bio-graphics 1.0 → 1.2

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Files changed (52) hide show
  1. data/doc/classes/Bio/Graphics.html +11 -1
  2. data/doc/classes/Bio/Graphics/Panel.html +5 -2
  3. data/doc/classes/Bio/Graphics/Panel.src/M000005.html +4 -4
  4. data/doc/classes/Bio/Graphics/Panel.src/M000006.html +3 -3
  5. data/doc/classes/Bio/Graphics/Panel.src/M000007.html +6 -5
  6. data/doc/classes/Bio/Graphics/Panel/Ruler.html +16 -16
  7. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +6 -14
  8. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +10 -41
  9. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +59 -0
  10. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +20 -0
  11. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +28 -0
  12. data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +59 -0
  13. data/doc/classes/Bio/Graphics/Panel/Track.html +30 -15
  14. data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +8 -5
  15. data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +2 -2
  16. data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +12 -245
  17. data/doc/classes/Bio/Graphics/Panel/Track/Feature.html +109 -0
  18. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +1 -1
  19. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +39 -0
  20. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000013.html +27 -0
  21. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +209 -49
  22. data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000015.html +48 -0
  23. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html +5 -5
  24. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000013.html +18 -0
  25. data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000016.html +18 -0
  26. data/doc/created.rid +1 -1
  27. data/doc/files/README_DEV.html +7 -11
  28. data/doc/files/TUTORIAL.html +3 -3
  29. data/doc/files/lib/bio-graphics_rb.html +3 -1
  30. data/doc/files/lib/bio/graphics/feature_rb.html +6 -11
  31. data/doc/files/lib/bio/graphics/image_map_rb.html +1 -1
  32. data/doc/files/lib/bio/graphics/panel_rb.html +1 -1
  33. data/doc/files/lib/bio/graphics/ruler_rb.html +1 -1
  34. data/doc/files/lib/bio/graphics/track_rb.html +1 -1
  35. data/doc/fr_method_index.html +8 -4
  36. data/doc/images/example_labels.png +0 -0
  37. data/doc/images/glyph_showcase.png +0 -0
  38. data/doc/images/terms.png +0 -0
  39. data/doc/index.html +2 -2
  40. data/images/example_labels.png +0 -0
  41. data/images/glyph_showcase.png +0 -0
  42. data/images/terms.png +0 -0
  43. data/images/terms.svg +146 -132
  44. data/lib/bio-graphics.rb +2 -1
  45. data/lib/bio/graphics/feature.rb +304 -0
  46. data/lib/bio/graphics/panel.rb +15 -11
  47. data/lib/bio/graphics/ruler.rb +1 -1
  48. data/lib/bio/graphics/track.rb +23 -254
  49. data/samples/arkdb_features.rb +8 -8
  50. data/samples/glyph_showcase.rb +10 -6
  51. data/test/unit/test_creation.rb +51 -0
  52. metadata +14 -2
data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html CHANGED
@@ -10,7 +10,7 @@
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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 37</span>
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 38</span>
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  <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">track</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">location</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'1..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>)
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  <span class="ruby-ivar">@track</span> = <span class="ruby-identifier">track</span>
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  <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html ADDED
@@ -0,0 +1,39 @@
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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>arrow (Bio::Graphics::Panel::Track::Feature)</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 129</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track</span>,<span class="ruby-identifier">direction</span>,<span class="ruby-identifier">x</span>,<span class="ruby-identifier">y</span>,<span class="ruby-identifier">size</span>)
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+ <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">direction</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:right</span>
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">x</span>,<span class="ruby-identifier">y</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:left</span>
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">x</span>,<span class="ruby-identifier">y</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:north</span>
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">x</span><span class="ruby-operator">-</span><span class="ruby-identifier">size</span>,<span class="ruby-identifier">y</span><span class="ruby-operator">+</span><span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-operator">-</span><span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:south</span>
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">x</span><span class="ruby-operator">-</span><span class="ruby-identifier">size</span>,<span class="ruby-identifier">y</span><span class="ruby-operator">-</span><span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-identifier">size</span>,<span class="ruby-operator">-</span><span class="ruby-identifier">size</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
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+ <span class="ruby-keyword kw">end</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.src/M000013.html ADDED
@@ -0,0 +1,27 @@
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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>connector (Bio::Graphics::Panel::Track::Feature)</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 156</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">connector</span>(<span class="ruby-identifier">track</span>,<span class="ruby-identifier">from</span>,<span class="ruby-identifier">to</span>,<span class="ruby-identifier">top</span>, <span class="ruby-identifier">color</span>)
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+ <span class="ruby-identifier">line_width</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">line_width</span>
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">set_source_rgb</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-identifier">track</span>.<span class="ruby-identifier">set_line_width</span>(<span class="ruby-value">0</span><span class="ruby-value">.5</span>)
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+ <span class="ruby-identifier">middle</span> = <span class="ruby-identifier">from</span> <span class="ruby-operator">+</span> ((<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">from</span>)<span class="ruby-operator">/</span><span class="ruby-value">2</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top</span><span class="ruby-operator">+</span><span class="ruby-value">2</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">middle</span>, <span class="ruby-identifier">top</span><span class="ruby-operator">+</span><span class="ruby-value">7</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top</span><span class="ruby-operator">+</span><span class="ruby-value">2</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">stroke</span>
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">set_line_width</span>(<span class="ruby-identifier">line_width</span>)
