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/MDArray.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: MDArray
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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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+ hasFrames = window.top.frames.main ? true : false;
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+ framesUrl = "frames.html#!MDArray.html";
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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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+ <span class="title">MDArray</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: MDArray
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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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+ <ul class="fullTree">
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+ <li>Object</li>
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+ <li class="next">MDArray</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">Includes:</dt>
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+ <dd class="r2"><span class='object_link'><a href="Renjin/RBSexp.html" title="Renjin::RBSexp (module)">Renjin::RBSexp</a></span></dd>
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+ <dt class="r1 last">Defined in:</dt>
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+ <dd class="r1 last">lib/JRubyR/ruby_classes.rb</dd>
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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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+ <h2>Instance Attribute Summary</h2>
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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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+ <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 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/MergeObservable.html ADDED
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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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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+ Module: MergeObservable
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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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+ framesUrl = "frames.html#!MergeObservable.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 (M)</a> &raquo;
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+ <span class="title">MergeObservable</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>Module: MergeObservable
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+ </h1>
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+ <dl class="box">
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+ <dt class="r1">Includes:</dt>
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+ <dd class="r1">Observable</dd>
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+ <dt class="r2">Included in:</dt>
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+ <dd class="r2"><span class='object_link'><a href="PackageManager/ParseXML.html" title="PackageManager::ParseXML (class)">PackageManager::ParseXML</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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+ 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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+ <ul class="summary">
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+ <a href="#merge_observers-instance_method" title="#merge_observers (instance method)">- (Object) <strong>merge_observers</strong> </a>
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+ <a href="#old_notify-instance_method" title="#old_notify (instance method)">- (Object) <strong>old_notify</strong> </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'></div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+
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+
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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="add_new_observer-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>add_new_observer</strong>(observer)
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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><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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+ 38
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+ 39
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+ 40
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+ 41</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 38</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_add_new_observer'>add_new_observer</span><span class='lparen'>(</span><span class='id identifier rubyid_observer'>observer</span><span class='rparen'>)</span>
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+ <span class='ivar'>@new_observers</span> <span class='op'>||=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
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+ <span class='ivar'>@new_observers</span> <span class='op'>&lt;&lt;</span> <span class='id identifier rubyid_observer'>observer</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="merge_observers-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>merge_observers</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><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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+ 43
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+ 44
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+ 45
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+ 46
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+ 47
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+ 48
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+ 49</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 43</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_merge_observers'>merge_observers</span>
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+ <span class='ivar'>@new_observers</span> <span class='op'>||=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
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+ <span class='ivar'>@new_observers</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_obs'>obs</span><span class='op'>|</span>
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+ <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_add_observer'>add_observer</span><span class='lparen'>(</span><span class='id identifier rubyid_obs'>obs</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span>
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+ <span class='ivar'>@new_observers</span> <span class='op'>=</span> <span class='kw'>nil</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="notify_observers-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>notify_observers</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><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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+ 51
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+ 52
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+ 53
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+ 54</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 51</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_notify_observers'>notify_observers</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='id identifier rubyid_merge_observers'>merge_observers</span>
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+ <span class='id identifier rubyid_old_notify'>old_notify</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='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="old_notify-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>old_notify</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><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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+ 36</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 36</span>
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+
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+ <span class='id identifier rubyid_alias_method'>alias_method</span> <span class='symbol'>:old_notify</span><span class='comma'>,</span> <span class='symbol'>:notify_observers</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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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Jul 14 18:12:22 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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+
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+ </body>
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+ </html>