sequenceserver 2.0.0.rc8 → 2.0.0

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Files changed (116) hide show
  1. checksums.yaml +4 -4
  2. data/bin/sequenceserver +22 -30
  3. data/lib/sequenceserver/api_errors.rb +5 -1
  4. data/lib/sequenceserver/blast/constants.rb +1 -1
  5. data/lib/sequenceserver/blast/hit.rb +5 -16
  6. data/lib/sequenceserver/blast/job.rb +9 -18
  7. data/lib/sequenceserver/blast/report.rb +5 -3
  8. data/lib/sequenceserver/config.rb +4 -1
  9. data/lib/sequenceserver/database.rb +69 -9
  10. data/lib/sequenceserver/job.rb +1 -1
  11. data/lib/sequenceserver/makeblastdb.rb +40 -45
  12. data/lib/sequenceserver/routes.rb +4 -0
  13. data/lib/sequenceserver/version.rb +1 -1
  14. data/lib/sequenceserver.rb +15 -11
  15. data/public/config.js +143 -142
  16. data/public/css/fonts.css +23 -22
  17. data/public/css/grapher.css +598 -594
  18. data/public/css/sequenceserver.css +86 -24
  19. data/public/css/sequenceserver.min.css +2 -2
  20. data/public/js/alignment_exporter.js +14 -14
  21. data/public/js/databases_tree.js +215 -0
  22. data/public/js/download_fasta.js +1 -1
  23. data/public/js/hit.js +6 -2
  24. data/public/js/hits_overview.js +1 -1
  25. data/public/js/length_distribution.js +5 -5
  26. data/public/js/query.js +4 -7
  27. data/public/js/report.js +12 -24
  28. data/public/js/search.js +21 -2
  29. data/public/js/sidebar.js +4 -4
  30. data/public/js/svgExporter.js +12 -12
  31. data/public/js/visualisation_helpers.js +4 -5
  32. data/public/sequenceserver-report.min.js +11 -11
  33. data/public/sequenceserver-search.min.js +15 -11
  34. data/public/vendor/github/vakata/jstree@3.3.8/LICENSE-MIT +22 -0
  35. data/public/vendor/github/vakata/jstree@3.3.8/README.md +663 -0
  36. data/public/vendor/github/vakata/jstree@3.3.8/bower.json +33 -0
  37. data/public/vendor/github/vakata/jstree@3.3.8/component.json +28 -0
  38. data/public/vendor/github/vakata/jstree@3.3.8/composer.json +46 -0
  39. data/public/vendor/github/vakata/jstree@3.3.8/demo/README.md +2 -0
  40. data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/index.html +146 -0
  41. data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/root.json +1 -0
  42. data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.js +8612 -0
  43. data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.min.js +6 -0
  44. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/32px.png +0 -0
  45. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/40px.png +0 -0
  46. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.css +1102 -0
  47. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.min.css +1 -0
  48. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/throbber.gif +0 -0
  49. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/32px.png +0 -0
  50. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/40px.png +0 -0
  51. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.css +1146 -0
  52. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.min.css +1 -0
  53. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/throbber.gif +0 -0
  54. data/public/vendor/github/vakata/jstree@3.3.8/gruntfile.js +242 -0
  55. data/public/vendor/github/vakata/jstree@3.3.8/jstree.jquery.json +28 -0
  56. data/public/vendor/github/vakata/jstree@3.3.8/package.json +58 -0
  57. data/public/vendor/github/vakata/jstree@3.3.8/src/intro.js +14 -0
  58. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.changed.js +69 -0
  59. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.checkbox.js +976 -0
  60. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.conditionalselect.js +38 -0
  61. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.contextmenu.js +661 -0
  62. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.dnd.js +669 -0
  63. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.js +4931 -0
  64. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.massload.js +137 -0
  65. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.search.js +421 -0
  66. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.sort.js +74 -0
  67. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.state.js +138 -0
  68. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.types.js +372 -0
  69. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.unique.js +164 -0
  70. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.wholerow.js +122 -0
  71. data/public/vendor/github/vakata/jstree@3.3.8/src/misc.js +656 -0
  72. data/public/vendor/github/vakata/jstree@3.3.8/src/outro.js +1 -0
  73. data/public/vendor/github/vakata/jstree@3.3.8/src/sample.js +93 -0
  74. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/base.less +93 -0
  75. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/32px.png +0 -0
  76. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/40px.png +0 -0
  77. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.css +1102 -0
  78. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.less +22 -0
  79. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/throbber.gif +0 -0
  80. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/32px.png +0 -0
  81. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/40px.png +0 -0
  82. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.css +1146 -0
  83. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.less +50 -0
  84. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/throbber.gif +0 -0
  85. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/main.less +77 -0
  86. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/mixins.less +104 -0
  87. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/responsive.less +67 -0
  88. data/public/vendor/github/vakata/jstree@3.3.8/src/vakata-jstree.js +38 -0
  89. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/index.html +16 -0
