bio-graphics 1.2 → 1.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (331) hide show
  1. data/doc/classes/Bio.html +4 -26
  2. data/doc/classes/Bio/Feature.html +350 -0
  3. data/doc/classes/Bio/Feature.src/M000010.html +21 -0
  4. data/doc/classes/Bio/Feature.src/M000011.html +20 -0
  5. data/doc/classes/Bio/Feature.src/M000012.html +19 -0
  6. data/doc/classes/Bio/Feature.src/M000014.html +21 -0
  7. data/doc/classes/Bio/Feature.src/M000016.html +21 -0
  8. data/doc/classes/Bio/Feature.src/M000034.html +21 -0
  9. data/doc/classes/Bio/Feature.src/M000035.html +20 -0
  10. data/doc/classes/Bio/Feature.src/M000036.html +19 -0
  11. data/doc/classes/Bio/Feature.src/M000038.html +21 -0
  12. data/doc/classes/Bio/Feature.src/M000040.html +21 -0
  13. data/doc/classes/Bio/Feature.src/M000042.html +21 -0
  14. data/doc/classes/Bio/Feature.src/M000043.html +20 -0
  15. data/doc/classes/Bio/Feature.src/M000044.html +21 -0
  16. data/doc/classes/Bio/Feature.src/M000045.html +20 -0
  17. data/doc/classes/Bio/Feature.src/M000046.html +19 -0
  18. data/doc/classes/Bio/Feature.src/M000048.html +21 -0
  19. data/doc/classes/Bio/Feature.src/M000050.html +21 -0
  20. data/doc/classes/Bio/Feature.src/M000074.html +21 -0
  21. data/doc/classes/Bio/Feature.src/M000075.html +20 -0
  22. data/doc/classes/Bio/Feature.src/M000076.html +19 -0
  23. data/doc/classes/Bio/Feature.src/M000078.html +21 -0
  24. data/doc/classes/Bio/Feature.src/M000080.html +21 -0
  25. data/doc/classes/Bio/Feature/Qualifier.html +189 -0
  26. data/doc/classes/Bio/Feature/Qualifier.src/M000017.html +18 -0
  27. data/doc/classes/Bio/Feature/Qualifier.src/M000041.html +18 -0
  28. data/doc/classes/Bio/Feature/Qualifier.src/M000049.html +18 -0
  29. data/doc/classes/Bio/Feature/Qualifier.src/M000051.html +18 -0
  30. data/doc/classes/Bio/Feature/Qualifier.src/M000081.html +18 -0
  31. data/doc/classes/Bio/Features.html +329 -0
  32. data/doc/classes/Bio/Features.src/M000004.html +18 -0
  33. data/doc/classes/Bio/Features.src/M000005.html +19 -0
  34. data/doc/classes/Bio/Features.src/M000006.html +21 -0
  35. data/doc/classes/Bio/Features.src/M000007.html +18 -0
  36. data/doc/classes/Bio/Features.src/M000008.html +18 -0
  37. data/doc/classes/Bio/Features.src/M000009.html +18 -0
  38. data/doc/classes/Bio/Features.src/M000028.html +18 -0
  39. data/doc/classes/Bio/Features.src/M000029.html +19 -0
  40. data/doc/classes/Bio/Features.src/M000030.html +21 -0
  41. data/doc/classes/Bio/Features.src/M000031.html +18 -0
  42. data/doc/classes/Bio/Features.src/M000032.html +18 -0
  43. data/doc/classes/Bio/Features.src/M000033.html +18 -0
  44. data/doc/classes/Bio/Features.src/M000036.html +18 -0
  45. data/doc/classes/Bio/Features.src/M000037.html +19 -0
  46. data/doc/classes/Bio/Features.src/M000038.html +18 -0
  47. data/doc/classes/Bio/Features.src/M000039.html +19 -0
  48. data/doc/classes/Bio/Features.src/M000040.html +21 -0
  49. data/doc/classes/Bio/Features.src/M000041.html +18 -0
  50. data/doc/classes/Bio/Features.src/M000042.html +18 -0
  51. data/doc/classes/Bio/Features.src/M000043.html +18 -0
  52. data/doc/classes/Bio/Features.src/M000068.html +18 -0
  53. data/doc/classes/Bio/Features.src/M000069.html +19 -0
  54. data/doc/classes/Bio/Features.src/M000070.html +21 -0
  55. data/doc/classes/Bio/Features.src/M000071.html +18 -0
  56. data/doc/classes/Bio/Features.src/M000072.html +18 -0
  57. data/doc/classes/Bio/Features.src/M000073.html +18 -0
  58. data/doc/classes/Bio/Graphics.html +28 -42
  59. data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} +98 -125
  60. data/doc/classes/Bio/Graphics/Feature.src/M000020.html +51 -0
  61. data/doc/classes/Bio/Graphics/Feature.src/M000021.html +65 -0
  62. data/doc/classes/Bio/Graphics/Feature.src/M000022.html +55 -0
  63. data/doc/classes/Bio/Graphics/Feature.src/M000023.html +66 -0
  64. data/doc/classes/Bio/Graphics/Feature.src/M000024.html +51 -0
  65. data/doc/classes/Bio/Graphics/Feature.src/M000025.html +65 -0
  66. data/doc/classes/Bio/Graphics/Feature.src/M000026.html +55 -0
  67. data/doc/classes/Bio/Graphics/Feature.src/M000054.html +51 -0
  68. data/doc/classes/Bio/Graphics/Feature.src/M000055.html +65 -0
  69. data/doc/classes/Bio/Graphics/Feature.src/M000056.html +55 -0
  70. data/doc/classes/Bio/Graphics/Feature/SubFeature.html +348 -0
  71. data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000025.html +68 -0
  72. data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000026.html +67 -0
  73. data/doc/classes/Bio/Graphics/Glyph.html +178 -0
  74. data/doc/classes/Bio/Graphics/Glyph/Box.html +139 -0
  75. data/doc/classes/Bio/Graphics/Glyph/Box.src/M000004.html +24 -0
  76. data/doc/classes/Bio/Graphics/Glyph/Box.src/M000032.html +24 -0
  77. data/doc/classes/Bio/Graphics/Glyph/Common.html +187 -0
  78. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html +18 -0
  79. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html +18 -0
