bio-graphics 1.0
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- data/doc/classes/Bio.html +135 -0
- data/doc/classes/Bio/Graphics.html +247 -0
- data/doc/classes/Bio/Graphics/Panel.html +344 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000005.html +29 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000006.html +19 -0
- data/doc/classes/Bio/Graphics/Panel.src/M000007.html +67 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.html +238 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +20 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +28 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +54 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +20 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +28 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +59 -0
- data/doc/classes/Bio/Graphics/Panel/Track.html +342 -0
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +23 -0
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +42 -0
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +285 -0
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +23 -0
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +43 -0
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +259 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.html +292 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +65 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +65 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html +155 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +18 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +18 -0
- data/doc/classes/ImageMap.html +185 -0
- data/doc/classes/ImageMap.src/M000001.html +18 -0
- data/doc/classes/ImageMap.src/M000002.html +24 -0
- data/doc/classes/ImageMap/ImageMapElement.html +187 -0
- data/doc/classes/ImageMap/ImageMapElement.src/M000003.html +19 -0
- data/doc/classes/ImageMap/ImageMapElement.src/M000004.html +20 -0
- data/doc/created.rid +1 -0
- data/doc/files/README_DEV.html +432 -0
- data/doc/files/TUTORIAL.html +358 -0
- data/doc/files/lib/bio-graphics_rb.html +121 -0
- data/doc/files/lib/bio/graphics/feature_rb.html +113 -0
- data/doc/files/lib/bio/graphics/image_map_rb.html +113 -0
- data/doc/files/lib/bio/graphics/panel_rb.html +113 -0
- data/doc/files/lib/bio/graphics/ruler_rb.html +113 -0
- data/doc/files/lib/bio/graphics/track_rb.html +113 -0
- data/doc/fr_class_index.html +35 -0
- data/doc/fr_file_index.html +34 -0
- data/doc/fr_method_index.html +41 -0
- data/doc/images/example.png +0 -0
- data/doc/images/glyph_showcase.png +0 -0
- data/doc/images/terms.png +0 -0
- data/doc/images/terms.svg +166 -0
- data/doc/index.html +24 -0
- data/images/example.png +0 -0
- data/images/glyph_showcase.png +0 -0
- data/images/terms.png +0 -0
- data/images/terms.svg +166 -0
- data/lib/bio-graphics.rb +18 -0
- data/lib/bio/graphics/feature.rb +136 -0
- data/lib/bio/graphics/image_map.rb +37 -0
- data/lib/bio/graphics/panel.rb +205 -0
- data/lib/bio/graphics/ruler.rb +96 -0
- data/lib/bio/graphics/track.rb +387 -0
- data/samples/arkdb_features.rb +37 -0
- data/samples/data.txt +32 -0
- data/samples/glyph_showcase.rb +29 -0
- metadata +137 -0
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.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">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">feature_colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>], <span class="ruby-identifier">feature_glyph</span> = <span class="ruby-value str">'generic'</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-identifier">name</span>
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<span class="ruby-ivar">@feature_colour</span> = <span class="ruby-identifier">feature_colour</span>
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<span class="ruby-ivar">@feature_glyph</span> = <span class="ruby-identifier">feature_glyph</span>
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<span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-ivar">@number_of_times_bumped</span> = <span class="ruby-value">0</span>
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<span class="ruby-keyword kw">end</span></pre>
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<title>add_feature (Bio::Graphics::Panel::Track)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 76</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">location_string</span> = <span class="ruby-value str">'1..'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@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-keyword kw">if</span> <span class="ruby-identifier">link</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
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<span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># Calculate the ultimate start and stop of the feature: the start
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<span class="ruby-comment cmt"># of the first subfeature (e.g. exon) and the stop of the last one.
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<span class="ruby-comment cmt"># The only reason we want to know these positions, is because we want
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<span class="ruby-comment cmt"># to determine if the feature falls within the view of the image or
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<span class="ruby-comment cmt"># not (see below).
