bio-graphics 1.2 → 1.4

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Files changed (331) hide show
  1. data/doc/classes/Bio.html +4 -26
  2. data/doc/classes/Bio/Feature.html +350 -0
  3. data/doc/classes/Bio/Feature.src/M000010.html +21 -0
  4. data/doc/classes/Bio/Feature.src/M000011.html +20 -0
  5. data/doc/classes/Bio/Feature.src/M000012.html +19 -0
  6. data/doc/classes/Bio/Feature.src/M000014.html +21 -0
  7. data/doc/classes/Bio/Feature.src/M000016.html +21 -0
  8. data/doc/classes/Bio/Feature.src/M000034.html +21 -0
  9. data/doc/classes/Bio/Feature.src/M000035.html +20 -0
  10. data/doc/classes/Bio/Feature.src/M000036.html +19 -0
  11. data/doc/classes/Bio/Feature.src/M000038.html +21 -0
  12. data/doc/classes/Bio/Feature.src/M000040.html +21 -0
  13. data/doc/classes/Bio/Feature.src/M000042.html +21 -0
  14. data/doc/classes/Bio/Feature.src/M000043.html +20 -0
  15. data/doc/classes/Bio/Feature.src/M000044.html +21 -0
  16. data/doc/classes/Bio/Feature.src/M000045.html +20 -0
  17. data/doc/classes/Bio/Feature.src/M000046.html +19 -0
  18. data/doc/classes/Bio/Feature.src/M000048.html +21 -0
  19. data/doc/classes/Bio/Feature.src/M000050.html +21 -0
  20. data/doc/classes/Bio/Feature.src/M000074.html +21 -0
  21. data/doc/classes/Bio/Feature.src/M000075.html +20 -0
  22. data/doc/classes/Bio/Feature.src/M000076.html +19 -0
  23. data/doc/classes/Bio/Feature.src/M000078.html +21 -0
  24. data/doc/classes/Bio/Feature.src/M000080.html +21 -0
  25. data/doc/classes/Bio/Feature/Qualifier.html +189 -0
  26. data/doc/classes/Bio/Feature/Qualifier.src/M000017.html +18 -0
  27. data/doc/classes/Bio/Feature/Qualifier.src/M000041.html +18 -0
  28. data/doc/classes/Bio/Feature/Qualifier.src/M000049.html +18 -0
  29. data/doc/classes/Bio/Feature/Qualifier.src/M000051.html +18 -0
  30. data/doc/classes/Bio/Feature/Qualifier.src/M000081.html +18 -0
  31. data/doc/classes/Bio/Features.html +329 -0
  32. data/doc/classes/Bio/Features.src/M000004.html +18 -0
  33. data/doc/classes/Bio/Features.src/M000005.html +19 -0
  34. data/doc/classes/Bio/Features.src/M000006.html +21 -0
  35. data/doc/classes/Bio/Features.src/M000007.html +18 -0
  36. data/doc/classes/Bio/Features.src/M000008.html +18 -0
  37. data/doc/classes/Bio/Features.src/M000009.html +18 -0
  38. data/doc/classes/Bio/Features.src/M000028.html +18 -0
  39. data/doc/classes/Bio/Features.src/M000029.html +19 -0
  40. data/doc/classes/Bio/Features.src/M000030.html +21 -0
  41. data/doc/classes/Bio/Features.src/M000031.html +18 -0
  42. data/doc/classes/Bio/Features.src/M000032.html +18 -0
  43. data/doc/classes/Bio/Features.src/M000033.html +18 -0
  44. data/doc/classes/Bio/Features.src/M000036.html +18 -0
  45. data/doc/classes/Bio/Features.src/M000037.html +19 -0
  46. data/doc/classes/Bio/Features.src/M000038.html +18 -0
  47. data/doc/classes/Bio/Features.src/M000039.html +19 -0
  48. data/doc/classes/Bio/Features.src/M000040.html +21 -0
  49. data/doc/classes/Bio/Features.src/M000041.html +18 -0
  50. data/doc/classes/Bio/Features.src/M000042.html +18 -0
  51. data/doc/classes/Bio/Features.src/M000043.html +18 -0
  52. data/doc/classes/Bio/Features.src/M000068.html +18 -0
  53. data/doc/classes/Bio/Features.src/M000069.html +19 -0
  54. data/doc/classes/Bio/Features.src/M000070.html +21 -0
  55. data/doc/classes/Bio/Features.src/M000071.html +18 -0
  56. data/doc/classes/Bio/Features.src/M000072.html +18 -0
  57. data/doc/classes/Bio/Features.src/M000073.html +18 -0
  58. data/doc/classes/Bio/Graphics.html +28 -42
  59. data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} +98 -125
  60. data/doc/classes/Bio/Graphics/Feature.src/M000020.html +51 -0
  61. data/doc/classes/Bio/Graphics/Feature.src/M000021.html +65 -0
  62. data/doc/classes/Bio/Graphics/Feature.src/M000022.html +55 -0
  63. data/doc/classes/Bio/Graphics/Feature.src/M000023.html +66 -0
  64. data/doc/classes/Bio/Graphics/Feature.src/M000024.html +51 -0
  65. data/doc/classes/Bio/Graphics/Feature.src/M000025.html +65 -0
  66. data/doc/classes/Bio/Graphics/Feature.src/M000026.html +55 -0
  67. data/doc/classes/Bio/Graphics/Feature.src/M000054.html +51 -0
  68. data/doc/classes/Bio/Graphics/Feature.src/M000055.html +65 -0
  69. data/doc/classes/Bio/Graphics/Feature.src/M000056.html +55 -0
  70. data/doc/classes/Bio/Graphics/Feature/SubFeature.html +348 -0
  71. data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000025.html +68 -0
  72. data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000026.html +67 -0
