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.
- data/doc/classes/Bio.html +4 -26
- data/doc/classes/Bio/Feature.html +350 -0
- data/doc/classes/Bio/Feature.src/M000010.html +21 -0
- data/doc/classes/Bio/Feature.src/M000011.html +20 -0
- data/doc/classes/Bio/Feature.src/M000012.html +19 -0
- data/doc/classes/Bio/Feature.src/M000014.html +21 -0
- data/doc/classes/Bio/Feature.src/M000016.html +21 -0
- data/doc/classes/Bio/Feature.src/M000034.html +21 -0
- data/doc/classes/Bio/Feature.src/M000035.html +20 -0
- data/doc/classes/Bio/Feature.src/M000036.html +19 -0
- data/doc/classes/Bio/Feature.src/M000038.html +21 -0
- data/doc/classes/Bio/Feature.src/M000040.html +21 -0
- data/doc/classes/Bio/Feature.src/M000042.html +21 -0
- data/doc/classes/Bio/Feature.src/M000043.html +20 -0
- data/doc/classes/Bio/Feature.src/M000044.html +21 -0
- data/doc/classes/Bio/Feature.src/M000045.html +20 -0
- data/doc/classes/Bio/Feature.src/M000046.html +19 -0
- data/doc/classes/Bio/Feature.src/M000048.html +21 -0
- data/doc/classes/Bio/Feature.src/M000050.html +21 -0
- data/doc/classes/Bio/Feature.src/M000074.html +21 -0
- data/doc/classes/Bio/Feature.src/M000075.html +20 -0
- data/doc/classes/Bio/Feature.src/M000076.html +19 -0
- data/doc/classes/Bio/Feature.src/M000078.html +21 -0
- data/doc/classes/Bio/Feature.src/M000080.html +21 -0
- data/doc/classes/Bio/Feature/Qualifier.html +189 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000017.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000041.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000049.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000051.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000081.html +18 -0
- data/doc/classes/Bio/Features.html +329 -0
- data/doc/classes/Bio/Features.src/M000004.html +18 -0
- data/doc/classes/Bio/Features.src/M000005.html +19 -0
- data/doc/classes/Bio/Features.src/M000006.html +21 -0
- data/doc/classes/Bio/Features.src/M000007.html +18 -0
- data/doc/classes/Bio/Features.src/M000008.html +18 -0
- data/doc/classes/Bio/Features.src/M000009.html +18 -0
- data/doc/classes/Bio/Features.src/M000028.html +18 -0
- data/doc/classes/Bio/Features.src/M000029.html +19 -0
- data/doc/classes/Bio/Features.src/M000030.html +21 -0
- data/doc/classes/Bio/Features.src/M000031.html +18 -0
- data/doc/classes/Bio/Features.src/M000032.html +18 -0
- data/doc/classes/Bio/Features.src/M000033.html +18 -0
- data/doc/classes/Bio/Features.src/M000036.html +18 -0
- data/doc/classes/Bio/Features.src/M000037.html +19 -0
- data/doc/classes/Bio/Features.src/M000038.html +18 -0
- data/doc/classes/Bio/Features.src/M000039.html +19 -0
- data/doc/classes/Bio/Features.src/M000040.html +21 -0
- data/doc/classes/Bio/Features.src/M000041.html +18 -0
- data/doc/classes/Bio/Features.src/M000042.html +18 -0
- data/doc/classes/Bio/Features.src/M000043.html +18 -0
- data/doc/classes/Bio/Features.src/M000068.html +18 -0
- data/doc/classes/Bio/Features.src/M000069.html +19 -0
- data/doc/classes/Bio/Features.src/M000070.html +21 -0
- data/doc/classes/Bio/Features.src/M000071.html +18 -0
- data/doc/classes/Bio/Features.src/M000072.html +18 -0
- data/doc/classes/Bio/Features.src/M000073.html +18 -0
- data/doc/classes/Bio/Graphics.html +28 -42
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} +98 -125
- data/doc/classes/Bio/Graphics/Feature.src/M000020.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000021.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000022.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000023.html +66 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000024.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000025.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000026.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000054.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000055.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000056.html +55 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000025.html +68 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000026.html +67 -0
- data/doc/classes/Bio/Graphics/Glyph.html +178 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000004.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000032.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.html +187 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html +40 -0
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.html} +16 -19
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Transcript.html +113 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html +21 -0
- data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.html} +50 -16
- data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} +3 -3
- data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000033.html +18 -0
- data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} +7 -4
- data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000062.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000064.html +27 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html +24 -0
- data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} +14 -14
- data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} +3 -3
- data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} +6 -4
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html +22 -0
- data/doc/classes/Bio/Graphics/Panel.html +70 -69
- data/doc/classes/Bio/Graphics/Panel.src/M000025.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000026.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000027.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000028.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000029.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000030.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000031.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000059.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000060.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000061.html +98 -0
