bio-graphics 1.2 → 1.4
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- data/doc/classes/Bio.html +4 -26
- data/doc/classes/Bio/Feature.html +350 -0
- data/doc/classes/Bio/Feature.src/M000010.html +21 -0
- data/doc/classes/Bio/Feature.src/M000011.html +20 -0
- data/doc/classes/Bio/Feature.src/M000012.html +19 -0
- data/doc/classes/Bio/Feature.src/M000014.html +21 -0
- data/doc/classes/Bio/Feature.src/M000016.html +21 -0
- data/doc/classes/Bio/Feature.src/M000034.html +21 -0
- data/doc/classes/Bio/Feature.src/M000035.html +20 -0
- data/doc/classes/Bio/Feature.src/M000036.html +19 -0
- data/doc/classes/Bio/Feature.src/M000038.html +21 -0
- data/doc/classes/Bio/Feature.src/M000040.html +21 -0
- data/doc/classes/Bio/Feature.src/M000042.html +21 -0
- data/doc/classes/Bio/Feature.src/M000043.html +20 -0
- data/doc/classes/Bio/Feature.src/M000044.html +21 -0
- data/doc/classes/Bio/Feature.src/M000045.html +20 -0
- data/doc/classes/Bio/Feature.src/M000046.html +19 -0
- data/doc/classes/Bio/Feature.src/M000048.html +21 -0
- data/doc/classes/Bio/Feature.src/M000050.html +21 -0
- data/doc/classes/Bio/Feature.src/M000074.html +21 -0
- data/doc/classes/Bio/Feature.src/M000075.html +20 -0
- data/doc/classes/Bio/Feature.src/M000076.html +19 -0
- data/doc/classes/Bio/Feature.src/M000078.html +21 -0
- data/doc/classes/Bio/Feature.src/M000080.html +21 -0
- data/doc/classes/Bio/Feature/Qualifier.html +189 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000017.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000041.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000049.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000051.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000081.html +18 -0
- data/doc/classes/Bio/Features.html +329 -0
- data/doc/classes/Bio/Features.src/M000004.html +18 -0
- data/doc/classes/Bio/Features.src/M000005.html +19 -0
- data/doc/classes/Bio/Features.src/M000006.html +21 -0
- data/doc/classes/Bio/Features.src/M000007.html +18 -0
- data/doc/classes/Bio/Features.src/M000008.html +18 -0
- data/doc/classes/Bio/Features.src/M000009.html +18 -0
- data/doc/classes/Bio/Features.src/M000028.html +18 -0
- data/doc/classes/Bio/Features.src/M000029.html +19 -0
- data/doc/classes/Bio/Features.src/M000030.html +21 -0
- data/doc/classes/Bio/Features.src/M000031.html +18 -0
- data/doc/classes/Bio/Features.src/M000032.html +18 -0
- data/doc/classes/Bio/Features.src/M000033.html +18 -0
- data/doc/classes/Bio/Features.src/M000036.html +18 -0
- data/doc/classes/Bio/Features.src/M000037.html +19 -0
- data/doc/classes/Bio/Features.src/M000038.html +18 -0
- data/doc/classes/Bio/Features.src/M000039.html +19 -0
- data/doc/classes/Bio/Features.src/M000040.html +21 -0
- data/doc/classes/Bio/Features.src/M000041.html +18 -0
- data/doc/classes/Bio/Features.src/M000042.html +18 -0
- data/doc/classes/Bio/Features.src/M000043.html +18 -0
- data/doc/classes/Bio/Features.src/M000068.html +18 -0
- data/doc/classes/Bio/Features.src/M000069.html +19 -0
- data/doc/classes/Bio/Features.src/M000070.html +21 -0
- data/doc/classes/Bio/Features.src/M000071.html +18 -0
- data/doc/classes/Bio/Features.src/M000072.html +18 -0
- data/doc/classes/Bio/Features.src/M000073.html +18 -0
- data/doc/classes/Bio/Graphics.html +28 -42
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} +98 -125
- data/doc/classes/Bio/Graphics/Feature.src/M000020.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000021.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000022.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000023.html +66 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000024.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000025.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000026.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000054.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000055.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000056.html +55 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000025.html +68 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000026.html +67 -0
- data/doc/classes/Bio/Graphics/Glyph.html +178 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000004.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000032.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.html +187 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html +40 -0
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.html} +16 -19
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Transcript.html +113 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html +21 -0
- data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.html} +50 -16
- data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} +3 -3
- data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000033.html +18 -0
- data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} +7 -4
- data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000062.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000064.html +27 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html +24 -0
- data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} +14 -14
- data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} +3 -3
- data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} +6 -4
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html +22 -0
- data/doc/classes/Bio/Graphics/Panel.html +70 -69
- data/doc/classes/Bio/Graphics/Panel.src/M000025.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000026.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000027.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000028.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000029.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000030.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000031.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000059.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000060.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000061.html +98 -0
- data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} +50 -21
- data/doc/classes/Bio/Graphics/Ruler.src/M000015.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000016.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000017.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000018.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000019.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000020.html +45 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000047.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000048.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000049.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000050.html +45 -0
