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 lib/bio/graphics/panel.rb, line 110</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">length</span>, <span class="ruby-identifier">opts</span> = {})
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<span class="ruby-ivar">@length</span> = <span class="ruby-identifier">length</span>
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<span class="ruby-identifier">opts</span> = {
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<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-constant">DEFAULT_PANEL_WIDTH</span>,
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<span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">></span> <span class="ruby-constant">Range</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">0</span>,<span class="ruby-ivar">@length</span>),
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<span class="ruby-identifier">:vertical</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>,
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<span class="ruby-identifier">:clickable</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>,
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<span class="ruby-identifier">:format</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:png</span>
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}.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
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<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:width</span>].<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@display_range</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:display_range</span>]
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<span class="ruby-ivar">@display_start</span> = [<span class="ruby-value">0</span>, <span class="ruby-ivar">@display_range</span>.<span class="ruby-identifier">lend</span>].<span class="ruby-identifier">max</span>
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<span class="ruby-ivar">@display_stop</span> = [<span class="ruby-ivar">@length</span>,<span class="ruby-ivar">@display_range</span>.<span class="ruby-identifier">rend</span>].<span class="ruby-identifier">min</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@display_stop</span> <span class="ruby-operator"><=</span> <span class="ruby-ivar">@display_start</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-value str">"[ERROR] Start coordinate to be displayed has to be smaller than stop coordinate."</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@display_range</span> = <span class="ruby-constant">Range</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@display_start</span>,<span class="ruby-ivar">@display_stop</span>)
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<span class="ruby-ivar">@vertical</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:vertical</span>]
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<span class="ruby-ivar">@clickable</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:clickable</span>]
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<span class="ruby-ivar">@format</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:format</span>]
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<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> [<span class="ruby-identifier">:png</span>, <span class="ruby-identifier">:svg</span>, <span class="ruby-identifier">:pdf</span>, <span class="ruby-identifier">:ps</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-ivar">@format</span>)
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<span class="ruby-identifier">raise</span> <span class="ruby-value str">"[ERROR] Format has to be one of :png, :svg, :pdf or :ps."</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@tracks</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
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<span class="ruby-ivar">@image_map</span> = <span class="ruby-constant">ImageMap</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-ivar">@rescale_factor</span> = (<span class="ruby-ivar">@display_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@display_start</span>).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@width</span>
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<span class="ruby-comment cmt"># To prevent that we do the whole drawing thing multiple times</span>
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<span class="ruby-ivar">@final_panel_destination</span> = <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">end</span></pre>
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<title>add_track (Bio::Graphics::Panel)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 166</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
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<span class="ruby-identifier">track</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Track</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span>)
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<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">track</span>)
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<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">track</span>
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<span class="ruby-keyword kw">end</span></pre>
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<title>draw (Bio::Graphics::Panel)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 179</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">file_name</span>)
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@final_panel_drawing</span>.<span class="ruby-identifier">nil?</span>
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<span class="ruby-comment cmt"># Create a panel that is huge vertically</span>
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<span class="ruby-identifier">huge_height</span> = <span class="ruby-value">2000</span>