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+ <span class="ruby-identifier">track</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-identifier">color</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.src/M000014.html CHANGED
@@ -5,60 +5,220 @@
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  <html>
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  <head>
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- <title>new (Bio::Graphics::Panel::Track::Feature)</title>
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+ <title>draw (Bio::Graphics::Panel::Track::Feature)</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 36</span>
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">track</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">location</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'0..'</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">width</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rescale_factor</span>).<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>)
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- <span class="ruby-ivar">@track</span> = <span class="ruby-identifier">track</span>
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- <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
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- <span class="ruby-ivar">@location</span> = <span class="ruby-identifier">location</span>
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- <span class="ruby-ivar">@start</span> = <span class="ruby-identifier">location</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
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- <span class="ruby-ivar">@stop</span> = <span class="ruby-identifier">location</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
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- <span class="ruby-ivar">@strand</span> = <span class="ruby-identifier">location</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">strand</span>.<span class="ruby-identifier">to_i</span>
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- <span class="ruby-ivar">@link</span> = <span class="ruby-identifier">link</span>
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- <span class="ruby-ivar">@pixel_range_collection</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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- <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">false</span>
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- <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">false</span>
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- <span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">false</span>
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- <span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">false</span>
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-
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- <span class="ruby-comment cmt"># Get all pixel ranges for the subfeatures
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- <span class="ruby-identifier">location</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span>
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- <span class="ruby-comment cmt"># xxxxxx [ ]
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- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
32
- <span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">true</span>
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- <span class="ruby-keyword kw">next</span>
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- <span class="ruby-comment cmt"># [ ] xxxxx
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- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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- <span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">true</span>
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- <span class="ruby-keyword kw">next</span>
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- <span class="ruby-comment cmt"># xxxx[xxx ]
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- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
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- <span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
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- <span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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- <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
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- <span class="ruby-comment cmt"># [ xxxx]xxxx
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- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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- <span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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- <span class="ruby-identifier">stop_pixel</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
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- <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
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- <span class="ruby-comment cmt"># xxxx[xxxxxxxxxx]xxxx
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- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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- <span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
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- <span class="ruby-identifier">stop_pixel</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
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- <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
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- <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
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- <span class="ruby-comment cmt"># [ xxxxx ]
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- <span class="ruby-keyword kw">else</span>
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- <span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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- <span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 178</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">track_drawing</span>)
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+ <span class="ruby-comment cmt"># We have to check if we want to change the glyph type from directed to
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+ <span class="ruby-comment cmt"># undirected
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+ <span class="ruby-comment cmt"># There are 2 cases where we don't want to draw arrows on
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+ <span class="ruby-comment cmt"># features:
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+ <span class="ruby-comment cmt"># (a) when the picture is really zoomed out, features are
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+ <span class="ruby-comment cmt"># so small that the arrow itself is too big
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+ <span class="ruby-comment cmt"># (b) if a directed feature on the fw strand extends beyond
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+ <span class="ruby-comment cmt"># the end of the picture, the arrow is out of view. This
23
+ <span class="ruby-comment cmt"># is the same as considering the feature as undirected.
24
+ <span class="ruby-comment cmt"># The same obviously goes for features on the reverse
25
+ <span class="ruby-comment cmt"># strand that extend beyond the left side of the image.
