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/feature.rb, line 38</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">track</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">location</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'1..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>)
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<span class="ruby-ivar">@track</span> = <span class="ruby-identifier">track</span>
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<span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
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<span class="ruby-ivar">@location</span> = <span class="ruby-identifier">location</span>
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<span class="ruby-ivar">@start</span> = <span class="ruby-identifier">location</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-identifier">location</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-identifier">location</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">@link</span> = <span class="ruby-identifier">link</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_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
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<span class="ruby-identifier">location</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 [ ]
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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-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
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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-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</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-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-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-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-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-comment cmt"># [ xxxx]xxxx
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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-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-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-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-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">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
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<span class="ruby-identifier">stop_pixel</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-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-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-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-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-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-ivar">@pixel_range_collection</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">PixelRange</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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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 129</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track</span>,<span class="ruby-identifier">direction</span>,<span class="ruby-identifier">x</span>,<span class="ruby-identifier">y</span>,<span class="ruby-identifier">size</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:north</span>
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">x</span><span class="ruby-operator">-</span><span class="ruby-identifier">size</span>,<span class="ruby-identifier">y</span><span class="ruby-operator">+</span><span class="ruby-identifier">size</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-operator">-</span><span class="ruby-identifier">size</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">x</span><span class="ruby-operator">-</span><span class="ruby-identifier">size</span>,<span class="ruby-identifier">y</span><span class="ruby-operator">-</span><span class="ruby-identifier">size</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-operator">-</span><span class="ruby-identifier">size</span>)
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 156</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">connector</span>(<span class="ruby-identifier">track</span>,<span class="ruby-identifier">from</span>,<span class="ruby-identifier">to</span>,<span class="ruby-identifier">top</span>, <span class="ruby-identifier">color</span>)
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<span class="ruby-identifier">line_width</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">line_width</span>
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<span class="ruby-identifier">track</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</span>.<span class="ruby-identifier">set_line_width</span>(<span class="ruby-value">0</span><span class="ruby-value">.5</span>)
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<span class="ruby-identifier">middle</span> = <span class="ruby-identifier">from</span> <span class="ruby-operator">+</span> ((<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">from</span>)<span class="ruby-operator">/</span><span class="ruby-value">2</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top</span><span class="ruby-operator">+</span><span class="ruby-value">2</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">middle</span>, <span class="ruby-identifier">top</span><span class="ruby-operator">+</span><span class="ruby-value">7</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top</span><span class="ruby-operator">+</span><span class="ruby-value">2</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">set_line_width</span>(<span class="ruby-identifier">line_width</span>)
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-identifier">color</span>)
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 178</span>
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|
-
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">track_drawing</span>)
|
|
15
|
-
<span class="ruby-comment cmt"># We have to check if we want to change the glyph type from directed to
|
|
16
|
-
<span class="ruby-comment cmt"># undirected
|
|
17
|
-
<span class="ruby-comment cmt"># There are 2 cases where we don't want to draw arrows on
|
|
18
|
-
<span class="ruby-comment cmt"># features:
|
|
19
|
-
<span class="ruby-comment cmt"># (a) when the picture is really zoomed out, features are
|
|
20
|
-
<span class="ruby-comment cmt"># so small that the arrow itself is too big
|
|
21
|
-
<span class="ruby-comment cmt"># (b) if a directed feature on the fw strand extends beyond
|
|
22
|
-
<span class="ruby-comment cmt"># the end of the picture, the arrow is out of view. This
|
|
23
|
-
<span class="ruby-comment cmt"># is the same as considering the feature as undirected.
|
|
24
|
-
<span class="ruby-comment cmt"># The same obviously goes for features on the reverse
|
|
25
|
-
<span class="ruby-comment cmt"># strand that extend beyond the left side of the image.