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<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-keyword kw">nil</span>
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<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-identifier">huge_height</span>)
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<span class="ruby-identifier">background</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">huge_panel_destination</span>)
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<span class="ruby-identifier">background</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">1</span>,<span class="ruby-value">1</span>,<span class="ruby-value">1</span>)
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<span class="ruby-identifier">background</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>,<span class="ruby-identifier">huge_height</span>).<span class="ruby-identifier">fill</span>
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<span class="ruby-comment cmt"># Add ruler</span>
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<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-value">0</span>
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<span class="ruby-identifier">ruler</span> = <span class="ruby-constant">Ruler</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>)
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<span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_destination</span>)
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<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">height</span>
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|
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<span class="ruby-comment cmt"># Add tracks</span>
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<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-identifier">vertical_offset</span>
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_destination</span>)
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<span class="ruby-ivar">@number_of_feature_rows</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span>
|
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+
<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> ( <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span><span class="ruby-operator">*</span>(<span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_V_DISTANCE</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)) <span class="ruby-operator">+</span> <span class="ruby-value">10</span> <span class="ruby-comment cmt"># '10' is for the header</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># And create a smaller version of the panel</span>
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<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">height</span>
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<span class="ruby-ivar">@height</span> <span class="ruby-operator">+=</span> <span class="ruby-value">20</span><span class="ruby-operator">*</span><span class="ruby-ivar">@number_of_feature_rows</span>
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+
<span class="ruby-ivar">@height</span> <span class="ruby-operator">+=</span> <span class="ruby-value">10</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">length</span> <span class="ruby-comment cmt">#To correct for the track headers</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@vertical</span>
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<span class="ruby-ivar">@image_map</span>.<span class="ruby-identifier">flip_orientation</span>(<span class="ruby-ivar">@width</span>)
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<span class="ruby-identifier">max_size</span> = [<span class="ruby-ivar">@height</span>, <span class="ruby-ivar">@width</span>].<span class="ruby-identifier">max</span>
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49
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+
<span class="ruby-identifier">rotated_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-identifier">max_size</span>, <span class="ruby-identifier">max_size</span>)
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+
<span class="ruby-identifier">rotated_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">rotated_destination</span>)
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<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">rotate</span>(<span class="ruby-value">3</span><span class="ruby-operator">*</span><span class="ruby-constant">PI</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
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<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-operator">-</span><span class="ruby-ivar">@width</span>, <span class="ruby-value">0</span>)
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<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-identifier">huge_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
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<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-identifier">max_size</span>, <span class="ruby-identifier">max_size</span>).<span class="ruby-identifier">fill</span>
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+
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+
<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span> = <span class="ruby-ivar">@height</span>, <span class="ruby-ivar">@width</span>
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57
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+
<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-identifier">rotated_destination</span>
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<span class="ruby-keyword kw">end</span>
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59
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|
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60
