bio 0.7.1 → 1.0.0

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Files changed (142) hide show
  1. data/bin/bioruby +71 -27
  2. data/bin/br_biofetch.rb +5 -17
  3. data/bin/br_bioflat.rb +14 -26
  4. data/bin/br_biogetseq.rb +6 -18
  5. data/bin/br_pmfetch.rb +6 -16
  6. data/doc/Changes-0.7.rd +35 -0
  7. data/doc/KEGG_API.rd +287 -172
  8. data/doc/KEGG_API.rd.ja +273 -160
  9. data/doc/Tutorial.rd +18 -9
  10. data/doc/Tutorial.rd.ja +656 -138
  11. data/lib/bio.rb +6 -24
  12. data/lib/bio/alignment.rb +5 -5
  13. data/lib/bio/appl/blast.rb +132 -98
  14. data/lib/bio/appl/blast/format0.rb +9 -19
  15. data/lib/bio/appl/blast/wublast.rb +5 -18
  16. data/lib/bio/appl/emboss.rb +40 -47
  17. data/lib/bio/appl/hmmer.rb +116 -82
  18. data/lib/bio/appl/hmmer/report.rb +509 -364
  19. data/lib/bio/appl/spidey/report.rb +7 -18
  20. data/lib/bio/data/na.rb +3 -21
  21. data/lib/bio/db.rb +3 -21
  22. data/lib/bio/db/aaindex.rb +147 -52
  23. data/lib/bio/db/embl/common.rb +27 -6
  24. data/lib/bio/db/embl/embl.rb +18 -10
  25. data/lib/bio/db/embl/sptr.rb +87 -67
  26. data/lib/bio/db/embl/swissprot.rb +32 -3
  27. data/lib/bio/db/embl/trembl.rb +32 -3
  28. data/lib/bio/db/embl/uniprot.rb +32 -3
  29. data/lib/bio/db/fasta.rb +327 -289
  30. data/lib/bio/db/medline.rb +25 -4
  31. data/lib/bio/db/nbrf.rb +12 -20
  32. data/lib/bio/db/pdb.rb +4 -1
  33. data/lib/bio/db/pdb/chemicalcomponent.rb +240 -0
  34. data/lib/bio/db/pdb/pdb.rb +13 -8
  35. data/lib/bio/db/rebase.rb +93 -97
  36. data/lib/bio/feature.rb +2 -31
  37. data/lib/bio/io/ddbjxml.rb +167 -139
  38. data/lib/bio/io/fastacmd.rb +89 -56
  39. data/lib/bio/io/flatfile.rb +994 -278
  40. data/lib/bio/io/flatfile/index.rb +257 -194
  41. data/lib/bio/io/flatfile/indexer.rb +37 -29
  42. data/lib/bio/reference.rb +147 -64
  43. data/lib/bio/sequence.rb +57 -417
  44. data/lib/bio/sequence/aa.rb +64 -0
  45. data/lib/bio/sequence/common.rb +175 -0
  46. data/lib/bio/sequence/compat.rb +68 -0
  47. data/lib/bio/sequence/format.rb +134 -0
  48. data/lib/bio/sequence/generic.rb +24 -0
  49. data/lib/bio/sequence/na.rb +189 -0
  50. data/lib/bio/shell.rb +9 -23
  51. data/lib/bio/shell/core.rb +130 -125
  52. data/lib/bio/shell/demo.rb +143 -0
  53. data/lib/bio/shell/{session.rb → interface.rb} +42 -40
  54. data/lib/bio/shell/object.rb +52 -0
  55. data/lib/bio/shell/plugin/codon.rb +4 -22
  56. data/lib/bio/shell/plugin/emboss.rb +23 -0
  57. data/lib/bio/shell/plugin/entry.rb +34 -25
  58. data/lib/bio/shell/plugin/flatfile.rb +5 -23
  59. data/lib/bio/shell/plugin/keggapi.rb +11 -24
  60. data/lib/bio/shell/plugin/midi.rb +5 -23
  61. data/lib/bio/shell/plugin/obda.rb +4 -22
  62. data/lib/bio/shell/plugin/seq.rb +6 -24
  63. data/lib/bio/shell/rails/Rakefile +10 -0
  64. data/lib/bio/shell/rails/app/controllers/application.rb +4 -0
  65. data/lib/bio/shell/rails/app/controllers/shell_controller.rb +94 -0
  66. data/lib/bio/shell/rails/app/helpers/application_helper.rb +3 -0
  67. data/lib/bio/shell/rails/app/models/shell_connection.rb +30 -0
  68. data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +37 -0
  69. data/lib/bio/shell/rails/app/views/shell/history.rhtml +5 -0
  70. data/lib/bio/shell/rails/app/views/shell/index.rhtml +2 -0
  71. data/lib/bio/shell/rails/app/views/shell/show.rhtml +13 -0
  72. data/lib/bio/shell/rails/config/boot.rb +19 -0
  73. data/lib/bio/shell/rails/config/database.yml +85 -0
  74. data/lib/bio/shell/rails/config/environment.rb +53 -0
  75. data/lib/bio/shell/rails/config/environments/development.rb +19 -0
  76. data/lib/bio/shell/rails/config/environments/production.rb +19 -0
  77. data/lib/bio/shell/rails/config/environments/test.rb +19 -0
  78. data/lib/bio/shell/rails/config/routes.rb +19 -0
  79. data/lib/bio/shell/rails/doc/README_FOR_APP +2 -0
  80. data/lib/bio/shell/rails/public/404.html +8 -0
  81. data/lib/bio/shell/rails/public/500.html +8 -0
  82. data/lib/bio/shell/rails/public/dispatch.cgi +10 -0
  83. data/lib/bio/shell/rails/public/dispatch.fcgi +24 -0
  84. data/lib/bio/shell/rails/public/dispatch.rb +10 -0
