scicom 0.3.0-java → 0.4.0-java

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Files changed (155) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +239 -55
  3. data/Rakefile +58 -5
  4. data/config.rb +34 -2
  5. data/doc/Array.html +153 -0
  6. data/doc/Java/OrgRenjinSexp/LogicalArrayVector.html +120 -0
  7. data/doc/Java/OrgRenjinSexp/StringArrayVector.html +133 -0
  8. data/doc/Java/RbScicom/MDDoubleVector.html +133 -0
  9. data/doc/MDArray.html +153 -0
  10. data/doc/MergeObservable.html +347 -0
  11. data/doc/NegRange.html +166 -0
  12. data/doc/PackageManager.html +823 -0
  13. data/doc/PackageManager/ParseXML.html +595 -0
  14. data/doc/Range.html +243 -0
  15. data/doc/Renjin.html +2210 -0
  16. data/doc/Renjin/Attributes.html +401 -0
  17. data/doc/Renjin/Closure.html +181 -0
  18. data/doc/Renjin/ComplexVector.html +557 -0
  19. data/doc/Renjin/DataFrame.html +258 -0
  20. data/doc/Renjin/Environment.html +279 -0
  21. data/doc/Renjin/Function.html +243 -0
  22. data/doc/Renjin/Index.html +628 -0
  23. data/doc/Renjin/List.html +398 -0
  24. data/doc/Renjin/Logical.html +352 -0
  25. data/doc/Renjin/Primitive.html +181 -0
  26. data/doc/Renjin/RBSexp.html +1151 -0
  27. data/doc/Renjin/RubySexp.html +498 -0
  28. data/doc/Renjin/Vector.html +3163 -0
  29. data/doc/RinRuby.html +2079 -0
  30. data/doc/_index.html +365 -0
  31. data/doc/class_list.html +58 -0
  32. data/doc/css/common.css +1 -0
  33. data/doc/css/full_list.css +57 -0
  34. data/doc/css/style.css +339 -0
  35. data/doc/file.README.html +159 -0
  36. data/doc/file_list.html +60 -0
  37. data/doc/frames.html +26 -0
  38. data/doc/index.html +159 -0
  39. data/doc/js/app.js +219 -0
  40. data/doc/js/full_list.js +181 -0
  41. data/doc/js/jquery.js +4 -0
  42. data/doc/method_list.html +939 -0
  43. data/doc/top-level-namespace.html +679 -0
  44. data/lib/JRubyR/attributes.rb +5 -2
  45. data/lib/JRubyR/callback.rb +115 -0
  46. data/lib/JRubyR/environment.rb +0 -1
  47. data/lib/JRubyR/indexed.rb +139 -0
  48. data/lib/JRubyR/list.rb +0 -16
  49. data/lib/JRubyR/logical_value.rb +0 -1
  50. data/lib/JRubyR/rbsexp.rb +20 -131
  51. data/lib/JRubyR/renjin.rb +201 -71
  52. data/lib/JRubyR/vector.rb +16 -15
  53. data/lib/scicom.rb +1 -3
  54. data/target/helper.jar +0 -0
  55. data/test/test_R_interface.rb +1 -1
  56. data/test/test_array.rb +1 -1
  57. data/test/test_assign_mdarray.rb +1 -1
  58. data/test/test_assign_mdarray_2d.rb +1 -1
  59. data/test/test_assign_mdarray_3d.rb +1 -1
  60. data/test/test_attributes.rb +1 -1
  61. data/test/test_basic.rb +7 -5
  62. data/test/test_callback.rb +176 -0
  63. data/test/test_complete.rb +1 -1
  64. data/test/test_creation.rb +29 -5
  65. data/test/test_dataframe.rb +1 -1
  66. data/test/test_factor.rb +1 -1
  67. data/test/test_functions.rb +13 -10
  68. data/test/test_linear_model.rb +1 -1
  69. data/test/test_list.rb +49 -10
  70. data/test/test_matrix.rb +6 -6
  71. data/test/test_operators.rb +1 -1
  72. data/test/test_package.rb +5 -5
  73. data/test/test_vector.rb +13 -7
  74. data/vendor/aether-api-1.0.2.v20150114.jar +0 -0
  75. data/vendor/aether-connector-basic-1.0.2.v20150114.jar +0 -0
  76. data/vendor/aether-impl-1.0.2.v20150114.jar +0 -0
  77. data/vendor/aether-spi-1.0.2.v20150114.jar +0 -0
  78. data/vendor/aether-transport-file-1.0.2.v20150114.jar +0 -0
  79. data/vendor/aether-transport-http-1.0.2.v20150114.jar +0 -0
  80. data/vendor/aether-util-1.0.2.v20150114.jar +0 -0
  81. data/vendor/aopalliance-1.0.jar +0 -0
  82. data/vendor/asm-3.3.1.jar +0 -0
  83. data/vendor/asm-5.0.4.jar +0 -0
  84. data/vendor/asm-commons-5.0.4.jar +0 -0
  85. data/vendor/asm-tree-5.0.4.jar +0 -0
  86. data/vendor/asm-util-5.0.4.jar +0 -0
  87. data/vendor/blas-0.8.jar +0 -0
  88. data/vendor/cdi-api-1.0.jar +0 -0
  89. data/vendor/codemodel-2.6.jar +0 -0
  90. data/vendor/collections-generic-4.01.jar +0 -0
  91. data/vendor/commons-codec-1.6.jar +0 -0
  92. data/vendor/commons-compress-1.4.1.jar +0 -0
  93. data/vendor/commons-logging-1.1.1.jar +0 -0
  94. data/vendor/commons-math-2.2.jar +0 -0
  95. data/vendor/commons-vfs2-2.0.jar +0 -0
  96. data/vendor/datasets-0.8.1891.jar +0 -0
  97. data/vendor/f2jutil-0.8.jar +0 -0
  98. data/vendor/gcc-runtime-0.8.1891.jar +0 -0
  99. data/vendor/grDevices-0.8.1891.jar +0 -0
  100. data/vendor/graphics-0.8.1891.jar +0 -0
  101. data/vendor/guava-17.0.jar +0 -0
  102. data/vendor/httpclient-4.2.6.jar +0 -0
  103. data/vendor/httpcore-4.2.5.jar +0 -0
  104. data/vendor/javax.inject-1.jar +0 -0
  105. data/vendor/jcl-over-slf4j-1.6.2.jar +0 -0
  106. data/vendor/joda-time-2.0.jar +0 -0
  107. data/vendor/jsr250-api-1.0.jar +0 -0
  108. data/vendor/jtransforms-2.4.jar +0 -0
  109. data/vendor/jung-api-2.0.1.jar +0 -0
