bio-graphics 1.2 → 1.4
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- data/doc/classes/Bio.html +4 -26
- data/doc/classes/Bio/Feature.html +350 -0
- data/doc/classes/Bio/Feature.src/M000010.html +21 -0
- data/doc/classes/Bio/Feature.src/M000011.html +20 -0
- data/doc/classes/Bio/Feature.src/M000012.html +19 -0
- data/doc/classes/Bio/Feature.src/M000014.html +21 -0
- data/doc/classes/Bio/Feature.src/M000016.html +21 -0
- data/doc/classes/Bio/Feature.src/M000034.html +21 -0
- data/doc/classes/Bio/Feature.src/M000035.html +20 -0
- data/doc/classes/Bio/Feature.src/M000036.html +19 -0
- data/doc/classes/Bio/Feature.src/M000038.html +21 -0
- data/doc/classes/Bio/Feature.src/M000040.html +21 -0
- data/doc/classes/Bio/Feature.src/M000042.html +21 -0
- data/doc/classes/Bio/Feature.src/M000043.html +20 -0
- data/doc/classes/Bio/Feature.src/M000044.html +21 -0
- data/doc/classes/Bio/Feature.src/M000045.html +20 -0
- data/doc/classes/Bio/Feature.src/M000046.html +19 -0
- data/doc/classes/Bio/Feature.src/M000048.html +21 -0
- data/doc/classes/Bio/Feature.src/M000050.html +21 -0
- data/doc/classes/Bio/Feature.src/M000074.html +21 -0
- data/doc/classes/Bio/Feature.src/M000075.html +20 -0
- data/doc/classes/Bio/Feature.src/M000076.html +19 -0
- data/doc/classes/Bio/Feature.src/M000078.html +21 -0
- data/doc/classes/Bio/Feature.src/M000080.html +21 -0
- data/doc/classes/Bio/Feature/Qualifier.html +189 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000017.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000041.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000049.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000051.html +18 -0
- data/doc/classes/Bio/Feature/Qualifier.src/M000081.html +18 -0
- data/doc/classes/Bio/Features.html +329 -0
- data/doc/classes/Bio/Features.src/M000004.html +18 -0
- data/doc/classes/Bio/Features.src/M000005.html +19 -0
- data/doc/classes/Bio/Features.src/M000006.html +21 -0
- data/doc/classes/Bio/Features.src/M000007.html +18 -0
- data/doc/classes/Bio/Features.src/M000008.html +18 -0
- data/doc/classes/Bio/Features.src/M000009.html +18 -0
- data/doc/classes/Bio/Features.src/M000028.html +18 -0
- data/doc/classes/Bio/Features.src/M000029.html +19 -0
- data/doc/classes/Bio/Features.src/M000030.html +21 -0
- data/doc/classes/Bio/Features.src/M000031.html +18 -0
- data/doc/classes/Bio/Features.src/M000032.html +18 -0
- data/doc/classes/Bio/Features.src/M000033.html +18 -0
- data/doc/classes/Bio/Features.src/M000036.html +18 -0
- data/doc/classes/Bio/Features.src/M000037.html +19 -0
- data/doc/classes/Bio/Features.src/M000038.html +18 -0
- data/doc/classes/Bio/Features.src/M000039.html +19 -0
- data/doc/classes/Bio/Features.src/M000040.html +21 -0
- data/doc/classes/Bio/Features.src/M000041.html +18 -0
- data/doc/classes/Bio/Features.src/M000042.html +18 -0
- data/doc/classes/Bio/Features.src/M000043.html +18 -0
- data/doc/classes/Bio/Features.src/M000068.html +18 -0
- data/doc/classes/Bio/Features.src/M000069.html +19 -0
- data/doc/classes/Bio/Features.src/M000070.html +21 -0
- data/doc/classes/Bio/Features.src/M000071.html +18 -0
- data/doc/classes/Bio/Features.src/M000072.html +18 -0
- data/doc/classes/Bio/Features.src/M000073.html +18 -0
- data/doc/classes/Bio/Graphics.html +28 -42
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature.html → Feature.html} +98 -125
- data/doc/classes/Bio/Graphics/Feature.src/M000020.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000021.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000022.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000023.html +66 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000024.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000025.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000026.html +55 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000054.html +51 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000055.html +65 -0
- data/doc/classes/Bio/Graphics/Feature.src/M000056.html +55 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000025.html +68 -0
- data/doc/classes/Bio/Graphics/Feature/SubFeature.src/M000026.html +67 -0
- data/doc/classes/Bio/Graphics/Glyph.html +178 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000004.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Box.src/M000032.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.html +187 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000004.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000005.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000006.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000007.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000033.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000034.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/Common.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyph.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/CustomTestGlyphInFile.src/M000038.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000009.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedBox.src/M000039.html +31 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000011.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000013.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedGeneric.src/M000043.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000008.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000010.html +40 -0
- data/doc/classes/Bio/Graphics/Glyph/DirectedSpliced.src/M000040.html +40 -0
- data/doc/classes/Bio/Graphics/{Panel/Track/Feature/PixelRange.html → Glyph/Dot.html} +16 -19
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000013.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000015.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Dot.src/M000045.html +22 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000009.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000011.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Generic.src/M000041.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000012.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000014.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/Line.src/M000044.html +20 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000014.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000016.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/LineWithHandles.src/M000046.html +28 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000010.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000012.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Spliced.src/M000042.html +19 -0
- data/doc/classes/Bio/Graphics/Glyph/Transcript.html +113 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.html +139 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000007.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000008.html +21 -0