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+
<span class="ruby-ivar">@final_panel_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
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+
<span class="ruby-identifier">resized_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@final_panel_destination</span>)
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62
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+
<span class="ruby-identifier">resized_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-identifier">huge_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
|
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63
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+
<span class="ruby-identifier">resized_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>).<span class="ruby-identifier">fill</span>
|
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+
<span class="ruby-keyword kw">end</span>
|
|
65
|
+
|
|
66
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+
<span class="ruby-comment cmt"># And print to file</span>
|
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+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@format</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:png</span>
|
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68
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+
<span class="ruby-ivar">@final_panel_destination</span>.<span class="ruby-identifier">write_to_png</span>(<span class="ruby-identifier">file_name</span>)
|
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+
<span class="ruby-keyword kw">else</span>
|
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70
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+
<span class="ruby-keyword kw">case</span> <span class="ruby-ivar">@format</span>
|
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|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:pdf</span>
|
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|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">PDFSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
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73
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+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:ps</span>
|
|
74
|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">PSSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
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+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:svg</span>
|
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|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">SVGSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
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+
<span class="ruby-keyword kw">end</span>
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78
|
+
|
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+
<span class="ruby-identifier">output_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">output_destination</span>)
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+
<span class="ruby-identifier">output_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-ivar">@final_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
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|
+
<span class="ruby-identifier">output_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>).<span class="ruby-identifier">fill</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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|
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|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@clickable</span> <span class="ruby-comment cmt"># create png and map</span>
|
|
86
|
+
<span class="ruby-identifier">html_filename</span> = <span class="ruby-identifier">file_name</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/\.[^.]+$/</span>, <span class="ruby-value str">'.html'</span>)
|
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|
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<span class="ruby-identifier">html</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">html_filename</span>,<span class="ruby-value str">'w'</span>)
|
|
88
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<html>"</span>
|
|
89
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<body>"</span>
|
|
90
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-ivar">@image_map</span>.<span class="ruby-identifier">to_s</span>
|
|
91
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<img border='1' src='"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">file_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"' usemap='#image_map' />"</span>
|
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|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"</body>"</span>
|
|
93
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"</html>"</span>
|
|
94
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">close</span>
|
|
95
|
+
<span class="ruby-keyword kw">end</span>
|
|
96
|
+
<span class="ruby-keyword kw">end</span></pre>
|
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|
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</body>
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</html>
|
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|
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<?xml version="1.0" encoding="iso-8859-1"?>
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<!DOCTYPE html
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PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html>
|
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<head>
|
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<title>add_track (Bio::Graphics::Panel)</title>
|
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9
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
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|
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</head>