  85. data/lib/bio/shell/rails/public/favicon.ico +0 -0
  86. data/lib/bio/shell/rails/public/images/icon.png +0 -0
  87. data/lib/bio/shell/rails/public/images/rails.png +0 -0
  88. data/lib/bio/shell/rails/public/index.html +277 -0
  89. data/lib/bio/shell/rails/public/javascripts/controls.js +750 -0
  90. data/lib/bio/shell/rails/public/javascripts/dragdrop.js +584 -0
  91. data/lib/bio/shell/rails/public/javascripts/effects.js +854 -0
  92. data/lib/bio/shell/rails/public/javascripts/prototype.js +1785 -0
  93. data/lib/bio/shell/rails/public/robots.txt +1 -0
  94. data/lib/bio/shell/rails/public/stylesheets/main.css +187 -0
  95. data/lib/bio/shell/rails/script/about +3 -0
  96. data/lib/bio/shell/rails/script/breakpointer +3 -0
  97. data/lib/bio/shell/rails/script/console +3 -0
  98. data/lib/bio/shell/rails/script/destroy +3 -0
  99. data/lib/bio/shell/rails/script/generate +3 -0
  100. data/lib/bio/shell/rails/script/performance/benchmarker +3 -0
  101. data/lib/bio/shell/rails/script/performance/profiler +3 -0
  102. data/lib/bio/shell/rails/script/plugin +3 -0
  103. data/lib/bio/shell/rails/script/process/reaper +3 -0
  104. data/lib/bio/shell/rails/script/process/spawner +3 -0
  105. data/lib/bio/shell/rails/script/process/spinner +3 -0
  106. data/lib/bio/shell/rails/script/runner +3 -0
  107. data/lib/bio/shell/rails/script/server +42 -0
  108. data/lib/bio/shell/rails/test/test_helper.rb +28 -0
  109. data/lib/bio/shell/web.rb +90 -0
  110. data/lib/bio/util/contingency_table.rb +231 -225
  111. data/sample/any2fasta.rb +59 -0
  112. data/test/data/HMMER/hmmpfam.out +64 -0
  113. data/test/data/HMMER/hmmsearch.out +88 -0
  114. data/test/data/aaindex/DAYM780301 +30 -0
  115. data/test/data/aaindex/PRAM900102 +20 -0
  116. data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
  117. data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
  118. data/test/data/blast/{eco:b0002.faa → b0002.faa} +0 -0
  119. data/test/data/blast/{eco:b0002.faa.m0 → b0002.faa.m0} +2 -2
  120. data/test/data/blast/{eco:b0002.faa.m7 → b0002.faa.m7} +1 -1
  121. data/test/data/blast/{eco:b0002.faa.m8 → b0002.faa.m8} +0 -0
  122. data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
  123. data/test/unit/bio/appl/blast/test_report.rb +15 -12
  124. data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -4
  125. data/test/unit/bio/appl/hmmer/test_report.rb +355 -0
  126. data/test/unit/bio/appl/test_blast.rb +5 -5
  127. data/test/unit/bio/data/test_na.rb +9 -18
  128. data/test/unit/bio/db/pdb/test_pdb.rb +169 -0
  129. data/test/unit/bio/db/test_aaindex.rb +197 -0
  130. data/test/unit/bio/io/test_fastacmd.rb +55 -0
  131. data/test/unit/bio/sequence/test_aa.rb +102 -0
  132. data/test/unit/bio/sequence/test_common.rb +178 -0
  133. data/test/unit/bio/sequence/test_compat.rb +82 -0
  134. data/test/unit/bio/sequence/test_na.rb +242 -0
  135. data/test/unit/bio/shell/plugin/test_seq.rb +29 -19
  136. data/test/unit/bio/test_alignment.rb +15 -7
  137. data/test/unit/bio/test_reference.rb +198 -0
  138. data/test/unit/bio/test_sequence.rb +4 -49
  139. data/test/unit/bio/test_shell.rb +2 -2
  140. metadata +118 -15
  141. data/lib/bio/io/brdb.rb +0 -103
  142. data/lib/bioruby.rb +0 -34
@@ -0,0 +1,750 @@
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+ // Copyright (c) 2005 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
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+ // (c) 2005 Ivan Krstic (http://blogs.law.harvard.edu/ivan)
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+ // (c) 2005 Jon Tirsen (http://www.tirsen.com)
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+ // Contributors:
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+ // Richard Livsey
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+ // Rahul Bhargava
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+ // Rob Wills
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+ //
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+ // See scriptaculous.js for full license.
