bio-graphics 1.2 → 1.4

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Files changed (331) hide show
  1. data/doc/classes/Bio.html +4 -26
  2. data/doc/classes/Bio/Feature.html +350 -0
  3. data/doc/classes/Bio/Feature.src/M000010.html +21 -0
  4. data/doc/classes/Bio/Feature.src/M000011.html +20 -0
  5. data/doc/classes/Bio/Feature.src/M000012.html +19 -0
  6. data/doc/classes/Bio/Feature.src/M000014.html +21 -0
  7. data/doc/classes/Bio/Feature.src/M000016.html +21 -0
  8. data/doc/classes/Bio/Feature.src/M000034.html +21 -0
  9. data/doc/classes/Bio/Feature.src/M000035.html +20 -0
  10. data/doc/classes/Bio/Feature.src/M000036.html +19 -0
  11. data/doc/classes/Bio/Feature.src/M000038.html +21 -0
  12. data/doc/classes/Bio/Feature.src/M000040.html +21 -0
  13. data/doc/classes/Bio/Feature.src/M000042.html +21 -0
  14. data/doc/classes/Bio/Feature.src/M000043.html +20 -0
  15. data/doc/classes/Bio/Feature.src/M000044.html +21 -0
  16. data/doc/classes/Bio/Feature.src/M000045.html +20 -0
  17. data/doc/classes/Bio/Feature.src/M000046.html +19 -0
  18. data/doc/classes/Bio/Feature.src/M000048.html +21 -0
  19. data/doc/classes/Bio/Feature.src/M000050.html +21 -0
  20. data/doc/classes/Bio/Feature.src/M000074.html +21 -0
  21. data/doc/classes/Bio/Feature.src/M000075.html +20 -0
  22. data/doc/classes/Bio/Feature.src/M000076.html +19 -0
  23. data/doc/classes/Bio/Feature.src/M000078.html +21 -0
  24. data/doc/classes/Bio/Feature.src/M000080.html +21 -0
  25. data/doc/classes/Bio/Feature/Qualifier.html +189 -0
  26. data/doc/classes/Bio/Feature/Qualifier.src/M000017.html +18 -0
  27. data/doc/classes/Bio/Feature/Qualifier.src/M000041.html +18 -0
  28. data/doc/classes/Bio/Feature/Qualifier.src/M000049.html +18 -0
  29. data/doc/classes/Bio/Feature/Qualifier.src/M000051.html +18 -0
  30. data/doc/classes/Bio/Feature/Qualifier.src/M000081.html +18 -0
  31. data/doc/classes/Bio/Features.html +329 -0
  32. data/doc/classes/Bio/Features.src/M000004.html +18 -0
  33. data/doc/classes/Bio/Features.src/M000005.html +19 -0
  34. data/doc/classes/Bio/Features.src/M000006.html +21 -0
  35. data/doc/classes/Bio/Features.src/M000007.html +18 -0
  36. data/doc/classes/Bio/Features.src/M000008.html +18 -0
  37. data/doc/classes/Bio/Features.src/M000009.html +18 -0
  38. data/doc/classes/Bio/Features.src/M000028.html +18 -0
  39. data/doc/classes/Bio/Features.src/M000029.html +19 -0
  40. data/doc/classes/Bio/Features.src/M000030.html +21 -0
  41. data/doc/classes/Bio/Features.src/M000031.html +18 -0
  42. data/doc/classes/Bio/Features.src/M000032.html +18 -0
  43. data/doc/classes/Bio/Features.src/M000033.html +18 -0
  44. data/doc/classes/Bio/Features.src/M000036.html +18 -0
  45. data/doc/classes/Bio/Features.src/M000037.html +19 -0
  46. data/doc/classes/Bio/Features.src/M000038.html +18 -0
  47. data/doc/classes/Bio/Features.src/M000039.html +19 -0
  48. data/doc/classes/Bio/Features.src/M000040.html +21 -0
  49. data/doc/classes/Bio/Features.src/M000041.html +18 -0
  50. data/doc/classes/Bio/Features.src/M000042.html +18 -0
  51. data/doc/classes/Bio/Features.src/M000043.html +18 -0
  52. data/doc/classes/Bio/Features.src/M000068.html +18 -0
  53. data/doc/classes/Bio/Features.src/M000069.html +19 -0
  54. data/doc/classes/Bio/Features.src/M000070.html +21 -0
  55. data/doc/classes/Bio/Features.src/M000071.html +18 -0
  56. data/doc/classes/Bio/Features.src/M000072.html +18 -0
  57. data/doc/classes/Bio/Features.src/M000073.html +18 -0
  58. data/doc/classes/Bio/Graphics.html +28 -42
  59. data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} +98 -125
  60. data/doc/classes/Bio/Graphics/Feature.src/M000020.html +51 -0
  61. data/doc/classes/Bio/Graphics/Feature.src/M000021.html +65 -0
  62. data/doc/classes/Bio/Graphics/Feature.src/M000022.html +55 -0
  63. data/doc/classes/Bio/Graphics/Feature.src/M000023.html +66 -0
  64. data/doc/classes/Bio/Graphics/Feature.src/M000024.html +51 -0
  65. data/doc/classes/Bio/Graphics/Feature.src/M000025.html +65 -0
  66. data/doc/classes/Bio/Graphics/Feature.src/M000026.html +55 -0
  67. data/doc/classes/Bio/Graphics/Feature.src/M000054.html +51 -0
  68. data/doc/classes/Bio/Graphics/Feature.src/M000055.html +65 -0
  69. data/doc/classes/Bio/Graphics/Feature.src/M000056.html +55 -0
  70. data/doc/classes/Bio/Graphics/Feature/SubFeature.html +348 -0
  71. data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000025.html +68 -0
  72. data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000026.html +67 -0
  73. data/doc/classes/Bio/Graphics/Glyph.html +178 -0
  74. data/doc/classes/Bio/Graphics/Glyph/Box.html +139 -0
  75. data/doc/classes/Bio/Graphics/Glyph/Box.src/M000004.html +24 -0
  76. data/doc/classes/Bio/Graphics/Glyph/Box.src/M000032.html +24 -0
  77. data/doc/classes/Bio/Graphics/Glyph/Common.html +187 -0
  78. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html +18 -0
  79. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html +18 -0
  80. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html +24 -0
  81. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html +24 -0
  82. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html +18 -0
  83. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html +24 -0
  84. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html +24 -0
  85. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html +139 -0
  86. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html +22 -0
  87. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html +139 -0
  88. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html +22 -0
  89. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.html +139 -0
  90. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html +31 -0
  91. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html +31 -0
  92. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html +139 -0
  93. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html +26 -0
  94. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html +26 -0
  95. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html +26 -0
  96. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html +139 -0
  97. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html +40 -0
  98. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html +40 -0
  99. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html +40 -0
