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/ImageMap.src/M000062.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>new (Bio::Graphics::ImageMap)</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/image_map.rb, line 9</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>
15
+ <span class="ruby-ivar">@elements</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
+ <span class="ruby-keyword kw">end</span></pre>
17
+ </body>
18
+ </html>
data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html ADDED
@@ -0,0 +1,18 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
8
+ <title>add_element (Bio::Graphics::ImageMap)</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/image_map.rb, line 14</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_element</span>(<span class="ruby-identifier">left</span>,<span class="ruby-identifier">top</span>,<span class="ruby-identifier">right</span>,<span class="ruby-identifier">bottom</span>,<span class="ruby-identifier">url</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <span class="ruby-ivar">@elements</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Element</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">left</span>,<span class="ruby-identifier">top</span>,<span class="ruby-identifier">right</span>,<span class="ruby-identifier">bottom</span>,<span class="ruby-identifier">url</span>))
16
+ <span class="ruby-keyword kw">end</span></pre>
17
+ </body>
18
+ </html>
data/doc/classes/Bio/Graphics/ImageMap.src/M000064.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>to_s (Bio::Graphics::ImageMap)</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>
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+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 18</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
15
+ <span class="ruby-identifier">output</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
+ <span class="ruby-identifier">output</span>.<span class="ruby-identifier">push</span>(<span class="ruby-value str">'&lt;map name=&quot;image_map&quot; border=&quot;1&quot;&gt;'</span>)
17
+ <span class="ruby-ivar">@elements</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">e</span><span class="ruby-operator">|</span>
18
+ <span class="ruby-identifier">area</span> = <span class="ruby-identifier">e</span>.<span class="ruby-identifier">to_s</span>
19
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">area</span> <span class="ruby-operator">!=</span> <span class="ruby-value str">''</span>
20
+ <span class="ruby-identifier">output</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">e</span>.<span class="ruby-identifier">to_s</span>)
21
+ <span class="ruby-keyword kw">end</span>
22
+ <span class="ruby-keyword kw">end</span>
23
+ <span class="ruby-identifier">output</span>.<span class="ruby-identifier">push</span>(<span class="ruby-value str">'&lt;/map&gt;'</span>)
24
+ <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">output</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">&quot;\n&quot;</span>)
25
+ <span class="ruby-keyword kw">end</span></pre>
26
+ </body>
27
+ </html>
data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html ADDED
@@ -0,0 +1,24 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
8
+ <title>flip_orientation (Bio::Graphics::ImageMap)</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/image_map.rb, line 33</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">flip_orientation</span>(<span class="ruby-identifier">width</span>)
15
+ <span class="ruby-ivar">@elements</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">element</span><span class="ruby-operator">|</span>
16
+ <span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span> = <span class="ruby-identifier">element</span>.<span class="ruby-identifier">left</span>, <span class="ruby-identifier">element</span>.<span class="ruby-identifier">top</span>, <span class="ruby-identifier">element</span>.<span class="ruby-identifier">right</span>, <span class="ruby-identifier">element</span>.<span class="ruby-identifier">bottom</span>
17
+ <span class="ruby-identifier">element</span>.<span class="ruby-identifier">left</span> = <span class="ruby-identifier">top</span>
18
+ <span class="ruby-identifier">element</span>.<span class="ruby-identifier">top</span> = <span class="ruby-identifier">width</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">right</span>
19
+ <span class="ruby-identifier">element</span>.<span class="ruby-identifier">right</span> = <span class="ruby-identifier">bottom</span>
20
+ <span class="ruby-identifier">element</span>.<span class="ruby-identifier">bottom</span> = <span class="ruby-identifier">width</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left</span>
21
+ <span class="ruby-keyword kw">end</span>
22
+ <span class="ruby-keyword kw">end</span></pre>
23
+ </body>
24
+ </html>
data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} RENAMED
@@ -5,10 +5,10 @@
5
5
 
