bio-graphics 1.0

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Files changed (63) hide show
  1. data/doc/classes/Bio.html +135 -0
  2. data/doc/classes/Bio/Graphics.html +247 -0
  3. data/doc/classes/Bio/Graphics/Panel.html +344 -0
  4. data/doc/classes/Bio/Graphics/Panel.src/M000005.html +29 -0
  5. data/doc/classes/Bio/Graphics/Panel.src/M000006.html +19 -0
  6. data/doc/classes/Bio/Graphics/Panel.src/M000007.html +67 -0
  7. data/doc/classes/Bio/Graphics/Panel/Ruler.html +238 -0
  8. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +20 -0
  9. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +28 -0
  10. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +54 -0
  11. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +20 -0
  12. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +28 -0
  13. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +59 -0
  14. data/doc/classes/Bio/Graphics/Panel/Track.html +342 -0
  15. data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +23 -0
  16. data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +42 -0
  17. data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +285 -0
  18. data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +23 -0
  19. data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +43 -0
  20. data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +259 -0
  21. data/doc/classes/Bio/Graphics/Panel/Track/Feature.html +292 -0
  22. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +65 -0
  23. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +65 -0
  24. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html +155 -0
  25. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +18 -0
  26. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +18 -0
  27. data/doc/classes/ImageMap.html +185 -0
  28. data/doc/classes/ImageMap.src/M000001.html +18 -0
  29. data/doc/classes/ImageMap.src/M000002.html +24 -0
  30. data/doc/classes/ImageMap/ImageMapElement.html +187 -0
  31. data/doc/classes/ImageMap/ImageMapElement.src/M000003.html +19 -0
  32. data/doc/classes/ImageMap/ImageMapElement.src/M000004.html +20 -0
  33. data/doc/created.rid +1 -0
  34. data/doc/files/README_DEV.html +432 -0
  35. data/doc/files/TUTORIAL.html +358 -0
  36. data/doc/files/lib/bio-graphics_rb.html +121 -0
  37. data/doc/files/lib/bio/graphics/feature_rb.html +113 -0
  38. data/doc/files/lib/bio/graphics/image_map_rb.html +113 -0
  39. data/doc/files/lib/bio/graphics/panel_rb.html +113 -0
  40. data/doc/files/lib/bio/graphics/ruler_rb.html +113 -0
  41. data/doc/files/lib/bio/graphics/track_rb.html +113 -0
  42. data/doc/fr_class_index.html +35 -0
  43. data/doc/fr_file_index.html +34 -0
  44. data/doc/fr_method_index.html +41 -0
  45. data/doc/images/example.png +0 -0
  46. data/doc/images/glyph_showcase.png +0 -0
  47. data/doc/images/terms.png +0 -0
  48. data/doc/images/terms.svg +166 -0
  49. data/doc/index.html +24 -0
  50. data/images/example.png +0 -0
  51. data/images/glyph_showcase.png +0 -0
  52. data/images/terms.png +0 -0
  53. data/images/terms.svg +166 -0
  54. data/lib/bio-graphics.rb +18 -0
  55. data/lib/bio/graphics/feature.rb +136 -0
  56. data/lib/bio/graphics/image_map.rb +37 -0
  57. data/lib/bio/graphics/panel.rb +205 -0
  58. data/lib/bio/graphics/ruler.rb +96 -0
  59. data/lib/bio/graphics/track.rb +387 -0
  60. data/samples/arkdb_features.rb +37 -0
  61. data/samples/data.txt +32 -0
  62. data/samples/glyph_showcase.rb +29 -0
  63. metadata +137 -0
data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.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::Ruler)</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/ruler.rb, line 28</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
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+ <span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
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+ <span class="ruby-ivar">@name</span> = <span class="ruby-value str">'ruler'</span>
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+ <span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">colour</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/Ruler.src/M000014.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>calculate_tick_distance (Bio::Graphics::Panel::Ruler)</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/ruler.rb, line 35</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">calculate_tick_distance</span>
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+ <span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">false</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-value">1</span> <span class="ruby-comment cmt"># in basepairs.
