bio-graphics 1.2 → 1.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/doc/classes/Bio.html +4 -26
- data/doc/classes/Bio/Feature.html +350 -0
- data/doc/classes/Bio/Feature.src/M000010.html +21 -0
- data/doc/classes/Bio/Feature.src/M000011.html +20 -0
- data/doc/classes/Bio/Feature.src/M000012.html +19 -0
- data/doc/classes/Bio/Feature.src/M000014.html +21 -0
- data/doc/classes/Bio/Feature.src/M000016.html +21 -0
- data/doc/classes/Bio/Feature.src/M000034.html +21 -0
- data/doc/classes/Bio/Feature.src/M000035.html +20 -0
- data/doc/classes/Bio/Feature.src/M000036.html +19 -0
- data/doc/classes/Bio/Feature.src/M000038.html +21 -0
- data/doc/classes/Bio/Feature.src/M000040.html +21 -0
- data/doc/classes/Bio/Feature.src/M000042.html +21 -0
- data/doc/classes/Bio/Feature.src/M000043.html +20 -0
- data/doc/classes/Bio/Feature.src/M000044.html +21 -0
- data/doc/classes/Bio/Feature.src/M000045.html +20 -0
- data/doc/classes/Bio/Feature.src/M000046.html +19 -0
- data/doc/classes/Bio/Feature.src/M000048.html +21 -0
- data/doc/classes/Bio/Feature.src/M000050.html +21 -0
- data/doc/classes/Bio/Feature.src/M000074.html +21 -0
- data/doc/classes/Bio/Feature.src/M000075.html +20 -0
- data/doc/classes/Bio/Feature.src/M000076.html +19 -0
- data/doc/classes/Bio/Feature.src/M000078.html +21 -0
- data/doc/classes/Bio/Feature.src/M000080.html +21 -0
- data/doc/classes/Bio/Feature/Qualifier.html +189 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000017.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000041.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000049.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000051.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000081.html +18 -0
- data/doc/classes/Bio/Features.html +329 -0
- data/doc/classes/Bio/Features.src/M000004.html +18 -0
- data/doc/classes/Bio/Features.src/M000005.html +19 -0
- data/doc/classes/Bio/Features.src/M000006.html +21 -0
- data/doc/classes/Bio/Features.src/M000007.html +18 -0
- data/doc/classes/Bio/Features.src/M000008.html +18 -0
- data/doc/classes/Bio/Features.src/M000009.html +18 -0
- data/doc/classes/Bio/Features.src/M000028.html +18 -0
- data/doc/classes/Bio/Features.src/M000029.html +19 -0
- data/doc/classes/Bio/Features.src/M000030.html +21 -0
- data/doc/classes/Bio/Features.src/M000031.html +18 -0
- data/doc/classes/Bio/Features.src/M000032.html +18 -0
- data/doc/classes/Bio/Features.src/M000033.html +18 -0
- data/doc/classes/Bio/Features.src/M000036.html +18 -0
- data/doc/classes/Bio/Features.src/M000037.html +19 -0
- data/doc/classes/Bio/Features.src/M000038.html +18 -0
- data/doc/classes/Bio/Features.src/M000039.html +19 -0
- data/doc/classes/Bio/Features.src/M000040.html +21 -0
- data/doc/classes/Bio/Features.src/M000041.html +18 -0
- data/doc/classes/Bio/Features.src/M000042.html +18 -0
- data/doc/classes/Bio/Features.src/M000043.html +18 -0
- data/doc/classes/Bio/Features.src/M000068.html +18 -0
- data/doc/classes/Bio/Features.src/M000069.html +19 -0
- data/doc/classes/Bio/Features.src/M000070.html +21 -0
- data/doc/classes/Bio/Features.src/M000071.html +18 -0
- data/doc/classes/Bio/Features.src/M000072.html +18 -0
- data/doc/classes/Bio/Features.src/M000073.html +18 -0
- data/doc/classes/Bio/Graphics.html +28 -42
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} +98 -125
- data/doc/classes/Bio/Graphics/Feature.src/M000020.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000021.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000022.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000023.html +66 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000024.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000025.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000026.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000054.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000055.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000056.html +55 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000025.html +68 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000026.html +67 -0
- data/doc/classes/Bio/Graphics/Glyph.html +178 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000004.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000032.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.html +187 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html +40 -0
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.html} +16 -19
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Transcript.html +113 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html +21 -0
- data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.html} +50 -16
- data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} +3 -3
- data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000033.html +18 -0
- data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} +7 -4
- data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000062.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000064.html +27 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html +24 -0
- data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} +14 -14
- data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} +3 -3
- data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} +6 -4
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html +22 -0
- data/doc/classes/Bio/Graphics/Panel.html +70 -69
- data/doc/classes/Bio/Graphics/Panel.src/M000025.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000026.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000027.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000028.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000029.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000030.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000031.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000059.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000060.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000061.html +98 -0