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<span class="ruby-identifier">location_object</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-identifier">location_string</span>)
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<span class="ruby-identifier">start</span> = <span class="ruby-identifier">location_object</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-identifier">stop</span> = <span class="ruby-identifier">location_object</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-comment cmt"># If the feature wouldn't show because it's not in the region we're
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<span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge
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<span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with
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<span class="ruby-comment cmt"># thousands of features.
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start >= panel.display_start and stop <= panel.display_stop
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Panel</span><span class="ruby-operator">::</span><span class="ruby-constant">Track</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">location_object</span>, <span class="ruby-identifier">link</span>))
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<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>
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<span class="ruby-keyword kw">end</span></pre>
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<title>draw (Bio::Graphics::Panel::Track)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 113</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">track_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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<span class="ruby-comment cmt"># Draw thin line above title
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<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">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">vertical_offset</span>)
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-identifier">vertical_offset</span>)
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-comment cmt"># Draw track title
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<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>)
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<span class="ruby-identifier">track_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">track_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
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<span class="ruby-comment cmt"># Draw the features
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<span class="ruby-identifier">grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">save</span> <span class="ruby-keyword kw">do</span>
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
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<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-ivar">@feature_colour</span>)
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<span class="ruby-comment cmt"># Now draw the features
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<span class="ruby-comment cmt"># These are the basic steps:
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<span class="ruby-comment cmt"># A. find out what row to draw it on
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<span class="ruby-comment cmt"># B. see 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"># C. draw the thing
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
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<span class="ruby-comment cmt"># Don't even bother if the feature is not in the view
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-keyword kw">next</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">feature_drawn</span> = <span class="ruby-keyword kw">false</span>
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<span class="ruby-comment cmt"># A. find out what row to draw it on
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<span class="ruby-identifier">feature_range</span> = (<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span><span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span>.<span class="ruby-identifier">ceil</span>)
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<span class="ruby-identifier">row</span> = <span class="ruby-value">1</span>
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<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
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<span class="ruby-keyword kw">until</span> <span class="ruby-identifier">feature_drawn</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
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<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>
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<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>)
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<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</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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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">row_available</span>
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<span class="ruby-identifier">row</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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<span class="ruby-identifier">row_available</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">if</span> <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
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<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-keyword kw">end</span>
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<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>)
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<span class="ruby-comment cmt"># B. see if we want to change the glyph type from directed to
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+
<span class="ruby-comment cmt"># undirected
|
|
74
|
+
<span class="ruby-comment cmt"># There are 2 cases where we don't want to draw arrows on
|
|
75
|
+
<span class="ruby-comment cmt"># features:
|
|
76
|
+
<span class="ruby-comment cmt"># (a) when the picture is really zoomed out, features are
|
|
77
|
+
<span class="ruby-comment cmt"># so small that the arrow itself is too big
|
|
78
|
+
<span class="ruby-comment cmt"># (b) if a directed feature on the fw strand extends beyond
|
|
79
|
+
<span class="ruby-comment cmt"># the end of the picture, the arrow is out of view. This
|
|
80
|
+
<span class="ruby-comment cmt"># is the same as considering the feature as undirected.
|
|
81
|
+
<span class="ruby-comment cmt"># The same obviously goes for features on the reverse
|
|
82
|
+
<span class="ruby-comment cmt"># strand that extend beyond the left side of the image.
|
|
83
|
+
<span class="ruby-comment cmt">#
|
|
84
|
+
<span class="ruby-comment cmt"># (a) Zoomed out
|
|
85
|
+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">false</span>
|
|
86
|
+
<span class="ruby-keyword kw">if</span> (<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span>).<span class="ruby-identifier">to_f</span><span class="ruby-operator">/</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"><</span> <span class="ruby-value">2</span>
|
|
87
|
+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
|
|
88
|
+
<span class="ruby-keyword kw">end</span>
|
|
89
|
+
<span class="ruby-comment cmt"># (b) Extending beyond borders picture
|
|
90
|
+
<span class="ruby-keyword kw">if</span> ( <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">chopped_at_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">1</span> ) <span class="ruby-keyword kw">or</span> ( <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">chopped_at_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">-1</span> )
|
|
91
|
+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
|
|
92
|
+
<span class="ruby-keyword kw">end</span>
|
|
93
|
+
|
|
94
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">nil</span>
|
|
95
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature_glyph</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'directed_generic'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
|
|
96
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-value str">'generic'</span>
|
|
97
|
+
<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">feature_glyph</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'directed_spliced'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
|
|
98
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-value str">'spliced'</span>
|
|
99
|
+
<span class="ruby-keyword kw">else</span>
|
|
100
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">feature_glyph</span>
|
|
101
|
+
<span class="ruby-keyword kw">end</span>
|
|
102
|
+
|
|
103
|
+
<span class="ruby-comment cmt"># C. And draw the thing.
