bio-graphics 1.2 → 1.4
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- 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
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000013.html +0 -27
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 37</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
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<span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
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<span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
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<span class="ruby-identifier">opts</span> = {
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<span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>,
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<span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:generic</span>,
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<span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
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}.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
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<span class="ruby-ivar">@show_label</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:label</span>]
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<span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:glyph</span>]
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<span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:colour</span>]
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<span class="ruby-comment cmt"># As far as I know, I can't do this in the glyph file for transcript, so we</span>
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<span class="ruby-comment cmt"># have to do it here instead.</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">:transcript</span>
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<span class="ruby-ivar">@glyph</span> = { <span class="ruby-value str">'utr5'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:box</span>, <span class="ruby-value str">'utr3'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:directed_box</span>, <span class="ruby-value str">'cds'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:spliced</span> }
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
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<span class="ruby-ivar">@vertical_offset</span> = <span class="ruby-value">0</span>
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<span class="ruby-ivar">@grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</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/track.rb, line 93</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span> = {})
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<span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start</span>
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<span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.</span>
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<span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want</span>
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<span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or</span>
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<span class="ruby-comment cmt"># not (see below).</span>
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<span class="ruby-identifier">start</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">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-identifier">stop</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">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-comment cmt"># If the feature wouldn't show because it's not in the region we're</span>
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<span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge</span>
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<span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with</span>
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<span class="ruby-comment cmt"># thousands of features.</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start >= panel.display_start and stop <= panel.display_stop</span>
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span>))
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<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</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/track.rb, line 123</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
|
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<span class="ruby-identifier">track_context</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_destination</span>)
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<span class="ruby-comment cmt"># Draw thin line above title</span>
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
|
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
|
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
|
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-comment cmt"># Draw track title</span>
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
|
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<span class="ruby-identifier">track_context</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>))
|
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_font_size</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">TRACK_HEADER_HEIGHT</span>)
|
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
|
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|
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
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<span class="ruby-comment cmt"># Draw the features</span>
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
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<span class="ruby-comment cmt"># Don't even bother if the feature is not in the view</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-keyword kw">next</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
|
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
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|
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<span class="ruby-ivar">@number_of_feature_rows</span> = ( <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
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|
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<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">panel_destination</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/track.rb, line 87</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">label</span> = <span class="ruby-value str">'anonymous'</span>, <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">glyph</span> = <span class="ruby-ivar">@glyph</span>, <span class="ruby-identifier">colour</span> = <span class="ruby-ivar">@colour</span>)
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">link</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
|
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<span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>
|
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<span class="ruby-keyword kw">end</span>
|
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|
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+
<span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start</span>
|
|
20
|
+
<span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.</span>
|
|
21
|
+
<span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want</span>
|
|
22
|
+
<span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or</span>
|
|
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|
+
<span class="ruby-comment cmt"># not (see below).</span>
|
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|
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<span class="ruby-identifier">start</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">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-identifier">stop</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">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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|
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<span class="ruby-comment cmt"># If the feature wouldn't show because it's not in the region we're</span>
|
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<span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge</span>
|
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<span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with</span>
|
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|
+
<span class="ruby-comment cmt"># thousands of features.</span>
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
|
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<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start >= panel.display_start and stop <= panel.display_stop</span>
|
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">label</span>, <span class="ruby-identifier">link</span>, <span class="ruby-identifier">glyph</span>, <span class="ruby-identifier">colour</span>))
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<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 37</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
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<span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
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<span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
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<span class="ruby-identifier">opts</span> = {
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<span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>,
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<span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:generic</span>,
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<span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
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}.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
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<span class="ruby-ivar">@show_label</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:label</span>]
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<span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:glyph</span>]
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<span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:colour</span>]
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<span class="ruby-comment cmt"># As far as I know, I can't do this in the glyph file for transcript, so we</span>
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<span class="ruby-comment cmt"># have to do it here instead.</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">:transcript</span>
|
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<span class="ruby-ivar">@glyph</span> = { <span class="ruby-value str">'utr5'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:box</span>, <span class="ruby-value str">'utr3'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:directed_box</span>, <span class="ruby-value str">'cds'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:spliced</span> }
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
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<span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
|
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<span class="ruby-ivar">@vertical_offset</span> = <span class="ruby-value">0</span>
|
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|
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<span class="ruby-ivar">@grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</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/track.rb, line 93</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span> = {})
|
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|