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+
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+ // Autocompleter.Base handles all the autocompletion functionality
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+ // that's independent of the data source for autocompletion. This
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+ // includes drawing the autocompletion menu, observing keyboard
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+ // and mouse events, and similar.
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+ //
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+ // Specific autocompleters need to provide, at the very least,
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+ // a getUpdatedChoices function that will be invoked every time
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+ // the text inside the monitored textbox changes. This method
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+ // should get the text for which to provide autocompletion by
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+ // invoking this.getToken(), NOT by directly accessing
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+ // this.element.value. This is to allow incremental tokenized
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+ // autocompletion. Specific auto-completion logic (AJAX, etc)
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+ // belongs in getUpdatedChoices.
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+ //
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+ // Tokenized incremental autocompletion is enabled automatically
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+ // when an autocompleter is instantiated with the 'tokens' option
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+ // in the options parameter, e.g.:
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+ // new Ajax.Autocompleter('id','upd', '/url/', { tokens: ',' });
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+ // will incrementally autocomplete with a comma as the token.
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+ // Additionally, ',' in the above example can be replaced with
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+ // a token array, e.g. { tokens: [',', '\n'] } which
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+ // enables autocompletion on multiple tokens. This is most
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+ // useful when one of the tokens is \n (a newline), as it
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+ // allows smart autocompletion after linebreaks.
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+
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+ var Autocompleter = {}
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+ Autocompleter.Base = function() {};
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+ Autocompleter.Base.prototype = {
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+ baseInitialize: function(element, update, options) {
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+ this.element = $(element);
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+ this.update = $(update);
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+ this.hasFocus = false;
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+ this.changed = false;
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+ this.active = false;
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+ this.index = 0;
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+ this.entryCount = 0;
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+
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+ if (this.setOptions)
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+ this.setOptions(options);
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+ else
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+ this.options = options || {};
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+
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+ this.options.paramName = this.options.paramName || this.element.name;
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+ this.options.tokens = this.options.tokens || [];
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+ this.options.frequency = this.options.frequency || 0.4;
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+ this.options.minChars = this.options.minChars || 1;
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+ this.options.onShow = this.options.onShow ||
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+ function(element, update){
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+ if(!update.style.position || update.style.position=='absolute') {
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+ update.style.position = 'absolute';
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+ Position.clone(element, update, {setHeight: false, offsetTop: element.offsetHeight});
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+ }
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+ Effect.Appear(update,{duration:0.15});
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+ };
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+ this.options.onHide = this.options.onHide ||
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+ function(element, update){ new Effect.Fade(update,{duration:0.15}) };
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+
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+ if (typeof(this.options.tokens) == 'string')
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+ this.options.tokens = new Array(this.options.tokens);
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+
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+ this.observer = null;
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+
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+ this.element.setAttribute('autocomplete','off');
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+
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+ Element.hide(this.update);
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+
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+ Event.observe(this.element, "blur", this.onBlur.bindAsEventListener(this));
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+ Event.observe(this.element, "keypress", this.onKeyPress.bindAsEventListener(this));
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+ },
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+
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+ show: function() {
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+ if(Element.getStyle(this.update, 'display')=='none') this.options.onShow(this.element, this.update);
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+ if(!this.iefix &&
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+ (navigator.appVersion.indexOf('MSIE')>0) &&
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+ (navigator.userAgent.indexOf('Opera')<0) &&
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+ (Element.getStyle(this.update, 'position')=='absolute')) {
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+ new Insertion.After(this.update,
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+ '<iframe id="' + this.update.id + '_iefix" '+
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+ 'style="display:none;position:absolute;filter:progid:DXImageTransform.Microsoft.Alpha(opacity=0);" ' +
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+ 'src="javascript:false;" frameborder="0" scrolling="no"></iframe>');
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+ this.iefix = $(this.update.id+'_iefix');
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+ }
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+ if(this.iefix) setTimeout(this.fixIEOverlapping.bind(this), 50);
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+ },
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+
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+ fixIEOverlapping: function() {
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+ Position.clone(this.update, this.iefix);
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+ this.iefix.style.zIndex = 1;
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+ this.update.style.zIndex = 2;
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+ Element.show(this.iefix);
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+ },
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+
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+ hide: function() {
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+ this.stopIndicator();
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+ if(Element.getStyle(this.update, 'display')!='none') this.options.onHide(this.element, this.update);
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+ if(this.iefix) Element.hide(this.iefix);
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+ },
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+
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+ startIndicator: function() {
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+ if(this.options.indicator) Element.show(this.options.indicator);
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+ },
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+
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+ stopIndicator: function() {
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+ if(this.options.indicator) Element.hide(this.options.indicator);
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+ },
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+
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+ onKeyPress: function(event) {
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+ if(this.active)