- data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} +50 -21
- data/doc/classes/Bio/Graphics/Ruler.src/M000015.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000016.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000017.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000018.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000019.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000020.html +45 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000047.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000048.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000049.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000050.html +45 -0
- data/doc/classes/Bio/Graphics/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000001.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000002.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000023.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000024.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000027.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000028.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000057.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000058.html +69 -0
- data/doc/classes/Bio/Graphics/{Panel/Track.html → Track.html} +67 -69
- data/doc/classes/Bio/Graphics/Track.src/M000017.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000018.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000019.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000020.html +41 -0
- data/doc/classes/Bio/Graphics/Track.src/M000021.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000022.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000023.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000051.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000052.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000053.html +45 -0
- data/doc/classes/Range.html +129 -0
- data/doc/classes/String.html +167 -0
- data/doc/classes/String.src/M000001.html +18 -0
- data/doc/classes/String.src/M000002.html +18 -0
- data/doc/classes/String.src/M000003.html +23 -0
- data/doc/classes/String.src/M000029.html +18 -0
- data/doc/classes/String.src/M000030.html +18 -0
- data/doc/classes/String.src/M000031.html +23 -0
- data/doc/classes/TestCustomGlyph.html +137 -0
- data/doc/classes/TestCustomGlyph.src/M000025.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.html +167 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000026.html +19 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000027.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000028.html +18 -0
- data/doc/classes/TestExtensions.html +152 -0
- data/doc/classes/TestExtensions.src/M000015.html +22 -0
- data/doc/classes/TestExtensions.src/M000016.html +25 -0
- data/doc/classes/TestFeature.html +152 -0
- data/doc/classes/TestFeature.src/M000017.html +19 -0
- data/doc/classes/TestFeature.src/M000018.html +21 -0
- data/doc/classes/TestImageMap.html +182 -0
- data/doc/classes/TestImageMap.src/M000019.html +22 -0
- data/doc/classes/TestImageMap.src/M000020.html +56 -0
- data/doc/classes/TestImageMap.src/M000021.html +56 -0
- data/doc/classes/TestImageMap.src/M000022.html +20 -0
- data/doc/classes/TestPanel.html +276 -0
- data/doc/classes/TestPanel.src/M000001.html +18 -0
- data/doc/classes/TestPanel.src/M000002.html +61 -0
- data/doc/classes/TestPanel.src/M000003.html +35 -0
- data/doc/classes/TestPanel.src/M000004.html +54 -0
- data/doc/classes/TestPanel.src/M000005.html +54 -0
- data/doc/classes/TestPanel.src/M000006.html +41 -0
- data/doc/classes/TestPanel.src/M000007.html +36 -0
- data/doc/classes/TestPanel.src/M000008.html +20 -0
- data/doc/classes/TestPanel.src/M000009.html +26 -0
- data/doc/classes/TestPanel.src/M000010.html +21 -0
- data/doc/classes/TestRuler.html +152 -0
- data/doc/classes/TestRuler.src/M000013.html +22 -0
- data/doc/classes/TestRuler.src/M000014.html +31 -0
- data/doc/classes/TestSubFeature.html +152 -0
- data/doc/classes/TestSubFeature.src/M000023.html +21 -0
- data/doc/classes/TestSubFeature.src/M000024.html +18 -0
- data/doc/classes/TestTrack.html +152 -0
- data/doc/classes/TestTrack.src/M000011.html +19 -0
- data/doc/classes/TestTrack.src/M000012.html +23 -0
- data/doc/created.rid +1 -1
- data/doc/files/README_DEV.html +399 -70
- data/doc/files/TUTORIAL.html +188 -67
- data/doc/files/lib/bio-graphics_rb.html +3 -2
- data/doc/files/lib/bio/graphics/feature_rb.html +12 -6
- data/doc/files/lib/bio/graphics/glyphs/box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/common_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/dot_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_with_handles_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/transcript_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/triangle_rb.html +113 -0
- data/doc/files/lib/bio/graphics/image_map_rb.html +3 -2
- data/doc/files/lib/bio/graphics/panel_rb.html +10 -2
- data/doc/files/lib/bio/graphics/ruler_rb.html +3 -2
- data/doc/files/lib/bio/graphics/subfeature_rb.html +114 -0
- data/doc/files/lib/bio/graphics/track_rb.html +3 -2
- data/doc/files/lib/feature_rb.html +101 -0
- data/doc/files/samples/arkdb_features_rb.html +101 -0
- data/doc/files/samples/glyph_showcase_rb.html +108 -0
- data/doc/files/samples/protein_domains_rb.html +115 -0
- data/doc/files/samples/subfeatures_rb.html +108 -0
- data/doc/files/scripts/gff2png_rb.html +154 -0
- data/doc/files/test/unit/custom_glyph_in_file_rb.html +101 -0
- data/doc/files/test/unit/test_class_extensions_rb.html +108 -0
- data/doc/files/test/unit/test_creation_rb.html +108 -0
- data/doc/files/test/unit/test_custom_glyph_rb.html +108 -0
- data/doc/files/test/unit/test_draw_rb.html +108 -0
- data/doc/files/test/unit/test_imagemap_rb.html +108 -0
