sequenceserver 3.1.2 → 3.1.3

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Files changed (41) hide show
  1. checksums.yaml +4 -4
  2. data/lib/sequenceserver/blast/tasks.rb +1 -1
  3. data/lib/sequenceserver/routes.rb +1 -1
  4. data/lib/sequenceserver/version.rb +1 -1
  5. data/lib/sequenceserver.rb +1 -1
  6. data/public/css/app.min.css +1 -1
  7. data/public/css/sequenceserver.css +0 -18
  8. data/public/css/sequenceserver.min.css +2 -2
  9. data/public/js/alignment_exporter.js +16 -28
  10. data/public/js/cloud_share_modal.js +42 -42
  11. data/public/js/form.js +12 -10
  12. data/public/js/grapher.js +4 -4
  13. data/public/js/hit.js +3 -3
  14. data/public/js/hits.js +276 -0
  15. data/public/js/jquery_world.js +1 -1
  16. data/public/js/mailto.js +1 -3
  17. data/public/js/null_plugins/report_plugins.js +1 -0
  18. data/public/js/options.js +2 -6
  19. data/public/js/query.js +1 -1
  20. data/public/js/report.js +68 -252
  21. data/public/js/report_root.js +7 -5
  22. data/public/js/search.js +28 -11
  23. data/public/js/sequence.js +158 -158
  24. data/public/js/sequence_modal.js +28 -36
  25. data/public/js/sidebar.js +7 -6
  26. data/public/js/tests/alignment_exporter.spec.js +38 -0
  27. data/public/js/tests/cloud_share_modal.spec.js +75 -0
  28. data/public/js/tests/report.spec.js +37 -15
  29. data/public/packages/jquery-ui@1.13.3.js +19070 -0
  30. data/public/sequenceserver-report.min.js +3 -2481
  31. data/public/sequenceserver-report.min.js.LICENSE.txt +300 -0
  32. data/public/sequenceserver-report.min.js.map +1 -0
  33. data/public/sequenceserver-search.min.js +3 -2382
  34. data/public/sequenceserver-search.min.js.LICENSE.txt +292 -0
  35. data/public/sequenceserver-search.min.js.map +1 -0
  36. data/views/layout.erb +3 -7
  37. data/views/search.erb +1 -1
  38. data/views/search_layout.erb +1 -1
  39. metadata +11 -5
  40. data/public/config.js +0 -147
  41. data/public/packages/jquery-ui@1.11.4.js +0 -16624
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+ /*!
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+ "shortcut" : 113,
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+ "shortcut_label" : 'F2',
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+ "icon" : "glyphicon glyphicon-leaf",
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+ */
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+
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+ /*!
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+ 'themes' : {
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+ 'name' : this.get_theme(),
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+ 'icons' : this._data.core.themes.icons,
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+ 'dots' : this._data.core.themes.dots
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+ },
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+ */
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+
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+ /*!
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+ .on("mousedown.jstree touchstart.jstree", ".jstree-wholerow", function (e) {
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+ if(e.target === e.currentTarget) {
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+ var a = $(e.currentTarget).closest(".jstree-node").children(".jstree-anchor");
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+ e.target = a[0];
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+ a.trigger(e);
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+ }
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+ })
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+ */
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+
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+ /*!
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+ if(!('oncontextmenu' in document.body) && ('ontouchstart' in document.body)) {
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+ var el = null, tm = null;
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+ this.element
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+ .on("touchstart", ".jstree-anchor", function (e) {
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+ el = e.currentTarget;
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+ tm = +new Date();
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+ $(document).one("touchend", function (e) {
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+ e.target = document.elementFromPoint(e.originalEvent.targetTouches[0].pageX - window.pageXOffset, e.originalEvent.targetTouches[0].pageY - window.pageYOffset);
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+ e.currentTarget = e.target;
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+ tm = ((+(new Date())) - tm);
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+ if(e.target === el && tm > 600 && tm < 1000) {
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+ e.preventDefault();
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+ $(el).trigger('contextmenu', e);
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+ }
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+ el = null;
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+ tm = null;
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+ });
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+ });
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+ }
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+ */
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+
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+ /*!
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+ oi = obj.children("i:visible"),
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+ ai = a.children("i:visible"),
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+ w1 = oi.width() * oi.length,
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+ w2 = ai.width() * ai.length,
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+ */
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+
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+ /*!
