bio-graphics 1.2 → 1.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
  305. data/doc/classes/Bio/Graphics/Panel.src/M000006.html +0 -19
  306. data/doc/classes/Bio/Graphics/Panel.src/M000007.html +0 -68
  307. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +0 -20
  308. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +0 -28
  309. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +0 -54
  310. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +0 -20
  311. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +0 -20
  312. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +0 -28
  313. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +0 -59
  314. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +0 -20
  315. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +0 -28
  316. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +0 -59
  317. data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +0 -26
  318. data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +0 -42
  319. data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +0 -52
  320. data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +0 -23
  321. data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +0 -43
  322. data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +0 -259
  323. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +0 -65
  324. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +0 -39
  325. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000013.html +0 -27
  326. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +0 -225
  327. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000015.html +0 -48
  328. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +0 -18
  329. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000013.html +0 -18
  330. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +0 -18
  331. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000016.html +0 -18
data/doc/classes/Bio/Features.src/M000072.html ADDED
@@ -0,0 +1,18 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>first (Bio::Features)</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 195</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">first</span>
15
+ <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">first</span>
16
+ <span class="ruby-keyword kw">end</span></pre>
17
+ </body>
18
+ </html>
data/doc/classes/Bio/Features.src/M000073.html ADDED
@@ -0,0 +1,18 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>last (Bio::Features)</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 200</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">last</span>
15
+ <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">last</span>
16
+ <span class="ruby-keyword kw">end</span></pre>
17
+ </body>
18
+ </html>
data/doc/classes/Bio/Graphics.html CHANGED
@@ -58,18 +58,6 @@
58
58
  <a href="../../files/lib/bio/graphics/panel_rb.html">
59
59
  lib/bio/graphics/panel.rb
60
60
  </a>
61
- <br />
62
- <a href="../../files/lib/bio/graphics/ruler_rb.html">
63
- lib/bio/graphics/ruler.rb
64
- </a>
65
- <br />
66
- <a href="../../files/lib/bio/graphics/feature_rb.html">
67
- lib/bio/graphics/feature.rb
68
- </a>
69
- <br />
70
- <a href="../../files/lib/bio/graphics/track_rb.html">
71
- lib/bio/graphics/track.rb
72
- </a>
73
61
  <br />
74
62
  </td>
75
63
  </tr>
@@ -134,30 +122,37 @@ Schematically:
134
122
  track1 = g.add_track('genes')
135
123
 
136
124
  # And put features in that track
137
- track1.add_feature('gene1',250,375)
138
- track1.add_feature('gene2',54,124)
139
- track1.add_feature('gene3',100,500)
125
+ track1.add_feature('gene1','250..375')
126
+ track1.add_feature('gene2','54..124')
127
+ track1.add_feature('gene3','100..500')
140
128
 
141
129
  # Add a second track (e.g. 'polymorphisms')
142
- track2 = g.add_track('polymorphisms',, false, 'red','triangle')
130
+ track2 = g.add_track('polymorphisms', false, [1,0,0], :triangle)
143
131
 
144
132
  # And put features on this one
145
- track2.add_feature('polymorphism 1',56,56)
146
- track2.add_feature('polymorphism 2',103,103)
133
+ track2.add_feature('polymorphism 1','56')
134
+ track2.add_feature('polymorphism 2','103')
147
135
 
148
136
  # Create the actual image as SVG text
149
137
  g.draw('my_picture.png')
150
138
  </pre>
151
- <h1>FUTURE PROSPECTS</h1>
139
+ <h1>NOTE ON ARGUMENTS</h1>
152
140
  <p>
153
- Any help from other developers is welcomed to work on these features:
141
+ As there can be an overwhelming number of arguments for some methods in <a
142
+ href="Graphics.html">Bio::Graphics</a>, any optional arguments have to be
143
+ provided as a hash. For example: the <a
144
+ href="Graphics/Track.html#M000022">Track#add_feature</a> method has only
145
+ one mandatory argument (the feature object) and several optional ones. This
146
+ is how you can use that method:
154
147
  </p>
155
- <ul>
156
- <li>Would be nice if this module would be easily accessible from any object
157
- that implements bioruby&#8216;s Bio::Map::ActsAsMap.
158
-
159
- </li>
160
- </ul>
148
+ <pre>
149
+ track.add_feature(my_feature_object,
150
+ :label =&gt; 'anonymous',
151
+ :link =&gt; 'http://www.google.com',
152
+ :glyph =&gt; :box,
153
+ :colour =&gt; [0,1,0]
154
+ )
155
+ </pre>
161
156
 