- data/doc/classes/Bio/Graphics/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000001.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000002.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000023.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000024.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000027.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000028.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000057.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000058.html +69 -0
- data/doc/classes/Bio/Graphics/{Panel/Track.html → Track.html} +67 -69
- data/doc/classes/Bio/Graphics/Track.src/M000017.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000018.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000019.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000020.html +41 -0
- data/doc/classes/Bio/Graphics/Track.src/M000021.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000022.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000023.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000051.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000052.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000053.html +45 -0
- data/doc/classes/Range.html +129 -0
- data/doc/classes/String.html +167 -0
- data/doc/classes/String.src/M000001.html +18 -0
- data/doc/classes/String.src/M000002.html +18 -0
- data/doc/classes/String.src/M000003.html +23 -0
- data/doc/classes/String.src/M000029.html +18 -0
- data/doc/classes/String.src/M000030.html +18 -0
- data/doc/classes/String.src/M000031.html +23 -0
- data/doc/classes/TestCustomGlyph.html +137 -0
- data/doc/classes/TestCustomGlyph.src/M000025.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.html +167 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000026.html +19 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000027.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000028.html +18 -0
- data/doc/classes/TestExtensions.html +152 -0
- data/doc/classes/TestExtensions.src/M000015.html +22 -0
- data/doc/classes/TestExtensions.src/M000016.html +25 -0
- data/doc/classes/TestFeature.html +152 -0
- data/doc/classes/TestFeature.src/M000017.html +19 -0
- data/doc/classes/TestFeature.src/M000018.html +21 -0
- data/doc/classes/TestImageMap.html +182 -0
- data/doc/classes/TestImageMap.src/M000019.html +22 -0
- data/doc/classes/TestImageMap.src/M000020.html +56 -0
- data/doc/classes/TestImageMap.src/M000021.html +56 -0
- data/doc/classes/TestImageMap.src/M000022.html +20 -0
- data/doc/classes/TestPanel.html +276 -0
- data/doc/classes/TestPanel.src/M000001.html +18 -0
- data/doc/classes/TestPanel.src/M000002.html +61 -0
- data/doc/classes/TestPanel.src/M000003.html +35 -0
- data/doc/classes/TestPanel.src/M000004.html +54 -0
- data/doc/classes/TestPanel.src/M000005.html +54 -0
- data/doc/classes/TestPanel.src/M000006.html +41 -0
- data/doc/classes/TestPanel.src/M000007.html +36 -0
- data/doc/classes/TestPanel.src/M000008.html +20 -0
- data/doc/classes/TestPanel.src/M000009.html +26 -0
- data/doc/classes/TestPanel.src/M000010.html +21 -0
- data/doc/classes/TestRuler.html +152 -0
- data/doc/classes/TestRuler.src/M000013.html +22 -0
- data/doc/classes/TestRuler.src/M000014.html +31 -0
- data/doc/classes/TestSubFeature.html +152 -0
- data/doc/classes/TestSubFeature.src/M000023.html +21 -0
- data/doc/classes/TestSubFeature.src/M000024.html +18 -0
- data/doc/classes/TestTrack.html +152 -0
- data/doc/classes/TestTrack.src/M000011.html +19 -0
- data/doc/classes/TestTrack.src/M000012.html +23 -0
- data/doc/created.rid +1 -1
- data/doc/files/README_DEV.html +399 -70
- data/doc/files/TUTORIAL.html +188 -67
- data/doc/files/lib/bio-graphics_rb.html +3 -2
- data/doc/files/lib/bio/graphics/feature_rb.html +12 -6
- data/doc/files/lib/bio/graphics/glyphs/box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/common_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/dot_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_with_handles_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/transcript_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/triangle_rb.html +113 -0
- data/doc/files/lib/bio/graphics/image_map_rb.html +3 -2
- data/doc/files/lib/bio/graphics/panel_rb.html +10 -2
- data/doc/files/lib/bio/graphics/ruler_rb.html +3 -2
- data/doc/files/lib/bio/graphics/subfeature_rb.html +114 -0
- data/doc/files/lib/bio/graphics/track_rb.html +3 -2
- data/doc/files/lib/feature_rb.html +101 -0
- data/doc/files/samples/arkdb_features_rb.html +101 -0
- data/doc/files/samples/glyph_showcase_rb.html +108 -0
- data/doc/files/samples/protein_domains_rb.html +115 -0
- data/doc/files/samples/subfeatures_rb.html +108 -0
- data/doc/files/scripts/gff2png_rb.html +154 -0
- data/doc/files/test/unit/custom_glyph_in_file_rb.html +101 -0
- data/doc/files/test/unit/test_class_extensions_rb.html +108 -0
- data/doc/files/test/unit/test_creation_rb.html +108 -0
- data/doc/files/test/unit/test_custom_glyph_rb.html +108 -0
- data/doc/files/test/unit/test_draw_rb.html +108 -0
- data/doc/files/test/unit/test_imagemap_rb.html +108 -0
- data/doc/files/test/unit/test_subfeatures_rb.html +108 -0
- data/doc/fr_class_index.html +24 -6
- data/doc/fr_file_index.html +14 -0
- data/doc/fr_method_index.html +51 -19
- data/doc/images/glyph_showcase.png +0 -0
- data/doc/images/terms.svg +146 -132
- data/images/glyph_showcase.png +0 -0
- data/lib/bio-graphics.rb +38 -6
- data/lib/bio/graphics/feature.rb +212 -440
- data/lib/bio/graphics/glyphs/box.rb +21 -0
- data/lib/bio/graphics/glyphs/common.rb +149 -0
- data/lib/bio/graphics/glyphs/directed_box.rb +28 -0
- data/lib/bio/graphics/glyphs/directed_generic.rb +23 -0
- data/lib/bio/graphics/glyphs/directed_spliced.rb +39 -0
- data/lib/bio/graphics/glyphs/dot.rb +21 -0
- data/lib/bio/graphics/glyphs/generic.rb +15 -0
- data/lib/bio/graphics/glyphs/line.rb +17 -0
- data/lib/bio/graphics/glyphs/line_with_handles.rb +25 -0
- data/lib/bio/graphics/glyphs/spliced.rb +16 -0
- data/lib/bio/graphics/glyphs/transcript.rb +12 -0
- data/lib/bio/graphics/glyphs/triangle.rb +18 -0
- data/lib/bio/graphics/image_map.rb +25 -4
- data/lib/bio/graphics/panel.rb +266 -209
- data/lib/bio/graphics/ruler.rb +95 -96
