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 +1,26 @@
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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>generic (Bio::Graphics::Glyph)</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/glyph.rb, line 59</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-identifier">args</span> = {
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+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
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+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'red'</span>,
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+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
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+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
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+ <span class="ruby-identifier">:x_round</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
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+ <span class="ruby-identifier">:y_round</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
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+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;fill-opacity:0.4;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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+ [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>, <span class="ruby-identifier">args</span>)]
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
@@ -0,0 +1,27 @@
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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>circle (Bio::Graphics::Glyph)</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/glyph.rb, line 103</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">circle</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-identifier">args</span> = {
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+ <span class="ruby-identifier">:radius</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
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+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'red'</span>,
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+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
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+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
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+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x_center</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>]
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+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y_center</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>]
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+ [<span class="ruby-identifier">:x</span>, <span class="ruby-identifier">:y</span>].<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">e</span><span class="ruby-operator">|</span> <span class="ruby-identifier">args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">e</span>)}
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+ [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:circle</span>, <span class="ruby-identifier">args</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>directed (Bio::Graphics::Glyph)</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/glyph.rb, line 151</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment cmt">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
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+ <span class="ruby-identifier">args</span> = {
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+
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+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
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+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'red'</span>,
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+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
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+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
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+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;fill-opacity:0.4;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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+
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'-'</span>
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+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:points</span>] = <span class="ruby-node">&quot;#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + args[:height] } #{args[:x]},#{args[:y] + (args[:height])} #{args[:x] - (args[:height] * 0.2)},#{args[:y] + (args[:height]/2)}&quot;</span>
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:points</span>] = <span class="ruby-node">&quot;#{args[:x]},#{args[:y]} #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + (args[:height]/2) } #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y] + args[:height]} #{args[:x]},#{args[:y] + args[:height]}&quot;</span>
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+
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+ <span class="ruby-keyword kw">end</span>
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+ [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:polygon</span>, <span class="ruby-identifier">args</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>down_triangle (Bio::Graphics::Glyph)</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/glyph.rb, line 200</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">down_triangle</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment cmt">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
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+ <span class="ruby-identifier">args</span> = {
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+
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+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
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+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'red'</span>,
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+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
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+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
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+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;fill-opacity:0.4;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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+
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+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:points</span>] = <span class="ruby-node">&quot;#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{ args[:x] + (args[:width]/2) },#{(args[:y] + args[:height]) }&quot;</span>
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+ [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:polygon</span>, <span class="ruby-identifier">args</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>up_triangle (Bio::Graphics::Glyph)</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/glyph.rb, line 245</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">up_triangle</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment cmt">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
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+ <span class="ruby-identifier">args</span> = {
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+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
17
