scicom 0.3.0-java → 0.4.0-java

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  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/NegRange.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: NegRange
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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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+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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+ <script type="text/javascript" charset="utf-8">
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+ hasFrames = window.top.frames.main ? true : false;
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+ framesUrl = "frames.html#!NegRange.html";
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+ </script>
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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+ </head>
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+ <body>
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+ <div id="header">
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+ <div id="menu">
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+ <a href="_index.html">Index (N)</a> &raquo;
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+ <span class="title">NegRange</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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+ <div id="search">
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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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+ <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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+ </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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+ <div id="content"><h1>Class: NegRange
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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"><span class='object_link'><a href="Range.html" title="Range (class)">Range</a></span></span>
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+
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+ <ul class="fullTree">
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+ <li>Object</li>
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+ <li class="next"><span class='object_link'><a href="Range.html" title="Range (class)">Range</a></span></li>
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+ <li class="next">NegRange</li>
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+ </ul>
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+ <a href="#" class="inheritanceTree">show all</a>
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+ <dt class="r2 last">Defined in:</dt>
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+ <dd class="r2 last">lib/JRubyR/ruby_classes.rb</dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+ <h6 id="label-"></h6>
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+
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+ <p>Class NegRange exists to represent a negative range, e.g., -(1...10). Such
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+ a range is used to index vectors and means all elements but the ones in the
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+ given range. Class NegRange is parsed to become "-(1:10)" in R.</p>
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+ <h6 id="label-"></h6>
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+ <h2>Instance Attribute Summary</h2>
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+ <h3 class="inherited">Attributes included from <span class='object_link'><a href="Renjin/RBSexp.html" title="Renjin::RBSexp (module)">Renjin::RBSexp</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="Renjin/RBSexp.html#attr-instance_method" title="Renjin::RBSexp#attr (method)">#attr</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#rvar-instance_method" title="Renjin::RBSexp#rvar (method)">#rvar</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#scope-instance_method" title="Renjin::RBSexp#scope (method)">#scope</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#sexp-instance_method" title="Renjin::RBSexp#sexp (method)">#sexp</a></span></p>
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+ <h2>Method Summary</h2>
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+ <h3 class="inherited">Methods inherited from <span class='object_link'><a href="Range.html" title="Range (class)">Range</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="Range.html#-%40-instance_method" title="Range#-@ (method)">#-@</a></span></p>
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+ <h3 class="inherited">Methods included from <span class='object_link'><a href="Renjin/RBSexp.html" title="Renjin::RBSexp (module)">Renjin::RBSexp</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="Renjin/RBSexp.html#destroy-instance_method" title="Renjin::RBSexp#destroy (method)">#destroy</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#ncol-instance_method" title="Renjin::RBSexp#ncol (method)">#ncol</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#nrow-instance_method" title="Renjin::RBSexp#nrow (method)">#nrow</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#pp-instance_method" title="Renjin::RBSexp#pp (method)">#pp</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#print-instance_method" title="Renjin::RBSexp#print (method)">#print</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#r-instance_method" title="Renjin::RBSexp#r (method)">#r</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#rclass-instance_method" title="Renjin::RBSexp#rclass (method)">#rclass</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#sexp%3F-instance_method" title="Renjin::RBSexp#sexp? (method)">#sexp?</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#typeof-instance_method" title="Renjin::RBSexp#typeof (method)">#typeof</a></span>, <span class='object_link'><a href="Renjin/RBSexp.html#unbind-instance_method" title="Renjin::RBSexp#unbind (method)">#unbind</a></span></p>
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Jul 14 18:12:24 2015 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.8.7.6 (ruby-1.9.3).
