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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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">length</span>, <span class="ruby-identifier">width</span> = <span class="ruby-constant">DEFAULT_PANEL_WIDTH</span>, <span class="ruby-identifier">clickable</span> = <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">display_start</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">display_stop</span> = <span class="ruby-keyword kw">nil</span>)
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<span class="ruby-ivar">@image_map</span> = ( <span class="ruby-identifier">clickable</span> ) <span class="ruby-operator">?</span> <span class="ruby-constant">ImageMap</span>.<span class="ruby-identifier">new</span> <span class="ruby-operator">:</span> <span class="ruby-keyword kw">nil</span>
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<span class="ruby-ivar">@display_start</span> = ( <span class="ruby-identifier">display_start</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">display_start</span> <span class="ruby-operator"><</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">0</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">display_start</span>
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<span class="ruby-ivar">@display_stop</span> = ( <span class="ruby-identifier">display_stop</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">display_stop</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@length</span> ) <span class="ruby-operator">?</span> <span class="ruby-ivar">@length</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">display_stop</span>
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<span class="ruby-ivar">@rescale_factor</span> = (<span class="ruby-ivar">@display_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@display_start</span>).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@width</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 139</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">label</span> = <span class="ruby-keyword kw">true</span>, <span class="ruby-identifier">feature_colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>], <span class="ruby-identifier">feature_glyph</span> = <span class="ruby-value str">'generic'</span>)
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<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Panel</span><span class="ruby-operator">::</span><span class="ruby-constant">Track</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">label</span>, <span class="ruby-identifier">feature_colour</span>, <span class="ruby-identifier">feature_glyph</span>))
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 151</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">file_name</span>)
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<span class="ruby-comment cmt"># Create a panel that is huge vertically
|
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|
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<span class="ruby-identifier">huge_panel_drawing</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-identifier">huge_height</span>)
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<span class="ruby-identifier">background</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">huge_panel_drawing</span>)
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<span class="ruby-identifier">background</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">1</span>,<span class="ruby-value">1</span>,<span class="ruby-value">1</span>)
|
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<span class="ruby-identifier">background</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>,<span class="ruby-identifier">huge_height</span>).<span class="ruby-identifier">fill</span>
|
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|
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<span class="ruby-comment cmt"># Add ruler
|
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<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-value">0</span>
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<span class="ruby-identifier">ruler</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">Panel</span><span class="ruby-operator">::</span><span class="ruby-constant">Ruler</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>)
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<span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_drawing</span>, <span class="ruby-identifier">vertical_offset</span>)
|
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<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">height</span>
|
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|
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|
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|
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<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
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|
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-identifier">vertical_offset</span>
|
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_drawing</span>)
|
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|
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<span class="ruby-ivar">@number_of_feature_rows</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span>
|
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|
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<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> ( <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span><span class="ruby-operator">*</span>(<span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_V_DISTANCE</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)) <span class="ruby-operator">+</span> <span class="ruby-value">10</span> <span class="ruby-comment cmt"># '10' is for the header
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<span class="ruby-keyword kw">end</span>
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|
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|
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<span class="ruby-identifier">height</span> <span class="ruby-operator">+=</span> <span class="ruby-value">20</span>
|
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|
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<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-comment cmt">#To correct for the track headers
|
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|
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|
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|
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<span class="ruby-identifier">resized_panel_drawing</span> = <span class="ruby-keyword kw">nil</span>
|
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<span class="ruby-identifier">resized_panel_drawing</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-identifier">height</span>)
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<span class="ruby-identifier">resizing_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">resized_panel_drawing</span>)
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<span class="ruby-identifier">resizing_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-identifier">huge_panel_drawing</span>, <span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
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<span class="ruby-identifier">resizing_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>, <span class="ruby-identifier">height</span>).<span class="ruby-identifier">fill</span>
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<span class="ruby-comment cmt"># And print to file
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@clickable</span> <span class="ruby-comment cmt"># create png and map
|
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<span class="ruby-identifier">html_filename</span> = <span class="ruby-identifier">file_name</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/\.[^.]+$/</span>, <span class="ruby-value str">'.html'</span>)
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<span class="ruby-identifier">html</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">html_filename</span>,<span class="ruby-value str">'w'</span>)
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|
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<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<img border='1' src='"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">file_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"' usemap='#image_map' />"</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 28</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</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-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
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<span class="ruby-ivar">@name</span> = <span class="ruby-value str">'ruler'</span>
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 35</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">calculate_tick_distance</span>
|
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<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-value">1</span> <span class="ruby-comment cmt"># in basepairs. Start with at least 10 bp distance
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<span class="ruby-keyword kw">while</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">min_tick_distance_requirement_met</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">/</span><span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span> <span class="ruby-operator">>=</span> <span class="ruby-constant">RULER_MIN_DISTANCE_TICKS_PIXEL</span>
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<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_drawing</span>, <span class="ruby-identifier">vertical_offset</span>)
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<span class="ruby-identifier">ruler_drawing</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_drawing</span>)
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<span class="ruby-comment cmt"># Draw line
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
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<span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</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-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">15</span>)
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<span class="ruby-comment cmt"># Draw tick number
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">select_font_face</span>(<span class="ruby-value str">'Georgia'</span>, <span class="ruby-value">1</span>, <span class="ruby-value">1</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">20</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">5</span>)
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<span class="ruby-ivar">@height</span> = <span class="ruby-value">25</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 28</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 28</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 35</span>
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|
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<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">false</span>
|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-value">1</span> <span class="ruby-comment cmt"># in basepairs.