- data/doc/classes/Bio/Graphics/Glyph/Triangle.src/M000036.html +21 -0
- data/doc/classes/{ImageMap.html → Bio/Graphics/ImageMap.html} +50 -16
- data/doc/classes/{ImageMap.src/M000001.html → Bio/Graphics/ImageMap.src/M000030.html} +3 -3
- data/doc/classes/Bio/Graphics/ImageMap.src/M000031.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000032.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000033.html +18 -0
- data/doc/classes/{ImageMap.src/M000002.html → Bio/Graphics/ImageMap.src/M000034.html} +7 -4
- data/doc/classes/Bio/Graphics/ImageMap.src/M000035.html +24 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000062.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000063.html +18 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000064.html +27 -0
- data/doc/classes/Bio/Graphics/ImageMap.src/M000065.html +24 -0
- data/doc/classes/{ImageMap/ImageMapElement.html → Bio/Graphics/ImageMap/Element.html} +14 -14
- data/doc/classes/{ImageMap/ImageMapElement.src/M000003.html → Bio/Graphics/ImageMap/Element.src/M000034.html} +3 -3
- data/doc/classes/{ImageMap/ImageMapElement.src/M000004.html → Bio/Graphics/ImageMap/Element.src/M000035.html} +6 -4
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000036.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000037.html +22 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000066.html +19 -0
- data/doc/classes/Bio/Graphics/ImageMap/Element.src/M000067.html +22 -0
- data/doc/classes/Bio/Graphics/Panel.html +70 -69
- data/doc/classes/Bio/Graphics/Panel.src/M000025.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000026.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000027.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000028.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000029.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000030.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000031.html +98 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000059.html +52 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000060.html +20 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000061.html +98 -0
- data/doc/classes/Bio/Graphics/{Panel/Ruler.html → Ruler.html} +50 -21
- data/doc/classes/Bio/Graphics/Ruler.src/M000015.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000016.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000017.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000018.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000019.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000020.html +45 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000047.html +30 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000048.html +20 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000049.html +26 -0
- data/doc/classes/Bio/Graphics/Ruler.src/M000050.html +45 -0
- data/doc/classes/Bio/Graphics/SubFeature.html +348 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000001.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000002.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000023.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000024.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000027.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000028.html +69 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000057.html +73 -0
- data/doc/classes/Bio/Graphics/SubFeature.src/M000058.html +69 -0
- data/doc/classes/Bio/Graphics/{Panel/Track.html → Track.html} +67 -69
- data/doc/classes/Bio/Graphics/Track.src/M000017.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000018.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000019.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000020.html +41 -0
- data/doc/classes/Bio/Graphics/Track.src/M000021.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000022.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000023.html +45 -0
- data/doc/classes/Bio/Graphics/Track.src/M000051.html +39 -0
- data/doc/classes/Bio/Graphics/Track.src/M000052.html +37 -0
- data/doc/classes/Bio/Graphics/Track.src/M000053.html +45 -0
- data/doc/classes/Range.html +129 -0
- data/doc/classes/String.html +167 -0
- data/doc/classes/String.src/M000001.html +18 -0
- data/doc/classes/String.src/M000002.html +18 -0
- data/doc/classes/String.src/M000003.html +23 -0
- data/doc/classes/String.src/M000029.html +18 -0
- data/doc/classes/String.src/M000030.html +18 -0
- data/doc/classes/String.src/M000031.html +23 -0
- data/doc/classes/TestCustomGlyph.html +137 -0
- data/doc/classes/TestCustomGlyph.src/M000025.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.html +167 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000026.html +19 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000027.html +25 -0
- data/doc/classes/TestCustomGlyphInFile.src/M000028.html +18 -0
- data/doc/classes/TestExtensions.html +152 -0
- data/doc/classes/TestExtensions.src/M000015.html +22 -0
- data/doc/classes/TestExtensions.src/M000016.html +25 -0
- data/doc/classes/TestFeature.html +152 -0
- data/doc/classes/TestFeature.src/M000017.html +19 -0
- data/doc/classes/TestFeature.src/M000018.html +21 -0
- data/doc/classes/TestImageMap.html +182 -0
- data/doc/classes/TestImageMap.src/M000019.html +22 -0
- data/doc/classes/TestImageMap.src/M000020.html +56 -0
- data/doc/classes/TestImageMap.src/M000021.html +56 -0
- data/doc/classes/TestImageMap.src/M000022.html +20 -0
- data/doc/classes/TestPanel.html +276 -0
- data/doc/classes/TestPanel.src/M000001.html +18 -0
- data/doc/classes/TestPanel.src/M000002.html +61 -0
- data/doc/classes/TestPanel.src/M000003.html +35 -0
- data/doc/classes/TestPanel.src/M000004.html +54 -0
- data/doc/classes/TestPanel.src/M000005.html +54 -0
- data/doc/classes/TestPanel.src/M000006.html +41 -0
- data/doc/classes/TestPanel.src/M000007.html +36 -0
- data/doc/classes/TestPanel.src/M000008.html +20 -0
- data/doc/classes/TestPanel.src/M000009.html +26 -0
- data/doc/classes/TestPanel.src/M000010.html +21 -0
- data/doc/classes/TestRuler.html +152 -0
- data/doc/classes/TestRuler.src/M000013.html +22 -0
- data/doc/classes/TestRuler.src/M000014.html +31 -0
- data/doc/classes/TestSubFeature.html +152 -0
- data/doc/classes/TestSubFeature.src/M000023.html +21 -0
- data/doc/classes/TestSubFeature.src/M000024.html +18 -0
- data/doc/classes/TestTrack.html +152 -0
- data/doc/classes/TestTrack.src/M000011.html +19 -0
- data/doc/classes/TestTrack.src/M000012.html +23 -0
- data/doc/created.rid +1 -1
- data/doc/files/README_DEV.html +399 -70
- data/doc/files/TUTORIAL.html +188 -67
- data/doc/files/lib/bio-graphics_rb.html +3 -2
- data/doc/files/lib/bio/graphics/feature_rb.html +12 -6