26
+ <span class="ruby-comment cmt">#
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+ <span class="ruby-comment cmt"># (a) Zoomed out
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+ <span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">false</span>
29
+ <span class="ruby-keyword kw">if</span> (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span>).<span class="ruby-identifier">to_f</span><span class="ruby-operator">/</span><span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">2</span>
30
+ <span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
31
+ <span class="ruby-keyword kw">end</span>
32
+ <span class="ruby-comment cmt"># (b) Extending beyond borders picture
33
+ <span class="ruby-keyword kw">if</span> ( <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">chopped_at_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">1</span> ) <span class="ruby-keyword kw">or</span> ( <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">chopped_at_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">-1</span> )
34
+ <span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
35
+ <span class="ruby-keyword kw">end</span>
36
+
37
+ <span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">nil</span>
38
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:directed_generic</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
39
+ <span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:generic</span>
40
+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:directed_spliced</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
41
+ <span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">:spliced</span>
42
+ <span class="ruby-keyword kw">else</span>
43
+ <span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span>
44
+ <span class="ruby-keyword kw">end</span>
45
+
46
+ <span class="ruby-comment cmt"># And draw the thing.
47
+ <span class="ruby-identifier">row</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">find_row</span>
48
+ <span class="ruby-identifier">top_pixel_of_feature</span> = <span class="ruby-constant">FEATURE_V_DISTANCE</span> <span class="ruby-operator">+</span> (<span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_V_DISTANCE</span>)<span class="ruby-operator">*</span><span class="ruby-identifier">row</span>
49
+ <span class="ruby-identifier">bottom_pixel_of_feature</span> = <span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-constant">FEATURE_HEIGHT</span>
50
+
51
+ <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">local_feature_glyph</span>
52
+ <span class="ruby-comment cmt"># triangles are typical for features which have a 1 bp position (start == stop)
53
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:triangle</span>
54
+ <span class="ruby-identifier">raise</span> <span class="ruby-value str">&quot;Start and stop are not the same (necessary if you want triangle glyphs)&quot;</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">stop</span>
55
+
56
+ <span class="ruby-comment cmt"># Need to get this for the imagemap
57
+ <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>
58
+ <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">+</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>
59
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:north</span>,<span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
60
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
61
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:line</span>
62
+ <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
63
+ <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
64
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">left_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
65
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">right_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
66
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
67
+
68
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>([<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
69
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">left_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
70
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
71
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">right_pixel_of_feature</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
72
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">stroke</span>
73
+
74
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span>)
75
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:directed_generic</span>
76
+ <span class="ruby-comment cmt"># Need to get this for the imagemap
77
+ <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
78
+ <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
79
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># Reverse strand
80
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
81
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">left_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
82
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
83
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand
84
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
85
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">right_pixel_of_feature</span><span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
86
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
87
+ <span class="ruby-keyword kw">end</span>
88
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:spliced</span>
89
+ <span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
90
+ <span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
91
+
92
+ <span class="ruby-comment cmt"># Need to get this for the imagemap
93
+ <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
94
+ <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
95
+
96
+ <span class="ruby-comment cmt"># First draw the parts
97
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span>
98
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, (<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>), <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
99
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">stop_pixel</span>)
100
+ <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>)
101
+ <span class="ruby-keyword kw">end</span>
102
+
103
+ <span class="ruby-comment cmt"># And then draw the connections in the gaps
104
+ <span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
105
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
106
+ <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
107
+
108
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap_number</span><span class="ruby-operator">|</span>
109
+ <span class="ruby-identifier">connector</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>,<span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span>)
110
+ <span class="ruby-keyword kw">end</span>
111
+
112
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
113
+ <span class="ruby-identifier">from</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
114
+ <span class="ruby-identifier">to</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
115
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
116
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
117
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
118
+ <span class="ruby-keyword kw">end</span>
119
+
120
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hidden_subfeatures_at_start</span>
121
+ <span class="ruby-identifier">from</span> = <span class="ruby-value">1</span>
122
+ <span class="ruby-identifier">to</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
