
},
|
|
902
|
+
|
|
903
|
+
setRange: function (start, end, update, keepLength) {
|
|
904
|
+
this.prev.start = this.start;
|
|
905
|
+
this.prev.end = this.end;
|
|
906
|
+
this.start = Math.min(Math.max(typeof start === 'number' ? Math.floor(start) : parseInt(start, 10), 1), this.chromosomeSize);
|
|
907
|
+
this.end = Math.max(Math.min(typeof end === 'number' ? Math.floor(end) : parseInt(end, 10), this.chromosomeSize), 1);
|
|
908
|
+
|
|
909
|
+
if (this.end < this.start) {
|
|
910
|
+
this.end = Math.min(this.start + this.defaultLength - 1, this.chromosomeSize);
|
|
911
|
+
}
|
|
912
|
+
|
|
913
|
+
if (keepLength && this.end - this.start + 1 !== this.length) {
|
|
914
|
+
if (this.end === this.chromosomeSize) {
|
|
915
|
+
this.start = this.end - this.length + 1;
|
|
916
|
+
} else {
|
|
917
|
+
const center = (this.start + this.end) / 2;
|
|
918
|
+
|
|
919
|
+
this.start = Math.max(Math.floor(center - this.length / 2), 1);
|
|
920
|
+
this.end = this.start + this.length - 1;
|
|
921
|
+
|
|
922
|
+
if (this.end > this.chromosomeSize) {
|
|
923
|
+
this.end = this.chromosomeSize;
|
|
924
|
+
this.start = this.end - this.length + 1;
|
|
925
|
+
}
|
|
926
|
+
}
|
|
927
|
+
} else {
|
|
928
|
+
this.length = this.end - this.start + 1;
|
|
929
|
+
}
|
|
930
|
+
|
|
931
|
+
this.setScale();
|
|
932
|
+
|
|
933
|
+
if (update === true && (this.prev.start !== this.start || this.prev.end !== this.end)) {
|
|
934
|
+
this.updateURL();
|
|
935
|
+
}
|
|
936
|
+
},
|
|
937
|
+
|
|
938
|
+
setScale: function () {
|
|
939
|
+
this.prev.scale = this.scale;
|
|
940
|
+
this.scale = this.width / this.length;
|
|
941
|
+
this.scaledStart = this.start * this.scale;
|
|
942
|
+
|
|
943
|
+
if (this.prev.scale !== this.scale) {
|
|
944
|
+
this.left = 0;
|
|
945
|
+
this.minLeft = Math.round((this.end - this.chromosomeSize) * this.scale);
|
|
946
|
+
this.maxLeft = Math.round((this.start - 1) * this.scale);
|
|
947
|
+
this.labelBuffer = Math.ceil(this.textWidth / this.scale) * this.longestLabel;
|
|
948
|
+
|
|
949
|
+
if (this.prev.scale) {
|
|
950
|
+
this.cancelSelect();
|
|
951
|
+
this.closeMenus();
|
|
952
|
+
}
|
|
953
|
+
|
|
954
|
+
this.onTracks('setScale');
|
|
955
|
+
this.onTracks('makeFirstImage');
|
|
956
|
+
}
|
|
957
|
+
},
|
|
958
|
+
|
|
959
|
+
checkTrackHeights: function () {
|
|
960
|
+
if (this.dragging) {
|
|
961
|
+
return;
|
|
962
|
+
}
|
|
963
|
+
|
|
964
|
+
this.onTracks('checkHeight');
|
|
965
|
+
},
|
|
966
|
+
|
|
967
|
+
resetTrackHeights: function () {
|
|
968
|
+
this.onTracks('resetHeight');
|
|
969
|
+
},
|
|
970
|
+
|
|
971
|
+
zoomIn: function (x) {
|
|
972
|
+
if (!x) {
|
|
973
|
+
x = this.width / 2;
|
|
974
|
+
}
|
|
975
|
+
|
|
976
|
+
const start = Math.round(this.start + x / (2 * this.scale));
|
|
977
|
+
const end = this.length === 2 ? start : Math.round(start + (this.length - 1) / 2);
|
|
978
|
+
|
|
979
|
+
this.setRange(start, end, true);
|
|
980
|
+
},
|
|
981
|
+
|
|
982
|
+
zoomOut: function (x) {
|
|
983
|
+
if (!x) {
|
|
984
|
+
x = this.width / 2;
|
|
985
|
+
}
|
|
986
|
+
|
|
987
|
+
const start = Math.round(this.start - x / this.scale);
|
|
988
|
+
const end = this.length === 1 ? start + 1 : Math.round(start + 2 * (this.length - 1));
|
|
989
|
+
|
|
990
|
+
this.setRange(start, end, true);
|
|
991
|
+
},
|
|
992
|
+
|
|
993
|
+
normaliseTrackDefinition: function (trackDefinition, baseObjName = 'Track') {
|
|
994
|
+
const baseObj = _get(Genoverse, baseObjName);
|
|
995
|
+
const baseObjNameArray = baseObjName.split('.');
|
|
996
|
+
|
|
997
|
+
const getObj = (t) => {
|
|
998
|
+
const objNameArray = t.split('.');
|
|
999
|
+
const objName = objNameArray.filter(n => n !== 'Genoverse' && !baseObjNameArray.includes(n)).join('.');
|
|
1000
|
+
|
|
1001
|
+
return objName === baseObjName ? baseObj : _get(baseObj, objName);
|
|
1002
|
+
};
|
|
1003