|
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<body class="standalone-code">
|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 148</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">opts</span> = {})
|
|
15
|
+
<span class="ruby-identifier">track</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Track</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">opts</span>)
|
|
16
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">track</span>)
|
|
17
|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">track</span>
|
|
18
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
19
|
+
</body>
|
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20
|
+
</html>
|
|
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|
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|
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<?xml version="1.0" encoding="iso-8859-1"?>
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+
<!DOCTYPE html
|
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3
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PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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4
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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|
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6
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<html>
|
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7
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<head>
|
|
8
|
+
<title>new (Bio::Graphics::Panel)</title>
|
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9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
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10
|
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<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
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+
</head>
|
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<body class="standalone-code">
|
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|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 110</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">length</span>, <span class="ruby-identifier">opts</span> = {})
|
|
15
|
+
<span class="ruby-ivar">@length</span> = <span class="ruby-identifier">length</span>
|
|
16
|
+
<span class="ruby-identifier">opts</span> = {
|
|
17
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-constant">DEFAULT_PANEL_WIDTH</span>,
|
|
18
|
+
<span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">></span> <span class="ruby-constant">Range</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">0</span>,<span class="ruby-ivar">@length</span>),
|
|
19
|
+
<span class="ruby-identifier">:vertical</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>,
|
|
20
|
+
<span class="ruby-identifier">:clickable</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>,
|
|
21
|
+
<span class="ruby-identifier">:format</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:png</span>
|
|
22
|
+
}.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
|
|
23
|
+
|
|
24
|
+
<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:width</span>].<span class="ruby-identifier">to_i</span>
|
|
25
|
+
|
|
26
|
+
<span class="ruby-ivar">@display_range</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:display_range</span>]
|
|
27
|
+
<span class="ruby-ivar">@display_start</span> = [<span class="ruby-value">0</span>, <span class="ruby-ivar">@display_range</span>.<span class="ruby-identifier">lend</span>].<span class="ruby-identifier">max</span>
|
|
28
|
+
<span class="ruby-ivar">@display_stop</span> = [<span class="ruby-ivar">@length</span>,<span class="ruby-ivar">@display_range</span>.<span class="ruby-identifier">rend</span>].<span class="ruby-identifier">min</span>
|
|
29
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@display_stop</span> <span class="ruby-operator"><=</span> <span class="ruby-ivar">@display_start</span>
|
|
30
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-value str">"[ERROR] Start coordinate to be displayed has to be smaller than stop coordinate."</span>
|
|
31
|
+
<span class="ruby-keyword kw">end</span>
|
|
32
|
+
<span class="ruby-ivar">@display_range</span> = <span class="ruby-constant">Range</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@display_start</span>,<span class="ruby-ivar">@display_stop</span>)
|
|
33
|
+
|
|
34
|
+
<span class="ruby-ivar">@vertical</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:vertical</span>]
|
|
35
|
+
<span class="ruby-ivar">@clickable</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:clickable</span>]
|
|
36
|
+
|
|
37
|
+
<span class="ruby-ivar">@format</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:format</span>]
|
|
38
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> [<span class="ruby-identifier">:png</span>, <span class="ruby-identifier">:svg</span>, <span class="ruby-identifier">:pdf</span>, <span class="ruby-identifier">:ps</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-ivar">@format</span>)
|
|
39
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-value str">"[ERROR] Format has to be one of :png, :svg, :pdf or :ps."</span>
|
|
40
|
+
<span class="ruby-keyword kw">end</span>
|
|
41
|
+
|
|
42
|
+
<span class="ruby-ivar">@tracks</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
43
|
+
<span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
|
|
44
|
+
<span class="ruby-ivar">@image_map</span> = <span class="ruby-constant">ImageMap</span>.<span class="ruby-identifier">new</span>
|
|
45
|
+
|
|
46
|
+
<span class="ruby-ivar">@rescale_factor</span> = (<span class="ruby-ivar">@display_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@display_start</span>).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@width</span>
|
|
47
|
+
|
|
48
|
+
<span class="ruby-comment cmt"># To prevent that we do the whole drawing thing multiple times</span>