  90. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.css +244 -0
  91. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.js +2212 -0
  92. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/test.js +11 -0
  93. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/desktop/index.html +44 -0
  94. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/mobile/index.html +42 -0
  95. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/desktop.png +0 -0
  96. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/home.png +0 -0
  97. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/home.png +0 -0
  98. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/mobile.png +0 -0
  99. data/public/vendor/github/vakata/jstree@3.3.8.js +3 -0
  100. data/public/vendor/system-csp-production.js +3 -3
  101. data/public/vendor/system-csp-production.js.map +1 -1
  102. data/public/vendor/system-csp-production.src.js +146 -140
  103. data/public/vendor/system-polyfills.js.map +1 -1
  104. data/public/vendor/system-polyfills.src.js +1 -0
  105. data/public/vendor/system.js +3 -3
  106. data/public/vendor/system.js.map +1 -1
  107. data/public/vendor/system.src.js +4771 -2383
  108. data/views/_options.erb +21 -0
  109. data/views/layout.erb +17 -18
  110. metadata +102 -43
  111. data/bin/chromedriver +0 -0
  112. data/bin/geckodriver +0 -0
  113. data/public/shims/form-core.js +0 -3
  114. data/public/shims/form-validation.js +0 -3
  115. data/public/shims/plugins/jquery.ui.position.js +0 -13
  116. data/public/shims/styles/shim.css +0 -1
@@ -0,0 +1,122 @@
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+ /**
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+ * ### Wholerow plugin
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+ *
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+ * Makes each node appear block level. Making selection easier. May cause slow down for large trees in old browsers.
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+ */
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+ /*globals jQuery, define, exports, require */
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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.wholerow', ['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 ($, jstree, undefined) {
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+ "use strict";
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+
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+ if($.jstree.plugins.wholerow) { return; }
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+
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+ var div = document.createElement('DIV');
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+ div.setAttribute('unselectable','on');
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+ div.setAttribute('role','presentation');
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+ div.className = 'jstree-wholerow';
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+ div.innerHTML = ' ';
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+ $.jstree.plugins.wholerow = function (options, parent) {
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+ this.bind = function () {
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+ parent.bind.call(this);
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+
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+ this.element
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+ .on('ready.jstree set_state.jstree', $.proxy(function () {
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+ this.hide_dots();
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+ }, this))
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+ .on("init.jstree loading.jstree ready.jstree", $.proxy(function () {
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+ //div.style.height = this._data.core.li_height + 'px';
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+ this.get_container_ul().addClass('jstree-wholerow-ul');
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+ }, this))
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+ .on("deselect_all.jstree", $.proxy(function (e, data) {
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+ this.element.find('.jstree-wholerow-clicked').removeClass('jstree-wholerow-clicked');
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+ }, this))
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+ .on("changed.jstree", $.proxy(function (e, data) {
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+ this.element.find('.jstree-wholerow-clicked').removeClass('jstree-wholerow-clicked');
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+ var tmp = false, i, j;
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+ for(i = 0, j = data.selected.length; i < j; i++) {
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+ tmp = this.get_node(data.selected[i], true);
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+ if(tmp && tmp.length) {
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+ tmp.children('.jstree-wholerow').addClass('jstree-wholerow-clicked');
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+ }
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+ }
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+ }, this))
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+ .on("open_node.jstree", $.proxy(function (e, data) {
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+ this.get_node(data.node, true).find('.jstree-clicked').parent().children('.jstree-wholerow').addClass('jstree-wholerow-clicked');
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+ }, this))
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+ .on("hover_node.jstree dehover_node.jstree", $.proxy(function (e, data) {
