bio-graphics 1.2 → 1.4
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +0 -225
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000015.html +0 -48
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +0 -18
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000013.html +0 -18
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +0 -18
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000016.html +0 -18
|
@@ -0,0 +1,154 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
+
<head>
|
|
8
|
+
<title>File: gff2png.rb</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
+
<link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
+
<script type="text/javascript">
|
|
13
|
+
// <![CDATA[
|
|
14
|
+
|
|
15
|
+
function popupCode( url ) {
|
|
16
|
+
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
+
}
|
|
18
|
+
|
|
19
|
+
function toggleCode( id ) {
|
|
20
|
+
if ( document.getElementById )
|
|
21
|
+
elem = document.getElementById( id );
|
|
22
|
+
else if ( document.all )
|
|
23
|
+
elem = eval( "document.all." + id );
|
|
24
|
+
else
|
|
25
|
+
return false;
|
|
26
|
+
|
|
27
|
+
elemStyle = elem.style;
|
|
28
|
+
|
|
29
|
+
if ( elemStyle.display != "block" ) {
|
|
30
|
+
elemStyle.display = "block"
|
|
31
|
+
} else {
|
|
32
|
+
elemStyle.display = "none"
|
|
33
|
+
}
|
|
34
|
+
|
|
35
|
+
return true;
|
|
36
|
+
}
|
|
37
|
+
|
|
38
|
+
// Make codeblocks hidden by default
|
|
39
|
+
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
+
|
|
41
|
+
// ]]>
|
|
42
|
+
</script>
|
|
43
|
+
|
|
44
|
+
</head>
|
|
45
|
+
<body>
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
|
|
49
|
+
<div id="fileHeader">
|
|
50
|
+
<h1>gff2png.rb</h1>
|
|
51
|
+
<table class="header-table">
|
|
52
|
+
<tr class="top-aligned-row">
|
|
53
|
+
<td><strong>Path:</strong></td>
|
|
54
|
+
<td>scripts/gff2png.rb
|
|
55
|
+
</td>
|
|
56
|
+
</tr>
|
|
57
|
+
<tr class="top-aligned-row">
|
|
58
|
+
<td><strong>Last Update:</strong></td>
|
|
59
|
+
<td>Fri Dec 14 09:29:08 +0000 2007</td>
|
|
60
|
+
</tr>
|
|
61
|
+
</table>
|
|
62
|
+
</div>
|
|
63
|
+
<!-- banner header -->
|
|
64
|
+
|
|
65
|
+
<div id="bodyContent">
|
|
66
|
+
|
|
67
|
+
|
|
68
|
+
|
|
69
|
+
<div id="contextContent">
|
|
70
|
+
|
|
71
|
+
<div id="description">
|
|
72
|
+
<h2>NAME</h2>
|
|
73
|
+
<p>
|
|
74
|
+
gff2png.rb
|
|
75
|
+
</p>
|
|
76
|
+
<h2>USAGE</h2>
|
|
77
|
+
<pre>
|
|
78
|
+
./gff2png.rb [ -h | --help ]
|
|
79
|
+
-l | --length length_of_sequence
|
|
80
|
+
[ -i | --infile | < ] your_gff_file.txt
|
|
81
|
+
-o | --outfile your_output.png
|
|
82
|
+
</pre>
|
|
83
|
+
<h2>DESCRIPTION</h2>
|
|
84
|
+
<p>
|
|
85
|
+
This script parses a GFF file and creates a picture using <a
|
|
86
|
+
href="../../classes/Bio/Graphics.html">Bio::Graphics</a>. The flavour of
|
|
87
|
+
GFF required is GFF3 (see <a
|
|
88
|
+
href="http://www.sequenceontology.org/gff3.shtml">www.sequenceontology.org/gff3.shtml</a>).
|
|
89
|
+
</p>
|
|
90
|
+
<h2>OPTIONS</h2>
|
|
91
|
+
<pre>
|
|
92
|
+
-h,--help:: Show help
|
|
93
|
+
-l,--length=LENGTH:: Length of sequence. Required.
|
|
94
|
+
-i,--infile=INFILE:: Name of input file. STDIN if not defined.
|
|
95
|
+
-o,--outfile=OUTFILE:: Name of output file. Required.
