bio-graphics 1.0

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  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/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.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>
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+ <head>
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+ <title>new (Bio::Graphics::Panel::Track::Feature::PixelRange)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 127</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>)
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+ <span class="ruby-ivar">@start_pixel</span>, <span class="ruby-ivar">@stop_pixel</span> = <span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.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>
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+ <head>
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+ <title>new (Bio::Graphics::Panel::Track::Feature::PixelRange)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 126</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>)
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+ <span class="ruby-ivar">@start_pixel</span>, <span class="ruby-ivar">@stop_pixel</span> = <span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/ImageMap.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>Class: ImageMap</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="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">ImageMap</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../files/lib/bio/graphics/image_map_rb.html">
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+ lib/bio/graphics/image_map.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ <td>
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+ Object
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+ </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 id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000001">new</a>&nbsp;&nbsp;
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+ <a href="#M000002">to_s</a>&nbsp;&nbsp;
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+ </div>
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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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+ <div id="class-list">
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+ <h3 class="section-bar">Classes and Modules</h3>
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+
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+ Class <a href="ImageMap/ImageMapElement.html" class="link">ImageMap::ImageMapElement</a><br />
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+
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+ </div>
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+
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+
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+
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+
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+ <div id="attribute-list">
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
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+ <table>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">elements</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ </table>
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+ </div>
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+ </div>
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+
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+ <div id="method-M000001" class="method-detail">
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+ <a name="M000001"></a>
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+
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+ <div class="method-heading">
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+ <a href="ImageMap.src/M000001.html" target="Code" class="method-signature"
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+ onclick="popupCode('ImageMap.src/M000001.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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+ </div>
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+
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+ <h3 class="section-bar">Public Instance methods</h3>
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+
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+ <div id="method-M000002" class="method-detail">
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+ <a name="M000002"></a>
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+
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+ <div class="method-heading">
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+ <a href="ImageMap.src/M000002.html" target="Code" class="method-signature"
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+ onclick="popupCode('ImageMap.src/M000002.html');return false;">
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+ <span class="method-name">to_s</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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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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+ <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/classes/ImageMap.src/M000001.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>
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+ <head>
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+ <title>new (ImageMap)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 8</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>
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+ <span class="ruby-ivar">@elements</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/ImageMap.src/M000002.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>
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+ <head>
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+ <title>to_s (ImageMap)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/image_map.rb, line 13</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
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+ <span class="ruby-identifier">output</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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+ <span class="ruby-identifier">output</span>.<span class="ruby-identifier">push</span>(<span class="ruby-value str">'&lt;map name=&quot;image_map&quot; border=&quot;1&quot;&gt;'</span>)
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+ <span class="ruby-ivar">@elements</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">e</span><span class="ruby-operator">|</span>
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+ <span class="ruby-identifier">output</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">e</span>.<span class="ruby-identifier">to_s</span>)
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-identifier">output</span>.<span class="ruby-identifier">push</span>(<span class="ruby-value str">'&lt;/map&gt;'</span>)
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+ <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">output</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">&quot;\n&quot;</span>)
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/ImageMap/ImageMapElement.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>Class: ImageMap::ImageMapElement</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="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">ImageMap::ImageMapElement</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../files/lib/bio/graphics/image_map_rb.html">
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+ lib/bio/graphics/image_map.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ <td>
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+ Object
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+ </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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+
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+
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000003">new</a>&nbsp;&nbsp;
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+ <a href="#M000004">to_s</a>&nbsp;&nbsp;
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+ </div>
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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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+
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+ <div id="attribute-list">
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
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+ <table>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">bottom</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">left</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">right</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">top</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">url</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ </table>
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+ </div>
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+ </div>
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+
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+ <div id="method-M000003" class="method-detail">
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+ <a name="M000003"></a>
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+
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+ <div class="method-heading">
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+ <a href="ImageMapElement.src/M000003.html" target="Code" class="method-signature"
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+ onclick="popupCode('ImageMapElement.src/M000003.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">(left, top, right, bottom, url = nil)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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+ </div>
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+
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+ <h3 class="section-bar">Public Instance methods</h3>
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+
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+ <div id="method-M000004" class="method-detail">
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+ <a name="M000004"></a>
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+
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+ <div class="method-heading">
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+ <a href="ImageMapElement.src/M000004.html" target="Code" class="method-signature"
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+ onclick="popupCode('ImageMapElement.src/M000004.html');return false;">
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+ <span class="method-name">to_s</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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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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+ <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>