  73. data/doc/classes/Bio/Graphics/Glyph.html +178 -0
  74. data/doc/classes/Bio/Graphics/Glyph/Box.html +139 -0
  75. data/doc/classes/Bio/Graphics/Glyph/Box.src/M000004.html +24 -0
  76. data/doc/classes/Bio/Graphics/Glyph/Box.src/M000032.html +24 -0
  77. data/doc/classes/Bio/Graphics/Glyph/Common.html +187 -0
  78. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html +18 -0
  79. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html +18 -0
  80. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html +24 -0
  81. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html +24 -0
  82. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html +18 -0
  83. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html +24 -0
  84. data/doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html +24 -0
  85. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html +139 -0
  86. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html +22 -0
  87. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html +139 -0
  88. data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html +22 -0
  89. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.html +139 -0
  90. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html +31 -0
  91. data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html +31 -0
  92. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html +139 -0
  93. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html +26 -0
  94. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html +26 -0
  95. data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html +26 -0
  96. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html +139 -0
  97. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html +40 -0
  98. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html +40 -0
  99. data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html +40 -0
  100. data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.html} +16 -19
  101. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html +22 -0
  102. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html +22 -0
  103. data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html +22 -0
  104. data/doc/classes/Bio/Graphics/Glyph/Generic.html +139 -0
  105. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html +18 -0
  106. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html +18 -0
  107. data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html +18 -0
  108. data/doc/classes/Bio/Graphics/Glyph/Line.html +139 -0
  109. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html +20 -0
  110. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html +20 -0
  111. data/doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html +20 -0
  112. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.html +139 -0
  113. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html +28 -0
  114. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html +28 -0
  115. data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html +28 -0
  116. data/doc/classes/Bio/Graphics/Glyph/Spliced.html +139 -0
  117. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html +19 -0
  118. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html +19 -0
  119. data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html +19 -0
  120. data/doc/classes/Bio/Graphics/Glyph/Transcript.html +113 -0
  121. data/doc/classes/Bio/Graphics/Glyph/Triangle.html +139 -0
  122. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html +21 -0
  123. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html +21 -0
  124. data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html +21 -0
  125. data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.html} +50 -16
  126. data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} +3 -3
  127. data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html +18 -0
  128. data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html +18 -0
  129. data/doc/classes/Bio/Graphics/ImageMap.src/M000033.html +18 -0
  130. data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} +7 -4
  131. data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html +24 -0
  132. data/doc/classes/Bio/Graphics/ImageMap.src/M000062.html +18 -0
  133. data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html +18 -0
  134. data/doc/classes/Bio/Graphics/ImageMap.src/M000064.html +27 -0
  135. data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html +24 -0
  136. data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} +14 -14