|
|
49
|
+
<span class="ruby-ivar">@final_panel_destination</span> = <span class="ruby-keyword kw">nil</span>
|
|
50
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
51
|
+
</body>
|
|
52
|
+
</html>
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>add_track (Bio::Graphics::Panel)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 166</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
|
|
15
|
+
<span class="ruby-identifier">track</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Track</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span>)
|
|
16
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">track</span>)
|
|
17
|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">track</span>
|
|
18
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
19
|
+
</body>
|
|
20
|
+
</html>
|
|
@@ -0,0 +1,98 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>draw (Bio::Graphics::Panel)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 179</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">file_name</span>)
|
|
15
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@final_panel_drawing</span>.<span class="ruby-identifier">nil?</span>
|
|
16
|
+
<span class="ruby-comment cmt"># Create a panel that is huge vertically</span>
|
|
17
|
+
<span class="ruby-identifier">huge_height</span> = <span class="ruby-value">2000</span>
|
|
18
|
+
|
|
19
|
+
<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-keyword kw">nil</span>
|
|
20
|
+
<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-identifier">huge_height</span>)
|
|
21
|
+
|
|
22
|
+
<span class="ruby-identifier">background</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">huge_panel_destination</span>)
|
|
23
|
+
<span class="ruby-identifier">background</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">1</span>,<span class="ruby-value">1</span>,<span class="ruby-value">1</span>)
|
|
24
|
+
<span class="ruby-identifier">background</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>,<span class="ruby-identifier">huge_height</span>).<span class="ruby-identifier">fill</span>
|
|
25
|
+
|
|
26
|
+
<span class="ruby-comment cmt"># Add ruler</span>
|
|
27
|
+
<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-value">0</span>
|
|
28
|
+
<span class="ruby-identifier">ruler</span> = <span class="ruby-constant">Ruler</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>)
|
|
29
|
+
<span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_destination</span>)
|
|
30
|
+
<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">height</span>
|
|
31
|
+
|
|
32
|
+
<span class="ruby-comment cmt"># Add tracks</span>
|
|
33
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
34
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-identifier">vertical_offset</span>
|
|
35
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_destination</span>)
|
|
36
|
+
<span class="ruby-ivar">@number_of_feature_rows</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span>
|
|
37
|
+
<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> ( <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span><span class="ruby-operator">*</span>(<span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_V_DISTANCE</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)) <span class="ruby-operator">+</span> <span class="ruby-value">10</span> <span class="ruby-comment cmt"># '10' is for the header</span>
|
|
38
|
+
<span class="ruby-keyword kw">end</span>
|
|
39
|
+
|
|
40
|
+
<span class="ruby-comment cmt"># And create a smaller version of the panel</span>
|
|
41
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">height</span>
|
|
42
|
+
<span class="ruby-ivar">@height</span> <span class="ruby-operator">+=</span> <span class="ruby-value">20</span><span class="ruby-operator">*</span><span class="ruby-ivar">@number_of_feature_rows</span>
|
|
43
|
+
<span class="ruby-ivar">@height</span> <span class="ruby-operator">+=</span> <span class="ruby-value">10</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">length</span> <span class="ruby-comment cmt">#To correct for the track headers</span>
|
|
44
|
+
|
|
45
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@vertical</span>
|
|
46
|
+
<span class="ruby-ivar">@image_map</span>.<span class="ruby-identifier">flip_orientation</span>(<span class="ruby-ivar">@width</span>)
|
|
47
|
+
|
|
48
|
+
<span class="ruby-identifier">max_size</span> = [<span class="ruby-ivar">@height</span>, <span class="ruby-ivar">@width</span>].<span class="ruby-identifier">max</span>
|
|
49
|
+
<span class="ruby-identifier">rotated_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-identifier">max_size</span>, <span class="ruby-identifier">max_size</span>)
|
|
50
|
+
<span class="ruby-identifier">rotated_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">rotated_destination</span>)
|
|
51
|
+
<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">rotate</span>(<span class="ruby-value">3</span><span class="ruby-operator">*</span><span class="ruby-constant">PI</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
52
|
+
<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-operator">-</span><span class="ruby-ivar">@width</span>, <span class="ruby-value">0</span>)
|
|
53
|
+
<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-identifier">huge_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
|
|
54
|
+
<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-identifier">max_size</span>, <span class="ruby-identifier">max_size</span>).<span class="ruby-identifier">fill</span>
|
|
55
|
+
|
|
56
|
+
<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span> = <span class="ruby-ivar">@height</span>, <span class="ruby-ivar">@width</span>
|
|
57
|
+
<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-identifier">rotated_destination</span>
|
|
58
|
+
<span class="ruby-keyword kw">end</span>
|
|
59
|
+
|
|
60