- data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} +50 -21
- data/doc/classes/Bio/Graphics/Ruler.src/M000015.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000016.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000017.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000018.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000019.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000020.html +45 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000047.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000048.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000049.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000050.html +45 -0
- data/doc/classes/Bio/Graphics/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000001.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000002.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000023.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000024.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000027.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000028.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000057.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000058.html +69 -0
- data/doc/classes/Bio/Graphics/{Panel/Track.html → Track.html} +67 -69
- data/doc/classes/Bio/Graphics/Track.src/M000017.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000018.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000019.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000020.html +41 -0
- data/doc/classes/Bio/Graphics/Track.src/M000021.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000022.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000023.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000051.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000052.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000053.html +45 -0
- data/doc/classes/Range.html +129 -0
- data/doc/classes/String.html +167 -0
- data/doc/classes/String.src/M000001.html +18 -0
- data/doc/classes/String.src/M000002.html +18 -0
- data/doc/classes/String.src/M000003.html +23 -0
- data/doc/classes/String.src/M000029.html +18 -0
- data/doc/classes/String.src/M000030.html +18 -0
- data/doc/classes/String.src/M000031.html +23 -0
- data/doc/classes/TestCustomGlyph.html +137 -0
- data/doc/classes/TestCustomGlyph.src/M000025.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.html +167 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000026.html +19 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000027.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000028.html +18 -0
- data/doc/classes/TestExtensions.html +152 -0
- data/doc/classes/TestExtensions.src/M000015.html +22 -0
- data/doc/classes/TestExtensions.src/M000016.html +25 -0
- data/doc/classes/TestFeature.html +152 -0
- data/doc/classes/TestFeature.src/M000017.html +19 -0
- data/doc/classes/TestFeature.src/M000018.html +21 -0
- data/doc/classes/TestImageMap.html +182 -0
- data/doc/classes/TestImageMap.src/M000019.html +22 -0
- data/doc/classes/TestImageMap.src/M000020.html +56 -0
- data/doc/classes/TestImageMap.src/M000021.html +56 -0
- data/doc/classes/TestImageMap.src/M000022.html +20 -0
- data/doc/classes/TestPanel.html +276 -0
- data/doc/classes/TestPanel.src/M000001.html +18 -0
- data/doc/classes/TestPanel.src/M000002.html +61 -0
- data/doc/classes/TestPanel.src/M000003.html +35 -0
- data/doc/classes/TestPanel.src/M000004.html +54 -0
- data/doc/classes/TestPanel.src/M000005.html +54 -0
- data/doc/classes/TestPanel.src/M000006.html +41 -0
- data/doc/classes/TestPanel.src/M000007.html +36 -0
- data/doc/classes/TestPanel.src/M000008.html +20 -0
- data/doc/classes/TestPanel.src/M000009.html +26 -0
- data/doc/classes/TestPanel.src/M000010.html +21 -0
- data/doc/classes/TestRuler.html +152 -0
- data/doc/classes/TestRuler.src/M000013.html +22 -0
- data/doc/classes/TestRuler.src/M000014.html +31 -0
- data/doc/classes/TestSubFeature.html +152 -0
- data/doc/classes/TestSubFeature.src/M000023.html +21 -0
- data/doc/classes/TestSubFeature.src/M000024.html +18 -0
- data/doc/classes/TestTrack.html +152 -0
- data/doc/classes/TestTrack.src/M000011.html +19 -0
- data/doc/classes/TestTrack.src/M000012.html +23 -0
- data/doc/created.rid +1 -1
- data/doc/files/README_DEV.html +399 -70
- data/doc/files/TUTORIAL.html +188 -67
- data/doc/files/lib/bio-graphics_rb.html +3 -2
- data/doc/files/lib/bio/graphics/feature_rb.html +12 -6
- data/doc/files/lib/bio/graphics/glyphs/box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/common_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/dot_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_with_handles_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/transcript_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/triangle_rb.html +113 -0
- data/doc/files/lib/bio/graphics/image_map_rb.html +3 -2
- data/doc/files/lib/bio/graphics/panel_rb.html +10 -2
- data/doc/files/lib/bio/graphics/ruler_rb.html +3 -2
- data/doc/files/lib/bio/graphics/subfeature_rb.html +114 -0
- data/doc/files/lib/bio/graphics/track_rb.html +3 -2
- data/doc/files/lib/feature_rb.html +101 -0
- data/doc/files/samples/arkdb_features_rb.html +101 -0
- data/doc/files/samples/glyph_showcase_rb.html +108 -0
- data/doc/files/samples/protein_domains_rb.html +115 -0
- data/doc/files/samples/subfeatures_rb.html +108 -0
- data/doc/files/scripts/gff2png_rb.html +154 -0
- data/doc/files/test/unit/custom_glyph_in_file_rb.html +101 -0
- data/doc/files/test/unit/test_class_extensions_rb.html +108 -0
