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
@@ -0,0 +1,137 @@
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/**
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* ### Massload plugin
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*
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* Adds massload functionality to jsTree, so that multiple nodes can be loaded in a single request (only useful with lazy loading).
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*/
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/*globals jQuery, define, exports, require, document */
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(function (factory) {
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"use strict";
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if (typeof define === 'function' && define.amd) {
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define('jstree.massload', ['jquery','jstree'], factory);
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}
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else if(typeof exports === 'object') {
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factory(require('jquery'), require('jstree'));
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}
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else {
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factory(jQuery, jQuery.jstree);
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}
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}(function ($, jstree, undefined) {
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"use strict";
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if($.jstree.plugins.massload) { return; }
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/**
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* massload configuration
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*
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* It is possible to set this to a standard jQuery-like AJAX config.
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* In addition to the standard jQuery ajax options here you can supply functions for `data` and `url`, the functions will be run in the current instance's scope and a param will be passed indicating which node IDs need to be loaded, the return value of those functions will be used.
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*
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* You can also set this to a function, that function will receive the node IDs being loaded as argument and a second param which is a function (callback) which should be called with the result.
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*
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* Both the AJAX and the function approach rely on the same return value - an object where the keys are the node IDs, and the value is the children of that node as an array.
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*
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* {
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* "id1" : [{ "text" : "Child of ID1", "id" : "c1" }, { "text" : "Another child of ID1", "id" : "c2" }],
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* "id2" : [{ "text" : "Child of ID2", "id" : "c3" }]
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* }
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*
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* @name $.jstree.defaults.massload
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* @plugin massload
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*/
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$.jstree.defaults.massload = null;
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$.jstree.plugins.massload = function (options, parent) {
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this.init = function (el, options) {
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this._data.massload = {};
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parent.init.call(this, el, options);
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};
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this._load_nodes = function (nodes, callback, is_callback, force_reload) {
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var s = this.settings.massload,
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nodesString = JSON.stringify(nodes),
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toLoad = [],
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m = this._model.data,
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i, j, dom;
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if (!is_callback) {
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for(i = 0, j = nodes.length; i < j; i++) {
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if(!m[nodes[i]] || ( (!m[nodes[i]].state.loaded && !m[nodes[i]].state.failed) || force_reload) ) {
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toLoad.push(nodes[i]);
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dom = this.get_node(nodes[i], true);
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if (dom && dom.length) {
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dom.addClass("jstree-loading").attr('aria-busy',true);
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}
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}
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}
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this._data.massload = {};
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if (toLoad.length) {
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if($.isFunction(s)) {
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return s.call(this, toLoad, $.proxy(function (data) {
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var i, j;
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if(data) {
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for(i in data) {
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if(data.hasOwnProperty(i)) {
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this._data.massload[i] = data[i];
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}
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}
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}
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for(i = 0, j = nodes.length; i < j; i++) {
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dom = this.get_node(nodes[i], true);
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if (dom && dom.length) {
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dom.removeClass("jstree-loading").attr('aria-busy',false);
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}
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}
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parent._load_nodes.call(this, nodes, callback, is_callback, force_reload);
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}, this));
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}
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if(typeof s === 'object' && s && s.url) {
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s = $.extend(true, {}, s);
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if($.isFunction(s.url)) {
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s.url = s.url.call(this, toLoad);
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}
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if($.isFunction(s.data)) {
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s.data = s.data.call(this, toLoad);
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}
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return $.ajax(s)
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.done($.proxy(function (data,t,x) {
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var i, j;
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if(data) {
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for(i in data) {
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if(data.hasOwnProperty(i)) {
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this._data.massload[i] = data[i];
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}
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}
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}
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for(i = 0, j = nodes.length; i < j; i++) {
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dom = this.get_node(nodes[i], true);
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if (dom && dom.length) {
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dom.removeClass("jstree-loading").attr('aria-busy',false);
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}
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}
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parent._load_nodes.call(this, nodes, callback, is_callback, force_reload);
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}, this))
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.fail($.proxy(function (f) {
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parent._load_nodes.call(this, nodes, callback, is_callback, force_reload);
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}, this));
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}
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}
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}
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return parent._load_nodes.call(this, nodes, callback, is_callback, force_reload);
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};
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this._load_node = function (obj, callback) {
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var data = this._data.massload[obj.id],
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rslt = null, dom;
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if(data) {
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rslt = this[typeof data === 'string' ? '_append_html_data' : '_append_json_data'](
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obj,
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typeof data === 'string' ? $($.parseHTML(data)).filter(function () { return this.nodeType !== 3; }) : data,
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function (status) { callback.call(this, status); }
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);
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dom = this.get_node(obj.id, true);
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if (dom && dom.length) {
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dom.removeClass("jstree-loading").attr('aria-busy',false);
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}
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delete this._data.massload[obj.id];
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return rslt;
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}
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return parent._load_node.call(this, obj, callback);
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};
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};
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}));
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/**
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* ### Search plugin
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*
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* Adds search functionality to jsTree.
