bio-svgenes 0.2.3 → 0.3.0
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/.DS_Store +0 -0
- data/VERSION +1 -1
- data/bio-svgenes.gemspec +59 -4
- data/doc/.DS_Store +0 -0
- data/doc/Bio.html +141 -0
- data/doc/Bio/.DS_Store +0 -0
- data/doc/Bio/Graphics.html +147 -0
- data/doc/Bio/Graphics/Glyph.html +1061 -0
- data/doc/Bio/Graphics/MiniFeature.html +342 -0
- data/doc/Bio/Graphics/Page.html +1200 -0
- data/doc/Bio/Graphics/Primitive.html +278 -0
- data/doc/Bio/Graphics/SVGEE.html +471 -0
- data/doc/Bio/Graphics/Track.html +506 -0
- data/doc/LICENSE_txt.html +118 -0
- data/doc/created.rid +9 -0
- data/doc/images/add.png +0 -0
- data/doc/images/arrow_up.png +0 -0
- data/doc/images/brick.png +0 -0
- data/doc/images/brick_link.png +0 -0
- data/doc/images/bug.png +0 -0
- data/doc/images/bullet_black.png +0 -0
- data/doc/images/bullet_toggle_minus.png +0 -0
- data/doc/images/bullet_toggle_plus.png +0 -0
- data/doc/images/date.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
- data/doc/images/macFFBgHack.png +0 -0
- data/doc/images/package.png +0 -0
- data/doc/images/page_green.png +0 -0
- data/doc/images/page_white_text.png +0 -0
- data/doc/images/page_white_width.png +0 -0
- data/doc/images/plugin.png +0 -0
- data/doc/images/ruby.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/images/tag_green.png +0 -0
- data/doc/images/transparent.png +0 -0
- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +94 -0
- data/doc/js/darkfish.js +155 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/rdoc.css +595 -0
- data/doc/table_of_contents.html +162 -0
- data/test/gene.gff +4 -0
- data/test/json_config.json +17 -0
- data/test/test_glyph.rb +33 -0
- data/test/test_mini_feature.rb +37 -0
- data/test/test_page.rb +127 -0
- data/test/test_primitive.rb +45 -0
- data/test/test_svgee.rb +73 -0
- data/test/test_track.rb +53 -0
- data/test/test_transcripts.gff +4 -0
- metadata +94 -14
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<h1 class="class">class Bio::Graphics::MiniFeature</h1>
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<p>The <a href="MiniFeature.html">MiniFeature</a> class represents any feature
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<p>Creates a new <a href="MiniFeature.html">MiniFeature</a></p>
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<p><em>Arguments</em></p>
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<p>start = the start position of the feature</p>
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<h2 id="method-c-new-label-Example+usage">Example usage<span><a href="#method-c-new-label-Example+usage">¶</a> <a href="#documentation">↑</a></span></h2>
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<pre class="ruby"><span class="ruby-ivar">@mini1</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">MiniFeature</span>.<span class="ruby-identifier">new</span>(:<span class="ruby-identifier">start=</span><span class="ruby-operator">></span><span class="ruby-value">3631</span>, :<span class="ruby-keyword">end</span>=<span class="ruby-operator">></span><span class="ruby-value">5899</span>, :<span class="ruby-identifier">strand=</span><span class="ruby-operator">></span><span class="ruby-string">'+'</span>,
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:<span class="ruby-identifier">exons=</span><span class="ruby-operator">></span>[<span class="ruby-value">4000</span>, <span class="ruby-value">4500</span>, <span class="ruby-value">4700</span>, <span class="ruby-value">5000</span>], :<span class="ruby-identifier">utrs=</span><span class="ruby-operator">></span>[<span class="ruby-value">3631</span>, <span class="ruby-value">3650</span>], :<span class="ruby-identifier">segment_height=</span><span class="ruby-operator">></span><span class="ruby-value">5</span>, :<span class="ruby-identifier">id=</span><span class="ruby-operator">></span><span class="ruby-string">"AT1G01010"</span>)
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<h1 class="class">class Bio::Graphics::Page</h1>
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<p>Calculates the colour or gradient for the supplied <a
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href="Track.html">Bio::Graphics::Track</a> objects and adds them to the <a
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 138</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">args</span>)
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[<span class="ruby-value">:fill_color</span>, <span class="ruby-value">:exon_fill_color</span>, <span class="ruby-value">:utr_fill_color</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">colour_tag</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword">if</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradients</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>])
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<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>]))
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<span class="ruby-keyword">end</span></pre>
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<p>Prints out the svg text</p>
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 332</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw</span>
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<span class="ruby-identifier">puts</span> <span class="ruby-identifier">get_markup</span>
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<span class="ruby-keyword">end</span></pre>
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<p><code>args</code> - an Array of <a
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 189</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_circle</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">circle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<span class="ruby-keyword">end</span></pre>
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<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
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<p><code>args</code> - an Array of <a
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 184</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_directed</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<span class="ruby-keyword">end</span></pre>
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</div><!-- draw_directed-method -->
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<div id="method-i-draw_down_triangle" class="method-detail ">
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<span class="method-name">draw_down_triangle</span><span
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class="method-args">(args)</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
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the <a href="SVGEE.html">SVGEE</a> object</p>
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<p><code>args</code> - an Array of <a
|
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href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
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type</p>