- data/doc/files/test/unit/test_subfeatures_rb.html +108 -0
- data/doc/fr_class_index.html +24 -6
- data/doc/fr_file_index.html +14 -0
- data/doc/fr_method_index.html +51 -19
- data/doc/images/glyph_showcase.png +0 -0
- data/doc/images/terms.svg +146 -132
- data/images/glyph_showcase.png +0 -0
- data/lib/bio-graphics.rb +38 -6
- data/lib/bio/graphics/feature.rb +212 -440
- data/lib/bio/graphics/glyphs/box.rb +21 -0
- data/lib/bio/graphics/glyphs/common.rb +149 -0
- data/lib/bio/graphics/glyphs/directed_box.rb +28 -0
- data/lib/bio/graphics/glyphs/directed_generic.rb +23 -0
- data/lib/bio/graphics/glyphs/directed_spliced.rb +39 -0
- data/lib/bio/graphics/glyphs/dot.rb +21 -0
- data/lib/bio/graphics/glyphs/generic.rb +15 -0
- data/lib/bio/graphics/glyphs/line.rb +17 -0
- data/lib/bio/graphics/glyphs/line_with_handles.rb +25 -0
- data/lib/bio/graphics/glyphs/spliced.rb +16 -0
- data/lib/bio/graphics/glyphs/transcript.rb +12 -0
- data/lib/bio/graphics/glyphs/triangle.rb +18 -0
- data/lib/bio/graphics/image_map.rb +25 -4
- data/lib/bio/graphics/panel.rb +266 -209
- data/lib/bio/graphics/ruler.rb +95 -96
- data/lib/bio/graphics/subfeature.rb +187 -0
- data/lib/bio/graphics/track.rb +155 -156
- data/lib/feature.rb +204 -0
- data/samples/arkdb_features.rb +10 -8
- data/samples/glyph_showcase.rb +58 -22
- data/samples/protein_domains.rb +19 -0
- data/samples/subfeatures.rb +31 -0
- data/test/unit/custom_glyph_in_file.rb +12 -0
- data/test/unit/data.txt +32 -0
- data/test/unit/test_class_extensions.rb +23 -0
- data/test/unit/test_creation.rb +43 -13
- data/test/unit/test_custom_glyph.rb +50 -0
- data/test/unit/test_draw.rb +211 -0
- data/test/unit/test_imagemap.rb +134 -0
- data/test/unit/test_subfeatures.rb +17 -0
- metadata +396 -119
- data/doc/classes/Bio/Graphics/Panel.src/M000005.html +0 -29
- data/doc/classes/Bio/Graphics/Panel.src/M000006.html +0 -19
- data/doc/classes/Bio/Graphics/Panel.src/M000007.html +0 -68
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +0 -54
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +0 -26
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +0 -42
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +0 -52
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +0 -23
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +0 -43
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +0 -259
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +0 -65
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +0 -39
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/subfeature.rb, line 21</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">feature</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">glyph</span>, <span class="ruby-identifier">colour</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">colour</span>)
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<span class="ruby-ivar">@feature</span> = <span class="ruby-identifier">feature</span>
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<span class="ruby-ivar">@feature_object</span> = <span class="ruby-identifier">feature_object</span>
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<span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">glyph</span>
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<span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">colour</span>
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<span class="ruby-ivar">@locations</span> = <span class="ruby-ivar">@feature_object</span>.<span class="ruby-identifier">locations</span>
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<span class="ruby-ivar">@start</span> = <span class="ruby-ivar">@locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@stop</span> = <span class="ruby-ivar">@locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@strand</span> = <span class="ruby-ivar">@locations</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">strand</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@pixel_range_collection</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-comment cmt"># Get all pixel ranges for the subfeatures</span>
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<span class="ruby-ivar">@locations</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span>
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<span class="ruby-comment cmt"># xxxxxx [ ]</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
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<span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">next</span>
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<span class="ruby-comment cmt"># [ ] xxxxx</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">next</span>
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<span class="ruby-comment cmt"># xxxx[xxx ]</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
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<span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
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<span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-comment cmt"># [ xxxx]xxxx</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-identifier">stop_pixel</span> = <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
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<span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-comment cmt"># xxxx[xxxxxxxxxx]xxxx</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
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<span class="ruby-identifier">stop_pixel</span> = <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
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<span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-comment cmt"># [ xxxxx ]</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@pixel_range_collection</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Range</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>))