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*/
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/*globals jQuery, define, exports, require, document */
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(function (factory) {
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"use strict";
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if (typeof define === 'function' && define.amd) {
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define('jstree.search', ['jquery','jstree'], factory);
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}
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else if(typeof exports === 'object') {
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factory(require('jquery'), require('jstree'));
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}
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else {
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factory(jQuery, jQuery.jstree);
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}
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}(function ($, jstree, undefined) {
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"use strict";
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if($.jstree.plugins.search) { return; }
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/**
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* stores all defaults for the search plugin
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* @name $.jstree.defaults.search
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* @plugin search
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*/
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$.jstree.defaults.search = {
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/**
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* a jQuery-like AJAX config, which jstree uses if a server should be queried for results.
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*
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* A `str` (which is the search string) parameter will be added with the request, an optional `inside` parameter will be added if the search is limited to a node id. The expected result is a JSON array with nodes that need to be opened so that matching nodes will be revealed.
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* Leave this setting as `false` to not query the server. You can also set this to a function, which will be invoked in the instance's scope and receive 3 parameters - the search string, the callback to call with the array of nodes to load, and the optional node ID to limit the search to
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* @name $.jstree.defaults.search.ajax
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* @plugin search
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*/
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ajax : false,
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/**
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* Indicates if the search should be fuzzy or not (should `chnd3` match `child node 3`). Default is `false`.
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* @name $.jstree.defaults.search.fuzzy
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* @plugin search
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*/
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fuzzy : false,
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/**
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* Indicates if the search should be case sensitive. Default is `false`.
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* @name $.jstree.defaults.search.case_sensitive
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* @plugin search
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*/
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case_sensitive : false,
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/**
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* Indicates if the tree should be filtered (by default) to show only matching nodes (keep in mind this can be a heavy on large trees in old browsers).
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* This setting can be changed at runtime when calling the search method. Default is `false`.
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* @name $.jstree.defaults.search.show_only_matches
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* @plugin search
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*/
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show_only_matches : false,
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/**
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* Indicates if the children of matched element are shown (when show_only_matches is true)
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* This setting can be changed at runtime when calling the search method. Default is `false`.
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* @name $.jstree.defaults.search.show_only_matches_children
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* @plugin search
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*/
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show_only_matches_children : false,
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|
+
/**
|
65
|
+
* Indicates if all nodes opened to reveal the search result, should be closed when the search is cleared or a new search is performed. Default is `true`.
|
66
|
+
* @name $.jstree.defaults.search.close_opened_onclear
|
67
|
+
* @plugin search
|
68
|
+
*/
|
69
|
+
close_opened_onclear : true,
|
70
|
+
/**
|
71
|
+
* Indicates if only leaf nodes should be included in search results. Default is `false`.
