bio-graphics 1.2 → 1.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/doc/classes/Bio.html +4 -26
- data/doc/classes/Bio/Feature.html +350 -0
- data/doc/classes/Bio/Feature.src/M000010.html +21 -0
- data/doc/classes/Bio/Feature.src/M000011.html +20 -0
- data/doc/classes/Bio/Feature.src/M000012.html +19 -0
- data/doc/classes/Bio/Feature.src/M000014.html +21 -0
- data/doc/classes/Bio/Feature.src/M000016.html +21 -0
- data/doc/classes/Bio/Feature.src/M000034.html +21 -0
- data/doc/classes/Bio/Feature.src/M000035.html +20 -0
- data/doc/classes/Bio/Feature.src/M000036.html +19 -0
- data/doc/classes/Bio/Feature.src/M000038.html +21 -0
- data/doc/classes/Bio/Feature.src/M000040.html +21 -0
- data/doc/classes/Bio/Feature.src/M000042.html +21 -0
- data/doc/classes/Bio/Feature.src/M000043.html +20 -0
- data/doc/classes/Bio/Feature.src/M000044.html +21 -0
- data/doc/classes/Bio/Feature.src/M000045.html +20 -0
- data/doc/classes/Bio/Feature.src/M000046.html +19 -0
- data/doc/classes/Bio/Feature.src/M000048.html +21 -0
- data/doc/classes/Bio/Feature.src/M000050.html +21 -0
- data/doc/classes/Bio/Feature.src/M000074.html +21 -0
- data/doc/classes/Bio/Feature.src/M000075.html +20 -0
- data/doc/classes/Bio/Feature.src/M000076.html +19 -0
- data/doc/classes/Bio/Feature.src/M000078.html +21 -0
- data/doc/classes/Bio/Feature.src/M000080.html +21 -0
- data/doc/classes/Bio/Feature/Qualifier.html +189 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000017.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000041.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000049.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000051.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000081.html +18 -0
- data/doc/classes/Bio/Features.html +329 -0
- data/doc/classes/Bio/Features.src/M000004.html +18 -0
- data/doc/classes/Bio/Features.src/M000005.html +19 -0
- data/doc/classes/Bio/Features.src/M000006.html +21 -0
- data/doc/classes/Bio/Features.src/M000007.html +18 -0
- data/doc/classes/Bio/Features.src/M000008.html +18 -0
- data/doc/classes/Bio/Features.src/M000009.html +18 -0
- data/doc/classes/Bio/Features.src/M000028.html +18 -0
- data/doc/classes/Bio/Features.src/M000029.html +19 -0
- data/doc/classes/Bio/Features.src/M000030.html +21 -0
- data/doc/classes/Bio/Features.src/M000031.html +18 -0
- data/doc/classes/Bio/Features.src/M000032.html +18 -0
- data/doc/classes/Bio/Features.src/M000033.html +18 -0
- data/doc/classes/Bio/Features.src/M000036.html +18 -0
- data/doc/classes/Bio/Features.src/M000037.html +19 -0
- data/doc/classes/Bio/Features.src/M000038.html +18 -0
- data/doc/classes/Bio/Features.src/M000039.html +19 -0
- data/doc/classes/Bio/Features.src/M000040.html +21 -0
- data/doc/classes/Bio/Features.src/M000041.html +18 -0
- data/doc/classes/Bio/Features.src/M000042.html +18 -0
- data/doc/classes/Bio/Features.src/M000043.html +18 -0
- data/doc/classes/Bio/Features.src/M000068.html +18 -0
- data/doc/classes/Bio/Features.src/M000069.html +19 -0
- data/doc/classes/Bio/Features.src/M000070.html +21 -0
- data/doc/classes/Bio/Features.src/M000071.html +18 -0
- data/doc/classes/Bio/Features.src/M000072.html +18 -0
- data/doc/classes/Bio/Features.src/M000073.html +18 -0
- data/doc/classes/Bio/Graphics.html +28 -42
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} +98 -125
- data/doc/classes/Bio/Graphics/Feature.src/M000020.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000021.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000022.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000023.html +66 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000024.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000025.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000026.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000054.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000055.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000056.html +55 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000025.html +68 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000026.html +67 -0
- data/doc/classes/Bio/Graphics/Glyph.html +178 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000004.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000032.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.html +187 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html +40 -0
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.html} +16 -19
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Transcript.html +113 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html +21 -0
- data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.html} +50 -16
- data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} +3 -3
- data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000033.html +18 -0
- data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} +7 -4
- data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000062.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000064.html +27 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html +24 -0
- data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} +14 -14
- data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} +3 -3
- data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} +6 -4
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html +22 -0
- data/doc/classes/Bio/Graphics/Panel.html +70 -69
- data/doc/classes/Bio/Graphics/Panel.src/M000025.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000026.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000027.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000028.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000029.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000030.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000031.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000059.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000060.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000061.html +98 -0
- data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} +50 -21
- data/doc/classes/Bio/Graphics/Ruler.src/M000015.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000016.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000017.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000018.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000019.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000020.html +45 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000047.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000048.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000049.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000050.html +45 -0
- data/doc/classes/Bio/Graphics/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000001.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000002.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000023.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000024.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000027.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000028.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000057.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000058.html +69 -0