  100. data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.html} +16 -19
  101. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html +22 -0
  102. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html +22 -0
  103. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html +22 -0
  104. data/doc/classes/Bio/Graphics/Glyph/Generic.html +139 -0
  105. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html +18 -0
  106. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html +18 -0
  107. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html +18 -0
  108. data/doc/classes/Bio/Graphics/Glyph/Line.html +139 -0
  109. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html +20 -0
  110. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html +20 -0
  111. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html +20 -0
  112. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.html +139 -0
  113. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html +28 -0
  114. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html +28 -0
  115. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html +28 -0
  116. data/doc/classes/Bio/Graphics/Glyph/Spliced.html +139 -0
  117. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html +19 -0
  118. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html +19 -0
  119. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html +19 -0
  120. data/doc/classes/Bio/Graphics/Glyph/Transcript.html +113 -0
  121. data/doc/classes/Bio/Graphics/Glyph/Triangle.html +139 -0
  122. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html +21 -0
  123. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html +21 -0
  124. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html +21 -0
  125. data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.html} +50 -16
  126. data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} +3 -3
  127. data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html +18 -0
  128. data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html +18 -0
  129. data/doc/classes/Bio/Graphics/ImageMap.src/M000033.html +18 -0
  130. data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} +7 -4
  131. data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html +24 -0
  132. data/doc/classes/Bio/Graphics/ImageMap.src/M000062.html +18 -0
  133. data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html +18 -0
  134. data/doc/classes/Bio/Graphics/ImageMap.src/M000064.html +27 -0
  135. data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html +24 -0
  136. data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} +14 -14
  137. data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} +3 -3
  138. data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} +6 -4
  139. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html +19 -0
  140. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html +22 -0
  141. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html +19 -0
  142. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html +22 -0
  143. data/doc/classes/Bio/Graphics/Panel.html +70 -69
  144. data/doc/classes/Bio/Graphics/Panel.src/M000025.html +52 -0
  145. data/doc/classes/Bio/Graphics/Panel.src/M000026.html +20 -0
  146. data/doc/classes/Bio/Graphics/Panel.src/M000027.html +98 -0
  147. data/doc/classes/Bio/Graphics/Panel.src/M000028.html +20 -0
  148. data/doc/classes/Bio/Graphics/Panel.src/M000029.html +52 -0
  149. data/doc/classes/Bio/Graphics/Panel.src/M000030.html +20 -0
  150. data/doc/classes/Bio/Graphics/Panel.src/M000031.html +98 -0
  151. data/doc/classes/Bio/Graphics/Panel.src/M000059.html +52 -0
  152. data/doc/classes/Bio/Graphics/Panel.src/M000060.html +20 -0
  153. data/doc/classes/Bio/Graphics/Panel.src/M000061.html +98 -0
  154. data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} +50 -21
  155. data/doc/classes/Bio/Graphics/Ruler.src/M000015.html +30 -0
  156. data/doc/classes/Bio/Graphics/Ruler.src/M000016.html +20 -0
  157. data/doc/classes/Bio/Graphics/Ruler.src/M000017.html +30 -0
  158. data/doc/classes/Bio/Graphics/Ruler.src/M000018.html +20 -0
  159. data/doc/classes/Bio/Graphics/Ruler.src/M000019.html +26 -0
  160. data/doc/classes/Bio/Graphics/Ruler.src/M000020.html +45 -0
  161. data/doc/classes/Bio/Graphics/Ruler.src/M000047.html +30 -0
  162. data/doc/classes/Bio/Graphics/Ruler.src/M000048.html +20 -0
  163. data/doc/classes/Bio/Graphics/Ruler.src/M000049.html +26 -0
  164. data/doc/classes/Bio/Graphics/Ruler.src/M000050.html +45 -0
  165. data/doc/classes/Bio/Graphics/SubFeature.html +348 -0
  166. data/doc/classes/Bio/Graphics/SubFeature.src/M000001.html +73 -0
  167. data/doc/classes/Bio/Graphics/SubFeature.src/M000002.html +69 -0
  168. data/doc/classes/Bio/Graphics/SubFeature.src/M000023.html +73 -0
  169. data/doc/classes/Bio/Graphics/SubFeature.src/M000024.html +69 -0
  170. data/doc/classes/Bio/Graphics/SubFeature.src/M000027.html +73 -0
  171. data/doc/classes/Bio/Graphics/SubFeature.src/M000028.html +69 -0
  172. data/doc/classes/Bio/Graphics/SubFeature.src/M000057.html +73 -0
  173. data/doc/classes/Bio/Graphics/SubFeature.src/M000058.html +69 -0
  174. data/doc/classes/Bio/Graphics/{Panel/Track.html → Track.html} +67 -69
  175. data/doc/classes/Bio/Graphics/Track.src/M000017.html +39 -0
  176. data/doc/classes/Bio/Graphics/Track.src/M000018.html +37 -0
  177. data/doc/classes/Bio/Graphics/Track.src/M000019.html +45 -0
  178. data/doc/classes/Bio/Graphics/Track.src/M000020.html +41 -0
  179. data/doc/classes/Bio/Graphics/Track.src/M000021.html +39 -0
  180. data/doc/classes/Bio/Graphics/Track.src/M000022.html +37 -0
  181. data/doc/classes/Bio/Graphics/Track.src/M000023.html +45 -0
  182. data/doc/classes/Bio/Graphics/Track.src/M000051.html +39 -0
  183. data/doc/classes/Bio/Graphics/Track.src/M000052.html +37 -0
  184. data/doc/classes/Bio/Graphics/Track.src/M000053.html +45 -0
  185. data/doc/classes/Range.html +129 -0
  186. data/doc/classes/String.html +167 -0
  187. data/doc/classes/String.src/M000001.html +18 -0
  188. data/doc/classes/String.src/M000002.html +18 -0
  189. data/doc/classes/String.src/M000003.html +23 -0
  190. data/doc/classes/String.src/M000029.html +18 -0
  191. data/doc/classes/String.src/M000030.html +18 -0
  192. data/doc/classes/String.src/M000031.html +23 -0
  193. data/doc/classes/TestCustomGlyph.html +137 -0
