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
  308. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +0 -28
  309. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +0 -54
  310. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +0 -20
  311. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +0 -20
  312. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +0 -28
  313. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +0 -59
  314. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +0 -20
  315. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +0 -28
  316. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +0 -59
  317. data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +0 -26
  318. data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +0 -42
  319. data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +0 -52
  320. data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +0 -23
  321. data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +0 -43
  322. data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +0 -259
  323. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +0 -65
  324. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +0 -39
  325. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000013.html +0 -27
  326. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +0 -225
  327. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000015.html +0 -48
  328. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +0 -18
  329. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000013.html +0 -18
  330. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +0 -18
  331. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000016.html +0 -18
data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} RENAMED
@@ -5,10 +5,10 @@
5
5
 
6
6
  <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
7
  <head>
8
- <title>Class: Bio::Graphics::Panel::Ruler</title>
8
+ <title>Class: Bio::Graphics::Ruler</title>
9
9
  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
10
  <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
- <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
12
12
  <script type="text/javascript">
13
13
  // <![CDATA[
14
14
 
@@ -50,12 +50,12 @@
50
50
  <table class="header-table">
51
51
  <tr class="top-aligned-row">
52
52
  <td><strong>Class</strong></td>
53
- <td class="class-name-in-header">Bio::Graphics::Panel::Ruler</td>
53
+ <td class="class-name-in-header">Bio::Graphics::Ruler</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/ruler_rb.html">
58
+ <a href="../../../files/lib/bio/graphics/ruler_rb.html">
59
59
  lib/bio/graphics/ruler.rb
60
60
  </a>
61
61
  <br />
@@ -80,10 +80,10 @@
80
80
 
81
81
  <div id="description">
82
82
  <p>
83
- The Bio::Graphics::Ruler class describes the ruler to be drawn on the
84
- graph. This is created automatically when creating the picture by using
85
- Bio::Graphics::Panel.to_svg. See BioExt::Graphics documentation for
86
- explanation of interplay between different classes.
83
+ The <a href="Ruler.html">Bio::Graphics::Ruler</a> class describes the ruler
84
+ to be drawn on the graph. This is created automatically when creating the
85
+ picture by using Bio::Graphics::Panel.to_svg. See BioExt::Graphics
86
+ documentation for explanation of interplay between different classes.
87
87
  </p>
88
88
 
89
89
  </div>
@@ -95,9 +95,10 @@ explanation of interplay between different classes.
95
95
  <h3 class="section-bar">Methods</h3>
96
96
 
97
97
  <div class="name-list">
98
- <a href="#M000018">calculate_tick_distance</a>&nbsp;&nbsp;
99
- <a href="#M000019">draw</a>&nbsp;&nbsp;
98
+ <a href="#M000020">draw</a>&nbsp;&nbsp;
99
+ <a href="#M000019">first_tick_position</a>&nbsp;&nbsp;
100
100
  <a href="#M000017">new</a>&nbsp;&nbsp;
101
+ <a href="#M000018">scaling_factor</a>&nbsp;&nbsp;
101
102
  </div>
102
103
  </div>
103
104
 
@@ -132,6 +133,11 @@ explanation of interplay between different classes.
132
133
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
133
134
  <td class="context-item-desc"></td>
134
135
  </tr>
136
+ <tr class="top-aligned-row context-row">
137
+ <td class="context-item-name">min_pixels_per_tick</td>
138
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
139
+ <td class="context-item-desc"></td>
140
+ </tr>
135
141
  <tr class="top-aligned-row context-row">
136
142
  <td class="context-item-name">minor_tick_distance</td>
137
143
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
@@ -147,6 +153,16 @@ explanation of interplay between different classes.
147
153
  <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
148
154
  <td class="context-item-desc"></td>
149
155
  </tr>
156
+ <tr class="top-aligned-row context-row">
157
+ <td class="context-item-name">tick_height</td>
158
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
159
+ <td class="context-item-desc"></td>
160
+ </tr>
161
+ <tr class="top-aligned-row context-row">
162
+ <td class="context-item-name">tick_text_height</td>
163
+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
164
+ <td class="context-item-desc"></td>
165
+ </tr>
150
166
  </table>
151
167
  </div>
152
168
  </div>
@@ -170,15 +186,14 @@ explanation of interplay between different classes.
170
186
  <div class="method-description">
171
187
  <p>
172
188
  Creates a <a href="Ruler.html#M000017">new</a> <a
173
- href="Ruler.html">Bio::Graphics::Panel::Ruler</a> object.
189
+ href="Ruler.html">Bio::Graphics::Ruler</a> object.
174
190
  </p>
175
191
  <hr size="1"></hr><p>
176
192
  <b>Arguments</b>:
177
193
  </p>
178
194
  <ul>
179
- <li><em>panel</em> (required) :: <a
180
- href="../Panel.html">Bio::Graphics::Panel</a> object that this ruler
181
- belongs to
195
+ <li><em>panel</em> (required) :: <a href="Panel.html">Bio::Graphics::Panel</a>
196
+ object that this ruler belongs to
182
197
 
