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/page.rb, line 111</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">parse_gff</span>(<span class="ruby-identifier">gff_file</span>)
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<span class="ruby-identifier">require</span> <span class="ruby-value str">'bio'</span>
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<span class="ruby-identifier">a</span> = []
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<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">gff_file</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">line</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^#/</span>
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<span class="ruby-identifier">a</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">GFF</span><span class="ruby-operator">::</span><span class="ruby-constant">GFF3</span><span class="ruby-operator">::</span><span class="ruby-constant">Record</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">a</span>
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<span class="ruby-keyword kw">end</span></pre>
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<title>add_track (Bio::Graphics::Page)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 206</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-comment cmt">#sort out the colour/gradient options</span>
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[<span class="ruby-identifier">:fill_color</span>, <span class="ruby-identifier">:exon_fill_color</span>, <span class="ruby-identifier">:utr_fill_color</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">colour_tag</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradients</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>])
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<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>]))
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>] = <span class="ruby-node">"url(##{args[colour_tag]})"</span>
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<span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>].<span class="ruby-identifier">instance_of?</span>(<span class="ruby-constant">Hash</span>)
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<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>])
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>] = <span class="ruby-node">"url(##{args[colour_tag][:id]})"</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@tracks</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Track</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">last</span>
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<span class="ruby-keyword kw">end</span></pre>
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<title>get_limits (Bio::Graphics::Page)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 222</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_limits</span>
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<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">lowest</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">x</span>, <span class="ruby-identifier">y</span><span class="ruby-operator">|</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">y</span>.<span class="ruby-identifier">start</span> }.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">start</span>
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<span class="ruby-identifier">highest</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">x</span>, <span class="ruby-identifier">y</span><span class="ruby-operator">|</span> <span class="ruby-identifier">y</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">end</span> }.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">end</span>
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<span class="ruby-ivar">@scale_start</span> = <span class="ruby-identifier">lowest</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">lowest</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@scale_start</span>
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<span class="ruby-ivar">@scale_stop</span> = <span class="ruby-identifier">highest</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">highest</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@scale_stop</span>
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<span class="ruby-ivar">@nt_per_px_x</span> = (<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@width</span>.<span class="ruby-identifier">to_f</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 233</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_scale</span>
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">scale</span>(<span class="ruby-identifier">:start</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@scale_start</span>,
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<span class="ruby-identifier">:stop</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@scale_stop</span>,
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<span class="ruby-identifier">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@num_intervals</span>, <span class="ruby-identifier">:page_width</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@width</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<span class="ruby-keyword kw">end</span></pre>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">label</span>(<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:text</span>],
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<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>]).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 248</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_generic</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment cmt">#remember presentation info comes from track@args when the track is defined</span>
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 252</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_directed</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 256</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_circle</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">circle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_transcript</span>(<span class="ruby-identifier">args</span>)
|
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|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">transcript</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 264</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_histogram</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 268</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_up_triangle</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">up_triangle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 272</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_down_triangle</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">down_triangle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 276</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_span</span>(<span class="ruby-identifier">args</span>)