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+ </div>
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+ </body>
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+ </html>
data/doc/PackageManager.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
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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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+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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+
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+ <script type="text/javascript" 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.html";
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+ </script>
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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+ </head>
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+ <body>
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+ <div id="header">
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+ <div id="menu">
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+ <a href="_index.html">Index (P)</a> &raquo;
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+ <span class="title">PackageManager</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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+ <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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+
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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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+
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+ <iframe id="search_frame"></iframe>
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+ <div id="content"><h1>Class: PackageManager
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+ </h1>
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+ <dl class="box">
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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</li>
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+ </ul>
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+ <a href="#" class="inheritanceTree">show all</a>
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+ </dd>
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+ <dt class="r2 last">Defined in:</dt>
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+ <dd class="r2 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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+ <h2>Defined Under Namespace</h2>
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+ <p class="children">
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+ <strong class="classes">Classes:</strong> <span class='object_link'><a href="PackageManager/ParseXML.html" title="PackageManager::ParseXML (class)">ParseXML</a></span>
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+ </p>
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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="#http_download_uri-instance_method" title="#http_download_uri (instance method)">- (Object) <strong>http_download_uri</strong>(uri, filename) </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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+ <li class="public ">
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+ <span class="summary_signature">
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+ <a href="#initialize-instance_method" title="#initialize (instance method)">- (PackageManager) <strong>initialize</strong> </a>
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+ </span>
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+ <span class="note title constructor">constructor</span>
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'>
171
+ <p>----------------------------------------------------------------------------------------.</p>
172
+ </div></span>
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+
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+ </li>
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+
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+
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+ <li class="public ">
178
+ <span class="summary_signature">
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+
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+ <a href="#load_package-instance_method" title="#load_package (instance method)">- (Object) <strong>load_package</strong>(name) </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'>
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+ <p>----------------------------------------------------------------------------------------
196
+ Installs a new package
197
+ ----------------------------------------------------------------------------------------.</p>
198
+ </div></span>
199
+
200
+ </li>
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+
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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="#new_text-instance_method" title="#new_text (instance method)">- (Object) <strong>new_text</strong>(text) </a>
207
+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'>
221
+ <p>----------------------------------------------------------------------------------------.</p>
222
+ </div></span>
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+
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+ </li>
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+
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+
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+ <li class="public ">
228
+ <span class="summary_signature">