162
157
  </div>
163
158
 
@@ -175,7 +170,13 @@ that implements bioruby&#8216;s Bio::Map::ActsAsMap.
175
170
  <div id="class-list">
176
171
  <h3 class="section-bar">Classes and Modules</h3>
177
172
 
178
- Class <a href="Graphics/Panel.html" class="link">Bio::Graphics::Panel</a><br />
173
+ Module <a href="Graphics/Glyph.html" class="link">Bio::Graphics::Glyph</a><br />
174
+ Class <a href="Graphics/Feature.html" class="link">Bio::Graphics::Feature</a><br />
175
+ Class <a href="Graphics/ImageMap.html" class="link">Bio::Graphics::ImageMap</a><br />
176
+ Class <a href="Graphics/Panel.html" class="link">Bio::Graphics::Panel</a><br />
177
+ Class <a href="Graphics/Ruler.html" class="link">Bio::Graphics::Ruler</a><br />
178
+ Class <a href="Graphics/SubFeature.html" class="link">Bio::Graphics::SubFeature</a><br />
179
+ Class <a href="Graphics/Track.html" class="link">Bio::Graphics::Track</a><br />
179
180
 
180
181
  </div>
181
182
 
@@ -214,25 +215,10 @@ The defaults
214
215
  <td>=</td>
215
216
  <td class="context-item-value">5</td>
216
217
  </tr>
217
- <tr class="top-aligned-row context-row">
218
- <td class="context-item-name">RULER_TEXT_HEIGHT</td>
219
- <td>=</td>
220
- <td class="context-item-value">10</td>
221
- </tr>
222
- <tr class="top-aligned-row context-row">
223
- <td class="context-item-name">RULER_MIN_DISTANCE_TICKS_PIXEL</td>
224
- <td>=</td>
225
- <td class="context-item-value">5</td>
226
- </tr>
227
218
  <tr class="top-aligned-row context-row">
228
219
  <td class="context-item-name">FONT</td>
229
220
  <td>=</td>
230
221
  <td class="context-item-value">['Georgia', 1, 1]</td>
231
- <td width="3em">&nbsp;</td>
232
- <td class="context-item-desc">
233
- consecutive ticks. This is used for the calculation of tick distance.
234
-
235
- </td>
236
222
  </tr>
237
223
  </table>
238
224
  </div>
data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} RENAMED
@@ -5,10 +5,10 @@
5
5
 
6
6
  <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
7
  <head>
8
- <title>Class: Bio::Graphics::Panel::Track::Feature</title>
8
+ <title>Class: Bio::Graphics::Feature</title>
9
9
  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
10
  <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
- <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
12
12
  <script type="text/javascript">
13
13
  // <![CDATA[
14
14
 
@@ -50,12 +50,12 @@
50
50
  <table class="header-table">
51
51
  <tr class="top-aligned-row">
52
52
  <td><strong>Class</strong></td>
53
- <td class="class-name-in-header">Bio::Graphics::Panel::Track::Feature</td>
53
+ <td class="class-name-in-header">Bio::Graphics::Feature</td>
54
54
  </tr>
55
55
  <tr class="top-aligned-row">
56
56
  <td><strong>In:</strong></td>
57
57
  <td>
58
- <a href="../../../../../files/lib/bio/graphics/feature_rb.html">
58
+ <a href="../../../files/lib/bio/graphics/feature_rb.html">
59
59
  lib/bio/graphics/feature.rb
60
60
  </a>
61
61
  <br />
@@ -80,14 +80,19 @@
80
80
 