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/subfeature.rb, line 128</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">feature_context</span>)
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<span class="ruby-comment cmt"># Set the glyph to be used. The glyph can be set as a symbol (e.g. :generic)</span>
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<span class="ruby-comment cmt"># or as a hash (e.g. {'utr' => :line, 'cds' => :directed_spliced}).</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">glyph</span>.<span class="ruby-identifier">class</span> <span class="ruby-operator">==</span> <span class="ruby-constant">Hash</span>
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<span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">glyph</span>[<span class="ruby-ivar">@feature_object</span>.<span class="ruby-identifier">feature</span>]
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">glyph</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># We have to check if we want to change the glyph type from directed to</span>
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<span class="ruby-comment cmt"># undirected</span>
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<span class="ruby-comment cmt"># There are 2 cases where we don't want to draw arrows on</span>
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<span class="ruby-comment cmt"># features:</span>
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<span class="ruby-comment cmt"># (a) when the picture is really zoomed out, features are</span>
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<span class="ruby-comment cmt"># so small that the arrow itself is too big</span>
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<span class="ruby-comment cmt"># (b) if a directed feature on the fw strand extends beyond</span>
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<span class="ruby-comment cmt"># the end of the picture, the arrow is out of view. This</span>
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<span class="ruby-comment cmt"># is the same as considering the feature as undirected.</span>
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<span class="ruby-comment cmt"># The same obviously goes for features on the reverse</span>
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<span class="ruby-comment cmt"># strand that extend beyond the left side of the image.</span>
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<span class="ruby-comment cmt">#</span>
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<span class="ruby-comment cmt"># (a) Zoomed out</span>
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<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-keyword kw">if</span> (<span class="ruby-ivar">@stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@start</span>).<span class="ruby-identifier">to_f</span><span class="ruby-operator">/</span><span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator"><</span> <span class="ruby-value">2</span>
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<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># (b) Extending beyond borders picture</span>
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<span class="ruby-keyword kw">if</span> ( <span class="ruby-ivar">@chopped_at_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@strand</span> = <span class="ruby-value">1</span> ) <span class="ruby-keyword kw">or</span> ( <span class="ruby-ivar">@chopped_at_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@strand</span> = <span class="ruby-value">-1</span> )
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<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:directed_generic</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
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<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:generic</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:directed_spliced</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
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<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:spliced</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-ivar">@glyph</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># And draw the thing.</span>
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<span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-ivar">@colour</span>)
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<span class="ruby-identifier">glyph</span> = (<span class="ruby-value str">"Bio::Graphics::Glyph::"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">local_feature_glyph</span>.<span class="ruby-identifier">to_s</span>.<span class="ruby-identifier">camel_case</span>).<span class="ruby-identifier">to_class</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_context</span>)
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<span class="ruby-identifier">glyph</span>.<span class="ruby-identifier">draw</span>
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<span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">left_pixel_of_subfeatures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">glyph</span>.<span class="ruby-identifier">left_pixel</span>)
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<span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">right_pixel_of_subfeatures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">glyph</span>.<span class="ruby-identifier">right_pixel</span>)
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<span class="ruby-keyword kw">end</span></pre>
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Class <a href="Glyph/Box.html" class="link">Bio::Graphics::Glyph::Box</a><br />
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