bio-svgenes 0.3.1 → 0.3.2
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- data/README.md +88 -0
- data/VERSION +1 -1
- data/bio-svgenes.gemspec +131 -8
- data/doc/classes/Bio.html +131 -0
- data/doc/classes/Bio/Graphics.html +142 -0
- data/doc/classes/Bio/Graphics/Glyph.html +987 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000001.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000002.html +27 -0
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- data/doc/classes/Bio/Graphics/Glyph.src/M000007.html +107 -0
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- data/doc/classes/Bio/Graphics/Glyph.src/M000009.html +23 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000010.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000011.html +75 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000012.html +51 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000013.html +23 -0
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- data/doc/classes/Bio/Graphics/Glyph.src/M000015.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000016.html +32 -0
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- data/doc/classes/Bio/Graphics/Glyph.src/M000018.html +25 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000019.html +29 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000020.html +107 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000021.html +51 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000022.html +23 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000023.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000024.html +75 -0
- data/doc/classes/Bio/Graphics/MiniFeature.html +243 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000001.html +25 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000003.html +25 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000024.html +25 -0
- data/doc/classes/Bio/Graphics/Page.html +705 -0
- data/doc/classes/Bio/Graphics/Page.src/M000010.html +35 -0
- data/doc/classes/Bio/Graphics/Page.src/M000011.html +83 -0
- data/doc/classes/Bio/Graphics/Page.src/M000012.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000013.html +29 -0
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- data/doc/classes/Bio/Graphics/Page.src/M000020.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000021.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000022.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000023.html +18 -0
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- data/doc/classes/Bio/Graphics/Page.src/M000025.html +35 -0
- data/doc/classes/Bio/Graphics/Page.src/M000026.html +83 -0
- data/doc/classes/Bio/Graphics/Page.src/M000027.html +24 -0
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- data/doc/classes/Bio/Graphics/Primitive.html +204 -0
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- data/doc/classes/Bio/Graphics/Primitive.src/M000008.html +21 -0
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- data/doc/classes/Bio/Graphics/Primitive.src/M000022.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000023.html +20 -0
- data/doc/classes/Bio/Graphics/SVGEE.html +290 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000002.html +24 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000003.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000004.html +24 -0
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- data/doc/classes/Bio/Graphics/SVGEE.src/M000020.html +27 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000021.html +23 -0
- data/doc/classes/Bio/Graphics/Track.html +473 -0
- data/doc/classes/Bio/Graphics/Track.src/M000001.html +35 -0
- data/doc/classes/Bio/Graphics/Track.src/M000002.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000003.html +28 -0
- data/doc/classes/Bio/Graphics/Track.src/M000004.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000010.html +35 -0
- data/doc/classes/Bio/Graphics/Track.src/M000011.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000012.html +28 -0
- data/doc/classes/Bio/Graphics/Track.src/M000013.html +18 -0
- data/doc/created.rid +1 -9
- data/doc/files/lib/bio-svgenes_rb.html +131 -0
- data/doc/files/lib/bio/graphics/glyph_rb.html +101 -0
- data/doc/files/lib/bio/graphics/mini_feature_rb.html +101 -0
- data/doc/files/lib/bio/graphics/page_rb.html +111 -0
- data/doc/files/lib/bio/graphics/primitive_rb.html +101 -0
- data/doc/files/lib/bio/graphics/svgee_rb.html +101 -0
- data/doc/files/lib/bio/graphics/track_rb.html +101 -0
- data/doc/fr_class_index.html +34 -0
- data/doc/fr_file_index.html +33 -0
- data/doc/fr_method_index.html +70 -0
- data/doc/index.html +21 -91
- data/doc/manual/bootstrap/css/bootstrap-responsive.css +1109 -0
- data/doc/manual/bootstrap/css/bootstrap-responsive.min.css +9 -0
- data/doc/manual/bootstrap/css/bootstrap.css +6158 -0
- data/doc/manual/bootstrap/css/bootstrap.min.css +9 -0
- data/doc/manual/bootstrap/img/glyphicons-halflings-white.png +0 -0
- data/doc/manual/bootstrap/img/glyphicons-halflings.png +0 -0
- data/doc/manual/bootstrap/js/bootstrap.js +2276 -0
- data/doc/manual/bootstrap/js/bootstrap.min.js +6 -0
- data/doc/manual/img/circle.png +0 -0
- data/doc/manual/img/directed.png +0 -0
- data/doc/manual/img/down_triangle.png +0 -0
- data/doc/manual/img/histogram.png +0 -0
- data/doc/manual/img/span.png +0 -0
- data/doc/manual/img/transcript.png +0 -0
- data/doc/manual/img/up_triangle.png +0 -0
- data/doc/manual/manual.html +360 -0
- data/doc/manual/manual.md +307 -0
- data/doc/rdoc-style.css +208 -0
- data/examples/example.rb +12 -8
- data/examples/{make_example.rb → example2.rb} +5 -16
- data/lib/bio/graphics/glyph.rb +293 -126
- data/lib/bio/graphics/mini_feature.rb +24 -17