|
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">span</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 284</span>
|
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|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw_features</span>(<span class="ruby-identifier">track</span>)
|
|
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|
+
<span class="ruby-keyword kw">if</span> [<span class="ruby-identifier">:histogram</span>, <span class="ruby-value str">"histogram"</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span>) <span class="ruby-comment cmt">#do different stuff for data tracks...</span>
|
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|
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<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>)
|
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<span class="ruby-identifier">max</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">max_y</span> <span class="ruby-value">? </span><span class="ruby-identifier">track</span>.<span class="ruby-identifier">max_y</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span>, <span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">segment_height</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">b</span>.<span class="ruby-identifier">segment_height</span> }.<span class="ruby-identifier">last</span>.<span class="ruby-identifier">segment_height</span>
|
|
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|
+
<span class="ruby-identifier">min</span> = <span class="ruby-value">0</span>
|
|
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|
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">label</span>
|
|
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|
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<span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">name</span>, <span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> <span class="ruby-value">30</span>, <span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-value">3</span>)
|
|
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|
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<span class="ruby-keyword kw">end</span>
|
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|
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<span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">max</span>, <span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">to_px</span>(<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">+</span> <span class="ruby-value">5</span>, <span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>)
|
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|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">min</span>, <span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">to_px</span>(<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">+</span> <span class="ruby-value">5</span>, <span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>)
|
|
25
|
+
<span class="ruby-identifier">data_interval</span> = <span class="ruby-identifier">max</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">min</span>
|
|
26
|
+
<span class="ruby-identifier">data_per_px</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">data_interval</span>.<span class="ruby-identifier">to_f</span>
|
|
27
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span>
|
|
28
|
+
<span class="ruby-identifier">x</span> = <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>)
|
|
29
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">f</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))
|
|
30
|
+
<span class="ruby-identifier">height</span> = <span class="ruby-identifier">f</span>.<span class="ruby-identifier">segment_height</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">data_per_px</span>
|
|
31
|
+
<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">height</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>
|
|
32
|
+
<span class="ruby-comment cmt">#$stderr.puts f.segment_height, data_per_px, data_interval, max, min, "------"</span>
|
|
33
|
+
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">send</span>(<span class="ruby-node">"draw_#{track.glyph}"</span>, {<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
34
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>,
|
|
35
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">width</span>,
|
|
36
|
+
<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">height</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">args</span>))
|
|
37
|
+
<span class="ruby-keyword kw">end</span>
|
|
38
|
+
<span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>) <span class="ruby-operator">+</span> <span class="ruby-value">20</span>
|
|
39
|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">##following stuff for the features</span>
|
|
40
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">label</span>
|
|
41
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">name</span>, <span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> <span class="ruby-value">30</span>, <span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-value">3</span>)
|
|
42
|
+
<span class="ruby-keyword kw">end</span>
|
|
43
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">get_rows</span> <span class="ruby-comment cmt">##work out how many rows and which features belong in each row...</span>
|
|
44
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span>, <span class="ruby-identifier">index</span><span class="ruby-operator">|</span>
|
|
45
|
+
<span class="ruby-identifier">x</span> = <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-comment cmt">#bottom left of feature</span>
|
|
46
|
+
<span class="ruby-identifier">all_sub_blocks</span> = []
|
|
47
|
+
|
|
48
|
+
<span class="ruby-comment cmt">#convert the exon and utr start stops to px start stops and px widths</span>
|
|
49
|
+
<span class="ruby-identifier">exons</span> = []
|
|
50
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>
|
|
51
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>.<span class="ruby-identifier">each_slice</span>(<span class="ruby-value">2</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">exon</span><span class="ruby-operator">|</span>
|
|
52
|
+
<span class="ruby-identifier">all_sub_blocks</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">exon</span>
|
|
53
|
+
<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">exon</span>.<span class="ruby-identifier">nil?</span>
|
|
54
|
+
<span class="ruby-identifier">exons</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">exon</span>[<span class="ruby-value">1</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
55
|
+
<span class="ruby-keyword kw">end</span>
|
|
56