6
6
  <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
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  <head>
8
- <title>Class: ImageMap::ImageMapElement</title>
8
+ <title>Class: Bio::Graphics::ImageMap::Element</title>
9
9
  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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  <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
12
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  <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">ImageMap::ImageMapElement</td>
53
+ <td class="class-name-in-header">Bio::Graphics::ImageMap::Element</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/image_map_rb.html">
58
+ <a href="../../../../files/lib/bio/graphics/image_map_rb.html">
59
59
  lib/bio/graphics/image_map.rb
60
60
  </a>
61
61
  <br />
@@ -86,8 +86,8 @@
86
86
  <h3 class="section-bar">Methods</h3>
87
87
 
88
88
  <div class="name-list">
89
- <a href="#M000003">new</a>&nbsp;&nbsp;
90
- <a href="#M000004">to_s</a>&nbsp;&nbsp;
89
+ <a href="#M000036">new</a>&nbsp;&nbsp;
90
+ <a href="#M000037">to_s</a>&nbsp;&nbsp;
91
91
  </div>
92
92
  </div>
93
93
 
@@ -142,12 +142,12 @@
142
142
  <div id="methods">
143
143
  <h3 class="section-bar">Public Class methods</h3>
144
144
 
145
- <div id="method-M000003" class="method-detail">
146
- <a name="M000003"></a>
145
+ <div id="method-M000036" class="method-detail">
146
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148
  <div class="method-heading">
149
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150
- onclick="popupCode('ImageMapElement.src/M000003.html');return false;">
149
+ <a href="Element.src/M000036.html" target="Code" class="method-signature"
150
+ onclick="popupCode('Element.src/M000036.html');return false;">
151
151
  <span class="method-name">new</span><span class="method-args">(left, top, right, bottom, url = nil)</span>
152
152
  </a>
153
153
  </div>
@@ -158,12 +158,12 @@
158
158
 
159
159
  <h3 class="section-bar">Public Instance methods</h3>
160
160
 
161
- <div id="method-M000004" class="method-detail">
162
- <a name="M000004"></a>
161
+ <div id="method-M000037" class="method-detail">
162
+ <a name="M000037"></a>
163
163
 
164
164
  <div class="method-heading">
165
- <a href="ImageMapElement.src/M000004.html" target="Code" class="method-signature"
166
- onclick="popupCode('ImageMapElement.src/M000004.html');return false;">
165
+ <a href="Element.src/M000037.html" target="Code" class="method-signature"
166
+ onclick="popupCode('Element.src/M000037.html');return false;">
167
167
  <span class="method-name">to_s</span><span class="method-args">()</span>
168
168
  </a>
169
169
  </div>
data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} RENAMED
@@ -5,12 +5,12 @@
5
5
 
6
6
  <html>
7
7
  <head>
8
- <title>new (ImageMap::ImageMapElement)</title>
8
+ <title>new (Bio::Graphics::ImageMap::Element)</title>
9
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" />
10
+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
11
  </head>
12
12
  <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 25</span>
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 44</span>
14
14
  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span>, <span class="ruby-identifier">url</span> = <span class="ruby-keyword kw">nil</span>)
15
15
  <span class="ruby-ivar">@left</span>, <span class="ruby-ivar">@top</span>, <span class="ruby-ivar">@right</span>, <span class="ruby-ivar">@bottom</span> = <span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span>
16
16
  <span class="ruby-ivar">@url</span> = ( <span class="ruby-identifier">url</span>.<span class="ruby-identifier">nil?</span> ) <span class="ruby-operator">?</span> <span class="ruby-value str">''</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">url</span>
data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} RENAMED
@@ -5,14 +5,16 @@
5
5
 