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+ switch(event.keyCode) {
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+ case Event.KEY_TAB:
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+ case Event.KEY_RETURN:
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+ this.selectEntry();
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+ Event.stop(event);
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+ case Event.KEY_ESC:
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+ this.hide();
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+ this.active = false;
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+ Event.stop(event);
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+ return;
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+ case Event.KEY_LEFT:
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+ case Event.KEY_RIGHT:
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+ return;
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+ case Event.KEY_UP:
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+ this.markPrevious();
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+ this.render();
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+ if(navigator.appVersion.indexOf('AppleWebKit')>0) Event.stop(event);
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+ return;
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+ case Event.KEY_DOWN:
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+ this.markNext();
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+ this.render();
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+ if(navigator.appVersion.indexOf('AppleWebKit')>0) Event.stop(event);
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+ return;
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+ }
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+ else
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+ if(event.keyCode==Event.KEY_TAB || event.keyCode==Event.KEY_RETURN)
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+ return;
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+
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+ this.changed = true;
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+ this.hasFocus = true;
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+
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+ if(this.observer) clearTimeout(this.observer);
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+ this.observer =
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+ setTimeout(this.onObserverEvent.bind(this), this.options.frequency*1000);
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+ },
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+
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+ onHover: function(event) {
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+ var element = Event.findElement(event, 'LI');
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+ if(this.index != element.autocompleteIndex)
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+ {
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+ this.index = element.autocompleteIndex;
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+ this.render();
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+ }
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+ Event.stop(event);
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+ },
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+
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+ onClick: function(event) {
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+ var element = Event.findElement(event, 'LI');
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+ this.index = element.autocompleteIndex;
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+ this.selectEntry();
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+ this.hide();
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+ },
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+
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+ onBlur: function(event) {
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+ // needed to make click events working
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+ setTimeout(this.hide.bind(this), 250);
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+ this.hasFocus = false;
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+ this.active = false;
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+ },
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+
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+ render: function() {
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+ if(this.entryCount > 0) {
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+ for (var i = 0; i < this.entryCount; i++)
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+ this.index==i ?
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+ Element.addClassName(this.getEntry(i),"selected") :
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+ Element.removeClassName(this.getEntry(i),"selected");
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+
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+ if(this.hasFocus) {
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+ this.show();
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+ this.active = true;
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+ }
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+ } else {
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+ this.active = false;
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+ this.hide();
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+ }
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+ },
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+
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+ markPrevious: function() {
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+ if(this.index > 0) this.index--
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+ else this.index = this.entryCount-1;
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+ },
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+
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+ markNext: function() {
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+ if(this.index < this.entryCount-1) this.index++
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+ else this.index = 0;
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+ },
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+
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+ getEntry: function(index) {
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+ return this.update.firstChild.childNodes[index];
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+ },
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+
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+ getCurrentEntry: function() {
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+ return this.getEntry(this.index);
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+ },
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+
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+ selectEntry: function() {
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+ this.active = false;
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+ this.updateElement(this.getCurrentEntry());
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+ },
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+
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+ updateElement: function(selectedElement) {
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+ if (this.options.updateElement) {
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+ this.options.updateElement(selectedElement);
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+ return;
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+ }
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+
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+ var value = Element.collectTextNodesIgnoreClass(selectedElement, 'informal');
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+ var lastTokenPos = this.findLastToken();
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+ if (lastTokenPos != -1) {
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+ var newValue = this.element.value.substr(0, lastTokenPos + 1);
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+ var whitespace = this.element.value.substr(lastTokenPos + 1).match(/^\s+/);
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+ if (whitespace)
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+ newValue += whitespace[0];
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+ this.element.value = newValue + value;
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+ } else {
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+ this.element.value = value;
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+ }
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+ this.element.focus();
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+
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+ if (this.options.afterUpdateElement)
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+ this.options.afterUpdateElement(this.element, selectedElement);
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+ },
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+
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+ updateChoices: function(choices) {
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+ if(!this.changed && this.hasFocus) {
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+ this.update.innerHTML = choices;
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+ Element.cleanWhitespace(this.update);