  110. data/vendor/jung-graph-impl-2.0.1.jar +0 -0
  111. data/vendor/lapack-0.8.jar +0 -0
  112. data/vendor/maven-aether-provider-3.1.0.jar +0 -0
  113. data/vendor/maven-model-3.1.0.jar +0 -0
  114. data/vendor/maven-model-builder-3.1.0.jar +0 -0
  115. data/vendor/maven-repository-metadata-3.1.0.jar +0 -0
  116. data/vendor/maven-scm-api-1.4.jar +0 -0
  117. data/vendor/maven-scm-provider-svn-commons-1.4.jar +0 -0
  118. data/vendor/maven-scm-provider-svnexe-1.4.jar +0 -0
  119. data/vendor/maven-settings-3.1.0.jar +0 -0
  120. data/vendor/maven-settings-builder-3.1.0.jar +0 -0
  121. data/vendor/methods-0.8.1891.jar +0 -0
  122. data/vendor/netlib-java-0.9.3-renjin-patched-2.jar +0 -0
  123. data/vendor/org.eclipse.sisu.inject-0.0.0.M2a.jar +0 -0
  124. data/vendor/org.eclipse.sisu.plexus-0.0.0.M2a.jar +0 -0
  125. data/vendor/plexus-cipher-1.4.jar +0 -0
  126. data/vendor/plexus-classworlds-2.4.jar +0 -0
  127. data/vendor/plexus-component-annotations-1.5.5.jar +0 -0
  128. data/vendor/plexus-interpolation-1.16.jar +0 -0
  129. data/vendor/plexus-sec-dispatcher-1.3.jar +0 -0
  130. data/vendor/plexus-utils-1.5.6.jar +0 -0
  131. data/vendor/plexus-utils-3.0.10.jar +0 -0
  132. data/vendor/regexp-1.3.jar +0 -0
  133. data/vendor/renjin-aether-package-loader-0.8.1891.jar +0 -0
  134. data/vendor/renjin-appl-0.8.1891.jar +0 -0
  135. data/vendor/renjin-core-0.8.1891.jar +0 -0
  136. data/vendor/renjin-gnur-runtime-0.8.1891.jar +0 -0
  137. data/vendor/renjin-script-engine-0.8.1891.jar +0 -0
  138. data/vendor/sisu-guice-3.1.0-no_aop.jar +0 -0
  139. data/vendor/slf4j-api-1.6.2.jar +0 -0
  140. data/vendor/stats-0.8.1891.jar +0 -0
  141. data/vendor/utils-0.8.1891.jar +0 -0
  142. data/vendor/xerbla-0.8.jar +0 -0
  143. data/vendor/xz-1.0.jar +0 -0
  144. data/version.rb +1 -1
  145. metadata +229 -127
  146. data/cran/AppliedPredictiveModeling.jar +0 -0
  147. data/cran/AppliedPredictiveModeling.xml +0 -25
  148. data/cran/AssetPricing.jar +0 -0
  149. data/cran/AssetPricing.xml +0 -25
  150. data/lib/env.rb +0 -12
  151. data/lib/rinruby.rb +0 -795
  152. data/test/env.rb +0 -2
  153. data/test/test_tmp.rb +0 -67
  154. data/vendor/Renjin.pdf +0 -0
  155. data/vendor/renjin-script-engine-0.7.0-RC7-SNAPSHOT-jar-with-dependencies.jar +0 -0
data/doc/PackageManager/ParseXML.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Class: PackageManager::ParseXML
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+
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+ &mdash; Documentation by YARD 0.8.7.6
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+ </title>
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+ <link rel="stylesheet" href="../css/style.css" type="text/css" charset="utf-8" />
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+ hasFrames = window.top.frames.main ? true : false;
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+ relpath = '../';
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+ framesUrl = "../frames.html#!PackageManager/ParseXML.html";
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+ </head>
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+ <body>
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+ <div id="header">
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+ <a href="../_index.html">Index (P)</a> &raquo;
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+ <span class='title'><span class='object_link'><a href="../PackageManager.html" title="PackageManager (class)">PackageManager</a></span></span>
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+ &raquo;
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+ <span class="title">ParseXML</span>
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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+ <div id="search">
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+
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+ <a class="full_list_link" id="class_list_link"
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+ href="../class_list.html">
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+ Class List
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+ </a>
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+ <a class="full_list_link" id="method_list_link"
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+ href="../method_list.html">
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+ Method List
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+ </a>
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+
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+ <a class="full_list_link" id="file_list_link"
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+ href="../file_list.html">
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+ File List