|
72
|
+
* @name $.jstree.defaults.search.search_leaves_only
|
73
|
+
* @plugin search
|
74
|
+
*/
|
75
|
+
search_leaves_only : false,
|
76
|
+
/**
|
77
|
+
* If set to a function it wil be called in the instance's scope with two arguments - search string and node (where node will be every node in the structure, so use with caution).
|
78
|
+
* If the function returns a truthy value the node will be considered a match (it might not be displayed if search_only_leaves is set to true and the node is not a leaf). Default is `false`.
|
79
|
+
* @name $.jstree.defaults.search.search_callback
|
80
|
+
* @plugin search
|
81
|
+
*/
|
82
|
+
search_callback : false
|
83
|
+
};
|
84
|
+
|
85
|
+
$.jstree.plugins.search = function (options, parent) {
|
86
|
+
this.bind = function () {
|
87
|
+
parent.bind.call(this);
|
88
|
+
|
89
|
+
this._data.search.str = "";
|
90
|
+
this._data.search.dom = $();
|
91
|
+
this._data.search.res = [];
|
92
|
+
this._data.search.opn = [];
|
93
|
+
this._data.search.som = false;
|
94
|
+
this._data.search.smc = false;
|
95
|
+
this._data.search.hdn = [];
|
96
|
+
|
97
|
+
this.element
|
98
|
+
.on("search.jstree", $.proxy(function (e, data) {
|
99
|
+
if(this._data.search.som && data.res.length) {
|
100
|
+
var m = this._model.data, i, j, p = [], k, l;
|
101
|
+
for(i = 0, j = data.res.length; i < j; i++) {
|
102
|
+
if(m[data.res[i]] && !m[data.res[i]].state.hidden) {
|
103
|
+
p.push(data.res[i]);
|
104
|
+
p = p.concat(m[data.res[i]].parents);
|
105
|
+
if(this._data.search.smc) {
|
106
|
+
for (k = 0, l = m[data.res[i]].children_d.length; k < l; k++) {
|
107
|
+
if (m[m[data.res[i]].children_d[k]] && !m[m[data.res[i]].children_d[k]].state.hidden) {
|
108
|
+
p.push(m[data.res[i]].children_d[k]);
|
109
|
+
}
|
110
|
+
}
|
111
|
+
}
|
112
|
+
}
|
113
|
+
}
|
114
|
+
p = $.vakata.array_remove_item($.vakata.array_unique(p), $.jstree.root);
|
115
|
+
this._data.search.hdn = this.hide_all(true);
|
116
|
+
this.show_node(p, true);
|
117
|
+
this.redraw(true);
|
118
|
+
}
|
119
|
+
}, this))
|
120
|
+
.on("clear_search.jstree", $.proxy(function (e, data) {
|
121
|
+
if(this._data.search.som && data.res.length) {
|
122
|
+
this.show_node(this._data.search.hdn, true);
|
123
|
+
this.redraw(true);
|
124
|
+
}
|
125
|
+
}, this));
|
126
|
+
};
|
127
|
+
/**
|
128
|
+
* used to search the tree nodes for a given string
|
129
|
+
* @name search(str [, skip_async])
|
130
|
+
* @param {String} str the search string
|
131
|
+
* @param {Boolean} skip_async if set to true server will not be queried even if configured
|
132
|
+
* @param {Boolean} show_only_matches if set to true only matching nodes will be shown (keep in mind this can be very slow on large trees or old browsers)
|
133
|
+
* @param {mixed} inside an optional node to whose children to limit the search
|
134
|
+
* @param {Boolean} append if set to true the results of this search are appended to the previous search
|
135
|
+
* @plugin search