|
+
|
|
1004
|
+
const normalise = t => ({
|
|
1005
|
+
...t,
|
|
1006
|
+
...(t.controller ? { controller: this.normaliseTrackDefinition(t.controller, 'Track.Controller') } : {}),
|
|
1007
|
+
...(t.model ? { model: this.normaliseTrackDefinition(t.model, 'Track.Model') } : {}),
|
|
1008
|
+
...(t.view ? { view: this.normaliseTrackDefinition(t.view, 'Track.View') } : {}),
|
|
1009
|
+
});
|
|
1010
|
+
|
|
1011
|
+
// e.g. 'Genoverse.Track.Foo' -> Genoverse.Track.Foo
|
|
1012
|
+
if (typeof trackDefinition === 'string') {
|
|
1013
|
+
return getObj(trackDefinition);
|
|
1014
|
+
}
|
|
1015
|
+
|
|
1016
|
+
// e.g. [ 'Genoverse.Track.Foo', { foo: true } ] -> Genoverse.Track.Foo.extend({ foo: true })
|
|
1017
|
+
if (Array.isArray(trackDefinition) && typeof trackDefinition[0] === 'string') {
|
|
1018
|
+
const obj = getObj(trackDefinition[0]);
|
|
1019
|
+
|
|
1020
|
+
return typeof trackDefinition[1] === 'object' && Object.keys(trackDefinition[1]).length ? obj.extend(normalise(trackDefinition[1])) : obj;
|
|
1021
|
+
}
|
|
1022
|
+
|
|
1023
|
+
// e.g. { foo: true } -> Genoverse.Track.extend({ foo: true })
|
|
1024
|
+
if (typeof trackDefinition === 'object' && Object.keys(trackDefinition).length) {
|
|
1025
|
+
return baseObj.extend(normalise(trackDefinition));
|
|
1026
|
+
}
|
|
1027
|
+
|
|
1028
|
+
return trackDefinition;
|
|
1029
|
+
},
|
|
1030
|
+
|
|
1031
|
+
addTrack: function (track, after) {
|
|
1032
|
+
return this.addTracks([ track ], after)[0];
|
|
1033
|
+
},
|
|
1034
|
+
|
|
1035
|
+
addTracks: function (tracks, after) {
|
|
1036
|
+
const jQuery = this.jQuery;
|
|
1037
|
+
|
|
1038
|
+
const defaults = {
|
|
1039
|
+
browser : this,
|
|
1040
|
+
width : Math.min(this.width, this.container.width()), // If this.container has borders, this.container.width() could be less than this.width
|
|
1041
|
+
};
|
|
1042
|
+
|
|
1043
|
+
const push = Boolean(tracks);
|
|
1044
|
+
|
|
1045
|
+
let order;
|
|
1046
|
+
|
|
1047
|
+
if (push && !this.tracks.filter(t => typeof t === 'function').length) {
|
|
1048
|
+
const [ insertAfter ] = (after ? this.tracks.filter(t => t.order < after) : this.tracks).sort((a, b) => b.order - a.order);
|
|
1049
|
+
|
|
1050
|
+
if (insertAfter) {
|
|
1051
|
+
order = insertAfter.order + 0.1;
|
|
1052
|
+
}
|
|
1053
|
+
}
|
|
1054
|
+
|
|
1055
|
+
tracks = tracks || [ ...this.tracks ];
|
|
1056
|
+
|
|
1057
|
+
for (let i = 0; i < tracks.length; i++) {
|
|
1058
|
+
const TrackClass = this.normaliseTrackDefinition(tracks[i]);
|
|
1059
|
+
|
|
1060
|
+
tracks[i] = new TrackClass({
|
|
1061
|
+
...defaults,
|
|
1062
|
+
namespace : Genoverse.getTrackNamespace(TrackClass),
|
|
1063
|
+
order : typeof order === 'number' ? order : i,
|
|
1064
|
+
config : this.savedConfig ? jQuery.extend(true, {}, this.savedConfig[TrackClass.prototype.id]) : undefined,
|
|
1065
|
+
});
|
|
1066
|
+
|
|
1067
|
+
if (tracks[i].id) {
|
|
1068
|
+
this.tracksById[tracks[i].id] = tracks[i];
|
|
1069
|
+
}
|
|
1070
|
+
|
|
1071
|
+
if (push) {
|
|
1072
|
+
this.tracks.push(tracks[i]);
|
|
1073
|
+
} else {
|
|
1074
|
+
this.tracks[i] = tracks[i];
|
|
1075
|
+
}
|
|
1076
|
+
}
|
|
1077
|
+
|
|
1078
|
+
this.sortTracks();
|
|
1079
|
+
this.saveConfig();
|
|
1080
|
+
|
|
1081
|
+
return tracks;
|
|
1082
|
+
},
|
|
1083
|
+
|
|
1084
|
+
removeTrack: function (track) {
|
|
1085
|
+
if (track) {
|
|
1086
|
+
this.removeTracks((track.prop('childTracks') || []).concat(track));
|
|
1087
|
+
}
|
|
1088
|
+
},
|
|
1089
|
+
|
|
1090
|
+
removeTracks: function (tracks) {
|
|
1091
|
+
let i = tracks.length;
|
|
1092
|
+
|
|
1093
|
+
while (i--) {
|
|
1094
|
+
const track = tracks[i];
|
|
1095
|
+
|
|
1096
|
+
let j = this.tracks.length;
|
|
1097
|
+
|
|
1098
|
+
while (j--) {
|
|
1099
|
+
if (track === this.tracks[j]) {
|
|
1100
|
+
this.tracks.splice(j, 1);
|
|
1101
|
+
|
|
1102
|
+
break;
|
|
1103