|
|
104
|
+
<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>
|
|
105
|
+
<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>
|
|
106
|
+
|
|
107
|
+
<span class="ruby-keyword kw">case</span> <span class="ruby-identifier">local_feature_glyph</span>
|
|
108
|
+
<span class="ruby-comment cmt"># triangles are typical for features which have a 1 bp position (start == stop)
|
|
109
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">'triangle'</span>
|
|
110
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-value str">"Start and stop are not the same (necessary if you want triangle glyphs)"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span>
|
|
111
|
+
|
|
112
|
+
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
113
|
+
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</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-value">3</span>
|
|
114
|
+
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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-value">3</span>
|
|
115
|
+
<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-operator">+</span> <span class="ruby-value">3</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
|
|
116
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">-3</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>)
|
|
117
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">6</span>, <span class="ruby-value">0</span>)
|
|
118
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
119
|
+
|
|
120
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">'directed_generic'</span>
|
|
121
|
+
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
122
|
+
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</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">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
124
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</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
|
|
125
|
+
<span class="ruby-comment cmt"># Draw main box
|
|
126
|
+
<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>
|
|
127
|
+
|
|
128
|
+
<span class="ruby-comment cmt"># Draw arrow
|
|
129
|
+
<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-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
|
|
130
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
131
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
132
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
133
|
+
|
|
134
|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand
|
|
135
|
+
<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>
|
|
136
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</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>)
|
|
137
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
138
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
139
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
140
|
+
<span class="ruby-keyword kw">end</span>
|
|
141
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">'spliced'</span>
|
|
142
|
+
<span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
143
|
+
<span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
144
|
+
|
|
145
|
+
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
146
|
+
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
147
|
+
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
148
|
+
|
|
149
|
+
<span class="ruby-comment cmt"># First draw the parts
|
|
150
|
+
<span class="ruby-identifier">feature</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>
|
|
151
|
+
<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>
|
|
152
|
+
<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>)
|
|
153
|
+
<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>)
|
|
154
|
+
<span class="ruby-keyword kw">end</span>
|
|
155
|
+
|
|
156
|
+
<span class="ruby-comment cmt"># And then draw the connections in the gaps
|
|
157
|
+
<span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
|
|
158
|
+
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
|
|
159
|
+
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
|
|
160
|
+
|
|
161
|
+
<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>
|
|
162
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
|
|
163
|
+
<span class="ruby-identifier">to</span> = <span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
|
|
164
|
+
<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>)
|
|
165
|
+
<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">2</span>)
|
|
166
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">middle</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">7</span>)
|
|
167
|
+
<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">2</span>)
|
|
168
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
169
|
+
<span class="ruby-keyword kw">end</span>
|
|
170
|
+
|
|
171
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
|
|
172
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-identifier">feature</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-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-value">5</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-value">5</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-identifier">feature</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-identifier">feature</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-value">5</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-value">5</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">when</span> <span class="ruby-value str">'directed_spliced'</span>