  194. data/doc/classes/TestCustomGlyph.src/M000025.html +25 -0
  195. data/doc/classes/TestCustomGlyphInFile.html +167 -0
  196. data/doc/classes/TestCustomGlyphInFile.src/M000026.html +19 -0
  197. data/doc/classes/TestCustomGlyphInFile.src/M000027.html +25 -0
  198. data/doc/classes/TestCustomGlyphInFile.src/M000028.html +18 -0
  199. data/doc/classes/TestExtensions.html +152 -0
  200. data/doc/classes/TestExtensions.src/M000015.html +22 -0
  201. data/doc/classes/TestExtensions.src/M000016.html +25 -0
  202. data/doc/classes/TestFeature.html +152 -0
  203. data/doc/classes/TestFeature.src/M000017.html +19 -0
  204. data/doc/classes/TestFeature.src/M000018.html +21 -0
  205. data/doc/classes/TestImageMap.html +182 -0
  206. data/doc/classes/TestImageMap.src/M000019.html +22 -0
  207. data/doc/classes/TestImageMap.src/M000020.html +56 -0
  208. data/doc/classes/TestImageMap.src/M000021.html +56 -0
  209. data/doc/classes/TestImageMap.src/M000022.html +20 -0
  210. data/doc/classes/TestPanel.html +276 -0
  211. data/doc/classes/TestPanel.src/M000001.html +18 -0
  212. data/doc/classes/TestPanel.src/M000002.html +61 -0
  213. data/doc/classes/TestPanel.src/M000003.html +35 -0
  214. data/doc/classes/TestPanel.src/M000004.html +54 -0
  215. data/doc/classes/TestPanel.src/M000005.html +54 -0
  216. data/doc/classes/TestPanel.src/M000006.html +41 -0
  217. data/doc/classes/TestPanel.src/M000007.html +36 -0
  218. data/doc/classes/TestPanel.src/M000008.html +20 -0
  219. data/doc/classes/TestPanel.src/M000009.html +26 -0
  220. data/doc/classes/TestPanel.src/M000010.html +21 -0
  221. data/doc/classes/TestRuler.html +152 -0
  222. data/doc/classes/TestRuler.src/M000013.html +22 -0
  223. data/doc/classes/TestRuler.src/M000014.html +31 -0
  224. data/doc/classes/TestSubFeature.html +152 -0
  225. data/doc/classes/TestSubFeature.src/M000023.html +21 -0
  226. data/doc/classes/TestSubFeature.src/M000024.html +18 -0
  227. data/doc/classes/TestTrack.html +152 -0
  228. data/doc/classes/TestTrack.src/M000011.html +19 -0
  229. data/doc/classes/TestTrack.src/M000012.html +23 -0
  230. data/doc/created.rid +1 -1
  231. data/doc/files/README_DEV.html +399 -70
  232. data/doc/files/TUTORIAL.html +188 -67
  233. data/doc/files/lib/bio-graphics_rb.html +3 -2
  234. data/doc/files/lib/bio/graphics/feature_rb.html +12 -6
  235. data/doc/files/lib/bio/graphics/glyphs/box_rb.html +113 -0
  236. data/doc/files/lib/bio/graphics/glyphs/common_rb.html +113 -0
  237. data/doc/files/lib/bio/graphics/glyphs/directed_box_rb.html +113 -0
  238. data/doc/files/lib/bio/graphics/glyphs/directed_generic_rb.html +113 -0
  239. data/doc/files/lib/bio/graphics/glyphs/directed_spliced_rb.html +113 -0
  240. data/doc/files/lib/bio/graphics/glyphs/dot_rb.html +113 -0
  241. data/doc/files/lib/bio/graphics/glyphs/generic_rb.html +113 -0
  242. data/doc/files/lib/bio/graphics/glyphs/line_rb.html +113 -0
  243. data/doc/files/lib/bio/graphics/glyphs/line_with_handles_rb.html +113 -0
  244. data/doc/files/lib/bio/graphics/glyphs/spliced_rb.html +113 -0
  245. data/doc/files/lib/bio/graphics/glyphs/transcript_rb.html +113 -0
  246. data/doc/files/lib/bio/graphics/glyphs/triangle_rb.html +113 -0
  247. data/doc/files/lib/bio/graphics/image_map_rb.html +3 -2
  248. data/doc/files/lib/bio/graphics/panel_rb.html +10 -2
  249. data/doc/files/lib/bio/graphics/ruler_rb.html +3 -2
  250. data/doc/files/lib/bio/graphics/subfeature_rb.html +114 -0
  251. data/doc/files/lib/bio/graphics/track_rb.html +3 -2
  252. data/doc/files/lib/feature_rb.html +101 -0
  253. data/doc/files/samples/arkdb_features_rb.html +101 -0
  254. data/doc/files/samples/glyph_showcase_rb.html +108 -0
  255. data/doc/files/samples/protein_domains_rb.html +115 -0
  256. data/doc/files/samples/subfeatures_rb.html +108 -0
  257. data/doc/files/scripts/gff2png_rb.html +154 -0
  258. data/doc/files/test/unit/custom_glyph_in_file_rb.html +101 -0
  259. data/doc/files/test/unit/test_class_extensions_rb.html +108 -0
  260. data/doc/files/test/unit/test_creation_rb.html +108 -0
  261. data/doc/files/test/unit/test_custom_glyph_rb.html +108 -0
  262. data/doc/files/test/unit/test_draw_rb.html +108 -0
  263. data/doc/files/test/unit/test_imagemap_rb.html +108 -0
  264. data/doc/files/test/unit/test_subfeatures_rb.html +108 -0
  265. data/doc/fr_class_index.html +24 -6
  266. data/doc/fr_file_index.html +14 -0
  267. data/doc/fr_method_index.html +51 -19
  268. data/doc/images/glyph_showcase.png +0 -0
  269. data/doc/images/terms.svg +146 -132
  270. data/images/glyph_showcase.png +0 -0
  271. data/lib/bio-graphics.rb +38 -6
  272. data/lib/bio/graphics/feature.rb +212 -440
  273. data/lib/bio/graphics/glyphs/box.rb +21 -0
  274. data/lib/bio/graphics/glyphs/common.rb +149 -0
  275. data/lib/bio/graphics/glyphs/directed_box.rb +28 -0
  276. data/lib/bio/graphics/glyphs/directed_generic.rb +23 -0
  277. data/lib/bio/graphics/glyphs/directed_spliced.rb +39 -0
  278. data/lib/bio/graphics/glyphs/dot.rb +21 -0
  279. data/lib/bio/graphics/glyphs/generic.rb +15 -0
  280. data/lib/bio/graphics/glyphs/line.rb +17 -0
  281. data/lib/bio/graphics/glyphs/line_with_handles.rb +25 -0
  282. data/lib/bio/graphics/glyphs/spliced.rb +16 -0
  283. data/lib/bio/graphics/glyphs/transcript.rb +12 -0
  284. data/lib/bio/graphics/glyphs/triangle.rb +18 -0
  285. data/lib/bio/graphics/image_map.rb +25 -4
  286. data/lib/bio/graphics/panel.rb +266 -209
  287. data/lib/bio/graphics/ruler.rb +95 -96
  288. data/lib/bio/graphics/subfeature.rb +187 -0
  289. data/lib/bio/graphics/track.rb +155 -156
  290. data/lib/feature.rb +204 -0
  291. data/samples/arkdb_features.rb +10 -8
  292. data/samples/glyph_showcase.rb +58 -22
  293. data/samples/protein_domains.rb +19 -0
  294. data/samples/subfeatures.rb +31 -0
  295. data/test/unit/custom_glyph_in_file.rb +12 -0
  296. data/test/unit/data.txt +32 -0
  297. data/test/unit/test_class_extensions.rb +23 -0
  298. data/test/unit/test_creation.rb +43 -13
  299. data/test/unit/test_custom_glyph.rb +50 -0
  300. data/test/unit/test_draw.rb +211 -0
  301. data/test/unit/test_imagemap.rb +134 -0
  302. data/test/unit/test_subfeatures.rb +17 -0
  303. metadata +396 -119
  304. data/doc/classes/Bio/Graphics/Panel.src/M000005.html +0 -29
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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>setup (TestPanel)</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 test/unit/test_draw.rb, line 5</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">setup</span>
