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
  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