|
+
<span class="ruby-ivar">@final_panel_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
|
61
|
+
<span class="ruby-identifier">resized_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@final_panel_destination</span>)
|
|
62
|
+
<span class="ruby-identifier">resized_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-identifier">huge_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
|
|
63
|
+
<span class="ruby-identifier">resized_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>).<span class="ruby-identifier">fill</span>
|
|
64
|
+
<span class="ruby-keyword kw">end</span>
|
|
65
|
+
|
|
66
|
+
<span class="ruby-comment cmt"># And print to file</span>
|
|
67
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@format</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:png</span>
|
|
68
|
+
<span class="ruby-ivar">@final_panel_destination</span>.<span class="ruby-identifier">write_to_png</span>(<span class="ruby-identifier">file_name</span>)
|
|
69
|
+
<span class="ruby-keyword kw">else</span>
|
|
70
|
+
<span class="ruby-keyword kw">case</span> <span class="ruby-ivar">@format</span>
|
|
71
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:pdf</span>
|
|
72
|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">PDFSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
|
73
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:ps</span>
|
|
74
|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">PSSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
|
75
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:svg</span>
|
|
76
|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">SVGSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
|
77
|
+
<span class="ruby-keyword kw">end</span>
|
|
78
|
+
|
|
79
|
+
<span class="ruby-identifier">output_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">output_destination</span>)
|
|
80
|
+
<span class="ruby-identifier">output_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-ivar">@final_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
|
|
81
|
+
<span class="ruby-identifier">output_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>).<span class="ruby-identifier">fill</span>
|
|
82
|
+
<span class="ruby-keyword kw">end</span>
|
|
83
|
+
|
|
84
|
+
|
|
85
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@clickable</span> <span class="ruby-comment cmt"># create png and map</span>
|
|
86
|
+
<span class="ruby-identifier">html_filename</span> = <span class="ruby-identifier">file_name</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/\.[^.]+$/</span>, <span class="ruby-value str">'.html'</span>)
|
|
87
|
+
<span class="ruby-identifier">html</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">html_filename</span>,<span class="ruby-value str">'w'</span>)
|
|
88
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<html>"</span>
|
|
89
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<body>"</span>
|
|
90
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-ivar">@image_map</span>.<span class="ruby-identifier">to_s</span>
|
|
91
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<img border='1' src='"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">file_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"' usemap='#image_map' />"</span>
|
|
92
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"</body>"</span>
|
|
93
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"</html>"</span>
|
|
94
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">close</span>
|
|
95
|
+
<span class="ruby-keyword kw">end</span>
|
|
96
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
97
|
+
</body>
|
|
98
|
+
</html>
|
|
@@ -0,0 +1,52 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>new (Bio::Graphics::Panel)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 110</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">length</span>, <span class="ruby-identifier">opts</span> = {})
|
|
15
|
+
<span class="ruby-ivar">@length</span> = <span class="ruby-identifier">length</span>
|
|
16
|
+
<span class="ruby-identifier">opts</span> = {
|
|
17
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-constant">DEFAULT_PANEL_WIDTH</span>,
|
|
18
|
+
<span class="ruby-identifier">:display_range</span> =<span class="ruby-operator">></span> <span class="ruby-constant">Range</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">0</span>,<span class="ruby-ivar">@length</span>),
|
|
19
|
+
<span class="ruby-identifier">:vertical</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>,
|
|
20
|
+
<span class="ruby-identifier">:clickable</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">false</span>,
|
|
21
|
+
<span class="ruby-identifier">:format</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:png</span>
|
|
22
|
+
}.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>)
|
|
23
|
+
|
|
24
|
+
<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:width</span>].<span class="ruby-identifier">to_i</span>
|
|
25
|
+
|
|
26
|
+
<span class="ruby-ivar">@display_range</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:display_range</span>]
|
|
27
|
+
<span class="ruby-ivar">@display_start</span> = [<span class="ruby-value">0</span>, <span class="ruby-ivar">@display_range</span>.<span class="ruby-identifier">lend</span>].<span class="ruby-identifier">max</span>
|
|
28
|
+
<span class="ruby-ivar">@display_stop</span> = [<span class="ruby-ivar">@length</span>,<span class="ruby-ivar">@display_range</span>.<span class="ruby-identifier">rend</span>].<span class="ruby-identifier">min</span>
|
|
29
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@display_stop</span> <span class="ruby-operator"><=</span> <span class="ruby-ivar">@display_start</span>
|
|
30
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-value str">"[ERROR] Start coordinate to be displayed has to be smaller than stop coordinate."</span>
|
|
31
|
+
<span class="ruby-keyword kw">end</span>