|
+
}
|
|
1104
|
+
}
|
|
1105
|
+
|
|
1106
|
+
if (track.id) {
|
|
1107
|
+
delete this.tracksById[track.id];
|
|
1108
|
+
}
|
|
1109
|
+
|
|
1110
|
+
track.destructor(); // Destroy DOM elements and track itself
|
|
1111
|
+
}
|
|
1112
|
+
|
|
1113
|
+
this.saveConfig();
|
|
1114
|
+
},
|
|
1115
|
+
|
|
1116
|
+
sortTracks: function () {
|
|
1117
|
+
const jQuery = this.jQuery;
|
|
1118
|
+
|
|
1119
|
+
if (this.tracks.some(track => typeof track !== 'object')) {
|
|
1120
|
+
return;
|
|
1121
|
+
}
|
|
1122
|
+
|
|
1123
|
+
const sorted = this.tracks.slice().sort((a, b) => a.order - b.order);
|
|
1124
|
+
const labels = jQuery();
|
|
1125
|
+
const containers = jQuery();
|
|
1126
|
+
|
|
1127
|
+
sorted.forEach(
|
|
1128
|
+
(track, i) => {
|
|
1129
|
+
if (track.prop('parentTrack')) {
|
|
1130
|
+
return;
|
|
1131
|
+
}
|
|
1132
|
+
|
|
1133
|
+
if (!track.prop('fixedOrder')) {
|
|
1134
|
+
track.prop('order', i);
|
|
1135
|
+
}
|
|
1136
|
+
|
|
1137
|
+
const container = track.prop('superContainer') || track.prop('container');
|
|
1138
|
+
|
|
1139
|
+
if (track.prop('menus').length) {
|
|
1140
|
+
track.prop('top', container.position().top);
|
|
1141
|
+
}
|
|
1142
|
+
|
|
1143
|
+
labels.push(track.prop('label')[0]);
|
|
1144
|
+
containers.push(container[0]);
|
|
1145
|
+
}
|
|
1146
|
+
);
|
|
1147
|
+
|
|
1148
|
+
this.labelContainer.append(labels);
|
|
1149
|
+
this.wrapper.append(containers);
|
|
1150
|
+
|
|
1151
|
+
// Correct the order
|
|
1152
|
+
this.tracks = sorted;
|
|
1153
|
+
|
|
1154
|
+
labels.map(function () { return jQuery(this).data('track'); }).each(function () {
|
|
1155
|
+
if (this.prop('menus').length) {
|
|
1156
|
+
const diff = (this.prop('superContainer') || this.prop('container')).position().top - this.prop('top');
|
|
1157
|
+
|
|
1158
|
+
this.prop('menus').css('top', (j, top) => parseInt(top, 10) + diff);
|
|
1159
|
+
this.prop('top', null);
|
|
1160
|
+
}
|
|
1161
|
+
});
|
|
1162
|
+
},
|
|
1163
|
+
|
|
1164
|
+
updateTrackOrder: function (e, ui) {
|
|
1165
|
+
const track = ui.item.data('track');
|
|
1166
|
+
|
|
1167
|
+
if (track.prop('unsortable') || track.prop('fixedOrder')) {
|
|
1168
|
+
return;
|
|
1169
|
+
}
|
|
1170
|
+
|
|
1171
|
+
const prev = ui.item.prev().data('track');
|
|
1172
|
+
const next = ui.item.next().data('track');
|
|
1173
|
+
const p = prev ? prev.prop('order') : 0;
|
|
1174
|
+
const n = next ? next.prop('order') : 0;
|
|
1175
|
+
const o = p || n;
|
|
1176
|
+
const order = (
|
|
1177
|
+
prev && next && Math.floor(n) === Math.floor(p)
|
|
1178
|
+
? p + (n - p) / 2
|
|
1179
|
+
: o + ((p ? 1 : -1) * Math.abs(Math.round(o) - o || 1)) / 2
|
|
1180
|
+
);
|
|
1181
|
+
|
|
1182
|
+
track.prop('order', order);
|
|
1183
|
+
|
|
1184
|
+
this.sortTracks();
|
|
1185
|
+
this.saveConfig();
|
|
1186
|
+
},
|
|
1187
|
+
|
|
1188
|
+
updateURL: function () {
|
|
1189
|
+
if (this.urlParamTemplate) {
|
|
1190
|
+
if (this.useHash) {
|
|
1191
|
+
window.location.hash = this.getQueryString();
|
|
1192
|
+
} else {
|
|
1193
|
+
window.history.pushState({}, '', this.getQueryString());
|
|
1194
|
+
}
|
|
1195
|
+
}
|
|
1196
|
+
},
|
|
1197
|
+
|
|
1198
|
+
popState: function () {
|
|
1199
|
+
if (this.baseURL && !window.location.href.match(this.baseURL)) {
|
|
1200
|
+
return;
|
|
1201
|
+
}
|
|
1202
|
+
|
|
1203
|
+
const coords = this.getCoords();
|
|
1204
|
+
const start = parseInt(coords.start, 10);
|
|
1205
|
+
const end = parseInt(coords.end, 10);
|
|
1206
|
+
|
|
1207
|
+
if (
|
|
1208
|
+
(coords.chr && String(coords.chr) !== String(this.chr)) ||
|
|
1209
|
+
(coords.start && !(start === this.start && end === this.end))
|
|
1210
|
+
) {
|
|
1211
|
+
// FIXME: a back action which changes scale or a zoom out will reset tracks, since scrollStart will not be the same as it was before
|
|
1212
|
+
this.moveTo(coords.chr, start, end);
|
