bio-svgenes 0.3.1 → 0.3.2

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Files changed (144) hide show
  1. data/README.md +88 -0
  2. data/VERSION +1 -1
  3. data/bio-svgenes.gemspec +131 -8
  4. data/doc/classes/Bio.html +131 -0
  5. data/doc/classes/Bio/Graphics.html +142 -0
  6. data/doc/classes/Bio/Graphics/Glyph.html +987 -0
  7. data/doc/classes/Bio/Graphics/Glyph.src/M000001.html +26 -0
  8. data/doc/classes/Bio/Graphics/Glyph.src/M000002.html +27 -0
  9. data/doc/classes/Bio/Graphics/Glyph.src/M000003.html +32 -0
  10. data/doc/classes/Bio/Graphics/Glyph.src/M000004.html +27 -0
  11. data/doc/classes/Bio/Graphics/Glyph.src/M000005.html +25 -0
  12. data/doc/classes/Bio/Graphics/Glyph.src/M000006.html +29 -0
  13. data/doc/classes/Bio/Graphics/Glyph.src/M000007.html +107 -0
  14. data/doc/classes/Bio/Graphics/Glyph.src/M000008.html +51 -0
  15. data/doc/classes/Bio/Graphics/Glyph.src/M000009.html +23 -0
  16. data/doc/classes/Bio/Graphics/Glyph.src/M000010.html +18 -0
  17. data/doc/classes/Bio/Graphics/Glyph.src/M000011.html +75 -0
  18. data/doc/classes/Bio/Graphics/Glyph.src/M000012.html +51 -0
  19. data/doc/classes/Bio/Graphics/Glyph.src/M000013.html +23 -0
  20. data/doc/classes/Bio/Graphics/Glyph.src/M000014.html +26 -0
  21. data/doc/classes/Bio/Graphics/Glyph.src/M000015.html +27 -0
  22. data/doc/classes/Bio/Graphics/Glyph.src/M000016.html +32 -0
  23. data/doc/classes/Bio/Graphics/Glyph.src/M000017.html +27 -0
  24. data/doc/classes/Bio/Graphics/Glyph.src/M000018.html +25 -0
  25. data/doc/classes/Bio/Graphics/Glyph.src/M000019.html +29 -0
  26. data/doc/classes/Bio/Graphics/Glyph.src/M000020.html +107 -0
  27. data/doc/classes/Bio/Graphics/Glyph.src/M000021.html +51 -0
  28. data/doc/classes/Bio/Graphics/Glyph.src/M000022.html +23 -0
  29. data/doc/classes/Bio/Graphics/Glyph.src/M000023.html +18 -0
  30. data/doc/classes/Bio/Graphics/Glyph.src/M000024.html +75 -0
  31. data/doc/classes/Bio/Graphics/MiniFeature.html +243 -0
  32. data/doc/classes/Bio/Graphics/MiniFeature.src/M000001.html +25 -0
  33. data/doc/classes/Bio/Graphics/MiniFeature.src/M000003.html +25 -0
  34. data/doc/classes/Bio/Graphics/MiniFeature.src/M000024.html +25 -0
  35. data/doc/classes/Bio/Graphics/Page.html +705 -0
  36. data/doc/classes/Bio/Graphics/Page.src/M000010.html +35 -0
  37. data/doc/classes/Bio/Graphics/Page.src/M000011.html +83 -0
  38. data/doc/classes/Bio/Graphics/Page.src/M000012.html +24 -0
  39. data/doc/classes/Bio/Graphics/Page.src/M000013.html +29 -0
  40. data/doc/classes/Bio/Graphics/Page.src/M000014.html +24 -0
  41. data/doc/classes/Bio/Graphics/Page.src/M000015.html +20 -0
  42. data/doc/classes/Bio/Graphics/Page.src/M000016.html +20 -0
  43. data/doc/classes/Bio/Graphics/Page.src/M000017.html +18 -0
  44. data/doc/classes/Bio/Graphics/Page.src/M000018.html +18 -0
  45. data/doc/classes/Bio/Graphics/Page.src/M000019.html +18 -0
  46. data/doc/classes/Bio/Graphics/Page.src/M000020.html +18 -0
  47. data/doc/classes/Bio/Graphics/Page.src/M000021.html +18 -0
  48. data/doc/classes/Bio/Graphics/Page.src/M000022.html +18 -0
  49. data/doc/classes/Bio/Graphics/Page.src/M000023.html +18 -0
  50. data/doc/classes/Bio/Graphics/Page.src/M000024.html +18 -0
  51. data/doc/classes/Bio/Graphics/Page.src/M000025.html +35 -0
  52. data/doc/classes/Bio/Graphics/Page.src/M000026.html +83 -0
  53. data/doc/classes/Bio/Graphics/Page.src/M000027.html +24 -0
  54. data/doc/classes/Bio/Graphics/Page.src/M000028.html +29 -0
  55. data/doc/classes/Bio/Graphics/Page.src/M000029.html +24 -0
  56. data/doc/classes/Bio/Graphics/Page.src/M000030.html +20 -0
  57. data/doc/classes/Bio/Graphics/Page.src/M000031.html +20 -0
  58. data/doc/classes/Bio/Graphics/Page.src/M000032.html +18 -0
  59. data/doc/classes/Bio/Graphics/Page.src/M000033.html +18 -0
  60. data/doc/classes/Bio/Graphics/Page.src/M000034.html +18 -0
  61. data/doc/classes/Bio/Graphics/Page.src/M000035.html +18 -0