81
81
  <div id="description">
82
82
  <p>
83
- The Bio::Graphics::Track::Feature class describes features to be placed on
84
- the graph. See <a href="../../../Graphics.html">Bio::Graphics</a>
85
- documentation for explanation of interplay between different classes.
83
+ The <a href="Feature.html">Bio::Graphics::Feature</a> class describes
84
+ features to be placed on the graph. See <a
85
+ href="../Graphics.html">Bio::Graphics</a> documentation for explanation of
86
+ interplay between different classes.
86
87
  </p>
87
88
  <p>
88
89
  The position of the <a href="Feature.html">Feature</a> is a Bio::Locations
89
90
  object to make it possible to transparently work with simple and spliced
90
91
  features.
92
+ </p>
93
+ <p>
94
+ The <a href="Feature.html">Bio::Graphics::Feature</a> class inherits from
95
+ <a href="../Feature.html">Bio::Feature</a>.
91
96
  </p>
92
97
 
93
98
  </div>
@@ -99,11 +104,9 @@ features.
99
104
  <h3 class="section-bar">Methods</h3>
100
105
 
101
106
  <div class="name-list">
102
- <a href="#M000012">arrow</a>&nbsp;&nbsp;
103
- <a href="#M000013">connector</a>&nbsp;&nbsp;
104
- <a href="#M000014">draw</a>&nbsp;&nbsp;
105
- <a href="#M000015">find_row</a>&nbsp;&nbsp;
106
- <a href="#M000011">new</a>&nbsp;&nbsp;
107
+ <a href="#M000025">draw</a>&nbsp;&nbsp;
108
+ <a href="#M000026">find_row</a>&nbsp;&nbsp;
109
+ <a href="#M000024">new</a>&nbsp;&nbsp;
107
110
  </div>
108
111
  </div>
109
112
 
@@ -114,14 +117,21 @@ features.
114
117
 
115
118
  <div id="section">
116
119
 
117
- <div id="class-list">
118
- <h3 class="section-bar">Classes and Modules</h3>
119
120
 
120
- Class <a href="Feature/PixelRange.html" class="link">Bio::Graphics::Panel::Track::Feature::PixelRange</a><br />
121
-
122
- </div>
123
121
 
122
+ <div id="aliases-list">
123
+ <h3 class="section-bar">External Aliases</h3>
124
124
 
125
+ <div class="name-list">
126
+ <table summary="aliases">
127
+ <tr class="top-aligned-row context-row">
128
+ <td class="context-item-name">label</td>
129
+ <td>-&gt;</td>
130
+ <td class="context-item-value">name</td>
131
+ </tr>
132
+ </table>
133
+ </div>
134
+ </div>
125
135
 
126
136
 
127
137
  <div id="attribute-list">
@@ -130,94 +140,90 @@ features.
130
140
  <div class="name-list">
131
141
  <table>
132
142
  <tr class="top-aligned-row context-row">
133
- <td class="context-item-name">chopped_at_start</td>
143
+ <td class="context-item-name">colour</td>
134
144
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
135
145
  <td class="context-item-desc">
136
- Is the first subfeature incomplete?
146
+ The colour to use to <a href="Feature.html#M000025">draw</a> this
147
+ (sub)feature
137
148
 
138
149
  </td>
139
150
  </tr>
140
151
  <tr class="top-aligned-row context-row">
141
- <td class="context-item-name">chopped_at_stop</td>
152
+ <td class="context-item-name">feature_object</td>
142
153
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
143
154
  <td class="context-item-desc">
144
- Is the last subfeature incomplete?
155
+ The bioruby <a href="../Feature.html">Bio::Feature</a> object
145
156
 
146
157
  </td>
147
158
  </tr>
148
159
  <tr class="top-aligned-row context-row">
149
- <td class="context-item-name">hidden_subfeatures_at_start</td>
160
+ <td class="context-item-name">glyph</td>
150
161
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
151
162
  <td class="context-item-desc">
152
- Are there subfeatures out of view at the left side of the picture?
163
+ The glyph to use to <a href="Feature.html#M000025">draw</a> this
164
+ (sub)feature
153
165
 
