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
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- 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
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<h1 id="label-bio-incanter">bio-incanter</h1>
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<p>bio-incanter is a Jruby bio-gem for use Incanter lib. Incanter is a Clojure
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lib to save and view graphics.</p>
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<h2 id="label-Use+">Use </h2>
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<ul><li>
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<p>Select your plot class</p>
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<p>Instance that class</p>
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<p>Call save method to save your plot</p>
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<p>Call view method to view your plot</p>
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<h2 id="label-Contributing+to+bio-incanter">Contributing to bio-incanter</h2>
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<ul><li>
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<p>Check out the latest master to make sure the feature hasn’t been
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implemented or the bug hasn’t been fixed yet.</p>
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</li><li>
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<p>Check out the issue tracker to make sure someone already hasn’t requested
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it and/or contributed it.</p>
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</li><li>
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<p>Fork the project.</p>
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</li><li>
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<p>Start a feature/bugfix branch.</p>
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</li><li>
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<p>Commit and push until you are happy with your contribution.</p>
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</li><li>
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<p>Make sure to add tests for it. This is important so I don’t break it in a
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future version unintentionally.</p>
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</li><li>
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<p>Please try not to mess with the Rakefile, version, or history. If you want
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to have your own version, or is otherwise necessary, that is fine, but
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please isolate to its own commit so I can cherry-pick around it.</p>
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</li></ul>
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<h2 id="label-Copyright">Copyright</h2>
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<p>Copyright © 2012 Matteo Picciolini. See <a
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href="LICENSE_txt.html">LICENSE.txt</a> for further details.</p>
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<pre><span class="ruby-comment"># File lib/scatter_plot/scatter_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">valuex</span>,<span class="ruby-identifier">valuey</span>,<span class="ruby-identifier">params</span>)
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<span class="ruby-ivar">@value_x</span>=<span class="ruby-identifier">check_val</span>(<span class="ruby-identifier">valuex</span>)
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<pre><span class="ruby-comment"># File lib/scatter_plot/scatter_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">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">"x_label"</span>,<span class="ruby-string">"y_label"</span>,<span class="ruby-string">"vertical"</span>,<span class="ruby-string">"n_bins"</span>,<span class="ruby-string">"density"</span>,<span class="ruby-string">"gruop_by"</span>,<span class="ruby-string">"gradient"</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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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"vertical"</span>]=<span class="ruby-keyword">true</span>
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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">"n_bins"</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">"n_bins"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"n_bins"</span>]
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"density"</span>]=<span class="ruby-keyword">false</span>
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"density"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"density"</span>]
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"group_by"</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">"group_by"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"group_by"</span>]
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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">"gradient"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"gradient"</span>]
|
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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">"width"</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">"width"</span>]=<span class="ruby-value">1500</span>
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|
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"width"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"width"</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">"height"</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">"height"</span>]=<span class="ruby-value">800</span>
|
|
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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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<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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<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>]
|
|
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|
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<span class="ruby-keyword">end</span>
|
|
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|
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|
|
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|
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<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>)
|
|
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|
+
<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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</div><!-- check_par-method -->
|
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|
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|
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|
|
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|
+
<div id="method-i-getParams" class="method-detail ">
|
|
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|
+
|
|
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|
+
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|
|
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+
<span class="method-name">getParams</span><span
|
|
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|
+
class="method-args">()</span>
|
|
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|
+
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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="getParams-source">
|
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|
+
<pre><span class="ruby-comment"># File lib/scatter_plot/scatter_plot.rb, line 103</span>
|
|
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|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getParams</span>
|
|
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|
+
<span class="ruby-ivar">@params</span>
|
|
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|
+
<span class="ruby-keyword">end</span></pre>
|
|
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|
+
</div><!-- getParams-source -->
|
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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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|
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|
+
</div><!-- getParams-method -->
|
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|
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|
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+
<div id="method-i-getValuex" class="method-detail ">
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|
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|
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<div class="method-heading">
|
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+
<span class="method-name">getValuex</span><span
|
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+
class="method-args">()</span>
|
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<span class="method-click-advice">click to toggle source</span>
|
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</div>
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<div class="method-description">
|
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|
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|
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|
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<div class="method-source-code" id="getValuex-source">
|
|
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|
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<pre><span class="ruby-comment"># File lib/scatter_plot/scatter_plot.rb, line 94</span>
|
|
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|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getValuex</span>
|
|
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|
+
<span class="ruby-ivar">@value_x</span>
|
|
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|
+
<span class="ruby-keyword">end</span></pre>
|
|
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|
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</div><!-- getValuex-source -->
|
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|
|
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|
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</div>
|
|
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</div><!-- getValuex-method -->
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<div id="method-i-getValuey" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">getValuey</span><span
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class="method-args">()</span>
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<pre><span class="ruby-comment"># File lib/scatter_plot/scatter_plot.rb, line 98</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">getValuey</span>
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<span class="ruby-ivar">@value_y</span>
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<span class="ruby-keyword">end</span></pre>
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<div id="method-i-save" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">save</span><span
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<pre><span class="ruby-comment"># File lib/scatter_plot/scatter_plot.rb, line 108</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">save</span>
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<span class="ruby-keyword">begin</span>
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<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>
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<span class="ruby-identifier">a</span>.<span class="ruby-identifier">save_scatter</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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<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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</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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<span class="method-name">view</span><span
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<span class="method-click-advice">click to toggle source</span>
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<div class="method-source-code" id="view-source">
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<pre><span class="ruby-comment"># File lib/scatter_plot/scatter_plot.rb, line 115</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">view</span>
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<span class="ruby-keyword">begin</span>
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<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>
|
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<span class="ruby-identifier">a</span>.<span class="ruby-identifier">view_scatter</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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<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-method -->
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</section><!-- public-instance-method-details -->
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</section><!-- 5Buntitled-5D -->
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</div><!-- documentation -->
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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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</footer>
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