6
6
  <html>
7
7
  <head>
8
- <title>to_s (ImageMap::ImageMapElement)</title>
8
+ <title>to_s (Bio::Graphics::ImageMap::Element)</title>
9
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" />
10
+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
11
  </head>
12
12
  <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 31</span>
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 50</span>
14
14
  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
15
- <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
15
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
16
+ <span class="ruby-keyword kw">return</span> <span class="ruby-value str">''</span>
17
+ <span class="ruby-keyword kw">else</span>
16
18
  <span class="ruby-keyword kw">return</span> <span class="ruby-value str">'&lt;area shape=&quot;rect&quot; coords=&quot;'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@left</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@top</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@right</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@bottom</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'&quot; href=&quot;'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'&quot;/&gt;'</span>
17
19
  <span class="ruby-keyword kw">end</span>
18
20
  <span class="ruby-keyword kw">end</span></pre>
data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html ADDED
@@ -0,0 +1,19 @@
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">
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+
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+ <html>
7
+ <head>
8
+ <title>new (Bio::Graphics::ImageMap::Element)</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/image_map.rb, line 44</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span>, <span class="ruby-identifier">url</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <span class="ruby-ivar">@left</span>, <span class="ruby-ivar">@top</span>, <span class="ruby-ivar">@right</span>, <span class="ruby-ivar">@bottom</span> = <span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span>
16
+ <span class="ruby-ivar">@url</span> = ( <span class="ruby-identifier">url</span>.<span class="ruby-identifier">nil?</span> ) <span class="ruby-operator">?</span> <span class="ruby-value str">''</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">url</span>
17
+ <span class="ruby-keyword kw">end</span></pre>
18
+ </body>
19
+ </html>
data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html ADDED
@@ -0,0 +1,22 @@
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>to_s (Bio::Graphics::ImageMap::Element)</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/image_map.rb, line 50</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
15
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
16
+ <span class="ruby-keyword kw">return</span> <span class="ruby-value str">''</span>
17
+ <span class="ruby-keyword kw">else</span>
18
+ <span class="ruby-keyword kw">return</span> <span class="ruby-value str">'&lt;area shape=&quot;rect&quot; coords=&quot;'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@left</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@top</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@right</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@bottom</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'&quot; href=&quot;'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'&quot;/&gt;'</span>
19
+ <span class="ruby-keyword kw">end</span>
20
+ <span class="ruby-keyword kw">end</span></pre>
21
+ </body>
22
+ </html>
data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html ADDED
@@ -0,0 +1,19 @@
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>new (Bio::Graphics::ImageMap::Element)</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/image_map.rb, line 44</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span>, <span class="ruby-identifier">url</span> = <span class="ruby-keyword kw">nil</span>)
15
+ <span class="ruby-ivar">@left</span>, <span class="ruby-ivar">@top</span>, <span class="ruby-ivar">@right</span>, <span class="ruby-ivar">@bottom</span> = <span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span>
16
+ <span class="ruby-ivar">@url</span> = ( <span class="ruby-identifier">url</span>.<span class="ruby-identifier">nil?</span> ) <span class="ruby-operator">?</span> <span class="ruby-value str">''</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">url</span>
17
+ <span class="ruby-keyword kw">end</span></pre>
18
+ </body>
19
+ </html>
data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html ADDED
@@ -0,0 +1,22 @@
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>to_s (Bio::Graphics::ImageMap::Element)</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/image_map.rb, line 50</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
15
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
16
+ <span class="ruby-keyword kw">return</span> <span class="ruby-value str">''</span>
17
+ <span class="ruby-keyword kw">else</span>
18
+ <span class="ruby-keyword kw">return</span> <span class="ruby-value str">'&lt;area shape=&quot;rect&quot; coords=&quot;'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@left</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@top</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@right</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@bottom</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'&quot; href=&quot;'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'&quot;/&gt;'</span>
19
+ <span class="ruby-keyword kw">end</span>
20
+ <span class="ruby-keyword kw">end</span></pre>
21
+ </body>
22
+ </html>
data/doc/classes/Bio/Graphics/Panel.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>
@@ -107,9 +95,9 @@ interplay between different classes.
107
95
  <h3 class="section-bar">Methods</h3>
108
96
 