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+
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+ <a href="#set_value-instance_method" title="#set_value (instance method)">- (Object) <strong>set_value</strong> </a>
231
+
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+
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+
234
+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'>
245
+ <p>----------------------------------------------------------------------------------------.</p>
246
+ </div></span>
247
+
248
+ </li>
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+
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+
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+ <li class="public ">
252
+ <span class="summary_signature">
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+
254
+ <a href="#tag_end-instance_method" title="#tag_end (instance method)">- (Object) <strong>tag_end</strong>(name) </a>
255
+
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+
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+
258
+ </span>
259
+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'>
269
+ <p>----------------------------------------------------------------------------------------.</p>
270
+ </div></span>
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+
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+ </li>
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+
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+
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+ <li class="public ">
276
+ <span class="summary_signature">
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+
278
+ <a href="#tag_start-instance_method" title="#tag_start (instance method)">- (Object) <strong>tag_start</strong>(name, value) </a>
279
+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'>
293
+ <p>----------------------------------------------------------------------------------------.</p>
294
+ </div></span>
295
+
296
+ </li>
297
+
298
+
299
+ <li class="public ">
300
+ <span class="summary_signature">
301
+
302
+ <a href="#update-instance_method" title="#update (instance method)">- (Object) <strong>update</strong>(type, name, attrs) </a>
303
+
304
+
305
+
306
+ </span>
307
+
308
+
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+
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+
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+
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+
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+
314
+
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+
316
+ <span class="summary_desc"><div class='inline'>
317
+ <p>----------------------------------------------------------------------------------------.</p>
318
+ </div></span>
319
+
320
+ </li>
321
+
322
+
323
+ </ul>
324
+
325
+
326
+ <div id="constructor_details" class="method_details_list">
327
+ <h2>Constructor Details</h2>
328
+
329
+ <div class="method_details first">
330
+ <h3 class="signature first" id="initialize-instance_method">
331
+
332
+ - (<tt><span class='object_link'><a href="" title="PackageManager (class)">PackageManager</a></span></tt>) <strong>initialize</strong>
333
+
334
+
335
+
336
+
337
+
338
+ </h3><div class="docstring">
339
+ <div class="discussion">
340
+ <hr>
341
+ <hr>
342
+
343
+
344
+ </div>
345
+ </div>
346
+ <div class="tags">
347
+
348
+
349
+ </div><table class="source_code">
350
+ <tr>
351
+ <td>
352
+ <pre class="lines">
353
+
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+
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+ 135
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+ 136
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+ 137
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+ 138</pre>
359
+ </td>
360
+ <td>
361
+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 135</span>
362
+
363
+ <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span>
364
+ <span class='ivar'>@properties</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
365
+ <span class='kw'>super</span>
366
+ <span class='kw'>end</span></pre>
367
+ </td>
368
+ </tr>
369
+ </table>
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+ </div>
371
+
372
+ </div>
373
+
374
+
375
+ <div id="instance_method_details" class="method_details_list">
376
+ <h2>Instance Method Details</h2>
377
+
378
+
379
+ <div class="method_details first">
380
+ <h3 class="signature first" id="http_download_uri-instance_method">
381
+
382
+ - (<tt>Object</tt>) <strong>http_download_uri</strong>(uri, filename)
383
+
384
+
385
+
386
+
387
+
388
+ </h3><div class="docstring">
389
+ <div class="discussion">
390
+ <hr>
391
+ <hr>
392
+
393
+
394
+ </div>
395
+ </div>
396
+ <div class="tags">
397
+
398
+
399
+ </div><table class="source_code">
400
+ <tr>
401
+ <td>
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+ <pre class="lines">
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+
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+
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+ 214
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+ 215
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+ 216
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+ 217
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+ 218
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+ 219
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+ 220
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+ 221
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+ 222
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+ 223
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+ 224
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+ 225
