RubyGems - bio-graphics - Versions diffs - 1.2 → 1.4 - Mend

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.

Files changed (331) hide show

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

data/doc/classes/Bio/Graphics/Track.src/M000017.html ADDED

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+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>new (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 37</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
+    <span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
+    <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
+    <span class="ruby-identifier">opts</span> = {
+      <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>,
+      <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:generic</span>,
+      <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
+    }.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
+    <span class="ruby-ivar">@show_label</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:label</span>]
+    <span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:glyph</span>]
+    <span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:colour</span>]
+    <span class="ruby-comment cmt"># As far as I know, I can't do this in the glyph file for transcript, so we</span>
+    <span class="ruby-comment cmt"># have to do it here instead.</span>
+    <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:transcript</span>
+      <span class="ruby-ivar">@glyph</span> = { <span class="ruby-value str">'utr5'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:box</span>, <span class="ruby-value str">'utr3'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:directed_box</span>, <span class="ruby-value str">'cds'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:spliced</span> }
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
+    <span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
+    <span class="ruby-ivar">@vertical_offset</span> = <span class="ruby-value">0</span>
+    <span class="ruby-ivar">@grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000018.html ADDED

@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>add_feature (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 93</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span> = {})
+    <span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start</span>
+    <span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.</span>
+    <span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want</span>
+    <span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or</span>
+    <span class="ruby-comment cmt"># not (see below).</span>
+    <span class="ruby-identifier">start</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
+    <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
+    <span class="ruby-comment cmt"># If the feature wouldn't show because it's not in the region we're</span>
+    <span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge</span>
+    <span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with</span>
+    <span class="ruby-comment cmt"># thousands of features.</span>
+    <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+      <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
+    <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start &gt;= panel.display_start and stop &lt;= panel.display_stop</span>
+      <span class="ruby-ivar">@features</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">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span>))
+      <span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000019.html ADDED

@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>draw (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 123</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
+    <span class="ruby-identifier">track_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_destination</span>)
+    <span class="ruby-comment cmt"># Draw thin line above title</span>
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">stroke</span>
+    <span class="ruby-comment cmt"># Draw track title</span>
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
+    <span class="ruby-identifier">track_context</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>))
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
+    <span class="ruby-comment cmt"># Draw the features</span>
+    <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
+      <span class="ruby-comment cmt"># Don't even bother if the feature is not in the view</span>
+      <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+        <span class="ruby-keyword kw">next</span>
+      <span class="ruby-keyword kw">else</span>
+        <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
+      <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-ivar">@number_of_feature_rows</span> = ( <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
+    <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">panel_destination</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000020.html ADDED

@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>add_feature (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 87</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">label</span> = <span class="ruby-value str">'anonymous'</span>, <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">glyph</span> = <span class="ruby-ivar">@glyph</span>, <span class="ruby-identifier">colour</span> = <span class="ruby-ivar">@colour</span>)
+    <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">link</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
+      <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start</span>
+    <span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.</span>
+    <span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want</span>
+    <span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or</span>
+    <span class="ruby-comment cmt"># not (see below).</span>
+    <span class="ruby-identifier">start</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
+    <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
+    <span class="ruby-comment cmt"># If the feature wouldn't show because it's not in the region we're</span>
+    <span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge</span>
+    <span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with</span>
+    <span class="ruby-comment cmt"># thousands of features.</span>
+    <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+      <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
+    <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start &gt;= panel.display_start and stop &lt;= panel.display_stop</span>
+      <span class="ruby-ivar">@features</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">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">label</span>, <span class="ruby-identifier">link</span>, <span class="ruby-identifier">glyph</span>, <span class="ruby-identifier">colour</span>))
+      <span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000021.html ADDED

@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>new (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 37</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
+    <span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
+    <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
+    <span class="ruby-identifier">opts</span> = {
+      <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>,
+      <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:generic</span>,
+      <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
+    }.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
+    <span class="ruby-ivar">@show_label</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:label</span>]
+    <span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:glyph</span>]
+    <span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:colour</span>]
+    <span class="ruby-comment cmt"># As far as I know, I can't do this in the glyph file for transcript, so we</span>
+    <span class="ruby-comment cmt"># have to do it here instead.</span>
+    <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:transcript</span>
+      <span class="ruby-ivar">@glyph</span> = { <span class="ruby-value str">'utr5'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:box</span>, <span class="ruby-value str">'utr3'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:directed_box</span>, <span class="ruby-value str">'cds'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:spliced</span> }
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
+    <span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
+    <span class="ruby-ivar">@vertical_offset</span> = <span class="ruby-value">0</span>
+    <span class="ruby-ivar">@grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000022.html ADDED