- data/doc/files/lib/bio/graphics/glyphs/box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/common_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_box_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/directed_spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/dot_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/generic_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/line_with_handles_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/spliced_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/transcript_rb.html +113 -0
- data/doc/files/lib/bio/graphics/glyphs/triangle_rb.html +113 -0
- data/doc/files/lib/bio/graphics/image_map_rb.html +3 -2
- data/doc/files/lib/bio/graphics/panel_rb.html +10 -2
- data/doc/files/lib/bio/graphics/ruler_rb.html +3 -2
- data/doc/files/lib/bio/graphics/subfeature_rb.html +114 -0
- data/doc/files/lib/bio/graphics/track_rb.html +3 -2
- data/doc/files/lib/feature_rb.html +101 -0
- data/doc/files/samples/arkdb_features_rb.html +101 -0
- data/doc/files/samples/glyph_showcase_rb.html +108 -0
- data/doc/files/samples/protein_domains_rb.html +115 -0
- data/doc/files/samples/subfeatures_rb.html +108 -0
- data/doc/files/scripts/gff2png_rb.html +154 -0
- data/doc/files/test/unit/custom_glyph_in_file_rb.html +101 -0
- data/doc/files/test/unit/test_class_extensions_rb.html +108 -0
- data/doc/files/test/unit/test_creation_rb.html +108 -0
- data/doc/files/test/unit/test_custom_glyph_rb.html +108 -0
- data/doc/files/test/unit/test_draw_rb.html +108 -0
- data/doc/files/test/unit/test_imagemap_rb.html +108 -0
- data/doc/files/test/unit/test_subfeatures_rb.html +108 -0
- data/doc/fr_class_index.html +24 -6
- data/doc/fr_file_index.html +14 -0
- data/doc/fr_method_index.html +51 -19
- data/doc/images/glyph_showcase.png +0 -0
- data/doc/images/terms.svg +146 -132
- data/images/glyph_showcase.png +0 -0
- data/lib/bio-graphics.rb +38 -6
- data/lib/bio/graphics/feature.rb +212 -440
- data/lib/bio/graphics/glyphs/box.rb +21 -0
- data/lib/bio/graphics/glyphs/common.rb +149 -0
- data/lib/bio/graphics/glyphs/directed_box.rb +28 -0
- data/lib/bio/graphics/glyphs/directed_generic.rb +23 -0
- data/lib/bio/graphics/glyphs/directed_spliced.rb +39 -0
- data/lib/bio/graphics/glyphs/dot.rb +21 -0
- data/lib/bio/graphics/glyphs/generic.rb +15 -0
- data/lib/bio/graphics/glyphs/line.rb +17 -0
- data/lib/bio/graphics/glyphs/line_with_handles.rb +25 -0
- data/lib/bio/graphics/glyphs/spliced.rb +16 -0
- data/lib/bio/graphics/glyphs/transcript.rb +12 -0
- data/lib/bio/graphics/glyphs/triangle.rb +18 -0
- data/lib/bio/graphics/image_map.rb +25 -4
- data/lib/bio/graphics/panel.rb +266 -209
- data/lib/bio/graphics/ruler.rb +95 -96
- data/lib/bio/graphics/subfeature.rb +187 -0
- data/lib/bio/graphics/track.rb +155 -156
- data/lib/feature.rb +204 -0
- data/samples/arkdb_features.rb +10 -8
- data/samples/glyph_showcase.rb +58 -22
- data/samples/protein_domains.rb +19 -0
- data/samples/subfeatures.rb +31 -0
- data/test/unit/custom_glyph_in_file.rb +12 -0
- data/test/unit/data.txt +32 -0
- data/test/unit/test_class_extensions.rb +23 -0
- data/test/unit/test_creation.rb +43 -13
- data/test/unit/test_custom_glyph.rb +50 -0
- data/test/unit/test_draw.rb +211 -0
- data/test/unit/test_imagemap.rb +134 -0
- data/test/unit/test_subfeatures.rb +17 -0
- metadata +396 -119
- data/doc/classes/Bio/Graphics/Panel.src/M000005.html +0 -29
- data/doc/classes/Bio/Graphics/Panel.src/M000006.html +0 -19
- data/doc/classes/Bio/Graphics/Panel.src/M000007.html +0 -68
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +0 -54
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +0 -20
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +0 -28
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +0 -59
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +0 -26
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +0 -42
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +0 -52
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +0 -23
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +0 -43
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +0 -259
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +0 -65
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +0 -39
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000013.html +0 -27
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<pre><span class="ruby-comment cmt"># File test/unit/test_draw.rb, line 9</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_draw_showcase</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">500</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1000</span>)
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<span class="ruby-identifier">generic_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'generic'</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">line_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'line'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:line</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></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-identifier">line_with_handles_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'line with handles'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:line_with_handles</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></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-identifier">directed_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'directed'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:directed_generic</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></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">triangle_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'triangle'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:triangle</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></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">dot_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'dot'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:dot</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">1</span>])
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<span class="ruby-identifier">spliced_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'spliced'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:spliced</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></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">directed_spliced_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'directed_spliced'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:directed_spliced</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>])
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<span class="ruby-identifier">generic_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-value str">'250..375'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'clone1'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.newsforge.com'</span>)
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<span class="ruby-identifier">generic_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-value str">'54..124'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'clone2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.thearkdb.org'</span>)