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+ <span class="ruby-keyword kw">while</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">min_tick_distance_requirement_met</span>
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">/</span><span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-constant">RULER_MIN_DISTANCE_TICKS_PIXEL</span>
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+ <span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">true</span>
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">*</span><span class="ruby-value">5</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">major_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</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/Ruler.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>draw (Bio::Graphics::Panel::Ruler)</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/ruler.rb, line 49</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_drawing</span>, <span class="ruby-identifier">vertical_offset</span>)
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+ <span class="ruby-identifier">ruler_drawing</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_drawing</span>)
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+
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">calculate_tick_distance</span>
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+
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+ <span class="ruby-comment cmt"># Draw line
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-value">10</span>)
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
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+
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+ <span class="ruby-comment cmt"># Draw ticks
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+ <span class="ruby-comment cmt"># * Find position of first tick.
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+ <span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first
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+ <span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the
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+ <span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:
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+ <span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.
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+ <span class="ruby-comment cmt"># So we want to find the position of the first tick.
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+ <span class="ruby-identifier">first_tick_position</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
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+ <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>
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+ <span class="ruby-identifier">first_tick_position</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ <span class="ruby-comment cmt"># * And start drawing the rest.
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+ <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">tick</span><span class="ruby-operator">|</span>
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+ <span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">5</span>)
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">15</span>)
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+
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+ <span class="ruby-comment cmt"># Draw tick number
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">select_font_face</span>(<span class="ruby-value str">'Georgia'</span>, <span class="ruby-value">1</span>, <span class="ruby-value">1</span>)
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">20</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">5</span>)
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+
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+
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+ <span class="ruby-ivar">@height</span> = <span class="ruby-value">25</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</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.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: Bio::Graphics::Panel::Track</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">Bio::Graphics::Panel::Track</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/feature_rb.html">
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+ lib/bio/graphics/feature.rb
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+ </a>
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+ <br />
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+ <a href="../../../../files/lib/bio/graphics/track_rb.html">
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+ lib/bio/graphics/track.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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+ <p>
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+ The Bio::Graphics::Track class describes the container for features of the
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+ same type. See <a href="../../Graphics.html">Bio::Graphics</a>
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+ documentation for explanation of interplay between different classes.
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+ </p>
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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="#M000009">add_feature</a>&nbsp;&nbsp;
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+ <a href="#M000010">draw</a>&nbsp;&nbsp;
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+ <a href="#M000008">new</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="Track/Feature.html" class="link">Bio::Graphics::Panel::Track::Feature</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">feature_colour</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">feature_glyph</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">features</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">height</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">name</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">number_of_times_bumped</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">panel</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-M000008" class="method-detail">
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+ <a name="M000008"></a>
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+
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+ <div class="method-heading">
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+ <a href="Track.src/M000008.html" target="Code" class="method-signature"
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+ onclick="popupCode('Track.src/M000008.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">(panel, name, feature_colour = [0,0,1], feature_glyph = 'generic')</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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+ <p>
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+ !!Not to be used directly. Use <a
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+ href="../Panel.html#M000006">Bio::Graphics::Panel.add_track</a> instead!! A
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+ track can not exist except within the confines of a <a
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+ href="../Panel.html">Bio::Graphics::Panel</a> object.
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+ </p>
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+ <hr size="1"></hr><p>
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+ <b>Arguments</b>:
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+ </p>
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+ <ul>
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+ <li><em>panel</em> (required) :: <a
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+ href="../Panel.html">Bio::Graphics::Panel</a> object that this track
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+ belongs to
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+
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+ </li>
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+ <li><em>name</em> (required) :: Name of the track to be displayed (e.g.
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+ &#8216;genes&#8217;)
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+
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+ </li>
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+ <li><em>colour</em> :: Colour to be used to <a
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+ href="Track.html#M000010">draw</a> the features within the track. Default =
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+ &#8216;blue&#8216;
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+
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+ </li>
209
+ <li><em>glyph</em> :: Glyph to use for drawing the features. Options are:
210
+ &#8216;generic&#8217;, &#8216;directed_generic&#8217;, &#8216;spliced,
211
+ &#8216;directed_spliced&#8217; and &#8216;triangle&#8217;. Triangles can be
212
+ used for features whose start and stop positions are the same (e.g. SNPs).
213
+ If you try to <a href="Track.html#M000010">draw</a> a feature that is
214
+ longer with triangles, an error will be shown.