183
198
  </li>
184
199
  <li><em>colour</em> :: colour of the ruler. Default = &#8216;black&#8216;
@@ -186,7 +201,7 @@ belongs to
186
201
  </li>
187
202
  </ul>
188
203
  <table>
189
- <tr><td valign="top"><b>Returns</b>:</td><td>Bio::Graphics::Ruler object
204
+ <tr><td valign="top"><b>Returns</b>:</td><td><a href="Ruler.html">Bio::Graphics::Ruler</a> object
190
205
 
191
206
  </td></tr>
192
207
  </table>
@@ -195,13 +210,13 @@ belongs to
195
210
 
196
211
  <h3 class="section-bar">Public Instance methods</h3>
197
212
 
198
- <div id="method-M000018" class="method-detail">
199
- <a name="M000018"></a>
213
+ <div id="method-M000020" class="method-detail">
214
+ <a name="M000020"></a>
200
215
 
201
216
  <div class="method-heading">
202
- <a href="Ruler.src/M000018.html" target="Code" class="method-signature"
203
- onclick="popupCode('Ruler.src/M000018.html');return false;">
204
- <span class="method-name">calculate_tick_distance</span><span class="method-args">()</span>
217
+ <a href="Ruler.src/M000020.html" target="Code" class="method-signature"
218
+ onclick="popupCode('Ruler.src/M000020.html');return false;">
219
+ <span class="method-name">draw</span><span class="method-args">(panel_drawing)</span>
205
220
  </a>
206
221
  </div>
207
222
 
@@ -215,7 +230,21 @@ belongs to
215
230
  <div class="method-heading">
216
231
  <a href="Ruler.src/M000019.html" target="Code" class="method-signature"
217
232
  onclick="popupCode('Ruler.src/M000019.html');return false;">
218
- <span class="method-name">draw</span><span class="method-args">(panel_drawing, vertical_offset)</span>
233
+ <span class="method-name">first_tick_position</span><span class="method-args">(start = @panel.display_start, minor_tick = @minor_tick_distance)</span>
234
+ </a>
235
+ </div>
236
+
237
+ <div class="method-description">
238
+ </div>
239
+ </div>
240
+
241
+ <div id="method-M000018" class="method-detail">
242
+ <a name="M000018"></a>
243
+
244
+ <div class="method-heading">
245
+ <a href="Ruler.src/M000018.html" target="Code" class="method-signature"
246
+ onclick="popupCode('Ruler.src/M000018.html');return false;">
247
+ <span class="method-name">scaling_factor</span><span class="method-args">(min_pixels_per_tick = @min_pixels_per_tick, rescale_factor = @panel.rescale_factor)</span>
219
248
  </a>
220
249
  </div>
221
250
 