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<span class="ruby-identifier">generic_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-value str">'100..449'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'clone3'</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-identifier">line_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">'primer'</span>, <span class="ruby-value str">'complement(200..320)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'primer1'</span>)
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<span class="ruby-identifier">line_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">'primer'</span>, <span class="ruby-value str">'355..480'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'primer2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.zdnet.co.uk'</span>)
|
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|
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<span class="ruby-identifier">line_with_handles_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">'primer'</span>, <span class="ruby-value str">'complement(200..320)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'primer1'</span>)
|
|
34
|
+
<span class="ruby-identifier">line_with_handles_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">'primer'</span>, <span class="ruby-value str">'355..480'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'primer2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.zdnet.co.uk'</span>)
|
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|
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<span class="ruby-identifier">directed_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-value str">'50..60'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'marker1'</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-identifier">directed_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-value str">'complement(80..120)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'marker2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.sourceforge.net'</span>)
|
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|
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<span class="ruby-identifier">triangle_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-value str">'56'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'snp1'</span>)
|
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+
<span class="ruby-identifier">triangle_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-value str">'103'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'snp2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://digg.com'</span>)
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|
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<span class="ruby-identifier">dot_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-value str">'56'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'thing1'</span>)
|
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<span class="ruby-identifier">dot_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-value str">'57'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'thing3'</span>)
|
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+
<span class="ruby-identifier">dot_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-value str">'114'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'thing2'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://digg.com'</span>)
|
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|
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<span class="ruby-identifier">spliced_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">'gene'</span>,<span class="ruby-value str">'join(34..52,109..183)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene1'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://news.bbc.co.uk'</span>)
|
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47
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+
<span class="ruby-identifier">spliced_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">'gene'</span>,<span class="ruby-value str">'complement(join(170..231,264..299,350..360,409..445))'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene2'</span>)
|
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<span class="ruby-identifier">spliced_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">'gene'</span>,<span class="ruby-value str">'join(134..152,209..283)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene3'</span>)
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|
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<span class="ruby-identifier">directed_spliced_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">'gene'</span>,<span class="ruby-value str">'join(34..52,109..183)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene4'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.vrtnieuws.net'</span>)
|
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+
<span class="ruby-identifier">directed_spliced_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">'gene'</span>,<span class="ruby-value str">'complement(join(170..231,264..299,350..360,409..445))'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene5'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://bioinformatics.roslin.ac.uk'</span>)
|
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52
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+
<span class="ruby-identifier">directed_spliced_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">'gene'</span>,<span class="ruby-value str">'join(134..152,209..283)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene6'</span>)
|
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|
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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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55
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+
<span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
|
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56
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+
|
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57
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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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58
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+
<span class="ruby-identifier">system</span>(<span class="ruby-value str">"display "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"& sleep 2 && kill $!"</span>)
|
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<span class="ruby-keyword kw">end</span></pre>
|