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+ 226
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+ 227
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+ 228
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+ 229
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+ 230
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+ 231
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+ 232
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+ 233
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+ 234
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+ 235</pre>
427
+ </td>
428
+ <td>
429
+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 214</span>
430
+
431
+ <span class='kw'>def</span> <span class='id identifier rubyid_http_download_uri'>http_download_uri</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='comma'>,</span> <span class='id identifier rubyid_filename'>filename</span><span class='rparen'>)</span>
432
+ <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Starting HTTP download for: </span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='id identifier rubyid_uri'>uri</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span>
433
+ <span class='id identifier rubyid_http_object'>http_object</span> <span class='op'>=</span> <span class='const'>Net</span><span class='op'>::</span><span class='const'>HTTP</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='period'>.</span><span class='id identifier rubyid_host'>host</span><span class='comma'>,</span> <span class='id identifier rubyid_uri'>uri</span><span class='period'>.</span><span class='id identifier rubyid_port'>port</span><span class='rparen'>)</span>
434
+ <span class='id identifier rubyid_http_object'>http_object</span><span class='period'>.</span><span class='id identifier rubyid_use_ssl'>use_ssl</span> <span class='op'>=</span> <span class='kw'>true</span> <span class='kw'>if</span> <span class='id identifier rubyid_uri'>uri</span><span class='period'>.</span><span class='id identifier rubyid_scheme'>scheme</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>https</span><span class='tstring_end'>'</span></span>
435
+ <span class='kw'>begin</span>
436
+ <span class='id identifier rubyid_http_object'>http_object</span><span class='period'>.</span><span class='id identifier rubyid_start'>start</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_http'>http</span><span class='op'>|</span>
437
+ <span class='id identifier rubyid_request'>request</span> <span class='op'>=</span> <span class='const'>Net</span><span class='op'>::</span><span class='const'>HTTP</span><span class='op'>::</span><span class='const'>Get</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='id identifier rubyid_uri'>uri</span><span class='period'>.</span><span class='id identifier rubyid_request_uri'>request_uri</span>
438
+ <span class='id identifier rubyid_http'>http</span><span class='period'>.</span><span class='id identifier rubyid_read_timeout'>read_timeout</span> <span class='op'>=</span> <span class='int'>500</span>
439
+ <span class='id identifier rubyid_http'>http</span><span class='period'>.</span><span class='id identifier rubyid_request'>request</span> <span class='id identifier rubyid_request'>request</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_response'>response</span><span class='op'>|</span>
440
+ <span class='id identifier rubyid_open'>open</span> <span class='id identifier rubyid_filename'>filename</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>wb</span><span class='tstring_end'>'</span></span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_io'>io</span><span class='op'>|</span>
441
+ <span class='id identifier rubyid_response'>response</span><span class='period'>.</span><span class='id identifier rubyid_read_body'>read_body</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_chunk'>chunk</span><span class='op'>|</span>
442
+ <span class='id identifier rubyid_io'>io</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span> <span class='id identifier rubyid_chunk'>chunk</span>
443
+ <span class='kw'>end</span>
444
+ <span class='kw'>end</span>
445
+ <span class='kw'>end</span>
446
+ <span class='kw'>end</span>
447
+ <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_e'>e</span>
448
+ <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>=&gt; Exception: '</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_e'>e</span><span class='rbrace'>}</span><span class='tstring_content'>'. Skipping download.</span><span class='tstring_end'>&quot;</span></span>
449
+ <span class='kw'>return</span>
450
+ <span class='kw'>end</span>
451
+ <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Stored download as </span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='id identifier rubyid_filename'>filename</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>.</span><span class='tstring_end'>&quot;</span></span>
452
+ <span class='kw'>end</span></pre>
453
+ </td>
454
+ </tr>
455
+ </table>
456
+ </div>
457
+
458
+ <div class="method_details ">
459
+ <h3 class="signature " id="load_package-instance_method">
460
+
461
+ - (<tt>Object</tt>) <strong>load_package</strong>(name)
462
+
463
+
464
+
465
+
466
+
467
+ </h3><div class="docstring">
468
+ <div class="discussion">
469
+ <hr>
470
+
471
+ <p>Installs a new package</p>
472
+ <hr>
473
+
474
+
475
+ </div>
476
+ </div>
477
+ <div class="tags">
478
+
479
+
480
+ </div><table class="source_code">
481
+ <tr>
482
+ <td>
483
+ <pre class="lines">
484
+
485
+
486
+ 241
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+ 242
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+ 243
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+ 244