|
1213
|
+
this.closeMenus();
|
|
1214
|
+
this.hideMessages();
|
|
1215
|
+
}
|
|
1216
|
+
},
|
|
1217
|
+
|
|
1218
|
+
getCoords: function () {
|
|
1219
|
+
const coords = {};
|
|
1220
|
+
|
|
1221
|
+
let match = `${decodeURIComponent(this.useHash ? window.location.hash.replace(/^#/, '?') || window.location.search : window.location.search)}&`.match(this.paramRegex);
|
|
1222
|
+
let i = 0;
|
|
1223
|
+
|
|
1224
|
+
if (!match) {
|
|
1225
|
+
return this.initialLocation;
|
|
1226
|
+
}
|
|
1227
|
+
|
|
1228
|
+
match = match.slice(2, -1);
|
|
1229
|
+
|
|
1230
|
+
this.urlParamTemplate.split('__').forEach(
|
|
1231
|
+
(part) => {
|
|
1232
|
+
const partMatch = part.match(/^(CHR|START|END)$/);
|
|
1233
|
+
|
|
1234
|
+
if (partMatch) {
|
|
1235
|
+
coords[partMatch[1].toLowerCase()] = partMatch[1] === 'CHR' ? match[i++] : parseInt(match[i++], 10);
|
|
1236
|
+
}
|
|
1237
|
+
}
|
|
1238
|
+
);
|
|
1239
|
+
|
|
1240
|
+
return (
|
|
1241
|
+
coords.chr && coords.start && coords.end && (this.genome ? this.genome[coords.chr] : true)
|
|
1242
|
+
? coords
|
|
1243
|
+
: this.initialLocation
|
|
1244
|
+
);
|
|
1245
|
+
},
|
|
1246
|
+
|
|
1247
|
+
getQueryString: function () {
|
|
1248
|
+
const location = this.urlParamTemplate
|
|
1249
|
+
.replace('__CHR__', this.chr)
|
|
1250
|
+
.replace('__START__', this.start)
|
|
1251
|
+
.replace('__END__', this.end);
|
|
1252
|
+
|
|
1253
|
+
const currentLocation = `${decodeURIComponent(this.useHash ? window.location.hash.replace(/^#/, '?') : window.location.search)}&`;
|
|
1254
|
+
|
|
1255
|
+
let newLocation = (
|
|
1256
|
+
currentLocation.match(this.paramRegex)
|
|
1257
|
+
? currentLocation.replace(this.paramRegex, `$1${location}$5`).slice(0, -1)
|
|
1258
|
+
: `${currentLocation}${location}`
|
|
1259
|
+
);
|
|
1260
|
+
|
|
1261
|
+
if (this.useHash) {
|
|
1262
|
+
newLocation = newLocation.replace(/^[&?]/, '');
|
|
1263
|
+
} else if (newLocation.indexOf('?') !== 0) {
|
|
1264
|
+
newLocation = `?${newLocation.replace(/^&/, '')}`;
|
|
1265
|
+
}
|
|
1266
|
+
|
|
1267
|
+
return newLocation;
|
|
1268
|
+
},
|
|
1269
|
+
|
|
1270
|
+
getChromosomeSize: function (chr) {
|
|
1271
|
+
return chr && this.genome && this.genome[chr] ? this.genome[chr].size : this.chromosomeSize;
|
|
1272
|
+
},
|
|
1273
|
+
|
|
1274
|
+
supported: function () {
|
|
1275
|
+
const el = document.createElement('canvas');
|
|
1276
|
+
|
|
1277
|
+
return !!(el.getContext && el.getContext('2d'));
|
|
1278
|
+
},
|
|
1279
|
+
|
|
1280
|
+
die: function (error, el) {
|
|
1281
|
+
if (el && el.length) {
|
|
1282
|
+
el.html(error);
|
|
1283
|
+
} else {
|
|
1284
|
+
throw error;
|
|
1285
|
+
}
|
|
1286
|
+
|
|
1287
|
+
this.failed = true;
|
|
1288
|
+
},
|
|
1289
|
+
|
|
1290
|
+
createMenuEl: function () {
|
|
1291
|
+
const jQuery = this.jQuery;
|
|
1292
|
+
|
|
1293
|
+
this.menuTemplate = this.menuTemplate || jQuery(`
|
|
1294
|
+
<div class="gv-menu">
|
|
1295
|
+
<div class="gv-close gv-menu-button fas fa-times-circle"></div>
|
|
1296
|
+
<div class="gv-menu-loading">Loading...</div>
|
|
1297
|
+
<div class="gv-menu-error">An error has occurred</div>
|
|
1298
|
+
<div class="gv-menu-content">
|
|
1299
|
+
<div class="gv-title"></div>
|
|
1300
|
+
<table class="gv-focus-highlight">
|
|
1301
|
+
<tr>
|
|
1302
|
+
<td><a class="gv-focus" href="#">Focus here</a></td>
|
|
1303
|
+
<td><a class="gv-highlight" href="#">Highlight this feature</a></td>
|
|
1304
|
+
</tr>
|
|
1305
|
+
</table>
|
|
1306
|
+
<table></table>
|
|
1307
|
+
</div>
|
|
1308
|
+
</div>
|
|
1309
|
+
`).on('click', function (e) {
|
|
1310
|
+
const menuEl = jQuery(this);
|
|
1311
|
+
|
|
1312
|
+
if (jQuery(e.target).hasClass('gv-close')) {
|
|
1313
|
+
menuEl.fadeOut('fast', function () {
|
|
1314
|
+
const data = menuEl.data();
|
|
1315
|
+
|
|
1316
|
+
if (data.track) {
|
|
1317
|
+