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<title>test_outside_border (TestPanel)</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_draw.rb, line 56</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_outside_border</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">500</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1000</span>, <span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">></span> <span class="ruby-value">100</span><span class="ruby-operator">..</span><span class="ruby-value">400</span>)
|
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<span class="ruby-identifier">spliced_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'spliced'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:spliced</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></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">directed_spliced_track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'directed_spliced'</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:directed_spliced</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> [<span class="ruby-value">1</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>])
|
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|
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20
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+
<span class="ruby-identifier">spliced_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">'gene'</span>,<span class="ruby-value str">'join(34..52,109..183)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene1'</span>,<span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://news.bbc.co.uk'</span>)
|
|
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+
<span class="ruby-identifier">spliced_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">'gene'</span>,<span class="ruby-value str">'complement(join(170..231,264..299,350..360,409..445))'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene2'</span>)
|
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<span class="ruby-identifier">spliced_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">'gene'</span>,<span class="ruby-value str">'join(134..152,209..283)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene3'</span>)
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+
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<span class="ruby-identifier">directed_spliced_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">'gene'</span>,<span class="ruby-value str">'join(34..52,109..183)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene4'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://www.vrtnieuws.net'</span>)
|
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+
<span class="ruby-identifier">directed_spliced_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">'gene'</span>,<span class="ruby-value str">'complement(join(170..231,264..299,350..360,409..445))'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene5'</span>, <span class="ruby-identifier">:link</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'http://bioinformatics.roslin.ac.uk'</span>)
|
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26
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+
<span class="ruby-identifier">directed_spliced_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">'gene'</span>,<span class="ruby-value str">'join(134..152,209..283)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'gene6'</span>)
|
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|
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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>
|
|
29
|
+
<span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
|
|
30
|
+
|
|
31
|
+
<span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
|
|
32
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-value str">"display "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"& sleep 2 && kill $!"</span>)
|
|
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|
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<span class="ruby-keyword kw">end</span></pre>
|
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PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<head>
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<title>test_arkdb_features (TestPanel)</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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</head>
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<body class="standalone-code">
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<pre><span class="ruby-comment cmt"># File test/unit/test_draw.rb, line 77</span>
|
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|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_arkdb_features</span>
|
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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">:vertical</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>)
|
|
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|
+
|
|
17
|
+
<span class="ruby-comment cmt">#Create and configure tracks</span>
|
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18
|
+
<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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19
|
+
<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>)
|
|
20
|
+
<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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24
|
+
<span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:triangle</span>
|
|
25
|
+
<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>]
|
|
26
|
+
|
|
27
|
+
<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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29
|
+
<span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp!</span>
|
|
30
|
+
<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>)
|
|
31
|
+
<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>
|
|
32
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">nil?</span>
|
|
33
|
+
<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>)
|
|
34
|
+
<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>)
|
|
36
|
+
<span class="ruby-keyword kw">end</span>
|
|
37
|
+
|
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38
|
+
<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-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
|
|
48
|
+
|
|
49
|
+
<span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
|
|
50
|
+
|
|
51
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-value str">"display "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"& sleep 2 && kill $!"</span>)
|
|
52
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
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|
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|
|
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|
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|