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+ if(e.type === "hover_node" && this.is_disabled(data.node)) { return; }
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+ this.get_node(data.node, true).children('.jstree-wholerow')[e.type === "hover_node"?"addClass":"removeClass"]('jstree-wholerow-hovered');
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+ }, this))
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+ .on("contextmenu.jstree", ".jstree-wholerow", $.proxy(function (e) {
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+ if (this._data.contextmenu) {
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+ e.preventDefault();
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+ var tmp = $.Event('contextmenu', { metaKey : e.metaKey, ctrlKey : e.ctrlKey, altKey : e.altKey, shiftKey : e.shiftKey, pageX : e.pageX, pageY : e.pageY });
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+ $(e.currentTarget).closest(".jstree-node").children(".jstree-anchor").first().trigger(tmp);
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+ }
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+ }, this))
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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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+ .on("click.jstree", ".jstree-wholerow", function (e) {
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+ e.stopImmediatePropagation();
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+ var tmp = $.Event('click', { metaKey : e.metaKey, ctrlKey : e.ctrlKey, altKey : e.altKey, shiftKey : e.shiftKey });
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+ $(e.currentTarget).closest(".jstree-node").children(".jstree-anchor").first().trigger(tmp).focus();
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+ })
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+ .on("dblclick.jstree", ".jstree-wholerow", function (e) {
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+ e.stopImmediatePropagation();
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+ var tmp = $.Event('dblclick', { metaKey : e.metaKey, ctrlKey : e.ctrlKey, altKey : e.altKey, shiftKey : e.shiftKey });
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+ $(e.currentTarget).closest(".jstree-node").children(".jstree-anchor").first().trigger(tmp).focus();
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+ })
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+ .on("click.jstree", ".jstree-leaf > .jstree-ocl", $.proxy(function (e) {
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+ e.stopImmediatePropagation();
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+ var tmp = $.Event('click', { metaKey : e.metaKey, ctrlKey : e.ctrlKey, altKey : e.altKey, shiftKey : e.shiftKey });
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+ $(e.currentTarget).closest(".jstree-node").children(".jstree-anchor").first().trigger(tmp).focus();
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+ }, this))
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+ .on("mouseover.jstree", ".jstree-wholerow, .jstree-icon", $.proxy(function (e) {
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+ e.stopImmediatePropagation();
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+ if(!this.is_disabled(e.currentTarget)) {
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+ this.hover_node(e.currentTarget);
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+ }
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+ return false;
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+ }, this))
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+ .on("mouseleave.jstree", ".jstree-node", $.proxy(function (e) {
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+ this.dehover_node(e.currentTarget);
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+ }, this));
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+ };
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+ this.teardown = function () {
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+ if(this.settings.wholerow) {
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+ this.element.find(".jstree-wholerow").remove();
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+ }
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+ parent.teardown.call(this);
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+ };
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+ this.redraw_node = function(obj, deep, callback, force_render) {
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+ obj = parent.redraw_node.apply(this, arguments);
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+ if(obj) {
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+ var tmp = div.cloneNode(true);
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+ //tmp.style.height = this._data.core.li_height + 'px';
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+ if($.inArray(obj.id, this._data.core.selected) !== -1) { tmp.className += ' jstree-wholerow-clicked'; }
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+ if(this._data.core.focused && this._data.core.focused === obj.id) { tmp.className += ' jstree-wholerow-hovered'; }
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+ obj.insertBefore(tmp, obj.childNodes[0]);
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+ }
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+ return obj;
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+ };
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+ };
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+ // include the wholerow plugin by default
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+ // $.jstree.defaults.plugins.push("wholerow");
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+ }));