|
|
188
|
+
<span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
189
|
+
<span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
190
|
+
<span class="ruby-comment cmt"># First draw the parts
|
|
191
|
+
<span class="ruby-identifier">locations</span> = <span class="ruby-identifier">feature</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>}
|
|
192
|
+
|
|
193
|
+
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
194
|
+
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
195
|
+
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
196
|
+
|
|
197
|
+
<span class="ruby-comment cmt"># Start with the one with the arrow
|
|
198
|
+
<span class="ruby-identifier">pixel_ranges</span> = <span class="ruby-identifier">feature</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>}
|
|
199
|
+
<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-keyword kw">nil</span>
|
|
200
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</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 => box with arrow is first one
|
|
201
|
+
<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">shift</span>
|
|
202
|
+
<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-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
203
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</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>)
|
|
204
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
205
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
206
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
207
|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># forward strand => box with arrow is last one
|
|
208
|
+
<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">pop</span>
|
|
209
|
+
<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-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
210
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</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>)
|
|
211
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
212
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
213
|
+
<span class="ruby-keyword kw">end</span>
|
|
214
|
+
<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>)
|
|
215
|
+
<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>)
|
|
216
|
+
|
|
217
|
+
<span class="ruby-comment cmt"># And then add the others
|
|
218
|
+
<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>
|
|
219
|
+
<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>
|
|
220
|
+
<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>)
|
|
221
|
+
<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>)
|
|
222
|
+
<span class="ruby-keyword kw">end</span>
|
|
223
|
+
|
|
224
|
+
<span class="ruby-comment cmt"># And then draw the connections in the gaps
|
|
225
|
+
<span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
|
|
226
|
+
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
|
|
227
|
+
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
|
|
228
|
+
|
|
229
|
+
<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>
|
|
230
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
|
|
231
|
+
<span class="ruby-identifier">to</span> = <span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
|
|
232
|
+
<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>)
|
|
233
|
+
<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">2</span>)
|
|
234
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">middle</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">7</span>)
|
|
235
|
+
<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">2</span>)
|
|
236
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
237
|
+
<span class="ruby-keyword kw">end</span>
|
|
238
|
+
|
|
239
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
|
|
240
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-identifier">feature</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>
|
|
241
|
+
<span class="ruby-identifier">to</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
|
|
242
|
+
<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>)
|
|
243
|
+
<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>)
|
|
244
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
245
|
+
<span class="ruby-keyword kw">end</span>
|
|
246
|
+
|
|
247
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_start</span>
|
|
248
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-value">1</span>
|
|
249
|
+
<span class="ruby-identifier">to</span> = <span class="ruby-identifier">feature</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>
|
|
250
|
+
<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>)
|
|
251
|
+
<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>)
|
|
252
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
253
|
+
<span class="ruby-keyword kw">end</span>
|
|
254
|
+
|
|
255
|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#treat as 'generic'
|
|
256
|
+
<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
257
|
+
<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>
|
|
258
|
+
<span class="ruby-keyword kw">end</span>
|
|
259
|
+
|
|
260
|
+
<span class="ruby-comment cmt"># And add the region to the image map
|
|
261
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">clickable</span>
|
|
262
|
+
<span class="ruby-comment cmt"># Comment: we have to add the vertical_offset and TRACK_HEADER_HEIGHT!
