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/test/unit/test_subfeatures.rb ADDED
@@ -0,0 +1,17 @@
1
+ require 'test/unit'
2
+ require File.dirname(__FILE__) + '/../../lib/bio-graphics'
3
+
4
+ class TestSubFeature < Test::Unit::TestCase
5
+ def setup
6
+ @utr5 = Bio::Feature.new('utr', '100..150')
7
+ @cds = Bio::Feature.new('cds', 'join(150..225, 250..275, 310..330)')
8
+ @utr3 = Bio::Feature.new('utr', '330..375')
9
+ @transcript = Bio::Feature.new('transcript', 'join(100..150, 150..225, 250..275, 310..330, 330..375)', [], nil, [@utr5,@cds,@utr3])
10
+ end
11
+
12
+ def test_existence_subfeatures
13
+ assert_equal(3, @transcript.subfeatures.length)
14
+ end
15
+
16
+
17
+ end
metadata CHANGED
@@ -1,149 +1,426 @@
1
1
  --- !ruby/object:Gem::Specification
2
- rubygems_version: 0.9.0
3
- specification_version: 1
4
2
  name: bio-graphics
5
3
  version: !ruby/object:Gem::Version
6
- version: "1.2"
7
- date: 2007-10-18 00:00:00 +01:00
8
- summary: Library for visualizing genomic regions
9
- require_paths:
10
- - lib
11
- email: jan.aerts@bbsrc.ac.uk
12
- homepage: http://bio-graphics.rubyforge.org/
13
- rubyforge_project:
14
- description:
15
- autorequire: bio-graphics
16
- default_executable:
17
- bindir: bin
18
- has_rdoc: true
19
- required_ruby_version: !ruby/object:Gem::Version::Requirement
20
- requirements:
21
- - - ">"
22
- - !ruby/object:Gem::Version
23
- version: 0.0.0
24
- version:
4
+ version: "1.4"
25
5
  platform: ruby
26
- signing_key:
27
- cert_chain:
28
- post_install_message:
29
6
  authors:
30
7
  - Jan Aerts
8
+ autorequire: bio-graphics
9
+ bindir: bin
10
+ cert_chain: []
11
+
12
+ date: 2008-01-24 00:00:00 +00:00
13
+ default_executable:
14
+ dependencies:
15
+ - !ruby/object:Gem::Dependency
16
+ name: bio
17
+ version_requirement:
18
+ version_requirements: !ruby/object:Gem::Requirement
19
+ requirements:
20
+ - - ">="
21
+ - !ruby/object:Gem::Version
22
+ version: "1"
23
+ version:
24
+ description:
25
+ email: jan.aerts@bbsrc.ac.uk
26
+ executables: []
27
+
28
+ extensions: []
29
+
30
+ extra_rdoc_files: []
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+
31
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254
+ - doc/classes/Bio/Graphics/Glyph/Common.html
255
+ - doc/classes/Bio/Graphics/Glyph/Triangle.src
256
+ - doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html
257
+ - doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html
258
+ - doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html
259
+ - doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html
260
+ - doc/classes/Bio/Graphics/Glyph/Generic.src
261
+ - doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html
262
+ - doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html
263
+ - doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html
264
+ - doc/classes/Bio/Graphics/Glyph/LineWithHandles.src
265
+ - doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html
266
+ - doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html
267
+ - doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html
268
+ - doc/classes/Bio/Graphics/Glyph/Spliced.html
269
+ - doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html
270
+ - doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html
271
+ - doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src
272
+ - doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html
273
+ - doc/classes/Bio/Graphics/Glyph/DirectedBox.html
274
+ - doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src
275
+ - doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html