15
+ <span class="ruby-ivar">@generated_pictures</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
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+ <html>
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+ <head>
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+ <title>test_draw_showcase (TestPanel)</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 test/unit/test_draw.rb, line 9</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_draw_showcase</span>
15
+ <span class="ruby-identifier">my_panel</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">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">500</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1000</span>)
16
+
17
+ <span class="ruby-identifier">generic_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'generic'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>)
18
+ <span class="ruby-identifier">line_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'line'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:line</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>])
19
+ <span class="ruby-identifier">line_with_handles_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'line with handles'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:line_with_handles</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>])
20
+ <span class="ruby-identifier">directed_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'directed'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:directed_generic</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">0</span>])
21
+ <span class="ruby-identifier">triangle_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'triangle'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:triangle</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
22
+ <span class="ruby-identifier">dot_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'dot'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:dot</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">1</span>])
23
+ <span class="ruby-identifier">spliced_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'spliced'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:spliced</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
24
+ <span class="ruby-identifier">directed_spliced_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'directed_spliced'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:directed_spliced</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>])
25
+
26
+ <span class="ruby-identifier">generic_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-value str">'250..375'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'clone1'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.newsforge.com'</span>)
27
+ <span class="ruby-identifier">generic_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-value str">'54..124'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'clone2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.thearkdb.org'</span>)
28
+ <span class="ruby-identifier">generic_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-value str">'100..449'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'clone3'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.google.com'</span>)
29
+
30
+ <span class="ruby-identifier">line_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'primer'</span>, <span class="ruby-value str">'complement(200..320)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'primer1'</span>)
31
+ <span class="ruby-identifier">line_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'primer'</span>, <span class="ruby-value str">'355..480'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'primer2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.zdnet.co.uk'</span>)
32
+
33
+ <span class="ruby-identifier">line_with_handles_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'primer'</span>, <span class="ruby-value str">'complement(200..320)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'primer1'</span>)
34
+ <span class="ruby-identifier">line_with_handles_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'primer'</span>, <span class="ruby-value str">'355..480'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'primer2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.zdnet.co.uk'</span>)
35
+
36
+ <span class="ruby-identifier">directed_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-value str">'50..60'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'marker1'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.google.com'</span>)
37
+ <span class="ruby-identifier">directed_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>,<span class="ruby-value str">'complement(80..120)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'marker2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.sourceforge.net'</span>)
38
+
39
+ <span class="ruby-identifier">triangle_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-value str">'56'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'snp1'</span>)
40
+ <span class="ruby-identifier">triangle_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-value str">'103'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'snp2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://digg.com'</span>)
41
+
42
+ <span class="ruby-identifier">dot_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-value str">'56'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'thing1'</span>)
43
+ <span class="ruby-identifier">dot_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-value str">'57'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'thing3'</span>)
44
+ <span class="ruby-identifier">dot_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-value str">'114'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'thing2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://digg.com'</span>)
45
+
46
+ <span class="ruby-identifier">spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'join(34..52,109..183)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene1'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://news.bbc.co.uk'</span>)
47