- data/lib/bio/graphics/page.rb +112 -54
- data/lib/bio/graphics/primitive.rb +12 -9
- data/lib/bio/graphics/svgee.rb +9 -11
- data/lib/bio/graphics/track.rb +92 -10
- metadata +132 -9
- data/README.rdoc +0 -19
- data/examples/annotate_snps.rb +0 -86
- data/examples/eg2.rb +0 -40
- data/examples/get_coverage_in_windows.rb +0 -176
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 13</span>
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<span class="ruby-keyword kw">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-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'100%'</span>, <span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'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-identifier">:width</span>]
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<span class="ruby-ivar">@supported_primitives</span> = [<span class="ruby-identifier">:circle</span>, <span class="ruby-identifier">:rectangle</span>, <span class="ruby-identifier">:ellipse</span>, <span class="ruby-identifier">:line</span>, <span class="ruby-identifier">:polyline</span>, <span class="ruby-identifier">:text</span>]
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<title>open_tag (Bio::Graphics::SVGEE)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 24</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">open_tag</span>
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<span class="ruby-node">%{<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 kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 13</span>
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<span class="ruby-keyword kw">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-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'100%'</span>, <span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'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-identifier">:width</span>]
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<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:height</span>]
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<span class="ruby-ivar">@supported_primitives</span> = [<span class="ruby-identifier">:circle</span>, <span class="ruby-identifier">:rectangle</span>, <span class="ruby-identifier">:ellipse</span>, <span class="ruby-identifier">:line</span>, <span class="ruby-identifier">:polyline</span>, <span class="ruby-identifier">:text</span>]
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 24</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">open_tag</span>
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<span class="ruby-node">%{<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 kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 29</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close_tag</span>
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<span class="ruby-value str">%{</svg>}</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 94</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">primitive_object</span>)
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<span class="ruby-identifier">args</span> = {}
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<span class="ruby-identifier">primitive_object</span>.<span class="ruby-identifier">instance_variables</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp re">/@/</span>,<span class="ruby-value str">""</span>).<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">primitive_object</span>.<span class="ruby-identifier">instance_variable_get</span>(<span class="ruby-identifier">v</span>) }
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<span class="ruby-identifier">primitive_string</span> = <span class="ruby-identifier">args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">:primitive</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-value str">"\n"</span> <span class="ruby-operator">+</span> <span class="ruby-node">%{<stop offset="#{s[:offset]}%" style="stop-color:#{s[:color]};stop-opacity:#{s[:opacity]}" />}</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 115</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
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<span class="ruby-identifier">head</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open_tag</span>
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<span class="ruby-identifier">defstring</span> = <span class="ruby-value str">"<defs>\n"</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">defs</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">"\n"</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">"\n </defs>\n"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">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 kw">self</span>.<span class="ruby-identifier">primitives</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">"\n"</span>)
|
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<span class="ruby-identifier">close</span> = <span class="ruby-keyword kw">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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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 17</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
|
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|
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<span class="ruby-identifier">opts</span> = {<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'100%'</span>, <span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'100%'</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
|
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|
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|