+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'red'</span>,
18
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
19
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
20
+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;fill-opacity:0.4;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
21
+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:points</span>] = <span class="ruby-node">&quot;#{args[:x]},#{args[:y] + args[:height]} #{args[:x] + args[:width]},#{args[:y] + args[:height]} #{ args[:x] + (args[:width]/2) },#{args[:y] }&quot;</span>
22
+ [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:polygon</span>, <span class="ruby-identifier">args</span>)]
23
+ <span class="ruby-keyword kw">end</span></pre>
24
+ </body>
25
+ </html>
@@ -0,0 +1,29 @@
1
+ <?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>span (Bio::Graphics::Glyph)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 289</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">span</span>(<span class="ruby-identifier">args</span>)
15
+ <span class="ruby-identifier">args</span> = {
16
+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
17
+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'red'</span>,
18
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
19
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
20
+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;fill-opacity:1;&quot;</span>
21
+ }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
22
+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x1</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>]
23
+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x2</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>] <span class="ruby-operator">+</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:width</span>]
24
+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y1</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>]
25
+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y2</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>]
26
+ [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:line</span>, <span class="ruby-identifier">args</span>)]
27
+ <span class="ruby-keyword kw">end</span></pre>
28
+ </body>
29
+ </html>
@@ -0,0 +1,107 @@
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>
7
+ <head>
8
+ <title>transcript (Bio::Graphics::Glyph)</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/glyph.rb, line 366</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">transcript</span>(<span class="ruby-identifier">args</span>)
15
+ <span class="ruby-identifier">args</span> = {
16
+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
17
+ <span class="ruby-identifier">:utr_fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'black'</span>,
18
+ <span class="ruby-identifier">:utr_stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
19
+ <span class="ruby-identifier">:utr_stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
20
+ <span class="ruby-identifier">:exon_fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'red'</span>,
21
+ <span class="ruby-identifier">:exon_stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
22
+ <span class="ruby-identifier">:exon_stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
23
+ <span class="ruby-identifier">:line_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'black'</span>,
24
+ <span class="ruby-identifier">:line_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
25
+ <span class="ruby-identifier">:exon_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;fill-opacity:0.4;&quot;</span>,
26
+ <span class="ruby-identifier">:utr_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;&quot;</span>,
27
+ <span class="ruby-identifier">:line_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;&quot;</span>,
28
+ <span class="ruby-identifier">:block_gaps</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;&quot;</span>,
29
+ <span class="ruby-identifier">:gap_marker</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;&quot;</span>
30
+ }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
31
+
32
+ <span class="ruby-identifier">composite</span> = []
33
+
34
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">not</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>].<span class="ruby-identifier">empty?</span> <span class="ruby-comment cmt">##draw the utr as terminal element...##terminal utr is the one with the point on...</span>
35
+ <span class="ruby-identifier">x</span>,<span class="ruby-identifier">width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'-'</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>].<span class="ruby-identifier">shift</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>].<span class="ruby-identifier">pop</span>
36
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">x</span>,
37
+ <span class="ruby-identifier">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
38
+ <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">width</span>,
39
+ <span class="ruby-identifier">:strand</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>],
40
+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>],
41
+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_fill_color</span>],
42
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span><span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_stroke</span>],
43
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_stroke_width</span>],
44
+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_style</span>] )
45
+ <span class="ruby-comment cmt">##draw the other(s!) </span>
46
+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">utr</span><span class="ruby-operator">|</span>
47
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>, {
48
+ <span class="ruby-identifier">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">first</span>,
49
+ <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">last</span>,
50
+ <span class="ruby-identifier">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
51
+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>],
52
+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_fill_color</span>],
53
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span><span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_stroke</span>],
54
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_stroke_width</span>],
55
+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_style</span>]} )
56
+ <span class="ruby-keyword kw">end</span>
57
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">## draw the terminal exon as terminal element </span>
58
+ <span class="ruby-identifier">points</span> = <span class="ruby-keyword kw">nil</span>
59
+ <span class="ruby-identifier">x</span>,<span class="ruby-identifier">width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'-'</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>].<span class="ruby-identifier">shift</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>].<span class="ruby-identifier">pop</span>
60
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">x</span>,
61
+ <span class="ruby-identifier">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
62
+ <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">width</span>,
63
+ <span class="ruby-identifier">:strand</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>],
64
+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>],
65
+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_fill_color</span>],
66