|
|
263
|
+
<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>,
|
|
264
|
+
<span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
|
|
265
|
+
<span class="ruby-identifier">right_pixel_of_feature</span>,
|
|
266
|
+
<span class="ruby-identifier">bottom_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
|
|
267
|
+
<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">link</span>
|
|
268
|
+
))
|
|
269
|
+
<span class="ruby-keyword kw">end</span>
|
|
270
|
+
|
|
271
|
+
|
|
272
|
+
<span class="ruby-identifier">feature_drawn</span> = <span class="ruby-keyword kw">true</span>
|
|
273
|
+
<span class="ruby-keyword kw">end</span>
|
|
274
|
+
<span class="ruby-keyword kw">end</span>
|
|
275
|
+
<span class="ruby-keyword kw">end</span>
|
|
276
|
+
<span class="ruby-keyword kw">end</span>
|
|
277
|
+
|
|
278
|
+
<span class="ruby-keyword kw">end</span>
|
|
279
|
+
|
|
280
|
+
<span class="ruby-ivar">@number_of_times_bumped</span> = ( <span class="ruby-identifier">grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
|
|
281
|
+
|
|
282
|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">panel_drawing</span>
|
|
283
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
284
|
+
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|
|
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|
+
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|
|
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|
|
|
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|
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|
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|
|
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|
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|
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|
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<html>
|
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|
+
<head>
|
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|
+
<title>new (Bio::Graphics::Panel::Track)</title>
|
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|
+
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|
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|
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|
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|
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|
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<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 38</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">feature_colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>], <span class="ruby-identifier">feature_glyph</span> = <span class="ruby-value str">'generic'</span>)
|
|
15
|
+
<span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
|
|
16
|
+
<span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
|
|
17
|
+
<span class="ruby-ivar">@feature_colour</span> = <span class="ruby-identifier">feature_colour</span>
|
|
18
|
+
<span class="ruby-ivar">@feature_glyph</span> = <span class="ruby-identifier">feature_glyph</span>
|
|
19
|
+
<span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
20
|
+
<span class="ruby-ivar">@number_of_times_bumped</span> = <span class="ruby-value">0</span>
|
|
21
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
22
|
+
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|
|
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|
+
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|
|
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|
|
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|
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|
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|
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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|
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<html>
|
|
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|
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<head>
|
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|
+
<title>add_feature (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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|
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|
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|
|
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|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 76</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">location_string</span> = <span class="ruby-value str">'0..'</span> <span class="ruby-operator">+</span> (<span class="ruby-ivar">@panel</span>.<span class="ruby-identifier">width</span> <span class="ruby-operator">*</span> <span class="ruby-ivar">@panel</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>)
|
|
15
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">link</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
|
|
16
|
+
<span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>
|
|
17
|
+
<span class="ruby-keyword kw">end</span>
|
|
18
|
+
<span class="ruby-identifier">location_object</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-identifier">location_string</span>)
|
|
19
|
+
<span class="ruby-identifier">start</span> = <span class="ruby-identifier">location_object</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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20
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<span class="ruby-identifier">stop</span> = <span class="ruby-identifier">location_object</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-comment cmt">#if start < 0 or stop > (panel.width.to_f * panel.rescale_factor.to_f).to_i
|
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23
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<span class="ruby-comment cmt"># raise "ERROR: feature " + name + " has coordinates that lie outside of panel"
|
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<span class="ruby-comment cmt">#end
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<span class="ruby-comment cmt">#@features.push(Bio::Graphics::Panel::Track::Feature.new(self, name, location_object, link))
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<span class="ruby-comment cmt">#return @features[-1]
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">></span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start >= panel.display_start and stop <= panel.display_stop
|
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Panel</span><span class="ruby-operator">::</span><span class="ruby-constant">Track</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">location_object</span>, <span class="ruby-identifier">link</span>))
