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 +1,93 @@
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+ /*global jQuery */
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+ // wrap in IIFE and pass jQuery as $
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+ (function ($, undefined) {
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+ "use strict";
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+
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+ // some private plugin stuff if needed
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+ var private_var = null;
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+
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+ // extending the defaults
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+ $.jstree.defaults.sample = {
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+ sample_option : 'sample_val'
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+ };
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+
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+ // the actual plugin code
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+ $.jstree.plugins.sample = function (options, parent) {
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+ // own function
17
+ this.sample_function = function (arg) {
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+ // you can chain this method if needed and available
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+ if(parent.sample_function) { parent.sample_function.call(this, arg); }
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+ };
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+
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+ // *SPECIAL* FUNCTIONS
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+ this.init = function (el, options) {
24
+ // do not forget parent
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+ parent.init.call(this, el, options);
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+ };
27
+ // bind events if needed
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+ this.bind = function () {
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+ // call parent function first
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+ parent.bind.call(this);
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+ // do(stuff);
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+ };
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+ // unbind events if needed (all in jquery namespace are taken care of by the core)
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+ this.unbind = function () {
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+ // do(stuff);
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+ // call parent function last
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+ parent.unbind.call(this);
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+ };
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+ this.teardown = function () {
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+ // do not forget parent
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+ parent.teardown.call(this);
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+ };
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+ // state management - get and restore
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+ this.get_state = function () {
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+ // always get state from parent first
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+ var state = parent.get_state.call(this);
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+ // add own stuff to state
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+ state.sample = { 'var' : 'val' };
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+ return state;
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+ };
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+ this.set_state = function (state, callback) {
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+ // only process your part if parent returns true
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+ // there will be multiple times with false
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+ if(parent.set_state.call(this, state, callback)) {
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+ // check the key you set above
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+ if(state.sample) {
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+ // do(stuff); // like calling this.sample_function(state.sample.var);
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+ // remove your part of the state, call again and RETURN FALSE, the next cycle will be TRUE
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+ delete state.sample;
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+ this.set_state(state, callback);
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+ return false;
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+ }
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+ // return true if your state is gone (cleared in the previous step)
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+ return true;
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+ }
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+ // parent was false - return false too
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+ return false;
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+ };
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+ // node transportation
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+ this.get_json = function (obj, options, flat) {
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+ // get the node from the parent
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+ var tmp = parent.get_json.call(this, obj, options, flat), i, j;
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+ if($.isArray(tmp)) {
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+ for(i = 0, j = tmp.length; i < j; i++) {
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+ tmp[i].sample = 'value';
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+ }
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+ }
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+ else {
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+ tmp.sample = 'value';
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+ }
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+ // return the original / modified node
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+ return tmp;
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+ };
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+ };
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+
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+ // attach to document ready if needed
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+ $(function () {
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+ // do(stuff);
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+ });
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+
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+ // you can include the sample plugin in all instances by default
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+ $.jstree.defaults.plugins.push("sample");
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+ })(jQuery);
@@ -0,0 +1,93 @@
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+ // base jstree
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+ .jstree-node, .jstree-children, .jstree-container-ul { display:block; margin:0; padding:0; list-style-type:none; list-style-image:none; }
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+ .jstree-node { white-space:nowrap; }
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+ .jstree-anchor { display:inline-block; color:black; white-space:nowrap; padding:0 4px 0 1px; margin:0; vertical-align:top; }
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+ .jstree-anchor:focus { outline:0; }
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+ .jstree-anchor, .jstree-anchor:link, .jstree-anchor:visited, .jstree-anchor:hover, .jstree-anchor:active { text-decoration:none; color:inherit; }
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+ .jstree-icon { display:inline-block; text-decoration:none; margin:0; padding:0; vertical-align:top; text-align:center; }
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+ .jstree-icon:empty { display:inline-block; text-decoration:none; margin:0; padding:0; vertical-align:top; text-align:center; }
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+ .jstree-ocl { cursor:pointer; }
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+ .jstree-leaf > .jstree-ocl { cursor:default; }