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|
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|
|
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|
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|
|
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|
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<span class="ruby-ivar">@defs</span> = []
|
|
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|
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<span class="ruby-ivar">@supported_primitives</span> = [<span class="ruby-identifier">:circle</span>, <span class="ruby-identifier">:rectangle</span>, <span class="ruby-identifier">:ellipse</span>, <span class="ruby-identifier">:line</span>, <span class="ruby-identifier">:polyline</span>, <span class="ruby-identifier">:text</span>]
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 27</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">open_tag</span>
|
|
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|
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<span class="ruby-node">%{<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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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 31</span>
|
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|
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|
|
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|
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<span class="ruby-value str">%{</svg>}</span>
|
|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 96</span>
|
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">primitive_object</span>)
|
|
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|
+
<span class="ruby-identifier">args</span> = {}
|
|
16
|
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<span class="ruby-identifier">primitive_object</span>.<span class="ruby-identifier">instance_variables</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp re">/@/</span>,<span class="ruby-value str">""</span>).<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">primitive_object</span>.<span class="ruby-identifier">instance_variable_get</span>(<span class="ruby-identifier">v</span>) }
|
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|
+
<span class="ruby-identifier">primitive_string</span> = <span class="ruby-identifier">args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">:primitive</span>)
|
|
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|
+
<span class="ruby-identifier">make_tag</span>(<span class="ruby-identifier">primitive_string</span>, <span class="ruby-identifier">args</span>)
|
|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 104</span>
|
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|
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<span class="ruby-keyword kw">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 kw">case</span> <span class="ruby-identifier">a</span>[<span class="ruby-identifier">:type</span>]
|
|
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|
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:radial</span>
|
|
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|
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<span class="ruby-node">%{<radialGradient id="#{a[:id]}" cx="#{a[:cx]}%" cy="#{a[:cy]}%" r="#{a[:r]}%" fx="#{a[:fx]}%" fy="#{a[:fy]}%">}</span>
|
|
18
|
+
<span class="ruby-keyword kw">else</span>
|
|
19
|
+
<span class="ruby-node">%{<linearGradient id="#{a[:id]}" x1="#{a[:x1]}%" x2="#{a[:x2]}%" y1="#{a[:y1]}%" y2="#{a[:y2]}%">}</span>
|
|
20
|
+
<span class="ruby-keyword kw">end</span>
|
|
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|
+
<span class="ruby-identifier">a</span>[<span class="ruby-identifier">:stops</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
|
|
22
|
+
<span class="ruby-identifier">definition_string</span> = <span class="ruby-identifier">definition_string</span> <span class="ruby-operator">+</span> <span class="ruby-value str">"\n"</span> <span class="ruby-operator">+</span> <span class="ruby-node">%{<stop offset="#{s[:offset]}%" style="stop-color:#{s[:color]};stop-opacity:#{s[:opacity]}" />}</span>
|
|
23
|
+
<span class="ruby-keyword kw">end</span>
|
|
24
|
+
<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-identifier">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-identifier">:linear</span> <span class="ruby-operator">?</span> <span class="ruby-value str">'</linearGradient>'</span> <span class="ruby-operator">:</span> <span class="ruby-value str">'</radialGradient>'</span>)
|
|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/svgee.rb, line 117</span>
|
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|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>
|
|
15
|
+
<span class="ruby-identifier">head</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open_tag</span>
|
|
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|
+
<span class="ruby-identifier">defstring</span> = <span class="ruby-value str">""</span>
|
|
17
|
+
<span class="ruby-identifier">defstring</span> = <span class="ruby-value str">"<defs>\n"</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">defs</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">"\n"</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">"\n </defs>\n"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">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 kw">self</span>.<span class="ruby-identifier">primitives</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">"\n"</span>)
|
|
19
|
+
<span class="ruby-identifier">close</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">close_tag</span>
|
|
20