data.track.prop('menus', data.track.prop('menus').not(this));
|
|
1318
|
+
}
|
|
1319
|
+
|
|
1320
|
+
data.browser.menus = data.browser.menus.not(this);
|
|
1321
|
+
});
|
|
1322
|
+
}
|
|
1323
|
+
});
|
|
1324
|
+
|
|
1325
|
+
return this.menuTemplate.clone(true).data({ browser: this });
|
|
1326
|
+
},
|
|
1327
|
+
|
|
1328
|
+
makeMenu: function (features, event, track) {
|
|
1329
|
+
const jQuery = this.jQuery;
|
|
1330
|
+
|
|
1331
|
+
if (!features) {
|
|
1332
|
+
return false;
|
|
1333
|
+
}
|
|
1334
|
+
|
|
1335
|
+
features = [].concat(features);
|
|
1336
|
+
|
|
1337
|
+
if (features.length === 0) {
|
|
1338
|
+
return false;
|
|
1339
|
+
}
|
|
1340
|
+
|
|
1341
|
+
if (features.length === 1) {
|
|
1342
|
+
return this.makeFeatureMenu(features[0], event, track);
|
|
1343
|
+
}
|
|
1344
|
+
|
|
1345
|
+
const menuEl = this.createMenuEl();
|
|
1346
|
+
const contentEl = jQuery('.gv-menu-content', menuEl).addClass('gv-menu-content-first');
|
|
1347
|
+
const table = jQuery('table:not(.gv-focus-highlight)', contentEl);
|
|
1348
|
+
|
|
1349
|
+
jQuery('.gv-focus-highlight, .gv-menu-loading', menuEl).remove();
|
|
1350
|
+
jQuery('.gv-title', menuEl).html(`${features.length} features`);
|
|
1351
|
+
|
|
1352
|
+
(track ? track.model.sortFeatures(features) : features.sort((a, b) => a.start - b.start)).forEach(
|
|
1353
|
+
(feature) => {
|
|
1354
|
+
const location = `${feature.chr}:${feature.start}${feature.end === feature.start ? '' : `-${feature.end}`}`;
|
|
1355
|
+
const title = feature.menuLabel || feature.name || (Array.isArray(feature.label) ? feature.label.join(' ') : feature.label) || String(feature.id);
|
|
1356
|
+
|
|
1357
|
+
jQuery('<a href="#">').html(title.match(location) ? title : `${location} ${title}`).on('click', (e) => {
|
|
1358
|
+
this.makeFeatureMenu(feature, e, track);
|
|
1359
|
+
|
|
1360
|
+
return false;
|
|
1361
|
+
}).appendTo(
|
|
1362
|
+
jQuery('<td>').appendTo(
|
|
1363
|
+
jQuery('<tr>').appendTo(table)
|
|
1364
|
+
)
|
|
1365
|
+
);
|
|
1366
|
+
}
|
|
1367
|
+
);
|
|
1368
|
+
|
|
1369
|
+
jQuery('<div class="gv-menu-scroll-wrapper">').append(table).appendTo(contentEl);
|
|
1370
|
+
|
|
1371
|
+
menuEl.appendTo(this.superContainer || this.container).show();
|
|
1372
|
+
|
|
1373
|
+
if (event) {
|
|
1374
|
+
menuEl.css({ left: 0, top: 0 }).position({ of: event, my: 'left top', collision: 'flipfit' });
|
|
1375
|
+
}
|
|
1376
|
+
|
|
1377
|
+
this.menus = this.menus.add(menuEl);
|
|
1378
|
+
|
|
1379
|
+
if (track) {
|
|
1380
|
+
track.prop('menus', track.prop('menus').add(menuEl));
|
|
1381
|
+
}
|
|
1382
|
+
|
|
1383
|
+
return menuEl;
|
|
1384
|
+
},
|
|
1385
|
+
|
|
1386
|
+
insertPropertiesIntoMenu: function (menuProperties, menuEl, contentEl, feature, track) {
|
|
1387
|
+
const jQuery = this.jQuery;
|
|
1388
|
+
|
|
1389
|
+
const focus = ({ currentTarget }) => {
|
|
1390
|
+
const data = jQuery(currentTarget).data();
|
|
1391
|
+
const length = data.end - data.start + 1;
|
|
1392
|
+
const context = Math.max(Math.round(length / 4), 25);
|
|
1393
|
+
|
|
1394
|
+
this.moveTo(data.chr, data.start - context, data.end + context, true);
|
|
1395
|
+
|
|
1396
|
+
return false;
|
|
1397
|
+
};
|
|
1398
|
+
|
|
1399
|
+
const highlight = ({ currentTarget }) => {
|
|
1400
|
+
this.addHighlight(jQuery(currentTarget).data());
|
|
1401
|
+
|
|
1402
|
+
return false;
|
|
1403
|
+
};
|
|
1404
|
+
|
|
1405
|
+
[].concat(menuProperties).forEach(
|
|
1406
|
+
(properties, i) => {
|
|
1407
|
+
const el = contentEl.clone().addClass(i ? '' : 'gv-menu-content-first').appendTo(menuEl);
|
|
1408
|
+
const chr = typeof properties.chr !== 'undefined' ? properties.chr : feature.chr;
|
|
1409
|
+
const start = parseInt(typeof properties.start !== 'undefined' ? properties.start : feature.start, 10);
|
|
1410
|
+
const end = parseInt(typeof properties.end !== 'undefined' ? properties.end : feature.end, 10);