|
136
|
+
* @trigger search.jstree
|
137
|
+
*/
|
138
|
+
this.search = function (str, skip_async, show_only_matches, inside, append, show_only_matches_children) {
|
139
|
+
if(str === false || $.trim(str.toString()) === "") {
|
140
|
+
return this.clear_search();
|
141
|
+
}
|
142
|
+
inside = this.get_node(inside);
|
143
|
+
inside = inside && inside.id ? inside.id : null;
|
144
|
+
str = str.toString();
|
145
|
+
var s = this.settings.search,
|
146
|
+
a = s.ajax ? s.ajax : false,
|
147
|
+
m = this._model.data,
|
148
|
+
f = null,
|
149
|
+
r = [],
|
150
|
+
p = [], i, j;
|
151
|
+
if(this._data.search.res.length && !append) {
|
152
|
+
this.clear_search();
|
153
|
+
}
|
154
|
+
if(show_only_matches === undefined) {
|
155
|
+
show_only_matches = s.show_only_matches;
|
156
|
+
}
|
157
|
+
if(show_only_matches_children === undefined) {
|
158
|
+
show_only_matches_children = s.show_only_matches_children;
|
159
|
+
}
|
160
|
+
if(!skip_async && a !== false) {
|
161
|
+
if($.isFunction(a)) {
|
162
|
+
return a.call(this, str, $.proxy(function (d) {
|
163
|
+
if(d && d.d) { d = d.d; }
|
164
|
+
this._load_nodes(!$.isArray(d) ? [] : $.vakata.array_unique(d), function () {
|
165
|
+
this.search(str, true, show_only_matches, inside, append, show_only_matches_children);
|
166
|
+
});
|
167
|
+
}, this), inside);
|
168
|
+
}
|
169
|
+
else {
|
170
|
+
a = $.extend({}, a);
|
171
|
+
if(!a.data) { a.data = {}; }
|
172
|
+
a.data.str = str;
|
173
|
+
if(inside) {
|
174
|
+
a.data.inside = inside;
|
175
|
+
}
|
176
|
+
if (this._data.search.lastRequest) {
|
177
|
+
this._data.search.lastRequest.abort();
|
178
|
+
}
|
179
|
+
this._data.search.lastRequest = $.ajax(a)
|
180
|
+
.fail($.proxy(function () {
|
181
|
+
this._data.core.last_error = { 'error' : 'ajax', 'plugin' : 'search', 'id' : 'search_01', 'reason' : 'Could not load search parents', 'data' : JSON.stringify(a) };
|
182
|
+
this.settings.core.error.call(this, this._data.core.last_error);
|
183
|
+
}, this))
|
184
|
+
.done($.proxy(function (d) {
|
185
|
+
if(d && d.d) { d = d.d; }
|
186
|
+
this._load_nodes(!$.isArray(d) ? [] : $.vakata.array_unique(d), function () {
|
187
|
+
this.search(str, true, show_only_matches, inside, append, show_only_matches_children);
|
188
|
+
});
|
189
|
+
}, this));
|
190
|
+
return this._data.search.lastRequest;
|
191
|
+
}
|
192
|
+
}
|
193
|
+
if(!append) {
|
194
|
+
this._data.search.str = str;
|
195
|
+
this._data.search.dom = $();
|
196
|
+
this._data.search.res = [];
|
197
|
+
this._data.search.opn = [];
|
198
|
+
this._data.search.som = show_only_matches;
|
199
|
+
this._data.search.smc = show_only_matches_children;
|
200
|
+
}
|
201
|
+
|
202
|
+
f = new $.vakata.search(str, true, { caseSensitive : s.case_sensitive, fuzzy : s.fuzzy });
|
203
|
+
$.each(m[inside ? inside : $.jstree.root].children_d, function (ii, i) {
|
204
|
+
var v = m[i];
|
205
|
+