- data/lib/bio/graphics/subfeature.rb +187 -0
- data/lib/bio/graphics/track.rb +155 -156
- data/lib/feature.rb +204 -0
- data/samples/arkdb_features.rb +10 -8
- data/samples/glyph_showcase.rb +58 -22
- data/samples/protein_domains.rb +19 -0
- data/samples/subfeatures.rb +31 -0
- data/test/unit/custom_glyph_in_file.rb +12 -0
- data/test/unit/data.txt +32 -0
- data/test/unit/test_class_extensions.rb +23 -0
- data/test/unit/test_creation.rb +43 -13
- data/test/unit/test_custom_glyph.rb +50 -0
- data/test/unit/test_draw.rb +211 -0
- data/test/unit/test_imagemap.rb +134 -0
- data/test/unit/test_subfeatures.rb +17 -0
- metadata +396 -119
- data/doc/classes/Bio/Graphics/Panel.src/M000005.html +0 -29
- data/doc/classes/Bio/Graphics/Panel.src/M000006.html +0 -19
- data/doc/classes/Bio/Graphics/Panel.src/M000007.html +0 -68
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +0 -54
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +0 -26
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +0 -42
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +0 -52
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +0 -23
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +0 -43
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +0 -259
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +0 -65
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +0 -39
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000013.html +0 -27
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 113</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
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<span class="ruby-identifier">feature_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_destination</span>)
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<span class="ruby-comment cmt"># Move the feature drawing down based on track it's in and the number</span>
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<span class="ruby-comment cmt"># of times is has to be bumped</span>
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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-ivar">@vertical_offset</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">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_V_DISTANCE</span>
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<span class="ruby-ivar">@vertical_offset</span> <span class="ruby-operator">+=</span> (<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">+</span><span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_V_DISTANCE</span>)<span class="ruby-operator">*</span><span class="ruby-identifier">row</span>
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<span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-value">0</span>, <span class="ruby-ivar">@vertical_offset</span>)
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<span class="ruby-comment cmt"># Let the subfeatures do the drawing.</span>
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<span class="ruby-ivar">@subfeatures</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">subfeature</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">subfeature</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">feature_context</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@left_pixel_of_feature</span> = <span class="ruby-ivar">@left_pixel_of_subfeatures</span>.<span class="ruby-identifier">min</span>
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<span class="ruby-ivar">@right_pixel_of_feature</span> = <span class="ruby-ivar">@right_pixel_of_subfeatures</span>.<span class="ruby-identifier">max</span>
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<span class="ruby-comment cmt"># Add the label for the feature</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@track</span>.<span class="ruby-identifier">show_label</span>
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<span class="ruby-identifier">pango_layout</span> = <span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">create_pango_layout</span>
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<span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">text</span> = <span class="ruby-ivar">@label</span>
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<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>)
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<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>)
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<span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">font_description</span> = <span class="ruby-identifier">fdesc</span>
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<span class="ruby-identifier">text_range</span> = <span class="ruby-ivar">@start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span>(<span class="ruby-ivar">@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-ivar">@track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>)
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@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>
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<span class="ruby-ivar">@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>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@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>)
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<span class="ruby-ivar">@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>)
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<span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-ivar">@left_pixel_of_feature</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
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<span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
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<span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">show_pango_layout</span>(<span class="ruby-identifier">pango_layout</span>)
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<span class="ruby-identifier">feature_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-ivar">@colour</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># And add the region to the image map</span>
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<span class="ruby-comment cmt"># Comment: we have to add the vertical_offset and TRACK_HEADER_HEIGHT!</span>