- data/doc/files/test/unit/test_creation_rb.html +108 -0
- data/doc/files/test/unit/test_custom_glyph_rb.html +108 -0
- data/doc/files/test/unit/test_draw_rb.html +108 -0
- data/doc/files/test/unit/test_imagemap_rb.html +108 -0
- data/doc/files/test/unit/test_subfeatures_rb.html +108 -0
- data/doc/fr_class_index.html +24 -6
- data/doc/fr_file_index.html +14 -0
- data/doc/fr_method_index.html +51 -19
- data/doc/images/glyph_showcase.png +0 -0
- data/doc/images/terms.svg +146 -132
- data/images/glyph_showcase.png +0 -0
- data/lib/bio-graphics.rb +38 -6
- data/lib/bio/graphics/feature.rb +212 -440
- data/lib/bio/graphics/glyphs/box.rb +21 -0
- data/lib/bio/graphics/glyphs/common.rb +149 -0
- data/lib/bio/graphics/glyphs/directed_box.rb +28 -0
- data/lib/bio/graphics/glyphs/directed_generic.rb +23 -0
- data/lib/bio/graphics/glyphs/directed_spliced.rb +39 -0
- data/lib/bio/graphics/glyphs/dot.rb +21 -0
- data/lib/bio/graphics/glyphs/generic.rb +15 -0
- data/lib/bio/graphics/glyphs/line.rb +17 -0
- data/lib/bio/graphics/glyphs/line_with_handles.rb +25 -0
- data/lib/bio/graphics/glyphs/spliced.rb +16 -0
- data/lib/bio/graphics/glyphs/transcript.rb +12 -0
- data/lib/bio/graphics/glyphs/triangle.rb +18 -0
- data/lib/bio/graphics/image_map.rb +25 -4
- data/lib/bio/graphics/panel.rb +266 -209
- data/lib/bio/graphics/ruler.rb +95 -96
- data/lib/bio/graphics/subfeature.rb +187 -0
- data/lib/bio/graphics/track.rb +155 -156
- data/lib/feature.rb +204 -0
- data/samples/arkdb_features.rb +10 -8
- data/samples/glyph_showcase.rb +58 -22
- data/samples/protein_domains.rb +19 -0
- data/samples/subfeatures.rb +31 -0
- data/test/unit/custom_glyph_in_file.rb +12 -0
- data/test/unit/data.txt +32 -0
- data/test/unit/test_class_extensions.rb +23 -0
- data/test/unit/test_creation.rb +43 -13
- data/test/unit/test_custom_glyph.rb +50 -0
- data/test/unit/test_draw.rb +211 -0
- data/test/unit/test_imagemap.rb +134 -0
- data/test/unit/test_subfeatures.rb +17 -0
- metadata +396 -119
- data/doc/classes/Bio/Graphics/Panel.src/M000005.html +0 -29
- data/doc/classes/Bio/Graphics/Panel.src/M000006.html +0 -19
- data/doc/classes/Bio/Graphics/Panel.src/M000007.html +0 -68
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +0 -54
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +0 -26
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +0 -42
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +0 -52
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +0 -23
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +0 -43
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +0 -259
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +0 -65
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +0 -39
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<pre><span class="ruby-comment cmt"># File test/unit/test_imagemap.rb, line 5</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">setup</span>
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<span class="ruby-ivar">@horizontal_imagemap</span> = <span class="ruby-value str">"<html>\n<body>\n<map name=\"image_map\" border=\"1\">\n<area shape=\"rect\" coords=\"209.075452640357 82 252.5194373852 92\" href=\"http://www.google.com\"/>\n<area shape=\"rect\" coords=\"253.957390519804 82 451.51613401821 92\" href=\"http://www.google.com\"/>\n<area shape=\"rect\" coords=\"132.966578121574 137 142.966578121574 147\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00049788\"/>\n<area shape=\"rect\" coords=\"135.392018720278 167 145.392018720278 177\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00033347\"/>\n<area shape=\"rect\" coords=\"181.068633829497 197 191.068633829497 207\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00049753\"/>\n<area shape=\"rect\" coords=\"205.969047559139 227 215.969047559139 237\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00049743\"/>\n<area shape=\"rect\" coords=\"217.47799253058 257 227.47799253058 267\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00050962\"/>\n<area shape=\"rect\" coords=\"430.77140269086 137 440.77140269086 147\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00049746\"/>\n</map>\n<img border='1' src='./test_horizontal_imagemap.png' usemap='#image_map' />\n</body>\n</html>\n"</span>
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<span class="ruby-ivar">@vertical_imagemap</span> = <span class="ruby-value str">"<html>\n<body>\n<map name=\"image_map\" border=\"1\">\n<area shape=\"rect\" coords=\"82 347.4805626148 92 390.924547359643\" href=\"http://www.google.com\"/>\n<area shape=\"rect\" coords=\"82 148.48386598179 92 346.042609480196\" href=\"http://www.google.com\"/>\n<area shape=\"rect\" coords=\"137 457.033421878426 147 467.033421878426\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00049788\"/>\n<area shape=\"rect\" coords=\"167 454.607981279722 177 464.607981279722\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00033347\"/>\n<area shape=\"rect\" coords=\"197 408.931366170503 207 418.931366170503\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00049753\"/>\n<area shape=\"rect\" coords=\"227 384.030952440861 237 394.030952440861\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00049743\"/>\n<area shape=\"rect\" coords=\"257 372.52200746942 267 382.52200746942\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00050962\"/>\n<area shape=\"rect\" coords=\"137 159.22859730914 147 169.22859730914\" href=\"http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=ARKMKR00049746\"/>\n</map>\n<img border='1' src='./test_vertical_imagemap.png' usemap='#image_map' />\n</body>\n</html>\n"</span>
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<pre><span class="ruby-comment cmt"># File test/unit/test_imagemap.rb, line 47</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_horizontal_imagemap</span>