  62. data/doc/classes/Bio/Graphics/Page.src/M000036.html +18 -0
  63. data/doc/classes/Bio/Graphics/Page.src/M000037.html +18 -0
  64. data/doc/classes/Bio/Graphics/Page.src/M000038.html +18 -0
  65. data/doc/classes/Bio/Graphics/Page.src/M000039.html +18 -0
  66. data/doc/classes/Bio/Graphics/Page.src/M000040.html +107 -0
  67. data/doc/classes/Bio/Graphics/Page.src/M000041.html +18 -0
  68. data/doc/classes/Bio/Graphics/Page.src/M000042.html +23 -0
  69. data/doc/classes/Bio/Graphics/Page.src/M000043.html +18 -0
  70. data/doc/classes/Bio/Graphics/Page.src/M000044.html +18 -0
  71. data/doc/classes/Bio/Graphics/Primitive.html +204 -0
  72. data/doc/classes/Bio/Graphics/Primitive.src/M000001.html +21 -0
  73. data/doc/classes/Bio/Graphics/Primitive.src/M000002.html +20 -0
  74. data/doc/classes/Bio/Graphics/Primitive.src/M000008.html +21 -0
  75. data/doc/classes/Bio/Graphics/Primitive.src/M000009.html +20 -0
  76. data/doc/classes/Bio/Graphics/Primitive.src/M000022.html +21 -0
  77. data/doc/classes/Bio/Graphics/Primitive.src/M000023.html +20 -0
  78. data/doc/classes/Bio/Graphics/SVGEE.html +290 -0
  79. data/doc/classes/Bio/Graphics/SVGEE.src/M000002.html +24 -0
  80. data/doc/classes/Bio/Graphics/SVGEE.src/M000003.html +18 -0
  81. data/doc/classes/Bio/Graphics/SVGEE.src/M000004.html +24 -0
  82. data/doc/classes/Bio/Graphics/SVGEE.src/M000005.html +18 -0
  83. data/doc/classes/Bio/Graphics/SVGEE.src/M000006.html +18 -0
  84. data/doc/classes/Bio/Graphics/SVGEE.src/M000007.html +21 -0
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  87. data/doc/classes/Bio/Graphics/SVGEE.src/M000016.html +24 -0
  88. data/doc/classes/Bio/Graphics/SVGEE.src/M000017.html +18 -0
  89. data/doc/classes/Bio/Graphics/SVGEE.src/M000018.html +18 -0
  90. data/doc/classes/Bio/Graphics/SVGEE.src/M000019.html +21 -0
  91. data/doc/classes/Bio/Graphics/SVGEE.src/M000020.html +27 -0
  92. data/doc/classes/Bio/Graphics/SVGEE.src/M000021.html +23 -0
  93. data/doc/classes/Bio/Graphics/Track.html +473 -0
  94. data/doc/classes/Bio/Graphics/Track.src/M000001.html +35 -0
  95. data/doc/classes/Bio/Graphics/Track.src/M000002.html +18 -0
  96. data/doc/classes/Bio/Graphics/Track.src/M000003.html +28 -0
  97. data/doc/classes/Bio/Graphics/Track.src/M000004.html +18 -0
  98. data/doc/classes/Bio/Graphics/Track.src/M000010.html +35 -0
  99. data/doc/classes/Bio/Graphics/Track.src/M000011.html +18 -0
  100. data/doc/classes/Bio/Graphics/Track.src/M000012.html +28 -0
  101. data/doc/classes/Bio/Graphics/Track.src/M000013.html +18 -0
  102. data/doc/created.rid +1 -9
  103. data/doc/files/lib/bio-svgenes_rb.html +131 -0
  104. data/doc/files/lib/bio/graphics/glyph_rb.html +101 -0
  105. data/doc/files/lib/bio/graphics/mini_feature_rb.html +101 -0
  106. data/doc/files/lib/bio/graphics/page_rb.html +111 -0
  107. data/doc/files/lib/bio/graphics/primitive_rb.html +101 -0
  108. data/doc/files/lib/bio/graphics/svgee_rb.html +101 -0
  109. data/doc/files/lib/bio/graphics/track_rb.html +101 -0
  110. data/doc/fr_class_index.html +34 -0
  111. data/doc/fr_file_index.html +33 -0
  112. data/doc/fr_method_index.html +70 -0
  113. data/doc/index.html +21 -91
  114. data/doc/manual/bootstrap/css/bootstrap-responsive.css +1109 -0
  115. data/doc/manual/bootstrap/css/bootstrap-responsive.min.css +9 -0
  116. data/doc/manual/bootstrap/css/bootstrap.css +6158 -0
  117. data/doc/manual/bootstrap/css/bootstrap.min.css +9 -0
  118. data/doc/manual/bootstrap/img/glyphicons-halflings-white.png +0 -0
  119. data/doc/manual/bootstrap/img/glyphicons-halflings.png +0 -0
  120. data/doc/manual/bootstrap/js/bootstrap.js +2276 -0
  121. data/doc/manual/bootstrap/js/bootstrap.min.js +6 -0
  122. data/doc/manual/img/circle.png +0 -0
  123. data/doc/manual/img/directed.png +0 -0
  124. data/doc/manual/img/down_triangle.png +0 -0
  125. data/doc/manual/img/histogram.png +0 -0
  126. data/doc/manual/img/span.png +0 -0
