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
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data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
8
+ <title>draw (Bio::Graphics::Glyph::DirectedGeneric)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyphs/directed_generic.rb, line 3</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
15
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># Reverse strand</span>
16
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
17
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
18
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
19
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand</span>
20
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span>, <span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span><span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
21
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span><span class="ruby-operator">-</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
22
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
23
+ <span class="ruby-keyword kw">end</span>
24
+ <span class="ruby-keyword kw">end</span></pre>
25
+ </body>
26
+ </html>
data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>draw (Bio::Graphics::Glyph::DirectedGeneric)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyphs/directed_generic.rb, line 11</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
15
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># Reverse strand</span>
16
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
17
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
18
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
19
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand</span>
20
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span>, <span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span><span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
21
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span><span class="ruby-operator">-</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
22
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
23
+ <span class="ruby-keyword kw">end</span>
24
+ <span class="ruby-keyword kw">end</span></pre>
25
+ </body>
26
+ </html>
data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html ADDED
@@ -0,0 +1,26 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
8
+ <title>draw (Bio::Graphics::Glyph::DirectedGeneric)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyphs/directed_generic.rb, line 11</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
15
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># Reverse strand</span>
16
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
17
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
18
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
19
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand</span>
20
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span>, <span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span><span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
21
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">right_pixel</span><span class="ruby-operator">-</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
22
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
23
+ <span class="ruby-keyword kw">end</span>
24
+ <span class="ruby-keyword kw">end</span></pre>
25
+ </body>
26
+ </html>
data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html ADDED
@@ -0,0 +1,139 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
+ <head>
8
+ <title>Class: Bio::Graphics::Glyph::DirectedSpliced</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
15
+ function popupCode( url ) {
16
+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
17
+ }
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+
19
+ function toggleCode( id ) {
20
+ if ( document.getElementById )
21
+ elem = document.getElementById( id );
22
+ else if ( document.all )
23
+ elem = eval( "document.all." + id );
24
+ else
25
+ return false;
26
+
27
+ elemStyle = elem.style;
28
+
29
+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
31
+ } else {
32
+ elemStyle.display = "none"
33
+ }
34
+
35
+ return true;
36
+ }
37
+
38
+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
40
+
41
+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
47
+
48
+
49
+ <div id="classHeader">
50
+ <table class="header-table">
51
+ <tr class="top-aligned-row">
52
+ <td><strong>Class</strong></td>
53
+ <td class="class-name-in-header">Bio::Graphics::Glyph::DirectedSpliced</td>
54
+ </tr>
55
+ <tr class="top-aligned-row">
56
+ <td><strong>In:</strong></td>
57
+ <td>
58
+ <a href="../../../../files/lib/bio/graphics/glyphs/directed_spliced_rb.html">
59
+ lib/bio/graphics/glyphs/directed_spliced.rb
60
+ </a>
61
+ <br />
62
+ </td>
63
+ </tr>
64
+
65
+ <tr class="top-aligned-row">
66
+ <td><strong>Parent:</strong></td>
67
+ <td>
68
+ <a href="Common.html">
69
+ Bio::Graphics::Glyph::Common
70
+ </a>
71
+ </td>
72
+ </tr>
73
+ </table>
74
+ </div>
75
+ <!-- banner header -->
76
+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+
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+
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+ </div>
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+
87
+ <div id="method-list">
88
+ <h3 class="section-bar">Methods</h3>
89
+
90
+ <div class="name-list">
91
+ <a href="#M000010">draw</a>&nbsp;&nbsp;
92
+ </div>
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+ </div>
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Instance methods</h3>
112
+
113
+ <div id="method-M000010" class="method-detail">
114
+ <a name="M000010"></a>
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+
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+ <div class="method-heading">
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+ <a href="DirectedSpliced.src/M000010.html" target="Code" class="method-signature"
118
+ onclick="popupCode('DirectedSpliced.src/M000010.html');return false;">
119
+ <span class="method-name">draw</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
135
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
138
+ </body>
139
+ </html>
data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html ADDED
@@ -0,0 +1,40 @@
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+ <?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
+
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+ <html>
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+ <head>
8
+ <title>draw (Bio::Graphics::Glyph::DirectedSpliced)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyphs/directed_spliced.rb, line 3</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
15
+ <span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
+ <span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