109
97
  <div class="name-list">
110
- <a href="#M000006">add_track</a>&nbsp;&nbsp;
111
- <a href="#M000007">draw</a>&nbsp;&nbsp;
112
- <a href="#M000005">new</a>&nbsp;&nbsp;
98
+ <a href="#M000030">add_track</a>&nbsp;&nbsp;
99
+ <a href="#M000031">draw</a>&nbsp;&nbsp;
100
+ <a href="#M000029">new</a>&nbsp;&nbsp;
113
101
  </div>
114
102
  </div>
115
103
 
@@ -120,13 +108,6 @@ interplay between different classes.
120
108
 
121
109
  <div id="section">
122
110
 
123
- <div id="class-list">
124
- <h3 class="section-bar">Classes and Modules</h3>
125
-
126
- Class <a href="Panel/Ruler.html" class="link">Bio::Graphics::Panel::Ruler</a><br />
127
- Class <a href="Panel/Track.html" class="link">Bio::Graphics::Panel::Track</a><br />
128
-
129
- </div>
130
111
 
131
112
 
132
113
 
@@ -141,6 +122,11 @@ Class <a href="Panel/Track.html" class="link">Bio::Graphics::Panel::Track</a><br
141
122
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
142
123
  <td class="context-item-desc"></td>
143
124
  </tr>
125
+ <tr class="top-aligned-row context-row">
126
+ <td class="context-item-name">display_range</td>
127
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
128
+ <td class="context-item-desc"></td>
129
+ </tr>
144
130
  <tr class="top-aligned-row context-row">
145
131
  <td class="context-item-name">display_start</td>
146
132
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
@@ -151,6 +137,16 @@ Class <a href="Panel/Track.html" class="link">Bio::Graphics::Panel::Track</a><br
151
137
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
152
138
  <td class="context-item-desc"></td>
153
139
  </tr>
140
+ <tr class="top-aligned-row context-row">
141
+ <td class="context-item-name">final_panel_destination</td>
142
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
143
+ <td class="context-item-desc"></td>
144
+ </tr>
145
+ <tr class="top-aligned-row context-row">
146
+ <td class="context-item-name">format</td>
147
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
148
+ <td class="context-item-desc"></td>
149
+ </tr>
154
150
  <tr class="top-aligned-row context-row">
155
151
  <td class="context-item-name">height</td>
156
152
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
@@ -181,6 +177,11 @@ Class <a href="Panel/Track.html" class="link">Bio::Graphics::Panel::Track</a><br
181
177
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
182
178
  <td class="context-item-desc"></td>
183
179
  </tr>
180
+ <tr class="top-aligned-row context-row">
181
+ <td class="context-item-name">vertical</td>
182
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
183
+ <td class="context-item-desc"></td>
184
+ </tr>
184
185
  <tr class="top-aligned-row context-row">
185
186
  <td class="context-item-name">width</td>
186
187
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
@@ -196,19 +197,19 @@ Class <a href="Panel/Track.html" class="link">Bio::Graphics::Panel::Track</a><br
196
197
  <div id="methods">
197
198
  <h3 class="section-bar">Public Class methods</h3>
198
199
 
199
- <div id="method-M000005" class="method-detail">
200
- <a name="M000005"></a>
200
+ <div id="method-M000029" class="method-detail">
201
+ <a name="M000029"></a>
201
202
 
202
203
  <div class="method-heading">
203
- <a href="Panel.src/M000005.html" target="Code" class="method-signature"
204
- onclick="popupCode('Panel.src/M000005.html');return false;">
205
- <span class="method-name">new</span><span class="method-args">(length, width = DEFAULT_PANEL_WIDTH, clickable = false, display_start = nil, display_stop = nil)</span>
204
+ <a href="Panel.src/M000029.html" target="Code" class="method-signature"
205
+ onclick="popupCode('Panel.src/M000029.html');return false;">
206
+ <span class="method-name">new</span><span class="method-args">(length, opts = {})</span>
206
207
  </a>
207
208
  </div>
208
209
 