+ <span class="ruby-identifier">spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'complement(join(170..231,264..299,350..360,409..445))'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene2'</span>)
48
+ <span class="ruby-identifier">spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'join(134..152,209..283)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene3'</span>)
49
+
50
+ <span class="ruby-identifier">directed_spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'join(34..52,109..183)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene4'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.vrtnieuws.net'</span>)
51
+ <span class="ruby-identifier">directed_spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'complement(join(170..231,264..299,350..360,409..445))'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene5'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://bioinformatics.roslin.ac.uk'</span>)
52
+ <span class="ruby-identifier">directed_spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'join(134..152,209..283)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene6'</span>)
53
+
54
+ <span class="ruby-identifier">output_file</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@method_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'.png'</span>
55
+ <span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
56
+
57
+ <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
58
+ <span class="ruby-identifier">system</span>(<span class="ruby-value str">&quot;display &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;&amp; sleep 2 &amp;&amp; kill $!&quot;</span>)
59
+ <span class="ruby-keyword kw">end</span></pre>
60
+ </body>
61
+ </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>test_outside_border (TestPanel)</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 test/unit/test_draw.rb, line 56</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_outside_border</span>
15
+ <span class="ruby-identifier">my_panel</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">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">500</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1000</span>, <span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">100</span><span class="ruby-operator">..</span><span class="ruby-value">400</span>)
16
+
17
+ <span class="ruby-identifier">spliced_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'spliced'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:spliced</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
18
+ <span class="ruby-identifier">directed_spliced_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'directed_spliced'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:directed_spliced</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>])
19
+
20
+ <span class="ruby-identifier">spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'join(34..52,109..183)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene1'</span>,<span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://news.bbc.co.uk'</span>)
21
+ <span class="ruby-identifier">spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'complement(join(170..231,264..299,350..360,409..445))'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene2'</span>)
22
+ <span class="ruby-identifier">spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'join(134..152,209..283)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene3'</span>)
23
+
24
+ <span class="ruby-identifier">directed_spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'join(34..52,109..183)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene4'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.vrtnieuws.net'</span>)
25
+ <span class="ruby-identifier">directed_spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'complement(join(170..231,264..299,350..360,409..445))'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene5'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://bioinformatics.roslin.ac.uk'</span>)
26
+ <span class="ruby-identifier">directed_spliced_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'gene'</span>,<span class="ruby-value str">'join(134..152,209..283)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'gene6'</span>)
27
+
28
+ <span class="ruby-identifier">output_file</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@method_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'.png'</span>
29
+ <span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
30
+
31
+ <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
32
+ <span class="ruby-identifier">system</span>(<span class="ruby-value str">&quot;display &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;&amp; sleep 2 &amp;&amp; kill $!&quot;</span>)
33
+ <span class="ruby-keyword kw">end</span></pre>
34
+ </body>
35
+ </html>
@@ -0,0 +1,54 @@
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>test_arkdb_features (TestPanel)</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>
12
+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File test/unit/test_draw.rb, line 77</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_arkdb_features</span>
15
+ <span class="ruby-identifier">my_panel</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">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">4173015</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">600</span>, <span class="ruby-identifier">:vertical</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>)
16
+
17
+ <span class="ruby-comment cmt">#Create and configure tracks</span>
18
+ <span class="ruby-identifier">scaffold_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>)
19
+ <span class="ruby-identifier">marker_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>)
20
+ <span class="ruby-identifier">clone_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>)
21
+
22
+ <span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>]
23
+ <span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">0</span>]
24
+ <span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:triangle</span>
25
+ <span class="ruby-identifier">clone_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
26
+
27
+ <span class="ruby-comment cmt"># Add data to tracks</span>
28
+ <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/data.txt'</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
29
+ <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp!</span>
30
