bio-svgenes 0.2.3 → 0.3.0

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  1. data/.DS_Store +0 -0
  2. data/VERSION +1 -1
  3. data/bio-svgenes.gemspec +59 -4
  4. data/doc/.DS_Store +0 -0
  5. data/doc/Bio.html +141 -0
  6. data/doc/Bio/.DS_Store +0 -0
  7. data/doc/Bio/Graphics.html +147 -0
  8. data/doc/Bio/Graphics/Glyph.html +1061 -0
  9. data/doc/Bio/Graphics/MiniFeature.html +342 -0
  10. data/doc/Bio/Graphics/Page.html +1200 -0
  11. data/doc/Bio/Graphics/Primitive.html +278 -0
  12. data/doc/Bio/Graphics/SVGEE.html +471 -0
  13. data/doc/Bio/Graphics/Track.html +506 -0
  14. data/doc/LICENSE_txt.html +118 -0
  15. data/doc/created.rid +9 -0
  16. data/doc/images/add.png +0 -0
  17. data/doc/images/arrow_up.png +0 -0
  18. data/doc/images/brick.png +0 -0
  19. data/doc/images/brick_link.png +0 -0
  20. data/doc/images/bug.png +0 -0
  21. data/doc/images/bullet_black.png +0 -0
  22. data/doc/images/bullet_toggle_minus.png +0 -0
  23. data/doc/images/bullet_toggle_plus.png +0 -0
  24. data/doc/images/date.png +0 -0
  25. data/doc/images/delete.png +0 -0
  26. data/doc/images/find.png +0 -0
  27. data/doc/images/loadingAnimation.gif +0 -0
  28. data/doc/images/macFFBgHack.png +0 -0
  29. data/doc/images/package.png +0 -0
  30. data/doc/images/page_green.png +0 -0
  31. data/doc/images/page_white_text.png +0 -0
  32. data/doc/images/page_white_width.png +0 -0
  33. data/doc/images/plugin.png +0 -0
  34. data/doc/images/ruby.png +0 -0
  35. data/doc/images/tag_blue.png +0 -0
  36. data/doc/images/tag_green.png +0 -0
  37. data/doc/images/transparent.png +0 -0
  38. data/doc/images/wrench.png +0 -0
  39. data/doc/images/wrench_orange.png +0 -0
  40. data/doc/images/zoom.png +0 -0
  41. data/doc/index.html +94 -0
  42. data/doc/js/darkfish.js +155 -0
  43. data/doc/js/jquery.js +18 -0
  44. data/doc/js/navigation.js +142 -0
  45. data/doc/js/search.js +94 -0
  46. data/doc/js/search_index.js +1 -0
  47. data/doc/js/searcher.js +228 -0
  48. data/doc/rdoc.css +595 -0
  49. data/doc/table_of_contents.html +162 -0
  50. data/test/gene.gff +4 -0
  51. data/test/json_config.json +17 -0
  52. data/test/test_glyph.rb +33 -0
  53. data/test/test_mini_feature.rb +37 -0
  54. data/test/test_page.rb +127 -0
  55. data/test/test_primitive.rb +45 -0
  56. data/test/test_svgee.rb +73 -0
  57. data/test/test_track.rb +53 -0
  58. data/test/test_transcripts.gff +4 -0
  59. metadata +94 -14
data/.DS_Store CHANGED
Binary file
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.2.3
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+ 0.3.0
data/bio-svgenes.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = "bio-svgenes"
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- s.version = "0.2.3"
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+ s.version = "0.3.0"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Dan MacLean"]
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- s.date = "2013-01-30"
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+ s.date = "2013-03-04"
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  s.description = "This bio-gem facilitates the creation of pretty, publication quality SVG images from feature data."
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  s.email = "maclean.daniel@gmail.com"
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  s.extra_rdoc_files = [
@@ -26,6 +26,52 @@ Gem::Specification.new do |s|
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  "Rakefile",
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  "VERSION",
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  "bio-svgenes.gemspec",
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+ "doc/.DS_Store",
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+ "doc/Bio.html",
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+ "doc/Bio/.DS_Store",
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+ "doc/Bio/Graphics.html",
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+ "doc/Bio/Graphics/Glyph.html",
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+ "doc/Bio/Graphics/MiniFeature.html",
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+ "doc/Bio/Graphics/Page.html",
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+ "doc/Bio/Graphics/Primitive.html",
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+ "doc/Bio/Graphics/SVGEE.html",
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+ "doc/Bio/Graphics/Track.html",
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+ "doc/LICENSE_txt.html",
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+ "doc/created.rid",
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+ "doc/images/add.png",
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+ "doc/images/arrow_up.png",
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+ "doc/images/brick.png",
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+ "doc/images/brick_link.png",
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+ "doc/images/bug.png",
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+ "doc/images/bullet_black.png",
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+ "doc/images/bullet_toggle_minus.png",
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+ "doc/images/bullet_toggle_plus.png",
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+ "doc/images/date.png",
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+ "doc/images/delete.png",
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+ "doc/images/find.png",
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+ "doc/images/loadingAnimation.gif",
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+ "doc/images/macFFBgHack.png",
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+ "doc/images/package.png",
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+ "doc/images/page_green.png",
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+ "doc/images/page_white_text.png",
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+ "doc/images/page_white_width.png",
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+ "doc/images/plugin.png",
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+ "doc/images/ruby.png",
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+ "doc/images/tag_blue.png",
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+ "doc/images/tag_green.png",
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+ "doc/images/transparent.png",
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+ "doc/images/wrench.png",
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+ "doc/images/wrench_orange.png",
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+ "doc/images/zoom.png",
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+ "doc/index.html",
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+ "doc/js/darkfish.js",
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+ "doc/js/jquery.js",
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+ "doc/js/navigation.js",
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+ "doc/js/search.js",
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+ "doc/js/search_index.js",
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+ "doc/js/searcher.js",
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+ "doc/rdoc.css",
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+ "doc/table_of_contents.html",
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  "examples/.DS_Store",
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  "examples/annotate_snps.rb",
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  "examples/data.txt",
@@ -49,13 +95,22 @@ Gem::Specification.new do |s|
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  "lib/bio/graphics/primitive.rb",
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  "lib/bio/graphics/svgee.rb",
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  "lib/bio/graphics/track.rb",
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+ "test/gene.gff",
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  "test/helper.rb",
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- "test/test_bio-svgenes.rb"
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+ "test/json_config.json",
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+ "test/test_bio-svgenes.rb",
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+ "test/test_glyph.rb",
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+ "test/test_mini_feature.rb",
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+ "test/test_page.rb",
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+ "test/test_primitive.rb",
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+ "test/test_svgee.rb",
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+ "test/test_track.rb",
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+ "test/test_transcripts.gff"
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  ]
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  s.homepage = "http://github.com/danmaclean/bioruby-svgenes"
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  s.licenses = ["MIT"]
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  s.require_paths = ["lib"]
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- s.rubygems_version = "1.8.10"
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+ s.rubygems_version = "1.8.25"
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  s.summary = "Create pretty SVG-format images of features, gene models and data tracks"
