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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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
8
+ <title>draw (Bio::Graphics::Feature)</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/feature.rb, line 113</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
15
+ <span class="ruby-identifier">feature_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_destination</span>)
16
+
17
+ <span class="ruby-comment cmt"># Move the feature drawing down based on track it's in and the number</span>
18
+ <span class="ruby-comment cmt"># of times is has to be bumped</span>
19
+ <span class="ruby-identifier">row</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">find_row</span>
20
+
21
+ <span class="ruby-ivar">@vertical_offset</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</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">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</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">FEATURE_V_DISTANCE</span>
22
+ <span class="ruby-ivar">@vertical_offset</span> <span class="ruby-operator">+=</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">FEATURE_HEIGHT</span><span class="ruby-operator">+</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">FEATURE_V_DISTANCE</span>)<span class="ruby-operator">*</span><span class="ruby-identifier">row</span>
23
+
24
+ <span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-value">0</span>, <span class="ruby-ivar">@vertical_offset</span>)
25
+
26
+ <span class="ruby-comment cmt"># Let the subfeatures do the drawing.</span>
27
+ <span class="ruby-ivar">@subfeatures</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">subfeature</span><span class="ruby-operator">|</span>
28
+ <span class="ruby-identifier">subfeature</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">feature_context</span>)
29
+ <span class="ruby-keyword kw">end</span>
30
+
31
+ <span class="ruby-ivar">@left_pixel_of_feature</span> = <span class="ruby-ivar">@left_pixel_of_subfeatures</span>.<span class="ruby-identifier">min</span>
32
+ <span class="ruby-ivar">@right_pixel_of_feature</span> = <span class="ruby-ivar">@right_pixel_of_subfeatures</span>.<span class="ruby-identifier">max</span>
33
+
34
+ <span class="ruby-comment cmt"># Add the label for the feature</span>
35
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">show_label</span>
36
+ <span class="ruby-identifier">pango_layout</span> = <span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">create_pango_layout</span>
37
+ <span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">text</span> = <span class="ruby-ivar">@label</span>
38
+ <span class="ruby-identifier">fdesc</span> = <span class="ruby-constant">Pango</span><span class="ruby-operator">::</span><span class="ruby-constant">FontDescription</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'Sans Serif'</span>)
39
+ <span class="ruby-identifier">fdesc</span>.<span class="ruby-identifier">set_size</span>(<span class="ruby-value">8</span> <span class="ruby-operator">*</span> <span class="ruby-constant">Pango</span><span class="ruby-operator">::</span><span class="ruby-constant">SCALE</span>)
40
+ <span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">font_description</span> = <span class="ruby-identifier">fdesc</span>
41
+
42
+ <span class="ruby-identifier">text_range</span> = <span class="ruby-ivar">@start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span>(<span class="ruby-ivar">@start</span>.<span class="ruby-identifier">floor</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">pixel_size</span>[<span class="ruby-value">0</span>]<span class="ruby-operator">*</span><span class="ruby-ivar">@track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>)
43
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>].<span class="ruby-identifier">nil?</span>
44
+ <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
45
+ <span class="ruby-keyword kw">end</span>
46
+ <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">text_range</span>)
47
+ <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">text_range</span>)
48
+ <span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-ivar">@left_pixel_of_feature</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">TRACK_HEADER_HEIGHT</span>)
49
+ <span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
50
+ <span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">show_pango_layout</span>(<span class="ruby-identifier">pango_layout</span>)
51
+ <span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-ivar">@colour</span>)
52
+ <span class="ruby-keyword kw">end</span>
53
+
54
+
55
+ <span class="ruby-comment cmt"># And add the region to the image map</span>
56
+ <span class="ruby-comment cmt"># Comment: we have to add the vertical_offset and TRACK_HEADER_HEIGHT!</span>
57
+ <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">image_map</span>.<span class="ruby-identifier">add_element</span>(<span class="ruby-ivar">@left_pixel_of_feature</span>,
58
+ <span class="ruby-ivar">@vertical_offset</span>,
59