- data/doc/classes/Bio/Graphics/{Panel/Track.html → Track.html} +67 -69
- data/doc/classes/Bio/Graphics/Track.src/M000017.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000018.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000019.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000020.html +41 -0
- data/doc/classes/Bio/Graphics/Track.src/M000021.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000022.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000023.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000051.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000052.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000053.html +45 -0
- data/doc/classes/Range.html +129 -0
- data/doc/classes/String.html +167 -0
- data/doc/classes/String.src/M000001.html +18 -0
- data/doc/classes/String.src/M000002.html +18 -0
- data/doc/classes/String.src/M000003.html +23 -0
- data/doc/classes/String.src/M000029.html +18 -0
- data/doc/classes/String.src/M000030.html +18 -0
- data/doc/classes/String.src/M000031.html +23 -0
- data/doc/classes/TestCustomGlyph.html +137 -0
- data/doc/classes/TestCustomGlyph.src/M000025.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.html +167 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000026.html +19 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000027.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000028.html +18 -0
- data/doc/classes/TestExtensions.html +152 -0
- data/doc/classes/TestExtensions.src/M000015.html +22 -0
- data/doc/classes/TestExtensions.src/M000016.html +25 -0
- data/doc/classes/TestFeature.html +152 -0
- data/doc/classes/TestFeature.src/M000017.html +19 -0
- data/doc/classes/TestFeature.src/M000018.html +21 -0
- data/doc/classes/TestImageMap.html +182 -0
- data/doc/classes/TestImageMap.src/M000019.html +22 -0
- data/doc/classes/TestImageMap.src/M000020.html +56 -0
- data/doc/classes/TestImageMap.src/M000021.html +56 -0
- data/doc/classes/TestImageMap.src/M000022.html +20 -0
- data/doc/classes/TestPanel.html +276 -0
- data/doc/classes/TestPanel.src/M000001.html +18 -0
- data/doc/classes/TestPanel.src/M000002.html +61 -0
- data/doc/classes/TestPanel.src/M000003.html +35 -0
- data/doc/classes/TestPanel.src/M000004.html +54 -0
- data/doc/classes/TestPanel.src/M000005.html +54 -0
- data/doc/classes/TestPanel.src/M000006.html +41 -0
- data/doc/classes/TestPanel.src/M000007.html +36 -0
- data/doc/classes/TestPanel.src/M000008.html +20 -0
- data/doc/classes/TestPanel.src/M000009.html +26 -0
- data/doc/classes/TestPanel.src/M000010.html +21 -0
- data/doc/classes/TestRuler.html +152 -0
- data/doc/classes/TestRuler.src/M000013.html +22 -0
- data/doc/classes/TestRuler.src/M000014.html +31 -0
- data/doc/classes/TestSubFeature.html +152 -0
- data/doc/classes/TestSubFeature.src/M000023.html +21 -0
- data/doc/classes/TestSubFeature.src/M000024.html +18 -0
- data/doc/classes/TestTrack.html +152 -0
- data/doc/classes/TestTrack.src/M000011.html +19 -0
- data/doc/classes/TestTrack.src/M000012.html +23 -0
- data/doc/created.rid +1 -1
- data/doc/files/README_DEV.html +399 -70
- data/doc/files/TUTORIAL.html +188 -67
- data/doc/files/lib/bio-graphics_rb.html +3 -2
- data/doc/files/lib/bio/graphics/feature_rb.html +12 -6
- data/doc/files/lib/bio/graphics/glyphs/box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/common_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/dot_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_with_handles_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/transcript_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/triangle_rb.html +113 -0
- data/doc/files/lib/bio/graphics/image_map_rb.html +3 -2
- data/doc/files/lib/bio/graphics/panel_rb.html +10 -2
- data/doc/files/lib/bio/graphics/ruler_rb.html +3 -2
- data/doc/files/lib/bio/graphics/subfeature_rb.html +114 -0
- data/doc/files/lib/bio/graphics/track_rb.html +3 -2
- data/doc/files/lib/feature_rb.html +101 -0
- data/doc/files/samples/arkdb_features_rb.html +101 -0
- data/doc/files/samples/glyph_showcase_rb.html +108 -0
- data/doc/files/samples/protein_domains_rb.html +115 -0
- data/doc/files/samples/subfeatures_rb.html +108 -0
- data/doc/files/scripts/gff2png_rb.html +154 -0
- data/doc/files/test/unit/custom_glyph_in_file_rb.html +101 -0
- data/doc/files/test/unit/test_class_extensions_rb.html +108 -0
- data/doc/files/test/unit/test_creation_rb.html +108 -0
- data/doc/files/test/unit/test_custom_glyph_rb.html +108 -0
- data/doc/files/test/unit/test_draw_rb.html +108 -0
- data/doc/files/test/unit/test_imagemap_rb.html +108 -0
- data/doc/files/test/unit/test_subfeatures_rb.html +108 -0
- data/doc/fr_class_index.html +24 -6
- data/doc/fr_file_index.html +14 -0
- data/doc/fr_method_index.html +51 -19
- data/doc/images/glyph_showcase.png +0 -0
- data/doc/images/terms.svg +146 -132
- data/images/glyph_showcase.png +0 -0
- data/lib/bio-graphics.rb +38 -6
- data/lib/bio/graphics/feature.rb +212 -440
- data/lib/bio/graphics/glyphs/box.rb +21 -0
- data/lib/bio/graphics/glyphs/common.rb +149 -0
- data/lib/bio/graphics/glyphs/directed_box.rb +28 -0
- data/lib/bio/graphics/glyphs/directed_generic.rb +23 -0
- data/lib/bio/graphics/glyphs/directed_spliced.rb +39 -0
- data/lib/bio/graphics/glyphs/dot.rb +21 -0
- data/lib/bio/graphics/glyphs/generic.rb +15 -0
- data/lib/bio/graphics/glyphs/line.rb +17 -0
- data/lib/bio/graphics/glyphs/line_with_handles.rb +25 -0
- data/lib/bio/graphics/glyphs/spliced.rb +16 -0
- data/lib/bio/graphics/glyphs/transcript.rb +12 -0
- data/lib/bio/graphics/glyphs/triangle.rb +18 -0
- data/lib/bio/graphics/image_map.rb +25 -4
- data/lib/bio/graphics/panel.rb +266 -209
- data/lib/bio/graphics/ruler.rb +95 -96
- data/lib/bio/graphics/subfeature.rb +187 -0
- data/lib/bio/graphics/track.rb +155 -156
- data/lib/feature.rb +204 -0
- data/samples/arkdb_features.rb +10 -8
- data/samples/glyph_showcase.rb +58 -22
- data/samples/protein_domains.rb +19 -0
- data/samples/subfeatures.rb +31 -0
- data/test/unit/custom_glyph_in_file.rb +12 -0
- data/test/unit/data.txt +32 -0
- data/test/unit/test_class_extensions.rb +23 -0
- data/test/unit/test_creation.rb +43 -13
- data/test/unit/test_custom_glyph.rb +50 -0
- data/test/unit/test_draw.rb +211 -0
- data/test/unit/test_imagemap.rb +134 -0
- data/test/unit/test_subfeatures.rb +17 -0
- metadata +396 -119
- data/doc/classes/Bio/Graphics/Panel.src/M000005.html +0 -29
- data/doc/classes/Bio/Graphics/Panel.src/M000006.html +0 -19
- data/doc/classes/Bio/Graphics/Panel.src/M000007.html +0 -68
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +0 -54
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +0 -26
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +0 -42
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +0 -52