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<div class="method-source-code" id="draw_down_triangle-source">
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 209</span>
|
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+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_down_triangle</span>(<span class="ruby-identifier">args</span>)
|
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+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">down_triangle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<span class="ruby-keyword">end</span></pre>
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</div>
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</div><!-- draw_down_triangle-method -->
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<div id="method-i-draw_features" class="method-detail ">
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<div class="method-heading">
|
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<span class="method-name">draw_features</span><span
|
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+
class="method-args">(track)</span>
|
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|
|
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<span class="method-click-advice">click to toggle source</span>
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|
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</div>
|
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|
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|
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<div class="method-description">
|
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|
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|
|
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|
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<p>Takes a <a href="Track.html">Bio::Graphics::Track</a> object and sorts out
|
|
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|
+
the input information into a user friendly format.</p>
|
|
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|
+
|
|
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|
+
<p>It examines the the type of track and calculates the required parameters</p>
|
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<ul><li>
|
|
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|
+
<p><code>args</code> - an Array of <a
|
|
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|
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href="Track.html">Bio::Graphics::Track</a> object</p>
|
|
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|
+
</li></ul>
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<div class="method-source-code" id="draw_features-source">
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 222</span>
|
|
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|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_features</span>(<span class="ruby-identifier">track</span>)
|
|
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|
+
<span class="ruby-keyword">if</span> [<span class="ruby-value">:histogram</span>, <span class="ruby-string">"histogram"</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span>) <span class="ruby-comment">#do different stuff for data tracks...</span>
|
|
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|
+
|
|
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|
+
<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>)
|
|
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|
+
<span class="ruby-identifier">max</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">max_y</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">max_y</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span>, <span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">segment_height</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">b</span>.<span class="ruby-identifier">segment_height</span> }.<span class="ruby-identifier">last</span>.<span class="ruby-identifier">segment_height</span>
|
|
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|
+
<span class="ruby-identifier">min</span> = <span class="ruby-value">0</span>
|
|
427
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">label</span>
|
|
428
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">name</span>, <span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> <span class="ruby-value">30</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-value">3</span>)
|
|
429
|
+
<span class="ruby-keyword">end</span>
|
|
430
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">max</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">to_px</span>(<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">+</span> <span class="ruby-value">5</span>, <span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>)
|
|
431
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">min</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">to_px</span>(<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">+</span> <span class="ruby-value">5</span>, <span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>)
|
|
432
|
+
<span class="ruby-identifier">data_interval</span> = <span class="ruby-identifier">max</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">min</span>
|
|
433
|
+
<span class="ruby-identifier">data_per_px</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">data_interval</span>.<span class="ruby-identifier">to_f</span>
|
|
434
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span>
|
|
435
|
+
<span class="ruby-identifier">x</span> = <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>)
|
|
436
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">f</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))
|
|
437
|
+
<span class="ruby-identifier">height</span> = <span class="ruby-identifier">f</span>.<span class="ruby-identifier">segment_height</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">data_per_px</span>
|
|
438
|
+
<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">height</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>
|
|
439
|
+
<span class="ruby-comment">#$stderr.puts f.segment_height, data_per_px, data_interval, max, min, "------"</span>
|
|
440
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">send</span>(<span class="ruby-node">"draw_#{track.glyph}"</span>, {<span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
441
|
+
<span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>,
|
|
442
|
+
<span class="ruby-value">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">width</span>,
|
|
443
|
+
<span class="ruby-value">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">height</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">args</span>))
|
|
444
|
+
<span class="ruby-keyword">end</span>
|
|
445
|
+
<span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>) <span class="ruby-operator">+</span> <span class="ruby-value">20</span>
|
|
446
|
+
<span class="ruby-keyword">else</span> <span class="ruby-comment">##following stuff for the features</span>
|
|
447