+ <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">type</span>, <span class="ruby-identifier">start</span>, <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\t/</span>)
31
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'scaffold'</span>
32
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">nil?</span>
33
+ <span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-value str">'1..4173015'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">accession</span>)
34
+ <span class="ruby-keyword kw">else</span>
35
+ <span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.google.com'</span>)
36
+ <span class="ruby-keyword kw">end</span>
37
+
38
+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'marker'</span>
39
+ <span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, ((<span class="ruby-identifier">start</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>.<span class="ruby-identifier">to_i</span>)<span class="ruby-operator">/</span><span class="ruby-value">2</span>).<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession='</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">accession</span>)
40
+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'clone'</span>
41
+ <span class="ruby-identifier">clone_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">accession</span>)
42
+ <span class="ruby-keyword kw">end</span>
43
+ <span class="ruby-keyword kw">end</span>
44
+
45
+ <span class="ruby-comment cmt"># And draw</span>
46
+ <span class="ruby-identifier">output_file</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@method_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'.png'</span>
47
+ <span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
48
+
49
+ <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
50
+
51
+ <span class="ruby-identifier">system</span>(<span class="ruby-value str">&quot;display &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;&amp; sleep 2 &amp;&amp; kill $!&quot;</span>)
52
+ <span class="ruby-keyword kw">end</span></pre>
53
+ </body>
54
+ </html>
@@ -0,0 +1,54 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!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">
5
+
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+ <html>
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+ <head>
8
+ <title>test_subregion (TestPanel)</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 test/unit/test_draw.rb, line 117</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_subregion</span>
15
+ <span class="ruby-identifier">my_panel</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">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">4173015</span>, <span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">2500000</span><span class="ruby-operator">..</span><span class="ruby-value">3500000</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">600</span>)
16
+
17
+ <span class="ruby-comment cmt">#Create and configure tracks</span>
18
+ <span class="ruby-identifier">scaffold_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>)
19
+ <span class="ruby-identifier">marker_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>)
20
+ <span class="ruby-identifier">clone_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>)
21
+
22
+ <span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>]
23
+ <span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">0</span>]
24
+ <span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:triangle</span>
25
+ <span class="ruby-identifier">clone_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
26
+
27
+ <span class="ruby-comment cmt"># Add data to tracks</span>
28
+ <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/data.txt'</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
29
+ <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp!</span>
30
+ <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">type</span>, <span class="ruby-identifier">start</span>, <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\t/</span>)
31
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'scaffold'</span>
32
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">nil?</span>
33
+ <span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-value str">'1..4173015'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">accession</span>)
34
+ <span class="ruby-keyword kw">else</span>
35
+ <span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.google.com'</span>)
36
+ <span class="ruby-keyword kw">end</span>
37
+
38
+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'marker'</span>
39
+ <span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, ((<span class="ruby-identifier">start</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>.<span class="ruby-identifier">to_i</span>)<span class="ruby-operator">/</span><span class="ruby-value">2</span>).<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession='</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">accession</span>)
40
+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'clone'</span>
41
+ <span class="ruby-identifier">clone_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">accession</span>)
42
+ <span class="ruby-keyword kw">end</span>
43
+ <span class="ruby-keyword kw">end</span>
44
+
45
+ <span class="ruby-comment cmt"># And draw</span>
46
+ <span class="ruby-identifier">output_file</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@method_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'.png'</span>
47
+ <span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
48
+
49
+ <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
50
+
51
+ <span class="ruby-identifier">system</span>(<span class="ruby-value str">&quot;display &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;&amp; sleep 2 &amp;&amp; kill $!&quot;</span>)
52
+ <span class="ruby-keyword kw">end</span></pre>
53
+ </body>
54
+ </html>
@@ -0,0 +1,41 @@
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">
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+
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+ <html>
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+ <head>
8
+ <title>test_subfeatures (TestPanel)</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">
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+ <pre><span class="ruby-comment cmt"># File test/unit/test_draw.rb, line 157</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_subfeatures</span>
