bio-svgenes 0.3.1 → 0.3.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
  85. data/doc/classes/Bio/Graphics/SVGEE.src/M000008.html +27 -0
  86. data/doc/classes/Bio/Graphics/SVGEE.src/M000009.html +23 -0
  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
@@ -0,0 +1,18 @@
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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>
8
+ <title>new (Bio::Graphics::Primitive)</title>
9
+ <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>
12
+ <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" />
11
+ </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>