data/doc/classes/Bio/Graphics/Ruler.src/M000015.html ADDED
@@ -0,0 +1,30 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>new (Bio::Graphics::Ruler)</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/ruler.rb, line 27</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
15
+ <span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
16
+ <span class="ruby-ivar">@name</span> = <span class="ruby-value str">'ruler'</span>
17
+ <span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">colour</span>
18
+
19
+ <span class="ruby-comment cmt"># Number of pixels between each tick, used to calculate tick spacing</span>
20
+ <span class="ruby-ivar">@min_pixels_per_tick</span> = <span class="ruby-value">5</span>
21
+ <span class="ruby-comment cmt"># The base height of minor ticks in pixels</span>
22
+ <span class="ruby-ivar">@tick_height</span> = <span class="ruby-value">5</span>
23
+ <span class="ruby-comment cmt"># The height of the text in pixels</span>
24
+ <span class="ruby-ivar">@tick_text_height</span> = <span class="ruby-value">10</span>
25
+
26
+ <span class="ruby-ivar">@minor_tick_distance</span> = <span class="ruby-ivar">@min_pixels_per_tick</span> <span class="ruby-operator">**</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">scaling_factor</span>
27
+ <span class="ruby-ivar">@major_tick_distance</span> = <span class="ruby-ivar">@minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
28
+ <span class="ruby-keyword kw">end</span></pre>
29
+ </body>
30
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000016.html ADDED
@@ -0,0 +1,20 @@
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>scaling_factor (Bio::Graphics::Ruler)</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/ruler.rb, line 46</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">scaling_factor</span>(<span class="ruby-identifier">min_pixels_per_tick</span> = <span class="ruby-ivar">@min_pixels_per_tick</span>,
15
+ <span class="ruby-identifier">rescale_factor</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">rescale_factor</span>)
16
+ (<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">rescale_factor</span>) <span class="ruby-operator">/</span>
17
+ <span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span>)).<span class="ruby-identifier">ceil</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000017.html ADDED
@@ -0,0 +1,30 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>new (Bio::Graphics::Ruler)</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/ruler.rb, line 27</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
15
+ <span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
16
+ <span class="ruby-ivar">@name</span> = <span class="ruby-value str">'ruler'</span>
17
+ <span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">colour</span>
18
+
19
+ <span class="ruby-comment cmt"># Number of pixels between each tick, used to calculate tick spacing</span>
20
+ <span class="ruby-ivar">@min_pixels_per_tick</span> = <span class="ruby-value">5</span>
21
+ <span class="ruby-comment cmt"># The base height of minor ticks in pixels</span>
22
+ <span class="ruby-ivar">@tick_height</span> = <span class="ruby-value">5</span>
23
+ <span class="ruby-comment cmt"># The height of the text in pixels</span>
24
+ <span class="ruby-ivar">@tick_text_height</span> = <span class="ruby-value">10</span>
25
+
26
+ <span class="ruby-ivar">@minor_tick_distance</span> = <span class="ruby-ivar">@min_pixels_per_tick</span> <span class="ruby-operator">**</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">scaling_factor</span>
27
+ <span class="ruby-ivar">@major_tick_distance</span> = <span class="ruby-ivar">@minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
28
+ <span class="ruby-keyword kw">end</span></pre>
29
+ </body>
30
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000018.html ADDED
@@ -0,0 +1,20 @@
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>scaling_factor (Bio::Graphics::Ruler)</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/ruler.rb, line 46</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">scaling_factor</span>(<span class="ruby-identifier">min_pixels_per_tick</span> = <span class="ruby-ivar">@min_pixels_per_tick</span>,
15
+ <span class="ruby-identifier">rescale_factor</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">rescale_factor</span>)
16
+ (<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">rescale_factor</span>) <span class="ruby-operator">/</span>
17
+ <span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span>)).<span class="ruby-identifier">ceil</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000019.html ADDED
@@ -0,0 +1,26 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>first_tick_position (Bio::Graphics::Ruler)</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/ruler.rb, line 52</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">first_tick_position</span>(<span class="ruby-identifier">start</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">display_start</span>,
15
+ <span class="ruby-identifier">minor_tick</span> = <span class="ruby-ivar">@minor_tick_distance</span>)
16
+ <span class="ruby-comment cmt"># * Find position of first tick.</span>
17
+ <span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first</span>
18
+ <span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the</span>
19
+ <span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:</span>
20
+ <span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.</span>
21
+ <span class="ruby-comment cmt"># So we want to find the position of the first tick.</span>
22
+ <span class="ruby-identifier">modulo_from_tick</span> = (<span class="ruby-identifier">start</span> <span class="ruby-operator">%</span> <span class="ruby-identifier">minor_tick</span>)
23
+ <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">modulo_from_tick</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span> <span class="ruby-operator">?</span> (<span class="ruby-identifier">minor_tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">modulo_from_tick</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>) <span class="ruby-operator">:</span> <span class="ruby-value">0</span>)
24
+ <span class="ruby-keyword kw">end</span></pre>
25
+ </body>
26
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000020.html ADDED
@@ -0,0 +1,45 @@
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::Ruler)</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/ruler.rb, line 64</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_drawing</span>)
15
+ <span class="ruby-identifier">ruler_drawing</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_drawing</span>)
16
+
17
+ <span class="ruby-comment cmt"># Draw line</span>
18
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-value">10</span>)
19
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
20
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
21
+
22
+ <span class="ruby-comment cmt"># Draw ticks</span>
23
+ <span class="ruby-comment cmt"># * And start drawing the rest.</span>
24
+ <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-ivar">@minor_tick_distance</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">tick</span><span class="ruby-operator">|</span>
25
+ <span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</span> <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">rescale_factor</span>
26
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-ivar">@min_pixels_per_tick</span>)
27
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-ivar">@major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