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+ Element.cleanWhitespace(this.update.firstChild);
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+
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+ if(this.update.firstChild && this.update.firstChild.childNodes) {
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+ this.entryCount =
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+ this.update.firstChild.childNodes.length;
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+ for (var i = 0; i < this.entryCount; i++) {
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+ var entry = this.getEntry(i);
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+ entry.autocompleteIndex = i;
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+ this.addObservers(entry);
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+ }
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+ } else {
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+ this.entryCount = 0;
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+ }
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+
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+ this.stopIndicator();
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+
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+ this.index = 0;
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+ this.render();
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+ }
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+ },
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+
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+ addObservers: function(element) {
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+ Event.observe(element, "mouseover", this.onHover.bindAsEventListener(this));
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+ Event.observe(element, "click", this.onClick.bindAsEventListener(this));
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+ },
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+
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+ onObserverEvent: function() {
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+ this.changed = false;
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+ if(this.getToken().length>=this.options.minChars) {
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+ this.startIndicator();
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+ this.getUpdatedChoices();
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+ } else {
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+ this.active = false;
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+ this.hide();
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+ }
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+ },
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+
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+ getToken: function() {
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+ var tokenPos = this.findLastToken();
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+ if (tokenPos != -1)
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+ var ret = this.element.value.substr(tokenPos + 1).replace(/^\s+/,'').replace(/\s+$/,'');
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+ else
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+ var ret = this.element.value;
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+
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+ return /\n/.test(ret) ? '' : ret;
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+ },
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+
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+ findLastToken: function() {
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+ var lastTokenPos = -1;
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+
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+ for (var i=0; i<this.options.tokens.length; i++) {
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+ var thisTokenPos = this.element.value.lastIndexOf(this.options.tokens[i]);
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+ if (thisTokenPos > lastTokenPos)
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+ lastTokenPos = thisTokenPos;
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+ }
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+ return lastTokenPos;
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+ }
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+ }
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+
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+ Ajax.Autocompleter = Class.create();
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+ Object.extend(Object.extend(Ajax.Autocompleter.prototype, Autocompleter.Base.prototype), {
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+ initialize: function(element, update, url, options) {
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+ this.baseInitialize(element, update, options);
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+ this.options.asynchronous = true;
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+ this.options.onComplete = this.onComplete.bind(this);
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+ this.options.defaultParams = this.options.parameters || null;
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+ this.url = url;
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+ },
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+
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+ getUpdatedChoices: function() {
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+ entry = encodeURIComponent(this.options.paramName) + '=' +
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+ encodeURIComponent(this.getToken());
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+
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+ this.options.parameters = this.options.callback ?
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+ this.options.callback(this.element, entry) : entry;
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+
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+ if(this.options.defaultParams)
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+ this.options.parameters += '&' + this.options.defaultParams;
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+
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+ new Ajax.Request(this.url, this.options);
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+ },
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+
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+ onComplete: function(request) {
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+ this.updateChoices(request.responseText);
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+ }
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+
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+ });
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+
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+ // The local array autocompleter. Used when you'd prefer to
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+ // inject an array of autocompletion options into the page, rather
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+ // than sending out Ajax queries, which can be quite slow sometimes.
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+ //
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+ // The constructor takes four parameters. The first two are, as usual,
339
+ // the id of the monitored textbox, and id of the autocompletion menu.
340
+ // The third is the array you want to autocomplete from, and the fourth
341
+ // is the options block.
342
+ //
343
+ // Extra local autocompletion options:
344
+ // - choices - How many autocompletion choices to offer
345
+ //
346
+ // - partialSearch - If false, the autocompleter will match entered
347
+ // text only at the beginning of strings in the
348
+ // autocomplete array. Defaults to true, which will
349
+ // match text at the beginning of any *word* in the
350
+ // strings in the autocomplete array. If you want to
351
+ // search anywhere in the string, additionally set
352
+ // the option fullSearch to true (default: off).
353
+ //
354
+ // - fullSsearch - Search anywhere in autocomplete array strings.
355
+ //
356
+ // - partialChars - How many characters to enter before triggering
357
+ // a partial match (unlike minChars, which defines
358
+ // how many characters are required to do any match
359
+ // at all). Defaults to 2.
360
+ //
361
+ // - ignoreCase - Whether to ignore case when autocompleting.
362
+ // Defaults to true.
363
+ //
364
+ // It's possible to pass in a custom function as the 'selector'
365
+ // option, if you prefer to write your own autocompletion logic.
366
+ // In that case, the other options above will not apply unless
367
+ // you support them.
368
+
369
+ Autocompleter.Local = Class.create();
370
+ Autocompleter.Local.prototype = Object.extend(new Autocompleter.Base(), {
371
+ initialize: function(element, update, array, options) {
372
+ this.baseInitialize(element, update, options);
373
+ this.options.array = array;
374
+ },
375
+
376
+ getUpdatedChoices: function() {
377
+ this.updateChoices(this.options.selector(this));
378
+ },
379
+
380
+ setOptions: function(options) {
381
+ this.options = Object.extend({
382
+ choices: 10,
383
+ partialSearch: true,
384
+ partialChars: 2,
385
+ ignoreCase: true,
386
+ fullSearch: false,
387
+ selector: function(instance) {
388
+ var ret = []; // Beginning matches
389
+ var partial = []; // Inside matches
390
+ var entry = instance.getToken();
391
+ var count = 0;
392
+
393
+ for (var i = 0; i < instance.options.array.length &&
394
+ ret.length < instance.options.choices ; i++) {
395
+
396
+ var elem = instance.options.array[i];
397
+ var foundPos = instance.options.ignoreCase ?