  127. data/doc/manual/img/transcript.png +0 -0
  128. data/doc/manual/img/up_triangle.png +0 -0
  129. data/doc/manual/manual.html +360 -0
  130. data/doc/manual/manual.md +307 -0
  131. data/doc/rdoc-style.css +208 -0
  132. data/examples/example.rb +12 -8
  133. data/examples/{make_example.rb → example2.rb} +5 -16
  134. data/lib/bio/graphics/glyph.rb +293 -126
  135. data/lib/bio/graphics/mini_feature.rb +24 -17
  136. data/lib/bio/graphics/page.rb +112 -54
  137. data/lib/bio/graphics/primitive.rb +12 -9
  138. data/lib/bio/graphics/svgee.rb +9 -11
  139. data/lib/bio/graphics/track.rb +92 -10
  140. metadata +132 -9
  141. data/README.rdoc +0 -19
  142. data/examples/annotate_snps.rb +0 -86
  143. data/examples/eg2.rb +0 -40
  144. data/examples/get_coverage_in_windows.rb +0 -176
data/doc/classes/Bio/Graphics/Page.src/M000044.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>write (Bio::Graphics::Page)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 396</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">write</span>(<span class="ruby-identifier">file</span>)
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+ <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">file</span>, <span class="ruby-value str">'w'</span>).<span class="ruby-identifier">write</span>(<span class="ruby-identifier">get_markup</span>)
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Graphics/Primitive.html ADDED
@@ -0,0 +1,204 @@
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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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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+ <title>Class: Bio::Graphics::Primitive</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">Bio::Graphics::Primitive</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../../files/lib/bio/graphics/primitive_rb.html">
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+ lib/bio/graphics/primitive.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ <td>
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+ Object
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <p>
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+ The <a href="Primitive.html">Bio::Graphics::Primitive</a> class is used to
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+ describe simple shapes. It is basically a simple data container that has
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+ lots of dynamically set instance variables including a name. The <a
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+ href="Primitive.html">Bio::Graphics::Primitive</a> object is later
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+ translated to an SVG string by the <a
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+ href="SVGEE.html">Bio::Graphics::SVGEE</a> class.
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+ </p>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000001">new</a>&nbsp;&nbsp;
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+ <a href="#M000002">update</a>&nbsp;&nbsp;
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+ </div>
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+ </div>
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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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="attribute-list">
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
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+ <table>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">primitive</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ </table>
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+ </div>
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+ </div>
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+
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+ <div id="method-M000001" class="method-detail">