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<span class="ruby-identifier">my_panel</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">4173015</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">600</span>, <span class="ruby-identifier">:clickable</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>)
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<span class="ruby-comment cmt">#Create and configure tracks</span>
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<span class="ruby-identifier">scaffold_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>)
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<span class="ruby-identifier">marker_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>)
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<span class="ruby-identifier">clone_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>)
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<span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>]
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<span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">0</span>]
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<span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:triangle</span>
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<span class="ruby-identifier">clone_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
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<span class="ruby-comment cmt"># Add data to tracks</span>
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<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/data.txt'</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp!</span>
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<span class="ruby-identifier">accession</span>, <span class="ruby-identifier">type</span>, <span class="ruby-identifier">start</span>, <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\t/</span>)
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'scaffold'</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">nil?</span>
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<span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-value str">'1..4173015'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">accession</span>)
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.google.com'</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'marker'</span>
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<span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, ((<span class="ruby-identifier">start</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>.<span class="ruby-identifier">to_i</span>)<span class="ruby-operator">/</span><span class="ruby-value">2</span>).<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession='</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">accession</span>)
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'clone'</span>
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<span class="ruby-identifier">clone_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">accession</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># And draw</span>
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<span class="ruby-identifier">output_file</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@method_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'.png'</span>
|
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+
<span class="ruby-identifier">html_file</span> = <span class="ruby-identifier">output_file</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/\.png$/</span>, <span class="ruby-value str">'.html'</span>)
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<span class="ruby-ivar">@generated_files</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
|
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<span class="ruby-ivar">@generated_files</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">html_file</span>)
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<span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
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+
|
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<span class="ruby-identifier">assert_equal</span>(<span class="ruby-ivar">@horizontal_imagemap</span>, <span class="ruby-constant">File</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">html_file</span>))
|
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<span class="ruby-keyword kw">end</span></pre>
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<title>test_vertical_imagemap (TestImageMap)</title>
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<pre><span class="ruby-comment cmt"># File test/unit/test_imagemap.rb, line 89</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_vertical_imagemap</span>
|
|
15
|
+
<span class="ruby-identifier">my_panel</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Panel</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">4173015</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">600</span>, <span class="ruby-identifier">:clickable</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>, <span class="ruby-identifier">:vertical</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>)
|
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|
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<span class="ruby-comment cmt">#Create and configure tracks</span>
|
|
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|
+
<span class="ruby-identifier">scaffold_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>)
|
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<span class="ruby-identifier">marker_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'marker'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>)