398
+ elem.toLowerCase().indexOf(entry.toLowerCase()) :
399
+ elem.indexOf(entry);
400
+
401
+ while (foundPos != -1) {
402
+ if (foundPos == 0 && elem.length != entry.length) {
403
+ ret.push("<li><strong>" + elem.substr(0, entry.length) + "</strong>" +
404
+ elem.substr(entry.length) + "</li>");
405
+ break;
406
+ } else if (entry.length >= instance.options.partialChars &&
407
+ instance.options.partialSearch && foundPos != -1) {
408
+ if (instance.options.fullSearch || /\s/.test(elem.substr(foundPos-1,1))) {
409
+ partial.push("<li>" + elem.substr(0, foundPos) + "<strong>" +
410
+ elem.substr(foundPos, entry.length) + "</strong>" + elem.substr(
411
+ foundPos + entry.length) + "</li>");
412
+ break;
413
+ }
414
+ }
415
+
416
+ foundPos = instance.options.ignoreCase ?
417
+ elem.toLowerCase().indexOf(entry.toLowerCase(), foundPos + 1) :
418
+ elem.indexOf(entry, foundPos + 1);
419
+
420
+ }
421
+ }
422
+ if (partial.length)
423
+ ret = ret.concat(partial.slice(0, instance.options.choices - ret.length))
424
+ return "<ul>" + ret.join('') + "</ul>";
425
+ }
426
+ }, options || {});
427
+ }
428
+ });
429
+
430
+ // AJAX in-place editor
431
+ //
432
+ // see documentation on http://wiki.script.aculo.us/scriptaculous/show/Ajax.InPlaceEditor
433
+
434
+ // Use this if you notice weird scrolling problems on some browsers,
435
+ // the DOM might be a bit confused when this gets called so do this
436
+ // waits 1 ms (with setTimeout) until it does the activation
437
+ Field.scrollFreeActivate = function(field) {
438
+ setTimeout(function() {
439
+ Field.activate(field);
440
+ }, 1);
441
+ }
442
+
443
+ Ajax.InPlaceEditor = Class.create();
444
+ Ajax.InPlaceEditor.defaultHighlightColor = "#FFFF99";
445
+ Ajax.InPlaceEditor.prototype = {
446
+ initialize: function(element, url, options) {
447
+ this.url = url;
448
+ this.element = $(element);
449
+
450
+ this.options = Object.extend({
451
+ okText: "ok",
452
+ cancelText: "cancel",
453
+ savingText: "Saving...",
454
+ clickToEditText: "Click to edit",
455
+ okText: "ok",
456
+ rows: 1,
457
+ onComplete: function(transport, element) {
458
+ new Effect.Highlight(element, {startcolor: this.options.highlightcolor});
459
+ },
460
+ onFailure: function(transport) {
461
+ alert("Error communicating with the server: " + transport.responseText.stripTags());
462
+ },
463
+ callback: function(form) {
464
+ return Form.serialize(form);
465
+ },
466
+ handleLineBreaks: true,
467
+ loadingText: 'Loading...',
468
+ savingClassName: 'inplaceeditor-saving',
469
+ loadingClassName: 'inplaceeditor-loading',
470
+ formClassName: 'inplaceeditor-form',
471
+ highlightcolor: Ajax.InPlaceEditor.defaultHighlightColor,
472
+ highlightendcolor: "#FFFFFF",
473
+ externalControl: null,
474
+ ajaxOptions: {}
475
+ }, options || {});
476
+
477
+ if(!this.options.formId && this.element.id) {
478
+ this.options.formId = this.element.id + "-inplaceeditor";
479
+ if ($(this.options.formId)) {
480
+ // there's already a form with that name, don't specify an id
481
+ this.options.formId = null;
482
+ }
483
+ }
484
+
485
+ if (this.options.externalControl) {
486
+ this.options.externalControl = $(this.options.externalControl);
487
+ }
488
+
489
+ this.originalBackground = Element.getStyle(this.element, 'background-color');
490
+ if (!this.originalBackground) {
491
+ this.originalBackground = "transparent";
492
+ }
493
+
494
+ this.element.title = this.options.clickToEditText;
495
+
496
+ this.onclickListener = this.enterEditMode.bindAsEventListener(this);
497
+ this.mouseoverListener = this.enterHover.bindAsEventListener(this);
498
+ this.mouseoutListener = this.leaveHover.bindAsEventListener(this);
499
+ Event.observe(this.element, 'click', this.onclickListener);
500
+ Event.observe(this.element, 'mouseover', this.mouseoverListener);
501
+ Event.observe(this.element, 'mouseout', this.mouseoutListener);
502
+ if (this.options.externalControl) {
503
+ Event.observe(this.options.externalControl, 'click', this.onclickListener);
504
+ Event.observe(this.options.externalControl, 'mouseover', this.mouseoverListener);
505
+ Event.observe(this.options.externalControl, 'mouseout', this.mouseoutListener);
506
+ }
507
+ },
508
+ enterEditMode: function(evt) {