276
+ - doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html
277
+ - doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html
278
+ - doc/classes/Bio/Graphics/Glyph/Line.src
279
+ - doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html
280
+ - doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html
281
+ - doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html
282
+ - doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src
283
+ - doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html
284
+ - doc/classes/Bio/Graphics/Glyph/DirectedBox.src
285
+ - doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html
286
+ - doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html
287
+ - doc/classes/Bio/Graphics/Glyph/Common.src
288
+ - doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html
289
+ - doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html
290
+ - doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html
291
+ - doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html
292
+ - doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html
293
+ - doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html
294
+ - doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html
295
+ - doc/classes/Bio/Graphics/Glyph/Dot.html
296
+ - doc/classes/Bio/Graphics/Glyph/Triangle.html
297
+ - doc/classes/Bio/Graphics/Glyph/Generic.html
298
+ - doc/classes/Bio/Graphics/Glyph/Transcript.html
299
+ - doc/classes/Bio/Graphics/Glyph/Line.html
300
+ - doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html
301
+ - doc/classes/Bio/Graphics/Glyph/Dot.src
302
+ - doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html
303
+ - doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html
304
+ - doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html
305
+ - doc/classes/Bio/Graphics/Glyph/Spliced.src
306
+ - doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html
307
+ - doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html
308
+ - doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html
309
+ - doc/classes/Bio/Graphics/Glyph/LineWithHandles.html
310
+ - doc/classes/Bio/Graphics/Glyph/Box.html
311
+ - doc/classes/Bio/Feature.html
312
+ - doc/classes/Bio/Feature.src
313
+ - doc/classes/Bio/Feature.src/M000080.html
314
+ - doc/classes/Bio/Feature.src/M000038.html
315
+ - doc/classes/Bio/Feature.src/M000078.html
316
+ - doc/classes/Bio/Feature.src/M000043.html
317
+ - doc/classes/Bio/Feature.src/M000014.html
318
+ - doc/classes/Bio/Feature.src/M000050.html
319
+ - doc/classes/Bio/Feature.src/M000048.html
320
+ - doc/classes/Bio/Feature.src/M000046.html
321
+ - doc/classes/Bio/Feature.src/M000045.html
322
+ - doc/classes/Bio/Feature.src/M000010.html
323
+ - doc/classes/Bio/Feature.src/M000016.html
324
+ - doc/classes/Bio/Feature.src/M000034.html
325
+ - doc/classes/Bio/Feature.src/M000035.html
326
+ - doc/classes/Bio/Feature.src/M000074.html
327
+ - doc/classes/Bio/Feature.src/M000040.html
328
+ - doc/classes/Bio/Feature.src/M000012.html
329
+ - doc/classes/Bio/Feature.src/M000011.html
330
+ - doc/classes/Bio/Feature.src/M000042.html
331
+ - doc/classes/Bio/Feature.src/M000075.html
332
+ - doc/classes/Bio/Feature.src/M000076.html
333
+ - doc/classes/Bio/Feature.src/M000036.html
334
+ - doc/classes/Bio/Feature.src/M000044.html
335
+ - doc/classes/TestExtensions.html
336
+ - doc/classes/TestRuler.html
337
+ - doc/classes/TestCustomGlyph.src
338
+ - doc/classes/TestCustomGlyph.src/M000025.html
339
+ - doc/classes/TestImageMap.html
340
+ - doc/classes/TestRuler.src