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+ <a name="M000001"></a>
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+
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+ <div class="method-heading">
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+ <a href="Primitive.src/M000001.html" target="Code" class="method-signature"
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+ onclick="popupCode('Primitive.src/M000001.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">(primitive,args)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ Creates a <a href="Primitive.html#M000001">new</a> <a
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+ href="Primitive.html">Primitive</a> and initialises instance variables
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+ dynamically from the args hash
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+ </p>
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+ <h2>args+</h2>
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+ <ul>
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+ <li>:primitive = the <a href="Primitive.html">Primitive</a> type
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+
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+ </li>
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+ <li>args = a hash of parameters needed to describe the attributes of the
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+ primitive type
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+
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+ </li>
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+ </ul>
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+ </div>
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+ </div>
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+
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+ <h3 class="section-bar">Public Instance methods</h3>
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+
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+ <div id="method-M000002" class="method-detail">
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+ <a name="M000002"></a>
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+
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+ <div class="method-heading">
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+ <a href="Primitive.src/M000002.html" target="Code" class="method-signature"
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+ onclick="popupCode('Primitive.src/M000002.html');return false;">
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+ <span class="method-name">update</span><span class="method-args">(args)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ Updates a <a href="Primitive.html">Primitive</a> and sets the provided
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+ values as instance variables
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+ </p>
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+ <h2>args</h2>
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+ <ul>
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+ <li>args = a hash of <a href="Primitive.html#M000001">new</a> parameters for
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+ the given primitive type
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+
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+ </li>
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+ </ul>
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+ </div>
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/Bio/Graphics/Primitive.src/M000001.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>new (Bio::Graphics::Primitive)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/primitive.rb, line 15</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">primitive</span>,<span class="ruby-identifier">args</span>)