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+ * if using jslint please allow for the jQuery global and use following options:
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+ * jslint: loopfunc: true, browser: true, ass: true, bitwise: true, continue: true, nomen: true, plusplus: true, regexp: true, unparam: true, todo: true, white: true
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+ */
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+
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+ /*!
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+ * jQuery JavaScript Library v3.7.1
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+ * https://jquery.com/
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license
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+ * https://jquery.org/license
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+ *
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+ * Date: 2023-08-28T13:37Z
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+ */
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+
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+ /*!
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+ * jQuery UI :data 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Autocomplete 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Button 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Checkboxradio 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Controlgroup 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Datepicker 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Dialog 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Draggable 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Droppable 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Effects 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Focusable 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Position 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ *
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+ * https://api.jqueryui.com/position/
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+ */
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+
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+ /*!
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+ * jQuery UI Resizable 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Spinner 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Support for jQuery core 1.8.x and newer 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ *
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+ */
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+
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+ /*!
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+ * jQuery UI Tabs 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Tooltip 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jQuery UI Widget 1.13.3
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+ * https://jqueryui.com
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+ *
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+ * Copyright OpenJS Foundation and other contributors
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+ * Released under the MIT license.
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+ * https://jquery.org/license
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+ */
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+
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+ /*!
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+ * jsTree 3.3.16
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+ * http://jstree.com/
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+ *
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+ * Copyright (c) 2014 Ivan Bozhanov (http://vakata.com)
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+ *
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+ * Licensed same as jquery - under the terms of the MIT License
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+ * http://www.opensource.org/licenses/mit-license.php
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+ */
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+
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+ /*! jQuery UI - v1.13.3 - 2024-04-26
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+ * https://jqueryui.com
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+ * Includes: widget.js, position.js, data.js, disable-selection.js, effect.js, effects/effect-blind.js, effects/effect-bounce.js, effects/effect-clip.js, effects/effect-drop.js, effects/effect-explode.js, effects/effect-fade.js, effects/effect-fold.js, effects/effect-highlight.js, effects/effect-puff.js, effects/effect-pulsate.js, effects/effect-scale.js, effects/effect-shake.js, effects/effect-size.js, effects/effect-slide.js, effects/effect-transfer.js, focusable.js, form-reset-mixin.js, jquery-patch.js, keycode.js, labels.js, scroll-parent.js, tabbable.js, unique-id.js, widgets/accordion.js, widgets/autocomplete.js, widgets/button.js, widgets/checkboxradio.js, widgets/controlgroup.js, widgets/datepicker.js, widgets/dialog.js, widgets/draggable.js, widgets/droppable.js, widgets/menu.js, widgets/mouse.js, widgets/progressbar.js, widgets/resizable.js, widgets/selectable.js, widgets/selectmenu.js, widgets/slider.js, widgets/sortable.js, widgets/spinner.js, widgets/tabs.js, widgets/tooltip.js
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+ * Copyright OpenJS Foundation and other contributors; Licensed MIT */
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+
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+ /**
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+ * @license React
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+ * react-dom.development.js
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+ *
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+ * Copyright (c) Facebook, Inc. and its affiliates.
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+ *
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+ * This source code is licensed under the MIT license found in the
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+ * LICENSE file in the root directory of this source tree.
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+ */
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+
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+ /**
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+ * @license React
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+ * react-jsx-runtime.development.js
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+ *
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+ * Copyright (c) Facebook, Inc. and its affiliates.
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+ *
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+ * This source code is licensed under the MIT license found in the
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+ * LICENSE file in the root directory of this source tree.
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+ */
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+
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+ /**
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+ * @license React
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+ * scheduler.development.js
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+ *
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+ * Copyright (c) Facebook, Inc. and its affiliates.
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+ *
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+ * This source code is licensed under the MIT license found in the
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+ * LICENSE file in the root directory of this source tree.
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+ */
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+
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+ /**
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+ * Checks if an event is supported in the current execution environment.
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+ *
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+ * NOTE: This will not work correctly for non-generic events such as `change`,
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+ * `reset`, `load`, `error`, and `select`.
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+ *
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+ * Borrows from Modernizr.
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+ *
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+ * @param {string} eventNameSuffix Event name, e.g. "click".
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+ * @return {boolean} True if the event is supported.
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+ * @internal
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+ * @license Modernizr 3.0.0pre (Custom Build) | MIT
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+ */