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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data/doc/classes/Bio/Feature.src/M000014.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html>
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+ <head>
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+ <title>each_subfeature (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 53</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_subfeature</span>(<span class="ruby-identifier">arg</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <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">x</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">arg</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">arg</span>
17
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">x</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Feature.src/M000016.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ <html>
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+ <head>
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+ <title>each_qualifier (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 65</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_qualifier</span>(<span class="ruby-identifier">arg</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <span class="ruby-ivar">@qualifiers</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">arg</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">qualifier</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">arg</span>
17
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">x</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Feature.src/M000034.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html>
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+ <head>
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+ <title>new (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 3</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">feature</span>, <span class="ruby-identifier">position</span>, <span class="ruby-identifier">qualifiers</span> = [], <span class="ruby-identifier">parent</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">subfeatures</span> = [])
15
+ <span class="ruby-ivar">@feature</span>, <span class="ruby-ivar">@position</span>, <span class="ruby-ivar">@qualifiers</span>, <span class="ruby-ivar">@parent</span> = <span class="ruby-identifier">feature</span>, <span class="ruby-identifier">position</span>, <span class="ruby-identifier">qualifiers</span>, <span class="ruby-identifier">parent</span>
16
+ <span class="ruby-ivar">@subfeatures</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
17
+ <span class="ruby-identifier">subfeatures</span>.<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">sf</span><span class="ruby-operator">|</span> <span class="ruby-identifier">add_subfeature</span>(<span class="ruby-identifier">sf</span>) }
18
+ <span class="ruby-ivar">@locations</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@position</span>)
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
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+ </html>
data/doc/classes/Bio/Feature.src/M000035.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>add_subfeature (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 32</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_subfeature</span>(<span class="ruby-identifier">sf</span>)
15
+ <span class="ruby-identifier">sf</span>.<span class="ruby-identifier">parent</span> = <span class="ruby-keyword kw">self</span>
16
+ <span class="ruby-ivar">@subfeatures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">sf</span>)
17
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
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+ </html>
data/doc/classes/Bio/Feature.src/M000036.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <html>
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+ <head>
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+ <title>add_qualifier (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 43</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_qualifier</span>(<span class="ruby-identifier">a</span>)
15
+ <span class="ruby-ivar">@qualifiers</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">a</span>) <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Qualifier</span>
16
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
17
+ <span class="ruby-keyword kw">end</span></pre>
18
+ </body>
19
+ </html>
data/doc/classes/Bio/Feature.src/M000038.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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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>each_subfeature (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 53</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_subfeature</span>(<span class="ruby-identifier">arg</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <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">x</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">arg</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">arg</span>
17
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">x</span>
18
+ <span class="ruby-keyword kw">end</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Feature.src/M000040.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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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>each_qualifier (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 65</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_qualifier</span>(<span class="ruby-identifier">arg</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <span class="ruby-ivar">@qualifiers</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">arg</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">qualifier</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">arg</span>
17
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">x</span>
18
+ <span class="ruby-keyword kw">end</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Feature.src/M000042.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>new (Bio::Feature)</title>
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+ <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/feature.rb, line 3</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">feature</span>, <span class="ruby-identifier">position</span>, <span class="ruby-identifier">qualifiers</span> = [], <span class="ruby-identifier">parent</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">subfeatures</span> = [])
15
+ <span class="ruby-ivar">@feature</span>, <span class="ruby-ivar">@position</span>, <span class="ruby-ivar">@qualifiers</span>, <span class="ruby-ivar">@parent</span> = <span class="ruby-identifier">feature</span>, <span class="ruby-identifier">position</span>, <span class="ruby-identifier">qualifiers</span>, <span class="ruby-identifier">parent</span>
