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_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
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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">'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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<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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+
<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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<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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<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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