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+ 245
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+ 248
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+ 249
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+ 251
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+ 252
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+ 282
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+ 283
529
+ 284</pre>
530
+ </td>
531
+ <td>
532
+ <pre class="code"><span class="info file"># File 'lib/JRubyR/package.rb', line 241</span>
533
+
534
+ <span class='kw'>def</span> <span class='id identifier rubyid_load_package'>load_package</span><span class='lparen'>(</span><span class='id identifier rubyid_name'>name</span><span class='rparen'>)</span>
535
+
536
+ <span class='comment'># create the cran_dir if it does not already exists
537
+ </span> <span class='const'>Dir</span><span class='period'>.</span><span class='id identifier rubyid_mkdir'>mkdir</span><span class='lparen'>(</span><span class='const'>SciCom</span><span class='period'>.</span><span class='id identifier rubyid_cran_dir'>cran_dir</span><span class='rparen'>)</span> <span class='kw'>if</span> <span class='op'>!</span><span class='const'>Dir</span><span class='period'>.</span><span class='id identifier rubyid_exists?'>exists?</span><span class='lparen'>(</span><span class='const'>SciCom</span><span class='period'>.</span><span class='id identifier rubyid_cran_dir'>cran_dir</span><span class='rparen'>)</span>
538
+
539
+ <span class='comment'># download address for Renjin packages
540
+ </span> <span class='id identifier rubyid_renjin_cran'>renjin_cran</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>http://nexus.bedatadriven.com/content/groups/public/org/renjin/cran/</span><span class='tstring_end'>'</span></span>
541
+
542
+ <span class='id identifier rubyid_package'>package</span> <span class='op'>=</span> <span class='id identifier rubyid_renjin_cran'>renjin_cran</span> <span class='op'>+</span> <span class='id identifier rubyid_name'>name</span>
543
+ <span class='id identifier rubyid_spec'>spec</span> <span class='op'>=</span> <span class='id identifier rubyid_package'>package</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>/</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>maven-metadata.xml</span><span class='tstring_end'>&quot;</span></span>
544
+ <span class='comment'># read the maven-metadata specification
545
+ </span> <span class='id identifier rubyid_uri'>uri</span> <span class='op'>=</span> <span class='const'>URI</span><span class='lparen'>(</span><span class='id identifier rubyid_spec'>spec</span><span class='rparen'>)</span>
546
+
547
+ <span class='comment'># parse the maven-metadata file
548
+ </span> <span class='id identifier rubyid_parse'>parse</span> <span class='op'>=</span> <span class='const'>ParseXML</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='const'>Net</span><span class='op'>::</span><span class='const'>HTTP</span><span class='period'>.</span><span class='id identifier rubyid_get'>get</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='rparen'>)</span><span class='rparen'>)</span>
549
+ <span class='id identifier rubyid_parse'>parse</span><span class='period'>.</span><span class='id identifier rubyid_add_observer'>add_observer</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span>
550
+ <span class='id identifier rubyid_parse'>parse</span><span class='period'>.</span><span class='id identifier rubyid_start'>start</span>
551
+
552
+ <span class='id identifier rubyid_download_dir'>download_dir</span> <span class='op'>=</span> <span class='id identifier rubyid_package'>package</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>/</span><span class='tstring_end'>'</span></span> <span class='op'>+</span> <span class='ivar'>@properties</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>latest</span><span class='tstring_end'>'</span></span><span class='rbracket'>]</span>
553
+ <span class='id identifier rubyid_spec2'>spec2</span> <span class='op'>=</span> <span class='id identifier rubyid_download_dir'>download_dir</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>/</span><span class='tstring_end'>'</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>maven-metadata.xml</span><span class='tstring_end'>&quot;</span></span>
554
+
555
+ <span class='comment'># parse the second maven-metadata file
556
+ </span> <span class='id identifier rubyid_uri'>uri</span> <span class='op'>=</span> <span class='const'>URI</span><span class='lparen'>(</span><span class='id identifier rubyid_spec2'>spec2</span><span class='rparen'>)</span>
557
+ <span class='comment'># download the spec file, so we know what version is actually installed
558
+ </span> <span class='id identifier rubyid_http_download_uri'>http_download_uri</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='comma'>,</span> <span class='const'>SciCom</span><span class='period'>.</span><span class='id identifier rubyid_cran_dir'>cran_dir</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>/</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_name'>name</span><span class='rbrace'>}</span><span class='tstring_content'>.xml</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
559
+
560
+ <span class='comment'># need to clear the properties. If the file has multiple properties with the same
561
+ </span> <span class='comment'># name, then only the last one will be kept. This might be a problem, but for
562
+ </span> <span class='comment'># now this does not seem to matter... We are only interested in the 'value'
563
+ </span> <span class='comment'># property that seems to always be the same for the 'pom' and 'jar' files.