  80. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html +24 -0
  81. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html +24 -0
  82. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html +18 -0
  83. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html +24 -0
  84. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html +24 -0
  85. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html +139 -0
  86. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html +22 -0
  87. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html +139 -0
  88. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html +22 -0
  89. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.html +139 -0
  90. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html +31 -0
  91. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html +31 -0
  92. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html +139 -0
  93. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html +26 -0
  94. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html +26 -0
  95. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html +26 -0
  96. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html +139 -0
  97. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html +40 -0
  98. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html +40 -0
  99. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html +40 -0
  100. data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.html} +16 -19
  101. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html +22 -0
  102. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html +22 -0
  103. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html +22 -0
  104. data/doc/classes/Bio/Graphics/Glyph/Generic.html +139 -0
  105. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html +18 -0
  106. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html +18 -0
  107. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html +18 -0
  108. data/doc/classes/Bio/Graphics/Glyph/Line.html +139 -0
  109. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html +20 -0
  110. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html +20 -0
  111. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html +20 -0
  112. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.html +139 -0
  113. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html +28 -0
  114. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html +28 -0
  115. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html +28 -0
  116. data/doc/classes/Bio/Graphics/Glyph/Spliced.html +139 -0
  117. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html +19 -0
  118. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html +19 -0
  119. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html +19 -0
  120. data/doc/classes/Bio/Graphics/Glyph/Transcript.html +113 -0
  121. data/doc/classes/Bio/Graphics/Glyph/Triangle.html +139 -0
  122. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html +21 -0
  123. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html +21 -0
  124. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html +21 -0
  125. data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.html} +50 -16
  126. data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} +3 -3
  127. data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html +18 -0
  128. data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html +18 -0
  129. data/doc/classes/Bio/Graphics/ImageMap.src/M000033.html +18 -0
  130. data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} +7 -4
  131. data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html +24 -0
  132. data/doc/classes/Bio/Graphics/ImageMap.src/M000062.html +18 -0
  133. data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html +18 -0
  134. data/doc/classes/Bio/Graphics/ImageMap.src/M000064.html +27 -0
  135. data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html +24 -0
  136. data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} +14 -14
  137. data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} +3 -3
  138. data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} +6 -4
  139. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html +19 -0
  140. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html +22 -0
  141. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html +19 -0
  142. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html +22 -0
  143. data/doc/classes/Bio/Graphics/Panel.html +70 -69
  144. data/doc/classes/Bio/Graphics/Panel.src/M000025.html +52 -0
  145. data/doc/classes/Bio/Graphics/Panel.src/M000026.html +20 -0
  146. data/doc/classes/Bio/Graphics/Panel.src/M000027.html +98 -0
  147. data/doc/classes/Bio/Graphics/Panel.src/M000028.html +20 -0
  148. data/doc/classes/Bio/Graphics/Panel.src/M000029.html +52 -0
  149. data/doc/classes/Bio/Graphics/Panel.src/M000030.html +20 -0
  150. data/doc/classes/Bio/Graphics/Panel.src/M000031.html +98 -0