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  if s.respond_to? :specification_version then
data/doc/.DS_Store ADDED
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data/doc/Bio.html ADDED
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <title>module Bio - RDoc Documentation</title>
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+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "./";
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+ </script>
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+
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+ <script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
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+ <body id="top" class="module">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="./index.html">Home</a>
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+ <a href="./table_of_contents.html#classes">Classes</a>
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+ <a href="./table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+ <div id="file-metadata">
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/bio/graphics/glyph.rb
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+ <li>lib/bio/graphics/mini_feature.rb
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+ <li>lib/bio/graphics/page.rb
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+ <li>lib/bio/graphics/primitive.rb
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+ <li>lib/bio/graphics/svgee.rb
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+ <li>lib/bio/graphics/track.rb
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+ </ul>
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+ </nav>
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+ </div>
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+ <div id="class-metadata">
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+ </div>
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+ <div id="project-metadata">
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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+ <ul>
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+ <li class="file"><a href="./LICENSE_txt.html">LICENSE</a>
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+
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+ </ul>
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+ </nav>
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+ <ul class="link-list">
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+
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+ <li><a href="./Bio.html">Bio</a>
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+
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+ <li><a href="./Bio/Graphics.html">Bio::Graphics</a>
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+
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+ <li><a href="./Bio/Graphics/Glyph.html">Bio::Graphics::Glyph</a>
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+
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+ <li><a href="./Bio/Graphics/MiniFeature.html">Bio::Graphics::MiniFeature</a>
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+
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+ <li><a href="./Bio/Graphics/Page.html">Bio::Graphics::Page</a>
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+
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+ <li><a href="./Bio/Graphics/Primitive.html">Bio::Graphics::Primitive</a>
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+
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+ <li><a href="./Bio/Graphics/SVGEE.html">Bio::Graphics::SVGEE</a>
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+
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+ <li><a href="./Bio/Graphics/Track.html">Bio::Graphics::Track</a>
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+
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+ </ul>
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+ </nav>
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+ </div>
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+ </nav>
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+ <div id="documentation">
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+ <h1 class="module">module Bio</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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+ </div><!-- documentation -->
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+ <footer id="validator-badges">
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+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.rc.2.1.
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+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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+
data/doc/Bio/.DS_Store ADDED
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data/doc/Bio/Graphics.html ADDED
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <title>class Bio::Graphics - RDoc Documentation</title>
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+
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+ <link type="text/css" media="screen" href="../rdoc.css" rel="stylesheet">
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+
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../";
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+ </script>
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+
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+ <script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/darkfish.js"></script>
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+
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+
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+ <body id="top" class="class">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../index.html">Home</a>
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+ <a href="../table_of_contents.html#classes">Classes</a>
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+ <a href="../table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+
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+
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/bio/graphics/glyph.rb
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+ <li>lib/bio/graphics/mini_feature.rb
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+ <li>lib/bio/graphics/page.rb
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+ <li>lib/bio/graphics/primitive.rb
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+ <li>lib/bio/graphics/svgee.rb
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+ <li>lib/bio/graphics/track.rb
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+ </ul>
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+ </nav>
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+ <div id="class-metadata">
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+ <nav id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+ <p class="link">Object
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+ </nav>
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+ <div id="project-metadata">
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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+ <ul>
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+ <li class="file"><a href="../LICENSE_txt.html">LICENSE</a>
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+ </ul>
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+ </nav>
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+
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="../Bio.html">Bio</a>
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+
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+ <li><a href="../Bio/Graphics.html">Bio::Graphics</a>
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+ <li><a href="../Bio/Graphics/Glyph.html">Bio::Graphics::Glyph</a>
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+ <li><a href="../Bio/Graphics/MiniFeature.html">Bio::Graphics::MiniFeature</a>
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+ <li><a href="../Bio/Graphics/Page.html">Bio::Graphics::Page</a>
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+ <li><a href="../Bio/Graphics/Primitive.html">Bio::Graphics::Primitive</a>
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+ <li><a href="../Bio/Graphics/SVGEE.html">Bio::Graphics::SVGEE</a>
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+ <li><a href="../Bio/Graphics/Track.html">Bio::Graphics::Track</a>
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+ </ul>
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+ </nav>
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+ </div>
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+ </nav>
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+ <div id="documentation">
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+ <h1 class="class">class Bio::Graphics</h1>
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+ <div id="description" class="description">
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+ </div><!-- description -->
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+ </div><!-- documentation -->
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+ <footer id="validator-badges">
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+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.rc.2.1.