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<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@features</span>[<span class="ruby-value">-1</span>]
|
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+
<span class="ruby-comment cmt"># TODO: chop bits of that extend beyond display
|
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34
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<span class="ruby-comment cmt">#elsif ( start >= panel.display_start and stop > panel.display_stop ) #Feature extends beyond right border
|
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35
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+
<span class="ruby-comment cmt"># new_location_object = Bio::Locations.new
|
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36
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<span class="ruby-comment cmt"># location_object.each do |l|
|
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37
|
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<span class="ruby-comment cmt"># if l.to <= panel.display_stop
|
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38
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<span class="ruby-comment cmt"># new_location_object.push(Bio::Location.new('l
|
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39
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<span class="ruby-comment cmt"># end
|
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40
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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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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 114</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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15
|
+
<span class="ruby-identifier">track_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-comment cmt"># Draw thin line above title
|
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18
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+
<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">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
|
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19
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">vertical_offset</span>)
|
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20
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-identifier">vertical_offset</span>)
|
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21
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
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22
|
+
|
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23
|
+
<span class="ruby-comment cmt"># Draw track title
|
|
24
|
+
<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>)
|
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25
|
+
<span class="ruby-identifier">track_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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26
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
|
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27
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
|
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28
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
|
|
29
|
+
|
|
30
|
+
<span class="ruby-comment cmt"># Draw the features
|
|
31
|
+
<span class="ruby-identifier">grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
|
|
32
|
+
|
|
33
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">save</span> <span class="ruby-keyword kw">do</span>
|
|
34
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
|
|
35
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-ivar">@feature_colour</span>)
|
|
36
|
+
|
|
37
|
+
<span class="ruby-comment cmt"># Now draw the features
|
|
38
|
+
<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
|
|
39
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator"><=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
|
|
40
|
+
<span class="ruby-keyword kw">next</span>
|
|
41
|
+
<span class="ruby-keyword kw">else</span>
|
|
42
|
+
|
|
43
|
+
<span class="ruby-identifier">feature_drawn</span> = <span class="ruby-keyword kw">false</span>
|
|
44
|
+
<span class="ruby-identifier">feature_range</span> = (<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span><span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span>.<span class="ruby-identifier">ceil</span>)
|
|
45
|
+
<span class="ruby-identifier">row</span> = <span class="ruby-value">1</span>
|
|
46
|
+
<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
|
|
47
|
+
<span class="ruby-keyword kw">until</span> <span class="ruby-identifier">feature_drawn</span>
|
|
48
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
|
|
49
|
+
<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>
|
|
50
|
+
<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>)
|
|
51
|
+
<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</span>
|
|
52
|
+
<span class="ruby-keyword kw">end</span>
|
|
53
|
+
<span class="ruby-keyword kw">end</span>
|
|
54
|
+
<span class="ruby-keyword kw">end</span>
|
|
55
|
+
|
|
56
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">row_available</span>
|
|
57
|
+
<span class="ruby-identifier">row</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
|
|
58
|
+
<span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
|
|
59
|
+
<span class="ruby-keyword kw">else</span>
|
|
60
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
|
|
61
|
+
<span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
62
|
+
<span class="ruby-keyword kw">end</span>
|
|
63
|
+
<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>)
|
|
64
|
+
|
|
65
|
+
<span class="ruby-comment cmt"># There are 2 cases where we don't want to draw arrows on
|
|
66
|
+
<span class="ruby-comment cmt"># features:
|
|
67
|
+
<span class="ruby-comment cmt"># (a) when the picture is really zoomed out, features are
|
|
68
|
+
<span class="ruby-comment cmt"># so small that the arrow itself is too big
|
|
69
|
+
<span class="ruby-comment cmt"># (b) if a directed feature on the fw strand extends beyond
|
|
70
|
+
<span class="ruby-comment cmt"># the end of the picture, the arrow is out of view. This
|
|
71
|
+
<span class="ruby-comment cmt"># is the same as considering the feature as undirected.
|
|
72
|
+
<span class="ruby-comment cmt"># The same obviously goes for features on the reverse
|
|
73
|
+
<span class="ruby-comment cmt"># strand that extend beyond the left side of the image.