209
210
  <div class="method-description">
210
211
  <p>
211
- Create a <a href="Panel.html#M000005">new</a> <a
212
+ Create a <a href="Panel.html#M000029">new</a> <a
212
213
  href="Panel.html">Bio::Graphics::Panel</a> object
213
214
  </p>
214
215
  <pre>
@@ -217,37 +218,42 @@ href="Panel.html">Bio::Graphics::Panel</a> object
217
218
  <p>
218
219
  The height of the image is calculated automatically depending on how many
219
220
  tracks and features it contains. The width of the image defaults to 800 pt
220
- but can be set manually by using a second argument:
221
+ but can be set manually by using the width argument to the opts hash:
221
222
  </p>
222
223
  <pre>
223
- g = Bio::Graphics::Panel.new(456, 400)
224
+ g = Bio::Graphics::Panel.new(456, :width =&gt; 1200)
224
225
  </pre>
225
226
  <p>
226
- See also: Bio::Graphics::Track, BioExt::Graphics::Feature
227
+ See also: <a href="Track.html">Bio::Graphics::Panel::Track</a>, <a
228
+ href="Feature.html">Bio::Graphics::Panel::Track::Feature</a>
227
229
  </p>
228
230
  <hr size="1"></hr><p>
229
231
  <b>Arguments</b>:
230
232
  </p>
231
233
  <ul>
232
234
  <li><em>length</em> :: length of the thing you want to visualize, e.g for
233
- visualizing a sequence that is 3.24 kb long, use 324.
235
+ visualizing a sequence that is 3.24 kb long, use 324. (required)
236
+
237
+ </li>
238
+ <li>_:width_ :: width of the resulting image in pixels. (default: 800)
239
+
240
+ </li>
241
+ <li>_:clickable_ :: whether the picture should have clickable glyphs or not
242
+ (default: false) If set to true, a html file will be created with the map.
234
243
 
235
244
  </li>
236
- <li><em>width</em> :: width of the resulting image in pt. This should be a
237
- string and not an integer. Default = &#8216;800&#8217; (Notice the
238
- quotes&#8230;).
245
+ <li>_:display_start_ :: start coordinate to be displayed (default: 1)
239
246
 
240
247
  </li>
241
- <li><em>clickable</em> :: whether the picture should have clickable glyphs or
242
- not (default: false) If set to true, a html file will be created with the
243
- map.
248
+ <li>_:display_stop_ :: stop coordinate to be displayed (default: length of
249
+ sequence)
244
250
 
245
251
  </li>
246
- <li><em>display_start</em> :: start coordinate to be displayed (default: 1)
252
+ <li>_:vertical_ :: Boolean: false = horizontal (= default)
247
253
 
248
254
  </li>
249
- <li><em>display_stop</em> :: stop coordinate to be displayed (default: length
250
- of sequence)
255
+ <li>_:format_ :: File format of the picture. Can be :png, :svg, :pdf or :ps
256
+ (default: :png)
251
257
 
252
258
  </li>
253
259
  </ul>
@@ -261,66 +267,61 @@ of sequence)
261
267
 
262
268
  <h3 class="section-bar">Public Instance methods</h3>
263
269
 
264
- <div id="method-M000006" class="method-detail">
265
- <a name="M000006"></a>
270
+ <div id="method-M000030" class="method-detail">
271
+ <a name="M000030"></a>
266
272
 
267
273
  <div class="method-heading">
268
- <a href="Panel.src/M000006.html" target="Code" class="method-signature"
269
- onclick="popupCode('Panel.src/M000006.html');return false;">
270
- <span class="method-name">add_track</span><span class="method-args">(name, label = true, feature_colour = [0,0,1], feature_glyph = 'generic')</span>
274
+ <a href="Panel.src/M000030.html" target="Code" class="method-signature"
275
+ onclick="popupCode('Panel.src/M000030.html');return false;">
276
+ <span class="method-name">add_track</span><span class="method-args">(name, opts = {})</span>
271
277
  </a>
272
278
  </div>
273
279
 