|
|
26
|
-
<span class="ruby-comment cmt">#
|
|
27
|
-
<span class="ruby-comment cmt"># (a) Zoomed out
|
|
28
|
-
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">false</span>
|
|
29
|
-
<span class="ruby-keyword kw">if</span> (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span>).<span class="ruby-identifier">to_f</span><span class="ruby-operator">/</span><span class="ruby-keyword kw">self</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>
|
|
30
|
-
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
|
|
31
|
-
<span class="ruby-keyword kw">end</span>
|
|
32
|
-
<span class="ruby-comment cmt"># (b) Extending beyond borders picture
|
|
33
|
-
<span class="ruby-keyword kw">if</span> ( <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">chopped_at_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">1</span> ) <span class="ruby-keyword kw">or</span> ( <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">chopped_at_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">-1</span> )
|
|
34
|
-
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
|
|
35
|
-
<span class="ruby-keyword kw">end</span>
|
|
36
|
-
|
|
37
|
-
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">nil</span>
|
|
38
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">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>
|
|
39
|
-
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:generic</span>
|
|
40
|
-
<span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">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>
|
|
41
|
-
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:spliced</span>
|
|
42
|
-
<span class="ruby-keyword kw">else</span>
|
|
43
|
-
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span>
|
|
44
|
-
<span class="ruby-keyword kw">end</span>
|
|
45
|
-
|
|
46
|
-
<span class="ruby-comment cmt"># And draw the thing.
|
|
47
|
-
<span class="ruby-identifier">row</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">find_row</span>
|
|
48
|
-
<span class="ruby-identifier">top_pixel_of_feature</span> = <span class="ruby-constant">FEATURE_V_DISTANCE</span> <span class="ruby-operator">+</span> (<span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_V_DISTANCE</span>)<span class="ruby-operator">*</span><span class="ruby-identifier">row</span>
|
|
49
|
-
<span class="ruby-identifier">bottom_pixel_of_feature</span> = <span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-constant">FEATURE_HEIGHT</span>
|
|
50
|
-
|
|
51
|
-
<span class="ruby-keyword kw">case</span> <span class="ruby-identifier">local_feature_glyph</span>
|
|
52
|
-
<span class="ruby-comment cmt"># triangles are typical for features which have a 1 bp position (start == stop)
|
|
53
|
-
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:triangle</span>
|
|
54
|
-
<span class="ruby-identifier">raise</span> <span class="ruby-value str">"Start and stop are not the same (necessary if you want triangle glyphs)"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">stop</span>
|
|
55
|
-
|
|
56
|
-
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
57
|
-
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>
|
|
58
|
-
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">+</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>
|
|
59
|
-
<span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:north</span>,<span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
60
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
|
|
61
|
-
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:line</span>
|
|
62
|
-
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
|
|
63
|
-
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
64
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">left_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
65
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">right_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
66
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
67
|
-
|
|
68
|
-
<span class="ruby-identifier">track_drawing</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>])
|
|
69
|
-
<span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">left_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
70
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
|
|
71
|
-
<span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">right_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
72
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
|
|
73
|
-
|
|
74
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span>)
|
|
75
|
-
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:directed_generic</span>
|
|
76
|
-
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
77
|
-
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
|
|
78
|
-
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
79
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># Reverse strand
|
|
80
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
81
|
-
<span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">left_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
82
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
83
|
-
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand
|
|
84
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
85
|
-
<span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">right_pixel_of_feature</span><span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
86
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
87
|
-
<span class="ruby-keyword kw">end</span>
|
|
88
|
-
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:spliced</span>
|
|
89
|
-
<span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
90
|
-
<span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
91
|
-
|
|
92
|
-
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
93
|
-
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
|
|
94
|
-
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
95
|
-
|
|
96
|
-
<span class="ruby-comment cmt"># First draw the parts
|
|
97
|
-
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span>
|
|
98
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, (<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>), <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
99
|
-
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">stop_pixel</span>)
|
|
100
|
-
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>)
|
|
101
|
-
<span class="ruby-keyword kw">end</span>
|
|
102
|
-
|
|
103
|
-
<span class="ruby-comment cmt"># And then draw the connections in the gaps
|
|
104
|
-
<span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
|
|
105
|
-
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
|
|
106
|
-
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
|
|
107
|
-
|
|
108
|
-
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap_number</span><span class="ruby-operator">|</span>
|
|
109
|
-
<span class="ruby-identifier">connector</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>,<span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span>)
|
|
110
|
-
<span class="ruby-keyword kw">end</span>
|
|
111
|
-
|
|
112
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
|
|
113
|
-
<span class="ruby-identifier">from</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
114
|
-
<span class="ruby-identifier">to</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
|
|
115
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
|
|
116
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
|
|
117
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
118
|
-
<span class="ruby-keyword kw">end</span>
|
|
119
|
-
|
|
120
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hidden_subfeatures_at_start</span>
|
|
121
|
-
<span class="ruby-identifier">from</span> = <span class="ruby-value">1</span>
|
|
122
|
-
<span class="ruby-identifier">to</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
|
|
123
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
|
|
124
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
|
|
125
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