if(v.text && !v.state.hidden && (!s.search_leaves_only || (v.state.loaded && v.children.length === 0)) && ( (s.search_callback && s.search_callback.call(this, str, v)) || (!s.search_callback && f.search(v.text).isMatch) ) ) {
|
206
|
+
r.push(i);
|
207
|
+
p = p.concat(v.parents);
|
208
|
+
}
|
209
|
+
});
|
210
|
+
if(r.length) {
|
211
|
+
p = $.vakata.array_unique(p);
|
212
|
+
for(i = 0, j = p.length; i < j; i++) {
|
213
|
+
if(p[i] !== $.jstree.root && m[p[i]] && this.open_node(p[i], null, 0) === true) {
|
214
|
+
this._data.search.opn.push(p[i]);
|
215
|
+
}
|
216
|
+
}
|
217
|
+
if(!append) {
|
218
|
+
this._data.search.dom = $(this.element[0].querySelectorAll('#' + $.map(r, function (v) { return "0123456789".indexOf(v[0]) !== -1 ? '\\3' + v[0] + ' ' + v.substr(1).replace($.jstree.idregex,'\\$&') : v.replace($.jstree.idregex,'\\$&'); }).join(', #')));
|
219
|
+
this._data.search.res = r;
|
220
|
+
}
|
221
|
+
else {
|
222
|
+
this._data.search.dom = this._data.search.dom.add($(this.element[0].querySelectorAll('#' + $.map(r, function (v) { return "0123456789".indexOf(v[0]) !== -1 ? '\\3' + v[0] + ' ' + v.substr(1).replace($.jstree.idregex,'\\$&') : v.replace($.jstree.idregex,'\\$&'); }).join(', #'))));
|
223
|
+
this._data.search.res = $.vakata.array_unique(this._data.search.res.concat(r));
|
224
|
+
}
|
225
|
+
this._data.search.dom.children(".jstree-anchor").addClass('jstree-search');
|
226
|
+
}
|
227
|
+
/**
|
228
|
+
* triggered after search is complete
|
229
|
+
* @event
|
230
|
+
* @name search.jstree
|
231
|
+
* @param {jQuery} nodes a jQuery collection of matching nodes
|
232
|
+
* @param {String} str the search string
|
233
|
+
* @param {Array} res a collection of objects represeing the matching nodes
|
234
|
+
* @plugin search
|
235
|
+
*/
|
236
|
+
this.trigger('search', { nodes : this._data.search.dom, str : str, res : this._data.search.res, show_only_matches : show_only_matches });
|
237
|
+
};
|
238
|
+
/**
|
239
|
+
* used to clear the last search (removes classes and shows all nodes if filtering is on)
|
240
|
+
* @name clear_search()
|
241
|
+
* @plugin search
|
242
|
+
* @trigger clear_search.jstree
|
243
|
+
*/
|
244
|
+
this.clear_search = function () {
|
245
|
+
if(this.settings.search.close_opened_onclear) {
|
246
|
+
this.close_node(this._data.search.opn, 0);
|
247
|
+
}
|
248
|
+
/**
|
249
|
+
* triggered after search is complete
|
250
|
+
* @event
|
251
|
+
* @name clear_search.jstree
|
252
|
+
* @param {jQuery} nodes a jQuery collection of matching nodes (the result from the last search)
|
253
|
+
* @param {String} str the search string (the last search string)
|
254
|
+
* @param {Array} res a collection of objects represeing the matching nodes (the result from the last search)
|
255
|
+
* @plugin search
|
256
|
+
*/
|
257
|
+
this.trigger('clear_search', { 'nodes' : this._data.search.dom, str : this._data.search.str, res : this._data.search.res });
|
258
|
+
if(this._data.search.res.length) {
|
259
|
+
