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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- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000013.html +0 -18
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +0 -18
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000016.html +0 -18
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<td><strong>Class</strong></td>
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<td class="class-name-in-header">Bio::Graphics::SubFeature</td>
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<td>
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<a href="../../../files/lib/bio/graphics/subfeature_rb.html">
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lib/bio/graphics/subfeature.rb
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Object
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<a href="#M000028">draw</a>
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<td class="context-item-name">chopped_at_start</td>
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<td class="context-item-value"> [RW] </td>
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<td class="context-item-desc">
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Is the first subfeature incomplete?
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<td class="context-item-value"> [RW] </td>
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Is the last subfeature incomplete?
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<td class="context-item-name">colour</td>
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The colour to use to <a href="SubFeature.html#M000028">draw</a> this
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(sub)feature
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<td class="context-item-name">feature</td>
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<td class="context-item-value"> [RW] </td>
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The feature that this subfeature belongs to
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<td class="context-item-value"> [RW] </td>
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The bioruby <a href="../Feature.html">Bio::Feature</a> object
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<td class="context-item-name">glyph</td>
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The glyph to use to <a href="SubFeature.html#M000028">draw</a> this
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(sub)feature
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<td class="context-item-name">hidden_subfeatures_at_start</td>
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<td class="context-item-value"> [RW] </td>
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Are there subfeatures out of view at the left side of the picture?
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Are there subfeatures out of view at the right side of the picture?
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The label of the feature
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The locations of the feature (which is a Bio::Locations object)
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<td class="context-item-value"> [RW] </td>
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The array keeping the pixel ranges for the sub-features. Unspliced features
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will just have one element, while spliced features will have more than one.
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The start position of the feature (in bp)
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The stop position of the feature (in bp)
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<td class="context-item-name">strand</td>
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The strand of the feature
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<h3 class="section-bar">Public Class methods</h3>
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<div id="method-M000027" class="method-detail">
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<a name="M000027"></a>
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<a href="SubFeature.src/M000027.html" target="Code" class="method-signature"
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onclick="popupCode('SubFeature.src/M000027.html');return false;">
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<span class="method-name">new</span><span class="method-args">(feature, feature_object, opts = {})</span>
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!!Not to be used directly.
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<b>Arguments</b>:
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</p>
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<li><em>feature</em> (required) :: <a
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href="Feature.html">Bio::Graphics::Feature</a> object that this subfeature
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belongs to
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<li><em>feature</em> <em>object</em> (required) :: A <a
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href="../Feature.html">Bio::Feature</a> object (see bioruby)
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<li>:glyph :: <a href="Glyph.html">Glyph</a> to use. Default = glyph of the
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track
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<li>:colour :: Colour. Default = colour of the track
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</li>
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<tr><td valign="top"><b>Returns</b>:</td><td><a href="SubFeature.html">Bio::Graphics::SubFeature</a> object
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<h3 class="section-bar">Public Instance methods</h3>
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<div id="method-M000028" class="method-detail">
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<a name="M000028"></a>
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<a href="SubFeature.src/M000028.html" target="Code" class="method-signature"
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onclick="popupCode('SubFeature.src/M000028.html');return false;">
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<span class="method-name">draw</span><span class="method-args">(feature_context)</span>
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<p>
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Adds the subfeature to the track cairo context. This method should not be
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used directly by the user, but is called by <a
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href="SubFeature.html#M000028">Bio::Graphics::Feature::SubFeature.draw</a>
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</p>
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<hr size="1"></hr><p>
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<b>Arguments</b>:
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</p>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/subfeature.rb, line 21</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">feature</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span> = {})
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<span class="ruby-ivar">@feature</span> = <span class="ruby-identifier">feature</span>
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<span class="ruby-ivar">@feature_object</span> = <span class="ruby-identifier">feature_object</span>
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<span class="ruby-identifier">opts</span> = {
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<span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">glyph</span>,
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<span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">colour</span>
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}.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
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<span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:glyph</span>]
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<span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:colour</span>]
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<span class="ruby-ivar">@locations</span> = <span class="ruby-ivar">@feature_object</span>.<span class="ruby-identifier">locations</span>
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<span class="ruby-ivar">@start</span> = <span class="ruby-ivar">@locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@stop</span> = <span class="ruby-ivar">@locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@strand</span> = <span class="ruby-ivar">@locations</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">strand</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@pixel_range_collection</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">false</span>
|
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<span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">false</span>
|
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<span class="ruby-comment cmt"># Get all pixel ranges for the subfeatures</span>
|
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<span class="ruby-ivar">@locations</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span>
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<span class="ruby-comment cmt"># xxxxxx [ ]</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
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<span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">next</span>
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<span class="ruby-comment cmt"># [ ] xxxxx</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">next</span>