|
|
32
|
+
<span class="ruby-ivar">@display_range</span> = <span class="ruby-constant">Range</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@display_start</span>,<span class="ruby-ivar">@display_stop</span>)
|
|
33
|
+
|
|
34
|
+
<span class="ruby-ivar">@vertical</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:vertical</span>]
|
|
35
|
+
<span class="ruby-ivar">@clickable</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:clickable</span>]
|
|
36
|
+
|
|
37
|
+
<span class="ruby-ivar">@format</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:format</span>]
|
|
38
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> [<span class="ruby-identifier">:png</span>, <span class="ruby-identifier">:svg</span>, <span class="ruby-identifier">:pdf</span>, <span class="ruby-identifier">:ps</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-ivar">@format</span>)
|
|
39
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-value str">"[ERROR] Format has to be one of :png, :svg, :pdf or :ps."</span>
|
|
40
|
+
<span class="ruby-keyword kw">end</span>
|
|
41
|
+
|
|
42
|
+
<span class="ruby-ivar">@tracks</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
43
|
+
<span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
|
|
44
|
+
<span class="ruby-ivar">@image_map</span> = <span class="ruby-constant">ImageMap</span>.<span class="ruby-identifier">new</span>
|
|
45
|
+
|
|
46
|
+
<span class="ruby-ivar">@rescale_factor</span> = (<span class="ruby-ivar">@display_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@display_start</span>).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@width</span>
|
|
47
|
+
|
|
48
|
+
<span class="ruby-comment cmt"># To prevent that we do the whole drawing thing multiple times</span>
|
|
49
|
+
<span class="ruby-ivar">@final_panel_destination</span> = <span class="ruby-keyword kw">nil</span>
|
|
50
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
51
|
+
</body>
|
|
52
|
+
</html>
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>add_track (Bio::Graphics::Panel)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 166</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span> = {})
|
|
15
|
+
<span class="ruby-identifier">track</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Track</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">opts</span>)
|
|
16
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">track</span>)
|
|
17
|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">track</span>
|
|
18
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
19
|
+
</body>
|
|
20
|
+
</html>
|
|
@@ -0,0 +1,98 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>draw (Bio::Graphics::Panel)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 179</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">file_name</span>)
|
|
15
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@final_panel_drawing</span>.<span class="ruby-identifier">nil?</span>
|
|
16
|
+
<span class="ruby-comment cmt"># Create a panel that is huge vertically</span>
|
|
17
|
+
<span class="ruby-identifier">huge_height</span> = <span class="ruby-value">2000</span>
|
|
18
|
+
|
|
19
|
+
<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-keyword kw">nil</span>
|
|
20
|
+
<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-identifier">huge_height</span>)
|
|
21
|
+
|
|
22
|
+
<span class="ruby-identifier">background</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">huge_panel_destination</span>)
|
|
23
|
+
<span class="ruby-identifier">background</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">1</span>,<span class="ruby-value">1</span>,<span class="ruby-value">1</span>)
|
|
24
|
+
<span class="ruby-identifier">background</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>,<span class="ruby-identifier">huge_height</span>).<span class="ruby-identifier">fill</span>
|
|
25
|
+
|
|
26
|
+
<span class="ruby-comment cmt"># Add ruler</span>
|
|
27
|
+
<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-value">0</span>
|
|
28
|
+
<span class="ruby-identifier">ruler</span> = <span class="ruby-constant">Ruler</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>)
|
|
29
|
+
<span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_destination</span>)
|
|
30
|
+
<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">height</span>
|
|
31
|
+
|
|
32
|
+
<span class="ruby-comment cmt"># Add tracks</span>
|
|
33
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
34
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-identifier">vertical_offset</span>
|
|
35
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_destination</span>)
|
|
36
|
+
<span class="ruby-ivar">@number_of_feature_rows</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span>
|
|
37
|
+
<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> ( <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span><span class="ruby-operator">*</span>(<span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_V_DISTANCE</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)) <span class="ruby-operator">+</span> <span class="ruby-value">10</span> <span class="ruby-comment cmt"># '10' is for the header</span>
|
|
38
|
+
<span class="ruby-keyword kw">end</span>
|
|
39
|
+
|
|
40
|
+
<span class="ruby-comment cmt"># And create a smaller version of the panel</span>
|
|
41
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">height</span>
|
|
42
|
+
<span class="ruby-ivar">@height</span> <span class="ruby-operator">+=</span> <span class="ruby-value">20</span><span class="ruby-operator">*</span><span class="ruby-ivar">@number_of_feature_rows</span>
|
|
43
|
+
<span class="ruby-ivar">@height</span> <span class="ruby-operator">+=</span> <span class="ruby-value">10</span><span class="ruby-operator">*</span><span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">length</span> <span class="ruby-comment cmt">#To correct for the track headers</span>