+ <span class="ruby-ivar">@right_pixel_of_feature</span>,
60
+ <span class="ruby-ivar">@vertical_offset</span> <span class="ruby-operator">+</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">FEATURE_HEIGHT</span>,
61
+ <span class="ruby-ivar">@link</span>
62
+ )
63
+ <span class="ruby-keyword kw">end</span></pre>
64
+ </body>
65
+ </html>
@@ -0,0 +1,55 @@
1
+ <?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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+
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+ <html>
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+ <head>
8
+ <title>find_row (Bio::Graphics::Feature)</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/feature.rb, line 171</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">find_row</span>
15
+ <span class="ruby-identifier">row_found</span> = <span class="ruby-keyword kw">false</span>
16
+
17
+ <span class="ruby-comment cmt"># We've got to find out what row to draw the feature on. If two </span>
18
+ <span class="ruby-comment cmt"># features overlap, one of them has to be 'bumped' down. So we'll</span>
19
+ <span class="ruby-comment cmt"># first try to draw a new feature at the top of the track. If</span>
20
+ <span class="ruby-comment cmt"># it however would overlap with another one, we'll bump it down</span>
21
+ <span class="ruby-comment cmt"># to the next row.</span>
22
+ <span class="ruby-identifier">feature_range</span> = (<span class="ruby-ivar">@start</span>.<span class="ruby-identifier">floor</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span><span class="ruby-operator">..</span><span class="ruby-ivar">@stop</span>.<span class="ruby-identifier">ceil</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>)
23
+ <span class="ruby-identifier">row</span> = <span class="ruby-value">1</span>
24
+ <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
25
+ <span class="ruby-keyword kw">until</span> <span class="ruby-identifier">row_found</span>
26
+ <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
27
+ <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">covered</span><span class="ruby-operator">|</span>
28
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">covered</span>.<span class="ruby-identifier">first</span>) <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">covered</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">first</span>)
29
+ <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</span>
30
+ <span class="ruby-keyword kw">end</span>
31
+ <span class="ruby-keyword kw">end</span>
32
+ <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>].<span class="ruby-identifier">nil?</span> <span class="ruby-comment cmt">#Still have to check if there is no label there.</span>
33
+ <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">covered</span><span class="ruby-operator">|</span>
34
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">covered</span>.<span class="ruby-identifier">first</span>) <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">covered</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">first</span>)
35
+ <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</span>
36
+ <span class="ruby-keyword kw">end</span>
37
+ <span class="ruby-keyword kw">end</span>
38
+ <span class="ruby-keyword kw">end</span>
39
+ <span class="ruby-keyword kw">end</span>
40
+
41
+ <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">row_available</span>
42
+ <span class="ruby-identifier">row</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
43
+ <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
44
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># We've found the place where to draw the feature.</span>
45
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
46
+ <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
47
+ <span class="ruby-keyword kw">end</span>
48
+ <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">feature_range</span>)
49
+ <span class="ruby-identifier">row_found</span> = <span class="ruby-keyword kw">true</span>
50
+ <span class="ruby-keyword kw">end</span>
51
+ <span class="ruby-keyword kw">end</span>
52
+ <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">row</span>
53
+ <span class="ruby-keyword kw">end</span></pre>
54
+ </body>
55
+ </html>
@@ -0,0 +1,348 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
+ <head>
8
+ <title>Class: Bio::Graphics::Feature::SubFeature</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
15
+ function popupCode( url ) {
16
+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
17
+ }
18
+
19
+ function toggleCode( id ) {
20
+ if ( document.getElementById )
21
+ elem = document.getElementById( id );
22
+ else if ( document.all )
23
+ elem = eval( "document.all." + id );
24
+ else
25
+ return false;
26
+
27
+ elemStyle = elem.style;
28
+
29
+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
31
+ } else {
32
+ elemStyle.display = "none"
33
+ }
34
+
35
+ return true;
36
+ }
37
+
38
+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
40
+
41
+ // ]]>
42
+ </script>
43
+
44
+ </head>
45
+ <body>
46
+
47
+
48
+
49
+ <div id="classHeader">