|
|
96
|
+
</pre>
|
|
97
|
+
<h2>FORMAT INPUT</h2>
|
|
98
|
+
<p>
|
|
99
|
+
GFF3. See <a
|
|
100
|
+
href="http://www.sequenceontology.org/gff3.shtml">www.sequenceontology.org/gff3.shtml</a>
|
|
101
|
+
</p>
|
|
102
|
+
<h2>FORMAT OUTPUT</h2>
|
|
103
|
+
<p>
|
|
104
|
+
A PNG picture.
|
|
105
|
+
</p>
|
|
106
|
+
<h2>AUTHOR</h2>
|
|
107
|
+
<pre>
|
|
108
|
+
Dr Jan Aerts
|
|
109
|
+
Bioinformatics Group
|
|
110
|
+
Roslin Institute
|
|
111
|
+
</pre>
|
|
112
|
+
|
|
113
|
+
</div>
|
|
114
|
+
|
|
115
|
+
<div id="requires-list">
|
|
116
|
+
<h3 class="section-bar">Required files</h3>
|
|
117
|
+
|
|
118
|
+
<div class="name-list">
|
|
119
|
+
../lib/bio-graphics
|
|
120
|
+
rdoc/usage
|
|
121
|
+
optparse
|
|
122
|
+
ostruct
|
|
123
|
+
</div>
|
|
124
|
+
</div>
|
|
125
|
+
|
|
126
|
+
</div>
|
|
127
|
+
|
|
128
|
+
|
|
129
|
+
</div>
|
|
130
|
+
|
|
131
|
+
|
|
132
|
+
<!-- if includes -->
|
|
133
|
+
|
|
134
|
+
<div id="section">
|
|
135
|
+
|
|
136
|
+
|
|
137
|
+
|
|
138
|
+
|
|
139
|
+
|
|
140
|
+
|
|
141
|
+
|
|
142
|
+
|
|
143
|
+
<!-- if method_list -->
|
|
144
|
+
|
|
145
|
+
|
|
146
|
+
</div>
|
|
147
|
+
|
|
148
|
+
|
|
149
|
+
<div id="validator-badges">
|
|
150
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
151
|
+
</div>
|
|
152
|
+
|
|
153
|
+
</body>
|
|
154
|
+
</html>
|
|
@@ -0,0 +1,101 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
+
<head>
|
|
8
|
+
<title>File: custom_glyph_in_file.rb</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
+
<link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
+
<script type="text/javascript">
|
|
13
|
+
// <![CDATA[
|
|
14
|
+
|
|
15
|
+
function popupCode( url ) {
|
|
16
|
+
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
+
}
|
|
18
|
+
|
|
19
|
+
function toggleCode( id ) {
|
|
20
|
+
if ( document.getElementById )
|
|
21
|
+
elem = document.getElementById( id );
|
|
22
|
+
else if ( document.all )
|
|
23
|
+
elem = eval( "document.all." + id );
|
|
24
|
+
else
|
|
25
|
+
return false;
|
|
26
|
+
|
|
27
|
+
elemStyle = elem.style;
|
|
28
|
+
|
|
29
|
+
if ( elemStyle.display != "block" ) {
|
|
30
|
+
elemStyle.display = "block"
|
|
31
|
+
} else {
|
|
32
|
+
elemStyle.display = "none"
|
|
33
|
+
}
|
|
34
|
+
|
|
35
|
+
return true;
|
|
36
|
+
}
|
|
37
|
+
|
|
38
|
+
// Make codeblocks hidden by default
|
|
39
|
+
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
+
|
|
41
|
+
// ]]>
|
|
42
|
+
</script>
|
|
43
|
+
|
|
44
|
+
</head>
|
|
45
|
+
<body>
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
|
|
49
|
+
<div id="fileHeader">
|
|
50
|
+
<h1>custom_glyph_in_file.rb</h1>
|
|
51
|
+
<table class="header-table">
|
|
52
|
+
<tr class="top-aligned-row">
|
|
53
|
+
<td><strong>Path:</strong></td>
|
|
54
|
+
<td>test/unit/custom_glyph_in_file.rb
|
|
55
|
+
</td>
|
|
56
|
+
</tr>
|
|
57
|
+
<tr class="top-aligned-row">
|
|
58
|
+
<td><strong>Last Update:</strong></td>
|
|
59
|
+
<td>Fri Dec 14 09:29:08 +0000 2007</td>
