sequenceserver 2.0.0.rc8 → 2.0.0
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- checksums.yaml +4 -4
- data/bin/sequenceserver +22 -30
- data/lib/sequenceserver/api_errors.rb +5 -1
- data/lib/sequenceserver/blast/constants.rb +1 -1
- data/lib/sequenceserver/blast/hit.rb +5 -16
- data/lib/sequenceserver/blast/job.rb +9 -18
- data/lib/sequenceserver/blast/report.rb +5 -3
- data/lib/sequenceserver/config.rb +4 -1
- data/lib/sequenceserver/database.rb +69 -9
- data/lib/sequenceserver/job.rb +1 -1
- data/lib/sequenceserver/makeblastdb.rb +40 -45
- data/lib/sequenceserver/routes.rb +4 -0
- data/lib/sequenceserver/version.rb +1 -1
- data/lib/sequenceserver.rb +15 -11
- data/public/config.js +143 -142
- data/public/css/fonts.css +23 -22
- data/public/css/grapher.css +598 -594
- data/public/css/sequenceserver.css +86 -24
- data/public/css/sequenceserver.min.css +2 -2
- data/public/js/alignment_exporter.js +14 -14
- data/public/js/databases_tree.js +215 -0
- data/public/js/download_fasta.js +1 -1
- data/public/js/hit.js +6 -2
- data/public/js/hits_overview.js +1 -1
- data/public/js/length_distribution.js +5 -5
- data/public/js/query.js +4 -7
- data/public/js/report.js +12 -24
- data/public/js/search.js +21 -2
- data/public/js/sidebar.js +4 -4
- data/public/js/svgExporter.js +12 -12
- data/public/js/visualisation_helpers.js +4 -5
- data/public/sequenceserver-report.min.js +11 -11
- data/public/sequenceserver-search.min.js +15 -11
- data/public/vendor/github/vakata/jstree@3.3.8/LICENSE-MIT +22 -0
- data/public/vendor/github/vakata/jstree@3.3.8/README.md +663 -0
- data/public/vendor/github/vakata/jstree@3.3.8/bower.json +33 -0
- data/public/vendor/github/vakata/jstree@3.3.8/component.json +28 -0
- data/public/vendor/github/vakata/jstree@3.3.8/composer.json +46 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/README.md +2 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/index.html +146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/root.json +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.js +8612 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.min.js +6 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.css +1102 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.min.css +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.css +1146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.min.css +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/gruntfile.js +242 -0
- data/public/vendor/github/vakata/jstree@3.3.8/jstree.jquery.json +28 -0
- data/public/vendor/github/vakata/jstree@3.3.8/package.json +58 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/intro.js +14 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.changed.js +69 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.checkbox.js +976 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.conditionalselect.js +38 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.contextmenu.js +661 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.dnd.js +669 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.js +4931 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.massload.js +137 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.search.js +421 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.sort.js +74 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.state.js +138 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.types.js +372 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.unique.js +164 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.wholerow.js +122 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/misc.js +656 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/outro.js +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/sample.js +93 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/base.less +93 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.css +1102 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.less +22 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.css +1146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.less +50 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/main.less +77 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/mixins.less +104 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/responsive.less +67 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/vakata-jstree.js +38 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/index.html +16 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.css +244 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.js +2212 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/test.js +11 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/desktop/index.html +44 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/mobile/index.html +42 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/desktop.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/home.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/home.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/mobile.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8.js +3 -0
- data/public/vendor/system-csp-production.js +3 -3
- data/public/vendor/system-csp-production.js.map +1 -1
- data/public/vendor/system-csp-production.src.js +146 -140
- data/public/vendor/system-polyfills.js.map +1 -1
- data/public/vendor/system-polyfills.src.js +1 -0
- data/public/vendor/system.js +3 -3
- data/public/vendor/system.js.map +1 -1
- data/public/vendor/system.src.js +4771 -2383
- data/views/_options.erb +21 -0
- data/views/layout.erb +17 -18
- metadata +102 -43
- data/bin/chromedriver +0 -0
- data/bin/geckodriver +0 -0
- data/public/shims/form-core.js +0 -3
- data/public/shims/form-validation.js +0 -3
- data/public/shims/plugins/jquery.ui.position.js +0 -13
- data/public/shims/styles/shim.css +0 -1
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{
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"name": "jstree",
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"license": "MIT",
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"version": "3.3.8",
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"main" : [
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"demo",
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"test",
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"libs",
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"jstree.jquery.json",
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"package.json",
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"bower.json",
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"component.json",
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"LICENCE-MIT",
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"dependencies": {
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"keywords": [
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"ui",
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"name": "jstree",
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"repo": "vakata/jstree",
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"description": "jsTree is jquery plugin, that provides interactive trees.",
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"version": "3.3.8",
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"license": "MIT",
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"keywords": [
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"ui",
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"scripts": [
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"images": [
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"name": "vakata/jstree",
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"description": "jsTree is jquery plugin, that provides interactive trees.",
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"type": "component",
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"homepage": "http://jstree.com",
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"license": "MIT",
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"support": {
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"issues": "https://github.com/vakata/jstree/issues",
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"forum": "https://groups.google.com/forum/#!forum/jstree",
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"source": "https://github.com/vakata/jstree"
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"authors": [
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{
