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/TracePlot.html
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<h1 class="class">class TracePlot</h1>
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<!-- Methods -->
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<h3 class="section-header">Public Class Methods</h3>
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class="method-args">(value,params)</span>
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<pre><span class="ruby-comment"># File lib/trace_plot/trace_plot.rb, line 2</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">value</span>,<span class="ruby-identifier">params</span>)
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class="method-args">(params)</span>
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<pre><span class="ruby-comment"># File lib/trace_plot/trace_plot.rb, line 7</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">"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">"vertical"</span>]<span class="ruby-operator">==</span><span class="ruby-keyword">nil</span>
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"width"</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">"width"</span>]=<span class="ruby-value">1500</span>
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data/doc/XyPlot.html
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|
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<h1 class="class">class XyPlot</h1>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">valuex</span>,<span class="ruby-identifier">valuey</span>,<span class="ruby-identifier">params</span>)
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<pre><span class="ruby-comment"># File lib/xy_plot/xy_plot.rb, line 8</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">"x_label"</span>,<span class="ruby-string">"y_label"</span>,<span class="ruby-string">"vertical"</span>,<span class="ruby-string">"points"</span>,<span class="ruby-string">"gruop_by"</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">raise</span> <span class="ruby-string">"Error : Permitted key are title,x_label,y_label,vertical,n_bins,density,group_by,gardient,legend,width,height"</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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|
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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-identifier">hash</span>[<span class="ruby-string">"height"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"height"</span>]
|
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|
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|
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|
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|
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"file_name"</span>]<span class="ruby-operator">==</span><span class="ruby-keyword">nil</span>
|
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|
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"file_name"</span>]=<span class="ruby-string">"sample.jpg"</span>
|
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|
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|
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|
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"file_name"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"file_name"</span>]
|
|
292
|
+
<span class="ruby-keyword">end</span>
|
|
293
|
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|
|
294
|
+
<span class="ruby-identifier">params_map</span> = <span class="ruby-constant">HashMap</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">hash</span>)
|
|
295
|
+
<span class="ruby-keyword">return</span> <span class="ruby-identifier">params_map</span>
|
|
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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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|
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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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|
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|
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|
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|
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|
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<pre><span class="ruby-comment"># File lib/xy_plot/xy_plot.rb, line 91</span>
|
|
324
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getParams</span>
|
|
325
|
+
<span class="ruby-ivar">@params</span>
|
|
326
|
+
<span class="ruby-keyword">end</span></pre>
|
|
327
|
+
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|
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|
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|
|
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|
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</div>
|
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+
|
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|
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|
+
|
|
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|
+
</div><!-- getParams-method -->
|
|
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|
+
|
|
336
|
+
|
|
337
|
+
<div id="method-i-getValuex" class="method-detail ">
|
|
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|
+
|
|
339
|
+
<div class="method-heading">
|
|
340
|
+
<span class="method-name">getValuex</span><span
|
|
341
|
+
class="method-args">()</span>
|
|
342
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
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|
+
</div>
|
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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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|
+
|
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351
|
+
|
|
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|
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<div class="method-source-code" id="getValuex-source">
|
|
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|
+
<pre><span class="ruby-comment"># File lib/xy_plot/xy_plot.rb, line 82</span>
|
|
354
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getValuex</span>
|
|
355
|
+
<span class="ruby-ivar">@value_x</span>
|
|
356
|
+
<span class="ruby-keyword">end</span></pre>
|
|
357
|
+
</div><!-- getValuex-source -->
|
|
358
|
+
|
|
359
|
+
</div>
|
|
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|
+
|
|
361
|
+
|
|
362
|
+
|
|
363
|
+
|
|
364
|
+
</div><!-- getValuex-method -->
|
|
365
|
+
|
|
366
|
+
|
|
367
|
+
<div id="method-i-getValuey" class="method-detail ">
|
|
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|
+
|
|
369
|
+
<div class="method-heading">
|
|
370
|
+
<span class="method-name">getValuey</span><span
|
|
371
|
+
class="method-args">()</span>
|
|
372
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
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</div>
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|
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|
+
|
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+
|
|
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|
+
|
|
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|
+
<div class="method-source-code" id="getValuey-source">
|
|
383
|
+
<pre><span class="ruby-comment"># File lib/xy_plot/xy_plot.rb, line 86</span>
|
|
384
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getValuey</span>
|
|
385
|
+
<span class="ruby-ivar">@value_y</span>
|
|
386
|
+
<span class="ruby-keyword">end</span></pre>
|
|
387
|
+
</div><!-- getValuey-source -->
|
|
388
|
+
|
|
389
|
+
</div>
|
|
390
|
+
|
|
391
|
+
|
|
392
|
+
|
|
393
|
+
|
|
394
|
+
</div><!-- getValuey-method -->
|
|
395
|
+
|
|
396
|
+
|
|
397
|
+
<div id="method-i-save" class="method-detail ">
|
|
398
|
+
|
|
399
|
+
<div class="method-heading">
|
|
400
|
+
<span class="method-name">save</span><span
|
|
401
|
+
class="method-args">()</span>
|
|
402
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
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|
+
</div>
|
|
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|
+
|
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|
+
|
|
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|
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|
|
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|
+
|
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|
+
|
|
409
|
+
|
|
410
|
+
|
|
411
|
+
|
|
412
|
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<div class="method-source-code" id="save-source">
|
|
413
|
+
<pre><span class="ruby-comment"># File lib/xy_plot/xy_plot.rb, line 96</span>
|
|
414
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">save</span>
|
|
415
|
+
<span class="ruby-keyword">begin</span>
|
|
416
|
+
<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>
|
|
417
|
+
<span class="ruby-identifier">a</span>.<span class="ruby-identifier">save_xy</span>(<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getValuex</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getValuey</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getParams</span>)
|
|
418
|
+
<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">ex</span>
|
|
419
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<span class="ruby-identifier">a</span>.<span class="ruby-identifier">view_xy</span>(<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getValuex</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getValuey</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getParams</span>)
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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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