15
+ <span class="ruby-identifier">my_panel</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">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">500</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">600</span>)
16
+
17
+ <span class="ruby-identifier">track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'mrna'</span>)
18
+
19
+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>]
20
+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:spliced</span>
21
+
22
+ <span class="ruby-comment cmt"># Add data to tracks</span>
23
+ <span class="ruby-identifier">utr5</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'utr'</span>, <span class="ruby-value str">'100..150'</span>)
24
+ <span class="ruby-identifier">cds</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'cds'</span>, <span class="ruby-value str">'join(150..225, 250..275, 310..330)'</span>)
25
+ <span class="ruby-identifier">utr3</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'utr'</span>, <span class="ruby-value str">'330..375'</span>)
26
+
27
+ <span class="ruby-identifier">transcript</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'transcript'</span>, <span class="ruby-value str">'join(100..225, 250..275, 310..375)'</span>, [], <span class="ruby-keyword kw">nil</span>, [<span class="ruby-identifier">utr5</span>, <span class="ruby-identifier">cds</span>, <span class="ruby-identifier">utr3</span>])
28
+
29
+ <span class="ruby-identifier">transcript_graphic</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">transcript</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'my_transcript'</span>)
30
+ <span class="ruby-identifier">transcript_graphic</span>.<span class="ruby-identifier">glyph</span> = { <span class="ruby-value str">'utr'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:line</span>, <span class="ruby-value str">'cds'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:spliced</span> }
31
+
32
+ <span class="ruby-comment cmt"># And draw</span>
33
+ <span class="ruby-identifier">output_file</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@method_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'.png'</span>
34
+ <span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
35
+
36
+ <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
37
+
38
+ <span class="ruby-identifier">system</span>(<span class="ruby-value str">&quot;display &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;&amp; sleep 2 &amp;&amp; kill $!&quot;</span>)
39
+ <span class="ruby-keyword kw">end</span></pre>
40
+ </body>
41
+ </html>
@@ -0,0 +1,36 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
7
+ <head>
8
+ <title>test_feature_specific_colouring (TestPanel)</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 test/unit/test_draw.rb, line 184</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_feature_specific_colouring</span>
15
+ <span class="ruby-identifier">my_panel</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">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">375</span>, <span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">100</span><span class="ruby-operator">..</span><span class="ruby-value">370</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">600</span>)
16
+
17
+ <span class="ruby-identifier">track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'mrna'</span>)
18
+
19
+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>]
20
+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:spliced</span>
21
+
22
+ <span class="ruby-comment cmt"># Add data to tracks</span>
23
+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'cds'</span>, <span class="ruby-value str">'join(100..200, 225..350)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'red_spliced'</span>)
24
+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'cds'</span>, <span class="ruby-value str">'join(100..200, 225..350)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'green_spliced'</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">0</span>])
25
+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'cds'</span>, <span class="ruby-value str">'join(100..200, 225..350)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'blue_generic'</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>])
26
+
27
+ <span class="ruby-comment cmt"># And draw</span>
28
+ <span class="ruby-identifier">output_file</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@method_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'.png'</span>
29
+ <span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
30
+
31
+ <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
32
+
33
+ <span class="ruby-identifier">system</span>(<span class="ruby-value str">&quot;display &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;&amp; sleep 2 &amp;&amp; kill $!&quot;</span>)
34
+ <span class="ruby-keyword kw">end</span></pre>
35
+ </body>
36
+ </html>
@@ -0,0 +1,20 @@
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>teardown (TestPanel)</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 test/unit/test_draw.rb, line 206</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">teardown</span>
15
+ <span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-constant">File</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">p</span>)
17
+ <span class="ruby-keyword kw">end</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
@@ -0,0 +1,26 @@
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">
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+
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+ <html>
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+ <head>
8
+ <title>test_panel_creation (TestPanel)</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">
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+ <pre><span class="ruby-comment cmt"># File test/unit/test_creation.rb, line 5</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_panel_creation</span>
15
+ <span class="ruby-identifier">panel</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">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1000</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">500</span>, <span class="ruby-identifier">:clickable</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>,
16