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PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>test_subregion (TestPanel)</title>
|
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|
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|
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</head>
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<body class="standalone-code">
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<pre><span class="ruby-comment cmt"># File test/unit/test_draw.rb, line 117</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_subregion</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">:display_range</span> =<span class="ruby-operator">></span> <span class="ruby-value">2500000</span><span class="ruby-operator">..</span><span class="ruby-value">3500000</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">600</span>)
|
|
16
|
+
|
|
17
|
+
<span class="ruby-comment cmt">#Create and configure tracks</span>
|
|
18
|
+
<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>)
|
|
19
|
+
<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>)
|
|
20
|
+
<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>)
|
|
21
|
+
|
|
22
|
+
<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>]
|
|
23
|
+
<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>]
|
|
24
|
+
<span class="ruby-identifier">marker_track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:triangle</span>
|
|
25
|
+
<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>]
|
|
26
|
+
|
|
27
|
+
<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>
|
|
29
|
+
<span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp!</span>
|
|
30
|
+
<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>)
|
|
31
|
+
<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>
|
|
32
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">nil?</span>
|
|
33
|
+
<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>)
|
|
34
|
+
<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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|
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|
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|
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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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|
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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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|
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<span class="ruby-keyword kw">end</span>
|
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|
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|
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|
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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-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
|
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|
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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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|
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<span class="ruby-identifier">system</span>(<span class="ruby-value str">"display "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"& sleep 2 && kill $!"</span>)
|
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File test/unit/test_draw.rb, line 157</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_subfeatures</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">500</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">600</span>)
|
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|
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<span class="ruby-identifier">track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'mrna'</span>)
|
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|
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|
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<span class="ruby-identifier">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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|
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:spliced</span>
|
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|
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|
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<span class="ruby-comment cmt"># Add data to tracks</span>
|
|
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|
+
<span class="ruby-identifier">utr5</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">'utr'</span>, <span class="ruby-value str">'100..150'</span>)
|
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|
+
<span class="ruby-identifier">cds</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">'cds'</span>, <span class="ruby-value str">'join(150..225, 250..275, 310..330)'</span>)
|
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|
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<span class="ruby-identifier">utr3</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">'utr'</span>, <span class="ruby-value str">'330..375'</span>)
|
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|
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|
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<span class="ruby-identifier">transcript</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">'transcript'</span>, <span class="ruby-value str">'join(100..225, 250..275, 310..375)'</span>, [], <span class="ruby-keyword kw">nil</span>, [<span class="ruby-identifier">utr5</span>, <span class="ruby-identifier">cds</span>, <span class="ruby-identifier">utr3</span>])
|
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|
+
|
|
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|
+
<span class="ruby-identifier">transcript_graphic</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">transcript</span>, <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'my_transcript'</span>)
|
|
30
|
+
<span class="ruby-identifier">transcript_graphic</span>.<span class="ruby-identifier">glyph</span> = { <span class="ruby-value str">'utr'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:line</span>, <span class="ruby-value str">'cds'</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:spliced</span> }
|
|
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|
+
|
|
32
|
+
<span class="ruby-comment cmt"># And draw</span>
|
|
33
|
+
<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>
|
|
34
|
+
<span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
|
|
35
|
+
|
|
36
|
+
<span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
|
|
37
|
+
|
|
38
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-value str">"display "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"& sleep 2 && kill $!"</span>)
|
|
39