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +0 -23
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +0 -43
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +0 -259
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +0 -65
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +0 -39
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/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-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-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-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-keyword kw">end</span>
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<span class="ruby-ivar">@pixel_range_collection</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">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-identifier">size</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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<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>)
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<span class="ruby-comment cmt"># We have to check if we want to change the glyph type from directed to
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<span class="ruby-comment cmt"># undirected
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<span class="ruby-comment cmt"># There are 2 cases where we don't want to draw arrows on
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<span class="ruby-comment cmt"># features:
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<span class="ruby-comment cmt"># (a) when the picture is really zoomed out, features are
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<span class="ruby-comment cmt"># so small that the arrow itself is too big
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<span class="ruby-comment cmt"># (b) if a directed feature on the fw strand extends beyond
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<span class="ruby-comment cmt"># the end of the picture, the arrow is out of view. This
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<span class="ruby-comment cmt"># is the same as considering the feature as undirected.
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<span class="ruby-comment cmt"># The same obviously goes for features on the reverse
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<span class="ruby-comment cmt"># strand that extend beyond the left side of the image.
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<span class="ruby-comment cmt">#
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<span class="ruby-comment cmt"># (a) Zoomed out
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<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-keyword kw">if</span> (<span class="ruby-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>
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<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># (b) Extending beyond borders picture
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<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> )
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<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-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>
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<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:generic</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-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>
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<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:spliced</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span>
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<span class="ruby-keyword kw">end</span>
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46
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<span class="ruby-comment cmt"># And draw the thing.
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<span class="ruby-identifier">row</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">find_row</span>
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<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>
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<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>
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51
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<span class="ruby-keyword kw">case</span> <span class="ruby-identifier">local_feature_glyph</span>
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<span class="ruby-comment cmt"># triangles are typical for features which have a 1 bp position (start == stop)
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:triangle</span>
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<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>
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56
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<span class="ruby-comment cmt"># Need to get this for the imagemap
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<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>
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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-value">0</span>].<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">+</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>
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<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>)
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:line</span>
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<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>
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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>
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64
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<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>)
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<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>)
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66
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
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67
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68
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<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>])
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69
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<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>)
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70
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
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71
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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">right_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
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72