|
|
1411
|
+
const columns = Math.max(...Object.values(properties).map(value => (Array.isArray(value) ? value.length : 1)));
|
|
1412
|
+
|
|
1413
|
+
let table = '';
|
|
1414
|
+
|
|
1415
|
+
jQuery('.gv-title', el)[properties.title ? 'html' : 'remove'](properties.title);
|
|
1416
|
+
|
|
1417
|
+
if (track && start && end && !this.isStatic) {
|
|
1418
|
+
const linkData = {
|
|
1419
|
+
chr : chr,
|
|
1420
|
+
start : start,
|
|
1421
|
+
end : Math.max(end, start),
|
|
1422
|
+
label : feature.label || (properties.title || '').replace(/<[^>]+>/g, ''),
|
|
1423
|
+
color : feature.color,
|
|
1424
|
+
};
|
|
1425
|
+
|
|
1426
|
+
jQuery('.gv-focus', el).data(linkData).on('click', focus);
|
|
1427
|
+
jQuery('.gv-highlight', el).data(linkData).on('click', highlight);
|
|
1428
|
+
} else {
|
|
1429
|
+
jQuery('.gv-focus-highlight', el).remove();
|
|
1430
|
+
}
|
|
1431
|
+
|
|
1432
|
+
Object.entries(properties).forEach(
|
|
1433
|
+
([ key, value ]) => {
|
|
1434
|
+
if (/^start|end$/.test(key) && value === false) {
|
|
1435
|
+
return;
|
|
1436
|
+
}
|
|
1437
|
+
|
|
1438
|
+
if (key !== 'title') {
|
|
1439
|
+
const colspan = value === '' ? ` colspan="${columns + 1}"` : '';
|
|
1440
|
+
|
|
1441
|
+
table += `<tr><td${colspan}>${key}</td>`;
|
|
1442
|
+
|
|
1443
|
+
if (!colspan) {
|
|
1444
|
+
if (Array.isArray(value)) {
|
|
1445
|
+
value.forEach(
|
|
1446
|
+
(prop) => {
|
|
1447
|
+
table += `<td>${prop}</td>`;
|
|
1448
|
+
}
|
|
1449
|
+
);
|
|
1450
|
+
} else if (columns === 1) {
|
|
1451
|
+
table += `<td>${value}</td>`;
|
|
1452
|
+
} else {
|
|
1453
|
+
table += `<td colspan="${columns}">${value}</td>`;
|
|
1454
|
+
}
|
|
1455
|
+
}
|
|
1456
|
+
|
|
1457
|
+
table += '</tr>';
|
|
1458
|
+
}
|
|
1459
|
+
}
|
|
1460
|
+
);
|
|
1461
|
+
|
|
1462
|
+
jQuery('table:not(.gv-focus-highlight)', el)[table ? 'html' : 'remove'](table);
|
|
1463
|
+
}
|
|
1464
|
+
);
|
|
1465
|
+
},
|
|
1466
|
+
|
|
1467
|
+
makeFeatureMenu: function (feature, e, track) {
|
|
1468
|
+
const jQuery = this.jQuery;
|
|
1469
|
+
const container = this.superContainer || this.container;
|
|
1470
|
+
|
|
1471
|
+
if (!feature.menuEl || feature.menuEl.data('hasErrored') === true) {
|
|
1472
|
+
const menuEl = this.createMenuEl().data({ feature });
|
|
1473
|
+
const contentEl = jQuery('.gv-menu-content', menuEl).remove();
|
|
1474
|
+
const loadingEl = jQuery('.gv-menu-loading', menuEl);
|
|
1475
|
+
|
|
1476
|
+
let getMenu;
|
|
1477
|
+
|
|
1478
|
+
try {
|
|
1479
|
+
getMenu = track ? track.controller.populateMenu(feature) : feature;
|
|
1480
|
+
} catch (error) {
|
|
1481
|
+
getMenu = jQuery.Deferred().reject(error);
|
|
1482
|
+
menuEl.data('hasErrored', true);
|
|
1483
|
+
}
|
|
1484
|
+
|
|
1485
|
+
const isDeferred = typeof getMenu === 'object' && typeof getMenu.promise === 'function';
|
|
1486
|
+
|
|
1487
|
+
if (!isDeferred) {
|
|
1488
|
+
loadingEl.hide();
|
|
1489
|
+
}
|
|
1490
|
+
|
|
1491
|
+
jQuery.when(getMenu).done(
|
|
1492
|
+
(menuProperties) => {
|
|
1493
|
+
(track?.controller || this).insertPropertiesIntoMenu(menuProperties, menuEl, contentEl, feature, track);
|
|
1494
|
+
|
|
1495
|
+
if (isDeferred) {
|
|
1496
|
+
loadingEl.hide();
|
|
1497
|
+
}
|
|
1498
|
+
}
|
|
1499
|
+
).fail(
|
|
1500
|
+
(error) => {
|
|
1501
|
+
loadingEl.hide();
|
|
1502
|
+
menuEl.data('hasErrored', true);
|
|
1503
|
+
jQuery('.gv-menu-error', menuEl).css('display', 'block');
|
|
1504
|
+
console.error(error); // eslint-disable-line no-console
|
|
1505
|
+
}
|
|
1506
|
+
);
|
|
1507
|
+
|
|
1508
|
+
if (track) {
|
|
1509
|
+
menuEl.addClass(track.id).data('track', track);
|
|
1510
|
+
}
|
|
1511
|
+
|
|
1512
|
+
feature.menuEl = menuEl.appendTo(container);
|
|
1513
|
+
} else {
|
|
1514
|
+
feature.menuEl.appendTo(container); // Move the menu to the end of the container again, so that it will always be on top of other menus