154
166
  </td>
155
167
  </tr>
156
168
  <tr class="top-aligned-row context-row">
157
- <td class="context-item-name">hidden_subfeatures_at_stop</td>
169
+ <td class="context-item-name">label</td>
158
170
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
159
171
  <td class="context-item-desc">
160
- Are there subfeatures out of view at the right side of the picture?
172
+ The label of the feature
161
173
 
162
174
  </td>
163
175
  </tr>
164
176
  <tr class="top-aligned-row context-row">
165
- <td class="context-item-name">link</td>
177
+ <td class="context-item-name">left_pixel_of_feature</td>
166
178
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
167
- <td class="context-item-desc">
168
- The URL to be followed when the glyph for this feature is clicked
169
-
170
- </td>
179
+ <td class="context-item-desc"></td>
171
180
  </tr>
172
181
  <tr class="top-aligned-row context-row">
173
- <td class="context-item-name">location</td>
182
+ <td class="context-item-name">left_pixel_of_subfeatures</td>
174
183
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
175
- <td class="context-item-desc">
176
- The location of the feature (which is a Bio::Locations object)
177
-
178
- </td>
184
+ <td class="context-item-desc"></td>
179
185
  </tr>
180
186
  <tr class="top-aligned-row context-row">
181
- <td class="context-item-name">name</td>
187
+ <td class="context-item-name">link</td>
182
188
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
183
189
  <td class="context-item-desc">
184
- The name of the feature
190
+ The URL to be followed when the glyph for this feature is clicked
185
191
 
186
192
  </td>
187
193
  </tr>
188
194
  <tr class="top-aligned-row context-row">
189
- <td class="context-item-name">pixel_range_collection</td>
195
+ <td class="context-item-name">locations</td>
190
196
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
191
- <td class="context-item-desc">
192
- The array keeping the pixel ranges for the sub-features. Unspliced features
193
- will just have one element, while spliced features will have more than one.
194
-
195
- </td>
197
+ <td class="context-item-desc"></td>
198
+ </tr>
199
+ <tr class="top-aligned-row context-row">
200
+ <td class="context-item-name">right_pixel_of_subfeatures</td>
201
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
202
+ <td class="context-item-desc"></td>
196
203
  </tr>
197
204
  <tr class="top-aligned-row context-row">
198
205
  <td class="context-item-name">start</td>
199
206
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
200
- <td class="context-item-desc">
201
- The start position of the feature (in bp)
202
-
203
- </td>
207
+ <td class="context-item-desc"></td>
204
208
  </tr>
205
209
  <tr class="top-aligned-row context-row">
206
210
  <td class="context-item-name">stop</td>
207
211
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
208
- <td class="context-item-desc">
209
- The stop position of the feature (in bp)
210
-
211
- </td>
212
+ <td class="context-item-desc"></td>
212
213
  </tr>
213
214
  <tr class="top-aligned-row context-row">
214
- <td class="context-item-name">strand</td>
215
+ <td class="context-item-name">subfeatures</td>
215
216
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
216
217
  <td class="context-item-desc">
217
- The strand of the feature
218
+ The <a href="../Graphics.html">Bio::Graphics</a> SubFeatures
218
219
 
219
220
  </td>
220
221
  </tr>
222
+ <tr class="top-aligned-row context-row">
223
+ <td class="context-item-name">top_pixel_of_feature</td>
224
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
225
+ <td class="context-item-desc"></td>
226
+ </tr>
221
227
  <tr class="top-aligned-row context-row">
222
228
  <td class="context-item-name">track</td>
223
229
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
@@ -226,6 +232,11 @@ The track that this feature belongs to
226
232
 
227
233
  </td>
228
234
  </tr>
235
+ <tr class="top-aligned-row context-row">
236
+ <td class="context-item-name">vertical_offset</td>
237
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
238
+ <td class="context-item-desc"></td>
239
+ </tr>
229
240
  </table>
230
241
  </div>
231
242
  </div>
@@ -236,45 +247,51 @@ The track that this feature belongs to
236
247
  <div id="methods">
237
248
  <h3 class="section-bar">Public Class methods</h3>
238
249
 