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+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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data/doc/Bio/Graphics/Glyph.html ADDED
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+ <title>class Bio::Graphics::Glyph - RDoc Documentation</title>
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+ <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../../";
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+ </script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
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+
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+ <body id="top" class="class">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../../index.html">Home</a>
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+ <a href="../../table_of_contents.html#classes">Classes</a>
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+ <a href="../../table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+
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+
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+ <div id="file-metadata">
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/bio/graphics/glyph.rb
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+ </ul>
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+ </nav>
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+
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+ </div>
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+
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+ <div id="class-metadata">
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+ <nav id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+
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+ <p class="link">Object
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+ </nav>
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+
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+ <!-- Method Quickref -->
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+ <nav id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+ <ul class="link-list">
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+
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+ <li ><a href="#method-c-circle">::circle</a>
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+ <li ><a href="#method-c-directed">::directed</a>
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+ <li ><a href="#method-c-down_triangle">::down_triangle</a>
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+ <li ><a href="#method-c-generic">::generic</a>
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+ <li ><a href="#method-c-gradient">::gradient</a>
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+ <li ><a href="#method-c-gradients">::gradients</a>
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+ <li ><a href="#method-c-label">::label</a>
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+ <li ><a href="#method-c-scale">::scale</a>
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+ <li ><a href="#method-c-span">::span</a>
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+ <li ><a href="#method-c-transcript">::transcript</a>
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+
96
+ <li ><a href="#method-c-up_triangle">::up_triangle</a>
97
+
98
+ </ul>
99
+ </nav>
100
+
101
+ </div>
102
+
103
+ <div id="project-metadata">
104
+ <nav id="fileindex-section" class="section project-section">
105
+ <h3 class="section-header">Pages</h3>
106
+
107
+ <ul>
108
+
109
+ <li class="file"><a href="../../LICENSE_txt.html">LICENSE</a>
110
+
111
+ </ul>
112
+ </nav>
113
+
114
+ <nav id="classindex-section" class="section project-section">
115
+ <h3 class="section-header">Class and Module Index</h3>
116
+
117
+ <ul class="link-list">
118
+
119
+ <li><a href="../../Bio.html">Bio</a>
120
+
121
+ <li><a href="../../Bio/Graphics.html">Bio::Graphics</a>
122
+
123
+ <li><a href="../../Bio/Graphics/Glyph.html">Bio::Graphics::Glyph</a>
124
+
125
+ <li><a href="../../Bio/Graphics/MiniFeature.html">Bio::Graphics::MiniFeature</a>
126
+
127
+ <li><a href="../../Bio/Graphics/Page.html">Bio::Graphics::Page</a>
128
+
129
+ <li><a href="../../Bio/Graphics/Primitive.html">Bio::Graphics::Primitive</a>
130
+
131
+ <li><a href="../../Bio/Graphics/SVGEE.html">Bio::Graphics::SVGEE</a>
132
+
133
+ <li><a href="../../Bio/Graphics/Track.html">Bio::Graphics::Track</a>
134
+
135
+ </ul>
136
+ </nav>
137
+
138
+ </div>
139
+ </nav>
140
+
141
+ <div id="documentation">
142
+ <h1 class="class">class Bio::Graphics::Glyph</h1>
143
+
144
+ <div id="description" class="description">
145
+
146
+ <p>A <a href="Glyph.html">Glyph</a> is an array of <a
147
+ href="Primitive.html">Primitive</a> objects, holding information about the
148
+ type of <a href="Glyph.html">Glyph</a> being created. Each different type
149
+ of <a href="Glyph.html">Glyph</a> has different arguments, pertaining to
150
+ how the <a href="Glyph.html">Glyph</a> will be drawn and the parameters
151
+ provided to <a href="SVGEE.html">SVGEE</a>.</p>
152
+
153
+ </div><!-- description -->
154
+
155
+
156
+
157
+
158
+ <section id="5Buntitled-5D" class="documentation-section">
159
+
160
+
161
+
162
+
163
+
164
+
165
+
166
+ <!-- Attributes -->
167
+ <section id="attribute-method-details" class="method-section section">
168
+ <h3 class="section-header">Attributes</h3>
169
+
170
+
171
+ <div id="attribute-i-glyphs" class="method-detail">
172
+ <div class="method-heading attribute-method-heading">
173
+ <span class="method-name">glyphs</span><span
174
+ class="attribute-access-type">[R]</span>
175
+ </div>
176
+
177
+ <div class="method-description">
178
+
179
+ <p>The different type of Glyphs are:</p>
180
+ <ul><li>
181
+ <p>generic</p>
182
+ </li><li>
183
+ <p>circle</p>
184
+ </li><li>
185
+ <p>directed</p>
186
+ </li><li>
187
+ <p>down_triangle</p>
188
+ </li><li>
189
+ <p>up_triangle</p>
190
+ </li><li>
191
+ <p>span</p>
192
+ </li><li>
193
+ <p>transcript</p>
194
+ </li><li>
195
+ <p>scale</p>
196
+ </li><li>
197
+ <p>label</p>
198
+ </li><li>
199
+ <p>histogram</p>
200
+ </li></ul>
201
+
202
+ </div>
203
+ </div>
204
+
205
+ </section><!-- attribute-method-details -->
206
+
207
+
208
+ <!-- Methods -->
209
+
210
+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
211
+ <h3 class="section-header">Public Class Methods</h3>
212
+
213
+
214
+ <div id="method-c-circle" class="method-detail ">
215
+
216
+ <div class="method-heading">
217
+ <span class="method-name">circle</span><span
218
+ class="method-args">(args)</span>
219
+
220
+ <span class="method-click-advice">click to toggle source</span>
221
+
222
+ </div>
223
+
224
+
225
+ <div class="method-description">
226
+
227
+ <p>Creates a circular <a href="Glyph.html">Glyph</a></p>
228
+
229
+ <p><code>args</code></p>
230
+ <ul><li>
231
+ <p>radius = the radius of the circle (10)</p>
232
+ </li><li>
233
+ <p>fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
234
+ (‘red’)</p>
235
+ </li><li>
236
+ <p>stroke = the outline colour of the <a href="Glyph.html">Glyph</a>
237
+ (“black”)</p>
238
+ </li><li>
239
+ <p>stroke_width = The width of the outline stroke (1)</p>
240
+ </li><li>
241
+ <p>style = the opacity of the fill color</p>
242
+ </li><li>
243
+ <p>x = x-axis centre of the circle</p>
244
+ </li><li>
245
+ <p>y = y-axis centre of the circle</p>
246
+ </li></ul>
247
+
248
+
249
+
250
+
251
+ <div class="method-source-code" id="circle-source">
252
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 60</span>
253
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">circle</span>(<span class="ruby-identifier">args</span>)
254
+ <span class="ruby-identifier">args</span> = {
255
+ <span class="ruby-value">:radius</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
256
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'red'</span>,
257
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
258
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
259
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
260
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:x_center</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-value">:x</span>]
261
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:y_center</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>]
262
+ [<span class="ruby-value">:x</span>, <span class="ruby-value">:y</span>].<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">e</span><span class="ruby-operator">|</span> <span class="ruby-identifier">args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">e</span>)}
263
+ [<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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:circle</span>, <span class="ruby-identifier">args</span>)]
264
+ <span class="ruby-keyword">end</span></pre>
265
+ </div><!-- circle-source -->
266
+
267
+ </div>
268
+
269
+
270
+
271
+
272
+ </div><!-- circle-method -->
273
+
274
+
275
+ <div id="method-c-directed" class="method-detail ">
276
+
277
+ <div class="method-heading">
278
+ <span class="method-name">directed</span><span
279
+ class="method-args">(args)</span>
280
+
281
+ <span class="method-click-advice">click to toggle source</span>
282
+
283
+ </div>
284
+
285
+
286
+ <div class="method-description">
287
+
288
+ <p>Creates a polygon <a href="Glyph.html">Glyph</a> to indicate the direction
289
+ in which the <a href="Glyph.html">Glyph</a> is pointing <code>args</code></p>
290
+ <ul><li>
291
+ <p>width = the width of the feature</p>
292
+ </li><li>
293
+ <p>fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
294
+ (‘red’)</p>
295
+ </li><li>
296
+ <p>stroke = the outline colour of the <a href="Glyph.html">Glyph</a>
297
+ (“black”)</p>
298
+ </li><li>
299
+ <p>stroke_width = The width of the outline stroke (1)</p>
300
+ </li><li>
301
+ <p>style = the opacity of the fill color</p>
302
+ </li><li>
303
+ <p>strand = the strand on which the <a href="Glyph.html">Glyph</a> is located.