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">label</span>
|
|
448
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">name</span>, <span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> <span class="ruby-value">30</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-value">3</span>)
|
|
449
|
+
<span class="ruby-keyword">end</span>
|
|
450
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">get_rows</span> <span class="ruby-comment">##work out how many rows and which features belong in each row...</span>
|
|
451
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span>, <span class="ruby-identifier">index</span><span class="ruby-operator">|</span>
|
|
452
|
+
<span class="ruby-identifier">x</span> = <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-comment">#bottom left of feature</span>
|
|
453
|
+
<span class="ruby-identifier">all_sub_blocks</span> = []
|
|
454
|
+
|
|
455
|
+
<span class="ruby-comment">#convert the exon and utr start stops to px start stops and px widths</span>
|
|
456
|
+
<span class="ruby-identifier">exons</span> = []
|
|
457
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>
|
|
458
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>.<span class="ruby-identifier">each_slice</span>(<span class="ruby-value">2</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">exon</span><span class="ruby-operator">|</span>
|
|
459
|
+
<span class="ruby-identifier">all_sub_blocks</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">exon</span>
|
|
460
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">exon</span>.<span class="ruby-identifier">nil?</span>
|
|
461
|
+
<span class="ruby-identifier">exons</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">exon</span>[<span class="ruby-value">1</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
462
|
+
<span class="ruby-keyword">end</span>
|
|
463
|
+
<span class="ruby-keyword">end</span>
|
|
464
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span> = <span class="ruby-identifier">exons</span>
|
|
465
|
+
|
|
466
|
+
<span class="ruby-identifier">utrs</span> = []
|
|
467
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>
|
|
468
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>.<span class="ruby-identifier">each_slice</span>(<span class="ruby-value">2</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">utr</span><span class="ruby-operator">|</span>
|
|
469
|
+
<span class="ruby-identifier">all_sub_blocks</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">utr</span>
|
|
470
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">nil?</span>
|
|
471
|
+
<span class="ruby-identifier">utrs</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">utr</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">utr</span>[<span class="ruby-value">1</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">utr</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
472
|
+
<span class="ruby-keyword">end</span>
|
|
473
|
+
<span class="ruby-keyword">end</span>
|
|
474
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span> = <span class="ruby-identifier">utrs</span>
|
|
475
|
+
|
|
476
|
+
<span class="ruby-comment">#if there are any intron like gaps.. get where they would be</span>
|
|
477
|
+
<span class="ruby-keyword">if</span> <span class="ruby-keyword">not</span> <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">empty?</span>
|
|
478
|
+
<span class="ruby-identifier">all_sub_blocks</span> = <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span>, <span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">b</span>.<span class="ruby-identifier">first</span> }
|
|
479
|
+
<span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">each_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
480
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">length</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">>=</span> <span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">first</span> <span class="ruby-comment">#skip if there is no gap</span>
|
|
481
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">block_gaps</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">first</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
482
|
+
<span class="ruby-keyword">end</span>
|
|
483
|
+
<span class="ruby-keyword">end</span>
|
|
484
|
+
|
|
485
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">f</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))
|
|
486
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">width</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span>
|
|
487
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span>
|
|
488
|
+
<span class="ruby-keyword">end</span>
|
|
489
|
+
<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_rows</span>[<span class="ruby-identifier">index</span>] <span class="ruby-operator">*</span> <span class="ruby-value">2</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span>)
|
|
490
|
+
|
|
491
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">send</span>(<span class="ruby-node">"draw_#{track.glyph}"</span>, {<span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
492
|
+
<span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>,
|
|
493
|
+
<span class="ruby-value">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">width</span>,
|
|
494
|
+
<span class="ruby-value">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">strand</span>,
|
|
495
|
+
<span class="ruby-value">:exons</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>,
|
|
496
|
+
<span class="ruby-value">:utrs</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>,
|
|
497
|
+
<span class="ruby-value">:block_gaps</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">block_gaps</span>,
|
|
498
|
+
<span class="ruby-value">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span>
|
|
499
|
+
}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">args</span>))
|
|
500
|
+
|
|
501
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">id</span>
|
|
502
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">width</span> <span class="ruby-value">+2</span>, <span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">id</span>)
|
|
503
|
+
<span class="ruby-keyword">end</span>
|
|
504
|
+
<span class="ruby-keyword">end</span>
|
|
505
|
+
<span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_rows</span> <span class="ruby-operator">*</span> <span class="ruby-value">2</span>) <span class="ruby-operator">+</span> <span class="ruby-value">20</span>
|
|
506
|
+
<span class="ruby-keyword">end</span>
|
|
507
|
+
|
|
508
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-value">100</span> <span class="ruby-comment">#fudge...</span>
|
|
509
|
+
<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">update_height</span>(<span class="ruby-ivar">@height</span>)
|
|
510
|
+
<span class="ruby-comment">#@svg.update_width(@width + 200)</span>
|
|
511
|
+
|
|
512
|
+
<span class="ruby-keyword">end</span></pre>
|
|
513
|
+
</div><!-- draw_features-source -->
|
|
514
|
+
|
|
515
|
+
</div>
|
|
516
|
+
|
|
517
|
+
|
|
518