126
|
-
<span class="ruby-keyword kw">end</span>
|
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127
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-
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128
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-
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:directed_spliced</span>
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129
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<span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
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131
|
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<span class="ruby-comment cmt"># First draw the parts
|
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132
|
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<span class="ruby-identifier">locations</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">location</span>.<span class="ruby-identifier">sort_by</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>}
|
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133
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-
|
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134
|
-
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
135
|
-
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
|
|
136
|
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<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
137
|
-
|
|
138
|
-
<span class="ruby-comment cmt"># Start with the one with the arrow
|
|
139
|
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<span class="ruby-identifier">pixel_ranges</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}
|
|
140
|
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<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-keyword kw">nil</span>
|
|
141
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># reverse strand => box with arrow is first one
|
|
142
|
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<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">shift</span>
|
|
143
|
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>((<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>)<span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
144
|
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<span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
145
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
146
|
-
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># forward strand => box with arrow is last one
|
|
147
|
-
<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">pop</span>
|
|
148
|
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
149
|
-
<span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span><span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
150
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
151
|
-
<span class="ruby-keyword kw">end</span>
|
|
152
|
-
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span>)
|
|
153
|
-
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>)
|
|
154
|
-
|
|
155
|
-
<span class="ruby-comment cmt"># And then add the others
|
|
156
|
-
<span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">range</span><span class="ruby-operator">|</span>
|
|
157
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
158
|
-
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">stop_pixel</span>)
|
|
159
|
-
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>)
|
|
160
|
-
<span class="ruby-keyword kw">end</span>
|
|
161
|
-
|
|
162
|
-
<span class="ruby-comment cmt"># And then draw the connections in the gaps
|
|
163
|
-
<span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
|
|
164
|
-
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
|
|
165
|
-
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
|
|
166
|
-
|
|
167
|
-
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap_number</span><span class="ruby-operator">|</span>
|
|
168
|
-
<span class="ruby-identifier">connector</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>,<span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span>)
|
|
169
|
-
<span class="ruby-keyword kw">end</span>
|
|
170
|
-
|
|
171
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
|
|
172
|
-
<span class="ruby-identifier">from</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
173
|
-
<span class="ruby-identifier">to</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
|
|
174
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
175
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
176
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
177
|
-
<span class="ruby-keyword kw">end</span>
|
|
178
|
-
|
|
179
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hidden_subfeatures_at_start</span>
|
|
180
|
-
<span class="ruby-identifier">from</span> = <span class="ruby-value">1</span>
|
|
181
|
-
<span class="ruby-identifier">to</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
|
|
182
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
183
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
|
|
184
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
185
|
-
<span class="ruby-keyword kw">end</span>
|
|
186
|
-
|
|
187
|
-
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#treat as 'generic'
|
|
188
|
-
<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
189
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, (<span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span>), <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
190
|
-
<span class="ruby-keyword kw">end</span>
|
|
191
|
-
|
|
192
|
-
<span class="ruby-comment cmt"># Add the label for the feature
|
|
193
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">show_label</span>
|
|
194
|
-
<span class="ruby-identifier">pango_layout</span> = <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">create_pango_layout</span>
|
|
195
|
-
<span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">text</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>
|
|
196
|
-
<span class="ruby-identifier">fdesc</span> = <span class="ruby-constant">Pango</span><span class="ruby-operator">::</span><span class="ruby-constant">FontDescription</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'Sans Serif'</span>)
|
|
197
|
-
<span class="ruby-identifier">fdesc</span>.<span class="ruby-identifier">set_size</span>(<span class="ruby-value">8</span> <span class="ruby-operator">*</span> <span class="ruby-constant">Pango</span><span class="ruby-operator">::</span><span class="ruby-constant">SCALE</span>)
|
|
198
|
-
<span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">font_description</span> = <span class="ruby-identifier">fdesc</span>
|
|
199
|
-
|
|
200
|
-
<span class="ruby-identifier">text_range</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">pixel_size</span>[<span class="ruby-value">0</span>]<span class="ruby-operator">*</span><span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>)
|
|
201
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>].<span class="ruby-identifier">nil?</span>
|
|
202
|
-
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
203
|
-
<span class="ruby-keyword kw">end</span>
|
|
204
|
-
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">text_range</span>)
|
|
205
|
-
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">text_range</span>)
|
|
206
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
|
|
207
|
-
<span class="ruby-identifier">track_drawing</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>)
|
|
208
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">show_pango_layout</span>(<span class="ruby-identifier">pango_layout</span>)
|
|
209
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span>)
|
|
210
|
-
<span class="ruby-keyword kw">end</span>
|
|
211
|
-
|
|
212
|
-
|
|
213
|
-
<span class="ruby-comment cmt"># And add the region to the image map
|
|
214
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">clickable</span>
|
|
215
|
-
<span class="ruby-comment cmt"># Comment: we have to add the vertical_offset and TRACK_HEADER_HEIGHT!
