bio-incanter 0.1.0
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/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
- data/doc/images/bullet_toggle_plus.png +0 -0
- 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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<section id="public-class-5Buntitled-5D-method-details" class="method-section section">
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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">@params</span>=<span class="ruby-keyword">self</span>.<span class="ruby-identifier">check_par</span>(<span class="ruby-identifier">params</span>)
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<span class="ruby-ivar">@function</span>=<span class="ruby-identifier">function</span>
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<span class="ruby-ivar">@min_x</span>=<span class="ruby-identifier">min_x</span>
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<span class="ruby-keyword">end</span></pre>
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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">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-identifier">hash</span>[<span class="ruby-string">"title"</span>]=<span class="ruby-string">"A sample Graph"</span>
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"vertical"</span>]<span class="ruby-operator">==</span><span class="ruby-keyword">nil</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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