|
+
|
|
519
|
+
|
|
520
|
+
</div><!-- draw_features-method -->
|
|
521
|
+
|
|
522
|
+
|
|
523
|
+
<div id="method-i-draw_generic" class="method-detail ">
|
|
524
|
+
|
|
525
|
+
<div class="method-heading">
|
|
526
|
+
<span class="method-name">draw_generic</span><span
|
|
527
|
+
class="method-args">(args)</span>
|
|
528
|
+
|
|
529
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
530
|
+
|
|
531
|
+
</div>
|
|
532
|
+
|
|
533
|
+
|
|
534
|
+
<div class="method-description">
|
|
535
|
+
|
|
536
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
537
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
538
|
+
<ul><li>
|
|
539
|
+
<p><code>args</code> - an Array of <a
|
|
540
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
541
|
+
type</p>
|
|
542
|
+
</li></ul>
|
|
543
|
+
|
|
544
|
+
|
|
545
|
+
|
|
546
|
+
|
|
547
|
+
<div class="method-source-code" id="draw_generic-source">
|
|
548
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 179</span>
|
|
549
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_generic</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment">#remember presentation info comes from track@args when the track is defined</span>
|
|
550
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
551
|
+
<span class="ruby-keyword">end</span></pre>
|
|
552
|
+
</div><!-- draw_generic-source -->
|
|
553
|
+
|
|
554
|
+
</div>
|
|
555
|
+
|
|
556
|
+
|
|
557
|
+
|
|
558
|
+
|
|
559
|
+
</div><!-- draw_generic-method -->
|
|
560
|
+
|
|
561
|
+
|
|
562
|
+
<div id="method-i-draw_histogram" class="method-detail ">
|
|
563
|
+
|
|
564
|
+
<div class="method-heading">
|
|
565
|
+
<span class="method-name">draw_histogram</span><span
|
|
566
|
+
class="method-args">(args)</span>
|
|
567
|
+
|
|
568
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
569
|
+
|
|
570
|
+
</div>
|
|
571
|
+
|
|
572
|
+
|
|
573
|
+
<div class="method-description">
|
|
574
|
+
|
|
575
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
576
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
577
|
+
<ul><li>
|
|
578
|
+
<p><code>args</code> - an Array of <a
|
|
579
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
580
|
+
type</p>
|
|
581
|
+
</li></ul>
|
|
582
|
+
|
|
583
|
+
|
|
584
|
+
|
|
585
|
+
|
|
586
|
+
<div class="method-source-code" id="draw_histogram-source">
|
|
587
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 199</span>
|
|
588
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_histogram</span>(<span class="ruby-identifier">args</span>)
|
|
589
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
590
|
+
<span class="ruby-keyword">end</span></pre>
|
|
591
|
+
</div><!-- draw_histogram-source -->
|
|
592
|
+
|
|
593
|
+
</div>
|
|
594
|
+
|
|
595
|
+
|
|
596
|
+
|
|
597
|
+
|
|
598
|
+
</div><!-- draw_histogram-method -->
|
|
599
|
+
|
|
600
|
+
|
|
601
|
+
<div id="method-i-draw_label" class="method-detail ">
|
|
602
|
+
|
|
603
|
+
<div class="method-heading">
|
|
604
|
+
<span class="method-name">draw_label</span><span
|
|
605
|
+
class="method-args">(args)</span>
|
|
606
|
+
|
|
607
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
608
|
+
|
|
609
|
+
</div>
|
|
610
|
+
|
|
611
|
+
|
|
612
|
+
<div class="method-description">
|
|
613
|
+
|
|
614
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
615
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
616
|
+
<ul><li>
|
|
617
|
+
<p><code>args</code> - an Array of <a
|
|
618
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> object</p>
|
|
619
|
+
</li></ul>
|
|
620
|
+
|
|
621
|
+
|
|
622
|
+
|
|
623
|
+
|
|
624
|
+
<div class="method-source-code" id="draw_label-source">
|
|
625
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 172</span>
|
|
626
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">args</span>)
|
|
627
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:text</span>],
|
|
628
|
+
<span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:x</span>],
|
|
629
|
+
<span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>]).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
630
|
+
<span class="ruby-keyword">end</span></pre>
|
|
631
|
+
</div><!-- draw_label-source -->
|
|
632
|
+
|
|
633
|
+
</div>
|
|
634
|
+
|
|
635
|
+
|
|
636
|
+
|
|
637
|
+
|
|
638
|
+
</div><!-- draw_label-method -->
|
|
639
|
+
|
|
640
|
+
|
|
641
|
+
<div id="method-i-draw_scale" class="method-detail ">
|
|
642
|
+
|
|
643
|
+
<div class="method-heading">
|
|
644
|
+
<span class="method-name">draw_scale</span><span
|
|
645
|
+
class="method-args">()</span>
|
|
646
|
+
|
|
647
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
648
|
+
|
|
649
|
+
</div>
|
|
650
|
+
|
|
651
|
+
|
|
652
|
+
<div class="method-description">
|
|
653
|
+
|
|
654
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
655
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
656
|
+
|
|
657
|
+
|
|
658
|
+
|
|
659
|
+
|
|
660
|
+
<div class="method-source-code" id="draw_scale-source">
|
|
661
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 165</span>
|
|
662
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_scale</span>
|
|
663
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">scale</span>(<span class="ruby-value">:start</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@scale_start</span>,
|
|
664
|
+
<span class="ruby-value">:stop</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@scale_stop</span>,
|
|
665
|
+
<span class="ruby-value">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@num_intervals</span>, <span class="ruby-value">:page_width</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@width</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
666
|
+
<span class="ruby-keyword">end</span></pre>
|
|
667
|
+
</div><!-- draw_scale-source -->
|
|
668
|
+
|
|
669
|
+
</div>
|
|
670
|
+
|
|
671
|
+
|
|
672
|
+
|
|
673
|
+
|
|
674
|
+
</div><!-- draw_scale-method -->
|
|
675
|
+
|
|
676
|
+
|
|
677
|
+
<div id="method-i-draw_span" class="method-detail ">
|
|
678
|
+
|
|
679
|
+
<div class="method-heading">
|
|
680
|
+
<span class="method-name">draw_span</span><span
|
|
681
|
+
class="method-args">(args)</span>
|
|
682
|
+
|
|
683
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
684
|
+
|
|
685
|
+
</div>
|
|
686
|
+
|
|
687
|
+
|
|
688
|
+
<div class="method-description">
|
|
689
|
+
|
|
690
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
691
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
692
|
+
<ul><li>
|
|
693
|
+
<p><code>args</code> - an Array of <a
|
|
694
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
695
|
+
type</p>
|
|
696
|
+
</li></ul>
|
|
697
|
+
|
|
698
|
+
|
|
699
|
+
|
|
700
|
+
|
|
701
|
+
<div class="method-source-code" id="draw_span-source">
|
|
702
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 214</span>
|
|
703
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_span</span>(<span class="ruby-identifier">args</span>)
|
|
704
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">span</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
705
|
+
<span class="ruby-keyword">end</span></pre>
|