this._data.search.dom = $(this.element[0].querySelectorAll('#' + $.map(this._data.search.res, function (v) {
|
260
|
+
return "0123456789".indexOf(v[0]) !== -1 ? '\\3' + v[0] + ' ' + v.substr(1).replace($.jstree.idregex,'\\$&') : v.replace($.jstree.idregex,'\\$&');
|
261
|
+
}).join(', #')));
|
262
|
+
this._data.search.dom.children(".jstree-anchor").removeClass("jstree-search");
|
263
|
+
}
|
264
|
+
this._data.search.str = "";
|
265
|
+
this._data.search.res = [];
|
266
|
+
this._data.search.opn = [];
|
267
|
+
this._data.search.dom = $();
|
268
|
+
};
|
269
|
+
|
270
|
+
this.redraw_node = function(obj, deep, callback, force_render) {
|
271
|
+
obj = parent.redraw_node.apply(this, arguments);
|
272
|
+
if(obj) {
|
273
|
+
if($.inArray(obj.id, this._data.search.res) !== -1) {
|
274
|
+
var i, j, tmp = null;
|
275
|
+
for(i = 0, j = obj.childNodes.length; i < j; i++) {
|
276
|
+
if(obj.childNodes[i] && obj.childNodes[i].className && obj.childNodes[i].className.indexOf("jstree-anchor") !== -1) {
|
277
|
+
tmp = obj.childNodes[i];
|
278
|
+
break;
|
279
|
+
}
|
280
|
+
}
|
281
|
+
if(tmp) {
|
282
|
+
tmp.className += ' jstree-search';
|
283
|
+
}
|
284
|
+
}
|
285
|
+
}
|
286
|
+
return obj;
|
287
|
+
};
|
288
|
+
};
|
289
|
+
|
290
|
+
// helpers
|
291
|
+
(function ($) {
|
292
|
+
// from http://kiro.me/projects/fuse.html
|
293
|
+
$.vakata.search = function(pattern, txt, options) {
|
294
|
+
options = options || {};
|
295
|
+
options = $.extend({}, $.vakata.search.defaults, options);
|
296
|
+
if(options.fuzzy !== false) {
|
297
|
+
options.fuzzy = true;
|
298
|
+
}
|
299
|
+
pattern = options.caseSensitive ? pattern : pattern.toLowerCase();
|
300
|
+
var MATCH_LOCATION = options.location,
|
301
|
+
MATCH_DISTANCE = options.distance,
|
302
|
+
MATCH_THRESHOLD = options.threshold,
|
303
|
+
patternLen = pattern.length,
|
304
|
+
matchmask, pattern_alphabet, match_bitapScore, search;
|
305
|
+
if(patternLen > 32) {
|
306
|
+
options.fuzzy = false;
|
307
|
+
}
|
308
|
+
if(options.fuzzy) {
|
309
|
+
matchmask = 1 << (patternLen - 1);
|
310
|
+
pattern_alphabet = (function () {
|
311
|
+
var mask = {},
|
312
|
+
i = 0;
|
313
|
+
for (i = 0; i < patternLen; i++) {
|
314
|
+
mask[pattern.charAt(i)] = 0;
|
315
|
+
}
|
316
|
+
for (i = 0; i < patternLen; i++) {
|
317
|
+
mask[pattern.charAt(i)] |= 1 << (patternLen - i - 1);
|
318
|
+
}
|
319
|
+
return mask;
|
320
|
+
}());
|
321
|
+
match_bitapScore = function (e, x) {
|
322
|
+
var accuracy = e / patternLen,
|
323
|
+
proximity = Math.abs(MATCH_LOCATION - x);
|
324
|
+
if(!MATCH_DISTANCE) {
|
325
|
+
return proximity ? 1.0 : accuracy;
|
326
|
+
}
|
327
|
+
return accuracy + (proximity / MATCH_DISTANCE);
|
328
|
+
};
|
329
|
+
}
|
330
|
+
search = function (text) {
|
331
|
+
text = options.caseSensitive ? text : text.toLowerCase();
|
332
|
+
if(pattern === text || text.indexOf(pattern) !== -1) {
|
333
|
+
return {
|
334
|
+
isMatch: true,
|
335
|
+
score: 0
|
336
|
+
};
|
337