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span><span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_stroke</span>],
67
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_stroke_width</span>],
68
+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_style</span>] )
69
+ <span class="ruby-keyword kw">end</span>
70
+ <span class="ruby-comment cmt">#draw any remaining exons</span>
71
+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">exon</span><span class="ruby-operator">|</span>
72
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>, {
73
+ <span class="ruby-identifier">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>],
74
+ <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">exon</span>[<span class="ruby-value">1</span>],
75
+ <span class="ruby-identifier">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
76
+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>],
77
+ <span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_fill_color</span>],
78
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span><span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_stroke</span>],
79
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_stroke_width</span>],
80
+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_style</span>]} )
81
+ <span class="ruby-keyword kw">end</span>
82
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:gap_marker</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">&quot;angled&quot;</span> <span class="ruby-keyword kw">and</span> <span class="ruby-keyword kw">not</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:block_gaps</span>].<span class="ruby-identifier">empty?</span>
83
+ <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:block_gaps</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap</span><span class="ruby-operator">|</span>
84
+ <span class="ruby-identifier">points</span> = <span class="ruby-node">&quot;#{gap.first},#{args[:y] + (args[:height]/2) } #{gap.first + (gap.last/2)},#{args[:y]} #{gap.first + gap.last},#{args[:y] + (args[:height]/2)}&quot;</span>
85
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:polyline</span>, {
86
+ <span class="ruby-identifier">:points</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">points</span>,
87
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_color</span>],
88
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_width</span>],
89
+ <span class="ruby-identifier">:fill</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;none&quot;</span>,
90
+ <span class="ruby-identifier">:line_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_style</span>]})
91
+ <span class="ruby-keyword kw">end</span>
92
+ <span class="ruby-keyword kw">else</span>
93
+ <span class="ruby-comment cmt">#add line</span>
94
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:line</span>, {
95
+ <span class="ruby-identifier">:x1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>],
96
+ <span class="ruby-identifier">:x2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{args[:x] + args[:width]}&quot;</span>,
97
+ <span class="ruby-identifier">:y1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>] <span class="ruby-operator">+</span> (<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>]<span class="ruby-operator">/</span><span class="ruby-value">2</span>),
98
+ <span class="ruby-identifier">:y2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>] <span class="ruby-operator">+</span> (<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>]<span class="ruby-operator">/</span><span class="ruby-value">2</span>),
99
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_color</span>],
100
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_width</span>],
101
+ <span class="ruby-identifier">:line_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_style</span>]})
102
+
103
+ <span class="ruby-keyword kw">end</span>
104
+ <span class="ruby-identifier">composite</span>
105
+ <span class="ruby-keyword kw">end</span></pre>
106
+ </body>
107
+ </html>
@@ -0,0 +1,51 @@
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>
7
+ <head>
8
+ <title>scale (Bio::Graphics::Glyph)</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/glyph.rb, line 470</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">scale</span>(<span class="ruby-identifier">args</span>)
15
+ <span class="ruby-identifier">first_mark</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:start</span>]
16
+ <span class="ruby-identifier">last_mark</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:stop</span>]
17
+ <span class="ruby-comment cmt">#(num.to_f / @nt_per_px_x.to_f)</span>
18
+ <span class="ruby-identifier">full_dist</span> = <span class="ruby-identifier">last_mark</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">first_mark</span>
19
+ <span class="ruby-identifier">interval_width</span> = <span class="ruby-identifier">full_dist</span> <span class="ruby-operator">/</span> (<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:number_of_intervals</span>] <span class="ruby-operator">-</span> <span class="ruby-value">1</span>)
20
+
21
+
22
+ <span class="ruby-identifier">a</span> = [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:line</span>,
23
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'black'</span>,
24
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
25
+ <span class="ruby-identifier">:x1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>, <span class="ruby-identifier">:x2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:page_width</span>],<span class="ruby-comment cmt"># * 1.1, </span>
26
+ <span class="ruby-identifier">:y1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;20&quot;</span>, <span class="ruby-identifier">:y2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;20&quot;</span> )]
27
+
28
+
29
+ <span class="ruby-identifier">marks</span> = (<span class="ruby-identifier">first_mark</span><span class="ruby-operator">..</span><span class="ruby-identifier">last_mark</span>).<span class="ruby-identifier">step</span>(<span class="ruby-identifier">interval_width</span>).<span class="ruby-identifier">to_a</span>
30
+
31
+ <span class="ruby-identifier">px_per_nt</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:page_width</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">full_dist</span>.<span class="ruby-identifier">to_f</span>
32
+ <span class="ruby-identifier">marks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">mark</span><span class="ruby-operator">|</span>
33
+ <span class="ruby-identifier">x</span> = (<span class="ruby-identifier">mark</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">first_mark</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">px_per_nt</span>
34
+ <span class="ruby-identifier">a</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>,
35
+ <span class="ruby-identifier">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">x</span>,
36
+ <span class="ruby-identifier">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">20</span>,
37
+ <span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'black'</span>,
38
+ <span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
39
+ <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
40
+ <span class="ruby-identifier">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">5</span> )
41
+
42
+ <span class="ruby-identifier">a</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:text</span>,
43
+ <span class="ruby-identifier">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">x</span>,
44