509
+ if (this.saving) return;
510
+ if (this.editing) return;
511
+ this.editing = true;
512
+ this.onEnterEditMode();
513
+ if (this.options.externalControl) {
514
+ Element.hide(this.options.externalControl);
515
+ }
516
+ Element.hide(this.element);
517
+ this.createForm();
518
+ this.element.parentNode.insertBefore(this.form, this.element);
519
+ Field.scrollFreeActivate(this.editField);
520
+ // stop the event to avoid a page refresh in Safari
521
+ if (evt) {
522
+ Event.stop(evt);
523
+ }
524
+ return false;
525
+ },
526
+ createForm: function() {
527
+ this.form = document.createElement("form");
528
+ this.form.id = this.options.formId;
529
+ Element.addClassName(this.form, this.options.formClassName)
530
+ this.form.onsubmit = this.onSubmit.bind(this);
531
+
532
+ this.createEditField();
533
+
534
+ if (this.options.textarea) {
535
+ var br = document.createElement("br");
536
+ this.form.appendChild(br);
537
+ }
538
+
539
+ okButton = document.createElement("input");
540
+ okButton.type = "submit";
541
+ okButton.value = this.options.okText;
542
+ this.form.appendChild(okButton);
543
+
544
+ cancelLink = document.createElement("a");
545
+ cancelLink.href = "#";
546
+ cancelLink.appendChild(document.createTextNode(this.options.cancelText));
547
+ cancelLink.onclick = this.onclickCancel.bind(this);
548
+ this.form.appendChild(cancelLink);
549
+ },
550
+ hasHTMLLineBreaks: function(string) {
551
+ if (!this.options.handleLineBreaks) return false;
552
+ return string.match(/<br/i) || string.match(/<p>/i);
553
+ },
554
+ convertHTMLLineBreaks: function(string) {
555
+ return string.replace(/<br>/gi, "\n").replace(/<br\/>/gi, "\n").replace(/<\/p>/gi, "\n").replace(/<p>/gi, "");
556
+ },
557
+ createEditField: function() {
558
+ var text;
559
+ if(this.options.loadTextURL) {
560
+ text = this.options.loadingText;
561
+ } else {
562
+ text = this.getText();
563
+ }
564
+
565
+ if (this.options.rows == 1 && !this.hasHTMLLineBreaks(text)) {
566
+ this.options.textarea = false;
567
+ var textField = document.createElement("input");
568
+ textField.type = "text";
569
+ textField.name = "value";
570
+ textField.value = text;
571
+ textField.style.backgroundColor = this.options.highlightcolor;
572
+ var size = this.options.size || this.options.cols || 0;
573
+ if (size != 0) textField.size = size;
574
+ this.editField = textField;
575
+ } else {
576
+ this.options.textarea = true;
577
+ var textArea = document.createElement("textarea");
578
+ textArea.name = "value";
579
+ textArea.value = this.convertHTMLLineBreaks(text);
580
+ textArea.rows = this.options.rows;
581
+ textArea.cols = this.options.cols || 40;
582
+ this.editField = textArea;
583
+ }
584
+
585
+ if(this.options.loadTextURL) {
586
+ this.loadExternalText();
587
+ }
588
+ this.form.appendChild(this.editField);
589
+ },
590
+ getText: function() {
591
+ return this.element.innerHTML;
592
+ },
593
+ loadExternalText: function() {
594
+ Element.addClassName(this.form, this.options.loadingClassName);
595
+ this.editField.disabled = true;
596
+ new Ajax.Request(
597
+ this.options.loadTextURL,
598
+ Object.extend({
599
+ asynchronous: true,
600
+ onComplete: this.onLoadedExternalText.bind(this)
601
+ }, this.options.ajaxOptions)
602
+ );
603
+ },
604
+ onLoadedExternalText: function(transport) {
605
+ Element.removeClassName(this.form, this.options.loadingClassName);
606
+ this.editField.disabled = false;
607
+ this.editField.value = transport.responseText.stripTags();
608
+ },
609
+ onclickCancel: function() {
610
+ this.onComplete();
611
+ this.leaveEditMode();
612
+ return false;
613
+ },
614
+ onFailure: function(transport) {
615
+ this.options.onFailure(transport);
616
+ if (this.oldInnerHTML) {
617
+ this.element.innerHTML = this.oldInnerHTML;
618
+ this.oldInnerHTML = null;
619
+ }
620
+ return false;
621
+ },
622
+ onSubmit: function() {
623
+ // onLoading resets these so we need to save them away for the Ajax call
624
+ var form = this.form;
625
+ var value = this.editField.value;
626
+
627
+ // do this first, sometimes the ajax call returns before we get a chance to switch on Saving...
628
+ // which means this will actually switch on Saving... *after* we've left edit mode causing Saving...