|
+
}
|
338
|
+
if(!options.fuzzy) {
|
339
|
+
return {
|
340
|
+
isMatch: false,
|
341
|
+
score: 1
|
342
|
+
};
|
343
|
+
}
|
344
|
+
var i, j,
|
345
|
+
textLen = text.length,
|
346
|
+
scoreThreshold = MATCH_THRESHOLD,
|
347
|
+
bestLoc = text.indexOf(pattern, MATCH_LOCATION),
|
348
|
+
binMin, binMid,
|
349
|
+
binMax = patternLen + textLen,
|
350
|
+
lastRd, start, finish, rd, charMatch,
|
351
|
+
score = 1,
|
352
|
+
locations = [];
|
353
|
+
if (bestLoc !== -1) {
|
354
|
+
scoreThreshold = Math.min(match_bitapScore(0, bestLoc), scoreThreshold);
|
355
|
+
bestLoc = text.lastIndexOf(pattern, MATCH_LOCATION + patternLen);
|
356
|
+
if (bestLoc !== -1) {
|
357
|
+
scoreThreshold = Math.min(match_bitapScore(0, bestLoc), scoreThreshold);
|
358
|
+
}
|
359
|
+
}
|
360
|
+
bestLoc = -1;
|
361
|
+
for (i = 0; i < patternLen; i++) {
|
362
|
+
binMin = 0;
|
363
|
+
binMid = binMax;
|
364
|
+
while (binMin < binMid) {
|
365
|
+
if (match_bitapScore(i, MATCH_LOCATION + binMid) <= scoreThreshold) {
|
366
|
+
binMin = binMid;
|
367
|
+
} else {
|
368
|
+
binMax = binMid;
|
369
|
+
}
|
370
|
+
binMid = Math.floor((binMax - binMin) / 2 + binMin);
|
371
|
+
}
|
372
|
+
binMax = binMid;
|
373
|
+
start = Math.max(1, MATCH_LOCATION - binMid + 1);
|
374
|
+
finish = Math.min(MATCH_LOCATION + binMid, textLen) + patternLen;
|
375
|
+
rd = new Array(finish + 2);
|
376
|
+
rd[finish + 1] = (1 << i) - 1;
|
377
|
+
for (j = finish; j >= start; j--) {
|
378
|
+
charMatch = pattern_alphabet[text.charAt(j - 1)];
|
379
|
+
if (i === 0) {
|
380
|
+
rd[j] = ((rd[j + 1] << 1) | 1) & charMatch;
|
381
|
+
} else {
|
382
|
+
rd[j] = ((rd[j + 1] << 1) | 1) & charMatch | (((lastRd[j + 1] | lastRd[j]) << 1) | 1) | lastRd[j + 1];
|
383
|
+
}
|
384
|
+
if (rd[j] & matchmask) {
|
385
|
+
score = match_bitapScore(i, j - 1);
|
386
|
+
if (score <= scoreThreshold) {
|
387
|
+
scoreThreshold = score;
|
388
|
+
bestLoc = j - 1;
|
389
|
+
locations.push(bestLoc);
|
390
|
+
if (bestLoc > MATCH_LOCATION) {
|
391
|
+
start = Math.max(1, 2 * MATCH_LOCATION - bestLoc);
|
392
|
+
} else {
|
393
|
+
break;
|
394
|
+
}
|
395
|
+
}
|
396
|
+
}
|
397
|
+
}
|
398
|
+
if (match_bitapScore(i + 1, MATCH_LOCATION) > scoreThreshold) {
|
399
|
+
break;
|
400
|
+
}
|
401
|
+
lastRd = rd;
|
402
|
+
}
|
403
|
+
return {
|
404
|
+
isMatch: bestLoc >= 0,
|
405
|
+
score: score
|
406
|
+
};
|
407
|
+
};
|
408
|
+
return txt === true ? { 'search' : search } : search(txt);
|
409
|
+
};
|
410
|
+
$.vakata.search.defaults = {
|
411
|
+
location : 0,
|
412
|
+
distance : 100,
|
413
|
+
threshold : 0.6,
|
414
|
+
fuzzy : false,
|
415
|
+
caseSensitive : false
|
416
|
+
};
|
417
|
+
}($));
|
418
|
+
|
419
|
+
// include the search plugin by default
|
420
|
+
// $.jstree.defaults.plugins.push("search");
|
421
|
+
}));
|
@@ -0,0 +1,74 @@
|
|
1
|
+
/**
|
2
|
+
* ### Sort plugin
|
3
|
+
*
|
4
|
+
* Automatically sorts all siblings in the tree according to a sorting function.