17
+
18
+ <span class="ruby-comment cmt"># Start with the one with the arrow</span>
19
+ <span class="ruby-identifier">pixel_ranges</span> = <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">lend</span>}
20
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-keyword kw">nil</span>
21
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># reverse strand =&gt; box with arrow is first one</span>
22
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">shift</span>
23
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>((<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>)<span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
24
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
25
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
26
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># forward strand =&gt; box with arrow is last one</span>
27
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">pop</span>
28
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>, <span class="ruby-value">0</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
29
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span><span class="ruby-operator">-</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
30
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
31
+ <span class="ruby-keyword kw">end</span>
32
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span>)
33
+ <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>)
34
+
35
+ <span class="ruby-comment cmt"># And then add the others</span>
36
+ <span class="ruby-identifier">draw_spliced</span>(<span class="ruby-ivar">@feature_context</span>, <span class="ruby-identifier">pixel_ranges</span>, <span class="ruby-identifier">gap_starts</span>, <span class="ruby-identifier">gap_stops</span>)
37
+
38
+ <span class="ruby-keyword kw">end</span></pre>
39
+ </body>
40
+ </html>
data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html ADDED
@@ -0,0 +1,40 @@
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>draw (Bio::Graphics::Glyph::DirectedSpliced)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyphs/directed_spliced.rb, line 11</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
15
+ <span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
+ <span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
17
+
18
+ <span class="ruby-comment cmt"># Start with the one with the arrow</span>
19
+ <span class="ruby-identifier">pixel_ranges</span> = <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">lend</span>}
20
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-keyword kw">nil</span>
21
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># reverse strand =&gt; box with arrow is first one</span>
22
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">shift</span>
23
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>((<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>)<span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
24
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
25
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
26
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># forward strand =&gt; box with arrow is last one</span>
27
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">pop</span>
28
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>, <span class="ruby-value">0</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
29
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span><span class="ruby-operator">-</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
30
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
31
+ <span class="ruby-keyword kw">end</span>
32
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span>)
33
+ <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>)
34
+
35
+ <span class="ruby-comment cmt"># And then add the others</span>
36
+ <span class="ruby-identifier">draw_spliced</span>(<span class="ruby-ivar">@feature_context</span>, <span class="ruby-identifier">pixel_ranges</span>, <span class="ruby-identifier">gap_starts</span>, <span class="ruby-identifier">gap_stops</span>)
37
+
38
+ <span class="ruby-keyword kw">end</span></pre>
39
+ </body>
40
+ </html>
data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html ADDED
@@ -0,0 +1,40 @@
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>draw (Bio::Graphics::Glyph::DirectedSpliced)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyphs/directed_spliced.rb, line 11</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
15
+ <span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
+ <span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
17
+
18
+ <span class="ruby-comment cmt"># Start with the one with the arrow</span>
19
+ <span class="ruby-identifier">pixel_ranges</span> = <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">lend</span>}
20
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-keyword kw">nil</span>
21
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># reverse strand =&gt; box with arrow is first one</span>
22
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">shift</span>
23
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>((<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>)<span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
24
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
25
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
26
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># forward strand =&gt; box with arrow is last one</span>
27
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">pop</span>
28
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>, <span class="ruby-value">0</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span> <span class="ruby-operator">-</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
29
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span><span class="ruby-operator">-</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
30
+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
31
+ <span class="ruby-keyword kw">end</span>
32
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">rend</span>)
33
+ <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">lend</span>)
34
+
35
+ <span class="ruby-comment cmt"># And then add the others</span>
36
+ <span class="ruby-identifier">draw_spliced</span>(<span class="ruby-ivar">@feature_context</span>, <span class="ruby-identifier">pixel_ranges</span>, <span class="ruby-identifier">gap_starts</span>, <span class="ruby-identifier">gap_stops</span>)
37
+
38
+ <span class="ruby-keyword kw">end</span></pre>
39
+ </body>
40
+ </html>
data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.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::PixelRange</title>
8
+ <title>Class: Bio::Graphics::Glyph::Dot</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
 