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+ </a>
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+
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+ </div>
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+ <div class="clear"></div>
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+ </div>
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1>Class: PackageManager::ParseXML
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+
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+ </h1>
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+
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+ <dl class="box">
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+
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+ <dt class="r1">Inherits:</dt>
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+ <dd class="r1">
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+ <span class="inheritName">Object</span>
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+
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+ <ul class="fullTree">
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+ <li>Object</li>
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+
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+ <li class="next">PackageManager::ParseXML</li>
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+
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+ </ul>
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+ <a href="#" class="inheritanceTree">show all</a>
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+
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+ </dd>
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+
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+ <dt class="r2">Includes:</dt>
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+ <dd class="r2"><span class='object_link'><a href="../MergeObservable.html" title="MergeObservable (module)">MergeObservable</a></span></dd>
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+ <dt class="r1 last">Defined in:</dt>
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+ <dd class="r1 last">lib/JRubyR/package.rb</dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+
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+ <p>Class to parse the maven-metadata.xml file for package management</p>
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+ </div>
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+ <h2>
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+ Instance Method Summary
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+ <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#initialize-instance_method" title="#initialize (instance method)">- (ParseXML) <strong>initialize</strong>(source) </a>
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+ </span>
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+ <span class="note title constructor">constructor</span>
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+ <span class="summary_desc"><div class='inline'>
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+ <p>----------------------------------------------------------------------------------------
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+ Parse the input_file and send parsed events to the given state machine.</p>
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+ </div></span>
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+ </li>
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+ <li class="public ">
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+ <span class="summary_signature">
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+ <a href="#method_missing-instance_method" title="#method_missing (instance method)">- (Object) <strong>method_missing</strong>(*args) </a>
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+ <span class="summary_desc"><div class='inline'>
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+ <p>----------------------------------------------------------------------------------------
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+ This method is necessary do ignore parsing events that are of no interest
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+ to our parsing.</p>
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+ </div></span>
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+ </li>
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+ <li class="public ">
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+ <span class="summary_signature">
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+ <a href="#start-instance_method" title="#start (instance method)">- (Object) <strong>start</strong> </a>