  151. data/doc/classes/Bio/Graphics/Panel.src/M000059.html +52 -0
  152. data/doc/classes/Bio/Graphics/Panel.src/M000060.html +20 -0
  153. data/doc/classes/Bio/Graphics/Panel.src/M000061.html +98 -0
  154. data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} +50 -21
  155. data/doc/classes/Bio/Graphics/Ruler.src/M000015.html +30 -0
  156. data/doc/classes/Bio/Graphics/Ruler.src/M000016.html +20 -0
  157. data/doc/classes/Bio/Graphics/Ruler.src/M000017.html +30 -0
  158. data/doc/classes/Bio/Graphics/Ruler.src/M000018.html +20 -0
  159. data/doc/classes/Bio/Graphics/Ruler.src/M000019.html +26 -0
  160. data/doc/classes/Bio/Graphics/Ruler.src/M000020.html +45 -0
  161. data/doc/classes/Bio/Graphics/Ruler.src/M000047.html +30 -0
  162. data/doc/classes/Bio/Graphics/Ruler.src/M000048.html +20 -0
  163. data/doc/classes/Bio/Graphics/Ruler.src/M000049.html +26 -0
  164. data/doc/classes/Bio/Graphics/Ruler.src/M000050.html +45 -0
  165. data/doc/classes/Bio/Graphics/SubFeature.html +348 -0
  166. data/doc/classes/Bio/Graphics/SubFeature.src/M000001.html +73 -0
  167. data/doc/classes/Bio/Graphics/SubFeature.src/M000002.html +69 -0
  168. data/doc/classes/Bio/Graphics/SubFeature.src/M000023.html +73 -0
  169. data/doc/classes/Bio/Graphics/SubFeature.src/M000024.html +69 -0
  170. data/doc/classes/Bio/Graphics/SubFeature.src/M000027.html +73 -0
  171. data/doc/classes/Bio/Graphics/SubFeature.src/M000028.html +69 -0
  172. data/doc/classes/Bio/Graphics/SubFeature.src/M000057.html +73 -0
  173. data/doc/classes/Bio/Graphics/SubFeature.src/M000058.html +69 -0
  174. data/doc/classes/Bio/Graphics/{Panel/Track.html → Track.html} +67 -69
  175. data/doc/classes/Bio/Graphics/Track.src/M000017.html +39 -0
  176. data/doc/classes/Bio/Graphics/Track.src/M000018.html +37 -0
  177. data/doc/classes/Bio/Graphics/Track.src/M000019.html +45 -0
  178. data/doc/classes/Bio/Graphics/Track.src/M000020.html +41 -0
  179. data/doc/classes/Bio/Graphics/Track.src/M000021.html +39 -0
  180. data/doc/classes/Bio/Graphics/Track.src/M000022.html +37 -0
  181. data/doc/classes/Bio/Graphics/Track.src/M000023.html +45 -0
  182. data/doc/classes/Bio/Graphics/Track.src/M000051.html +39 -0
  183. data/doc/classes/Bio/Graphics/Track.src/M000052.html +37 -0
  184. data/doc/classes/Bio/Graphics/Track.src/M000053.html +45 -0
  185. data/doc/classes/Range.html +129 -0
  186. data/doc/classes/String.html +167 -0
  187. data/doc/classes/String.src/M000001.html +18 -0
  188. data/doc/classes/String.src/M000002.html +18 -0
  189. data/doc/classes/String.src/M000003.html +23 -0
  190. data/doc/classes/String.src/M000029.html +18 -0
  191. data/doc/classes/String.src/M000030.html +18 -0
  192. data/doc/classes/String.src/M000031.html +23 -0
  193. data/doc/classes/TestCustomGlyph.html +137 -0
  194. data/doc/classes/TestCustomGlyph.src/M000025.html +25 -0
  195. data/doc/classes/TestCustomGlyphInFile.html +167 -0
  196. data/doc/classes/TestCustomGlyphInFile.src/M000026.html +19 -0
  197. data/doc/classes/TestCustomGlyphInFile.src/M000027.html +25 -0
  198. data/doc/classes/TestCustomGlyphInFile.src/M000028.html +18 -0
  199. data/doc/classes/TestExtensions.html +152 -0
  200. data/doc/classes/TestExtensions.src/M000015.html +22 -0
  201. data/doc/classes/TestExtensions.src/M000016.html +25 -0
  202. data/doc/classes/TestFeature.html +152 -0
  203. data/doc/classes/TestFeature.src/M000017.html +19 -0
  204. data/doc/classes/TestFeature.src/M000018.html +21 -0
  205. data/doc/classes/TestImageMap.html +182 -0
  206. data/doc/classes/TestImageMap.src/M000019.html +22 -0
  207. data/doc/classes/TestImageMap.src/M000020.html +56 -0
  208. data/doc/classes/TestImageMap.src/M000021.html +56 -0
  209. data/doc/classes/TestImageMap.src/M000022.html +20 -0
  210. data/doc/classes/TestPanel.html +276 -0
  211. data/doc/classes/TestPanel.src/M000001.html +18 -0
  212. data/doc/classes/TestPanel.src/M000002.html +61 -0
  213. data/doc/classes/TestPanel.src/M000003.html +35 -0
  214. data/doc/classes/TestPanel.src/M000004.html +54 -0
  215. data/doc/classes/TestPanel.src/M000005.html +54 -0
  216. data/doc/classes/TestPanel.src/M000006.html +41 -0
  217. data/doc/classes/TestPanel.src/M000007.html +36 -0
  218. data/doc/classes/TestPanel.src/M000008.html +20 -0
  219. data/doc/classes/TestPanel.src/M000009.html +26 -0
  220. data/doc/classes/TestPanel.src/M000010.html +21 -0
  221. data/doc/classes/TestRuler.html +152 -0
  222. data/doc/classes/TestRuler.src/M000013.html +22 -0
  223. data/doc/classes/TestRuler.src/M000014.html +31 -0
  224. data/doc/classes/TestSubFeature.html +152 -0
  225. data/doc/classes/TestSubFeature.src/M000023.html +21 -0
  226. data/doc/classes/TestSubFeature.src/M000024.html +18 -0
  227. data/doc/classes/TestTrack.html +152 -0
  228. data/doc/classes/TestTrack.src/M000011.html +19 -0
  229. data/doc/classes/TestTrack.src/M000012.html +23 -0
  230. data/doc/created.rid +1 -1
  231. data/doc/files/README_DEV.html +399 -70
  232. data/doc/files/TUTORIAL.html +188 -67