304
+ May be ‘+’ or ‘-’</p>
305
+ </li><li>
306
+ <p>points = the x and y axis points used to calculate the shape of the polygon</p>
307
+ </li><li>
308
+ <p>x = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the x-axis</p>
309
+ </li><li>
310
+ <p>y = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the y-axis</p>
311
+ </li></ul>
312
+
313
+ <p>The points of the polygon are calculated form the <code>x</code> and
314
+ <code>y</code> co-ordinates</p>
315
+
316
+
317
+
318
+
319
+ <div class="method-source-code" id="directed-source">
320
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 85</span>
321
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
322
+ <span class="ruby-identifier">args</span> = {
323
+
324
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
325
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'red'</span>,
326
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
327
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
328
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;fill-opacity:0.4;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
329
+
330
+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'-'</span>
331
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:points</span>] = <span class="ruby-node">&quot;#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + args[:height] } #{args[:x]},#{args[:y] + (args[:height])} #{args[:x] - (args[:height] * 0.2)},#{args[:y] + (args[:height]/2)}&quot;</span>
332
+ <span class="ruby-keyword">else</span>
333
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:points</span>] = <span class="ruby-node">&quot;#{args[:x]},#{args[:y]} #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + (args[:height]/2) } #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y] + args[:height]} #{args[:x]},#{args[:y] + args[:height]}&quot;</span>
334
+
335
+ <span class="ruby-keyword">end</span>
336
+ [<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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:polygon</span>, <span class="ruby-identifier">args</span>)]
337
+ <span class="ruby-keyword">end</span></pre>
338
+ </div><!-- directed-source -->
339
+
340
+ </div>
341
+
342
+
343
+
344
+
345
+ </div><!-- directed-method -->
346
+
347
+
348
+ <div id="method-c-down_triangle" class="method-detail ">
349
+
350
+ <div class="method-heading">
351
+ <span class="method-name">down_triangle</span><span
352
+ class="method-args">(args)</span>
353
+
354
+ <span class="method-click-advice">click to toggle source</span>
355
+
356
+ </div>
357
+
358
+
359
+ <div class="method-description">
360
+
361
+ <p>Creates a polygon <a href="Glyph.html">Glyph</a> for a downward-pointing
362
+ triangle <code>args</code></p>
363
+ <ul><li>
364
+ <p>height = the height of the <a href="Glyph.html">Glyph</a> (10)</p>
365
+ </li><li>
366
+ <p>fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
367
+ (‘red’)</p>
368
+ </li><li>
369
+ <p>stroke = the outline colour of the <a href="Glyph.html">Glyph</a>
370
+ (“black”)</p>
371
+ </li><li>
372
+ <p>stroke_width = The width of the outline stroke (1)</p>
373
+ </li><li>
374
+ <p>style = the opacity of the fill color (“fill-opacity:0.4;”)</p>
375
+ </li><li>
376
+ <p>x = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the x-axis</p>
377
+ </li><li>
378
+ <p>y = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the y-axis</p>
379
+ </li></ul>
380
+
381
+ <p>The points of the triangle are calculated form the <code>x</code> and
382
+ <code>y</code> co-ordinates</p>
383
+
384
+
385
+
386
+
387
+ <div class="method-source-code" id="down_triangle-source">
388
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 113</span>
389
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">down_triangle</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
390
+ <span class="ruby-identifier">args</span> = {
391
+
392
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
393
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'red'</span>,
394
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
395
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
396
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;fill-opacity:0.4;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
397
+
398
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:points</span>] = <span class="ruby-node">&quot;#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{ args[:x] + (args[:width]/2) },#{(args[:y] + args[:height]) }&quot;</span>
399
+ [<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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:polygon</span>, <span class="ruby-identifier">args</span>)]
400
+ <span class="ruby-keyword">end</span></pre>
401
+ </div><!-- down_triangle-source -->
402
+
403
+ </div>
404
+
405
+
406
+
407
+
408
+ </div><!-- down_triangle-method -->
409
+
410
+
411
+ <div id="method-c-generic" class="method-detail ">
412
+
413
+ <div class="method-heading">
414
+ <span class="method-name">generic</span><span
415
+ class="method-args">(args)</span>
416
+
417
+ <span class="method-click-advice">click to toggle source</span>
418
+
419
+ </div>
420
+
421
+
422
+ <div class="method-description">
423
+
424
+ <p>Creates a generic glyph, which is a rectangle</p>
425
+
426
+ <p><code>args</code></p>
427
+ <ul><li>
428
+ <p>height = the height of the <a href="Glyph.html">Glyph</a> (10)</p>
429
+ </li><li>
430
+ <p>fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
431
+ (‘red’)</p>
432
+ </li><li>
433
+ <p>stroke = the outline colour of the <a href="Glyph.html">Glyph</a>
434
+ (“black”)</p>
435
+ </li><li>
436
+ <p>stroke_width = The width of the outline stroke (1)</p>
437
+ </li><li>
438
+ <p>x_round = x-axis radius of the ellipse used to round off the corners of the
439
+ rectangle (1)</p>
440
+ </li><li>
441
+ <p>y_round = y-axis radius of the ellipse used to round off the corners of the
442
+ rectangle (1)</p>
443
+ </li><li>
444
+ <p>style = the opacity of the fill color (“fill-opacity:0.4;”)</p>
445
+ </li><li>
446
+ <p>x = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the x-axis</p>
447
+ </li><li>
448
+ <p>y = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the y-axis</p>
449
+ </li></ul>
450
+
451
+
452
+
453
+
454
+ <div class="method-source-code" id="generic-source">
455
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 37</span>
456
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height, </span>
457
+ <span class="ruby-identifier">args</span> = {
458
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
459
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'red'</span>,
460
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
461
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
462
+ <span class="ruby-value">:x_round</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
463
+ <span class="ruby-value">:y_round</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
464
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;fill-opacity:0.4;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
465
+ [<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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:rectangle</span>, <span class="ruby-identifier">args</span>)]
466
+ <span class="ruby-keyword">end</span></pre>
467
+ </div><!-- generic-source -->
468
+
469
+ </div>
470
+
471
+
472
+
473
+
474
+ </div><!-- generic-method -->
475
+
476
+
477
+ <div id="method-c-gradient" class="method-detail ">
478
+
479
+ <div class="method-heading">
480
+ <span class="method-name">gradient</span><span
481
+ class="method-args">(gradient)</span>
482
+
483
+ <span class="method-click-advice">click to toggle source</span>
484
+
485
+ </div>
486
+
487
+
488
+ <div class="method-description">
489
+
490
+ <p>Sets the the type (linear or radial) and colour of gradient for a
491
+ pre-defined gradient along with the pertinent parameters for that type</p>
492
+
493
+ <p><code>args</code></p>
494
+ <ul><li>
495
+ <p>gradient = a pre-defined gradient</p>
496
+ </li></ul>
497
+
498
+ <p>The types of gradient are:</p>
499
+ <ul><li>
500
+ <p>red_white_h</p>
501
+ </li><li>
502