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<span class="ruby-comment cmt"># xxxx[xxx ]</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
|
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<span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
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<span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-comment cmt"># [ xxxx]xxxx</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
|
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<span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
|
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<span class="ruby-identifier">stop_pixel</span> = <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
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<span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
|
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<span class="ruby-comment cmt"># xxxx[xxxxxxxxxx]xxxx</span>
|
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
|
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<span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
|
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<span class="ruby-identifier">stop_pixel</span> = <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
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<span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-comment cmt"># [ xxxxx ]</span>
|
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<span class="ruby-keyword kw">else</span>
|
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<span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
|
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<span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
|
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<span class="ruby-keyword kw">end</span>
|
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|
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<span class="ruby-ivar">@pixel_range_collection</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Range</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>))
|
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|
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<span class="ruby-keyword kw">end</span>
|
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<span class="ruby-keyword kw">end</span></pre>
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<title>draw (Bio::Graphics::SubFeature)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/subfeature.rb, line 133</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">feature_context</span>)
|
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+
<span class="ruby-comment cmt"># Set the glyph to be used. The glyph can be set as a symbol (e.g. :generic)</span>
|
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+
<span class="ruby-comment cmt"># or as a hash (e.g. {'utr' => :line, 'cds' => :directed_spliced}).</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">glyph</span>.<span class="ruby-identifier">class</span> <span class="ruby-operator">==</span> <span class="ruby-constant">Hash</span>
|
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18
|
+
<span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">glyph</span>[<span class="ruby-ivar">@feature_object</span>.<span class="ruby-identifier">feature</span>]
|
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|
+
<span class="ruby-keyword kw">else</span>
|
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+
<span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">glyph</span>
|
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|
+
<span class="ruby-keyword kw">end</span>
|
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+
|
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+
<span class="ruby-comment cmt"># We have to check if we want to change the glyph type from directed to</span>
|
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24
|
+
<span class="ruby-comment cmt"># undirected</span>
|
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25
|
+
<span class="ruby-comment cmt"># There are 2 cases where we don't want to draw arrows on</span>
|
|
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|
+
<span class="ruby-comment cmt"># features:</span>
|
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+
<span class="ruby-comment cmt"># (a) when the picture is really zoomed out, features are</span>
|
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|
+
<span class="ruby-comment cmt"># so small that the arrow itself is too big</span>
|
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|
+
<span class="ruby-comment cmt"># (b) if a directed feature on the fw strand extends beyond</span>
|
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<span class="ruby-comment cmt"># the end of the picture, the arrow is out of view. This</span>
|
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+
<span class="ruby-comment cmt"># is the same as considering the feature as undirected.</span>
|
|
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|
+
<span class="ruby-comment cmt"># The same obviously goes for features on the reverse</span>
|
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|
+
<span class="ruby-comment cmt"># strand that extend beyond the left side of the image.</span>
|
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|
+
<span class="ruby-comment cmt">#</span>
|
|
35
|
+
<span class="ruby-comment cmt"># (a) Zoomed out</span>
|
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|
+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">false</span>
|
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+
<span class="ruby-keyword kw">if</span> (<span class="ruby-ivar">@stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@start</span>).<span class="ruby-identifier">to_f</span><span class="ruby-operator">/</span><span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator"><</span> <span class="ruby-value">2</span>
|
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|
+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
|
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39
|
+
<span class="ruby-keyword kw">end</span>
|
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40
|
+
<span class="ruby-comment cmt"># (b) Extending beyond borders picture</span>
|
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41
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+
<span class="ruby-keyword kw">if</span> ( <span class="ruby-ivar">@chopped_at_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@strand</span> = <span class="ruby-value">1</span> ) <span class="ruby-keyword kw">or</span> ( <span class="ruby-ivar">@chopped_at_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@strand</span> = <span class="ruby-value">-1</span> )
|
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+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
|
|
43
|
+
<span class="ruby-keyword kw">end</span>
|
|
44
|
+
|
|
45
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">nil</span>
|
|
46
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+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:directed_generic</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
|
|
47
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:generic</span>
|
|
48
|
+
<span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:directed_spliced</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
|
|
49
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:spliced</span>
|
|
50
|
+
<span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:directed_box</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
|
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51
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:box</span>
|
|
52
|
+
<span class="ruby-keyword kw">else</span>
|
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53
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-ivar">@glyph</span>
|
|
54
|
+
<span class="ruby-keyword kw">end</span>
|
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55
|
+
|
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56
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+
<span class="ruby-comment cmt"># And draw the thing.</span>
|
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57
|
+
|
|
58
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+
<span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-ivar">@colour</span>)
|
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59
|
+
|
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+
<span class="ruby-identifier">glyph</span> = (<span class="ruby-value str">"Bio::Graphics::Glyph::"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">local_feature_glyph</span>.<span class="ruby-identifier">to_s</span>.<span class="ruby-identifier">camel_case</span>).<span class="ruby-identifier">to_class</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_context</span>)
|
|
61
|
+
<span class="ruby-identifier">glyph</span>.<span class="ruby-identifier">draw</span>
|
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|
+
|
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+
<span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">left_pixel_of_subfeatures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">glyph</span>.<span class="ruby-identifier">left_pixel</span>)
|
|
64
|
+
<span class="ruby-ivar">@feature</span>.<span class="ruby-identifier">right_pixel_of_subfeatures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">glyph</span>.<span class="ruby-identifier">right_pixel</span>)
|
|
65
|
+
|
|
66
|
+
|
|
67
|
+
<span class="ruby-keyword kw">end</span></pre>
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|
68
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+
</body>
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69
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+
</html>
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