274
280
  <div class="method-description">
275
281
  <p>
276
- Adds a Bio::Graphics::Track container to this panel. A panel contains a
277
- logical grouping of features, e.g. (for sequence annotation:) genes,
278
- polymorphisms, ESTs, etc.
282
+ Adds a <a href="Track.html">Bio::Graphics::Track</a> container to this
283
+ panel. A panel contains a logical grouping of features, e.g. (for sequence
284
+ annotation:) genes, polymorphisms, ESTs, etc.
279
285
  </p>
280
286
  <pre>
281
- est_track = g.add_track('ESTs')
282
- gene_track = g.add_track('genes')
287
+ est_track = g.add_track('ESTs', :label =&gt; false, :glyph =&gt; :directed_generic)
288
+ gene_track = g.add_track('genes', :label =&gt; true)
283
289
  </pre>
284
290
  <hr size="1"></hr><p>
285
291
  <b>Arguments</b>:
286
292
  </p>
287
293
  <ul>
288
- <li><em>name</em> (required) :: Name of the track to be displayed (e.g.
289
- &#8216;genes&#8217;)
294
+ <li><em>name</em> :: Name to be displayed at the top of the track. (Required)
290
295
 
291
296
  </li>
292
- <li>_label) :: Whether the feature labels should be displayed or not
297
+ <li>_:label_ :: boolean. Whether or not to display the labels for the features.
298
+ (Default = true)
293
299
 
294
300
  </li>
295
- <li><em>colour</em> :: Colour to be used to <a
296
- href="Panel.html#M000007">draw</a> the features within the track. Default =
297
- &#8216;blue&#8216;
301
+ <li>_:glyph_ :: Default glyph for features in this track. For more info, see
302
+ the lib/bio/graphics/glyph directory. (Default = :generic)
298
303
 
299
304
  </li>
300
- <li><em>glyph</em> :: Glyph to use for drawing the features. Options are:
301
- &#8216;generic&#8217;, &#8216;directed_generic&#8217;,
302
- &#8216;spliced&#8217;, &#8216;directed_spliced&#8217; and
303
- &#8216;triangle&#8217;. Triangles can be used for features whose start and
304
- stop positions are the same (e.g. SNPs). If you try to <a
305
- href="Panel.html#M000007">draw</a> a feature that is longer with triangles,
306
- an error will be shown.
305
+ <li>_:colour_ :: Default colour for features in this track, in RGB (Default =
306
+ [0,0,1])
307
307
 
308
308
  </li>
309
309
  </ul>
310
310
  <table>
311
- <tr><td valign="top"><b>Returns</b>:</td><td>Bio::Graphics::Track object that has just been created
311
+ <tr><td valign="top"><b>Returns</b>:</td><td><a href="Track.html">Bio::Graphics::Track</a> object that has just been
312
+ created
312
313
 
313
314
  </td></tr>
314
315
  </table>
315
316
  </div>
316
317
  </div>
317
318
 
318
- <div id="method-M000007" class="method-detail">
319
- <a name="M000007"></a>
319
+ <div id="method-M000031" class="method-detail">
320
+ <a name="M000031"></a>
320
321
 
321
322
  <div class="method-heading">
322
- <a href="Panel.src/M000007.html" target="Code" class="method-signature"
323
- onclick="popupCode('Panel.src/M000007.html');return false;">
323
+ <a href="Panel.src/M000031.html" target="Code" class="method-signature"
324
+ onclick="popupCode('Panel.src/M000031.html');return false;">
324
325
  <span class="method-name">draw</span><span class="method-args">(file_name)</span>
325
326
  </a>
326
327
  </div>