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
  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
@@ -0,0 +1,35 @@
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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::Track)</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/track.rb, line 93</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-ivar">@args</span> = {<span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:generic</span>,
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+ <span class="ruby-identifier">:name</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;feature_track&quot;</span>,
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+ <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>,
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+ <span class="ruby-identifier">:feature_height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
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+ <span class="ruby-identifier">:track_height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">nil</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:glyph</span>]
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+ <span class="ruby-ivar">@name</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:name</span>]
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+ <span class="ruby-ivar">@label</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:label</span>]
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+ <span class="ruby-ivar">@track_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:track_height</span>]
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+ <span class="ruby-ivar">@features</span> = []
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+ <span class="ruby-ivar">@feature_rows</span> = []
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+ <span class="ruby-ivar">@scale</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:scale</span>]
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+ <span class="ruby-ivar">@feature_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:feature_height</span>]
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+ <span class="ruby-ivar">@number_of_rows</span> = <span class="ruby-value">1</span>
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+ <span class="ruby-ivar">@max_y</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:max_y</span>]
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+ <span class="ruby-ivar">@min_width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:min_width</span>]
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+
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+
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
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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>add (Bio::Graphics::Track)</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/track.rb, line 115</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">feature</span>)
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+ <span class="ruby-ivar">@features</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">feature</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
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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>get_rows (Bio::Graphics::Track)</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/track.rb, line 121</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_rows</span>
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+ <span class="ruby-identifier">current_row</span> = <span class="ruby-value">1</span>
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+ <span class="ruby-ivar">@feature_rows</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">length</span>,<span class="ruby-value">1</span>)
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+ <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f1</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
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+ <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f2</span>, <span class="ruby-identifier">j</span><span class="ruby-operator">|</span>
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+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">j</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">j</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-identifier">i</span>
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>,<span class="ruby-identifier">f2</span>)
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+ <span class="ruby-ivar">@feature_rows</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-ivar">@number_rows</span> = <span class="ruby-ivar">@feature_rows</span>.<span class="ruby-identifier">max</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>
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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>overlaps (Bio::Graphics::Track)</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/track.rb, line 140</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>, <span class="ruby-identifier">f2</span>)
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+ (<span class="ruby-identifier">f1</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">f1</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">end</span>) <span class="ruby-keyword kw">or</span> (<span class="ruby-identifier">f1</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">f1</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">end</span>)
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
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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::Track)</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/track.rb, line 93</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-ivar">@args</span> = {<span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:generic</span>,
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+ <span class="ruby-identifier">:name</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;feature_track&quot;</span>,
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+ <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>,
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+ <span class="ruby-identifier">:feature_height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
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+ <span class="ruby-identifier">:track_height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">nil</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:glyph</span>]
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+ <span class="ruby-ivar">@name</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:name</span>]
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+ <span class="ruby-ivar">@label</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:label</span>]
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+ <span class="ruby-ivar">@track_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:track_height</span>]
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+ <span class="ruby-ivar">@features</span> = []
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+ <span class="ruby-ivar">@feature_rows</span> = []
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+ <span class="ruby-ivar">@scale</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:scale</span>]
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+ <span class="ruby-ivar">@feature_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:feature_height</span>]
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+ <span class="ruby-ivar">@number_of_rows</span> = <span class="ruby-value">1</span>
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+ <span class="ruby-ivar">@max_y</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:max_y</span>]
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+ <span class="ruby-ivar">@min_width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:min_width</span>]
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+
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+