|
5
|
+
*/
|
6
|
+
/*globals jQuery, define, exports, require */
|
7
|
+
(function (factory) {
|
8
|
+
"use strict";
|
9
|
+
if (typeof define === 'function' && define.amd) {
|
10
|
+
define('jstree.sort', ['jquery','jstree'], factory);
|
11
|
+
}
|
12
|
+
else if(typeof exports === 'object') {
|
13
|
+
factory(require('jquery'), require('jstree'));
|
14
|
+
}
|
15
|
+
else {
|
16
|
+
factory(jQuery, jQuery.jstree);
|
17
|
+
}
|
18
|
+
}(function ($, jstree, undefined) {
|
19
|
+
"use strict";
|
20
|
+
|
21
|
+
if($.jstree.plugins.sort) { return; }
|
22
|
+
|
23
|
+
/**
|
24
|
+
* the settings function used to sort the nodes.
|
25
|
+
* It is executed in the tree's context, accepts two nodes as arguments and should return `1` or `-1`.
|
26
|
+
* @name $.jstree.defaults.sort
|
27
|
+
* @plugin sort
|
28
|
+
*/
|
29
|
+
$.jstree.defaults.sort = function (a, b) {
|
30
|
+
//return this.get_type(a) === this.get_type(b) ? (this.get_text(a) > this.get_text(b) ? 1 : -1) : this.get_type(a) >= this.get_type(b);
|
31
|
+
return this.get_text(a) > this.get_text(b) ? 1 : -1;
|
32
|
+
};
|
33
|
+
$.jstree.plugins.sort = function (options, parent) {
|
34
|
+
this.bind = function () {
|
35
|
+
parent.bind.call(this);
|
36
|
+
this.element
|
37
|
+
.on("model.jstree", $.proxy(function (e, data) {
|
38
|
+
this.sort(data.parent, true);
|
39
|
+
}, this))
|
40
|
+
.on("rename_node.jstree create_node.jstree", $.proxy(function (e, data) {
|
41
|
+
this.sort(data.parent || data.node.parent, false);
|
42
|
+
this.redraw_node(data.parent || data.node.parent, true);
|
43
|
+
}, this))
|
44
|
+
.on("move_node.jstree copy_node.jstree", $.proxy(function (e, data) {
|
45
|
+
this.sort(data.parent, false);
|
46
|
+
this.redraw_node(data.parent, true);
|
47
|
+
}, this));
|
48
|
+
};
|
49
|
+
/**
|
50
|
+
* used to sort a node's children
|
51
|
+
* @private
|
52
|
+
* @name sort(obj [, deep])
|
53
|
+
* @param {mixed} obj the node
|
54
|
+
* @param {Boolean} deep if set to `true` nodes are sorted recursively.
|
55
|
+
* @plugin sort
|
56
|
+
* @trigger search.jstree
|
57
|
+
*/
|
58
|
+
this.sort = function (obj, deep) {
|
59
|
+
var i, j;
|
60
|
+
obj = this.get_node(obj);
|
61
|
+
if(obj && obj.children && obj.children.length) {
|
62
|
+
obj.children.sort($.proxy(this.settings.sort, this));
|
63
|
+
if(deep) {
|
64
|
+
for(i = 0, j = obj.children_d.length; i < j; i++) {
|
65
|
+
this.sort(obj.children_d[i], false);
|
66
|
+
}
|
67
|
+
}
|
68
|
+
}
|
69
|
+
};
|
70
|
+
};
|
71
|
+
|
72
|
+
// include the sort plugin by default
|
73
|
+
// $.jstree.defaults.plugins.push("sort");
|
74
|
+
}));
|