|
706
|
+
</div><!-- draw_span-source -->
|
|
707
|
+
|
|
708
|
+
</div>
|
|
709
|
+
|
|
710
|
+
|
|
711
|
+
|
|
712
|
+
|
|
713
|
+
</div><!-- draw_span-method -->
|
|
714
|
+
|
|
715
|
+
|
|
716
|
+
<div id="method-i-draw_transcript" class="method-detail ">
|
|
717
|
+
|
|
718
|
+
<div class="method-heading">
|
|
719
|
+
<span class="method-name">draw_transcript</span><span
|
|
720
|
+
class="method-args">(args)</span>
|
|
721
|
+
|
|
722
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
723
|
+
|
|
724
|
+
</div>
|
|
725
|
+
|
|
726
|
+
|
|
727
|
+
<div class="method-description">
|
|
728
|
+
|
|
729
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
730
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
731
|
+
<ul><li>
|
|
732
|
+
<p><code>args</code> - an Array of <a
|
|
733
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
734
|
+
type</p>
|
|
735
|
+
</li></ul>
|
|
736
|
+
|
|
737
|
+
|
|
738
|
+
|
|
739
|
+
|
|
740
|
+
<div class="method-source-code" id="draw_transcript-source">
|
|
741
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 194</span>
|
|
742
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_transcript</span>(<span class="ruby-identifier">args</span>)
|
|
743
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">transcript</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
744
|
+
<span class="ruby-keyword">end</span></pre>
|
|
745
|
+
</div><!-- draw_transcript-source -->
|
|
746
|
+
|
|
747
|
+
</div>
|
|
748
|
+
|
|
749
|
+
|
|
750
|
+
|
|
751
|
+
|
|
752
|
+
</div><!-- draw_transcript-method -->
|
|
753
|
+
|
|
754
|
+
|
|
755
|
+
<div id="method-i-draw_up_triangle" class="method-detail ">
|
|
756
|
+
|
|
757
|
+
<div class="method-heading">
|
|
758
|
+
<span class="method-name">draw_up_triangle</span><span
|
|
759
|
+
class="method-args">(args)</span>
|
|
760
|
+
|
|
761
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
762
|
+
|
|
763
|
+
</div>
|
|
764
|
+
|
|
765
|
+
|
|
766
|
+
<div class="method-description">
|
|
767
|
+
|
|
768
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
769
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
770
|
+
<ul><li>
|
|
771
|
+
<p><code>args</code> - an Array of <a
|
|
772
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
773
|
+
type</p>
|
|
774
|
+
</li></ul>
|
|
775
|
+
|
|
776
|
+
|
|
777
|
+
|
|
778
|
+
|
|
779
|
+
<div class="method-source-code" id="draw_up_triangle-source">
|
|
780
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 204</span>
|
|
781
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_up_triangle</span>(<span class="ruby-identifier">args</span>)
|
|
782
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">up_triangle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
783
|
+
<span class="ruby-keyword">end</span></pre>
|
|
784
|
+
</div><!-- draw_up_triangle-source -->
|
|
785
|
+
|
|
786
|
+
</div>
|
|
787
|
+
|
|
788
|
+
|
|
789
|
+
|
|
790
|
+
|
|
791
|
+
</div><!-- draw_up_triangle-method -->
|
|
792
|
+
|
|
793
|
+
|
|
794
|
+
<div id="method-i-get_limits" class="method-detail ">
|
|
795
|
+
|
|
796
|
+
<div class="method-heading">
|
|
797
|
+
<span class="method-name">get_limits</span><span
|
|
798
|
+
class="method-args">()</span>
|
|
799
|
+
|
|
800
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
801
|
+
|
|
802
|
+
</div>
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
<div class="method-description">
|
|
806
|
+
|
|
807
|
+
<p>Calculates the <a href="Page.html">Page</a> scale-start and scale-stop
|
|
808
|
+
position and the nucleotides per pixel for the current <a
|
|
809
|
+
href="Page.html">Page</a></p>
|
|
810
|
+
|
|
811
|
+
|
|
812
|
+
|
|
813
|
+
|
|
814
|
+
<div class="method-source-code" id="get_limits-source">
|
|
815
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 154</span>
|
|
816
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">get_limits</span>
|
|
817
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
818
|
+
<span class="ruby-identifier">lowest</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">x</span>, <span class="ruby-identifier">y</span><span class="ruby-operator">|</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">y</span>.<span class="ruby-identifier">start</span> }.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">start</span>
|
|
819
|
+
<span class="ruby-identifier">highest</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">x</span>, <span class="ruby-identifier">y</span><span class="ruby-operator">|</span> <span class="ruby-identifier">y</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">end</span> }.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">end</span>
|
|
820
|
+
<span class="ruby-ivar">@scale_start</span> = <span class="ruby-identifier">lowest</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">lowest</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@scale_start</span>
|
|
821
|
+
<span class="ruby-ivar">@scale_stop</span> = <span class="ruby-identifier">highest</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">highest</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@scale_stop</span>
|
|
822
|
+
<span class="ruby-ivar">@nt_per_px_x</span> = (<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@width</span>.<span class="ruby-identifier">to_f</span>
|
|
823
|
+
<span class="ruby-keyword">end</span>
|
|
824
|
+
<span class="ruby-keyword">end</span></pre>
|
|
825
|
+
</div><!-- get_limits-source -->
|
|
826
|
+
|
|
827
|
+
</div>
|
|
828
|
+
|
|
829
|
+
|
|
830
|
+
|
|
831
|
+
|
|
832
|
+
</div><!-- get_limits-method -->
|
|
833
|
+
|
|
834
|
+
|
|
835
|
+
<div id="method-i-get_markup" class="method-detail ">
|
|
836
|
+
|
|
837
|
+
<div class="method-heading">
|
|
838
|
+
<span class="method-name">get_markup</span><span
|
|
839
|
+
class="method-args">()</span>
|
|
840
|
+
|
|
841
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
842
|
+
|
|
843
|
+
</div>
|
|
844
|
+
|
|
845
|
+
|
|
846
|
+
<div class="method-description">
|
|
847
|
+
|
|
848
|
+
<p>Pulls together all track information to create svg text which will draw all
|
|
849
|
+
the features on the page to scale Uses the methods <code>get_limits</code>
|
|
850
|
+
and <code>draw_scale</code> and then <code>draw_feature</code> for each
|
|
851
|
+
track on the page</p>
|
|
852
|
+
|
|
853
|
+
|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
<div class="method-source-code" id="get_markup-source">
|
|
857
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 323</span>
|
|
858
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">get_markup</span>
|
|
859
|
+
<span class="ruby-identifier">get_limits</span>
|
|
860
|
+
<span class="ruby-identifier">draw_scale</span>
|
|
861
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
862
|
+
<span class="ruby-identifier">draw_features</span>(<span class="ruby-identifier">track</span>)
|
|
863
|
+
<span class="ruby-keyword">end</span>
|
|
864
|
+
<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">draw</span>
|
|
865
|
+
<span class="ruby-keyword">end</span></pre>
|
|
866
|
+
</div><!-- get_markup-source -->