  137. data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} +3 -3
  138. data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} +6 -4
  139. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html +19 -0
  140. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html +22 -0
  141. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html +19 -0
  142. data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html +22 -0
  143. data/doc/classes/Bio/Graphics/Panel.html +70 -69
  144. data/doc/classes/Bio/Graphics/Panel.src/M000025.html +52 -0
  145. data/doc/classes/Bio/Graphics/Panel.src/M000026.html +20 -0
  146. data/doc/classes/Bio/Graphics/Panel.src/M000027.html +98 -0
  147. data/doc/classes/Bio/Graphics/Panel.src/M000028.html +20 -0
  148. data/doc/classes/Bio/Graphics/Panel.src/M000029.html +52 -0
  149. data/doc/classes/Bio/Graphics/Panel.src/M000030.html +20 -0
  150. data/doc/classes/Bio/Graphics/Panel.src/M000031.html +98 -0
  151. data/doc/classes/Bio/Graphics/Panel.src/M000059.html +52 -0
  152. data/doc/classes/Bio/Graphics/Panel.src/M000060.html +20 -0
  153. data/doc/classes/Bio/Graphics/Panel.src/M000061.html +98 -0
  154. data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} +50 -21
  155. data/doc/classes/Bio/Graphics/Ruler.src/M000015.html +30 -0
  156. data/doc/classes/Bio/Graphics/Ruler.src/M000016.html +20 -0
  157. data/doc/classes/Bio/Graphics/Ruler.src/M000017.html +30 -0
  158. data/doc/classes/Bio/Graphics/Ruler.src/M000018.html +20 -0
  159. data/doc/classes/Bio/Graphics/Ruler.src/M000019.html +26 -0
  160. data/doc/classes/Bio/Graphics/Ruler.src/M000020.html +45 -0
  161. data/doc/classes/Bio/Graphics/Ruler.src/M000047.html +30 -0
  162. data/doc/classes/Bio/Graphics/Ruler.src/M000048.html +20 -0
  163. data/doc/classes/Bio/Graphics/Ruler.src/M000049.html +26 -0
  164. data/doc/classes/Bio/Graphics/Ruler.src/M000050.html +45 -0
  165. data/doc/classes/Bio/Graphics/SubFeature.html +348 -0
  166. data/doc/classes/Bio/Graphics/SubFeature.src/M000001.html +73 -0
  167. data/doc/classes/Bio/Graphics/SubFeature.src/M000002.html +69 -0
  168. data/doc/classes/Bio/Graphics/SubFeature.src/M000023.html +73 -0
  169. data/doc/classes/Bio/Graphics/SubFeature.src/M000024.html +69 -0
  170. data/doc/classes/Bio/Graphics/SubFeature.src/M000027.html +73 -0
  171. data/doc/classes/Bio/Graphics/SubFeature.src/M000028.html +69 -0
  172. data/doc/classes/Bio/Graphics/SubFeature.src/M000057.html +73 -0
  173. data/doc/classes/Bio/Graphics/SubFeature.src/M000058.html +69 -0
  174. data/doc/classes/Bio/Graphics/{Panel/Track.html → Track.html} +67 -69
  175. data/doc/classes/Bio/Graphics/Track.src/M000017.html +39 -0
  176. data/doc/classes/Bio/Graphics/Track.src/M000018.html +37 -0
  177. data/doc/classes/Bio/Graphics/Track.src/M000019.html +45 -0
  178. data/doc/classes/Bio/Graphics/Track.src/M000020.html +41 -0
  179. data/doc/classes/Bio/Graphics/Track.src/M000021.html +39 -0
  180. data/doc/classes/Bio/Graphics/Track.src/M000022.html +37 -0
  181. data/doc/classes/Bio/Graphics/Track.src/M000023.html +45 -0
  182. data/doc/classes/Bio/Graphics/Track.src/M000051.html +39 -0
  183. data/doc/classes/Bio/Graphics/Track.src/M000052.html +37 -0
  184. data/doc/classes/Bio/Graphics/Track.src/M000053.html +45 -0
  185. data/doc/classes/Range.html +129 -0
  186. data/doc/classes/String.html +167 -0
  187. data/doc/classes/String.src/M000001.html +18 -0
  188. data/doc/classes/String.src/M000002.html +18 -0
  189. data/doc/classes/String.src/M000003.html +23 -0
  190. data/doc/classes/String.src/M000029.html +18 -0
  191. data/doc/classes/String.src/M000030.html +18 -0
  192. data/doc/classes/String.src/M000031.html +23 -0
  193. data/doc/classes/TestCustomGlyph.html +137 -0
  194. data/doc/classes/TestCustomGlyph.src/M000025.html +25 -0
  195. data/doc/classes/TestCustomGlyphInFile.html +167 -0
  196. data/doc/classes/TestCustomGlyphInFile.src/M000026.html +19 -0
  197. data/doc/classes/TestCustomGlyphInFile.src/M000027.html +25 -0
  198. data/doc/classes/TestCustomGlyphInFile.src/M000028.html +18 -0
  199. data/doc/classes/TestExtensions.html +152 -0
  200. data/doc/classes/TestExtensions.src/M000015.html +22 -0
  201. data/doc/classes/TestExtensions.src/M000016.html +25 -0
  202. data/doc/classes/TestFeature.html +152 -0
  203. data/doc/classes/TestFeature.src/M000017.html +19 -0
  204. data/doc/classes/TestFeature.src/M000018.html +21 -0
  205. data/doc/classes/TestImageMap.html +182 -0
  206. data/doc/classes/TestImageMap.src/M000019.html +22 -0