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+ <span class="ruby-ivar">@primitive</span> = <span class="ruby-identifier">primitive</span>
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+ <span class="ruby-identifier">args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">instance_variable_set</span>(<span class="ruby-node">&quot;@#{k}&quot;</span>, <span class="ruby-identifier">args</span>[<span class="ruby-identifier">k</span>])
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Graphics/Primitive.src/M000002.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>update (Bio::Graphics::Primitive)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/primitive.rb, line 26</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">update</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-identifier">args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">instance_variable_set</span>(<span class="ruby-node">&quot;@#{k}&quot;</span>, <span class="ruby-identifier">args</span>[<span class="ruby-identifier">k</span>])
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Graphics/Primitive.src/M000008.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>new (Bio::Graphics::Primitive)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/primitive.rb, line 15</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">primitive</span>,<span class="ruby-identifier">args</span>)
15
+ <span class="ruby-ivar">@primitive</span> = <span class="ruby-identifier">primitive</span>
16
+ <span class="ruby-identifier">args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
17
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">instance_variable_set</span>(<span class="ruby-node">&quot;@#{k}&quot;</span>, <span class="ruby-identifier">args</span>[<span class="ruby-identifier">k</span>])
18
+ <span class="ruby-keyword kw">end</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Graphics/Primitive.src/M000009.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>update (Bio::Graphics::Primitive)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/primitive.rb, line 26</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">update</span>(<span class="ruby-identifier">args</span>)
15
+ <span class="ruby-identifier">args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">instance_variable_set</span>(<span class="ruby-node">&quot;@#{k}&quot;</span>, <span class="ruby-identifier">args</span>[<span class="ruby-identifier">k</span>])
17
+ <span class="ruby-keyword kw">end</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
data/doc/classes/Bio/Graphics/Primitive.src/M000022.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>new (Bio::Graphics::Primitive)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/primitive.rb, line 15</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">primitive</span>,<span class="ruby-identifier">args</span>)
15
+ <span class="ruby-ivar">@primitive</span> = <span class="ruby-identifier">primitive</span>
16
+ <span class="ruby-identifier">args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
17
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">instance_variable_set</span>(<span class="ruby-node">&quot;@#{k}&quot;</span>, <span class="ruby-identifier">args</span>[<span class="ruby-identifier">k</span>])
18
+ <span class="ruby-keyword kw">end</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Graphics/Primitive.src/M000023.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>update (Bio::Graphics::Primitive)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/primitive.rb, line 26</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">update</span>(<span class="ruby-identifier">args</span>)
15
+ <span class="ruby-identifier">args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">instance_variable_set</span>(<span class="ruby-node">&quot;@#{k}&quot;</span>, <span class="ruby-identifier">args</span>[<span class="ruby-identifier">k</span>])
