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
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- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
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- data/doc/images/page_white_text.png +0 -0
- data/doc/images/page_white_width.png +0 -0
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- data/doc/images/ruby.png +0 -0
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- 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/BarChart.html
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<h1 class="class">class BarChart</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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<h3 class="section-header">Public Class Methods</h3>
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<div id="method-c-new" class="method-detail ">
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class="method-args">(group,value,params)</span>
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<h4 id="method-c-new-label-Attributes++">Attributes </h4>
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<ul><li>
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<p><code>group</code> - a vector of String categories</p>
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<p><code>value</code> - a vector of Float numeric value</p>
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<p><code>parms</code> - an Hash whit parametrs value</p>
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<h4 id="method-c-new-label-Parms++">Parms </h4>
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<p>This Hash contain parmas . List of key permitted .</p>
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<ul><li>
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<p><code>:title</code> - (default “A sample Graph”) Graph main title</p>
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<p><code>:x_label</code> - (default ‘Categories’) Label of x ass</p>
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<p><code>:y_label</code> - (default ‘Value’) Label of y ass</p>
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<p><code>:legend</code> - (default false) Prints legend</p>
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<p><code>:vertical</code> - (default true) The orientation of the plot</p>
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<p><code>:group_by</code> - (default nil) A vector of values used to group
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the values into series within each category.</p>
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<p><code>:height</code> - (default 1500) Graph height</p>
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<p><code>:width</code> - (default 800) Graph width</p>
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<p><code>:file_name</code> - (default sample.jpg) Graph File Name/Path to save
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plot. You can chose jpg or pdf</p>
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<h4 id="method-c-new-label-Examples++">Examples </h4>
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<p>Class Usage:</p>
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<pre class="ruby"><span class="ruby-identifier">categories</span> = [<span class="ruby-string">"uman"</span>,<span class="ruby-string">"elf"</span>,<span class="ruby-string">"dwarfs"</span>]
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<span class="ruby-identifier">values</span> = [<span class="ruby-value">1.0</span>,<span class="ruby-value">2.0</span>,<span class="ruby-value">3.0</span>]
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<span class="ruby-identifier">params</span> = {<span class="ruby-string">"title"</span> =<span class="ruby-operator">></span> <span class="ruby-string">"Popolation of middle heart"</span>,<span class="ruby-string">"x_label"</span>=<span class="ruby-operator">></span><span class="ruby-string">"Popolation"</span>,<span class="ruby-string">"y_label"</span>=<span class="ruby-operator">></span><span class="ruby-string">"greed"</span>}
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<span class="ruby-identifier">plot</span> = <span class="ruby-constant">BarChart</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">categories</span>,<span class="ruby-identifier">values</span>,<span class="ruby-identifier">params</span>)
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<span class="ruby-comment">#To view</span>
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<span class="ruby-identifier">plot</span>.<span class="ruby-identifier">view</span>
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<span class="ruby-comment">#to save</span>
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<span class="ruby-identifier">plot</span>.<span class="ruby-identifier">save</span>
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</pre>
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<pre><span class="ruby-comment"># File lib/bar_chart/bar_chart.rb, line 38</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">group</span>,<span class="ruby-identifier">value</span>,<span class="ruby-identifier">params</span>)
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<span class="ruby-ivar">@group</span>=<span class="ruby-identifier">check_grp</span>(<span class="ruby-identifier">group</span>)
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<span class="ruby-ivar">@value</span>=<span class="ruby-identifier">check_val</span>(<span class="ruby-identifier">value</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-keyword">end</span></pre>
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<pre><span class="ruby-comment"># File lib/bar_chart/bar_chart.rb, line 44</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">"group_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">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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<span class="ruby-identifier">raise</span> <span class="ruby-string">"Error : Permitted key are title,x_label,y_label,vertical,group_by,legend,width,height"</span>
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<span class="ruby-keyword">end</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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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"x_label"</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">"x_label"</span>]=<span class="ruby-string">"Categories"</span>
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"x_label"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"x_label"</span>]
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"y_label"</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">"y_label"</span>]=<span class="ruby-string">"Values"</span>
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<span class="ruby-keyword">else</span>
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"y_label"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"y_label"</span>]
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<span class="ruby-keyword">end</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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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"vertical"</span>]=<span class="ruby-keyword">true</span>