+ <span class="ruby-identifier">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">40</span>, <span class="ruby-identifier">:fill</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'black'</span>,
45
+ <span class="ruby-identifier">:text</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">mark</span>,
46
+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;font-family:Arial;font-style:italic&quot;</span>)
47
+ <span class="ruby-keyword kw">end</span>
48
+ <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">a</span>
49
+ <span class="ruby-keyword kw">end</span></pre>
50
+ </body>
51
+ </html>
@@ -0,0 +1,23 @@
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>
7
+ <head>
8
+ <title>label (Bio::Graphics::Glyph)</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/glyph.rb, line 515</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">label</span>(<span class="ruby-identifier">args</span>)
15
+ [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:text</span>,
16
+ <span class="ruby-identifier">:text</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:text</span>],
17
+ <span class="ruby-identifier">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>],
18
+ <span class="ruby-identifier">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
19
+ <span class="ruby-identifier">:fill</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;black&quot;</span>,
20
+ <span class="ruby-identifier">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;font-family:monospace;&quot;</span>)]
21
+ <span class="ruby-keyword kw">end</span></pre>
22
+ </body>
23
+ </html>
@@ -0,0 +1,18 @@
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>
7
+ <head>
8
+ <title>gradients (Bio::Graphics::Glyph)</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/glyph.rb, line 525</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">gradients</span> <span class="ruby-comment cmt">#needs to know which of its gradients are predefined</span>
15
+ [<span class="ruby-identifier">:red_white_h</span>, <span class="ruby-identifier">:green_white_h</span>, <span class="ruby-identifier">:blue_white_h</span>, <span class="ruby-identifier">:yellow_white_h</span>, <span class="ruby-identifier">:red_white_radial</span>, <span class="ruby-identifier">:green_white_radial</span>, <span class="ruby-identifier">:blue_white_radial</span>, <span class="ruby-identifier">:yellow_white_radial</span> ]
16
+ <span class="ruby-keyword kw">end</span></pre>
17
+ </body>
18
+ </html>
@@ -0,0 +1,75 @@
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>
7
+ <head>
8
+ <title>gradient (Bio::Graphics::Glyph)</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/glyph.rb, line 534</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">gradient</span>)
15
+ <span class="ruby-identifier">type</span>, <span class="ruby-identifier">color</span> = <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">gradient</span>
16
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:red_white_h</span>
17
+ [<span class="ruby-identifier">:linear</span>, <span class="ruby-value str">&quot;red&quot;</span>]
18
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:green_white_h</span>
19
+ [<span class="ruby-identifier">:linear</span>, <span class="ruby-value str">&quot;green&quot;</span>]
20
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:blue_white_h</span>
21
+ [<span class="ruby-identifier">:linear</span>, <span class="ruby-value str">&quot;blue&quot;</span>]
22
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:yellow_white_h</span>
23
+ [<span class="ruby-identifier">:linear</span>, <span class="ruby-value str">&quot;yellow&quot;</span>]
24
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:red_white_radial</span>
25
+ [<span class="ruby-identifier">:radial</span>, <span class="ruby-value str">&quot;red&quot;</span>]
26
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:green_white_radial</span>
27
+ [<span class="ruby-identifier">:radial</span>, <span class="ruby-value str">&quot;green&quot;</span>]
28
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:blue_white_radial</span>
29
+ [<span class="ruby-identifier">:radial</span>, <span class="ruby-value str">&quot;blue&quot;</span>]
30
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:yellow_white_radial</span>
31
+ [<span class="ruby-identifier">:radial</span>, <span class="ruby-value str">&quot;yellow&quot;</span>]
32
+ <span class="ruby-keyword kw">end</span>
33
+
34
+ <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>
35
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:linear</span>
36
+ {<span class="ruby-identifier">:type</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:linear</span>,
37
+ <span class="ruby-identifier">:id</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">gradient</span>,
38
+ <span class="ruby-identifier">:x1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>, <span class="ruby-identifier">:y1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>,
39
+ <span class="ruby-identifier">:x2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>, <span class="ruby-identifier">:y2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">100</span>,
40
+ <span class="ruby-identifier">:stops</span> =<span class="ruby-operator">&gt;</span> [
41
+ {
42
+ <span class="ruby-identifier">:color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">color</span>,
43
+ <span class="ruby-identifier">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>,
44
+ <span class="ruby-identifier">:opacity=</span><span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>
45
+ },
46
+ {
47
+ <span class="ruby-identifier">:color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;white&quot;</span>,
48
+ <span class="ruby-identifier">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">100</span>,
49
+ <span class="ruby-identifier">:opacity=</span><span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>
50
+ }
51
+ ]
52
+ }
53
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:radial</span>
54
+ {
55
+ <span class="ruby-identifier">:type</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:radial</span>,
56
+ <span class="ruby-identifier">:id</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">gradient</span>,
57
+ <span class="ruby-identifier">:cx</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>, <span class="ruby-identifier">:cy</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>,
58
+ <span class="ruby-identifier">:r</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>, <span class="ruby-identifier">:fx</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>, <span class="ruby-identifier">:fy</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>,
59
+ <span class="ruby-identifier">:stops</span> =<span class="ruby-operator">&gt;</span> [
60
+ {<span class="ruby-identifier">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>,
61
+ <span class="ruby-identifier">:color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">&quot;white&quot;</span>,
62
+ <span class="ruby-identifier">:opacity</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
63
+ },
64
+ {
65
+ <span class="ruby-identifier">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">100</span>,
66
+ <span class="ruby-identifier">:color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">color</span>,
67
+ <span class="ruby-identifier">:opacity</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>
68
+ }
69
+ ]
70
+ }
71
+ <span class="ruby-keyword kw">end</span>
72
+
73
+ <span class="ruby-keyword kw">end</span></pre>
74
+ </body>
75
+ </html>