  233. data/doc/files/lib/bio-graphics_rb.html +3 -2
  234. data/doc/files/lib/bio/graphics/feature_rb.html +12 -6
  235. data/doc/files/lib/bio/graphics/glyphs/box_rb.html +113 -0
  236. data/doc/files/lib/bio/graphics/glyphs/common_rb.html +113 -0
  237. data/doc/files/lib/bio/graphics/glyphs/directed_box_rb.html +113 -0
  238. data/doc/files/lib/bio/graphics/glyphs/directed_generic_rb.html +113 -0
  239. data/doc/files/lib/bio/graphics/glyphs/directed_spliced_rb.html +113 -0
  240. data/doc/files/lib/bio/graphics/glyphs/dot_rb.html +113 -0
  241. data/doc/files/lib/bio/graphics/glyphs/generic_rb.html +113 -0
  242. data/doc/files/lib/bio/graphics/glyphs/line_rb.html +113 -0
  243. data/doc/files/lib/bio/graphics/glyphs/line_with_handles_rb.html +113 -0
  244. data/doc/files/lib/bio/graphics/glyphs/spliced_rb.html +113 -0
  245. data/doc/files/lib/bio/graphics/glyphs/transcript_rb.html +113 -0
  246. data/doc/files/lib/bio/graphics/glyphs/triangle_rb.html +113 -0
  247. data/doc/files/lib/bio/graphics/image_map_rb.html +3 -2
  248. data/doc/files/lib/bio/graphics/panel_rb.html +10 -2
  249. data/doc/files/lib/bio/graphics/ruler_rb.html +3 -2
  250. data/doc/files/lib/bio/graphics/subfeature_rb.html +114 -0
  251. data/doc/files/lib/bio/graphics/track_rb.html +3 -2
  252. data/doc/files/lib/feature_rb.html +101 -0
  253. data/doc/files/samples/arkdb_features_rb.html +101 -0
  254. data/doc/files/samples/glyph_showcase_rb.html +108 -0
  255. data/doc/files/samples/protein_domains_rb.html +115 -0
  256. data/doc/files/samples/subfeatures_rb.html +108 -0
  257. data/doc/files/scripts/gff2png_rb.html +154 -0
  258. data/doc/files/test/unit/custom_glyph_in_file_rb.html +101 -0
  259. data/doc/files/test/unit/test_class_extensions_rb.html +108 -0
  260. data/doc/files/test/unit/test_creation_rb.html +108 -0
  261. data/doc/files/test/unit/test_custom_glyph_rb.html +108 -0
  262. data/doc/files/test/unit/test_draw_rb.html +108 -0
  263. data/doc/files/test/unit/test_imagemap_rb.html +108 -0
  264. data/doc/files/test/unit/test_subfeatures_rb.html +108 -0
  265. data/doc/fr_class_index.html +24 -6
  266. data/doc/fr_file_index.html +14 -0
  267. data/doc/fr_method_index.html +51 -19
  268. data/doc/images/glyph_showcase.png +0 -0
  269. data/doc/images/terms.svg +146 -132
  270. data/images/glyph_showcase.png +0 -0
  271. data/lib/bio-graphics.rb +38 -6
  272. data/lib/bio/graphics/feature.rb +212 -440
  273. data/lib/bio/graphics/glyphs/box.rb +21 -0
  274. data/lib/bio/graphics/glyphs/common.rb +149 -0
  275. data/lib/bio/graphics/glyphs/directed_box.rb +28 -0
  276. data/lib/bio/graphics/glyphs/directed_generic.rb +23 -0
  277. data/lib/bio/graphics/glyphs/directed_spliced.rb +39 -0
  278. data/lib/bio/graphics/glyphs/dot.rb +21 -0
  279. data/lib/bio/graphics/glyphs/generic.rb +15 -0
  280. data/lib/bio/graphics/glyphs/line.rb +17 -0
  281. data/lib/bio/graphics/glyphs/line_with_handles.rb +25 -0
  282. data/lib/bio/graphics/glyphs/spliced.rb +16 -0
  283. data/lib/bio/graphics/glyphs/transcript.rb +12 -0
  284. data/lib/bio/graphics/glyphs/triangle.rb +18 -0
  285. data/lib/bio/graphics/image_map.rb +25 -4
  286. data/lib/bio/graphics/panel.rb +266 -209
  287. data/lib/bio/graphics/ruler.rb +95 -96
  288. data/lib/bio/graphics/subfeature.rb +187 -0
  289. data/lib/bio/graphics/track.rb +155 -156
  290. data/lib/feature.rb +204 -0
  291. data/samples/arkdb_features.rb +10 -8
  292. data/samples/glyph_showcase.rb +58 -22
  293. data/samples/protein_domains.rb +19 -0
  294. data/samples/subfeatures.rb +31 -0
  295. data/test/unit/custom_glyph_in_file.rb +12 -0
  296. data/test/unit/data.txt +32 -0
  297. data/test/unit/test_class_extensions.rb +23 -0
  298. data/test/unit/test_creation.rb +43 -13
  299. data/test/unit/test_custom_glyph.rb +50 -0
  300. data/test/unit/test_draw.rb +211 -0
  301. data/test/unit/test_imagemap.rb +134 -0
  302. data/test/unit/test_subfeatures.rb +17 -0
  303. metadata +396 -119
  304. data/doc/classes/Bio/Graphics/Panel.src/M000005.html +0 -29
  305. data/doc/classes/Bio/Graphics/Panel.src/M000006.html +0 -19
  306. data/doc/classes/Bio/Graphics/Panel.src/M000007.html +0 -68
  307. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +0 -20
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  320. data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +0 -23
  321. data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +0 -43
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  328. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +0 -18
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data/doc/classes/Bio/Graphics/Glyph/Triangle.html ADDED
@@ -0,0 +1,139 @@
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"
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+ "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">
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+ <head>