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"name": "Ivan Bozhanov",
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"email": "jstree@jstree.com"
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"require": {
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"suggest": {
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"robloach/component-installer": "Allows installation of Components via Composer"
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"files": [
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<title>jstree basic demos</title>
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<style>
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html { margin:0; padding:0; font-size:62.5%; }
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body { max-width:800px; min-width:300px; margin:0 auto; padding:20px 10px; font-size:14px; font-size:1.4em; }
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h1 { font-size:1.8em; }
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.demo { overflow:auto; border:1px solid silver; min-height:100px; }
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<link rel="stylesheet" href="./../../dist/themes/default/style.min.css" />
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</head>
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<body>
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<h1>HTML demo</h1>
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<div id="html" class="demo">
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<ul>
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<li data-jstree='{ "opened" : true }'>Root node
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<ul>
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<li data-jstree='{ "selected" : true }'>Child node 1</li>
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<li>Child node 2</li>
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</ul>
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</li>
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</ul>
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</div>
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<h1>Inline data demo</h1>
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<div id="data" class="demo"></div>
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<h1>Data format demo</h1>
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<div id="frmt" class="demo"></div>
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<h1>AJAX demo</h1>
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<div id="ajax" class="demo"></div>
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<h1>Lazy loading demo</h1>
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<div id="lazy" class="demo"></div>
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<h1>Callback function data demo</h1>
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<div id="clbk" class="demo"></div>
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<h1>Interaction and events demo</h1>
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<button id="evts_button">select node with id 1</button> <em>either click the button or a node in the tree</em>
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<div id="evts" class="demo"></div>
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<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
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<script src="./../../dist/jstree.min.js"></script>
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<script>
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// html demo
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$('#html').jstree();
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// inline data demo
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$('#data').jstree({
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'core' : {
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'data' : [
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{ "text" : "Root node", "children" : [
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{ "text" : "Child node 1" },
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{ "text" : "Child node 2" }
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});
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// data format demo
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$('#frmt').jstree({
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'core' : {
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'data' : [
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{
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"text" : "Root node",
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"state" : { "opened" : true },
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"children" : [
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"text" : "Child node 1",
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"state" : { "selected" : true },
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"icon" : "jstree-file"
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},
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{ "text" : "Child node 2", "state" : { "disabled" : true } }
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]
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}
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});
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// ajax demo
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$('#ajax').jstree({
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'core' : {
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'data' : {
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"url" : "./root.json",
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"dataType" : "json" // needed only if you do not supply JSON headers
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}
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}
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});
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// lazy demo
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$('#lazy').jstree({
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'core' : {
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'data' : {
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"url" : "//www.jstree.com/fiddle/?lazy",
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"data" : function (node) {
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return { "id" : node.id };
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}
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});
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// data from callback
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$('#clbk').jstree({
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'core' : {
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'data' : function (node, cb) {
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if(node.id === "#") {
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cb([{"text" : "Root", "id" : "1", "children" : true}]);
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}
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else {
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cb(["Child"]);
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}
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}
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}
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|
+
});
|
120
|
+
|
121
|
+
// interaction and events
|
122
|
+
$('#evts_button').on("click", function () {
|
123
|
+
var instance = $('#evts').jstree(true);
|
124
|
+
instance.deselect_all();
|
125
|
+
instance.select_node('1');
|
126
|
+
});
|
127
|
+
$('#evts')
|
128
|
+
.on("changed.jstree", function (e, data) {
|
129
|
+
if(data.selected.length) {
|
130
|
+
alert('The selected node is: ' + data.instance.get_node(data.selected[0]).text);
|
131
|
+
}
|
132
|
+
})
|
133
|
+
.jstree({
|
134
|
+
'core' : {
|
135
|
+
'multiple' : false,
|
136
|
+
'data' : [
|
137
|
+
{ "text" : "Root node", "children" : [
|
138
|
+
{ "text" : "Child node 1", "id" : 1 },
|
139
|
+
{ "text" : "Child node 2" }
|
140
|
+
]}
|
141
|
+
]
|
142
|
+
}
|
143
|
+
});
|
144
|
+
</script>
|
145
|
+
</body>
|
146
|
+
</html>
|
@@ -0,0 +1 @@
|
|
1
|
+
[{"id":1,"text":"Root node","children":[{"id":2,"text":"Child node 1"},{"id":3,"text":"Child node 2"}]}]
|