+ <p>green_white_h</p>
503
+ </li><li>
504
+ <p>blue_white_h</p>
505
+ </li><li>
506
+ <p>yellow_white_h</p>
507
+ </li><li>
508
+ <p>red_white_radial</p>
509
+ </li><li>
510
+ <p>green_white_radial</p>
511
+ </li><li>
512
+ <p>blue_white_radial</p>
513
+ </li><li>
514
+ <p>yellow_white_radial</p>
515
+ </li></ul>
516
+
517
+
518
+
519
+
520
+ <div class="method-source-code" id="gradient-source">
521
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 367</span>
522
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">gradient</span>)
523
+ <span class="ruby-identifier">type</span>, <span class="ruby-identifier">color</span> = <span class="ruby-keyword">case</span> <span class="ruby-identifier">gradient</span>
524
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:red_white_h</span>
525
+ [<span class="ruby-value">:linear</span>, <span class="ruby-string">&quot;red&quot;</span>]
526
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:green_white_h</span>
527
+ [<span class="ruby-value">:linear</span>, <span class="ruby-string">&quot;green&quot;</span>]
528
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:blue_white_h</span>
529
+ [<span class="ruby-value">:linear</span>, <span class="ruby-string">&quot;blue&quot;</span>]
530
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:yellow_white_h</span>
531
+ [<span class="ruby-value">:linear</span>, <span class="ruby-string">&quot;yellow&quot;</span>]
532
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:red_white_radial</span>
533
+ [<span class="ruby-value">:radial</span>, <span class="ruby-string">&quot;red&quot;</span>]
534
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:green_white_radial</span>
535
+ [<span class="ruby-value">:radial</span>, <span class="ruby-string">&quot;green&quot;</span>]
536
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:blue_white_radial</span>
537
+ [<span class="ruby-value">:radial</span>, <span class="ruby-string">&quot;blue&quot;</span>]
538
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:yellow_white_radial</span>
539
+ [<span class="ruby-value">:radial</span>, <span class="ruby-string">&quot;yellow&quot;</span>]
540
+ <span class="ruby-keyword">end</span>
541
+
542
+ <span class="ruby-keyword">case</span> <span class="ruby-identifier">type</span>
543
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:linear</span>
544
+ {<span class="ruby-value">:type</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:linear</span>,
545
+ <span class="ruby-value">:id</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">gradient</span>,
546
+ <span class="ruby-value">:x1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>, <span class="ruby-value">:y1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>,
547
+ <span class="ruby-value">:x2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>, <span class="ruby-value">:y2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">100</span>,
548
+ <span class="ruby-value">:stops</span> =<span class="ruby-operator">&gt;</span> [
549
+ {
550
+ <span class="ruby-value">:color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">color</span>,
551
+ <span class="ruby-value">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>,
552
+ <span class="ruby-value">:opacity=</span><span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>
553
+ },
554
+ {
555
+ <span class="ruby-value">:color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;white&quot;</span>,
556
+ <span class="ruby-value">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">100</span>,
557
+ <span class="ruby-value">:opacity=</span><span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>
558
+ }
559
+ ]
560
+ }
561
+ <span class="ruby-keyword">when</span> <span class="ruby-value">:radial</span>
562
+ {
563
+ <span class="ruby-value">:type</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:radial</span>,
564
+ <span class="ruby-value">:id</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">gradient</span>,
565
+ <span class="ruby-value">:cx</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>, <span class="ruby-value">:cy</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>,
566
+ <span class="ruby-value">:r</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>, <span class="ruby-value">:fx</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>, <span class="ruby-value">:fy</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">50</span>,
567
+ <span class="ruby-value">:stops</span> =<span class="ruby-operator">&gt;</span> [
568
+ {<span class="ruby-value">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>,
569
+ <span class="ruby-value">:color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;white&quot;</span>,
570
+ <span class="ruby-value">:opacity</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
571
+ },
572
+ {
573
+ <span class="ruby-value">:offset</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">100</span>,
574
+ <span class="ruby-value">:color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">color</span>,
575
+ <span class="ruby-value">:opacity</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>
576
+ }
577
+ ]
578
+ }
579
+ <span class="ruby-keyword">end</span>
580
+
581
+ <span class="ruby-keyword">end</span></pre>
582
+ </div><!-- gradient-source -->
583
+
584
+ </div>
585
+
586
+
587
+
588
+
589
+ </div><!-- gradient-method -->
590
+
591
+
592
+ <div id="method-c-gradients" class="method-detail ">
593
+
594
+ <div class="method-heading">
595
+ <span class="method-name">gradients</span><span
596
+ class="method-args">()</span>
597
+
598
+ <span class="method-click-advice">click to toggle source</span>
599
+
600
+ </div>
601
+
602
+
603
+ <div class="method-description">
604
+
605
+ <p>The list of pre-defined gradients</p>
606
+
607
+
608
+
609
+
610
+ <div class="method-source-code" id="gradients-source">
611
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 348</span>
612
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">gradients</span> <span class="ruby-comment">#needs to know which of its gradients are predefined</span>
613
+ [<span class="ruby-value">:red_white_h</span>, <span class="ruby-value">:green_white_h</span>, <span class="ruby-value">:blue_white_h</span>, <span class="ruby-value">:yellow_white_h</span>, <span class="ruby-value">:red_white_radial</span>, <span class="ruby-value">:green_white_radial</span>, <span class="ruby-value">:blue_white_radial</span>, <span class="ruby-value">:yellow_white_radial</span> ]
614
+ <span class="ruby-keyword">end</span></pre>
615
+ </div><!-- gradients-source -->
616
+
617
+ </div>
618
+
619
+
620
+
621
+
622
+ </div><!-- gradients-method -->
623
+
624
+
625
+ <div id="method-c-label" class="method-detail ">
626
+
627
+ <div class="method-heading">
628
+ <span class="method-name">label</span><span
629
+ class="method-args">(args)</span>
630
+
631
+ <span class="method-click-advice">click to toggle source</span>
632
+
633
+ </div>
634
+
635
+
636
+ <div class="method-description">
637
+
638
+ <p>Creates a label <a href="Glyph.html">Glyph</a> to write text</p>
639
+
640
+ <p><code>args</code></p>
641
+ <ul><li>
642
+ <p>text = the text to write</p>
643
+ </li><li>
644
+ <p>fill = the colour of the text (“black”)</p>
645
+ </li><li>
646
+ <p>style = the style of writing (“font-family:monospace;”)</p>
647
+ </li><li>
648
+ <p>x = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the x-axis</p>
649
+ </li><li>
650
+ <p>y = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the y-axis</p>
651
+ </li></ul>
652
+
653
+
654
+
655
+
656
+ <div class="method-source-code" id="label-source">
657
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 339</span>
658
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">label</span>(<span class="ruby-identifier">args</span>)
659
+ [<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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:text</span>,
660
+ <span class="ruby-value">:text</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:text</span>],
661
+ <span class="ruby-value">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:x</span>],