|
|
74
|
+
<span class="ruby-comment cmt">#
|
|
75
|
+
<span class="ruby-comment cmt"># (a) Zoomed out
|
|
76
|
+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">false</span>
|
|
77
|
+
<span class="ruby-keyword kw">if</span> (<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span>).<span class="ruby-identifier">to_f</span><span class="ruby-operator">/</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"><</span> <span class="ruby-value">2</span>
|
|
78
|
+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
|
|
79
|
+
<span class="ruby-keyword kw">end</span>
|
|
80
|
+
<span class="ruby-comment cmt"># (b) Extending beyond borders picture
|
|
81
|
+
<span class="ruby-keyword kw">if</span> ( <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">chopped_at_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">1</span> ) <span class="ruby-keyword kw">or</span> ( <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">chopped_at_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">-1</span> )
|
|
82
|
+
<span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
|
|
83
|
+
<span class="ruby-keyword kw">end</span>
|
|
84
|
+
|
|
85
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">nil</span>
|
|
86
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature_glyph</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'directed_generic'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
|
|
87
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-value str">'generic'</span>
|
|
88
|
+
<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">feature_glyph</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'directed_spliced'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
|
|
89
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-value str">'spliced'</span>
|
|
90
|
+
<span class="ruby-keyword kw">else</span>
|
|
91
|
+
<span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">feature_glyph</span>
|
|
92
|
+
<span class="ruby-keyword kw">end</span>
|
|
93
|
+
|
|
94
|
+
<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>
|
|
95
|
+
<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>
|
|
96
|
+
|
|
97
|
+
<span class="ruby-keyword kw">case</span> <span class="ruby-identifier">local_feature_glyph</span>
|
|
98
|
+
<span class="ruby-comment cmt"># triangles are typical for features which have a 1 bp position (start == stop)
|
|
99
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">'triangle'</span>
|
|
100
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-value str">"Start and stop are not the same (necessary if you want triangle glyphs)"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span>
|
|
101
|
+
|
|
102
|
+
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
103
|
+
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</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-value">3</span>
|
|
104
|
+
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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-value">3</span>
|
|
105
|
+
<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-operator">+</span> <span class="ruby-value">3</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
|
|
106
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">-3</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>)
|
|
107
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">6</span>, <span class="ruby-value">0</span>)
|
|
108
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
109
|
+
|
|
110
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">'directed_generic'</span>
|
|
111
|
+
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
112
|
+
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
113
|
+
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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-keyword kw">if</span> <span class="ruby-identifier">feature</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
|
|
115
|
+
<span class="ruby-comment cmt"># Draw main box
|
|
116
|
+
<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>
|
|
117
|
+
|
|
118
|
+
<span class="ruby-comment cmt"># Draw arrow
|
|
119
|
+
<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-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
|
|
120
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
121
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
122
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
123
|
+
|
|
124
|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand
|
|
125
|
+
<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>
|
|
126
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</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>)
|
|
127
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
128
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
129
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
130
|
+
<span class="ruby-keyword kw">end</span>
|
|
131
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">'spliced'</span>
|
|
132
|
+
<span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
133
|
+
<span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
134
|
+
|
|
135
|
+
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
136
|
+
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
137
|
+
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
138
|
+
|
|
139
|
+
<span class="ruby-comment cmt"># First draw the parts
|
|
140
|
+
<span class="ruby-identifier">feature</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>
|
|
141
|
+
<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>
|
|
142
|
+
<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>)
|
|
143
|
+
<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>)
|
|
144
|
+
<span class="ruby-keyword kw">end</span>
|
|
145
|
+
|
|
146
|
+
<span class="ruby-comment cmt"># And then draw the connections in the gaps
|
|
147
|
+
<span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
|
|
148
|
+
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
|
|
149
|
+
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
|
|
150
|
+
|
|
151
|
+
<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>
|
|
152
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
|
|
153
|
+
<span class="ruby-identifier">to</span> = <span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
|
|
154
|
+
<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>)
|
|
155
|
+
<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">2</span>)
|
|
156
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">middle</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">7</span>)
|
|
157
|
+
<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">2</span>)
|
|
158
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
159
|
+
<span class="ruby-keyword kw">end</span>
|
|
160
|
+
|
|
161
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
|
|
162
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-identifier">feature</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>