  207. data/doc/classes/TestImageMap.src/M000020.html +56 -0
  208. data/doc/classes/TestImageMap.src/M000021.html +56 -0
  209. data/doc/classes/TestImageMap.src/M000022.html +20 -0
  210. data/doc/classes/TestPanel.html +276 -0
  211. data/doc/classes/TestPanel.src/M000001.html +18 -0
  212. data/doc/classes/TestPanel.src/M000002.html +61 -0
  213. data/doc/classes/TestPanel.src/M000003.html +35 -0
  214. data/doc/classes/TestPanel.src/M000004.html +54 -0
  215. data/doc/classes/TestPanel.src/M000005.html +54 -0
  216. data/doc/classes/TestPanel.src/M000006.html +41 -0
  217. data/doc/classes/TestPanel.src/M000007.html +36 -0
  218. data/doc/classes/TestPanel.src/M000008.html +20 -0
  219. data/doc/classes/TestPanel.src/M000009.html +26 -0
  220. data/doc/classes/TestPanel.src/M000010.html +21 -0
  221. data/doc/classes/TestRuler.html +152 -0
  222. data/doc/classes/TestRuler.src/M000013.html +22 -0
  223. data/doc/classes/TestRuler.src/M000014.html +31 -0
  224. data/doc/classes/TestSubFeature.html +152 -0
  225. data/doc/classes/TestSubFeature.src/M000023.html +21 -0
  226. data/doc/classes/TestSubFeature.src/M000024.html +18 -0
  227. data/doc/classes/TestTrack.html +152 -0
  228. data/doc/classes/TestTrack.src/M000011.html +19 -0
  229. data/doc/classes/TestTrack.src/M000012.html +23 -0
  230. data/doc/created.rid +1 -1
  231. data/doc/files/README_DEV.html +399 -70
  232. data/doc/files/TUTORIAL.html +188 -67
  233. data/doc/files/lib/bio-graphics_rb.html +3 -2
  234. data/doc/files/lib/bio/graphics/feature_rb.html +12 -6
  235. data/doc/files/lib/bio/graphics/glyphs/box_rb.html +113 -0
  236. data/doc/files/lib/bio/graphics/glyphs/common_rb.html +113 -0
  237. data/doc/files/lib/bio/graphics/glyphs/directed_box_rb.html +113 -0
  238. data/doc/files/lib/bio/graphics/glyphs/directed_generic_rb.html +113 -0
  239. data/doc/files/lib/bio/graphics/glyphs/directed_spliced_rb.html +113 -0
  240. data/doc/files/lib/bio/graphics/glyphs/dot_rb.html +113 -0
  241. data/doc/files/lib/bio/graphics/glyphs/generic_rb.html +113 -0
  242. data/doc/files/lib/bio/graphics/glyphs/line_rb.html +113 -0
  243. data/doc/files/lib/bio/graphics/glyphs/line_with_handles_rb.html +113 -0
  244. data/doc/files/lib/bio/graphics/glyphs/spliced_rb.html +113 -0
  245. data/doc/files/lib/bio/graphics/glyphs/transcript_rb.html +113 -0
  246. data/doc/files/lib/bio/graphics/glyphs/triangle_rb.html +113 -0
  247. data/doc/files/lib/bio/graphics/image_map_rb.html +3 -2
  248. data/doc/files/lib/bio/graphics/panel_rb.html +10 -2
  249. data/doc/files/lib/bio/graphics/ruler_rb.html +3 -2
  250. data/doc/files/lib/bio/graphics/subfeature_rb.html +114 -0
  251. data/doc/files/lib/bio/graphics/track_rb.html +3 -2
  252. data/doc/files/lib/feature_rb.html +101 -0
  253. data/doc/files/samples/arkdb_features_rb.html +101 -0
  254. data/doc/files/samples/glyph_showcase_rb.html +108 -0
  255. data/doc/files/samples/protein_domains_rb.html +115 -0
  256. data/doc/files/samples/subfeatures_rb.html +108 -0
  257. data/doc/files/scripts/gff2png_rb.html +154 -0
  258. data/doc/files/test/unit/custom_glyph_in_file_rb.html +101 -0
  259. data/doc/files/test/unit/test_class_extensions_rb.html +108 -0
  260. data/doc/files/test/unit/test_creation_rb.html +108 -0
  261. data/doc/files/test/unit/test_custom_glyph_rb.html +108 -0
  262. data/doc/files/test/unit/test_draw_rb.html +108 -0
  263. data/doc/files/test/unit/test_imagemap_rb.html +108 -0
  264. data/doc/files/test/unit/test_subfeatures_rb.html +108 -0
  265. data/doc/fr_class_index.html +24 -6
  266. data/doc/fr_file_index.html +14 -0
  267. data/doc/fr_method_index.html +51 -19
  268. data/doc/images/glyph_showcase.png +0 -0
  269. data/doc/images/terms.svg +146 -132
  270. data/images/glyph_showcase.png +0 -0
  271. data/lib/bio-graphics.rb +38 -6
  272. data/lib/bio/graphics/feature.rb +212 -440
  273. data/lib/bio/graphics/glyphs/box.rb +21 -0
  274. data/lib/bio/graphics/glyphs/common.rb +149 -0
  275. data/lib/bio/graphics/glyphs/directed_box.rb +28 -0
  276. data/lib/bio/graphics/glyphs/directed_generic.rb +23 -0
  277. data/lib/bio/graphics/glyphs/directed_spliced.rb +39 -0
  278. data/lib/bio/graphics/glyphs/dot.rb +21 -0
  279. data/lib/bio/graphics/glyphs/generic.rb +15 -0
  280. data/lib/bio/graphics/glyphs/line.rb +17 -0
  281. data/lib/bio/graphics/glyphs/line_with_handles.rb +25 -0
  282. data/lib/bio/graphics/glyphs/spliced.rb +16 -0
  283. data/lib/bio/graphics/glyphs/transcript.rb +12 -0
  284. data/lib/bio/graphics/glyphs/triangle.rb +18 -0