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+ <title>Class: Bio::Graphics::Glyph::Triangle</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <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" />
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+ <script type="text/javascript">
13
+ // <![CDATA[
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+
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+ 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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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
21
+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
24
+ else
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+ return false;
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+ elemStyle = elem.style;
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+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
31
+ } else {
32
+ elemStyle.display = "none"
33
+ }
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+
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+ return true;
36
+ }
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+
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+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <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::Triangle</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/triangle_rb.html">
59
+ lib/bio/graphics/glyphs/triangle.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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+
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+ <div id="method-list">
88
+ <h3 class="section-bar">Methods</h3>
89
+
90
+ <div class="name-list">
91
+ <a href="#M000008">draw</a>&nbsp;&nbsp;
92
+ </div>
93
+ </div>
94
+
95
+ </div>
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+
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+
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+ <!-- if includes -->
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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 -->
110
+ <div id="methods">
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+ <h3 class="section-bar">Public Instance methods</h3>
112
+
113
+ <div id="method-M000008" class="method-detail">
114
+ <a name="M000008"></a>
115
+
116
+ <div class="method-heading">
117
+ <a href="Triangle.src/M000008.html" target="Code" class="method-signature"
118
+ onclick="popupCode('Triangle.src/M000008.html');return false;">
119
+ <span class="method-name">draw</span><span class="method-args">()</span>
120
+ </a>
121
+ </div>
122
+
123
+ <div class="method-description">
124
+ </div>
125
+ </div>
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+
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+
128
+ </div>
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+
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+
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+ </div>
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+
133
+
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+ <div id="validator-badges">
135
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
136
+ </div>
137
+
138
+ </body>
139
+ </html>
data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html ADDED
@@ -0,0 +1,21 @@
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::Triangle)</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/triangle.rb, line 3</span>
14
+ <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>
16
+
17
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:north</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">stroke</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html ADDED
@@ -0,0 +1,21 @@
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::Triangle)</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/triangle.rb, line 11</span>
14
+ <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>
16
+
17
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:north</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">stroke</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html ADDED
@@ -0,0 +1,21 @@
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::Triangle)</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/triangle.rb, line 11</span>
14
+ <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>
16
+
17
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-ivar">@feature_context</span>,<span class="ruby-identifier">:north</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">stroke</span>
19
+ <span class="ruby-keyword kw">end</span></pre>
20
+ </body>
21
+ </html>
data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.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: ImageMap</title>
8
+ <title>Class: Bio::Graphics::ImageMap</title>
9
9
  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
10
  <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
11
+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
12
12
  <script type="text/javascript">
13
13
  // <![CDATA[
14
14
 