|
|
163
|
+
<span class="ruby-identifier">to</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
|
|
164
|
+
<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>)
|
|
165
|
+
<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>)
|
|
166
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
167
|
+
<span class="ruby-keyword kw">end</span>
|
|
168
|
+
|
|
169
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_start</span>
|
|
170
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-value">1</span>
|
|
171
|
+
<span class="ruby-identifier">to</span> = <span class="ruby-identifier">feature</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>
|
|
172
|
+
<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>)
|
|
173
|
+
<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>)
|
|
174
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
175
|
+
<span class="ruby-keyword kw">end</span>
|
|
176
|
+
|
|
177
|
+
<span class="ruby-keyword kw">when</span> <span class="ruby-value str">'directed_spliced'</span>
|
|
178
|
+
<span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
179
|
+
<span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
180
|
+
<span class="ruby-comment cmt"># First draw the parts
|
|
181
|
+
<span class="ruby-identifier">locations</span> = <span class="ruby-identifier">feature</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>}
|
|
182
|
+
|
|
183
|
+
<span class="ruby-comment cmt"># Need to get this for the imagemap
|
|
184
|
+
<span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
185
|
+
<span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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>
|
|
186
|
+
|
|
187
|
+
<span class="ruby-comment cmt"># Start with the one with the arrow
|
|
188
|
+
<span class="ruby-identifier">pixel_ranges</span> = <span class="ruby-identifier">feature</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>}
|
|
189
|
+
<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-keyword kw">nil</span>
|
|
190
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</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 => box with arrow is first one
|
|
191
|
+
<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">shift</span>
|
|
192
|
+
<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-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
193
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</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>)
|
|
194
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
195
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
196
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
|
|
197
|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># forward strand => box with arrow is last one
|
|
198
|
+
<span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">pop</span>
|
|
199
|
+
<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-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
|
|
200
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</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>)
|
|
201
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
202
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
|
|
203
|
+
<span class="ruby-keyword kw">end</span>
|
|
204
|
+
<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>)
|
|
205
|
+
<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>)
|
|
206
|
+
|
|
207
|
+
<span class="ruby-comment cmt"># And then add the others
|
|
208
|
+
<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>
|
|
209
|
+
<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>
|
|
210
|
+
<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>)
|
|
211
|
+
<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>)
|
|
212
|
+
<span class="ruby-keyword kw">end</span>
|
|
213
|
+
|
|
214
|
+
<span class="ruby-comment cmt"># And then draw the connections in the gaps
|
|
215
|
+
<span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
|
|
216
|
+
<span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
|
|
217
|
+
<span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
|
|
218
|
+
|
|
219
|
+
<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>
|
|
220
|
+
<span class="ruby-identifier">from</span> = <span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
|
|
221
|
+
<span class="ruby-identifier">to</span> = <span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
|
|
222
|
+
<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>)
|
|
223
|
+
<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">2</span>)
|
|
224
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">middle</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">7</span>)
|
|
225
|
+
<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">2</span>)
|
|
226
|
+
<span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
|
|
227
|
+
<span class="ruby-keyword kw">end</span>
|
|
228
|
+
|
|
229
|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#treat as 'generic'
|
|
230
|
+
<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</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-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">stop_pixel</span>
|
|
231
|
+
<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>
|
|
232
|
+
<span class="ruby-keyword kw">end</span>
|
|
233
|
+
|
|
234
|
+
<span class="ruby-comment cmt"># And add the region to the image map
|
|
235
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">clickable</span>
|
|
236
|
+
<span class="ruby-comment cmt"># Comment: we have to add the vertical_offset and TRACK_HEADER_HEIGHT!
|
|
237
|
+
<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>,
|
|
238
|
+
<span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
|
|
239
|
+
<span class="ruby-identifier">right_pixel_of_feature</span>,
|
|
240
|
+
<span class="ruby-identifier">bottom_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
|
|
241
|
+
<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">link</span>
|
|
242
|
+
))
|
|
243
|
+
<span class="ruby-keyword kw">end</span>
|
|
244
|
+
|
|
245
|
+
|
|
246
|
+
<span class="ruby-identifier">feature_drawn</span> = <span class="ruby-keyword kw">true</span>
|
|
247
|
+
<span class="ruby-keyword kw">end</span>
|
|
248
|
+
<span class="ruby-keyword kw">end</span>
|
|
249
|
+
<span class="ruby-keyword kw">end</span>
|
|
250
|
+
<span class="ruby-keyword kw">end</span>
|
|
251
|
+
|
|
252
|
+
<span class="ruby-keyword kw">end</span>
|
|
253
|
+
|
|
254
|
+
<span class="ruby-ivar">@number_of_times_bumped</span> = ( <span class="ruby-identifier">grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
|
|
255
|
+
|
|
256
|
+
<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">panel_drawing</span>
|
|
257
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
258
|
+
</body>
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259
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+
</html>
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