|
+
<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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|
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<span class="ruby-keyword kw">end</span></pre>
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<td><strong>Class</strong></td>
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<td class="class-name-in-header">Bio::Graphics::Track</td>
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<a href="../../../files/lib/bio/graphics/track_rb.html">
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Object
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The <a href="Track.html">Bio::Graphics::Track</a> object acts as a
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container for <a href="MiniFeature.html">Bio::Graphics::MiniFeature</a>
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objects. The <a href="Track.html">Bio::Graphics::Track</a> takes style
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information on instantiation. Style information is applied to each feature
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in the track by the track
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<a href="#M000011">add</a>
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<a href="#M000012">get_rows</a>
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<a href="#M000010">new</a>
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<span class="method-name">new</span><span class="method-args">(args)</span>
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href="Track.html">Bio::Graphics::Track</a>
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<h2>args</h2>
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[:generic, :directed, :transcript, :scale, :label, :histogram, :circle, :down_triangle, :up_triangle, :span]
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<li>:stroke_color = the outline colour of the glyphs in the track (default =
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<li>:fill_color = the fill colour of the glyphs in the track (default =
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‘red’), can be any SVG colour eg rgb(256,0,0) or FF0000, or one
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of the built in gradient types <a
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href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
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</li>
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</ul>
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<pre>
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[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
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</pre>
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<p>
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or a custom definition of a gradient
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</p>
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<pre>
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{:type => :radial,
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:id => :custom,
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:fx => 50,
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}, {
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</pre>
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<li>:track_height = minimum height for the track, will be modified
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automatically if more space is needed e.g for overlapping features (default
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= auto),
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<li>:x_round = x radius of the ellipse used to round off the corners of
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rectangles (default = 1)
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<li>:y_round = y radius of the ellipse used to round off the corners of
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rectangles (default = 1)
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:utr_fill_color = the fill colour of the utr part of the glyph (default =
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‘black’), can be any SVG colour eg rgb(256,0,0) or FF0000, or
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one of the built in gradient types <a
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href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
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</p>
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<pre>
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[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
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<p>
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or a custom definition of a gradient
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<pre>
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{:type => :radial,
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}, {
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}
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</pre>
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<ul>
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<li>:utr_stroke = the outline colour of the utr part of the glyph (default =
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"black"), can be any SVG colour eg rgb(256,0,0) or FF0000
|
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</li>
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<li>:utr_stroke_width = The width of the outline stroke for the utr part of the