|
|
1515
|
+
}
|
|
1516
|
+
|
|
1517
|
+
this.menus = this.menus.add(feature.menuEl);
|
|
1518
|
+
|
|
1519
|
+
if (track) {
|
|
1520
|
+
track.prop('menus', track.prop('menus').add(feature.menuEl));
|
|
1521
|
+
}
|
|
1522
|
+
|
|
1523
|
+
feature.menuEl.show(); // Must show before positioning, else position will be wrong
|
|
1524
|
+
|
|
1525
|
+
if (e) {
|
|
1526
|
+
feature.menuEl.css({ left: 0, top: 0 }).position({ of: e, my: 'left top', collision: 'flipfit' });
|
|
1527
|
+
}
|
|
1528
|
+
|
|
1529
|
+
return feature.menuEl;
|
|
1530
|
+
},
|
|
1531
|
+
|
|
1532
|
+
closeMenus: function (obj) {
|
|
1533
|
+
obj = obj || this;
|
|
1534
|
+
|
|
1535
|
+
obj.menus.filter(':visible').children('.gv-close').trigger('click');
|
|
1536
|
+
obj.menus = this.jQuery();
|
|
1537
|
+
},
|
|
1538
|
+
|
|
1539
|
+
hideMessages: function () {
|
|
1540
|
+
if (this.autoHideMessages) {
|
|
1541
|
+
this.wrapper.find('.gv-message-container').addClass('gv-collapsed');
|
|
1542
|
+
}
|
|
1543
|
+
},
|
|
1544
|
+
|
|
1545
|
+
getSelectorPosition: function () {
|
|
1546
|
+
const left = this.selector.position().left;
|
|
1547
|
+
const width = this.selector.outerWidth(true);
|
|
1548
|
+
const start = Math.round(left / this.scale) + this.start;
|
|
1549
|
+
|
|
1550
|
+
let end = Math.round((left + width) / this.scale) + this.start - 1;
|
|
1551
|
+
|
|
1552
|
+
end = end <= start ? start : end;
|
|
1553
|
+
|
|
1554
|
+
return {
|
|
1555
|
+
start,
|
|
1556
|
+
end,
|
|
1557
|
+
left,
|
|
1558
|
+
width,
|
|
1559
|
+
};
|
|
1560
|
+
},
|
|
1561
|
+
|
|
1562
|
+
addHighlight: function (highlight) {
|
|
1563
|
+
this.addHighlights([ highlight ]);
|
|
1564
|
+
},
|
|
1565
|
+
|
|
1566
|
+
addHighlights: function (highlights) {
|
|
1567
|
+
if (!this.tracksById.highlights) {
|
|
1568
|
+
this.addTrack(HighlightRegionTrack);
|
|
1569
|
+
}
|
|
1570
|
+
|
|
1571
|
+
this.tracksById.highlights.addHighlights(highlights);
|
|
1572
|
+
},
|
|
1573
|
+
|
|
1574
|
+
on: function (events, obj, fn, once) {
|
|
1575
|
+
const eventMap = {};
|
|
1576
|
+
|
|
1577
|
+
function makeEventMap(types, handler) {
|
|
1578
|
+
types.split(' ').forEach(
|
|
1579
|
+
(type) => {
|
|
1580
|
+
eventMap[type] = (eventMap[type] || []).concat(handler);
|
|
1581
|
+
}
|
|
1582
|
+
);
|
|
1583
|
+
}
|
|
1584
|
+
|
|
1585
|
+
if (typeof events === 'object') {
|
|
1586
|
+
Object.entries(events).forEach(
|
|
1587
|
+
([ key, value ]) => makeEventMap(key, value)
|
|
1588
|
+
);
|
|
1589
|
+
|
|
1590
|
+
obj = obj || this;
|
|
1591
|
+
} else {
|
|
1592
|
+
if (typeof fn === 'undefined') {
|
|
1593
|
+
fn = obj;
|
|
1594
|
+
obj = this;
|
|
1595
|
+
}
|
|
1596
|
+
|
|
1597
|
+
makeEventMap(events, fn);
|
|
1598
|
+
}
|
|
1599
|
+
|
|
1600
|
+
const type = obj instanceof Track || obj === 'tracks' ? 'tracks' : 'browser';
|
|
1601
|
+
|
|
1602
|
+
Object.entries(eventMap).forEach(
|
|
1603
|
+
([ key, value ]) => {
|
|
1604
|
+
const event = `${key}${once ? '.once' : ''}`;
|
|
1605
|
+
const fnStrings = value.map(func => func.toString());
|
|
1606
|
+
|
|
1607
|
+
this.events[type][event] = this.events[type][event] || [];
|
|
1608
|
+
|
|
1609
|
+
if (
|
|
1610
|
+
!this.events[type][event].some(
|
|
1611
|
+
(func) => {
|
|
1612
|
+
const f = func.toString();
|
|
1613
|
+
|
|
1614
|
+
return fnStrings.some(fnString => fnString === f);
|
|
1615
|
+
}
|
|
1616
|
+
)
|
|
1617
|
+
) {
|
|
1618
|
+
this.events[type][event].push(...value);
|
|
1619
|
+
}
|
|
1620
|
+
}
|
|
1621
|
+
);
|
|
1622
|
+
},
|
|
1623
|
+
|
|
1624
|
+
once: function (events, obj, fn) {
|
|
1625
|
+
this.on(events, obj, fn, true);
|
|
1626
|
+
},
|
|
1627
|
+
|
|
1628
|
+
destroy: function () {
|
|
1629
|
+
this.destroying = true;
|
|
1630
|
+
|
|
1631
|
+
this.onTracks('destructor');
|
|
1632
|
+
(this.superContainer || this.container).empty();
