bio-graphics 1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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<?xml version="1.0" encoding="iso-8859-1"?>
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<title>new (Bio::Graphics::Panel::Track)</title>
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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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<html>
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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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<html>
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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
|
|
73
|
+
<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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