bio-graphics 1.0

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Files changed (63) hide show
  1. data/doc/classes/Bio.html +135 -0
  2. data/doc/classes/Bio/Graphics.html +247 -0
  3. data/doc/classes/Bio/Graphics/Panel.html +344 -0
  4. data/doc/classes/Bio/Graphics/Panel.src/M000005.html +29 -0
  5. data/doc/classes/Bio/Graphics/Panel.src/M000006.html +19 -0
  6. data/doc/classes/Bio/Graphics/Panel.src/M000007.html +67 -0
  7. data/doc/classes/Bio/Graphics/Panel/Ruler.html +238 -0
  8. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +20 -0
  9. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +28 -0
  10. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +54 -0
  11. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +20 -0
  12. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +28 -0
  13. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +59 -0
  14. data/doc/classes/Bio/Graphics/Panel/Track.html +342 -0
  15. data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +23 -0
  16. data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +42 -0
  17. data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +285 -0
  18. data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +23 -0
  19. data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +43 -0
  20. data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +259 -0
  21. data/doc/classes/Bio/Graphics/Panel/Track/Feature.html +292 -0
  22. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +65 -0
  23. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +65 -0
  24. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html +155 -0
  25. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +18 -0
  26. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +18 -0
  27. data/doc/classes/ImageMap.html +185 -0
  28. data/doc/classes/ImageMap.src/M000001.html +18 -0
  29. data/doc/classes/ImageMap.src/M000002.html +24 -0
  30. data/doc/classes/ImageMap/ImageMapElement.html +187 -0
  31. data/doc/classes/ImageMap/ImageMapElement.src/M000003.html +19 -0
  32. data/doc/classes/ImageMap/ImageMapElement.src/M000004.html +20 -0
  33. data/doc/created.rid +1 -0
  34. data/doc/files/README_DEV.html +432 -0
  35. data/doc/files/TUTORIAL.html +358 -0
  36. data/doc/files/lib/bio-graphics_rb.html +121 -0
  37. data/doc/files/lib/bio/graphics/feature_rb.html +113 -0
  38. data/doc/files/lib/bio/graphics/image_map_rb.html +113 -0
  39. data/doc/files/lib/bio/graphics/panel_rb.html +113 -0
  40. data/doc/files/lib/bio/graphics/ruler_rb.html +113 -0
  41. data/doc/files/lib/bio/graphics/track_rb.html +113 -0
  42. data/doc/fr_class_index.html +35 -0
  43. data/doc/fr_file_index.html +34 -0
  44. data/doc/fr_method_index.html +41 -0
  45. data/doc/images/example.png +0 -0
  46. data/doc/images/glyph_showcase.png +0 -0
  47. data/doc/images/terms.png +0 -0
  48. data/doc/images/terms.svg +166 -0
  49. data/doc/index.html +24 -0
  50. data/images/example.png +0 -0
  51. data/images/glyph_showcase.png +0 -0
  52. data/images/terms.png +0 -0
  53. data/images/terms.svg +166 -0
  54. data/lib/bio-graphics.rb +18 -0
  55. data/lib/bio/graphics/feature.rb +136 -0
  56. data/lib/bio/graphics/image_map.rb +37 -0
  57. data/lib/bio/graphics/panel.rb +205 -0
  58. data/lib/bio/graphics/ruler.rb +96 -0
  59. data/lib/bio/graphics/track.rb +387 -0
  60. data/samples/arkdb_features.rb +37 -0
  61. data/samples/data.txt +32 -0
  62. data/samples/glyph_showcase.rb +29 -0
  63. metadata +137 -0
@@ -0,0 +1,29 @@
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+ require '../lib/bio-graphics'
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+
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+ my_panel = Bio::Graphics::Panel.new(500, 1000, true)
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+
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+ generic_track = my_panel.add_track('generic')
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+ directed_track = my_panel.add_track('directed',[0,1,0],'directed_generic')
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+ triangle_track = my_panel.add_track('triangle',[1,0,0],'triangle')
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+ spliced_track = my_panel.add_track('spliced',[1,0,0],'spliced')
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+ directed_spliced_track = my_panel.add_track('directed_spliced',[1,0,1],'directed_spliced')
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+
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+ generic_track.add_feature('clone1','250..375', 'http://www.newsforge.com')
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+ generic_track.add_feature('clone2','54..124', 'http://www.thearkdb.org')
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+ generic_track.add_feature('clone3','100..449', 'http://www.google.com')
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+
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+ directed_track.add_feature('marker1','50..60', 'http://www.google.com')
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+ directed_track.add_feature('marker2','complement(80..120)', 'http://www.sourceforge.net')
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+
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+ triangle_track.add_feature('snp1','56')
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+ triangle_track.add_feature('snp2','103','http://digg.com')
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+
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+ spliced_track.add_feature('gene1','join(34..52,109..183)','http://news.bbc.co.uk')
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+ spliced_track.add_feature('gene2','complement(join(170..231,264..299,350..360,409..445))')
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+ spliced_track.add_feature('gene3','join(134..152,209..283)')
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+
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+ directed_spliced_track.add_feature('gene4','join(34..52,109..183)', 'http://www.vrtnieuws.net')
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+ directed_spliced_track.add_feature('gene5','complement(join(170..231,264..299,350..360,409..445))', 'http://bioinformatics.roslin.ac.uk')
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+ directed_spliced_track.add_feature('gene6','join(134..152,209..283)')
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+
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+ my_panel.draw('glyph_showcase.png')
metadata ADDED
@@ -0,0 +1,137 @@
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+ --- !ruby/object:Gem::Specification
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+ rubygems_version: 0.9.0
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+ specification_version: 1
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+ name: bio-graphics
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+ version: !ruby/object:Gem::Version
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+ version: "1.0"
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+ date: 2007-10-01 00:00:00 +01:00
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+ summary: Library for visualizing genomic regions
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+ require_paths:
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+ - lib
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+ email: jan.aerts@bbsrc.ac.uk
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+ homepage: http://bio-graphics.rubyforge.org/
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+ rubyforge_project:
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+ description:
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+ autorequire: bio-graphics
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+ default_executable:
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+ bindir: bin
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+ has_rdoc: true
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+ required_ruby_version: !ruby/object:Gem::Version::Requirement
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+ requirements:
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+ - - ">"
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+ - !ruby/object:Gem::Version
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+ version: 0.0.0
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+ version:
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+ platform: ruby
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+ signing_key:
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+ cert_chain:
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+ post_install_message:
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+ authors:
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+ - Jan Aerts
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+ files:
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+ - doc/images
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+ - doc/fr_file_index.html
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+ - doc/fr_class_index.html
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+ - doc/index.html
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+ - doc/fr_method_index.html
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+ - doc/classes
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+ - doc/created.rid
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+ - doc/files
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+ - doc/images/terms.svg
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+ - doc/images/terms.png
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+ - doc/images/glyph_showcase.png
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+ - doc/images/example.png
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+ - doc/classes/Bio
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+ - doc/classes/ImageMap.html
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+ - doc/classes/ImageMap
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+ - doc/classes/ImageMap.src
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+ - doc/classes/Bio.html
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+ - doc/classes/Bio/Graphics.html
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+ - doc/classes/Bio/Graphics
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+ - doc/classes/Bio/Graphics/Panel
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+ - doc/classes/Bio/Graphics/Panel.src
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+ - doc/classes/Bio/Graphics/Panel.html
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+ - doc/classes/Bio/Graphics/Panel/Track
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+ - doc/classes/Bio/Graphics/Panel/Ruler.html
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+ - doc/classes/Bio/Graphics/Panel/Track.html
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+ - doc/classes/Bio/Graphics/Panel/Track.src
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+ - doc/classes/Bio/Graphics/Panel/Ruler.src
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature.html
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature.src
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html
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+ - doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html
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+ - doc/classes/Bio/Graphics/Panel/Track.src/M000013.html
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+ - doc/classes/Bio/Graphics/Panel/Track.src/M000012.html
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+ - doc/classes/Bio/Graphics/Panel/Track.src/M000009.html
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+ - doc/classes/Bio/Graphics/Panel/Track.src/M000011.html
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+ - doc/classes/Bio/Graphics/Panel/Track.src/M000010.html
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+ - doc/classes/Bio/Graphics/Panel/Track.src/M000008.html
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+ - doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html
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+ - doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html
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+ - doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html
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+ - doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html
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+ - doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html
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+ - doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html
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+ - doc/classes/Bio/Graphics/Panel.src/M000007.html
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+ - doc/classes/Bio/Graphics/Panel.src/M000005.html
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+ - doc/classes/Bio/Graphics/Panel.src/M000006.html
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+ - doc/classes/ImageMap/ImageMapElement.src
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+ - doc/classes/ImageMap/ImageMapElement.html
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+ - doc/classes/ImageMap/ImageMapElement.src/M000003.html
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+ - doc/classes/ImageMap/ImageMapElement.src/M000004.html
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+ - doc/classes/ImageMap.src/M000001.html
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+ - doc/classes/ImageMap.src/M000002.html
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+ - doc/files/lib
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+ - doc/files/README_DEV.html
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+ - doc/files/TUTORIAL.html
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+ - doc/files/lib/bio-graphics_rb.html
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+ - doc/files/lib/bio
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+ - doc/files/lib/bio/graphics
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+ - doc/files/lib/bio/graphics/panel_rb.html
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+ - doc/files/lib/bio/graphics/track_rb.html
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+ - doc/files/lib/bio/graphics/image_map_rb.html
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+ - doc/files/lib/bio/graphics/feature_rb.html
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+ - doc/files/lib/bio/graphics/ruler_rb.html
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+ - lib/bio
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+ - lib/bio-graphics.rb
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+ - lib/bio/graphics
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+ - lib/bio/graphics/panel.rb
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+ - lib/bio/graphics/ruler.rb
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+ - lib/bio/graphics/feature.rb
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+ - lib/bio/graphics/track.rb
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+ - lib/bio/graphics/image_map.rb
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+ - samples/arkdb_features.rb
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+ - samples/data.txt
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+ - samples/glyph_showcase.rb
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+ - test/unit
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+ - images/terms.svg
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+ - images/terms.png
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+ - images/glyph_showcase.png
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+ - images/example.png
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+ test_files: []
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+
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+ rdoc_options: []
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+
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+ extra_rdoc_files: []
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+
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+ executables: []
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+
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+ extensions: []
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+
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+ requirements: []
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+
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bio
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Version::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "1"
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+ version: