bio-graphics 1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (63) hide show
  1. data/doc/classes/Bio.html +135 -0
  2. data/doc/classes/Bio/Graphics.html +247 -0
  3. data/doc/classes/Bio/Graphics/Panel.html +344 -0
  4. data/doc/classes/Bio/Graphics/Panel.src/M000005.html +29 -0
  5. data/doc/classes/Bio/Graphics/Panel.src/M000006.html +19 -0
  6. data/doc/classes/Bio/Graphics/Panel.src/M000007.html +67 -0
  7. data/doc/classes/Bio/Graphics/Panel/Ruler.html +238 -0
  8. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +20 -0
  9. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +28 -0
  10. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +54 -0
  11. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +20 -0
  12. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +28 -0
  13. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +59 -0
  14. data/doc/classes/Bio/Graphics/Panel/Track.html +342 -0
  15. data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +23 -0
  16. data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +42 -0
  17. data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +285 -0
  18. data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +23 -0
  19. data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +43 -0
  20. data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +259 -0
  21. data/doc/classes/Bio/Graphics/Panel/Track/Feature.html +292 -0
  22. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +65 -0
  23. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +65 -0
  24. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html +155 -0
  25. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +18 -0
  26. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +18 -0
  27. data/doc/classes/ImageMap.html +185 -0
  28. data/doc/classes/ImageMap.src/M000001.html +18 -0
  29. data/doc/classes/ImageMap.src/M000002.html +24 -0
  30. data/doc/classes/ImageMap/ImageMapElement.html +187 -0
  31. data/doc/classes/ImageMap/ImageMapElement.src/M000003.html +19 -0
  32. data/doc/classes/ImageMap/ImageMapElement.src/M000004.html +20 -0
  33. data/doc/created.rid +1 -0
  34. data/doc/files/README_DEV.html +432 -0
  35. data/doc/files/TUTORIAL.html +358 -0
  36. data/doc/files/lib/bio-graphics_rb.html +121 -0
  37. data/doc/files/lib/bio/graphics/feature_rb.html +113 -0
  38. data/doc/files/lib/bio/graphics/image_map_rb.html +113 -0
  39. data/doc/files/lib/bio/graphics/panel_rb.html +113 -0
  40. data/doc/files/lib/bio/graphics/ruler_rb.html +113 -0
  41. data/doc/files/lib/bio/graphics/track_rb.html +113 -0
  42. data/doc/fr_class_index.html +35 -0
  43. data/doc/fr_file_index.html +34 -0
  44. data/doc/fr_method_index.html +41 -0
  45. data/doc/images/example.png +0 -0
  46. data/doc/images/glyph_showcase.png +0 -0
  47. data/doc/images/terms.png +0 -0
  48. data/doc/images/terms.svg +166 -0
  49. data/doc/index.html +24 -0
  50. data/images/example.png +0 -0
  51. data/images/glyph_showcase.png +0 -0
  52. data/images/terms.png +0 -0
  53. data/images/terms.svg +166 -0
  54. data/lib/bio-graphics.rb +18 -0
  55. data/lib/bio/graphics/feature.rb +136 -0
  56. data/lib/bio/graphics/image_map.rb +37 -0
  57. data/lib/bio/graphics/panel.rb +205 -0
  58. data/lib/bio/graphics/ruler.rb +96 -0
  59. data/lib/bio/graphics/track.rb +387 -0
  60. data/samples/arkdb_features.rb +37 -0
  61. data/samples/data.txt +32 -0
  62. data/samples/glyph_showcase.rb +29 -0
  63. metadata +137 -0
data/doc/files/lib/bio/graphics/feature_rb.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>File: feature.rb</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ elemStyle.display = "none"
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+ }
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="fileHeader">
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+ <h1>feature.rb</h1>
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Path:</strong></td>
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+ <td>lib/bio/graphics/feature.rb
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>Last Update:</strong></td>
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+ <td>Fri Sep 28 20:39:05 +0100 2007</td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <h1>bio/graphics/feature.rb - feature class</h1>
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+ <table>
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+ <tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
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+
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+ </td></tr>
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+ <tr><td valign="top">License:</td><td>The Ruby License
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+
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+ </td></tr>
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+ </table>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+ <!-- if method_list -->
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/files/lib/bio/graphics/image_map_rb.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>File: image_map.rb</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="fileHeader">
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+ <h1>image_map.rb</h1>
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Path:</strong></td>
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+ <td>lib/bio/graphics/image_map.rb
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>Last Update:</strong></td>
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+ <td>Fri Sep 28 20:03:31 +0100 2007</td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <h1>bio/graphics/image_map.rb - create the image map for clickable images</h1>
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+ <table>
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+ <tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
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+
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+ </td></tr>
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+ <tr><td valign="top">License:</td><td>Ruby&#8216;s
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+
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+ </td></tr>
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+ </table>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+ <!-- if method_list -->
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/files/lib/bio/graphics/panel_rb.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>File: panel.rb</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="fileHeader">
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+ <h1>panel.rb</h1>
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Path:</strong></td>
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+ <td>lib/bio/graphics/panel.rb
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>Last Update:</strong></td>
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+ <td>Mon Oct 01 11:00:37 +0100 2007</td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <h1>bio/graphics/panel - panel class</h1>
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+ <table>
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+ <tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
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+
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+ </td></tr>
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+ <tr><td valign="top">License:</td><td>The Ruby License
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+
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+ </td></tr>
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+ </table>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <!-- if method_list -->
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/files/lib/bio/graphics/ruler_rb.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>File: ruler.rb</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="fileHeader">
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+ <h1>ruler.rb</h1>
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Path:</strong></td>
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+ <td>lib/bio/graphics/ruler.rb
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>Last Update:</strong></td>
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+ <td>Sat Sep 29 19:35:12 +0100 2007</td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <h1>bio/graphics/ruler - ruler class</h1>
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+ <table>
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+ <tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
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+
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+ </td></tr>
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+ <tr><td valign="top">License:</td><td>The Ruby License
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+
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+ </td></tr>
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+ </table>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <!-- if method_list -->
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>