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+ <span class="summary_desc"><div class='inline'>
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+ <p>----------------------------------------------------------------------------------------
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+ start parsing the file.</p>
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+ </div></span>
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+ </li>
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+ <li class="public ">
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+ <span class="summary_signature">
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+ <a href="#tag_end-instance_method" title="#tag_end (instance method)">- (Object) <strong>tag_end</strong>(name) </a>
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+ <span class="summary_desc"><div class='inline'>
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+ <p>----------------------------------------------------------------------------------------
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+ Called when receiving a tag_end event
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+ ----------------------------------------------------------------------------------------.</p>
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+ </div></span>
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+ </li>
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+ <li class="public ">
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+ <span class="summary_signature">
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+ <a href="#tag_start-instance_method" title="#tag_start (instance method)">- (Object) <strong>tag_start</strong>(name, attrs) </a>
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+ <span class="summary_desc"><div class='inline'>
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+ <p>----------------------------------------------------------------------------------------
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+ Called when receiving a tag_start event
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+ ----------------------------------------------------------------------------------------.</p>
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+ </div></span>
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+ </li>
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+ <li class="public ">
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+ <a href="#text-instance_method" title="#text (instance method)">- (Object) <strong>text</strong>(text) </a>
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+ <span class="summary_desc"><div class='inline'>
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+ <p>----------------------------------------------------------------------------------------.</p>
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+ </div></span>
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+ </li>
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+ </ul>
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+ <h3 class="inherited">Methods included from <span class='object_link'><a href="../MergeObservable.html" title="MergeObservable (module)">MergeObservable</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="../MergeObservable.html#add_new_observer-instance_method" title="MergeObservable#add_new_observer (method)">#add_new_observer</a></span>, <span class='object_link'><a href="../MergeObservable.html#merge_observers-instance_method" title="MergeObservable#merge_observers (method)">#merge_observers</a></span>, <span class='object_link'><a href="../MergeObservable.html#notify_observers-instance_method" title="MergeObservable#notify_observers (method)">#notify_observers</a></span>, <span class='object_link'><a href="../MergeObservable.html#old_notify-instance_method" title="MergeObservable#old_notify (method)">#old_notify</a></span></p>
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+
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+ <div id="constructor_details" class="method_details_list">
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+ <h2>Constructor Details</h2>
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="initialize-instance_method">
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+
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+ - (<tt><span class='object_link'><a href="" title="PackageManager::ParseXML (class)">ParseXML</a></span></tt>) <strong>initialize</strong>(source)
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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+
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+ <p>Parse the input_file and send parsed events to the given state machine.
