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/ruler.rb, line 27</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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<span class="ruby-ivar">@minor_tick_distance</span> = <span class="ruby-ivar">@min_pixels_per_tick</span> <span class="ruby-operator">**</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">scaling_factor</span>
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<span class="ruby-ivar">@major_tick_distance</span> = <span class="ruby-ivar">@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 46</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">scaling_factor</span>(<span class="ruby-identifier">min_pixels_per_tick</span> = <span class="ruby-ivar">@min_pixels_per_tick</span>,
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<span class="ruby-identifier">rescale_factor</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">rescale_factor</span>)
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(<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">rescale_factor</span>) <span class="ruby-operator">/</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 27</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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<span class="ruby-ivar">@major_tick_distance</span> = <span class="ruby-ivar">@minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">scaling_factor</span>(<span class="ruby-identifier">min_pixels_per_tick</span> = <span class="ruby-ivar">@min_pixels_per_tick</span>,
|
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(<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">rescale_factor</span>) <span class="ruby-operator">/</span>
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<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span>)).<span class="ruby-identifier">ceil</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 52</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">first_tick_position</span>(<span class="ruby-identifier">start</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">display_start</span>,
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<span class="ruby-identifier">minor_tick</span> = <span class="ruby-ivar">@minor_tick_distance</span>)
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<span class="ruby-comment cmt"># * Find position of first tick.</span>
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<span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first</span>
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<span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the</span>
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<span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:</span>
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<span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.</span>
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<span class="ruby-comment cmt"># So we want to find the position of the first tick.</span>
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<span class="ruby-identifier">modulo_from_tick</span> = (<span class="ruby-identifier">start</span> <span class="ruby-operator">%</span> <span class="ruby-identifier">minor_tick</span>)
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<span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">modulo_from_tick</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span> <span class="ruby-operator">?</span> (<span class="ruby-identifier">minor_tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">modulo_from_tick</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>) <span class="ruby-operator">:</span> <span class="ruby-value">0</span>)
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 64</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>)
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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</span>
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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-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-comment cmt"># Draw ticks</span>
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<span class="ruby-comment cmt"># * And start drawing the rest.</span>
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<span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-ivar">@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-ivar">@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-ivar">@min_pixels_per_tick</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-ivar">@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">3</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span>)
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<span class="ruby-comment cmt"># Draw tick number</span>
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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">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</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-ivar">@tick_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">4</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@tick_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-keyword kw">else</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-ivar">@tick_height</span>)
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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">end</span>
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<span class="ruby-ivar">@height</span> = <span class="ruby-value">5</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@tick_text_height</span>
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 27</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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<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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<span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">colour</span>
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<span class="ruby-comment cmt"># Number of pixels between each tick, used to calculate tick spacing</span>
|
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<span class="ruby-ivar">@min_pixels_per_tick</span> = <span class="ruby-value">5</span>
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<span class="ruby-comment cmt"># The base height of minor ticks in pixels</span>
|
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<span class="ruby-ivar">@tick_height</span> = <span class="ruby-value">5</span>
|
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<span class="ruby-comment cmt"># The height of the text in pixels</span>
|
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<span class="ruby-ivar">@tick_text_height</span> = <span class="ruby-value">10</span>
|
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<span class="ruby-ivar">@minor_tick_distance</span> = <span class="ruby-ivar">@min_pixels_per_tick</span> <span class="ruby-operator">**</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">scaling_factor</span>
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<span class="ruby-ivar">@major_tick_distance</span> = <span class="ruby-ivar">@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 46</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">scaling_factor</span>(<span class="ruby-identifier">min_pixels_per_tick</span> = <span class="ruby-ivar">@min_pixels_per_tick</span>,
|
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<span class="ruby-identifier">rescale_factor</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">rescale_factor</span>)
|
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|
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(<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">rescale_factor</span>) <span class="ruby-operator">/</span>
|
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<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">min_pixels_per_tick</span>)).<span class="ruby-identifier">ceil</span>
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 52</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">first_tick_position</span>(<span class="ruby-identifier">start</span> = <span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">display_start</span>,
|
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<span class="ruby-identifier">minor_tick</span> = <span class="ruby-ivar">@minor_tick_distance</span>)
|
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<span class="ruby-comment cmt"># * Find position of first tick.</span>
|
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<span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first</span>
|
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<span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the</span>
|
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|
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<span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:</span>
|
|
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|
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<span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.</span>
|
|
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|
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<span class="ruby-comment cmt"># So we want to find the position of the first tick.</span>
|
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<span class="ruby-identifier">modulo_from_tick</span> = (<span class="ruby-identifier">start</span> <span class="ruby-operator">%</span> <span class="ruby-identifier">minor_tick</span>)
|
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<span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">modulo_from_tick</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span> <span class="ruby-operator">?</span> (<span class="ruby-identifier">minor_tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">modulo_from_tick</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>) <span class="ruby-operator">:</span> <span class="ruby-value">0</span>)
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 64</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>)
|
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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</span>
|
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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-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
|
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<span class="ruby-comment cmt"># Draw ticks</span>
|
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<span class="ruby-comment cmt"># * And start drawing the rest.</span>
|
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<span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-ivar">@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-ivar">@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-ivar">@min_pixels_per_tick</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-ivar">@major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
|
|
28
|
+
<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">3</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span>)
|
|
29
|
+
|
|
30
|
+
<span class="ruby-comment cmt"># Draw tick number</span>
|
|
31
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">select_font_face</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">FONT</span>)
|
|
32
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-ivar">@tick_text_height</span>)
|
|
33
|
+
<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">4</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@tick_text_height</span>)
|
|
34
|
+
<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>)
|
|
35
|
+
<span class="ruby-keyword kw">else</span>
|
|
36
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-ivar">@tick_height</span>)
|
|
37
|
+
|
|
38
|
+
<span class="ruby-keyword kw">end</span>
|
|
39
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
40
|
+
<span class="ruby-keyword kw">end</span>
|
|
41
|
+
|
|
42
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-value">5</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tick_height</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@tick_text_height</span>
|
|
43
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
44
|
+
</body>
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45
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+
</html>
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