|
|
216
|
-
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">image_map</span>.<span class="ruby-identifier">elements</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">ImageMap</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageMapElement</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">left_pixel_of_feature</span>,
|
|
217
|
-
<span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
|
|
218
|
-
<span class="ruby-identifier">right_pixel_of_feature</span>,
|
|
219
|
-
<span class="ruby-identifier">bottom_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
|
|
220
|
-
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">link</span>
|
|
221
|
-
))
|
|
222
|
-
<span class="ruby-keyword kw">end</span>
|
|
223
|
-
<span class="ruby-keyword kw">end</span></pre>
|
|
224
|
-
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|
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|
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|
|
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<html>
|
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7
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-
<head>
|
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8
|
-
<title>find_row (Bio::Graphics::Panel::Track::Feature)</title>
|
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|
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<body class="standalone-code">
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13
|
-
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 396</span>
|
|
14
|
-
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">find_row</span>
|
|
15
|
-
<span class="ruby-identifier">row_found</span> = <span class="ruby-keyword kw">false</span>
|
|
16
|
-
|
|
17
|
-
<span class="ruby-comment cmt"># We've got to find out what row to draw the feature on. If two
|
|
18
|
-
<span class="ruby-comment cmt"># features overlap, one of them has to be 'bumped' down. So we'll
|
|
19
|
-
<span class="ruby-comment cmt"># first try to draw a new feature at the top of the track. If
|
|
20
|
-
<span class="ruby-comment cmt"># it however would overlap with another one, we'll bump it down
|
|
21
|
-
<span class="ruby-comment cmt"># to the next row.
|
|
22
|
-
<span class="ruby-identifier">feature_range</span> = (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span><span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">stop</span>.<span class="ruby-identifier">ceil</span>)
|
|
23
|
-
<span class="ruby-identifier">row</span> = <span class="ruby-value">1</span>
|
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<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
|
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<span class="ruby-keyword kw">until</span> <span class="ruby-identifier">row_found</span>
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">covered</span><span class="ruby-operator">|</span>
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">covered</span>.<span class="ruby-identifier">first</span>) <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">covered</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">first</span>)
|
|
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|
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<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</span>
|
|
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|
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<span class="ruby-keyword kw">end</span>
|
|
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|
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<span class="ruby-keyword kw">end</span>
|
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|
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<span class="ruby-keyword kw">end</span>
|
|
33
|
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|
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34
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">row_available</span>
|
|
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|
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<span class="ruby-identifier">row</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
|
|
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|
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<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
|
|
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|
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<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># We've found the place where to draw the feature.
|
|
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|
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<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
|
|
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|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
40
|
-
<span class="ruby-keyword kw">end</span>
|
|
41
|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">feature_range</span>)
|
|
42
|
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<span class="ruby-identifier">row_found</span> = <span class="ruby-keyword kw">true</span>
|
|
43
|
-
<span class="ruby-keyword kw">end</span>
|
|
44
|
-
<span class="ruby-keyword kw">end</span>
|
|
45
|
-
<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">row</span>
|
|
46
|
-
<span class="ruby-keyword kw">end</span></pre>
|
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 127</span>
|
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>)
|
|
15
|
-
<span class="ruby-ivar">@start_pixel</span>, <span class="ruby-ivar">@stop_pixel</span> = <span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>
|
|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 337</span>
|
|
14
|
-
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>)
|
|
15
|
-
<span class="ruby-ivar">@start_pixel</span>, <span class="ruby-ivar">@stop_pixel</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></pre>
|
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