+ <span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">1000</span>)
17
+ <span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">1000</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">length</span>)
18
+ <span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">500</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>)
19
+ <span class="ruby-identifier">assert_equal</span>(<span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">clickable</span>)
20
+ <span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>)
21
+ <span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">1000</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>)
22
+ <span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">1000</span><span class="ruby-operator">/</span><span class="ruby-value">500</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>)
23
+ <span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">tracks</span>.<span class="ruby-identifier">length</span>)
24
+ <span class="ruby-keyword kw">end</span></pre>
25
+ </body>
26
+ </html>
@@ -0,0 +1,21 @@
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>test_panel_creation_out_of_boundaries (TestPanel)</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 test/unit/test_creation.rb, line 17</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_panel_creation_out_of_boundaries</span>
15
+ <span class="ruby-identifier">panel</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">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1000</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">500</span>, <span class="ruby-identifier">:clickable</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span>,
16
+ <span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">-7</span><span class="ruby-operator">..</span><span class="ruby-value">5000</span>)
17
+ <span class="ruby-identifier">assert_same</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>)
18
+ <span class="ruby-identifier">assert_same</span>(<span class="ruby-value">1000</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>)
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
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+ </html>
@@ -0,0 +1,152 @@
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+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ 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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+
6
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
8
+ <title>Class: TestRuler</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
+
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+ function popupCode( url ) {
16
+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
17
+ }
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+
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+ function toggleCode( id ) {
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+ 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
+ }
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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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+
48
+
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+ <div id="classHeader">
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+ <table class="header-table">
51
+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
53
+ <td class="class-name-in-header">TestRuler</td>
54
+ </tr>
55
+ <tr class="top-aligned-row">
56
+ <td><strong>In:</strong></td>
57
+ <td>
58
+ <a href="../files/test/unit/test_creation_rb.html">
59
+ test/unit/test_creation.rb
60
+ </a>
61
+ <br />
62
+ </td>
63
+ </tr>
64
+
65
+ <tr class="top-aligned-row">
66
+ <td><strong>Parent:</strong></td>
67
+ <td>
68
+ Test::Unit::TestCase
69
+ </td>
70
+ </tr>
71
+ </table>
72
+ </div>
73
+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+
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+
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+ </div>
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+
85
+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
87
+
88
+ <div class="name-list">
89
+ <a href="#M000014">test_drawing</a>&nbsp;&nbsp;
90
+ <a href="#M000013">test_scaling_factor</a>&nbsp;&nbsp;
91
+ </div>
92
+ </div>
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+
94
+ </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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+ <div id="methods">
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+ <h3 class="section-bar">Public Instance methods</h3>
111
+
112
+ <div id="method-M000014" class="method-detail">
113
+ <a name="M000014"></a>
114
+
115
+ <div class="method-heading">
116
+ <a href="TestRuler.src/M000014.html" target="Code" class="method-signature"
117
+ onclick="popupCode('TestRuler.src/M000014.html');return false;">
118
+ <span class="method-name">test_drawing</span><span class="method-args">()</span>
119
+ </a>
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+ </div>
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+
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+ <div class="method-description">
123
+ </div>
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+ </div>
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+
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+ <div id="method-M000013" class="method-detail">
127
+ <a name="M000013"></a>
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+
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+ <div class="method-heading">
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+ <a href="TestRuler.src/M000013.html" target="Code" class="method-signature"
131
+ onclick="popupCode('TestRuler.src/M000013.html');return false;">
132
+ <span class="method-name">test_scaling_factor</span><span class="method-args">()</span>
133
+ </a>
134
+ </div>
135
+
136
+ <div class="method-description">
137
+ </div>
138
+ </div>
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+
140
+
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+ </div>
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+
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+
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+ </div>
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+
146
+
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+ <div id="validator-badges">
148
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>