bio-svgenes 0.3.1 → 0.3.2
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/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
- data/doc/classes/Bio/Graphics/Glyph.src/M000003.html +32 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000004.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000005.html +25 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000006.html +29 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000007.html +107 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000008.html +51 -0
- 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
- data/doc/classes/Bio/Graphics/Glyph.src/M000014.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000015.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000016.html +32 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000017.html +27 -0
- 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
- data/doc/classes/Bio/Graphics/Page.src/M000014.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000015.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000016.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000017.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000018.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000019.html +18 -0
- 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
- data/doc/classes/Bio/Graphics/Page.src/M000024.html +18 -0
- 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
- data/doc/classes/Bio/Graphics/Page.src/M000028.html +29 -0
- data/doc/classes/Bio/Graphics/Page.src/M000029.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000030.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000031.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000032.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000033.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000034.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000035.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000036.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000037.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000038.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000039.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000040.html +107 -0
- data/doc/classes/Bio/Graphics/Page.src/M000041.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000042.html +23 -0
- data/doc/classes/Bio/Graphics/Page.src/M000043.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000044.html +18 -0
- data/doc/classes/Bio/Graphics/Primitive.html +204 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000001.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000002.html +20 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000008.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000009.html +20 -0
- 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
- data/doc/classes/Bio/Graphics/SVGEE.src/M000005.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000006.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000007.html +21 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000008.html +27 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000009.html +23 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000016.html +24 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000017.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000018.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000019.html +21 -0
- 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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<title>new (Bio::Graphics::SVGEE)</title>
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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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<span class="ruby-keyword kw">end</span></pre>
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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 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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<title>add_primitive (Bio::Graphics::SVGEE)</title>
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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">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>
|