16
+ <span class="ruby-ivar">@subfeatures</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
17
+ <span class="ruby-identifier">subfeatures</span>.<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">sf</span><span class="ruby-operator">|</span> <span class="ruby-identifier">add_subfeature</span>(<span class="ruby-identifier">sf</span>) }
18
+ <span class="ruby-ivar">@locations</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@position</span>)
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Feature.src/M000043.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>add_subfeature (Bio::Feature)</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 lib/feature.rb, line 32</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_subfeature</span>(<span class="ruby-identifier">sf</span>)
15
+ <span class="ruby-identifier">sf</span>.<span class="ruby-identifier">parent</span> = <span class="ruby-keyword kw">self</span>
16
+ <span class="ruby-ivar">@subfeatures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">sf</span>)
17
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
data/doc/classes/Bio/Feature.src/M000044.html ADDED
@@ -0,0 +1,21 @@
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>new (Bio::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/feature.rb, line 3</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">feature</span>, <span class="ruby-identifier">position</span>, <span class="ruby-identifier">qualifiers</span> = [], <span class="ruby-identifier">parent</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">subfeatures</span> = [])
15
+ <span class="ruby-ivar">@feature</span>, <span class="ruby-ivar">@position</span>, <span class="ruby-ivar">@qualifiers</span>, <span class="ruby-ivar">@parent</span> = <span class="ruby-identifier">feature</span>, <span class="ruby-identifier">position</span>, <span class="ruby-identifier">qualifiers</span>, <span class="ruby-identifier">parent</span>
16
+ <span class="ruby-ivar">@subfeatures</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
17
+ <span class="ruby-identifier">subfeatures</span>.<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">sf</span><span class="ruby-operator">|</span> <span class="ruby-identifier">add_subfeature</span>(<span class="ruby-identifier">sf</span>) }
18
+ <span class="ruby-ivar">@locations</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@position</span>)
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Feature.src/M000045.html ADDED
@@ -0,0 +1,20 @@
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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>add_subfeature (Bio::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/feature.rb, line 32</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_subfeature</span>(<span class="ruby-identifier">sf</span>)
15
+ <span class="ruby-identifier">sf</span>.<span class="ruby-identifier">parent</span> = <span class="ruby-keyword kw">self</span>
16
+ <span class="ruby-ivar">@subfeatures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">sf</span>)
17
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
data/doc/classes/Bio/Feature.src/M000046.html ADDED
@@ -0,0 +1,19 @@
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>add_qualifier (Bio::Feature)</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" />
11
+ </head>
12
+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 43</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_qualifier</span>(<span class="ruby-identifier">a</span>)
15
+ <span class="ruby-ivar">@qualifiers</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">a</span>) <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Qualifier</span>
16
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
17
+ <span class="ruby-keyword kw">end</span></pre>
18
+ </body>
19
+ </html>
data/doc/classes/Bio/Feature.src/M000048.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>each_subfeature (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 53</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_subfeature</span>(<span class="ruby-identifier">arg</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <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">x</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">arg</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">arg</span>
17
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">x</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Feature.src/M000050.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>each_qualifier (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 65</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_qualifier</span>(<span class="ruby-identifier">arg</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <span class="ruby-ivar">@qualifiers</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">arg</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">qualifier</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">arg</span>
17
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">x</span>
18
+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Feature.src/M000074.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>new (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 3</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">feature</span>, <span class="ruby-identifier">position</span>, <span class="ruby-identifier">qualifiers</span> = [], <span class="ruby-identifier">parent</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">subfeatures</span> = [])
15
+ <span class="ruby-ivar">@feature</span>, <span class="ruby-ivar">@position</span>, <span class="ruby-ivar">@qualifiers</span>, <span class="ruby-ivar">@parent</span> = <span class="ruby-identifier">feature</span>, <span class="ruby-identifier">position</span>, <span class="ruby-identifier">qualifiers</span>, <span class="ruby-identifier">parent</span>
16
+ <span class="ruby-ivar">@subfeatures</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
17
+ <span class="ruby-identifier">subfeatures</span>.<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">sf</span><span class="ruby-operator">|</span> <span class="ruby-identifier">add_subfeature</span>(<span class="ruby-identifier">sf</span>) }
18
+ <span class="ruby-ivar">@locations</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@position</span>)
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Feature.src/M000075.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>add_subfeature (Bio::Feature)</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 lib/feature.rb, line 32</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_subfeature</span>(<span class="ruby-identifier">sf</span>)