@@ -50,12 +50,12 @@
50
50
  <table class="header-table">
51
51
  <tr class="top-aligned-row">
52
52
  <td><strong>Class</strong></td>
53
- <td class="class-name-in-header">ImageMap</td>
53
+ <td class="class-name-in-header">Bio::Graphics::ImageMap</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 />
@@ -81,7 +81,8 @@
81
81
  <div id="description">
82
82
  <h1>bio/graphics/image_map.rb - create the image map for clickable images</h1>
83
83
  <table>
84
- <tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
84
+ <tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt; Charles Comstock
85
+ &lt;dgtized@gmail.com&gt;
85
86
 
86
87
  </td></tr>
87
88
  <tr><td valign="top">License:</td><td>Ruby&#8216;s
@@ -98,8 +99,10 @@
98
99
  <h3 class="section-bar">Methods</h3>
99
100
 
100
101
  <div class="name-list">
101
- <a href="#M000001">new</a>&nbsp;&nbsp;
102
- <a href="#M000002">to_s</a>&nbsp;&nbsp;
102
+ <a href="#M000033">add_element</a>&nbsp;&nbsp;
103
+ <a href="#M000035">flip_orientation</a>&nbsp;&nbsp;
104
+ <a href="#M000032">new</a>&nbsp;&nbsp;
105
+ <a href="#M000034">to_s</a>&nbsp;&nbsp;
103
106
  </div>
104
107
  </div>
105
108
 