|
|
867
|
+
|
|
868
|
+
</div>
|
|
869
|
+
|
|
870
|
+
|
|
871
|
+
|
|
872
|
+
|
|
873
|
+
</div><!-- get_markup-method -->
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
<div id="method-i-to_px" class="method-detail ">
|
|
877
|
+
|
|
878
|
+
<div class="method-heading">
|
|
879
|
+
<span class="method-name">to_px</span><span
|
|
880
|
+
class="method-args">(num)</span>
|
|
881
|
+
|
|
882
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
883
|
+
|
|
884
|
+
</div>
|
|
885
|
+
|
|
886
|
+
|
|
887
|
+
<div class="method-description">
|
|
888
|
+
|
|
889
|
+
<p>Provides the number of pixels required for a given number of nucleotides,
|
|
890
|
+
e.g the length of a certain exon</p>
|
|
891
|
+
<ul><li>
|
|
892
|
+
<p><code>num</code> - the number of nucleotides</p>
|
|
893
|
+
</li><li>
|
|
894
|
+
<p><code>returns</code> - the required number of pixels to draw the object</p>
|
|
895
|
+
</li></ul>
|
|
896
|
+
|
|
897
|
+
|
|
898
|
+
|
|
899
|
+
|
|
900
|
+
<div class="method-source-code" id="to_px-source">
|
|
901
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 317</span>
|
|
902
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">num</span>)
|
|
903
|
+
(<span class="ruby-identifier">num</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@nt_per_px_x</span>.<span class="ruby-identifier">to_f</span>)
|
|
904
|
+
<span class="ruby-keyword">end</span></pre>
|
|
905
|
+
</div><!-- to_px-source -->
|
|
906
|
+
|
|
907
|
+
</div>
|
|
908
|
+
|
|
909
|
+
|
|
910
|
+
|
|
911
|
+
|
|
912
|
+
</div><!-- to_px-method -->
|
|
913
|
+
|
|
914
|
+
|
|
915
|
+
<div id="method-i-write" class="method-detail ">
|
|
916
|
+
|
|
917
|
+
<div class="method-heading">
|
|
918
|
+
<span class="method-name">write</span><span
|
|
919
|
+
class="method-args">(file)</span>
|
|
920
|
+
|
|
921
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
922
|
+
|
|
923
|
+
</div>
|
|
924
|
+
|
|
925
|
+
|
|
926
|
+
<div class="method-description">
|
|
927
|
+
|
|
928
|
+
<p>Writes the svg text to a file</p>
|
|
929
|
+
<ul><li>
|
|
930
|
+
<p><code>file</code> - the file to which the svg text should be written</p>
|
|
931
|
+
</li></ul>
|
|
932
|
+
|
|
933
|
+
|
|
934
|
+
|
|
935
|
+
|
|
936
|
+
<div class="method-source-code" id="write-source">
|
|
937
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 338</span>
|
|
938
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">write</span>(<span class="ruby-identifier">file</span>)
|
|
939
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">file</span>, <span class="ruby-string">'w'</span>).<span class="ruby-identifier">write</span>(<span class="ruby-identifier">get_markup</span>)
|
|
940
|
+
<span class="ruby-keyword">end</span></pre>
|
|
941
|
+
</div><!-- write-source -->
|
|
942
|
+
|
|
943
|
+
</div>
|
|
944
|
+
|
|
945
|
+
|
|
946
|
+
|
|
947
|
+
|
|
948
|
+
</div><!-- write-method -->
|
|
949
|
+
|
|
950
|
+
|
|
951
|
+
</section><!-- public-instance-method-details -->
|
|
952
|
+
|
|
953
|
+
<section id="public-class-5Buntitled-5D-method-details" class="method-section section">
|
|
954
|
+
<h3 class="section-header">Public Class Methods</h3>
|
|
955
|
+
|
|
956
|
+
|
|
957
|
+
<div id="method-c-from_json" class="method-detail ">
|
|
958
|
+
|
|
959
|
+
<div class="method-heading">
|
|
960
|
+
<span class="method-name">from_json</span><span
|
|
961
|
+
class="method-args">(args)</span>
|
|
962
|
+
|
|
963
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
964
|
+
|
|
965
|
+
</div>
|
|
966
|
+
|
|
967
|
+
|
|
968
|
+
<div class="method-description">
|
|
969
|
+
|
|
970
|
+
<p>Takes a custom-written json file and writes an svg page to file which will
|
|
971
|
+
contain the given features described within the json file.</p>
|
|
972
|
+
<ul><li>
|
|
973
|
+
<p><code>args</code> - a custom-written json file describing the parameters
|
|
974
|
+
and resources needed for a new page</p>
|
|
975
|
+
</li></ul>
|
|
976
|
+
|
|
977
|
+
|
|
978
|
+
|
|
979
|
+
|
|
980
|
+
<div class="method-source-code" id="from_json-source">
|
|
981
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 53</span>
|
|
982
|
+
<span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">from_json</span>(<span class="ruby-identifier">args</span>)
|
|
983
|
+
<span class="ruby-identifier">require</span> <span class="ruby-string">'rubygems'</span>
|
|
984
|
+
<span class="ruby-identifier">require</span> <span class="ruby-string">'json'</span>
|
|
985
|
+
<span class="ruby-identifier">data</span> = <span class="ruby-constant">JSON</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">args</span>[<span class="ruby-value">:json</span>], <span class="ruby-string">'r'</span>).<span class="ruby-identifier">read</span>)
|
|
986
|
+
<span class="ruby-identifier">p</span> = <span class="ruby-constant">Page</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-string">"Page"</span>][<span class="ruby-string">"width"</span>],
|
|
987
|
+
<span class="ruby-value">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-string">"Page"</span>][<span class="ruby-string">"height"</span>],
|
|
988
|
+
<span class="ruby-value">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-string">"Page"</span>][<span class="ruby-string">"intervals"</span>])
|
|
989
|
+
<span class="ruby-identifier">data</span>[<span class="ruby-string">"Tracks"</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
990
|
+
<span class="ruby-comment">#prep the track args</span>
|
|
991
|
+
<span class="ruby-identifier">track_args</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">dup</span>
|
|
992
|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-string">"file"</span>)
|
|
993
|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-string">"file_type"</span>)
|
|
994
|
+
<span class="ruby-identifier">track_args</span> = <span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">inject</span>({}) { <span class="ruby-operator">|</span><span class="ruby-identifier">memo</span>, (<span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span>)<span class="ruby-operator">|</span> <span class="ruby-identifier">memo</span>[<span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">v</span>; <span class="ruby-identifier">memo</span> }
|
|
995
|
+
<span class="ruby-comment">##convert any of the pre-made gradient strings in the keys to symbol</span>
|
|
996
|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
|
|
997
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">respond_to?</span>(<span class="ruby-value">:to_sym</span>)
|
|
998
|
+
<span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>] = <span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_sym</span> <span class="ruby-keyword">if</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradients</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_sym</span>)
|
|
999
|
+
<span class="ruby-keyword">end</span>
|
|
1000
|
+
|
|
1001
|
+
<span class="ruby-identifier">svg_track</span> = <span class="ruby-identifier">p</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">track_args</span>)
|
|
1002
|
+