17
+ <span class="ruby-keyword kw">end</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
data/doc/classes/Bio/Graphics/SVGEE.html ADDED
@@ -0,0 +1,290 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
+ <head>
8
+ <title>Class: Bio::Graphics::SVGEE</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
15
+ function popupCode( url ) {
16
+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
17
+ }
18
+
19
+ function toggleCode( id ) {
20
+ if ( document.getElementById )
21
+ elem = document.getElementById( id );
22
+ else if ( document.all )
23
+ elem = eval( "document.all." + id );
24
+ else
25
+ return false;
26
+
27
+ elemStyle = elem.style;
28
+
29
+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
31
+ } else {
32
+ elemStyle.display = "none"
33
+ }
34
+
35
+ return true;
36
+ }
37
+
38
+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
40
+
41
+ // ]]>
42
+ </script>
43
+
44
+ </head>
45
+ <body>
46
+
47
+
48
+
49
+ <div id="classHeader">
50
+ <table class="header-table">
51
+ <tr class="top-aligned-row">
52
+ <td><strong>Class</strong></td>
53
+ <td class="class-name-in-header">Bio::Graphics::SVGEE</td>
54
+ </tr>
55
+ <tr class="top-aligned-row">
56
+ <td><strong>In:</strong></td>
57
+ <td>
58
+ <a href="../../../files/lib/bio/graphics/svgee_rb.html">
59
+ lib/bio/graphics/svgee.rb
60
+ </a>
61
+ <br />
62
+ </td>
63
+ </tr>
64
+
65
+ <tr class="top-aligned-row">
66
+ <td><strong>Parent:</strong></td>
67
+ <td>
68
+ Object
69
+ </td>
70
+ </tr>
71
+ </table>
72
+ </div>
73
+ <!-- banner header -->
74
+
75
+ <div id="bodyContent">
76
+
77
+
78
+
79
+ <div id="contextContent">
80
+
81
+ <div id="description">
82
+ <p>
83
+ The <a href="SVGEE.html">Bio::Graphics::SVGEE</a> class takes argument
84
+ information in a hash and creates SVG Markup tags, which it will <a
85
+ href="SVGEE.html#M000009">draw</a>
86
+ </p>
87
+
88
+ </div>
89
+
90
+
91
+ </div>
92
+
93
+ <div id="method-list">
94
+ <h3 class="section-bar">Methods</h3>
95
+
96
+ <div class="name-list">
97
+ <a href="#M000007">add_primitive</a>&nbsp;&nbsp;
98
+ <a href="#M000006">close_tag</a>&nbsp;&nbsp;
99
+ <a href="#M000009">draw</a>&nbsp;&nbsp;
100
+ <a href="#M000008">gradient</a>&nbsp;&nbsp;
101
+ <a href="#M000004">new</a>&nbsp;&nbsp;
102
+ <a href="#M000005">open_tag</a>&nbsp;&nbsp;
103
+ </div>
104
+ </div>
105
+
106
+ </div>
107
+
108
+
109
+ <!-- if includes -->
110
+
111
+ <div id="section">
112
+
113
+
114
+
115
+
116
+
117
+ <div id="attribute-list">
118
+ <h3 class="section-bar">Attributes</h3>
119
+
120
+ <div class="name-list">
121
+ <table>
122
+ <tr class="top-aligned-row context-row">
123
+ <td class="context-item-name">defs</td>
124
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
125
+ <td class="context-item-desc"></td>
126
+ </tr>
127
+ <tr class="top-aligned-row context-row">
128
+ <td class="context-item-name">primitives</td>
129
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
130
+ <td class="context-item-desc"></td>
131
+ </tr>
132
+ <tr class="top-aligned-row context-row">
133
+ <td class="context-item-name">supported_primitives</td>
134
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
135
+ <td class="context-item-desc"></td>
136
+ </tr>
137
+ </table>
138
+ </div>
139
+ </div>
140
+
141
+
142
+
143
+ <!-- if method_list -->
144
+ <div id="methods">
145
+ <h3 class="section-bar">Public Class methods</h3>
146
+
147
+ <div id="method-M000004" class="method-detail">
148
+ <a name="M000004"></a>
149
+
150
+ <div class="method-heading">
151
+ <a href="SVGEE.src/M000004.html" target="Code" class="method-signature"
152
+ onclick="popupCode('SVGEE.src/M000004.html');return false;">
153
+ <span class="method-name">new</span><span class="method-args">(args)</span>
154
+ </a>
155
+ </div>
156
+
157
+ <div class="method-description">
158
+ <p>
159
+ Creates a <a href="SVGEE.html#M000004">new</a> <a
160
+ href="SVGEE.html">Bio::Graphics::SVGEE</a> object which will contain all