28
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">3</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span>)
29
+
30
+ <span class="ruby-comment cmt"># Draw tick number</span>
31
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">select_font_face</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">FONT</span>)
32
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-ivar">@tick_text_height</span>)
33
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">4</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@tick_text_height</span>)
34
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
35
+ <span class="ruby-keyword kw">else</span>
36
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-ivar">@tick_height</span>)
37
+
38
+ <span class="ruby-keyword kw">end</span>
39
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
40
+ <span class="ruby-keyword kw">end</span>
41
+
42
+ <span class="ruby-ivar">@height</span> = <span class="ruby-value">5</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@tick_text_height</span>
43
+ <span class="ruby-keyword kw">end</span></pre>
44
+ </body>
45
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000047.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>new (Bio::Graphics::Ruler)</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/ruler.rb, line 27</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
15
+ <span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
16
+ <span class="ruby-ivar">@name</span> = <span class="ruby-value str">'ruler'</span>
17
+ <span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">colour</span>
18
+
19
+ <span class="ruby-comment cmt"># Number of pixels between each tick, used to calculate tick spacing</span>
20
+ <span class="ruby-ivar">@min_pixels_per_tick</span> = <span class="ruby-value">5</span>
21
+ <span class="ruby-comment cmt"># The base height of minor ticks in pixels</span>
22
+ <span class="ruby-ivar">@tick_height</span> = <span class="ruby-value">5</span>
23
+ <span class="ruby-comment cmt"># The height of the text in pixels</span>
24
+ <span class="ruby-ivar">@tick_text_height</span> = <span class="ruby-value">10</span>
25
+
26
+ <span class="ruby-ivar">@minor_tick_distance</span> = <span class="ruby-ivar">@min_pixels_per_tick</span> <span class="ruby-operator">**</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">scaling_factor</span>
27
+ <span class="ruby-ivar">@major_tick_distance</span> = <span class="ruby-ivar">@minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
28
+ <span class="ruby-keyword kw">end</span></pre>
29
+ </body>
30
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000048.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>scaling_factor (Bio::Graphics::Ruler)</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/ruler.rb, line 46</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">scaling_factor</span>(<span class="ruby-identifier">min_pixels_per_tick</span> = <span class="ruby-ivar">@min_pixels_per_tick</span>,
15
+ <span class="ruby-identifier">rescale_factor</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">rescale_factor</span>)
16
+ (<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">rescale_factor</span>) <span class="ruby-operator">/</span>
17
+ <span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span>)).<span class="ruby-identifier">ceil</span>
18
+ <span class="ruby-keyword kw">end</span></pre>
19
+ </body>
20
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000049.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>first_tick_position (Bio::Graphics::Ruler)</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/ruler.rb, line 52</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">first_tick_position</span>(<span class="ruby-identifier">start</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">display_start</span>,
15
+ <span class="ruby-identifier">minor_tick</span> = <span class="ruby-ivar">@minor_tick_distance</span>)
16
+ <span class="ruby-comment cmt"># * Find position of first tick.</span>
17
+ <span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first</span>
18
+ <span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the</span>
19
+ <span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:</span>
20
+ <span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.</span>
21
+ <span class="ruby-comment cmt"># So we want to find the position of the first tick.</span>
22
+ <span class="ruby-identifier">modulo_from_tick</span> = (<span class="ruby-identifier">start</span> <span class="ruby-operator">%</span> <span class="ruby-identifier">minor_tick</span>)
23
+ <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">modulo_from_tick</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span> <span class="ruby-operator">?</span> (<span class="ruby-identifier">minor_tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">modulo_from_tick</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>) <span class="ruby-operator">:</span> <span class="ruby-value">0</span>)
24
+ <span class="ruby-keyword kw">end</span></pre>
25
+ </body>
26
+ </html>
data/doc/classes/Bio/Graphics/Ruler.src/M000050.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>
8
+ <title>draw (Bio::Graphics::Ruler)</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/ruler.rb, line 64</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_drawing</span>)
15
+ <span class="ruby-identifier">ruler_drawing</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_drawing</span>)
16
+
17
+ <span class="ruby-comment cmt"># Draw line</span>
18
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-value">10</span>)
19
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
20
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
21
+
22
+ <span class="ruby-comment cmt"># Draw ticks</span>
23
+ <span class="ruby-comment cmt"># * And start drawing the rest.</span>
24
+ <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-ivar">@minor_tick_distance</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">tick</span><span class="ruby-operator">|</span>
25
+ <span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</span> <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">rescale_factor</span>
26
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-ivar">@min_pixels_per_tick</span>)
27
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-ivar">@major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
28
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">3</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span>)
29
+
30
+ <span class="ruby-comment cmt"># Draw tick number</span>
31
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">select_font_face</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">FONT</span>)
32
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-ivar">@tick_text_height</span>)
33
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">4</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@tick_text_height</span>)
34
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
35
+ <span class="ruby-keyword kw">else</span>
36
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-ivar">@tick_height</span>)
37
+
38
+ <span class="ruby-keyword kw">end</span>
39
+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
40
+ <span class="ruby-keyword kw">end</span>
41
+
42
+ <span class="ruby-ivar">@height</span> = <span class="ruby-value">5</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@tick_text_height</span>
43
+ <span class="ruby-keyword kw">end</span></pre>
44
+ </body>
45
+ </html>