662
+ <span class="ruby-value">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>],
663
+ <span class="ruby-value">:fill</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
664
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;font-family:monospace;&quot;</span>)]
665
+ <span class="ruby-keyword">end</span></pre>
666
+ </div><!-- label-source -->
667
+
668
+ </div>
669
+
670
+
671
+
672
+
673
+ </div><!-- label-method -->
674
+
675
+
676
+ <div id="method-c-scale" class="method-detail ">
677
+
678
+ <div class="method-heading">
679
+ <span class="method-name">scale</span><span
680
+ class="method-args">(args)</span>
681
+
682
+ <span class="method-click-advice">click to toggle source</span>
683
+
684
+ </div>
685
+
686
+
687
+ <div class="method-description">
688
+
689
+ <p>Creates the scale across the top of the SVG page</p>
690
+
691
+ <p><code>args</code></p>
692
+ <ul><li>
693
+ <p>start = the start of the scale</p>
694
+ </li><li>
695
+ <p>stop = the end of the scale</p>
696
+ </li><li>
697
+ <p>number_of_intervals = the number of tick-marks on the scale to show the
698
+ current position</p>
699
+ </li><li>
700
+ <p>page_width = the width of the page</p>
701
+ </li></ul>
702
+
703
+ <p><code>returns</code></p>
704
+ <ul><li>
705
+ <p>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of <a
706
+ href="Primitive.html">Primitive</a> objects (of type ‘line’,
707
+ ‘rectangle’ and ‘text’)</p>
708
+ </li></ul>
709
+
710
+
711
+
712
+
713
+ <div class="method-source-code" id="scale-source">
714
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 294</span>
715
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">scale</span>(<span class="ruby-identifier">args</span>)
716
+ <span class="ruby-identifier">first_mark</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:start</span>]
717
+ <span class="ruby-identifier">last_mark</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:stop</span>]
718
+ <span class="ruby-comment">#(num.to_f / @nt_per_px_x.to_f)</span>
719
+ <span class="ruby-identifier">full_dist</span> = <span class="ruby-identifier">last_mark</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">first_mark</span>
720
+ <span class="ruby-identifier">interval_width</span> = <span class="ruby-identifier">full_dist</span> <span class="ruby-operator">/</span> (<span class="ruby-identifier">args</span>[<span class="ruby-value">:number_of_intervals</span>] <span class="ruby-operator">-</span> <span class="ruby-value">1</span>)
721
+
722
+
723
+ <span class="ruby-identifier">a</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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:line</span>,
724
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'black'</span>,
725
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
726
+ <span class="ruby-value">:x1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>, <span class="ruby-value">:x2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:page_width</span>],<span class="ruby-comment"># * 1.1, </span>
727
+ <span class="ruby-value">:y1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;20&quot;</span>, <span class="ruby-value">:y2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;20&quot;</span> )]
728
+
729
+
730
+ <span class="ruby-identifier">marks</span> = (<span class="ruby-identifier">first_mark</span><span class="ruby-operator">..</span><span class="ruby-identifier">last_mark</span>).<span class="ruby-identifier">step</span>(<span class="ruby-identifier">interval_width</span>).<span class="ruby-identifier">to_a</span>
731
+
732
+ <span class="ruby-identifier">px_per_nt</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:page_width</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">full_dist</span>.<span class="ruby-identifier">to_f</span>
733
+ <span class="ruby-identifier">marks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">mark</span><span class="ruby-operator">|</span>
734
+ <span class="ruby-identifier">x</span> = (<span class="ruby-identifier">mark</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">first_mark</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">px_per_nt</span>
735
+ <span class="ruby-identifier">a</span> <span class="ruby-operator">&lt;&lt;</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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:rectangle</span>,
736
+ <span class="ruby-value">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">x</span>,
737
+ <span class="ruby-value">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">20</span>,
738
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'black'</span>,
739
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
740
+ <span class="ruby-value">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
741
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">5</span> )
742
+
743
+ <span class="ruby-identifier">a</span> <span class="ruby-operator">&lt;&lt;</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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:text</span>,
744
+ <span class="ruby-value">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">x</span>,
745
+ <span class="ruby-value">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">40</span>, <span class="ruby-value">:fill</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'black'</span>,
746
+ <span class="ruby-value">:text</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">mark</span>,
747
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;font-family:Arial;font-style:italic&quot;</span>)
748
+ <span class="ruby-keyword">end</span>
749
+ <span class="ruby-keyword">return</span> <span class="ruby-identifier">a</span>
750
+ <span class="ruby-keyword">end</span></pre>
751
+ </div><!-- scale-source -->
752
+
753
+ </div>
754
+
755
+
756
+
757
+
758
+ </div><!-- scale-method -->
759
+
760
+
761
+ <div id="method-c-span" class="method-detail ">
762
+
763
+ <div class="method-heading">
764
+ <span class="method-name">span</span><span
765
+ class="method-args">(args)</span>
766
+
767
+ <span class="method-click-advice">click to toggle source</span>
768
+
769
+ </div>
770
+
771
+
772
+ <div class="method-description">
773
+
774
+ <p>Creates a span glyph, which is a line</p>
775
+
776
+ <p><code>args</code></p>
777
+ <ul><li>
778
+ <p>height = the height of the <a href="Glyph.html">Glyph</a> (10)</p>
779
+ </li><li>
780
+ <p>fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
781
+ (‘red’)</p>
782
+ </li><li>
783
+ <p>stroke = the outline colour of the <a href="Glyph.html">Glyph</a>
784
+ (“black”)</p>
785
+ </li><li>
786
+ <p>stroke_width = The width of the outline stroke (1)</p>
787
+ </li><li>
788
+ <p>style = the opacity of the fill color (“fill-opacity:0.4;”)</p>
789
+ </li><li>
790
+ <p>x = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the x-axis</p>
791
+ </li><li>
792
+ <p>y = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the y-axis</p>
793
+ </li></ul>
794
+
795
+
796
+
797
+
798
+ <div class="method-source-code" id="span-source">
799
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 156</span>
800
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">span</span>(<span class="ruby-identifier">args</span>)
801
+ <span class="ruby-identifier">args</span> = {
802
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
803
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'red'</span>,
804
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
805
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
806
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;fill-opacity:1;&quot;</span>
807
+ }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
808
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:x1</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-value">:x</span>]
809
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:x2</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-value">:x</span>] <span class="ruby-operator">+</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:width</span>]
810