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
40
|
+
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|
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|
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|
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|
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|
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<title>test_feature_specific_colouring (TestPanel)</title>
|
|
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|
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
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<body class="standalone-code">
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<pre><span class="ruby-comment cmt"># File test/unit/test_draw.rb, line 184</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_feature_specific_colouring</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">375</span>, <span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">></span> <span class="ruby-value">100</span><span class="ruby-operator">..</span><span class="ruby-value">370</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">600</span>)
|
|
16
|
+
|
|
17
|
+
<span class="ruby-identifier">track</span> = <span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value str">'mrna'</span>)
|
|
18
|
+
|
|
19
|
+
<span class="ruby-identifier">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>]
|
|
20
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:spliced</span>
|
|
21
|
+
|
|
22
|
+
<span class="ruby-comment cmt"># Add data to tracks</span>
|
|
23
|
+
<span class="ruby-identifier">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">'cds'</span>, <span class="ruby-value str">'join(100..200, 225..350)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'red_spliced'</span>)
|
|
24
|
+
<span class="ruby-identifier">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">'cds'</span>, <span class="ruby-value str">'join(100..200, 225..350)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'green_spliced'</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> [<span class="ruby-value">0</span>,<span class="ruby-value">1</span>,<span class="ruby-value">0</span>])
|
|
25
|
+
<span class="ruby-identifier">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">'cds'</span>, <span class="ruby-value str">'join(100..200, 225..350)'</span>), <span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'blue_generic'</span>, <span class="ruby-identifier">:colour</span> =<span class="ruby-operator">></span> [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>])
|
|
26
|
+
|
|
27
|
+
<span class="ruby-comment cmt"># And draw</span>
|
|
28
|
+
<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>
|
|
29
|
+
<span class="ruby-ivar">@generated_pictures</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">output_file</span>)
|
|
30
|
+
|
|
31
|
+
<span class="ruby-identifier">my_panel</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">output_file</span>)
|
|
32
|
+
|
|
33
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-value str">"display "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">output_file</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"& sleep 2 && kill $!"</span>)
|
|
34
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
35
|
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|
|
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|
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|
|
@@ -0,0 +1,20 @@
|
|
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|
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|
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|
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|
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<head>
|
|
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|
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<title>teardown (TestPanel)</title>
|
|
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|
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
+
<pre><span class="ruby-comment cmt"># File test/unit/test_draw.rb, line 206</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">teardown</span>
|
|
15
|
+
<span class="ruby-ivar">@generated_pictures</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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|
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|
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@@ -0,0 +1,26 @@
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<title>test_panel_creation (TestPanel)</title>
|
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<pre><span class="ruby-comment cmt"># File test/unit/test_creation.rb, line 5</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_panel_creation</span>
|
|
15
|
+
<span class="ruby-identifier">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">1000</span>, <span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">500</span>, <span class="ruby-identifier">:clickable</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>,
|
|
16
|
+
<span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">></span> <span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">1000</span>)
|
|
17
|
+
<span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">1000</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">length</span>)
|
|
18
|
+
<span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">500</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>)
|
|
19
|
+
<span class="ruby-identifier">assert_equal</span>(<span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">clickable</span>)
|
|
20
|
+
<span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>)
|
|
21
|
+
<span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">1000</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>)
|
|
22
|
+
<span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">1000</span><span class="ruby-operator">/</span><span class="ruby-value">500</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>)
|
|
23
|
+
<span class="ruby-identifier">assert_equal</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">tracks</span>.<span class="ruby-identifier">length</span>)
|
|
24
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
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|
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|
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|
|
@@ -0,0 +1,21 @@
|
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|
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|
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<title>test_panel_creation_out_of_boundaries (TestPanel)</title>
|
|
9
|
+
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">test_panel_creation_out_of_boundaries</span>
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