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
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73
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-
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74
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<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>)
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75
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:directed_generic</span>
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76
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<span class="ruby-comment cmt"># Need to get this for the imagemap
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77
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<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>
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78
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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>
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<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
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80
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-
<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>
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81
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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">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>)
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|
82
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
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|
83
|
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<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand
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|
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>
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|
85
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<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>)
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|
86
|
-
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
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|
87
|
-
<span class="ruby-keyword kw">end</span>
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|
88
|
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<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>
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|
90
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-
<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>
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94
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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>
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|
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>
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|
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>
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|
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>)
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|
100
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-
<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.
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|
105
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-
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
|
|
106
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-
<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>
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109
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-
<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>
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|
114
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-
<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>
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|
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
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-
<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>)
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117
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<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>
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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>)
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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>
|
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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
|
-
<span class="ruby-comment cmt"># First draw the parts
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132
|
-
<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
|
-
|
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138
|
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<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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<head>
|
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|
-
<title>find_row (Bio::Graphics::Panel::Track::Feature)</title>
|
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|
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|
-
<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>)
|
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<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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<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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<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>
|
|
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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">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>)
|
|
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|
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<span class="ruby-identifier">row_found</span> = <span class="ruby-keyword kw">true</span>
|
|
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|
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<span class="ruby-keyword kw">end</span>
|
|
44
|
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<span class="ruby-keyword kw">end</span>
|
|
45
|
-
<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">row</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/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>)
|
|
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|
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<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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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 337</span>
|
|
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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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|
-
<span class="ruby-keyword kw">end</span></pre>
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