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<span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start</span>
|
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<span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.</span>
|
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<span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want</span>
|
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<span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or</span>
|
|
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|
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<span class="ruby-comment cmt"># not (see below).</span>
|
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|
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<span class="ruby-identifier">start</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">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-identifier">stop</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">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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+
|
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<span class="ruby-comment cmt"># If the feature wouldn't show because it's not in the region we're</span>
|
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|
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<span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge</span>
|
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<span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with</span>
|
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|
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<span class="ruby-comment cmt"># thousands of features.</span>
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
|
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|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
|
|
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|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start >= panel.display_start and stop <= panel.display_stop</span>
|
|
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|
+
<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span>))
|
|
31
|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
|
|
32
|
+
<span class="ruby-keyword kw">end</span>
|
|
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|
+
|
|
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|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
|
|
35
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 123</span>
|
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
|
|
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|
+
<span class="ruby-identifier">track_context</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_destination</span>)
|
|
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|
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|
|
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|
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<span class="ruby-comment cmt"># Draw thin line above title</span>
|
|
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|
+
<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
|
|
19
|
+
<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
|
|
20
|
+
<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
|
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|
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">stroke</span>
|
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|
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|
|
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|
+
<span class="ruby-comment cmt"># Draw track title</span>
|
|
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|
+
<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
|
|
25
|
+
<span class="ruby-identifier">track_context</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>))
|
|
26
|
+
<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_font_size</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">TRACK_HEADER_HEIGHT</span>)
|
|
27
|
+
<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
|
|
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|
+
<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
|
|
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|
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|
|
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|
+
<span class="ruby-comment cmt"># Draw the features</span>
|
|
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|
+
<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
|
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|
+
<span class="ruby-comment cmt"># Don't even bother if the feature is not in the view</span>
|
|
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|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
|
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|
+
<span class="ruby-keyword kw">next</span>
|
|
35
|
+
<span class="ruby-keyword kw">else</span>
|
|
36
|
+
<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
|
|
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|
+
<span class="ruby-keyword kw">end</span>
|
|
38
|
+
<span class="ruby-keyword kw">end</span>
|
|
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|
+
|
|
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|
+
<span class="ruby-ivar">@number_of_feature_rows</span> = ( <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
|
|
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|
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|
|
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|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">panel_destination</span>
|
|
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|
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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/track.rb, line 37</span>
|
|
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|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
|
|
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|
+
<span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
|
|
16
|
+
<span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
|
|
17
|
+
<span class="ruby-identifier">opts</span> = {
|
|
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|
+
<span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>,
|
|
19
|
+
<span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:generic</span>,
|
|
20
|
+
<span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
|
|
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|
+
}.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
|
|
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|
+
|
|
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|
+
<span class="ruby-ivar">@show_label</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:label</span>]
|
|
24
|
+
<span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:glyph</span>]
|
|
25
|
+
<span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:colour</span>]
|
|
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|
+
|
|
27
|
+
<span class="ruby-comment cmt"># As far as I know, I can't do this in the glyph file for transcript, so we</span>
|
|
28
|
+
<span class="ruby-comment cmt"># have to do it here instead.</span>
|
|
29
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:transcript</span>
|
|
30
|
+
<span class="ruby-ivar">@glyph</span> = { <span class="ruby-value str">'utr5'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:box</span>, <span class="ruby-value str">'utr3'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:directed_box</span>, <span class="ruby-value str">'cds'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:spliced</span> }
|
|
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|
+
<span class="ruby-keyword kw">end</span>
|
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|
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|
|
33
|
+
<span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
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|
+
<span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
|
|
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|
+
<span class="ruby-ivar">@vertical_offset</span> = <span class="ruby-value">0</span>
|
|
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|
+
<span class="ruby-ivar">@grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
|
|
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|
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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/track.rb, line 93</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span> = {})
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<span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start</span>
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<span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.</span>
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<span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want</span>
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<span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or</span>
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<span class="ruby-comment cmt"># not (see below).</span>
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<span class="ruby-identifier">start</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">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-identifier">stop</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">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-comment cmt"># If the feature wouldn't show because it's not in the region we're</span>
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<span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge</span>
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<span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with</span>
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<span class="ruby-comment cmt"># thousands of features.</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start >= panel.display_start and stop <= panel.display_stop</span>
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span>))
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<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</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/track.rb, line 123</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
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<span class="ruby-identifier">track_context</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_destination</span>)
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<span class="ruby-comment cmt"># Draw thin line above title</span>
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
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<span class="ruby-comment cmt"># Draw track title</span>
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
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<span class="ruby-identifier">track_context</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>))
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_font_size</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">TRACK_HEADER_HEIGHT</span>)
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
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<span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
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<span class="ruby-comment cmt"># Draw the features</span>
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
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<span class="ruby-comment cmt"># Don't even bother if the feature is not in the view</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-ivar">@number_of_feature_rows</span> = ( <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
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