341
+ - doc/classes/TestRuler.src/M000013.html
342
+ - doc/classes/TestRuler.src/M000014.html
343
+ - doc/classes/TestTrack.html
344
+ - doc/classes/TestSubFeature.src
345
+ - doc/classes/TestSubFeature.src/M000024.html
346
+ - doc/classes/TestSubFeature.src/M000023.html
347
+ - doc/classes/TestCustomGlyphInFile.src
348
+ - doc/classes/TestCustomGlyphInFile.src/M000028.html
349
+ - doc/classes/TestCustomGlyphInFile.src/M000026.html
350
+ - doc/classes/TestCustomGlyphInFile.src/M000027.html
351
+ - doc/classes/TestCustomGlyphInFile.html
352
+ - doc/classes/TestFeature.html
353
+ - doc/classes/TestCustomGlyph.html
354
+ - doc/fr_method_index.html
355
+ - doc/index.html
356
+ - doc/fr_file_index.html
111
357
  - lib/bio-graphics.rb
358
+ - lib/feature.rb
359
+ - lib/bio
112
360
  - lib/bio/graphics
113
- - lib/bio/graphics/panel.rb
114
- - lib/bio/graphics/ruler.rb
115
361
  - lib/bio/graphics/feature.rb
116
- - lib/bio/graphics/track.rb
117
362
  - lib/bio/graphics/image_map.rb
363
+ - lib/bio/graphics/glyphs
364
+ - lib/bio/graphics/glyphs/transcript.rb
365
+ - lib/bio/graphics/glyphs/directed_spliced.rb
366
+ - lib/bio/graphics/glyphs/dot.rb
367
+ - lib/bio/graphics/glyphs/generic.rb
368
+ - lib/bio/graphics/glyphs/common.rb
369
+ - lib/bio/graphics/glyphs/line.rb
370
+ - lib/bio/graphics/glyphs/box.rb
371
+ - lib/bio/graphics/glyphs/directed_generic.rb
372
+ - lib/bio/graphics/glyphs/line_with_handles.rb
373
+ - lib/bio/graphics/glyphs/directed_box.rb
374
+ - lib/bio/graphics/glyphs/triangle.rb
375
+ - lib/bio/graphics/glyphs/spliced.rb
376
+ - lib/bio/graphics/track.rb
377
+ - lib/bio/graphics/ruler.rb
378
+ - lib/bio/graphics/panel.rb
379
+ - lib/bio/graphics/subfeature.rb
380
+ - samples/glyph_showcase.rb
118
381
  - samples/arkdb_features.rb
382
+ - samples/protein_domains.rb
119
383
  - samples/data.txt
120
- - samples/glyph_showcase.rb
384
+ - samples/subfeatures.rb
121
385
  - test/unit
386
+ - test/unit/test_class_extensions.rb
387
+ - test/unit/custom_glyph_in_file.rb
388
+ - test/unit/data.txt
389
+ - test/unit/test_subfeatures.rb
390
+ - test/unit/test_custom_glyph.rb
391
+ - test/unit/test_imagemap.rb
392
+ - test/unit/test_draw.rb
122
393
  - test/unit/test_creation.rb
123
- - images/terms.svg
124
- - images/terms.png
125
- - images/glyph_showcase.png
126
394
  - images/example_labels.png
395
+ - images/terms.png
396
+ - images/terms.svg
127
397
  - images/example.png
128
- test_files: []
129
-
398
+ - images/glyph_showcase.png
399
+ has_rdoc: true
400
+ homepage: http://bio-graphics.rubyforge.org/
401
+ post_install_message:
130
402
  rdoc_options: []
131
403
 
132
- extra_rdoc_files: []
133
-
134
- executables: []
135
-
136
- extensions: []
137
-
404
+ require_paths:
405
+ - lib
406
+ required_ruby_version: !ruby/object:Gem::Requirement
407
+ requirements:
408
+ - - ">="
409
+ - !ruby/object:Gem::Version
410
+ version: "0"
411
+ version:
412
+ required_rubygems_version: !ruby/object:Gem::Requirement
413
+ requirements:
414
+ - - ">="
415
+ - !ruby/object:Gem::Version
416
+ version: "0"
417
+ version:
138
418
  requirements: []
139
419
 
140
- dependencies:
141
- - !ruby/object:Gem::Dependency
142
- name: bio
143
- version_requirement:
144
- version_requirements: !ruby/object:Gem::Version::Requirement
145
- requirements:
146
- - - ">="
147
- - !ruby/object:Gem::Version
148
- version: "1"
149
- version:
420
+ rubyforge_project:
421
+ rubygems_version: 0.9.5
422
+ signing_key:
423
+ specification_version: 2
424
+ summary: Library for visualizing genomic regions
425
+ test_files: []
426
+