564
+ </span> <span class='ivar'>@properties</span><span class='period'>.</span><span class='id identifier rubyid_clear'>clear</span>
565
+ <span class='id identifier rubyid_parse'>parse</span> <span class='op'>=</span> <span class='const'>ParseXML</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='const'>Net</span><span class='op'>::</span><span class='const'>HTTP</span><span class='period'>.</span><span class='id identifier rubyid_get'>get</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='rparen'>)</span><span class='rparen'>)</span>
566
+ <span class='id identifier rubyid_parse'>parse</span><span class='period'>.</span><span class='id identifier rubyid_add_observer'>add_observer</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span>
567
+ <span class='id identifier rubyid_parse'>parse</span><span class='period'>.</span><span class='id identifier rubyid_start'>start</span>
568
+
569
+ <span class='id identifier rubyid_filename'>filename</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>/</span><span class='tstring_end'>'</span></span> <span class='op'>+</span> <span class='id identifier rubyid_name'>name</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span> <span class='op'>+</span> <span class='ivar'>@properties</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>value</span><span class='tstring_end'>'</span></span><span class='rbracket'>]</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>.jar</span><span class='tstring_end'>&quot;</span></span>
570
+
571
+ <span class='id identifier rubyid_download_file'>download_file</span> <span class='op'>=</span> <span class='id identifier rubyid_download_dir'>download_dir</span> <span class='op'>+</span> <span class='id identifier rubyid_filename'>filename</span>
572
+ <span class='id identifier rubyid_target_file'>target_file</span> <span class='op'>=</span> <span class='const'>SciCom</span><span class='period'>.</span><span class='id identifier rubyid_cran_dir'>cran_dir</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>/</span><span class='tstring_end'>'</span></span> <span class='op'>+</span> <span class='id identifier rubyid_name'>name</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>.jar</span><span class='tstring_end'>&quot;</span></span>
573
+
574
+ <span class='id identifier rubyid_uri'>uri</span> <span class='op'>=</span> <span class='const'>URI</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_download_file'>download_file</span><span class='rparen'>)</span>
575
+ <span class='id identifier rubyid_http_download_uri'>http_download_uri</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='comma'>,</span> <span class='id identifier rubyid_target_file'>target_file</span><span class='rparen'>)</span>
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+
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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>
582
+
583
+ <div class="method_details ">
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+ <h3 class="signature " id="new_text-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>new_text</strong>(text)
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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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+ <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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+ 187
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+ 188
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+ 189</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 187</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_new_text'>new_text</span><span class='lparen'>(</span><span class='id identifier rubyid_text'>text</span><span class='rparen'>)</span>
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+ <span class='ivar'>@text</span> <span class='op'>=</span> <span class='id identifier rubyid_text'>text</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="set_value-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>set_value</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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+ <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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+ 162
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+ 163
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+ 164</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 162</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_set_value'>set_value</span>
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+ <span class='ivar'>@properties</span><span class='lbracket'>[</span><span class='ivar'>@name</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='ivar'>@text</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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+ <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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+ 179
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+ 180
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+ 181</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 179</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_value_read'>value_read</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, value)
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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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+ <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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+ 170
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+ 171
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+ 172
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+ 173</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 170</span>
739
+
740
+ <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_value'>value</span><span class='rparen'>)</span>
741
+ <span class='ivar'>@name</span> <span class='op'>=</span> <span class='id identifier rubyid_name'>name</span>
742
+ <span class='id identifier rubyid_read_value'>read_value</span>
743
+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
746
+ </table>
747
+ </div>
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+
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+ <div class="method_details ">
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+ <h3 class="signature " id="update-instance_method">
751
+
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+ - (<tt>Object</tt>) <strong>update</strong>(type, name, attrs)
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+
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+
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+
756
+
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+
758
+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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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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+ 195
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+ 196
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+ 197
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+ 198
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+ 199
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+ 200
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+ 201
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+ 202
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+ 203
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+ 204
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+ 205
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+ 206
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+ 207
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+ 208</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 195</span>
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+
793
+ <span class='kw'>def</span> <span class='id identifier rubyid_update'>update</span><span class='lparen'>(</span><span class='id identifier rubyid_type'>type</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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+
795
+ <span class='kw'>case</span> <span class='id identifier rubyid_type'>type</span>
796
+ <span class='kw'>when</span> <span class='symbol'>:tag_start</span>
797
+ <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>
798
+ <span class='kw'>when</span> <span class='symbol'>:tag_end</span>
799
+ <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>
800
+ <span class='kw'>when</span> <span class='symbol'>:new_text</span>
801
+ <span class='id identifier rubyid_new_text'>new_text</span><span class='lparen'>(</span><span class='id identifier rubyid_name'>name</span><span class='rparen'>)</span>
802
+ <span class='kw'>else</span>
803
+ <span class='id identifier rubyid_raise'>raise</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Unknown type </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_type'>type</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
804
+ <span class='kw'>end</span>
805
+
806
+ <span class='kw'>end</span></pre>
807
+ </td>
808
+ </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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+ </div>
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+
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+ <div id="footer">
817
+ Generated on Tue Jul 14 18:12:23 2015 by
818
+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 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>