239
- <div id="method-M000011" class="method-detail">
240
- <a name="M000011"></a>
250
+ <div id="method-M000024" class="method-detail">
251
+ <a name="M000024"></a>
241
252
 
242
253
  <div class="method-heading">
243
- <a href="Feature.src/M000011.html" target="Code" class="method-signature"
244
- onclick="popupCode('Feature.src/M000011.html');return false;">
245
- <span class="method-name">new</span><span class="method-args">(track, name, location = Bio::Locations.new('1..' + track.panel.length.to_s), link = nil)</span>
254
+ <a href="Feature.src/M000024.html" target="Code" class="method-signature"
255
+ onclick="popupCode('Feature.src/M000024.html');return false;">
256
+ <span class="method-name">new</span><span class="method-args">(track, feature_object, opts = {})</span>
246
257
  </a>
247
258
  </div>
248
259
 
249
260
  <div class="method-description">
250
261
  <p>
251
262
  !!Not to be used directly. Use <a
252
- href="../Track.html#M000009">Bio::Graphics::Panel::Track.add_feature</a>
253
- instead!! A feature can not exist except within the confines of a <a
254
- href="../Track.html">Bio::Graphics::Panel::Track</a> object.
263
+ href="Track.html#M000022">Bio::Graphics::Track.add_feature</a> instead!! A
264
+ feature can not exist except within the confines of a <a
265
+ href="Track.html">Bio::Graphics::Track</a> object.
255
266
  </p>
256
267
  <hr size="1"></hr><p>
257
268
  <b>Arguments</b>:
258
269
  </p>
259
270
  <ul>
260
- <li><em>panel</em> (required) :: <a
261
- href="../Track.html">Bio::Graphics::Panel::Track</a> object that this
262
- feature belongs to
271
+ <li><em>track</em> (required) :: <a href="Track.html">Bio::Graphics::Track</a>
272
+ object that this feature belongs to
273
+
274
+ </li>
275
+ <li><em>feature</em> <em>object</em> (required) :: A <a
276
+ href="../Feature.html">Bio::Feature</a> object (see bioruby)
277
+
278
+ </li>
279
+ <li>_:label_ :: Label of the feature. Default = &#8216;anonymous&#8216;
263
280
 
264
281
  </li>
265
- <li><em>name</em> (required) :: Name of the feature
282
+ <li>_:link_ :: URL for clickable images. Default = nil
266
283
 
267
284
  </li>
268
- <li><em>location</em> :: Bio::Locations object. Default = whole panel, forward
269
- strand
285
+ <li>_:glyph_ :: <a href="Glyph.html">Glyph</a> to use. Default = glyph of the
286
+ track
270
287
 
271
288
  </li>
272
- <li><em>link</em> :: URL for clickable images
289
+ <li>_:colour_ :: Colour. Default = colour of the track
273
290
 
274
291
  </li>
275
292
  </ul>
276
293
  <table>
277
- <tr><td valign="top"><b>Returns</b>:</td><td>Bio::Graphics::Track::Feature object
294
+ <tr><td valign="top"><b>Returns</b>:</td><td><a href="Feature.html">Bio::Graphics::Feature</a> object
278
295
 