|
|
60
|
+
</tr>
|
|
61
|
+
</table>
|
|
62
|
+
</div>
|
|
63
|
+
<!-- banner header -->
|
|
64
|
+
|
|
65
|
+
<div id="bodyContent">
|
|
66
|
+
|
|
67
|
+
|
|
68
|
+
|
|
69
|
+
<div id="contextContent">
|
|
70
|
+
|
|
71
|
+
|
|
72
|
+
|
|
73
|
+
</div>
|
|
74
|
+
|
|
75
|
+
|
|
76
|
+
</div>
|
|
77
|
+
|
|
78
|
+
|
|
79
|
+
<!-- if includes -->
|
|
80
|
+
|
|
81
|
+
<div id="section">
|
|
82
|
+
|
|
83
|
+
|
|
84
|
+
|
|
85
|
+
|
|
86
|
+
|
|
87
|
+
|
|
88
|
+
|
|
89
|
+
|
|
90
|
+
<!-- if method_list -->
|
|
91
|
+
|
|
92
|
+
|
|
93
|
+
</div>
|
|
94
|
+
|
|
95
|
+
|
|
96
|
+
<div id="validator-badges">
|
|
97
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
98
|
+
</div>
|
|
99
|
+
|
|
100
|
+
</body>
|
|
101
|
+
</html>
|
|
@@ -0,0 +1,108 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
+
<head>
|
|
8
|
+
<title>File: test_class_extensions.rb</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
+
<link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
+
<script type="text/javascript">
|
|
13
|
+
// <![CDATA[
|
|
14
|
+
|
|
15
|
+
function popupCode( url ) {
|
|
16
|
+
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
+
}
|
|
18
|
+
|
|
19
|
+
function toggleCode( id ) {
|
|
20
|
+
if ( document.getElementById )
|
|
21
|
+
elem = document.getElementById( id );
|
|
22
|
+
else if ( document.all )
|
|
23
|
+
elem = eval( "document.all." + id );
|
|
24
|
+
else
|
|
25
|
+
return false;
|
|
26
|
+
|
|
27
|
+
elemStyle = elem.style;
|
|
28
|
+
|
|
29
|
+
if ( elemStyle.display != "block" ) {
|
|
30
|
+
elemStyle.display = "block"
|
|
31
|
+
} else {
|
|
32
|
+
elemStyle.display = "none"
|
|
33
|
+
}
|
|
34
|
+
|
|
35
|
+
return true;
|
|
36
|
+
}
|
|
37
|
+
|
|
38
|
+
// Make codeblocks hidden by default
|
|
39
|
+
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
+
|
|
41
|
+
// ]]>
|
|
42
|
+
</script>
|
|
43
|
+
|
|
44
|
+
</head>
|
|
45
|
+
<body>
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
|
|
49
|
+
<div id="fileHeader">
|
|
50
|
+
<h1>test_class_extensions.rb</h1>
|
|
51
|
+
<table class="header-table">
|
|
52
|
+
<tr class="top-aligned-row">
|
|
53
|
+
<td><strong>Path:</strong></td>
|
|
54
|
+
<td>test/unit/test_class_extensions.rb
|
|
55
|
+
</td>
|
|
56
|
+
</tr>
|
|
57
|
+
<tr class="top-aligned-row">
|
|
58
|
+
<td><strong>Last Update:</strong></td>
|
|
59
|
+
<td>Fri Dec 14 09:29:08 +0000 2007</td>
|
|
60
|
+
</tr>
|
|
61
|
+
</table>
|
|
62
|
+
</div>
|
|
63
|
+
<!-- banner header -->
|
|
64
|
+
|
|
65
|
+
<div id="bodyContent">
|
|
66
|
+
|
|
67
|
+
|
|
68
|
+
|
|
69
|
+
<div id="contextContent">
|
|
70
|
+
|
|
71
|
+
|
|
72
|
+
<div id="requires-list">
|
|
73
|
+
<h3 class="section-bar">Required files</h3>
|
|
74
|
+
|
|
75
|
+
<div class="name-list">
|
|
76
|
+
test/unit
|
|
77
|
+
</div>
|
|
78
|
+
</div>
|
|
79
|
+
|
|
80
|
+
</div>
|
|
81
|
+
|
|
82
|
+
|
|
83
|
+
</div>
|
|
84
|
+
|
|
85
|
+
|
|
86
|
+
<!-- if includes -->
|
|
87
|
+