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:y1</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>]
811
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:y2</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>]
812
+ [<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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:line</span>, <span class="ruby-identifier">args</span>)]
813
+ <span class="ruby-keyword">end</span></pre>
814
+ </div><!-- span-source -->
815
+
816
+ </div>
817
+
818
+
819
+
820
+
821
+ </div><!-- span-method -->
822
+
823
+
824
+ <div id="method-c-transcript" class="method-detail ">
825
+
826
+ <div class="method-heading">
827
+ <span class="method-name">transcript</span><span
828
+ class="method-args">(args)</span>
829
+
830
+ <span class="method-click-advice">click to toggle source</span>
831
+
832
+ </div>
833
+
834
+
835
+ <div class="method-description">
836
+
837
+ <p>Creates a transcript glyph, which is a number of different types of <a
838
+ href="Glyph.html">Glyph</a>, depending on the features within the
839
+ transcript</p>
840
+
841
+ <p><code>args</code></p>
842
+ <ul><li>
843
+ <p>height = the height of the <a href="Glyph.html">Glyph</a> (10)</p>
844
+ </li><li>
845
+ <p>utr_fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
846
+ (‘black’)</p>
847
+ </li><li>
848
+ <p>utr_stroke = the outline colour of the <a href="Glyph.html">Glyph</a>
849
+ (“black”)</p>
850
+ </li><li>
851
+ <p>utr_stroke_width = The width of the outline stroke (1)</p>
852
+ </li><li>
853
+ <p>exon_fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
854
+ (‘red’)</p>
855
+ </li><li>
856
+ <p>exon_stroke = the outline colour of the <a href="Glyph.html">Glyph</a>
857
+ (“black”)</p>
858
+ </li><li>
859
+ <p>exon_stroke_width = The width of the outline stroke (1)</p>
860
+ </li><li>
861
+ <p>line_color = the colour for any line Glyphs</p>
862
+ </li><li>
863
+ <p>line_width = the width for any line Glyphs</p>
864
+ </li><li>
865
+ <p>exon_style = the opacity of the fill color for exons
866
+ (“fill-opacity:0.4;”)</p>
867
+ </li><li>
868
+ <p>utr_style = the opacity of the fill color for utrs</p>
869
+ </li><li>
870
+ <p>line_style = the opacity of the fill color for lines</p>
871
+ </li><li>
872
+ <p>block_gaps = ****I’m not sure what these are****</p>
873
+ </li><li>
874
+ <p>gap_marker = ****I’m not sure what these are****</p>
875
+ </li><li>
876
+ <p>x = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the x-axis</p>
877
+ </li><li>
878
+ <p>y = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the y-axis</p>
879
+ </li></ul>
880
+
881
+
882
+
883
+
884
+ <div class="method-source-code" id="transcript-source">
885
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 190</span>
886
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">transcript</span>(<span class="ruby-identifier">args</span>)
887
+ <span class="ruby-identifier">args</span> = {
888
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
889
+ <span class="ruby-value">:utr_fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'black'</span>,
890
+ <span class="ruby-value">:utr_stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
891
+ <span class="ruby-value">:utr_stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
892
+ <span class="ruby-value">:exon_fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'red'</span>,
893
+ <span class="ruby-value">:exon_stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
894
+ <span class="ruby-value">:exon_stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
895
+ <span class="ruby-value">:line_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'black'</span>,
896
+ <span class="ruby-value">:line_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
897
+ <span class="ruby-value">:exon_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;fill-opacity:0.4;&quot;</span>,
898
+ <span class="ruby-value">:utr_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;&quot;</span>,
899
+ <span class="ruby-value">:line_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;&quot;</span>,
900
+ <span class="ruby-value">:block_gaps</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;&quot;</span>,
901
+ <span class="ruby-value">:gap_marker</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;&quot;</span>
902
+ }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
903
+
904
+ <span class="ruby-identifier">composite</span> = []
905
+
906
+ <span class="ruby-keyword">if</span> <span class="ruby-keyword">not</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utrs</span>].<span class="ruby-identifier">empty?</span> <span class="ruby-comment">##draw the utr as terminal element...##terminal utr is the one with the point on...</span>
907
+ <span class="ruby-identifier">x</span>,<span class="ruby-identifier">width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'-'</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utrs</span>].<span class="ruby-identifier">shift</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utrs</span>].<span class="ruby-identifier">pop</span>
908
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-value">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">x</span>,
909
+ <span class="ruby-value">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>],
910
+ <span class="ruby-value">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">width</span>,
911
+ <span class="ruby-value">:strand</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:strand</span>],
912
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:height</span>],
913
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utr_fill_color</span>],
914
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span><span class="ruby-identifier">args</span>[<span class="ruby-value">:utr_stroke</span>],
915
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utr_stroke_width</span>],
916
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utr_style</span>] )
917
+ <span class="ruby-comment">##draw the other(s!) </span>
918
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:utrs</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">utr</span><span class="ruby-operator">|</span>
919
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">&lt;&lt;</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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:rectangle</span>, {
920
+ <span class="ruby-value">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">first</span>,
921
+ <span class="ruby-value">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">last</span>,
922
+ <span class="ruby-value">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>],
923
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:height</span>],
924
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utr_fill_color</span>],
925
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span><span class="ruby-identifier">args</span>[<span class="ruby-value">:utr_stroke</span>],
926
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utr_stroke_width</span>],
927
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:utr_style</span>]} )
928
+ <span class="ruby-keyword">end</span>
929
+ <span class="ruby-keyword">else</span> <span class="ruby-comment">## draw the terminal exon as terminal element </span>
930
+ <span class="ruby-identifier">points</span> = <span class="ruby-keyword">nil</span>
931
+ <span class="ruby-identifier">x</span>,<span class="ruby-identifier">width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'-'</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:exons</span>].<span class="ruby-identifier">shift</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:exons</span>].<span class="ruby-identifier">pop</span>
932
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-value">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">x</span>,
933
+ <span class="ruby-value">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>],
934
+ <span class="ruby-value">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">width</span>,
935
+ <span class="ruby-value">:strand</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:strand</span>],