279
296
  </td></tr>
280
297
  </table>
@@ -283,51 +300,13 @@ strand
283
300
 
284
301
  <h3 class="section-bar">Public Instance methods</h3>
285
302
 
286
- <div id="method-M000012" class="method-detail">
287
- <a name="M000012"></a>
288
-
289
- <div class="method-heading">
290
- <a href="Feature.src/M000012.html" target="Code" class="method-signature"
291
- onclick="popupCode('Feature.src/M000012.html');return false;">
292
- <span class="method-name">arrow</span><span class="method-args">(track,direction,x,y,size)</span>
293
- </a>
294
- </div>
295
-
296
- <div class="method-description">
297
- <p>
298
- Method to <a href="Feature.html#M000014">draw</a> the arrows of directed
299
- glyphs. Not to be used directly, but called by <a
300
- href="Feature.html#M000014">Feature#draw</a>.
301
- </p>
302
- </div>
303
- </div>
304
-
305
- <div id="method-M000013" class="method-detail">
306
- <a name="M000013"></a>
307
-
308
- <div class="method-heading">
309
- <a href="Feature.src/M000013.html" target="Code" class="method-signature"
310
- onclick="popupCode('Feature.src/M000013.html');return false;">
311
- <span class="method-name">connector</span><span class="method-args">(track,from,to,top, color)</span>
312
- </a>
313
- </div>
314
-
315
- <div class="method-description">
316
- <p>
317
- Method to <a href="Feature.html#M000014">draw</a> the connections (introns)
318
- of spliced glyphs. Not to be used directly, but called by <a
319
- href="Feature.html#M000014">Feature#draw</a>.
320
- </p>
321
- </div>
322
- </div>
323
-
324
- <div id="method-M000014" class="method-detail">
325
- <a name="M000014"></a>
303
+ <div id="method-M000025" class="method-detail">
304
+ <a name="M000025"></a>
326
305
 
327
306
  <div class="method-heading">
328
- <a href="Feature.src/M000014.html" target="Code" class="method-signature"
329
- onclick="popupCode('Feature.src/M000014.html');return false;">
330
- <span class="method-name">draw</span><span class="method-args">(track_drawing)</span>
307
+ <a href="Feature.src/M000025.html" target="Code" class="method-signature"
308
+ onclick="popupCode('Feature.src/M000025.html');return false;">
309
+ <span class="method-name">draw</span><span class="method-args">(panel_destination)</span>
331
310
  </a>
332
311
  </div>
333
312
 
@@ -335,20 +314,14 @@ href="Feature.html#M000014">Feature#draw</a>.
335
314
  <p>
336
315
  Adds the feature to the track cairo context. This method should not be used
337
316
  directly by the user, but is called by <a
338
- href="../Track.html#M000010">Bio::Graphics::Panel::Track.draw</a>
317
+ href="Track.html#M000023">Bio::Graphics::Track.draw</a>
339
318
  </p>
340
319
  <hr size="1"></hr><p>
341
320
  <b>Arguments</b>:
342
321
  </p>
343
322
  <ul>
344
- <li><em>trackdrawing</em> (required) :: the track cairo object
345
-
346
- </li>
347
- <li><em>row</em> (required) :: row within the track that this feature has
323
+ <li><em>track_drawing</em> (required) :: the track cairo object
348
324
 
349
- <pre>
350
- been bumped to
351
- </pre>
352
325
  </li>
353
326
  </ul>
354
327
  <table>
@@ -359,12 +332,12 @@ href="../Track.html#M000010">Bio::Graphics::Panel::Track.draw</a>
359
332
  </div>
360
333
  </div>
361
334
 
362
- <div id="method-M000015" class="method-detail">
363
- <a name="M000015"></a>
335
+ <div id="method-M000026" class="method-detail">
336
+ <a name="M000026"></a>
364
337
 
365
338
  <div class="method-heading">
366
- <a href="Feature.src/M000015.html" target="Code" class="method-signature"
367
- onclick="popupCode('Feature.src/M000015.html');return false;">
339
+ <a href="Feature.src/M000026.html" target="Code" class="method-signature"
340
+ onclick="popupCode('Feature.src/M000026.html');return false;">
368
341
  <span class="method-name">find_row</span><span class="method-args">()</span>
369
342
  </a>
370
343
  </div>
@@ -373,7 +346,7 @@ href="../Track.html#M000010">Bio::Graphics::Panel::Track.draw</a>
373
346
  <p>
374
347
  Calculates the row within the track where this feature should be drawn.
375
348
  This method should not be used directly by the user, but is called by <a
376
- href="Feature.html#M000014">Bio::Graphics::Panel::Track::Feature.draw</a>
349
+ href="Feature.html#M000025">Bio::Graphics::Feature.draw</a>
377
350
  </p>
378
351
  <hr size="1"></hr><table>
379
352
  <tr><td valign="top"><b>Arguments</b>:</td><td>none