|
|
1633
|
+
|
|
1634
|
+
if (this.zoomInHighlight) {
|
|
1635
|
+
this.zoomInHighlight.add(this.zoomOutHighlight).remove();
|
|
1636
|
+
}
|
|
1637
|
+
|
|
1638
|
+
this.container.off(this.eventNamespace);
|
|
1639
|
+
this.jQuery(window).add(document).off(this.eventNamespace);
|
|
1640
|
+
|
|
1641
|
+
Object.keys(this).forEach(
|
|
1642
|
+
(key) => { delete this[key]; }
|
|
1643
|
+
);
|
|
1644
|
+
},
|
|
1645
|
+
}, {
|
|
1646
|
+
id : 0,
|
|
1647
|
+
Track : Track,
|
|
1648
|
+
jQuery : $,
|
|
1649
|
+
|
|
1650
|
+
configure: ({
|
|
1651
|
+
tracks = {},
|
|
1652
|
+
plugins = {},
|
|
1653
|
+
genomes = {},
|
|
1654
|
+
css = true,
|
|
1655
|
+
fontawesome = true,
|
|
1656
|
+
force = false,
|
|
1657
|
+
} = {}) => {
|
|
1658
|
+
if (force || !Genoverse.configured) {
|
|
1659
|
+
importTracks(Track, require.context('./Track', true, /\.js$/), { exclude: tracks.exclude });
|
|
1660
|
+
|
|
1661
|
+
if (tracks.include) {
|
|
1662
|
+
importTracks(Track, tracks.include);
|
|
1663
|
+
}
|
|
1664
|
+
|
|
1665
|
+
const importAll = r => r.keys().forEach(r);
|
|
1666
|
+
|
|
1667
|
+
if (plugins.include) {
|
|
1668
|
+
importAll(plugins.include);
|
|
1669
|
+
}
|
|
1670
|
+
|
|
1671
|
+
if (genomes.include) {
|
|
1672
|
+
importAll(genomes.include);
|
|
1673
|
+
}
|
|
1674
|
+
|
|
1675
|
+
Genoverse.importCSS = css;
|
|
1676
|
+
Genoverse.importFontAwesome = fontawesome;
|
|
1677
|
+
}
|
|
1678
|
+
|
|
1679
|
+
Genoverse.configured = true;
|
|
1680
|
+
},
|
|
1681
|
+
|
|
1682
|
+
getAllTrackTypes: function (namespace, n) {
|
|
1683
|
+
namespace = namespace || Track;
|
|
1684
|
+
|
|
1685
|
+
if (n) {
|
|
1686
|
+
namespace = namespace[n];
|
|
1687
|
+
}
|
|
1688
|
+
|
|
1689
|
+
if (!namespace) {
|
|
1690
|
+
return [];
|
|
1691
|
+
}
|
|
1692
|
+
|
|
1693
|
+
const trackTypes = {};
|
|
1694
|
+
|
|
1695
|
+
Object.entries(namespace).forEach(
|
|
1696
|
+
([ type, func ]) => {
|
|
1697
|
+
if (typeof func === 'function' && !Base[type] && !/^(Controller|Model|View)$/.test(type)) {
|
|
1698
|
+
Object.entries(Genoverse.getAllTrackTypes(namespace, type)).forEach(
|
|
1699
|
+
([ subtype, fn ]) => {
|
|
1700
|
+
if (typeof fn === 'function') {
|
|
1701
|
+
trackTypes[`${type}.${subtype}`] = fn;
|
|
1702
|
+
}
|
|
1703
|
+
}
|
|
1704
|
+
);
|
|
1705
|
+
|
|
1706
|
+
trackTypes[type] = func;
|
|
1707
|
+
}
|
|
1708
|
+
}
|
|
1709
|
+
);
|
|
1710
|
+
|
|
1711
|
+
return trackTypes;
|
|
1712
|
+
},
|
|
1713
|
+
|
|
1714
|
+
getTrackNamespace: function (track) {
|
|
1715
|
+
const trackTypes = Genoverse.getAllTrackTypes();
|
|
1716
|
+
const namespaces = Object.entries(trackTypes).map(
|
|
1717
|
+
([ name, constructor ]) => (track === constructor || track.prototype instanceof constructor ? name : false) // Find all namespaces which this track could be
|
|
1718
|
+
).filter(Boolean);
|
|
1719
|
+
|
|
1720
|
+
let j = namespaces.length;
|
|
1721
|
+
|
|
1722
|
+
// Find the most specific namespace for this track - the one which isn't a parent of any other namespaces this track could be
|
|
1723
|
+
while (namespaces.length > 1) {
|
|
1724
|
+
for (let i = 0; i < namespaces.length - 1; i++) {
|
|
1725
|
+
if (trackTypes[namespaces[i]].prototype instanceof trackTypes[namespaces[i + 1]]) {
|
|
1726
|
+
namespaces.splice(i + 1, 1);
|
|
1727
|
+
|
|
1728
|
+
break;
|
|
1729
|
+
} else if (trackTypes[namespaces[i + 1]].prototype instanceof trackTypes[namespaces[i]]) {
|
|
1730
|
+
namespaces.splice(i, 1);
|
|
1731
|
+
|
|
1732
|
+
break;
|
|
1733
|
+
}
|
|
1734
|
+
}
|
|
1735
|
+
|
|
1736
|
+
if (j-- < 0) {
|
|
1737
|
+
break; // Stop infinite loop if something went really wrong
|
|
1738
|
+
}
|
|
1739
|
+
}
|
|
1740
|
+
|
|
1741
|
+
return namespaces[0];
|
|
1742
|
+
},
|
|
1743
|
+
});
|
|
1744
|
+
|
|
1745
|
+
global.Genoverse = Genoverse;
|
|
1746
|
+
|
|
1747
|
+
export default Genoverse;
|