50
+ <table class="header-table">
51
+ <tr class="top-aligned-row">
52
+ <td><strong>Class</strong></td>
53
+ <td class="class-name-in-header">Bio::Graphics::Feature::SubFeature</td>
54
+ </tr>
55
+ <tr class="top-aligned-row">
56
+ <td><strong>In:</strong></td>
57
+ <td>
58
+ <a href="../../../../files/lib/bio/graphics/subfeature_rb.html">
59
+ lib/bio/graphics/subfeature.rb
60
+ </a>
61
+ <br />
62
+ </td>
63
+ </tr>
64
+
65
+ <tr class="top-aligned-row">
66
+ <td><strong>Parent:</strong></td>
67
+ <td>
68
+ Object
69
+ </td>
70
+ </tr>
71
+ </table>
72
+ </div>
73
+ <!-- banner header -->
74
+
75
+ <div id="bodyContent">
76
+
77
+
78
+
79
+ <div id="contextContent">
80
+
81
+ <div id="description">
82
+ <p>
83
+ TODO: Documentation for <a href="SubFeature.html">SubFeature</a>
84
+ </p>
85
+
86
+ </div>
87
+
88
+
89
+ </div>
90
+
91
+ <div id="method-list">
92
+ <h3 class="section-bar">Methods</h3>
93
+
94
+ <div class="name-list">
95
+ <a href="#M000026">draw</a>&nbsp;&nbsp;
96
+ <a href="#M000025">new</a>&nbsp;&nbsp;
97
+ </div>
98
+ </div>
99
+
100
+ </div>
101
+
102
+
103
+ <!-- if includes -->
104
+
105
+ <div id="section">
106
+
107
+
108
+
109
+ <div id="aliases-list">
110
+ <h3 class="section-bar">External Aliases</h3>
111
+
112
+ <div class="name-list">
113
+ <table summary="aliases">
114
+ <tr class="top-aligned-row context-row">
115
+ <td class="context-item-name">label</td>
116
+ <td>-&gt;</td>
117
+ <td class="context-item-value">name</td>
118
+ </tr>
119
+ <tr class="top-aligned-row context-row">
120
+ <td class="context-item-name">locations</td>
121
+ <td>-&gt;</td>
122
+ <td class="context-item-value">location</td>
123
+ </tr>
124
+ </table>
125
+ </div>
126
+ </div>
127
+
128
+
129
+ <div id="attribute-list">
130
+ <h3 class="section-bar">Attributes</h3>
131
+
132
+ <div class="name-list">
133
+ <table>
134
+ <tr class="top-aligned-row context-row">
135
+ <td class="context-item-name">chopped_at_start</td>
136
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
137
+ <td class="context-item-desc">
138
+ Is the first subfeature incomplete?
139
+
140
+ </td>
141
+ </tr>
142
+ <tr class="top-aligned-row context-row">
143
+ <td class="context-item-name">chopped_at_stop</td>
144
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
145
+ <td class="context-item-desc">
146
+ Is the last subfeature incomplete?
147
+
148
+ </td>
149
+ </tr>
150
+ <tr class="top-aligned-row context-row">
151
+ <td class="context-item-name">colour</td>
152
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
153
+ <td class="context-item-desc">
154
+ The colour to use to <a href="SubFeature.html#M000026">draw</a> this
155
+ (sub)feature
156
+
157
+ </td>
158
+ </tr>
159
+ <tr class="top-aligned-row context-row">
160
+ <td class="context-item-name">feature</td>
161
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
162
+ <td class="context-item-desc">
163
+ The feature that this subfeature belongs to
164
+
165
+ </td>
166
+ </tr>
167
+ <tr class="top-aligned-row context-row">
168
+ <td class="context-item-name">feature_object</td>
169
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
170
+ <td class="context-item-desc">
171
+ The bioruby <a href="../../Feature.html">Bio::Feature</a> object
172
+
173
+ </td>
174
+ </tr>
175
+ <tr class="top-aligned-row context-row">
176
+ <td class="context-item-name">glyph</td>
177
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
178
+ <td class="context-item-desc">
179
+ The glyph to use to <a href="SubFeature.html#M000026">draw</a> this
180
+ (sub)feature
181
+
182
+ </td>
183
+ </tr>
184
+ <tr class="top-aligned-row context-row">
185
+ <td class="context-item-name">hidden_subfeatures_at_start</td>
186
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
187
+ <td class="context-item-desc">
188
+ Are there subfeatures out of view at the left side of the picture?
189
+
190
+ </td>
191
+ </tr>
192
+ <tr class="top-aligned-row context-row">
193
+ <td class="context-item-name">hidden_subfeatures_at_stop</td>
194
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
195
+ <td class="context-item-desc">
196
+ Are there subfeatures out of view at the right side of the picture?
197
+
198
+ </td>
199
+ </tr>
200
+ <tr class="top-aligned-row context-row">
201
+ <td class="context-item-name">label</td>
202
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
203
+ <td class="context-item-desc">
204
+ The label of the feature
205
+
206
+ </td>
207
+ </tr>
208
+ <tr class="top-aligned-row context-row">
209
+ <td class="context-item-name">locations</td>
210
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
211
+ <td class="context-item-desc">
212
+ The locations of the feature (which is a Bio::Locations object)
213
+
214
+ </td>
215
+ </tr>
216
+ <tr class="top-aligned-row context-row">
217
+ <td class="context-item-name">pixel_range_collection</td>
218
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
219
+ <td class="context-item-desc">
220
+ The array keeping the pixel ranges for the sub-features. Unspliced features
221
+ will just have one element, while spliced features will have more than one.