<span class="ruby-identifier">features</span> = [] <span class="ruby-comment">##set up the features...</span>
|
|
1003
|
+
|
|
1004
|
+
<span class="ruby-keyword">case</span> <span class="ruby-identifier">track</span>[<span class="ruby-string">"file_type"</span>] <span class="ruby-comment">##deal with the gff and data files</span>
|
|
1005
|
+
<span class="ruby-keyword">when</span> <span class="ruby-string">"gff"</span>
|
|
1006
|
+
<span class="ruby-identifier">groups</span> = {}
|
|
1007
|
+
<span class="ruby-identifier">parentless_features</span> = []
|
|
1008
|
+
<span class="ruby-constant">Page</span>.<span class="ruby-identifier">parse_gff</span>(<span class="ruby-identifier">track</span>[<span class="ruby-string">"file"</span>]).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gff</span><span class="ruby-operator">|</span> <span class="ruby-comment">#gets features in a list and links their children to them as members of the array at the key</span>
|
|
1009
|
+
<span class="ruby-identifier">parent_id</span> = <span class="ruby-identifier">gff</span>.<span class="ruby-identifier">attributes</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-string">'Parent'</span> }
|
|
1010
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">empty?</span>
|
|
1011
|
+
<span class="ruby-identifier">parentless_features</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
1012
|
+
<span class="ruby-keyword">else</span>
|
|
1013
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>].<span class="ruby-identifier">nil?</span>
|
|
1014
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] = []
|
|
1015
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
1016
|
+
<span class="ruby-keyword">else</span>
|
|
1017
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
1018
|
+
<span class="ruby-keyword">end</span>
|
|
1019
|
+
<span class="ruby-keyword">end</span>
|
|
1020
|
+
<span class="ruby-keyword">end</span>
|
|
1021
|
+
<span class="ruby-comment">#now flick through the parentless features and add any exons / UTRs</span>
|
|
1022
|
+
<span class="ruby-identifier">parentless_features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">plf</span><span class="ruby-operator">|</span>
|
|
1023
|
+
<span class="ruby-identifier">require</span> <span class="ruby-string">'pp'</span>
|
|
1024
|
+
<span class="ruby-comment">#pp parentless_features</span>
|
|
1025
|
+
<span class="ruby-identifier">gff_id</span> = <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">attributes</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-string">'ID'</span> }
|
|
1026
|
+
<span class="ruby-identifier">gff_id</span> = <span class="ruby-identifier">gff_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>
|
|
1027
|
+
<span class="ruby-identifier">exons</span> = []
|
|
1028
|
+
<span class="ruby-identifier">utrs</span> = []
|
|
1029
|
+
<span class="ruby-identifier">children</span> = <span class="ruby-identifier">groups</span>[<span class="ruby-identifier">gff_id</span>] <span class="ruby-operator">||</span> <span class="ruby-identifier">children</span> = []
|
|
1030
|
+
<span class="ruby-identifier">children</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">child</span><span class="ruby-operator">|</span>
|
|
1031
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">==</span> <span class="ruby-string">'exon'</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">==</span> <span class="ruby-string">'CDS'</span>
|
|
1032
|
+
<span class="ruby-identifier">exons</span> <span class="ruby-operator">+=</span> [<span class="ruby-identifier">child</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">child</span>.<span class="ruby-identifier">end</span>]
|
|
1033
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp">/utr/</span>
|
|
1034
|
+
<span class="ruby-identifier">utrs</span> <span class="ruby-operator">+=</span> [<span class="ruby-identifier">child</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">child</span>.<span class="ruby-identifier">end</span>]
|
|
1035
|
+
<span class="ruby-keyword">end</span>
|
|
1036
|
+
<span class="ruby-keyword">end</span>
|
|
1037
|
+
<span class="ruby-identifier">features</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">start</span>, <span class="ruby-value">:end</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">end</span>, <span class="ruby-value">:exons</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">exons</span>, <span class="ruby-value">:utrs</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">utrs</span>, <span class="ruby-value">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">strand</span>, <span class="ruby-value">:id</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">gff_id</span>)
|
|
1038
|
+
<span class="ruby-keyword">end</span> <span class="ruby-comment">#parentless features end</span>
|
|
1039
|
+
<span class="ruby-keyword">when</span> <span class="ruby-string">"data"</span>
|
|
1040
|
+
<span class="ruby-comment">##each line is a data feature</span>
|
|
1041
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">track</span>[<span class="ruby-string">"file"</span>], <span class="ruby-string">"r"</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
|
1042
|
+
<span class="ruby-identifier">start</span>, <span class="ruby-identifier">stop</span>, <span class="ruby-identifier">value</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
|
|
1043
|
+
<span class="ruby-identifier">features</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:end</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">stop</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:segment_height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">value</span>.<span class="ruby-identifier">to_f</span>)
|
|
1044
|
+
<span class="ruby-keyword">end</span>
|
|
1045
|
+
<span class="ruby-keyword">end</span> <span class="ruby-comment">#data end</span>
|
|
1046
|
+
<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">svg_track</span>.<span class="ruby-identifier">add</span>(<span class="ruby-identifier">f</span>) }
|
|
1047
|
+
<span class="ruby-keyword">end</span> <span class="ruby-comment">#track end</span>
|
|
1048
|
+
<span class="ruby-identifier">p</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">args</span>[<span class="ruby-value">:outfile</span>])
|
|
1049
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1050
|
+
</div><!-- from_json-source -->
|
|
1051
|
+
|
|
1052
|
+
</div>
|
|
1053
|
+
|
|
1054
|
+
|
|
1055
|
+
|
|
1056
|
+
|
|
1057
|
+
</div><!-- from_json-method -->
|
|
1058
|
+
|
|
1059
|
+
|
|
1060
|
+
<div id="method-c-new" class="method-detail ">
|
|
1061
|
+
|
|
1062
|
+
<div class="method-heading">
|
|
1063
|
+
<span class="method-name">new</span><span
|
|
1064
|
+
class="method-args">(args)</span>
|
|
1065
|
+
|
|
1066
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1067
|
+
|
|
1068
|
+
</div>
|
|
1069
|
+
|
|
1070
|
+
|
|
1071
|
+
<div class="method-description">
|
|
1072
|
+
|
|
1073
|
+
<p>Creates a new <a href="Page.html">Page</a> object.</p>
|
|
1074
|
+
|
|
1075
|
+
