bio-incanter 0.1.0
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- data/Gemfile +14 -0
- data/Gemfile.lock +35 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +26 -0
- data/Rakefile +51 -0
- data/VERSION +1 -0
- data/bio-incanter.gemspec +136 -0
- data/doc/AreaChart.html +473 -0
- data/doc/BarChart.html +519 -0
- data/doc/BlandAltman.html +453 -0
- data/doc/BoxPlot.html +474 -0
- data/doc/FunctionPlot.html +496 -0
- data/doc/HeatMap.html +554 -0
- data/doc/Histogram.html +444 -0
- data/doc/LICENSE_txt.html +130 -0
- data/doc/LineChart.html +479 -0
- data/doc/Object.html +278 -0
- data/doc/PieChart.html +455 -0
- data/doc/README_rdoc.html +152 -0
- data/doc/ScatterPlot.html +489 -0
- data/doc/TimeChart.html +473 -0
- data/doc/TracePlot.html +416 -0
- data/doc/XyPlot.html +477 -0
- data/doc/created.rid +18 -0
- data/doc/images/add.png +0 -0
- data/doc/images/brick.png +0 -0
- data/doc/images/brick_link.png +0 -0
- data/doc/images/bug.png +0 -0
- data/doc/images/bullet_black.png +0 -0
- data/doc/images/bullet_toggle_minus.png +0 -0
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- data/doc/images/date.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
- data/doc/images/macFFBgHack.png +0 -0
- data/doc/images/package.png +0 -0
- data/doc/images/page_green.png +0 -0
- data/doc/images/page_white_text.png +0 -0
- data/doc/images/page_white_width.png +0 -0
- data/doc/images/plugin.png +0 -0
- data/doc/images/ruby.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/images/tag_green.png +0 -0
- data/doc/images/transparent.png +0 -0
- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +106 -0
- data/doc/js/darkfish.js +153 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/rdoc.css +543 -0
- data/doc/table_of_contents.html +295 -0
- data/lib/area_chart/area_chart.rb +106 -0
- data/lib/bar_chart/bar_chart.rb +142 -0
- data/lib/bio-incanter.rb +108 -0
- data/lib/bland_altman/bland_altman.rb +120 -0
- data/lib/box_plot/box_plot.rb +136 -0
- data/lib/function_plot/function_plot.rb +137 -0
- data/lib/histogram/histogram.rb +139 -0
- data/lib/java/clocomics-1.0.0-standalone.jar +0 -0
- data/lib/line_chart/line_chart.rb +148 -0
- data/lib/pie_chart/pie_chart.rb +121 -0
- data/lib/qq_plot/qq_plot.rb +105 -0
- data/lib/scatter_plot/scatter_plot.rb +162 -0
- data/lib/time_chart/time_chart.rb +142 -0
- data/lib/trace_plot/trace_plot.rb +108 -0
- data/lib/xy_plot/xy_plot.rb +149 -0
- data/spec/bar_chart_spec.rb +25 -0
- data/spec/bland_altman_spec.rb +26 -0
- data/spec/box_plot_spec.rb +25 -0
- data/spec/function_plot_spec.rb +27 -0
- data/spec/histogram_spec.rb +24 -0
- data/spec/line_chart_spec.rb +25 -0
- data/spec/pie_chart_spec.rb +25 -0
- data/spec/qq_plot_spec.rb +24 -0
- data/spec/scatter_plot_spec.rb +26 -0
- data/spec/spec_helper.rb +13 -0
- data/spec/time_chart_spec.rb +26 -0
- data/spec/trace_plot_spec.rb +24 -0
- data/spec/xy_plot_spec.rb +25 -0
- metadata +196 -0
data/doc/HeatMap.html
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<h1 class="class">class HeatMap</h1>
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<!-- Methods -->
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class="method-args">(function,min_x,max_x,min_y,max_y,params)</span>
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 2</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">function</span>,<span class="ruby-identifier">min_x</span>,<span class="ruby-identifier">max_x</span>,<span class="ruby-identifier">min_y</span>,<span class="ruby-identifier">max_y</span>,<span class="ruby-identifier">params</span>)
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<span class="ruby-ivar">@min_x</span>=<span class="ruby-identifier">min_x</span>
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 11</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">check_par</span>(<span class="ruby-identifier">params</span>)
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<span class="ruby-identifier">hash</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-identifier">permitted</span> = [<span class="ruby-string">"title"</span>,<span class="ruby-string">"vertical"</span>,<span class="ruby-string">"legend"</span>,<span class="ruby-string">"width"</span>,<span class="ruby-string">"height"</span>,<span class="ruby-string">"file_name"</span>]
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<span class="ruby-identifier">keys</span> = <span class="ruby-identifier">params</span>.<span class="ruby-identifier">keys</span>
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<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">key</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">permitted</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">key</span>)<span class="ruby-operator">==</span><span class="ruby-keyword">false</span>
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}
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"title"</span>]<span class="ruby-operator">==</span><span class="ruby-keyword">nil</span>
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"title"</span>]=<span class="ruby-string">"A sample Graph"</span>
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 61</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">getFunction</span>
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 69</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">getMaxX</span>
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 77</span>
|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">getMaxY</span>
|
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<span class="ruby-ivar">@max_y</span>
|
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<div id="method-i-getMinX" class="method-detail ">
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 65</span>
|
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399
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getMinX</span>
|
|
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|
+
<span class="ruby-ivar">@min_x</span>
|
|
401
|
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<span class="ruby-keyword">end</span></pre>
|
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|
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|
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|
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|
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|
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<div id="method-i-getMinY" class="method-detail ">
|