215
+
216
+ </li>
217
+ </ul>
218
+ <table>
219
+ <tr><td valign="top"><b>Returns</b>:</td><td>Bio::Graphics::Track object
220
+
221
+ </td></tr>
222
+ </table>
223
+ </div>
224
+ </div>
225
+
226
+ <h3 class="section-bar">Public Instance methods</h3>
227
+
228
+ <div id="method-M000009" class="method-detail">
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+ <a name="M000009"></a>
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+
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+ <div class="method-heading">
232
+ <a href="Track.src/M000009.html" target="Code" class="method-signature"
233
+ onclick="popupCode('Track.src/M000009.html');return false;">
234
+ <span class="method-name">add_feature</span><span class="method-args">(name, location_string = '1..' + @panel.length.to_s, link = nil)</span>
235
+ </a>
236
+ </div>
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+
238
+ <div class="method-description">
239
+ <p>
240
+ Adds a <a
241
+ href="Track/Feature.html">Bio::Graphics::Panel::Track::Feature</a> to this
242
+ track. A track contains features of the same type, e.g. (for sequence
243
+ annotation:) genes, polymorphisms, ESTs, etc.
244
+ </p>
245
+ <pre>
246
+ est_track.add_feature('EST1','50..60')
247
+ est_track.add_feature('EST2','52..73')
248
+ est_track.add_feature('EST3','41..69')
249
+ gene_track.add_feature('gene2','39..73')
250
+ </pre>
251
+ <p>
252
+ For spliced features:
253
+ </p>
254
+ <pre>
255
+ est_track.add_feature('EST4','join(34..53,153..191)')
256
+ </pre>
257
+ <p>
258
+ Or on the complement strand:
259
+ </p>
260
+ <pre>
261
+ est_track.add_feature('EST5','complement(join(34..53,153..191))')
262
+ </pre>
263
+ <p>
264
+ See the documentation in Bio::Locations for a full description of how
265
+ locations can be defined.
266
+ </p>
267
+ <p>
268
+ Features are only added if they are at least partly in the displayed
269
+ region. If a feature is completely outside of the region, it&#8216;s not
270
+ added. If it should be only partly visible, it is added completely.
271
+ </p>
272
+ <hr size="1"></hr><p>
273
+ <b>Arguments</b>:
274
+ </p>
275
+ <ul>
276
+ <li><em>name</em> (required) :: Name of the feature
277
+
278
+ </li>
279
+ <li><em>location</em> :: String. Default: whole of panel, forward strand.
280
+
281
+ </li>
282
+ <li><em>link</em> :: URL to link to for this glyph
283
+
284
+ </li>
285
+ </ul>
286
+ <table>
287
+ <tr><td valign="top"><b>Returns</b>:</td><td>Bio::Graphics::Track::Feature object that was created or nil
288
+
289
+ </td></tr>
290
+ </table>
291
+ </div>
292
+ </div>
293
+
294
+ <div id="method-M000010" class="method-detail">
295
+ <a name="M000010"></a>
296
+
297
+ <div class="method-heading">
298
+ <a href="Track.src/M000010.html" target="Code" class="method-signature"
299
+ onclick="popupCode('Track.src/M000010.html');return false;">
300
+ <span class="method-name">draw</span><span class="method-args">(panel_drawing, vertical_offset)</span>
301
+ </a>
302
+ </div>
303
+
304
+ <div class="method-description">
305
+ <p>
306
+ Adds the track to a cairo drawing. This method should not be used directly
307
+ by the user, but is called by <a
308
+ href="../Panel.html#M000007">Bio::Graphics::Panel.draw</a>
309
+ </p>
310
+ <hr size="1"></hr><p>
311
+ <b>Arguments</b>:
312
+ </p>
313
+ <ul>
314
+ <li><em>paneldrawing</em> (required) :: the panel cairo object
315
+
316
+ </li>
317
+ <li><em>verticaloffset</em> (required) :: number of pixels to offset the track
318
+ downwards, based on the height of other tracks that were drawn above it
319
+
320
+ </li>
321
+ </ul>
322
+ <table>
323
+ <tr><td valign="top"><b>Returns</b>:</td><td>FIXME: I don&#8216;t know
324
+
325
+ </td></tr>
326
+ </table>
327
+ </div>
328
+ </div>
329
+
330
+
331
+ </div>
332
+
333
+
334
+ </div>
335
+
336
+
337
+ <div id="validator-badges">
338
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
339
+ </div>
340
+
341
+ </body>
342
+ </html>