  285. data/lib/bio/graphics/image_map.rb +25 -4
  286. data/lib/bio/graphics/panel.rb +266 -209
  287. data/lib/bio/graphics/ruler.rb +95 -96
  288. data/lib/bio/graphics/subfeature.rb +187 -0
  289. data/lib/bio/graphics/track.rb +155 -156
  290. data/lib/feature.rb +204 -0
  291. data/samples/arkdb_features.rb +10 -8
  292. data/samples/glyph_showcase.rb +58 -22
  293. data/samples/protein_domains.rb +19 -0
  294. data/samples/subfeatures.rb +31 -0
  295. data/test/unit/custom_glyph_in_file.rb +12 -0
  296. data/test/unit/data.txt +32 -0
  297. data/test/unit/test_class_extensions.rb +23 -0
  298. data/test/unit/test_creation.rb +43 -13
  299. data/test/unit/test_custom_glyph.rb +50 -0
  300. data/test/unit/test_draw.rb +211 -0
  301. data/test/unit/test_imagemap.rb +134 -0
  302. data/test/unit/test_subfeatures.rb +17 -0
  303. metadata +396 -119
  304. data/doc/classes/Bio/Graphics/Panel.src/M000005.html +0 -29
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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" />
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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" />
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+ <script type="text/javascript">
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+ // <![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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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
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+ } else {
32
+ elemStyle.display = "none"
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+ }
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+
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+ return true;
36
+ }
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+
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+ // Make codeblocks hidden by default
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+ 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">
50
+ <table class="header-table">
51
+ <tr class="top-aligned-row">
52
+ <td><strong>Class</strong></td>
53
+ <td class="class-name-in-header">Bio::Graphics::Glyph::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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+
87
+ <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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+
97
+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <!-- if method_list -->
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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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
135
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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>
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+ </html>
data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html ADDED
@@ -0,0 +1,18 @@
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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>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
12
+ <body class="standalone-code">
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+ <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>
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+ </body>
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+ </html>
data/doc/classes/Bio/Graphics/ImageMap.src/M000033.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>add_element (Bio::Graphics::ImageMap)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/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>
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+ </html>
data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} RENAMED
@@ -5,17 +5,20 @@
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  <html>
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  <head>
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- <title>to_s (ImageMap)</title>
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+ <title>to_s (Bio::Graphics::ImageMap)</title>
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  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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  </head>
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  <body class="standalone-code">
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- <pre><span class="ruby-comment cmt"># File lib/bio/graphics/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
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+ <?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>