123
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
124
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
125
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
126
+ <span class="ruby-keyword kw">end</span>
127
+
128
+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:directed_spliced</span>
129
+ <span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
130
+ <span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
131
+ <span class="ruby-comment cmt"># First draw the parts
132
+ <span class="ruby-identifier">locations</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">location</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}
133
+
134
+ <span class="ruby-comment cmt"># Need to get this for the imagemap
135
+ <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
136
+ <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
137
+
138
+ <span class="ruby-comment cmt"># Start with the one with the arrow
139
+ <span class="ruby-identifier">pixel_ranges</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}
140
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-keyword kw">nil</span>
141
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># reverse strand =&gt; box with arrow is first one
142
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">shift</span>
143
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>((<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>)<span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
144
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:left</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
145
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
146
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># forward strand =&gt; box with arrow is last one
147
+ <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">pop</span>
148
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
149
+ <span class="ruby-identifier">arrow</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">:right</span>,<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span><span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
150
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
151
+ <span class="ruby-keyword kw">end</span>
152
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span>)
153
+ <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>)
154
+
155
+ <span class="ruby-comment cmt"># And then add the others
156
+ <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">range</span><span class="ruby-operator">|</span>
157
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
158
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">stop_pixel</span>)
159
+ <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>)
160
+ <span class="ruby-keyword kw">end</span>
161
+
162
+ <span class="ruby-comment cmt"># And then draw the connections in the gaps
163
+ <span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
164
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
165
+ <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
166
+
167
+ <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap_number</span><span class="ruby-operator">|</span>
168
+ <span class="ruby-identifier">connector</span>(<span class="ruby-identifier">track_drawing</span>,<span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>,<span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>,<span class="ruby-identifier">top_pixel_of_feature</span>,<span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span>)
169
+ <span class="ruby-keyword kw">end</span>
170
+
171
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
172
+ <span class="ruby-identifier">from</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
173
+ <span class="ruby-identifier">to</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
174
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
175
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
176
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
177
+ <span class="ruby-keyword kw">end</span>
178
+
179
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hidden_subfeatures_at_start</span>
180
+ <span class="ruby-identifier">from</span> = <span class="ruby-value">1</span>
181
+ <span class="ruby-identifier">to</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
182
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
183
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>)
184
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
185
+ <span class="ruby-keyword kw">end</span>
186
+
187
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#treat as 'generic'
188
+ <span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">stop_pixel</span>
189
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, (<span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span>), <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
190
+ <span class="ruby-keyword kw">end</span>
191
+
192
+ <span class="ruby-comment cmt"># Add the label for the feature
193
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">show_label</span>
194
+ <span class="ruby-identifier">pango_layout</span> = <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">create_pango_layout</span>
195
+ <span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">text</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>
196
+ <span class="ruby-identifier">fdesc</span> = <span class="ruby-constant">Pango</span><span class="ruby-operator">::</span><span class="ruby-constant">FontDescription</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'Sans Serif'</span>)
197
+ <span class="ruby-identifier">fdesc</span>.<span class="ruby-identifier">set_size</span>(<span class="ruby-value">8</span> <span class="ruby-operator">*</span> <span class="ruby-constant">Pango</span><span class="ruby-operator">::</span><span class="ruby-constant">SCALE</span>)
198
+ <span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">font_description</span> = <span class="ruby-identifier">fdesc</span>
199
+
200
+ <span class="ruby-identifier">text_range</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">pango_layout</span>.<span class="ruby-identifier">pixel_size</span>[<span class="ruby-value">0</span>]<span class="ruby-operator">*</span><span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>)
201
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>].<span class="ruby-identifier">nil?</span>
202
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
58
203
  <span class="ruby-keyword kw">end</span>
59
-
60
- <span class="ruby-ivar">@pixel_range_collection</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">PixelRange</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>))
61
-
204
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">text_range</span>)
205
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span><span class="ruby-operator">+</span><span class="ruby-value">1</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">text_range</span>)
206
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
207
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
208
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">show_pango_layout</span>(<span class="ruby-identifier">pango_layout</span>)
209
+ <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">colour</span>)
210
+ <span class="ruby-keyword kw">end</span>
211
+
212
+
213
+ <span class="ruby-comment cmt"># And add the region to the image map
214
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">clickable</span>
215
+ <span class="ruby-comment cmt"># Comment: we have to add the vertical_offset and TRACK_HEADER_HEIGHT!