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+ .jstree .jstree-open > .jstree-children { display:block; }
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+ .jstree .jstree-closed > .jstree-children,
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+ .jstree .jstree-leaf > .jstree-children { display:none; }
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+ .jstree-anchor > .jstree-themeicon { margin-right:2px; }
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+ .jstree-no-icons .jstree-themeicon,
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+ .jstree-anchor > .jstree-themeicon-hidden { display:none; }
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+ .jstree-hidden, .jstree-node.jstree-hidden { display:none; }
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+
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+ // base jstree rtl
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+ .jstree-rtl {
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+ .jstree-anchor { padding:0 1px 0 4px; }
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+ .jstree-anchor > .jstree-themeicon { margin-left:2px; margin-right:0; }
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+ .jstree-node { margin-left:0; }
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+ .jstree-container-ul > .jstree-node { margin-right:0; }
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+ }
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+
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+ // base jstree wholerow
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+ .jstree-wholerow-ul {
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+ position:relative;
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+ display:inline-block;
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+ min-width:100%;
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+ .jstree-leaf > .jstree-ocl { cursor:pointer; }
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+ .jstree-anchor, .jstree-icon { position:relative; }
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+ .jstree-wholerow { width:100%; cursor:pointer; position:absolute; left:0; -webkit-user-select:none; -moz-user-select:none; -ms-user-select:none; user-select:none; }
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+ }
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+
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+ // base contextmenu
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+ .jstree-contextmenu .jstree-anchor {
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+ -webkit-user-select: none; /* disable selection/Copy of UIWebView */
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+ -webkit-touch-callout: none; /* disable the IOS popup when long-press on a link */
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+ }
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+ .vakata-context {
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+ display:none;
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+ &, ul { margin:0; padding:2px; position:absolute; background:#f5f5f5; border:1px solid #979797; box-shadow:2px 2px 2px #999999; }
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+ ul { list-style:none; left:100%; margin-top:-2.7em; margin-left:-4px; }
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+ .vakata-context-right ul { left:auto; right:100%; margin-left:auto; margin-right:-4px; }
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+ li {
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+ list-style:none;
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+ > a {
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+ display:block; padding:0 2em 0 2em; text-decoration:none; width:auto; color:black; white-space:nowrap; line-height:2.4em; text-shadow:1px 1px 0 white; border-radius:1px;
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+ &:hover { position:relative; background-color:#e8eff7; box-shadow:0 0 2px #0a6aa1; }
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+ &.vakata-context-parent { background-image:url("data:image/gif;base64,R0lGODlhCwAHAIAAACgoKP///yH5BAEAAAEALAAAAAALAAcAAAIORI4JlrqN1oMSnmmZDQUAOw=="); background-position:right center; background-repeat:no-repeat; }
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+ }
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+ > a:focus { outline:0; }
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+ }
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+ .vakata-context-hover > a { position:relative; background-color:#e8eff7; box-shadow:0 0 2px #0a6aa1; }
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+ .vakata-context-separator {
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+ > a, > a:hover { background:white; border:0; border-top:1px solid #e2e3e3; height:1px; min-height:1px; max-height:1px; padding:0; margin:0 0 0 2.4em; border-left:1px solid #e0e0e0; text-shadow:0 0 0 transparent; box-shadow:0 0 0 transparent; border-radius:0; }
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+ }
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+ .vakata-contextmenu-disabled {
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+ a, a:hover { color:silver; background-color:transparent; border:0; box-shadow:0 0 0; }
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+ > a > i { filter: grayscale(100%); }
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+ }
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+ li > a {
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+ > i { text-decoration:none; display:inline-block; width:2.4em; height:2.4em; background:transparent; margin:0 0 0 -2em; vertical-align:top; text-align:center; line-height:2.4em; }
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+ > i:empty { width:2.4em; line-height:2.4em; }
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+ .vakata-contextmenu-sep { display:inline-block; width:1px; height:2.4em; background:white; margin:0 0.5em 0 0; border-left:1px solid #e2e3e3; }
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+ }
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+ .vakata-contextmenu-shortcut { font-size:0.8em; color:silver; opacity:0.5; display:none; }
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+ }
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+ .vakata-context-rtl {
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+ ul { left:auto; right:100%; margin-left:auto; margin-right:-4px; }
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+ li > a.vakata-context-parent { background-image:url("data:image/gif;base64,R0lGODlhCwAHAIAAACgoKP///yH5BAEAAAEALAAAAAALAAcAAAINjI+AC7rWHIsPtmoxLAA7"); background-position:left center; background-repeat:no-repeat; }
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+ .vakata-context-separator > a { margin:0 2.4em 0 0; border-left:0; border-right:1px solid #e2e3e3;}
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+ .vakata-context-left ul { right:auto; left:100%; margin-left:-4px; margin-right:auto; }
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+ li > a {
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+ > i { margin:0 -2em 0 0; }
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+ .vakata-contextmenu-sep { margin:0 0 0 0.5em; border-left-color:white; background:#e2e3e3; }
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+ }
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+ }
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+
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+ // base drag'n'drop
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+ #jstree-marker { position: absolute; top:0; left:0; margin:-5px 0 0 0; padding:0; border-right:0; border-top:5px solid transparent; border-bottom:5px solid transparent; border-left:5px solid; width:0; height:0; font-size:0; line-height:0; }
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+ #jstree-dnd {
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+ line-height:16px;
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+ margin:0;
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+ padding:4px;
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+ .jstree-icon,
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+ .jstree-copy { display:inline-block; text-decoration:none; margin:0 2px 0 0; padding:0; width:16px; height:16px; }
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+ .jstree-ok { background:green; }
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+ .jstree-er { background:red; }
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+ .jstree-copy { margin:0 2px 0 2px; }
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+ }