|
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|
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|
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|
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<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">/</span><span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span> <span class="ruby-operator">>=</span> <span class="ruby-constant">RULER_MIN_DISTANCE_TICKS_PIXEL</span>
|
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<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">true</span>
|
|
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|
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|
|
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|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">*</span><span class="ruby-value">5</span>
|
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|
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|
|
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|
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|
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|
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|
|
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|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">major_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 49</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_drawing</span>, <span class="ruby-identifier">vertical_offset</span>)
|
|
15
|
-
<span class="ruby-identifier">ruler_drawing</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_drawing</span>)
|
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|
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|
|
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<span class="ruby-comment cmt"># Draw line
|
|
20
|
-
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-value">10</span>)
|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
|
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|
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|
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|
|
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|
-
<span class="ruby-comment cmt"># * Find position of first tick.
|
|
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|
-
<span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first
|
|
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<span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the
|
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<span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:
|
|
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|
-
<span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.
|
|
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|
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<span class="ruby-comment cmt"># So we want to find the position of the first tick.
|
|
31
|
-
<span class="ruby-identifier">first_tick_position</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
|
|
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|
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<span class="ruby-keyword kw">while</span> <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>
|
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<span class="ruby-identifier">first_tick_position</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
|
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|
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|
|
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|
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|
|
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|
-
<span class="ruby-comment cmt"># * And start drawing the rest.
|
|
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|
-
<span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">tick</span><span class="ruby-operator">|</span>
|
|
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|
-
<span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
|
|
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|
-
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">5</span>)
|
|
40
|
-
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
|
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41
|
-
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">15</span>)
|
|
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|
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|
|
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|
-
<span class="ruby-comment cmt"># Draw tick number
|
|
44
|
-
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">select_font_face</span>(<span class="ruby-value str">'Georgia'</span>, <span class="ruby-value">1</span>, <span class="ruby-value">1</span>)
|
|
45
|
-
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
|
|
46
|
-
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">20</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
|
|
47
|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
|
|
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|
-
<span class="ruby-keyword kw">else</span>
|
|
49
|
-
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">5</span>)
|
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|
-
|
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|
-
<span class="ruby-keyword kw">end</span>
|
|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 35</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">calculate_tick_distance</span>
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<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-value">1</span> <span class="ruby-comment cmt"># in basepairs.
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<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">/</span><span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span> <span class="ruby-operator">>=</span> <span class="ruby-constant">RULER_MIN_DISTANCE_TICKS_PIXEL</span>
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<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">*</span><span class="ruby-value">5</span>
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">major_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 49</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_drawing</span>, <span class="ruby-identifier">vertical_offset</span>)
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<span class="ruby-identifier">ruler_drawing</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_drawing</span>)
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<span class="ruby-comment cmt"># Draw line
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-value">10</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
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<span class="ruby-comment cmt"># Draw ticks
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<span class="ruby-comment cmt"># * Find position of first tick.
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<span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first
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<span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the
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<span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:
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<span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.
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<span class="ruby-identifier">first_tick_position</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
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<span class="ruby-keyword kw">while</span> <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>
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<span class="ruby-identifier">first_tick_position</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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<span class="ruby-comment cmt"># * And start drawing the rest.
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<span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">tick</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">5</span>)
|
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">15</span>)
|
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|
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|
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<span class="ruby-comment cmt"># Draw tick number
|
|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">select_font_face</span>(<span class="ruby-operator">*</span>(<span class="ruby-constant">FONT</span>))
|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">20</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
|
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|
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<span class="ruby-keyword kw">else</span>
|
|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">5</span>)
|
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|
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|
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|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
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|
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|
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|
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|
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|
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|
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|
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<span class="ruby-ivar">@height</span> = <span class="ruby-value">25</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>
|
|
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|
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