216
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">image_map</span>.<span class="ruby-identifier">elements</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">ImageMap</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageMapElement</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">left_pixel_of_feature</span>,
217
+ <span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
218
+ <span class="ruby-identifier">right_pixel_of_feature</span>,
219
+ <span class="ruby-identifier">bottom_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
220
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">link</span>
221
+ ))
62
222
  <span class="ruby-keyword kw">end</span>
63
223
  <span class="ruby-keyword kw">end</span></pre>
64
224
  </body>
data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000015.html ADDED
@@ -0,0 +1,48 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>find_row (Bio::Graphics::Panel::Track::Feature)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 396</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">find_row</span>
15
+ <span class="ruby-identifier">row_found</span> = <span class="ruby-keyword kw">false</span>
16
+
17
+ <span class="ruby-comment cmt"># We've got to find out what row to draw the feature on. If two
18
+ <span class="ruby-comment cmt"># features overlap, one of them has to be 'bumped' down. So we'll
19
+ <span class="ruby-comment cmt"># first try to draw a new feature at the top of the track. If
20
+ <span class="ruby-comment cmt"># it however would overlap with another one, we'll bump it down
21
+ <span class="ruby-comment cmt"># to the next row.
22
+ <span class="ruby-identifier">feature_range</span> = (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span><span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">stop</span>.<span class="ruby-identifier">ceil</span>)
23
+ <span class="ruby-identifier">row</span> = <span class="ruby-value">1</span>
24
+ <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
25
+ <span class="ruby-keyword kw">until</span> <span class="ruby-identifier">row_found</span>
26
+ <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
27
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">covered</span><span class="ruby-operator">|</span>
28
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">covered</span>.<span class="ruby-identifier">first</span>) <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">covered</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">first</span>)
29
+ <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</span>
30
+ <span class="ruby-keyword kw">end</span>
31
+ <span class="ruby-keyword kw">end</span>
32
+ <span class="ruby-keyword kw">end</span>
33
+
34
+ <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">row_available</span>
35
+ <span class="ruby-identifier">row</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
36
+ <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
37
+ <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># We've found the place where to draw the feature.
38
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
39
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
40
+ <span class="ruby-keyword kw">end</span>
41
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">track</span>.<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">feature_range</span>)
42
+ <span class="ruby-identifier">row_found</span> = <span class="ruby-keyword kw">true</span>
43
+ <span class="ruby-keyword kw">end</span>
44
+ <span class="ruby-keyword kw">end</span>
45
+ <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">row</span>
46
+ <span class="ruby-keyword kw">end</span></pre>
47
+ </body>
48
+ </html>
data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html CHANGED
@@ -86,7 +86,7 @@
86
86
  <h3 class="section-bar">Methods</h3>
87
87
 
88
88
  <div class="name-list">
89
- <a href="#M000012">new</a>&nbsp;&nbsp;
89
+ <a href="#M000016">new</a>&nbsp;&nbsp;
90
90
  </div>
91
91
  </div>
92
92
 
@@ -126,12 +126,12 @@
126
126
  <div id="methods">
127
127
  <h3 class="section-bar">Public Class methods</h3>
128
128
 
129
- <div id="method-M000012" class="method-detail">
130
- <a name="M000012"></a>
129
+ <div id="method-M000016" class="method-detail">
130
+ <a name="M000016"></a>
131
131
 
132
132
  <div class="method-heading">
133
- <a href="PixelRange.src/M000012.html" target="Code" class="method-signature"
134
- onclick="popupCode('PixelRange.src/M000012.html');return false;">
133
+ <a href="PixelRange.src/M000016.html" target="Code" class="method-signature"
134
+ onclick="popupCode('PixelRange.src/M000016.html');return false;">
135
135
  <span class="method-name">new</span><span class="method-args">(start_pixel, stop_pixel)</span>
136
136
  </a>
137
137
  </div>
data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000013.html ADDED
@@ -0,0 +1,18 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>new (Bio::Graphics::Panel::Track::Feature::PixelRange)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 337</span>
14
+ <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>)
15
+ <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>
16
+ <span class="ruby-keyword kw">end</span></pre>
17
+ </body>
18
+ </html>
data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000016.html ADDED
@@ -0,0 +1,18 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>new (Bio::Graphics::Panel::Track::Feature::PixelRange)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 431</span>
14
+ <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>)
15
+ <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>
16
+ <span class="ruby-keyword kw">end</span></pre>
17
+ </body>
18
+ </html>