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<span class="ruby-ivar">@track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">image_map</span>.<span class="ruby-identifier">add_element</span>(<span class="ruby-ivar">@left_pixel_of_feature</span>,
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<span class="ruby-ivar">@vertical_offset</span>,
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<span class="ruby-ivar">@right_pixel_of_feature</span>,
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<span class="ruby-ivar">@vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">FEATURE_HEIGHT</span>,
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<span class="ruby-ivar">@link</span>
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)
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<span class="ruby-keyword kw">end</span></pre>
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<title>find_row (Bio::Graphics::Feature)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 171</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">find_row</span>
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<span class="ruby-identifier">row_found</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-comment cmt"># We've got to find out what row to draw the feature on. If two </span>
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<span class="ruby-comment cmt"># features overlap, one of them has to be 'bumped' down. So we'll</span>
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<span class="ruby-comment cmt"># first try to draw a new feature at the top of the track. If</span>
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<span class="ruby-comment cmt"># it however would overlap with another one, we'll bump it down</span>
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<span class="ruby-comment cmt"># to the next row.</span>
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<span class="ruby-identifier">feature_range</span> = (<span class="ruby-ivar">@start</span>.<span class="ruby-identifier">floor</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span><span class="ruby-operator">..</span><span class="ruby-ivar">@stop</span>.<span class="ruby-identifier">ceil</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</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-ivar">@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-ivar">@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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<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</span>
|
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-ivar">@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> <span class="ruby-comment cmt">#Still have to check if there is no label there.</span>
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<span class="ruby-ivar">@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">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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<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</span>
|
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
|
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<span class="ruby-keyword kw">end</span>
|
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|
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<span class="ruby-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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<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
|
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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.</span>
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@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-ivar">@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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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@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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<span class="ruby-identifier">row_found</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-keyword kw">end</span>
|
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<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">row</span>
|
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<span class="ruby-keyword kw">end</span></pre>
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<head>
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<title>Class: Bio::Graphics::Feature::SubFeature</title>
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// <![CDATA[
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// Make codeblocks hidden by default
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document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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// ]]>
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</script>
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<div id="classHeader">
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<table class="header-table">
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<tr class="top-aligned-row">
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<td><strong>Class</strong></td>
|
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<td class="class-name-in-header">Bio::Graphics::Feature::SubFeature</td>
|
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</tr>
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<tr class="top-aligned-row">
|
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<td><strong>In:</strong></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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</a>
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<td>-></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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The colour to use to <a href="SubFeature.html#M000026">draw</a> this
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(sub)feature
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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-value"> [RW] </td>
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The glyph to use to <a href="SubFeature.html#M000026">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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<td class="context-item-desc">
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Are there subfeatures out of view at the left side of the picture?