936
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:height</span>],
937
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:exon_fill_color</span>],
938
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span><span class="ruby-identifier">args</span>[<span class="ruby-value">:exon_stroke</span>],
939
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:exon_stroke_width</span>],
940
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:exon_style</span>] )
941
+ <span class="ruby-keyword">end</span>
942
+ <span class="ruby-comment">#draw any remaining exons</span>
943
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:exons</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">exon</span><span class="ruby-operator">|</span>
944
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">&lt;&lt;</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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:rectangle</span>, {
945
+ <span class="ruby-value">:x</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>],
946
+ <span class="ruby-value">:width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">exon</span>[<span class="ruby-value">1</span>],
947
+ <span class="ruby-value">:y</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>],
948
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:height</span>],
949
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:exon_fill_color</span>],
950
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span><span class="ruby-identifier">args</span>[<span class="ruby-value">:exon_stroke</span>],
951
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:exon_stroke_width</span>],
952
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:exon_style</span>]} )
953
+ <span class="ruby-keyword">end</span>
954
+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:gap_marker</span>] <span class="ruby-operator">==</span> <span class="ruby-string">&quot;angled&quot;</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">not</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:block_gaps</span>].<span class="ruby-identifier">empty?</span>
955
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:block_gaps</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap</span><span class="ruby-operator">|</span>
956
+ <span class="ruby-identifier">points</span> = <span class="ruby-node">&quot;#{gap.first},#{args[:y] + (args[:height]/2) } #{gap.first + (gap.last/2)},#{args[:y]} #{gap.first + gap.last},#{args[:y] + (args[:height]/2)}&quot;</span>
957
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">&lt;&lt;</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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:polyline</span>, {
958
+ <span class="ruby-value">:points</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">points</span>,
959
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:line_color</span>],
960
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:line_width</span>],
961
+ <span class="ruby-value">:fill</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;none&quot;</span>,
962
+ <span class="ruby-value">:line_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:line_style</span>]})
963
+ <span class="ruby-keyword">end</span>
964
+ <span class="ruby-keyword">else</span>
965
+ <span class="ruby-comment">#add line</span>
966
+ <span class="ruby-identifier">composite</span> <span class="ruby-operator">&lt;&lt;</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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:line</span>, {
967
+ <span class="ruby-value">:x1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:x</span>],
968
+ <span class="ruby-value">:x2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{args[:x] + args[:width]}&quot;</span>,
969
+ <span class="ruby-value">:y1</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>] <span class="ruby-operator">+</span> (<span class="ruby-identifier">args</span>[<span class="ruby-value">:height</span>]<span class="ruby-operator">/</span><span class="ruby-value">2</span>),
970
+ <span class="ruby-value">:y2</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>] <span class="ruby-operator">+</span> (<span class="ruby-identifier">args</span>[<span class="ruby-value">:height</span>]<span class="ruby-operator">/</span><span class="ruby-value">2</span>),
971
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:line_color</span>],
972
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:line_width</span>],
973
+ <span class="ruby-value">:line_style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:line_style</span>]})
974
+
975
+ <span class="ruby-keyword">end</span>
976
+ <span class="ruby-identifier">composite</span>
977
+ <span class="ruby-keyword">end</span></pre>
978
+ </div><!-- transcript-source -->
979
+
980
+ </div>
981
+
982
+
983
+
984
+
985
+ </div><!-- transcript-method -->
986
+
987
+
988
+ <div id="method-c-up_triangle" class="method-detail ">
989
+
990
+ <div class="method-heading">
991
+ <span class="method-name">up_triangle</span><span
992
+ class="method-args">(args)</span>
993
+
994
+ <span class="method-click-advice">click to toggle source</span>
995
+
996
+ </div>
997
+
998
+
999
+ <div class="method-description">
1000
+
1001
+ <p>Creates a polygon <a href="Glyph.html">Glyph</a> for an upward-pointing
1002
+ triangle <code>args</code></p>
1003
+ <ul><li>
1004
+ <p>height = the height of the <a href="Glyph.html">Glyph</a> (10)</p>
1005
+ </li><li>
1006
+ <p>fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
1007
+ (‘red’)</p>
1008
+ </li><li>
1009
+ <p>stroke = the outline colour of the <a href="Glyph.html">Glyph</a>
1010
+ (“black”)</p>
1011
+ </li><li>
1012
+ <p>stroke_width = The width of the outline stroke (1)</p>
1013
+ </li><li>
1014
+ <p>style = the opacity of the fill color (“fill-opacity:0.4;”)</p>
1015
+ </li><li>
1016
+ <p>x = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the x-axis</p>
1017
+ </li><li>
1018
+ <p>y = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the y-axis</p>
1019
+ </li></ul>
1020
+
1021
+ <p>The points of the triangle are calculated form the <code>x</code> and
1022
+ <code>y</code> co-ordinates</p>
1023
+
1024
+
1025
+
1026
+
1027
+ <div class="method-source-code" id="up_triangle-source">
1028
+ <pre><span class="ruby-comment"># File lib/bio/graphics/glyph.rb, line 136</span>
1029
+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">up_triangle</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
1030
+ <span class="ruby-identifier">args</span> = {
1031
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
1032
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'red'</span>,
1033
+ <span class="ruby-value">:stroke</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;black&quot;</span>,
1034
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
1035
+ <span class="ruby-value">:style</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&quot;fill-opacity:0.4;&quot;</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
1036
+ <span class="ruby-identifier">args</span>[<span class="ruby-value">:points</span>] = <span class="ruby-node">&quot;#{args[:x]},#{args[:y] + args[:height]} #{args[:x] + args[:width]},#{args[:y] + args[:height]} #{ args[:x] + (args[:width]/2) },#{args[:y] }&quot;</span>
1037
+ [<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">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:polygon</span>, <span class="ruby-identifier">args</span>)]
1038
+ <span class="ruby-keyword">end</span></pre>
1039
+ </div><!-- up_triangle-source -->
1040
+
1041
+ </div>
1042
+
1043
+
1044
+
1045
+
1046
+ </div><!-- up_triangle-method -->
1047
+
1048
+
1049
+ </section><!-- public-class-method-details -->
1050
+
1051
+ </section><!-- 5Buntitled-5D -->
1052
+
1053
+ </div><!-- documentation -->
1054
+
1055
+
1056
+ <footer id="validator-badges">
1057
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
1058
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.rc.2.1.
1059
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
1060
+ </footer>
1061
+