@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>add_feature (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 93</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span> = {})
+    <span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start</span>
+    <span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.</span>
+    <span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want</span>
+    <span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or</span>
+    <span class="ruby-comment cmt"># not (see below).</span>
+    <span class="ruby-identifier">start</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
+    <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
+    <span class="ruby-comment cmt"># If the feature wouldn't show because it's not in the region we're</span>
+    <span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge</span>
+    <span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with</span>
+    <span class="ruby-comment cmt"># thousands of features.</span>
+    <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+      <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
+    <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start &gt;= panel.display_start and stop &lt;= panel.display_stop</span>
+      <span class="ruby-ivar">@features</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">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span>))
+      <span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000023.html ADDED

@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>draw (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 123</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
+    <span class="ruby-identifier">track_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_destination</span>)
+    <span class="ruby-comment cmt"># Draw thin line above title</span>
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">stroke</span>
+    <span class="ruby-comment cmt"># Draw track title</span>
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
+    <span class="ruby-identifier">track_context</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>))
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
+    <span class="ruby-comment cmt"># Draw the features</span>
+    <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
+      <span class="ruby-comment cmt"># Don't even bother if the feature is not in the view</span>
+      <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+        <span class="ruby-keyword kw">next</span>
+      <span class="ruby-keyword kw">else</span>
+        <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
+      <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-ivar">@number_of_feature_rows</span> = ( <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
+    <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">panel_destination</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000051.html ADDED

@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>new (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 37</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
+    <span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
+    <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
+    <span class="ruby-identifier">opts</span> = {
+      <span class="ruby-identifier">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>,
+      <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:generic</span>,
+      <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">&gt;</span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
+    }.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
+    <span class="ruby-ivar">@show_label</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:label</span>]
+    <span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:glyph</span>]
+    <span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:colour</span>]
+    <span class="ruby-comment cmt"># As far as I know, I can't do this in the glyph file for transcript, so we</span>
+    <span class="ruby-comment cmt"># have to do it here instead.</span>
+    <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:transcript</span>
+      <span class="ruby-ivar">@glyph</span> = { <span class="ruby-value str">'utr5'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:box</span>, <span class="ruby-value str">'utr3'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:directed_box</span>, <span class="ruby-value str">'cds'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">:spliced</span> }
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
+    <span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
+    <span class="ruby-ivar">@vertical_offset</span> = <span class="ruby-value">0</span>
+    <span class="ruby-ivar">@grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000052.html ADDED

@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>add_feature (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 93</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span> = {})
+    <span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start</span>
+    <span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.</span>
+    <span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want</span>
+    <span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or</span>
+    <span class="ruby-comment cmt"># not (see below).</span>
+    <span class="ruby-identifier">start</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
+    <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">feature_object</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
+    <span class="ruby-comment cmt"># If the feature wouldn't show because it's not in the region we're</span>
+    <span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge</span>
+    <span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with</span>
+    <span class="ruby-comment cmt"># thousands of features.</span>
+    <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+      <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
+    <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start &gt;= panel.display_start and stop &lt;= panel.display_stop</span>
+      <span class="ruby-ivar">@features</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">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">feature_object</span>, <span class="ruby-identifier">opts</span>))
+      <span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Track.src/M000053.html ADDED

@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+  <title>draw (Bio::Graphics::Track)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 123</span>
+  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
+    <span class="ruby-identifier">track_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_destination</span>)
+    <span class="ruby-comment cmt"># Draw thin line above title</span>
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">stroke</span>
+    <span class="ruby-comment cmt"># Draw track title</span>
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
+    <span class="ruby-identifier">track_context</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>))
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
+    <span class="ruby-identifier">track_context</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
+    <span class="ruby-comment cmt"># Draw the features</span>
+    <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
+      <span class="ruby-comment cmt"># Don't even bother if the feature is not in the view</span>
+      <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+        <span class="ruby-keyword kw">next</span>
+      <span class="ruby-keyword kw">else</span>
+        <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_destination</span>)
+      <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">end</span>
+    <span class="ruby-ivar">@number_of_feature_rows</span> = ( <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
+    <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">panel_destination</span>
+  <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Range.html ADDED

@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>Class: Range</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Class</strong></td>
+          <td class="class-name-in-header">Range</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../files/lib/bio-graphics_rb.html">
+                lib/bio-graphics.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                Object
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+   </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <div id="aliases-list">
+      <h3 class="section-bar">External Aliases</h3>
+      <div class="name-list">
+                        <table summary="aliases">
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">begin</td>
+          <td>-&gt;</td>
+          <td class="context-item-value">lend</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">end</td>
+          <td>-&gt;</td>
+          <td class="context-item-value">rend</td>
+        </tr>
+                        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>