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<td class="context-item-value"> [RW] </td>
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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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<td class="context-item-name">locations</td>
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<td class="context-item-value"> [RW] </td>
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The locations of the feature (which is a Bio::Locations object)
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<td class="context-item-name">pixel_range_collection</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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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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<td class="context-item-name">stop</td>
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The stop position of the feature (in bp)
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</td>
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<td class="context-item-name">strand</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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|
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The strand of the feature
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|
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</td>
|
|
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|
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</table>
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<!-- if method_list -->
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<div id="methods">
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<h3 class="section-bar">Public Class methods</h3>
|
|
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|
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<div id="method-M000025" class="method-detail">
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<a name="M000025"></a>
|
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|
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<div class="method-heading">
|
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<a href="SubFeature.src/M000025.html" target="Code" class="method-signature"
|
|
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|
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onclick="popupCode('SubFeature.src/M000025.html');return false;">
|
|
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|
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<span class="method-name">new</span><span class="method-args">(feature, feature_object, glyph = feature.glyph, colour = feature.colour)</span>
|
|
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</a>
|
|
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|
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</div>
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|
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|
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<div class="method-description">
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<p>
|
|
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|
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!!Not to be used directly.
|
|
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|
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</p>
|
|
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|
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<hr size="1"></hr><p>
|
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|
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<b>Arguments</b>:
|
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|
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</p>
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<ul>
|
|
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|
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<li><em>feature</em> (required) :: <a
|
|
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|
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href="../Feature.html">Bio::Graphics::Feature</a> object that this
|
|
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|
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subfeature belongs to
|
|
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|
|
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</li>
|
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<li><em>feature</em> <em>object</em> (required) :: A <a
|
|
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|
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href="../../Feature.html">Bio::Feature</a> object (see bioruby)
|
|
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|
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|
|
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</li>
|
|
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|
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<li><em>glyph</em> :: <a href="../Glyph.html">Glyph</a> to use. Default = glyph
|
|
287
|
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of the track
|
|
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|
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|
|
289
|
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</li>
|
|
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|
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<li><em>colour</em> :: Colour. Default = colour of the track
|
|
291
|
+
|
|
292
|
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</li>
|
|
293
|
+
</ul>
|
|
294
|
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<table>
|
|
295
|
+
<tr><td valign="top"><b>Returns</b>:</td><td><a href="SubFeature.html">Bio::Graphics::Feature::SubFeature</a> object
|
|
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|
+
|
|
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|
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</td></tr>
|
|
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|
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</table>
|
|
299
|
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</div>
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|
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|
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</div>
|
|
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|
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|
|
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|
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<h3 class="section-bar">Public Instance methods</h3>
|
|
303
|
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|
|
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|
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<div id="method-M000026" class="method-detail">
|
|
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|
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<a name="M000026"></a>
|
|
306
|
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|
|
307
|
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<div class="method-heading">
|
|
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|
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<a href="SubFeature.src/M000026.html" target="Code" class="method-signature"
|
|
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|
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onclick="popupCode('SubFeature.src/M000026.html');return false;">
|
|
310
|
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<span class="method-name">draw</span><span class="method-args">(feature_context)</span>
|
|
311
|
+
</a>
|
|
312
|
+
</div>
|
|
313
|
+
|
|
314
|
+
<div class="method-description">
|
|
315
|
+
<p>
|
|
316
|
+
Adds the subfeature to the track cairo context. This method should not be
|
|
317
|
+
used directly by the user, but is called by <a
|
|
318
|
+
href="SubFeature.html#M000026">Bio::Graphics::Feature::SubFeature.draw</a>
|
|
319
|
+
</p>
|
|
320
|
+
<hr size="1"></hr><p>
|
|
321
|
+
<b>Arguments</b>:
|
|
322
|
+
</p>
|
|
323
|
+
<ul>
|
|
324
|
+
<li><em>track_drawing</em> (required) :: the track cairo object
|
|
325
|
+
|
|
326
|
+
</li>
|
|
327
|
+
</ul>
|
|
328
|
+
<table>
|
|
329
|
+
<tr><td valign="top"><b>Returns</b>:</td><td>FIXME: I don‘t know
|
|
330
|
+
|
|
331
|
+
</td></tr>
|
|
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|
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</table>
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|
333
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</div>
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|
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</div>
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|
335
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|
|
336
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|
|
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</div>
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|
338
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|
|
339
|
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|
|
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|
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</div>
|
|
341
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|
|
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|
|
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|
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<div id="validator-badges">
|
|
344
|
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<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
345
|
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|
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</body>
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</html>
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