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|
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|
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|
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<span class="method-name">getMinY</span><span
|
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416
|
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class="method-args">()</span>
|
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<div class="method-source-code" id="getMinY-source">
|
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|
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 73</span>
|
|
429
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getMinY</span>
|
|
430
|
+
<span class="ruby-ivar">@min_y</span>
|
|
431
|
+
<span class="ruby-keyword">end</span></pre>
|
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|
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</div><!-- getMinY-source -->
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<div id="method-i-getParams" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">getParams</span><span
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class="method-args">()</span>
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<div class="method-source-code" id="getParams-source">
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 81</span>
|
|
459
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getParams</span>
|
|
460
|
+
<span class="ruby-ivar">@params</span>
|
|
461
|
+
<span class="ruby-keyword">end</span></pre>
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</div><!-- getParams-source -->
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</div><!-- getParams-method -->
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<div id="method-i-save" class="method-detail ">
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<div class="method-heading">
|
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475
|
+
<span class="method-name">save</span><span
|
|
476
|
+
class="method-args">()</span>
|
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+
<span class="method-click-advice">click to toggle source</span>
|
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478
|
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</div>
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479
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480
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|
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<div class="method-description">
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|
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<div class="method-source-code" id="save-source">
|
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488
|
+
<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 86</span>
|
|
489
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">save</span>
|
|
490
|
+
<span class="ruby-keyword">begin</span>
|
|
491
|
+
<span class="ruby-identifier">a</span> = <span class="ruby-constant">Java</span><span class="ruby-operator">::</span><span class="ruby-constant">ComDomain</span><span class="ruby-operator">::</span><span class="ruby-identifier">clocomics</span>
|
|
492
|
+
<span class="ruby-identifier">a</span>.<span class="ruby-identifier">save_heat</span>(<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getFunction</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getMinX</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getMaxX</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getMinY</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getMaxY</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getParams</span>)
|
|
493
|
+
<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">ex</span>
|
|
494
|
+
<span class="ruby-keyword">end</span>
|
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495
|
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<span class="ruby-keyword">end</span></pre>
|
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</div><!-- save-source -->
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</div><!-- save-method -->
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<div id="method-i-view" class="method-detail ">
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<div class="method-heading">
|
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509
|
+
<span class="method-name">view</span><span
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|
+
class="method-args">()</span>
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<pre><span class="ruby-comment"># File lib/heat_map/heat_map.rb, line 93</span>
|
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523
|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">view</span>
|
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524
|
+
<span class="ruby-keyword">begin</span>
|
|
525
|
+
<span class="ruby-identifier">a</span> = <span class="ruby-constant">Java</span><span class="ruby-operator">::</span><span class="ruby-constant">ComDomain</span><span class="ruby-operator">::</span><span class="ruby-identifier">clocomics</span>
|
|
526
|
+
<span class="ruby-identifier">a</span>.<span class="ruby-identifier">view_heat</span>(<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getFunction</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getMinX</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getMaxX</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getMinY</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getMaxY</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getParams</span>)
|
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<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">ex</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">end</span></pre>
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</div><!-- view-source -->
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</div><!-- view-method -->
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</section><!-- public-instance-method-details -->
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</section><!-- 5Buntitled-5D -->
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<footer id="validator-badges">
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<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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<p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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