@@ -113,7 +116,7 @@
113
116
  <div id="class-list">
114
117
  <h3 class="section-bar">Classes and Modules</h3>
115
118
 
116
- Class <a href="ImageMap/ImageMapElement.html" class="link">ImageMap::ImageMapElement</a><br />
119
+ Class <a href="ImageMap/Element.html" class="link">Bio::Graphics::ImageMap::Element</a><br />
117
120
 
118
121
  </div>
119
122
 
@@ -140,12 +143,12 @@
140
143
  <div id="methods">
141
144
  <h3 class="section-bar">Public Class methods</h3>
142
145
 
143
- <div id="method-M000001" class="method-detail">
144
- <a name="M000001"></a>
146
+ <div id="method-M000032" class="method-detail">
147
+ <a name="M000032"></a>
145
148
 
146
149
  <div class="method-heading">
147
- <a href="ImageMap.src/M000001.html" target="Code" class="method-signature"
148
- onclick="popupCode('ImageMap.src/M000001.html');return false;">
150
+ <a href="ImageMap.src/M000032.html" target="Code" class="method-signature"
151
+ onclick="popupCode('ImageMap.src/M000032.html');return false;">
149
152
  <span class="method-name">new</span><span class="method-args">()</span>
150
153
  </a>
151
154
  </div>
@@ -156,12 +159,43 @@
156
159
 
157
160
  <h3 class="section-bar">Public Instance methods</h3>
158
161
 
159
- <div id="method-M000002" class="method-detail">
160
- <a name="M000002"></a>
162
+ <div id="method-M000033" class="method-detail">
163
+ <a name="M000033"></a>
161
164
 
162
165
  <div class="method-heading">
163
- <a href="ImageMap.src/M000002.html" target="Code" class="method-signature"
164
- onclick="popupCode('ImageMap.src/M000002.html');return false;">
166
+ <a href="ImageMap.src/M000033.html" target="Code" class="method-signature"
167
+ onclick="popupCode('ImageMap.src/M000033.html');return false;">
168
+ <span class="method-name">add_element</span><span class="method-args">(left,top,right,bottom,url = nil)</span>
169
+ </a>
170
+ </div>
171
+
172
+ <div class="method-description">
173
+ </div>
174
+ </div>
175
+
176
+ <div id="method-M000035" class="method-detail">
177
+ <a name="M000035"></a>
178
+
179
+ <div class="method-heading">
180
+ <a href="ImageMap.src/M000035.html" target="Code" class="method-signature"
181
+ onclick="popupCode('ImageMap.src/M000035.html');return false;">
182
+ <span class="method-name">flip_orientation</span><span class="method-args">(width)</span>
183
+ </a>
184
+ </div>
185
+
186
+ <div class="method-description">
187
+ <p>
188
+ Switch horizontal to vertical orientation
189
+ </p>
190
+ </div>
191
+ </div>
192
+
193
+ <div id="method-M000034" class="method-detail">
194
+ <a name="M000034"></a>
195
+
196
+ <div class="method-heading">
197
+ <a href="ImageMap.src/M000034.html" target="Code" class="method-signature"
198
+ onclick="popupCode('ImageMap.src/M000034.html');return false;">
165
199
  <span class="method-name">to_s</span><span class="method-args">()</span>
166
200
  </a>
167
201
  </div>
data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} RENAMED
@@ -5,12 +5,12 @@
5
5
 
6
6
  <html>
7
7
  <head>
8
- <title>new (ImageMap)</title>
8
+ <title>new (Bio::Graphics::ImageMap)</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 8</span>
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 9</span>
14
14
  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>
15
15
  <span class="ruby-ivar">@elements</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
16
  <span class="ruby-keyword kw">end</span></pre>
data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html ADDED
@@ -0,0 +1,18 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>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/M000032.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>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/M000033.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"
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>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/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} RENAMED
@@ -5,17 +5,20 @@
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5
 
6
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  <html>
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  <head>
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- <title>to_s (ImageMap)</title>
8
+ <title>to_s (Bio::Graphics::ImageMap)</title>
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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 13</span>
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 18</span>
14
14
  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
15
15
  <span class="ruby-identifier">output</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
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
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">output</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">e</span>.<span class="ruby-identifier">to_s</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>
19
22
  <span class="ruby-keyword kw">end</span>
20
23
  <span class="ruby-identifier">output</span>.<span class="ruby-identifier">push</span>(<span class="ruby-value str">'&lt;/map&gt;'</span>)
21
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>)
data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html ADDED
@@ -0,0 +1,24 @@
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>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>