629
+ // to be displayed indefinitely
630
+ this.onLoading();
631
+
632
+ new Ajax.Updater(
633
+ {
634
+ success: this.element,
635
+ // don't update on failure (this could be an option)
636
+ failure: null
637
+ },
638
+ this.url,
639
+ Object.extend({
640
+ parameters: this.options.callback(form, value),
641
+ onComplete: this.onComplete.bind(this),
642
+ onFailure: this.onFailure.bind(this)
643
+ }, this.options.ajaxOptions)
644
+ );
645
+ // stop the event to avoid a page refresh in Safari
646
+ if (arguments.length > 1) {
647
+ Event.stop(arguments[0]);
648
+ }
649
+ return false;
650
+ },
651
+ onLoading: function() {
652
+ this.saving = true;
653
+ this.removeForm();
654
+ this.leaveHover();
655
+ this.showSaving();
656
+ },
657
+ showSaving: function() {
658
+ this.oldInnerHTML = this.element.innerHTML;
659
+ this.element.innerHTML = this.options.savingText;
660
+ Element.addClassName(this.element, this.options.savingClassName);
661
+ this.element.style.backgroundColor = this.originalBackground;
662
+ Element.show(this.element);
663
+ },
664
+ removeForm: function() {
665
+ if(this.form) {
666
+ if (this.form.parentNode) Element.remove(this.form);
667
+ this.form = null;
668
+ }
669
+ },
670
+ enterHover: function() {
671
+ if (this.saving) return;
672
+ this.element.style.backgroundColor = this.options.highlightcolor;
673
+ if (this.effect) {
674
+ this.effect.cancel();
675
+ }
676
+ Element.addClassName(this.element, this.options.hoverClassName)
677
+ },
678
+ leaveHover: function() {
679
+ if (this.options.backgroundColor) {
680
+ this.element.style.backgroundColor = this.oldBackground;
681
+ }
682
+ Element.removeClassName(this.element, this.options.hoverClassName)
683
+ if (this.saving) return;
684
+ this.effect = new Effect.Highlight(this.element, {
685
+ startcolor: this.options.highlightcolor,
686
+ endcolor: this.options.highlightendcolor,
687
+ restorecolor: this.originalBackground
688
+ });
689
+ },
690
+ leaveEditMode: function() {
691
+ Element.removeClassName(this.element, this.options.savingClassName);
692
+ this.removeForm();
693
+ this.leaveHover();
694
+ this.element.style.backgroundColor = this.originalBackground;
695
+ Element.show(this.element);
696
+ if (this.options.externalControl) {
697
+ Element.show(this.options.externalControl);
698
+ }
699
+ this.editing = false;
700
+ this.saving = false;
701
+ this.oldInnerHTML = null;
702
+ this.onLeaveEditMode();
703
+ },
704
+ onComplete: function(transport) {
705
+ this.leaveEditMode();
706
+ this.options.onComplete.bind(this)(transport, this.element);
707
+ },
708
+ onEnterEditMode: function() {},
709
+ onLeaveEditMode: function() {},
710
+ dispose: function() {
711
+ if (this.oldInnerHTML) {
712
+ this.element.innerHTML = this.oldInnerHTML;
713
+ }
714
+ this.leaveEditMode();
715
+ Event.stopObserving(this.element, 'click', this.onclickListener);
716
+ Event.stopObserving(this.element, 'mouseover', this.mouseoverListener);
717
+ Event.stopObserving(this.element, 'mouseout', this.mouseoutListener);
718
+ if (this.options.externalControl) {
719
+ Event.stopObserving(this.options.externalControl, 'click', this.onclickListener);
720
+ Event.stopObserving(this.options.externalControl, 'mouseover', this.mouseoverListener);
721
+ Event.stopObserving(this.options.externalControl, 'mouseout', this.mouseoutListener);
722
+ }
723
+ }
724
+ };
725
+
726
+ // Delayed observer, like Form.Element.Observer,
727
+ // but waits for delay after last key input
728
+ // Ideal for live-search fields
729
+
730
+ Form.Element.DelayedObserver = Class.create();
731
+ Form.Element.DelayedObserver.prototype = {
732
+ initialize: function(element, delay, callback) {
733
+ this.delay = delay || 0.5;
734
+ this.element = $(element);
735
+ this.callback = callback;
736
+ this.timer = null;
737
+ this.lastValue = $F(this.element);
738
+ Event.observe(this.element,'keyup',this.delayedListener.bindAsEventListener(this));
739
+ },
740
+ delayedListener: function(event) {
741
+ if(this.lastValue == $F(this.element)) return;
742
+ if(this.timer) clearTimeout(this.timer);
743
+ this.timer = setTimeout(this.onTimerEvent.bind(this), this.delay * 1000);
744
+ this.lastValue = $F(this.element);
745
+ },
746
+ onTimerEvent: function() {
747
+ this.timer = null;
748
+ this.callback(this.element, $F(this.element));
749
+ }
750
+ };