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
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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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+ <head>
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+ <title>add (Bio::Graphics::Track)</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/track.rb, line 115</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">feature</span>)
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+ <span class="ruby-ivar">@features</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">feature</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
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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>get_rows (Bio::Graphics::Track)</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/track.rb, line 121</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_rows</span>
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+ <span class="ruby-identifier">current_row</span> = <span class="ruby-value">1</span>
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+ <span class="ruby-ivar">@feature_rows</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">length</span>,<span class="ruby-value">1</span>)
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+ <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f1</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
18
+ <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f2</span>, <span class="ruby-identifier">j</span><span class="ruby-operator">|</span>
19
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">j</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">j</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-identifier">i</span>
20
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>,<span class="ruby-identifier">f2</span>)
21
+ <span class="ruby-ivar">@feature_rows</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-ivar">@number_rows</span> = <span class="ruby-ivar">@feature_rows</span>.<span class="ruby-identifier">max</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>
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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>overlaps (Bio::Graphics::Track)</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/track.rb, line 140</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>, <span class="ruby-identifier">f2</span>)
15
+ (<span class="ruby-identifier">f1</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">f1</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">end</span>) <span class="ruby-keyword kw">or</span> (<span class="ruby-identifier">f1</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">f1</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">end</span>)
16
+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
@@ -1,9 +1 @@
1
- Fri, 01 Mar 2013 15:52:41 +0000
2
- ./lib/bio/graphics/primitive.rb Fri, 01 Mar 2013 13:01:51 +0000
3
- ./lib/bio/graphics/svgee.rb Fri, 01 Mar 2013 14:31:26 +0000
4
- ./lib/bio-svgenes.rb Tue, 12 Feb 2013 12:53:21 +0000
5
- ./lib/bio/graphics/track.rb Fri, 01 Mar 2013 15:38:24 +0000
6
- ./lib/bio/graphics/glyph.rb Fri, 01 Mar 2013 14:55:52 +0000
7
- ./LICENSE.txt Tue, 12 Feb 2013 12:53:20 +0000
8
- ./lib/bio/graphics/mini_feature.rb Fri, 01 Mar 2013 15:52:40 +0000
9
- ./lib/bio/graphics/page.rb Fri, 01 Mar 2013 14:34:28 +0000
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+ Thu, 04 Apr 2013 16:23:02 +0100
@@ -0,0 +1,131 @@
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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>File: bio-svgenes.rb</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" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
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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"
33
+ }
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+
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+ return true;
36
+ }
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+
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+ // Make codeblocks hidden by default
39
+ 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="fileHeader">
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+ <h1>bio-svgenes.rb</h1>
51
+ <table class="header-table">
52
+ <tr class="top-aligned-row">
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+ <td><strong>Path:</strong></td>
54
+ <td>lib/bio-svgenes.rb
55
+ </td>
56
+ </tr>
57
+ <tr class="top-aligned-row">
58
+ <td><strong>Last Update:</strong></td>
59
+ <td>Mon Mar 04 12:51:41 +0000 2013</td>
60
+ </tr>
61
+ </table>
62
+ </div>
63
+ <!-- banner header -->
64
+
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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>
73
+ Please require your code below, respecting the bioruby directory tree. For
74
+ instance, perhaps the only uncommented line in this file might be something
75
+ like this:
76
+ </p>
77
+ <pre>
78
+ require 'bio/sequence/awesome_sequence_plugin_thingy'
79
+ </pre>
80
+ <p>
81
+ and then create the ruby file
82
+ &#8216;lib/bio/sequence/awesome_sequence_thingy.rb&#8217; and put your
83
+ plugin&#8216;s code there. It is bad practice to write other code directly
84
+ into this file, because doing so causes confusion if this biogem was ever
85
+ to get merged into the main bioruby tree.
86
+ </p>
87
+
88
+ </div>
89
+
90
+ <div id="requires-list">
91
+ <h3 class="section-bar">Required files</h3>
92
+
93
+ <div class="name-list">
94
+ bio/graphics/svgee&nbsp;&nbsp;
95
+ bio/graphics/glyph&nbsp;&nbsp;
96
+ bio/graphics/page&nbsp;&nbsp;
97
+ bio/graphics/track&nbsp;&nbsp;
98
+ bio/graphics/mini_feature&nbsp;&nbsp;
99
+ bio/graphics/primitive&nbsp;&nbsp;
100
+ </div>
101
+ </div>
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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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+ <!-- 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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+
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+
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+
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+ <!-- if method_list -->
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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">
127
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
128
+ </div>
129
+
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+ </body>
131
+ </html>
@@ -0,0 +1,101 @@
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
+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
+ <head>
8
+ <title>File: glyph.rb</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>
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+
44
+ </head>
45
+ <body>
46
+
47
+
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+
49
+ <div id="fileHeader">
50
+ <h1>glyph.rb</h1>
51
+ <table class="header-table">
52
+ <tr class="top-aligned-row">
53
+ <td><strong>Path:</strong></td>
54
+ <td>lib/bio/graphics/glyph.rb
55
+ </td>
56
+ </tr>
57
+ <tr class="top-aligned-row">
58
+ <td><strong>Last Update:</strong></td>
59
+ <td>Thu Apr 04 15:40:52 +0100 2013</td>
60
+ </tr>
61
+ </table>
62
+ </div>
63
+ <!-- banner header -->
64
+
65
+ <div id="bodyContent">
66
+
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+
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+
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+ <div id="contextContent">
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+
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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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+
79
+ <!-- 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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+
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+
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+
90
+ <!-- if method_list -->
91
+
92
+
93
+ </div>
94
+
95
+
96
+ <div id="validator-badges">
97
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
98
+ </div>
99
+
100
+ </body>
101
+ </html>