@@ -50,13 +50,13 @@
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::PixelRange</td>
53
+ <td class="class-name-in-header">Bio::Graphics::Glyph::Dot</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">
59
- lib/bio/graphics/feature.rb
58
+ <a href="../../../../files/lib/bio/graphics/glyphs/dot_rb.html">
59
+ lib/bio/graphics/glyphs/dot.rb
60
60
  </a>
61
61
  <br />
62
62
  </td>
@@ -65,7 +65,9 @@
65
65
  <tr class="top-aligned-row">
66
66
  <td><strong>Parent:</strong></td>
67
67
  <td>
68
- Object
68
+ <a href="Common.html">
69
+ Bio::Graphics::Glyph::Common
70
+ </a>
69
71
  </td>
70
72
  </tr>
71
73
  </table>
@@ -86,7 +88,7 @@
86
88
  <h3 class="section-bar">Methods</h3>
87
89
 
88
90
  <div class="name-list">
89
- <a href="#M000016">new</a>&nbsp;&nbsp;
91
+ <a href="#M000015">draw</a>&nbsp;&nbsp;
90
92
  </div>
91
93
  </div>
92
94
 
@@ -107,12 +109,7 @@
107
109
  <div class="name-list">
108
110
  <table>
109
111
  <tr class="top-aligned-row context-row">
110
- <td class="context-item-name">start_pixel</td>
111
- <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
112
- <td class="context-item-desc"></td>
113
- </tr>
114
- <tr class="top-aligned-row context-row">
115
- <td class="context-item-name">stop_pixel</td>
112
+ <td class="context-item-name">radius</td>
116
113
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
117
114
  <td class="context-item-desc"></td>
118
115
  </tr>
@@ -124,15 +121,15 @@
124
121
 
125
122
  <!-- if method_list -->
126
123
  <div id="methods">
127
- <h3 class="section-bar">Public Class methods</h3>
124
+ <h3 class="section-bar">Public Instance methods</h3>
128
125
 
129
- <div id="method-M000016" class="method-detail">
130
- <a name="M000016"></a>
126
+ <div id="method-M000015" class="method-detail">
127
+ <a name="M000015"></a>
131
128
 
132
129
  <div class="method-heading">
133
- <a href="PixelRange.src/M000016.html" target="Code" class="method-signature"
134
- onclick="popupCode('PixelRange.src/M000016.html');return false;">
135
- <span class="method-name">new</span><span class="method-args">(start_pixel, stop_pixel)</span>
130
+ <a href="Dot.src/M000015.html" target="Code" class="method-signature"
131
+ onclick="popupCode('Dot.src/M000015.html');return false;">
132
+ <span class="method-name">draw</span><span class="method-args">()</span>
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  </a>
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  </div>
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data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>draw (Bio::Graphics::Glyph::Dot)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyphs/dot.rb, line 5</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
15
+ <span class="ruby-identifier">raise</span> <span class="ruby-value str">&quot;Start and stop are not the same (necessary if you want triangle glyphs)&quot;</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">!=</span> <span class="ruby-ivar">@subfeature</span>.<span class="ruby-identifier">stop</span>
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+
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+ <span class="ruby-ivar">@radius</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>
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+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">circle</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">left_pixel</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@radius</span>, <span class="ruby-ivar">@radius</span>, <span class="ruby-ivar">@radius</span>).<span class="ruby-identifier">fill</span>
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+ <span class="ruby-ivar">@feature_context</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>