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+ Results should be stored in the output_dir</p>
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+ <hr>
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+ </div>
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+ </div>
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+ <div class="tags">
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+ 76
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+ 77
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+ 78</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 76</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_source'>source</span><span class='rparen'>)</span>
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+ <span class='ivar'>@source</span> <span class='op'>=</span> <span class='id identifier rubyid_source'>source</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+ <div id="method_missing_details" class="method_details_list">
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+ <h2>Dynamic Method Handling</h2>
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+ <p class="notice this">
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+ This class handles dynamic methods through the <tt>method_missing</tt> method
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+
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+ </p>
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="method_missing-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>method_missing</strong>(*args)
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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+
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+ <p>This method is necessary do ignore parsing events that are of no interest
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+ to our parsing.</p>
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+ <hr>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+ 94
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+ 95
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+ 96</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 94</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_method_missing'>method_missing</span><span class='lparen'>(</span><span class='op'>*</span><span class='id identifier rubyid_args'>args</span><span class='rparen'>)</span>
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+ <span class='comment'># p args
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+ </span><span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+
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+ <div id="instance_method_details" class="method_details_list">
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+ <h2>Instance Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="start-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>start</strong>
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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+
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+ <p>start parsing the file. This class will receive the events and redirect
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+ them to listeners</p>
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+ <hr>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 85
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+ 86
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+ 87</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 85</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_start'>start</span>
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+ <span class='const'>REXML</span><span class='op'>::</span><span class='const'>Document</span><span class='period'>.</span><span class='id identifier rubyid_parse_stream'>parse_stream</span><span class='lparen'>(</span><span class='ivar'>@source</span><span class='comma'>,</span> <span class='kw'>self</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ <div class="method_details ">
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+ <h3 class="signature " id="tag_end-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>tag_end</strong>(name)
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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+
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+ <p>Called when receiving a tag_end event</p>
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+ <hr>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 111
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+ 112
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+ 113
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+ 114</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 111</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_tag_end'>tag_end</span><span class='lparen'>(</span><span class='id identifier rubyid_name'>name</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_changed'>changed</span>
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+ <span class='id identifier rubyid_notify_observers'>notify_observers</span><span class='lparen'>(</span><span class='symbol'>:tag_end</span><span class='comma'>,</span> <span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='kw'>nil</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ <div class="method_details ">
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+ <h3 class="signature " id="tag_start-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>tag_start</strong>(name, attrs)
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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+
509
+ <p>Called when receiving a tag_start event</p>
510
+ <hr>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 102
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+ 103
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+ 104
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+ 105</pre>
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+ </td>
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+ <td>
530
+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 102</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_tag_start'>tag_start</span><span class='lparen'>(</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='id identifier rubyid_attrs'>attrs</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_changed'>changed</span>
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+ <span class='id identifier rubyid_notify_observers'>notify_observers</span><span class='lparen'>(</span><span class='symbol'>:tag_start</span><span class='comma'>,</span> <span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='id identifier rubyid_attrs'>attrs</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
541
+ <div class="method_details ">
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+ <h3 class="signature " id="text-instance_method">
543
+
544
+ - (<tt>Object</tt>) <strong>text</strong>(text)
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+
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+
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+
548
+
549
+
550
+ </h3><div class="docstring">
551
+ <div class="discussion">
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+ <hr>
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+ <hr>
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+
555
+
556
+ </div>
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+ </div>
558
+ <div class="tags">
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+
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+
561
+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 120
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+ 121
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+ 122
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+ 123</pre>
571
+ </td>
572
+ <td>
573
+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 120</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_text'>text</span><span class='lparen'>(</span><span class='id identifier rubyid_text'>text</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_changed'>changed</span>
577
+ <span class='id identifier rubyid_notify_observers'>notify_observers</span><span class='lparen'>(</span><span class='symbol'>:new_text</span><span class='comma'>,</span> <span class='id identifier rubyid_text'>text</span><span class='comma'>,</span> <span class='kw'>nil</span><span class='rparen'>)</span>
578
+ <span class='kw'>end</span></pre>
579
+ </td>
580
+ </tr>
581
+ </table>
582
+ </div>
583
+
584
+ </div>
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+
586
+ </div>
587
+
588
+ <div id="footer">
589
+ Generated on Tue Jul 14 18:12:23 2015 by
590
+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
591
+ 0.8.7.6 (ruby-1.9.3).
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+ </div>
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+
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+ </body>
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+ </html>