<p>A new <a href="Page.html">Page</a> contains the following arguments:</p>
|
|
1076
|
+
<ul><li>
|
|
1077
|
+
<p>height = the height of the page</p>
|
|
1078
|
+
</li><li>
|
|
1079
|
+
<p>width = the width of the page</p>
|
|
1080
|
+
</li><li>
|
|
1081
|
+
<p>style = includes the a background colour</p>
|
|
1082
|
+
</li><li>
|
|
1083
|
+
<p>svg = a new <a href="SVGEE.html">SVGEE</a> object</p>
|
|
1084
|
+
</li><li>
|
|
1085
|
+
<p>scale_start = the scale-start of the page (1.0/0.0)</p>
|
|
1086
|
+
</li><li>
|
|
1087
|
+
<p>scale_stop = the scale-stop of the page (-1.0/0.0)</p>
|
|
1088
|
+
</li><li>
|
|
1089
|
+
<p>tracks = an array of track objects with loads of features in it…</p>
|
|
1090
|
+
</li><li>
|
|
1091
|
+
<p>nt_per_percent = the number of nucleotides that are represented by 1% of
|
|
1092
|
+
the page (1);</p>
|
|
1093
|
+
</li><li>
|
|
1094
|
+
<p>num_intervals = the number of intervals</p>
|
|
1095
|
+
</li><li>
|
|
1096
|
+
<p>track_top = the position of the top of the first track (30)</p>
|
|
1097
|
+
</li></ul>
|
|
1098
|
+
|
|
1099
|
+
<p>A new page maybe set up as follows:</p>
|
|
1100
|
+
|
|
1101
|
+
<pre class="ruby"><span class="ruby-ivar">@page</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">Page</span>.<span class="ruby-identifier">new</span>(:<span class="ruby-identifier">width</span> =<span class="ruby-operator">></span> <span class="ruby-value">800</span>,
|
|
1102
|
+
:<span class="ruby-identifier">height</span> =<span class="ruby-operator">></span> <span class="ruby-value">110</span>, :<span class="ruby-identifier">number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>)
|
|
1103
|
+
</pre>
|
|
1104
|
+
|
|
1105
|
+
|
|
1106
|
+
|
|
1107
|
+
|
|
1108
|
+
<div class="method-source-code" id="new-source">
|
|
1109
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 30</span>
|
|
1110
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
|
|
1111
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:height</span>]
|
|
1112
|
+
<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:width</span>]
|
|
1113
|
+
<span class="ruby-identifier">args</span>[<span class="ruby-value">:style</span>] = <span class="ruby-node">"background-color:#{args[:background_color]};"</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:background_color</span>]
|
|
1114
|
+
<span class="ruby-ivar">@svg</span> = <span class="ruby-constant">SVGEE</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">args</span>)
|
|
1115
|
+
<span class="ruby-ivar">@scale_start</span> = <span class="ruby-value">1.0</span><span class="ruby-operator">/</span><span class="ruby-value">0.0</span>
|
|
1116
|
+
<span class="ruby-ivar">@scale_stop</span> = <span class="ruby-value">-1.0</span><span class="ruby-operator">/</span><span class="ruby-value">0.0</span>
|
|
1117
|
+
<span class="ruby-ivar">@tracks</span> = [] <span class="ruby-comment">#array of track objects with loads of features in it...</span>
|
|
1118
|
+
<span class="ruby-ivar">@nt_per_percent</span> = <span class="ruby-value">1</span>;
|
|
1119
|
+
<span class="ruby-ivar">@num_intervals</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:number_of_intervals</span>]
|
|
1120
|
+
<span class="ruby-ivar">@track_top</span> = <span class="ruby-value">30</span>
|
|
1121
|
+
|
|
1122
|
+
<span class="ruby-keyword">def</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">update_height</span>(<span class="ruby-identifier">height</span>)
|
|
1123
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">height</span>
|
|
1124
|
+
<span class="ruby-keyword">end</span>
|
|
1125
|
+
|
|
1126
|
+
<span class="ruby-comment">#def @svg.update_width(width)</span>
|
|
1127
|
+
<span class="ruby-comment"># @width = width</span>
|
|
1128
|
+
<span class="ruby-comment">#end</span>
|
|
1129
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1130
|
+
</div><!-- new-source -->
|
|
1131
|
+
|
|
1132
|
+
</div>
|
|
1133
|
+
|
|
1134
|
+
|
|
1135
|
+
|
|
1136
|
+
|
|
1137
|
+
</div><!-- new-method -->
|
|
1138
|
+
|
|
1139
|
+
|
|
1140
|
+
<div id="method-c-parse_gff" class="method-detail ">
|
|
1141
|
+
|
|
1142
|
+
<div class="method-heading">
|
|
1143
|
+
<span class="method-name">parse_gff</span><span
|
|
1144
|
+
class="method-args">(gff_file)</span>
|
|
1145
|
+
|
|
1146
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1147
|
+
|
|
1148
|
+
</div>
|
|
1149
|
+
|
|
1150
|
+
|
|
1151
|
+
<div class="method-description">
|
|
1152
|
+
|
|
1153
|
+
<p>Parses a GFF file into an Array of <a
|
|
1154
|
+
href="http://bioruby.org/rdoc/Bio/GFF/GFF3/Record.html">Bio::GFF::GFF3::Record</a>
|
|
1155
|
+
objects</p>
|
|
1156
|
+
<ul><li>
|
|
1157
|
+
<p><code>gff_file</code> - a GFF-formatted file</p>
|
|
1158
|
+
</li><li>
|
|
1159
|
+
<p><code>returns</code> - an Array of <a
|
|
1160
|
+
href="http://bioruby.org/rdoc/Bio/GFF/GFF3/Record.html">Bio::GFF::GFF3::Record</a>
|
|
1161
|
+
objects</p>
|
|
1162
|
+
</li></ul>
|
|
1163
|
+
|
|
1164
|
+
|
|
1165
|
+
|
|
1166
|
+
|
|
1167
|
+
<div class="method-source-code" id="parse_gff-source">
|
|
1168
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 125</span>
|
|
1169
|
+
<span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">parse_gff</span>(<span class="ruby-identifier">gff_file</span>)
|
|
1170
|
+
<span class="ruby-identifier">require</span> <span class="ruby-string">'bio'</span>
|
|
1171
|
+
<span class="ruby-identifier">a</span> = []
|
|
1172
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">gff_file</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
|
1173
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span> <span class="ruby-operator">=~</span> <span class="ruby-node">/^#/</span>
|
|
1174
|
+
<span class="ruby-identifier">a</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">GFF</span><span class="ruby-operator">::</span><span class="ruby-constant">GFF3</span><span class="ruby-operator">::</span><span class="ruby-constant">Record</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
|
|
1175
|
+
<span class="ruby-keyword">end</span>
|
|
1176
|
+
<span class="ruby-identifier">a</span>
|
|
1177
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1178
|
+
</div><!-- parse_gff-source -->
|
|
1179
|
+
|
|
1180
|
+
</div>
|
|
1181
|
+
|
|
1182
|
+
|
|
1183
|
+
|
|
1184
|
+
|
|
1185
|
+
</div><!-- parse_gff-method -->
|
|
1186
|
+
|
|
1187
|
+
|
|
1188
|
+
</section><!-- public-class-method-details -->
|
|
1189
|
+
|
|
1190
|
+
</section><!-- 5Buntitled-5D -->
|
|
1191
|
+
|
|
1192
|
+
</div><!-- documentation -->
|
|
1193
|
+
|
|
1194
|
+
|
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1195
|
+
<footer id="validator-badges">
|
|
1196
|
+
<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
|
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1197
|
+
<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.rc.2.1.
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1198
|
+
<p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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</footer>
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