|
+
<span class="ruby-keyword kw">end</span>
|
|
57
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span> = <span class="ruby-identifier">exons</span>
|
|
58
|
+
|
|
59
|
+
<span class="ruby-identifier">utrs</span> = []
|
|
60
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>
|
|
61
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>.<span class="ruby-identifier">each_slice</span>(<span class="ruby-value">2</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">utr</span><span class="ruby-operator">|</span>
|
|
62
|
+
<span class="ruby-identifier">all_sub_blocks</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">utr</span>
|
|
63
|
+
<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">nil?</span>
|
|
64
|
+
<span class="ruby-identifier">utrs</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">utr</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">utr</span>[<span class="ruby-value">1</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">utr</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
65
|
+
<span class="ruby-keyword kw">end</span>
|
|
66
|
+
<span class="ruby-keyword kw">end</span>
|
|
67
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span> = <span class="ruby-identifier">utrs</span>
|
|
68
|
+
|
|
69
|
+
<span class="ruby-comment cmt">#if there are any intron like gaps.. get where they would be</span>
|
|
70
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">not</span> <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">empty?</span>
|
|
71
|
+
<span class="ruby-identifier">all_sub_blocks</span> = <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span>, <span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">b</span>.<span class="ruby-identifier">first</span> }
|
|
72
|
+
<span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">each_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
73
|
+
<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">length</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">>=</span> <span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">first</span> <span class="ruby-comment cmt">#skip if there is no gap</span>
|
|
74
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">block_gaps</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">first</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
75
|
+
<span class="ruby-keyword kw">end</span>
|
|
76
|
+
<span class="ruby-keyword kw">end</span>
|
|
77
|
+
|
|
78
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">f</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))
|
|
79
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">width</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span>
|
|
80
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span>
|
|
81
|
+
<span class="ruby-keyword kw">end</span>
|
|
82
|
+
<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_rows</span>[<span class="ruby-identifier">index</span>] <span class="ruby-operator">*</span> <span class="ruby-value">2</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span>)
|
|
83
|
+
|
|
84
|
+
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">send</span>(<span class="ruby-node">"draw_#{track.glyph}"</span>, {<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
85
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>,
|
|
86
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">width</span>,
|
|
87
|
+
<span class="ruby-identifier">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">strand</span>,
|
|
88
|
+
<span class="ruby-identifier">:exons</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>,
|
|
89
|
+
<span class="ruby-identifier">:utrs</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>,
|
|
90
|
+
<span class="ruby-identifier">:block_gaps</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">block_gaps</span>,
|
|
91
|
+
<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span>
|
|
92
|
+
}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">args</span>))
|
|
93
|
+
|
|
94
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">id</span>
|
|
95
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>, <span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">width</span> <span class="ruby-value">+2</span>, <span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">id</span>)
|
|
96
|
+
<span class="ruby-keyword kw">end</span>
|
|
97
|
+
<span class="ruby-keyword kw">end</span>
|
|
98
|
+
<span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_rows</span> <span class="ruby-operator">*</span> <span class="ruby-value">2</span>) <span class="ruby-operator">+</span> <span class="ruby-value">20</span>
|
|
99
|
+
<span class="ruby-keyword kw">end</span>
|
|
100
|
+
|
|
101
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-value">100</span> <span class="ruby-comment cmt">#fudge...</span>
|
|
102
|
+
<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">update_height</span>(<span class="ruby-ivar">@height</span>)
|
|
103
|
+
<span class="ruby-comment cmt">#@svg.update_width(@width + 200)</span>
|
|
104
|
+
|
|
105
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
106
|
+
</body>
|
|
107
|
+
</html>
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>to_px (Bio::Graphics::Page)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 377</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">num</span>)
|
|
15
|
+
(<span class="ruby-identifier">num</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@nt_per_px_x</span>.<span class="ruby-identifier">to_f</span>)
|
|
16
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
17
|
+
</body>
|
|
18
|
+
</html>
|
|
@@ -0,0 +1,23 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>get_markup (Bio::Graphics::Page)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 382</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_markup</span>
|
|
15
|
+
<span class="ruby-identifier">get_limits</span>
|
|
16
|
+
<span class="ruby-identifier">draw_scale</span>
|
|
17
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
18
|
+
<span class="ruby-identifier">draw_features</span>(<span class="ruby-identifier">track</span>)
|
|
19
|
+
<span class="ruby-keyword kw">end</span>
|
|
20
|
+
<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">draw</span>
|
|
21
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
22
|
+
</body>
|
|
23
|
+
</html>
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html>
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<head>
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<title>draw (Bio::Graphics::Page)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/page.rb, line 391</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">puts</span> <span class="ruby-identifier">get_markup</span>
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<span class="ruby-keyword kw">end</span></pre>
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