161
+ the necessary objects to display all the features on a page
162
+ </p>
163
+ <h2>args</h2>
164
+ <ul>
165
+ <li>:width = the width of the SVG page (100%)
166
+
167
+ </li>
168
+ <li>:height = the amount of the page height the svg should take up (100%)
169
+
170
+ </li>
171
+ <li>:style = the svg style information
172
+
173
+ </li>
174
+ </ul>
175
+ </div>
176
+ </div>
177
+
178
+ <h3 class="section-bar">Public Instance methods</h3>
179
+
180
+ <div id="method-M000007" class="method-detail">
181
+ <a name="M000007"></a>
182
+
183
+ <div class="method-heading">
184
+ <a href="SVGEE.src/M000007.html" target="Code" class="method-signature"
185
+ onclick="popupCode('SVGEE.src/M000007.html');return false;">
186
+ <span class="method-name">add_primitive</span><span class="method-args">(primitive_object)</span>
187
+ </a>
188
+ </div>
189
+
190
+ <div class="method-description">
191
+ <p>
192
+ Adds a <a href="Primitive.html">Primitive</a> object to the <a
193
+ href="SVGEE.html">SVGEE</a> object and makes the svg text for that <a
194
+ href="Primitive.html">Primitive</a>
195
+ </p>
196
+ </div>
197
+ </div>
198
+
199
+ <div id="method-M000006" class="method-detail">
200
+ <a name="M000006"></a>
201
+
202
+ <div class="method-heading">
203
+ <a href="SVGEE.src/M000006.html" target="Code" class="method-signature"
204
+ onclick="popupCode('SVGEE.src/M000006.html');return false;">
205
+ <span class="method-name">close_tag</span><span class="method-args">()</span>
206
+ </a>
207
+ </div>
208
+
209
+ <div class="method-description">
210
+ <p>
211
+ Produces the closing text for an svg file
212
+ </p>
213
+ </div>
214
+ </div>
215
+
216
+ <div id="method-M000009" class="method-detail">
217
+ <a name="M000009"></a>
218
+
219
+ <div class="method-heading">
220
+ <a href="SVGEE.src/M000009.html" target="Code" class="method-signature"
221
+ onclick="popupCode('SVGEE.src/M000009.html');return false;">
222
+ <span class="method-name">draw</span><span class="method-args">()</span>
223
+ </a>
224
+ </div>
225
+
226
+ <div class="method-description">
227
+ <p>
228
+ Produces the svg text to display all the features on a <a
229
+ href="Page.html">Page</a>
230
+ </p>
231
+ </div>
232
+ </div>
233
+
234
+ <div id="method-M000008" class="method-detail">
235
+ <a name="M000008"></a>
236
+
237
+ <div class="method-heading">
238
+ <a href="SVGEE.src/M000008.html" target="Code" class="method-signature"
239
+ onclick="popupCode('SVGEE.src/M000008.html');return false;">
240
+ <span class="method-name">gradient</span><span class="method-args">(a)</span>
241
+ </a>
242
+ </div>
243
+
244
+ <div class="method-description">
245
+ <p>
246
+ Takes the <a href="SVGEE.html#M000008">gradient</a> information from a <a
247
+ href="Glyph.html">Glyph</a>, which must be of type &#8216;radial&#8217; or
248
+ &#8216;linear&#8217; and creates the svg text for that <a
249
+ href="SVGEE.html#M000008">gradient</a>
250
+ </p>
251
+ <ul>
252
+ <li><tt>a</tt> = a <a href="SVGEE.html#M000008">gradient</a> (a <a
253
+ href="SVGEE.html#M000008">gradient</a> type, a colour and the parameters
254
+ for a given type)
255
+
256
+ </li>
257
+ </ul>
258
+ </div>
259
+ </div>
260
+
261
+ <div id="method-M000005" class="method-detail">
262
+ <a name="M000005"></a>
263
+
264
+ <div class="method-heading">
265
+ <a href="SVGEE.src/M000005.html" target="Code" class="method-signature"
266
+ onclick="popupCode('SVGEE.src/M000005.html');return false;">
267
+ <span class="method-name">open_tag</span><span class="method-args">()</span>
268
+ </a>
269
+ </div>
270
+
271
+ <div class="method-description">
272
+ <p>
273
+ Produces the opening text for an svg file
274
+ </p>
275
+ </div>
276
+ </div>
277
+
278
+
279
+ </div>
280
+
281
+
282
+ </div>
283
+
284
+
285
+ <div id="validator-badges">
286
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
287
+ </div>
288
+
289
+ </body>
290
+ </html>