|
|
44
|
+
|
|
45
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@vertical</span>
|
|
46
|
+
<span class="ruby-ivar">@image_map</span>.<span class="ruby-identifier">flip_orientation</span>(<span class="ruby-ivar">@width</span>)
|
|
47
|
+
|
|
48
|
+
<span class="ruby-identifier">max_size</span> = [<span class="ruby-ivar">@height</span>, <span class="ruby-ivar">@width</span>].<span class="ruby-identifier">max</span>
|
|
49
|
+
<span class="ruby-identifier">rotated_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-identifier">max_size</span>, <span class="ruby-identifier">max_size</span>)
|
|
50
|
+
<span class="ruby-identifier">rotated_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">rotated_destination</span>)
|
|
51
|
+
<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">rotate</span>(<span class="ruby-value">3</span><span class="ruby-operator">*</span><span class="ruby-constant">PI</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
52
|
+
<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-operator">-</span><span class="ruby-ivar">@width</span>, <span class="ruby-value">0</span>)
|
|
53
|
+
<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-identifier">huge_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
|
|
54
|
+
<span class="ruby-identifier">rotated_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-identifier">max_size</span>, <span class="ruby-identifier">max_size</span>).<span class="ruby-identifier">fill</span>
|
|
55
|
+
|
|
56
|
+
<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span> = <span class="ruby-ivar">@height</span>, <span class="ruby-ivar">@width</span>
|
|
57
|
+
<span class="ruby-identifier">huge_panel_destination</span> = <span class="ruby-identifier">rotated_destination</span>
|
|
58
|
+
<span class="ruby-keyword kw">end</span>
|
|
59
|
+
|
|
60
|
+
<span class="ruby-ivar">@final_panel_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">1</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
|
61
|
+
<span class="ruby-identifier">resized_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@final_panel_destination</span>)
|
|
62
|
+
<span class="ruby-identifier">resized_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-identifier">huge_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
|
|
63
|
+
<span class="ruby-identifier">resized_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>).<span class="ruby-identifier">fill</span>
|
|
64
|
+
<span class="ruby-keyword kw">end</span>
|
|
65
|
+
|
|
66
|
+
<span class="ruby-comment cmt"># And print to file</span>
|
|
67
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@format</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:png</span>
|
|
68
|
+
<span class="ruby-ivar">@final_panel_destination</span>.<span class="ruby-identifier">write_to_png</span>(<span class="ruby-identifier">file_name</span>)
|
|
69
|
+
<span class="ruby-keyword kw">else</span>
|
|
70
|
+
<span class="ruby-keyword kw">case</span> <span class="ruby-ivar">@format</span>
|
|
71
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:pdf</span>
|
|
72
|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">PDFSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
|
73
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:ps</span>
|
|
74
|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">PSSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
|
75
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:svg</span>
|
|
76
|
+
<span class="ruby-identifier">output_destination</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">SVGSurface</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">file_name</span>, <span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>)
|
|
77
|
+
<span class="ruby-keyword kw">end</span>
|
|
78
|
+
|
|
79
|
+
<span class="ruby-identifier">output_context</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">output_destination</span>)
|
|
80
|
+
<span class="ruby-identifier">output_context</span>.<span class="ruby-identifier">set_source</span>(<span class="ruby-ivar">@final_panel_destination</span>, <span class="ruby-value">0</span>, <span class="ruby-value">0</span>)
|
|
81
|
+
<span class="ruby-identifier">output_context</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-ivar">@width</span>, <span class="ruby-ivar">@height</span>).<span class="ruby-identifier">fill</span>
|
|
82
|
+
<span class="ruby-keyword kw">end</span>
|
|
83
|
+
|
|
84
|
+
|
|
85
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@clickable</span> <span class="ruby-comment cmt"># create png and map</span>
|
|
86
|
+
<span class="ruby-identifier">html_filename</span> = <span class="ruby-identifier">file_name</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/\.[^.]+$/</span>, <span class="ruby-value str">'.html'</span>)
|
|
87
|
+
<span class="ruby-identifier">html</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">html_filename</span>,<span class="ruby-value str">'w'</span>)
|
|
88
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<html>"</span>
|
|
89
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<body>"</span>
|
|
90
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-ivar">@image_map</span>.<span class="ruby-identifier">to_s</span>
|
|
91
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"<img border='1' src='"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">file_name</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"' usemap='#image_map' />"</span>
|
|
92
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"</body>"</span>
|
|
93
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">puts</span> <span class="ruby-value str">"</html>"</span>
|
|
94
|
+
<span class="ruby-identifier">html</span>.<span class="ruby-identifier">close</span>
|
|
95
|
+
<span class="ruby-keyword kw">end</span>
|
|
96
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
97
|
+
</body>
|
|
98
|
+
</html>
|