|
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<span class="ruby-identifier">clone_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>)
|
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|
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<span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>]
|
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|
+
<span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">0</span>]
|
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+
<span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:triangle</span>
|
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|
+
<span class="ruby-identifier">clone_track</span>.<span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>]
|
|
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|
+
|
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|
+
<span class="ruby-comment cmt"># Add data to tracks</span>
|
|
28
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/data.txt'</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
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<span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp!</span>
|
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+
<span class="ruby-identifier">accession</span>, <span class="ruby-identifier">type</span>, <span class="ruby-identifier">start</span>, <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\t/</span>)
|
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+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'scaffold'</span>
|
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+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">nil?</span>
|
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|
+
<span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-value str">'1..4173015'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">accession</span>)
|
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+
<span class="ruby-keyword kw">else</span>
|
|
35
|
+
<span class="ruby-identifier">scaffold_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'scaffold'</span>, <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.google.com'</span>)
|
|
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<span class="ruby-keyword kw">end</span>
|
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'marker'</span>
|
|
39
|
+
<span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'marker'</span>, ((<span class="ruby-identifier">start</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>.<span class="ruby-identifier">to_i</span>)<span class="ruby-operator">/</span><span class="ruby-value">2</span>).<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">accession</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession='</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">accession</span>)
|
|
40
|
+
<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'clone'</span>
|
|
41
|
+
<span class="ruby-identifier">clone_track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'clone'</span>, <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">stop</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">accession</span>)
|
|
42
|
+
<span class="ruby-keyword kw">end</span>
|
|
43
|
+
<span class="ruby-keyword kw">end</span>
|
|
44
|
+
|
|
45
|
+
<span class="ruby-comment cmt"># And draw</span>
|
|
46
|
+
<span class="ruby-identifier">output_file</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword kw">__FILE__</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@method_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'.png'</span>
|
|
47
|
+
<span class="ruby-identifier">html_file</span> = <span class="ruby-identifier">output_file</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/\.png$/</span>, <span class="ruby-value str">'.html'</span>)
|
|
48
|
+
<span class="ruby-ivar">@generated_files</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
|
|
49
|
+
<span class="ruby-ivar">@generated_files</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">html_file</span>)
|
|
50
|
+
|
|
51
|
+
<span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
|
|
52
|
+
|
|
53
|
+
<span class="ruby-identifier">assert_equal</span>(<span class="ruby-ivar">@vertical_imagemap</span>, <span class="ruby-constant">File</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">html_file</span>))
|
|
54
|
+
<span class="ruby-keyword kw">end</span></pre>
|
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|
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@@ -0,0 +1,20 @@
|
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<html>
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<head>
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<title>teardown (TestImageMap)</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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<pre><span class="ruby-comment cmt"># File test/unit/test_imagemap.rb, line 131</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">teardown</span>
|
|
15
|
+
<span class="ruby-ivar">@generated_files</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span><span class="ruby-operator">|</span>
|
|
16
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">p</span>)
|
|
17
|
+
<span class="ruby-keyword kw">end</span>
|
|
18
|
+
<span class="ruby-keyword kw">end</span></pre>
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test/unit/test_draw.rb
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test/unit/test_creation.rb
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Test::Unit::TestCase
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<a href="#M000001">setup</a>
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