222
+
223
+ </td>
224
+ </tr>
225
+ <tr class="top-aligned-row context-row">
226
+ <td class="context-item-name">start</td>
227
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
228
+ <td class="context-item-desc">
229
+ The start position of the feature (in bp)
230
+
231
+ </td>
232
+ </tr>
233
+ <tr class="top-aligned-row context-row">
234
+ <td class="context-item-name">stop</td>
235
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
236
+ <td class="context-item-desc">
237
+ The stop position of the feature (in bp)
238
+
239
+ </td>
240
+ </tr>
241
+ <tr class="top-aligned-row context-row">
242
+ <td class="context-item-name">strand</td>
243
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
244
+ <td class="context-item-desc">
245
+ The strand of the feature
246
+
247
+ </td>
248
+ </tr>
249
+ </table>
250
+ </div>
251
+ </div>
252
+
253
+
254
+
255
+ <!-- if method_list -->
256
+ <div id="methods">
257
+ <h3 class="section-bar">Public Class methods</h3>
258
+
259
+ <div id="method-M000025" class="method-detail">
260
+ <a name="M000025"></a>
261
+
262
+ <div class="method-heading">
263
+ <a href="SubFeature.src/M000025.html" target="Code" class="method-signature"
264
+ onclick="popupCode('SubFeature.src/M000025.html');return false;">
265
+ <span class="method-name">new</span><span class="method-args">(feature, feature_object, glyph = feature.glyph, colour = feature.colour)</span>
266
+ </a>
267
+ </div>
268
+
269
+ <div class="method-description">
270
+ <p>
271
+ !!Not to be used directly.
272
+ </p>
273
+ <hr size="1"></hr><p>
274
+ <b>Arguments</b>:
275
+ </p>
276
+ <ul>
277
+ <li><em>feature</em> (required) :: <a
278
+ href="../Feature.html">Bio::Graphics::Feature</a> object that this
279
+ subfeature belongs to
280
+
281
+ </li>
282
+ <li><em>feature</em> <em>object</em> (required) :: A <a
283
+ href="../../Feature.html">Bio::Feature</a> object (see bioruby)
284
+
285
+ </li>
286
+ <li><em>glyph</em> :: <a href="../Glyph.html">Glyph</a> to use. Default = glyph
287
+ of the track
288
+
289
+ </li>
290
+ <li><em>colour</em> :: Colour. Default = colour of the track
291
+
292
+ </li>
293
+ </ul>
294
+ <table>
295
+ <tr><td valign="top"><b>Returns</b>:</td><td><a href="SubFeature.html">Bio::Graphics::Feature::SubFeature</a> object
296
+
297
+ </td></tr>
298
+ </table>
299
+ </div>
300
+ </div>
301
+
302
+ <h3 class="section-bar">Public Instance methods</h3>
303
+
304
+ <div id="method-M000026" class="method-detail">
305
+ <a name="M000026"></a>
306
+
307
+ <div class="method-heading">
308
+ <a href="SubFeature.src/M000026.html" target="Code" class="method-signature"
309
+ onclick="popupCode('SubFeature.src/M000026.html');return false;">
310
+ <span class="method-name">draw</span><span class="method-args">(feature_context)</span>
311
+ </a>
312
+ </div>
313
+
314
+ <div class="method-description">
315
+ <p>
316
+ Adds the subfeature to the track cairo context. This method should not be
317
+ used directly by the user, but is called by <a
318
+ href="SubFeature.html#M000026">Bio::Graphics::Feature::SubFeature.draw</a>
319
+ </p>
320
+ <hr size="1"></hr><p>
321
+ <b>Arguments</b>:
322
+ </p>
323
+ <ul>
324
+ <li><em>track_drawing</em> (required) :: the track cairo object
325
+
326
+ </li>
327
+ </ul>
328
+ <table>
329
+ <tr><td valign="top"><b>Returns</b>:</td><td>FIXME: I don&#8216;t know
330
+
331
+ </td></tr>
332
+ </table>
333
+ </div>
334
+ </div>
335
+
336
+
337
+ </div>
338
+
339
+
340
+ </div>
341
+
342
+
343
+ <div id="validator-badges">
344
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
345
+ </div>
346
+
347
+ </body>
348
+ </html>