bio-svgenes 0.2.3 → 0.3.0
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- 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
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- 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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<p>The <a href="Primitive.html">Primitive</a> class is used to hold
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information about Glyphs. They contain a <a href="Glyph.html">Glyph</a>
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<p>args = a hash of new parameters for the given <a
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<span class="ruby-keyword">self</span>.<span class="ruby-identifier">instance_variable_set</span>(<span class="ruby-node">"@#{k}"</span>, <span class="ruby-identifier">args</span>[<span class="ruby-identifier">k</span>])
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<pre><span class="ruby-comment"># File lib/bio/graphics/primitive.rb, line 12</span>
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<h1 class="class">class Bio::Graphics::SVGEE</h1>
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<p>Adds a <a href="Primitive.html">Primitive</a> object to the <a
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<pre><span class="ruby-comment"># File lib/bio/graphics/svgee.rb, line 96</span>
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<p>Produces the closing text for an svg file</p>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">close_tag</span>
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<p>Produces the svg text to display all the features on a <a
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<pre><span class="ruby-comment"># File lib/bio/graphics/svgee.rb, line 117</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">defstring</span> = <span class="ruby-string">""</span>
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<span class="ruby-identifier">defstring</span> = <span class="ruby-string">"<defs>\n"</span> <span class="ruby-operator">+</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">defs</span>.<span class="ruby-identifier">join</span>(<span class="ruby-string">"\n"</span>) <span class="ruby-operator">+</span> <span class="ruby-string">"\n </defs>\n"</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">not</span> <span class="ruby-identifier">defs</span>.<span class="ruby-identifier">empty?</span>
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<span class="ruby-identifier">shapes</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">primitives</span>.<span class="ruby-identifier">join</span>(<span class="ruby-string">"\n"</span>)
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<span class="ruby-identifier">close</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">close_tag</span>
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<span class="ruby-identifier">head</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">defstring</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">shapes</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">close</span>
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class="method-args">(a)</span>
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<p>Takes the gradient information from a <a href="Glyph.html">Glyph</a>, which
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must be of type ‘radial’ or ‘linear’ and creates the svg text for
|
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that gradient</p>
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<p><code>a</code> = a gradient (a gradient type, a colour and the parameters
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for a given type)</p>
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<pre><span class="ruby-comment"># File lib/bio/graphics/svgee.rb, line 104</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">a</span>)
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<span class="ruby-identifier">definition_string</span> = <span class="ruby-keyword">case</span> <span class="ruby-identifier">a</span>[<span class="ruby-value">:type</span>]
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<span class="ruby-keyword">when</span> <span class="ruby-value">:radial</span>
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<span class="ruby-node">%Q{<radialGradient id="#{a[:id]}" cx="#{a[:cx]}%" cy="#{a[:cy]}%" r="#{a[:r]}%" fx="#{a[:fx]}%" fy="#{a[:fy]}%">}</span>
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<span class="ruby-keyword">else</span>
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<span class="ruby-node">%Q{<linearGradient id="#{a[:id]}" x1="#{a[:x1]}%" x2="#{a[:x2]}%" y1="#{a[:y1]}%" y2="#{a[:y2]}%">}</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-identifier">a</span>[<span class="ruby-value">:stops</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">definition_string</span> = <span class="ruby-identifier">definition_string</span> <span class="ruby-operator">+</span> <span class="ruby-string">"\n"</span> <span class="ruby-operator">+</span> <span class="ruby-node">%Q{<stop offset="#{s[:offset]}%" style="stop-color:#{s[:color]};stop-opacity:#{s[:opacity]}" />}</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-identifier">add_def</span> <span class="ruby-identifier">definition_string</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">a</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value">:linear</span> <span class="ruby-operator">?</span> <span class="ruby-string">'</linearGradient>'</span> <span class="ruby-operator">:</span> <span class="ruby-string">'</radialGradient>'</span>)
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<span class="ruby-keyword">end</span></pre>
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<span class="method-name">open_tag</span><span
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class="method-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>Produces the opening text for an svg file</p>
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<pre><span class="ruby-comment"># File lib/bio/graphics/svgee.rb, line 27</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">open_tag</span>
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<span class="ruby-node">%Q{<svg xmlns="http://www.w3.org/2000/svg" version="1.1" width="#{@width}" height="#{@height}" style="#{@style}" xmlns:xlink="http://www.w3.org/1999/xlink">}</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- open_tag-source -->
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</div>
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</div><!-- open_tag-method -->
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</section><!-- public-instance-method-details -->
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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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<div class="method-description">
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<p>Creates a new <a href="SVGEE.html">SVGEE</a> object which will contain all
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the necessary objects to display all the features on a page</p>
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<p><code>args</code></p>
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<ul><li>
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<p>width = the amount of the page width the svg should take up (100%)</p>
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</li><li>
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<p>height = the amount of the page height the svg should take up (100%)</p>
|
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</li><li>
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<p>style = the svg style information</p>
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</li><li>
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<p>primitives = an array of glyphs</p>
|
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</li><li>
|
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<p>defs = the gradients that will be used in the SVG</p>
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</li><li>
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<p>supported_primitives = a list of permitted Glyphs</p>
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</li></ul>
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<div class="method-source-code" id="new-source">
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<pre><span class="ruby-comment"># File lib/bio/graphics/svgee.rb, line 17</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-identifier">opts</span> = {<span class="ruby-value">:width</span> =<span class="ruby-operator">></span> <span class="ruby-string">'100%'</span>, <span class="ruby-value">:height</span> =<span class="ruby-operator">></span> <span class="ruby-string">'100%'</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:width</span>]
|
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<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:height</span>]
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<span class="ruby-ivar">@style</span>= <span class="ruby-identifier">opts</span>[<span class="ruby-value">:style</span>]
|
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<span class="ruby-ivar">@primitives</span> = []
|
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<span class="ruby-ivar">@defs</span> = []
|
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<span class="ruby-ivar">@supported_primitives</span> = [<span class="ruby-value">:circle</span>, <span class="ruby-value">:rectangle</span>, <span class="ruby-value">:ellipse</span>, <span class="ruby-value">:line</span>, <span class="ruby-value">:polyline</span>, <span class="ruby-value">:text</span>]
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<span class="ruby-keyword">end</span></pre>
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<footer id="validator-badges">
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<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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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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