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::Track</h1>
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<p>The <a href="Track.html">Track</a> class holds and organises the features,
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<h3 class="section-header">Public Instance Methods</h3>
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<div id="method-i-add" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">add</span><span
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class="method-args">(feature)</span>
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</div>
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<div class="method-description">
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<p>Adds a new <a href="MiniFeature.html">MiniFeature</a> to the the @features
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array</p>
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<div class="method-source-code" id="add-source">
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<pre><span class="ruby-comment"># File lib/bio/graphics/track.rb, line 31</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">feature</span>)
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<span class="ruby-ivar">@features</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">feature</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- add-source -->
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<div class="method-heading">
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<span class="method-name">get_rows</span><span
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class="method-args">()</span>
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</div>
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<p>Calculates how many rows are needed per track for overlapping features and
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which row each feature should be in</p>
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<pre><span class="ruby-comment"># File lib/bio/graphics/track.rb, line 38</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">get_rows</span>
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<span class="ruby-identifier">current_row</span> = <span class="ruby-value">1</span>
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<span class="ruby-ivar">@feature_rows</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">length</span>,<span class="ruby-value">1</span>)
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<span class="ruby-ivar">@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">f1</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
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<span class="ruby-ivar">@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">f2</span>, <span class="ruby-identifier">j</span><span class="ruby-operator">|</span>
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<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-identifier">j</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">j</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">i</span>
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>,<span class="ruby-identifier">f2</span>)
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<span class="ruby-ivar">@feature_rows</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-ivar">@number_rows</span> = <span class="ruby-ivar">@feature_rows</span>.<span class="ruby-identifier">max</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">end</span></pre>
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<span class="method-name">overlaps</span><span
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class="method-args">(f1, f2)</span>
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</div>
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<p>Calculates if two <a href="MiniFeature.html">MiniFeature</a> objects
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overlap by examining their start and end positions. If two features overlap
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then then will be placed on separate rows of the track</p>
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<p><code>args</code></p>
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<ul><li>
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<p>f1 - a <a href="MiniFeature.html">MiniFeature</a> object</p>
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</li><li>
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<p>f2 - a <a href="MiniFeature.html">MiniFeature</a> object</p>
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<pre><span class="ruby-comment"># File lib/bio/graphics/track.rb, line 58</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>, <span class="ruby-identifier">f2</span>)
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(<span class="ruby-identifier">f1</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">start</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">f1</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">end</span>) <span class="ruby-keyword">or</span> (<span class="ruby-identifier">f1</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">>=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">start</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">f1</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">end</span>)
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<span class="ruby-keyword">end</span></pre>
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<section id="public-class-5Buntitled-5D-method-details" class="method-section section">
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<h3 class="section-header">Public Class Methods</h3>
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<div id="method-c-new" class="method-detail ">
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<span class="method-name">new</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>Creates a new <a href="Track.html">Track</a></p>
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<pre><span class="ruby-comment"># File lib/bio/graphics/track.rb, line 9</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-ivar">@args</span> = {<span class="ruby-value">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-value">:generic</span>,
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<span class="ruby-value">:name</span> =<span class="ruby-operator">></span> <span class="ruby-string">"feature_track"</span>,
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<span class="ruby-value">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">true</span>,
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<span class="ruby-value">:feature_height</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>,
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<span class="ruby-value">:track_height</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">nil</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:glyph</span>]
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<span class="ruby-ivar">@name</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:name</span>]
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<span class="ruby-ivar">@label</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:label</span>]
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<span class="ruby-ivar">@track_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:track_height</span>]
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<span class="ruby-ivar">@features</span> = []
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<span class="ruby-ivar">@feature_rows</span> = []
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<span class="ruby-ivar">@scale</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:scale</span>]
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<span class="ruby-ivar">@feature_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:feature_height</span>]
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<span class="ruby-ivar">@number_of_rows</span> = <span class="ruby-value">1</span>
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<span class="ruby-ivar">@max_y</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:max_y</span>]
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<span class="ruby-ivar">@min_width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:min_width</span>]
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<span class="ruby-keyword">end</span></pre>
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<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.rc.2.1.
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<p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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