15
+ <span class="ruby-identifier">sf</span>.<span class="ruby-identifier">parent</span> = <span class="ruby-keyword kw">self</span>
16
+ <span class="ruby-ivar">@subfeatures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">sf</span>)
17
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
data/doc/classes/Bio/Feature.src/M000076.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>add_qualifier (Bio::Feature)</title>
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+ <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>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 43</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_qualifier</span>(<span class="ruby-identifier">a</span>)
15
+ <span class="ruby-ivar">@qualifiers</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">a</span>) <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Qualifier</span>
16
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
17
+ <span class="ruby-keyword kw">end</span></pre>
18
+ </body>
19
+ </html>
data/doc/classes/Bio/Feature.src/M000078.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>each_subfeature (Bio::Feature)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
12
+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 53</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_subfeature</span>(<span class="ruby-identifier">arg</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <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">x</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">arg</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">arg</span>
17
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">x</span>
18
+ <span class="ruby-keyword kw">end</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Feature.src/M000080.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>each_qualifier (Bio::Feature)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/feature.rb, line 65</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_qualifier</span>(<span class="ruby-identifier">arg</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <span class="ruby-ivar">@qualifiers</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">arg</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">qualifier</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">arg</span>
17
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">x</span>
18
+ <span class="ruby-keyword kw">end</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Feature/Qualifier.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Class: Bio::Feature::Qualifier</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
15
+ 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 ) {
20
+ if ( document.getElementById )
21
+ elem = document.getElementById( id );
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+ else if ( document.all )
23
+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
27
+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
31
+ } else {
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+ elemStyle.display = "none"
33
+ }
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+
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+ return true;
36
+ }
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+
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+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
41
+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
46
+
47
+
48
+
49
+ <div id="classHeader">
50
+ <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">Bio::Feature::Qualifier</td>
54
+ </tr>
55
+ <tr class="top-aligned-row">
56
+ <td><strong>In:</strong></td>
57
+ <td>
58
+ <a href="../../../files/lib/feature_rb.html">
59
+ lib/feature.rb
60
+ </a>
61
+ <br />
62
+ </td>
63
+ </tr>
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+
65
+ <tr class="top-aligned-row">
66
+ <td><strong>Parent:</strong></td>
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+ <td>
68
+ Object
69
+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
79
+ <div id="contextContent">
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+
81
+ <div id="description">
82
+ <p>
83
+ Container for qualifier-value pairs for sequence features.
84
+ </p>
85
+
86
+ </div>
87
+
88
+
89
+ </div>
90
+
91
+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000051">new</a>&nbsp;&nbsp;
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+ </div>
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+ </div>
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+
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+ <div id="attribute-list">
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
114
+ <table>
115
+ <tr class="top-aligned-row context-row">
116
+ <td class="context-item-name">qualifier</td>
117
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
118
+ <td class="context-item-desc">
119
+ <a href="Qualifier.html">Qualifier</a> name in <a
120
+ href="../../String.html">String</a>
121
+
122
+ </td>
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+ </tr>
124
+ <tr class="top-aligned-row context-row">
125
+ <td class="context-item-name">value</td>
126
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
127
+ <td class="context-item-desc">
128
+ <a href="Qualifier.html">Qualifier</a> value in <a
129
+ href="../../String.html">String</a>
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+
131
+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+ </div>
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
142
+
143
+ <div id="method-M000051" class="method-detail">
144
+ <a name="M000051"></a>
145
+
146
+ <div class="method-heading">
147
+ <a href="Qualifier.src/M000051.html" target="Code" class="method-signature"
148
+ onclick="popupCode('Qualifier.src/M000051.html');return false;">
149
+ <span class="method-name">new</span><span class="method-args">(key, value)</span>
150
+ </a>
151
+ </div>
152
+
153
+ <div class="method-description">
154
+ <p>
155
+ Creates a <a href="Qualifier.html#M000051">new</a> <a
156
+ href="Qualifier.html">Bio::Feature::Qualifier</a> object
157
+ </p>
158
+ <p>
159
+ <b>Arguments</b>:
160
+ </p>
161
+ <ul>
162
+ <li>(required) <em>key</em>: key of the qualifier (e.g. &quot;gene&quot;)
163
+
164
+ </li>
165
+ <li>(required) <em>value</em>: value of the qualifier (e.g. &quot;CYP2D6&quot;)
166
+
167
+ </li>
168
+ </ul>
169
+ <table>
170
+ <tr><td valign="top"><b>Returns</b>:</td><td><a href="Qualifier.html">Bio::Feature::Qualifier</a> object
171
+
172
+ </td></tr>
173
+ </table>
174
+ </div>
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+ </div>
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+
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+
178
+ </div>
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
189
+ </html>