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glyph (default = 1)
|
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</li>
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<li>:exon_fill_color = the fill colour of the utr part of the glyph (default =
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‘red’), can be any SVG colour eg rgb(256,0,0) or FF0000, or one
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of the built in gradient types <a
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href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a> or a custom
|
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definition of a gradient
|
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328
|
+
|
|
329
|
+
</li>
|
|
330
|
+
</ul>
|
|
331
|
+
<pre>
|
|
332
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
333
|
+
</pre>
|
|
334
|
+
<p>
|
|
335
|
+
or a custom definition of a gradient
|
|
336
|
+
</p>
|
|
337
|
+
<pre>
|
|
338
|
+
{:type => :radial,
|
|
339
|
+
:id => :custom,
|
|
340
|
+
:cx => 5,
|
|
341
|
+
:cy => 5,
|
|
342
|
+
:r => 50,
|
|
343
|
+
:fx => 50,
|
|
344
|
+
:fy => 50,
|
|
345
|
+
:stops => [ {
|
|
346
|
+
:offset => 0,
|
|
347
|
+
:color => 'rgb(255,255,255)',
|
|
348
|
+
:opacity => 0
|
|
349
|
+
}, {
|
|
350
|
+
:offset => 100,
|
|
351
|
+
:color => 'rgb(0,127,200)',
|
|
352
|
+
:opacity => 1
|
|
353
|
+
}, ]
|
|
354
|
+
</pre>
|
|
355
|
+
<ul>
|
|
356
|
+
<li>:exon_stroke = the outline colour of the exon part of the glyph (default =
|
|
357
|
+
"black") can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
358
|
+
|
|
359
|
+
</li>
|
|
360
|
+
<li>:exon_stroke_width = The width of the outline stroke for the exon part of
|
|
361
|
+
the glyph (default = 1)
|
|
362
|
+
|
|
363
|
+
</li>
|
|
364
|
+
<li>:line_color = the colour for the line part that joins the blocks (default =
|
|
365
|
+
‘black’) can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
366
|
+
|
|
367
|
+
</li>
|
|
368
|
+
<li>:line_width = the width ffor the line part that joins the blocks (default =
|
|
369
|
+
1)
|
|
370
|
+
|
|
371
|
+
</li>
|
|
372
|
+
<li>:exon_style = an arbitrary SVG compliant style string eg
|
|
373
|
+
"fill-opacity:0.4;"
|
|
374
|
+
|
|
375
|
+
</li>
|
|
376
|
+
<li>:utr_style = an arbitrary SVG compliant style string eg
|
|
377
|
+
"fill-opacity:0.4;"
|
|
378
|
+
|
|
379
|
+
</li>
|
|
380
|
+
<li>:line_style = an arbitrary SVG compliant style string eg
|
|
381
|
+
"fill-opacity:0.4;"
|
|
382
|
+
|
|
383
|
+
</li>
|
|
384
|
+
<li>:gap_marker = style of the line between blocks - either angled or straight
|
|
385
|
+
|
|
386
|
+
</li>
|
|
387
|
+
</ul>
|
|
388
|
+
</div>
|
|
389
|
+
</div>
|
|
390
|
+
|
|
391
|
+
<h3 class="section-bar">Public Instance methods</h3>
|
|
392
|
+
|
|
393
|
+
<div id="method-M000011" class="method-detail">
|
|
394
|
+
<a name="M000011"></a>
|
|
395
|
+
|
|
396
|
+
<div class="method-heading">
|
|
397
|
+
<a href="Track.src/M000011.html" target="Code" class="method-signature"
|
|
398
|
+
onclick="popupCode('Track.src/M000011.html');return false;">
|
|
399
|
+
<span class="method-name">add</span><span class="method-args">(feature)</span>
|
|
400
|
+
</a>
|
|
401
|
+
</div>
|
|
402
|
+
|
|
403
|
+
<div class="method-description">
|
|
404
|
+
<p>
|
|
405
|
+
Adds a <a href="Track.html#M000010">new</a> <a
|
|
406
|
+
href="MiniFeature.html">Bio::Graphics::MiniFeature</a> object to the
|
|
407
|
+
current <a href="Track.html">Bio::Graphics::Track</a>
|
|
408
|
+
</p>
|
|
409
|
+
</div>
|
|
410
|
+
</div>
|
|
411
|
+
|
|
412
|
+
<div id="method-M000012" class="method-detail">
|
|
413
|
+
<a name="M000012"></a>
|
|
414
|
+
|
|
415
|
+
<div class="method-heading">
|
|
416
|
+
<a href="Track.src/M000012.html" target="Code" class="method-signature"
|
|
417
|
+
onclick="popupCode('Track.src/M000012.html');return false;">
|
|
418
|
+
<span class="method-name">get_rows</span><span class="method-args">()</span>
|
|
419
|
+
</a>
|
|
420
|
+
</div>
|
|
421
|
+
|
|
422
|
+
<div class="method-description">
|
|
423
|
+
<p>
|
|
424
|
+
Calculates how many rows are needed per track for overlapping features and
|
|
425
|
+
which row each feature should be in. Usually only called by the enclosing
|
|
426
|
+
<a href="Page.html">Bio::Graphics::Page</a> object.
|
|
427
|
+
</p>
|
|
428
|
+
</div>
|
|
429
|
+
</div>
|
|
430
|
+
|
|
431
|
+
<div id="method-M000013" class="method-detail">
|
|
432
|
+
<a name="M000013"></a>
|
|
433
|
+
|
|
434
|
+
<div class="method-heading">
|
|
435
|
+
<a href="Track.src/M000013.html" target="Code" class="method-signature"
|
|
436
|
+
onclick="popupCode('Track.src/M000013.html');return false;">
|
|
437
|
+
<span class="method-name">overlaps</span><span class="method-args">(f1, f2)</span>
|
|
438
|
+
</a>
|
|
439
|
+
</div>
|
|
440
|
+
|
|
441
|
+
<div class="method-description">
|
|
442
|
+
<p>
|
|
443
|
+
Calculates whether two <a
|
|
444
|
+
href="MiniFeature.html">Bio::Graphics::MiniFeature</a> objects overlap by
|
|
445
|
+
examining their start and end positions.
|
|
446
|
+
</p>
|
|
447
|
+
<p>
|
|
448
|
+
<tt>args</tt>
|
|
449
|
+
</p>
|
|
450
|
+
<ul>
|
|
451
|
+
<li>f1 - a <a href="MiniFeature.html">Bio::Graphics::MiniFeature</a> object
|
|
452
|
+
|
|
453
|
+
</li>
|
|
454
|
+
<li>f2 - a <a href="MiniFeature.html">Bio::Graphics::MiniFeature</a> object
|
|
455
|
+
|
|
456
|
+
</li>
|
|
457
|
+
</ul>
|
|
458
|
+
</div>
|
|
459
|
+
</div>
|
|
460
|
+
|
|
461
|
+
|
|
462
|
+
</div>
|
|
463
|
+
|
|
464
|
+
|
|
465
|
+
</div>
|
|
466
|
+
|
|
467
|
+
|
|
468
|
+
<div id="validator-badges">
|
|
469
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
470
|
+
</div>
|
|
471
|
+
|
|
472
|
+
</body>
|
|
473
|
+
</html>
|