|
|
88
|
+
<div id="section">
|
|
89
|
+
|
|
90
|
+
|
|
91
|
+
|
|
92
|
+
|
|
93
|
+
|
|
94
|
+
|
|
95
|
+
|
|
96
|
+
|
|
97
|
+
<!-- if method_list -->
|
|
98
|
+
|
|
99
|
+
|
|
100
|
+
</div>
|
|
101
|
+
|
|
102
|
+
|
|
103
|
+
<div id="validator-badges">
|
|
104
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
105
|
+
</div>
|
|
106
|
+
|
|
107
|
+
</body>
|
|
108
|
+
</html>
|
|
@@ -0,0 +1,108 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
+
<head>
|
|
8
|
+
<title>File: test_creation.rb</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
+
<link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
+
<script type="text/javascript">
|
|
13
|
+
// <![CDATA[
|
|
14
|
+
|
|
15
|
+
function popupCode( url ) {
|
|
16
|
+
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
+
}
|
|
18
|
+
|
|
19
|
+
function toggleCode( id ) {
|
|
20
|
+
if ( document.getElementById )
|
|
21
|
+
elem = document.getElementById( id );
|
|
22
|
+
else if ( document.all )
|
|
23
|
+
elem = eval( "document.all." + id );
|
|
24
|
+
else
|
|
25
|
+
return false;
|
|
26
|
+
|
|
27
|
+
elemStyle = elem.style;
|
|
28
|
+
|
|
29
|
+
if ( elemStyle.display != "block" ) {
|
|
30
|
+
elemStyle.display = "block"
|
|
31
|
+
} else {
|
|
32
|
+
elemStyle.display = "none"
|
|
33
|
+
}
|
|
34
|
+
|
|
35
|
+
return true;
|
|
36
|
+
}
|
|
37
|
+
|
|
38
|
+
// Make codeblocks hidden by default
|
|
39
|
+
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
+
|
|
41
|
+
// ]]>
|
|
42
|
+
</script>
|
|
43
|
+
|
|
44
|
+
</head>
|
|
45
|
+
<body>
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
|
|
49
|
+
<div id="fileHeader">
|
|
50
|
+
<h1>test_creation.rb</h1>
|
|
51
|
+
<table class="header-table">
|
|
52
|
+
<tr class="top-aligned-row">
|
|
53
|
+
<td><strong>Path:</strong></td>
|
|
54
|
+
<td>test/unit/test_creation.rb
|
|
55
|
+
</td>
|
|
56
|
+
</tr>
|
|
57
|
+
<tr class="top-aligned-row">
|
|
58
|
+
<td><strong>Last Update:</strong></td>
|
|
59
|
+
<td>Thu Jan 24 17:02:37 +0000 2008</td>
|
|
60
|
+
</tr>
|
|
61
|
+
</table>
|
|
62
|
+
</div>
|
|
63
|
+
<!-- banner header -->
|
|
64
|
+
|
|
65
|
+
<div id="bodyContent">
|
|
66
|
+
|
|
67
|
+
|
|
68
|
+
|
|
69
|
+
<div id="contextContent">
|
|
70
|
+
|
|
71
|
+
|
|
72
|
+
<div id="requires-list">
|
|
73
|
+
<h3 class="section-bar">Required files</h3>
|
|
74
|
+
|
|
75
|
+
<div class="name-list">
|
|
76
|
+
test/unit
|
|
77
|
+
</div>
|
|
78
|
+
</div>
|
|
79
|
+
|
|
80
|
+
</div>
|
|
81
|
+
|
|
82
|
+
|
|
83
|
+
</div>
|
|
84
|
+
|
|
85
|
+
|
|
86
|
+
<!-- if includes -->
|
|
87
|
+
|
|
88
|
+
<div id="section">
|
|
89
|
+
|
|
90
|
+
|
|
91
|
+
|
|
92
|
+
|
|
93
|
+
|
|
94
|
+
|
|
95
|
+
|
|
96
|
+
|
|
97
|
+
<!-- if method_list -->
|
|
98
|
+
|
|
99
|
+
|
|
100
|
+
</div>
|
|
101
|
+
|
|
102
|
+
|
|
103
|
+
<div id="validator-badges">
|
|
104
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
105
|
+
</div>
|
|
106
|
+
|
|
107
|
+
</body>
|
|
108
|
+
</html>
|