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<span class="ruby-keyword">else</span>
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"vertical"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"vertical"</span>]
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"legend"</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">"legend"</span>]=<span class="ruby-keyword">false</span>
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<span class="ruby-keyword">else</span>
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<span class="ruby-identifier">hash</span>[<span class="ruby-string">"legend"</span>]=<span class="ruby-identifier">params</span>[<span class="ruby-string">"legend"</span>]
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-string">"gruop_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-keyword">nil</span>
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<span class="ruby-keyword">else</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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<span class="ruby-keyword">end</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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<span class="ruby-keyword">else</span>
|
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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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<span class="ruby-keyword">end</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">"height"</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">"height"</span>]=<span class="ruby-value">800</span>
|
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<span class="ruby-keyword">else</span>
|
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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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<span class="ruby-keyword">end</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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329
|
+
<span class="ruby-identifier">hash</span>[<span class="ruby-string">"file_name"</span>]=<span class="ruby-string">"sample.jpg"</span>
|
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|
+
<span class="ruby-keyword">else</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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332
|
+
<span class="ruby-keyword">end</span>
|
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333
|
+
|
|
334
|
+
<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>)
|
|
335
|
+
<span class="ruby-keyword">return</span> <span class="ruby-identifier">params_map</span>
|
|
336
|
+
<span class="ruby-keyword">end</span></pre>
|
|
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|
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</div><!-- check_par-source -->
|
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|
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|
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</div>
|
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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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|
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|
+
<div id="method-i-getGroup" class="method-detail ">
|
|
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|
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|
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|
+
<div class="method-heading">
|
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350
|
+
<span class="method-name">getGroup</span><span
|
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|
+
class="method-args">()</span>
|
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</div>
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<div class="method-source-code" id="getGroup-source">
|
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|
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<pre><span class="ruby-comment"># File lib/bar_chart/bar_chart.rb, line 112</span>
|
|
364
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getGroup</span>
|
|
365
|
+
<span class="ruby-ivar">@group</span>
|
|
366
|
+
<span class="ruby-keyword">end</span></pre>
|
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367
|
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</div><!-- getGroup-source -->
|
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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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|
|
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|
+
</div><!-- getGroup-method -->
|
|
375
|
+
|
|
376
|
+
|
|
377
|
+
<div id="method-i-getParams" class="method-detail ">
|
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378
|
+
|
|
379
|
+
<div class="method-heading">
|
|
380
|
+
<span class="method-name">getParams</span><span
|
|
381
|
+
class="method-args">()</span>
|
|
382
|
+
<span class="method-click-advice">click to toggle source</span>
|
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383
|
+
</div>
|
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+
|
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+
|
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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="getParams-source">
|
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393
|
+
<pre><span class="ruby-comment"># File lib/bar_chart/bar_chart.rb, line 120</span>
|
|
394
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getParams</span>
|
|
395
|
+
<span class="ruby-ivar">@params</span>
|
|
396
|
+
<span class="ruby-keyword">end</span></pre>
|
|
397
|
+
</div><!-- getParams-source -->
|
|
398
|
+
|
|
399
|
+
</div>
|
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|
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401
|
+
|
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|
+
|
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|
+
|
|
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|
+
</div><!-- getParams-method -->
|
|
405
|
+
|
|
406
|
+
|
|
407
|
+
<div id="method-i-getValue" class="method-detail ">
|
|
408
|
+
|
|
409
|
+
<div class="method-heading">
|
|
410
|
+
<span class="method-name">getValue</span><span
|
|
411
|
+
class="method-args">()</span>
|
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412
|
+
<span class="method-click-advice">click to toggle source</span>
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</div>
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|
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<div class="method-source-code" id="getValue-source">
|
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|
+
<pre><span class="ruby-comment"># File lib/bar_chart/bar_chart.rb, line 116</span>
|
|
424
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">getValue</span>
|
|
425
|
+
<span class="ruby-ivar">@value</span>
|
|
426
|
+
<span class="ruby-keyword">end</span></pre>
|
|
427
|
+
</div><!-- getValue-source -->
|
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428
|
+
|
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429
|
+
</div>
|
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|
+
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431
|
+
|
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|
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433
|
+
|
|
434
|
+
</div><!-- getValue-method -->
|
|
435
|
+
|
|
436
|
+
|
|
437
|
+
<div id="method-i-save" class="method-detail ">
|
|
438
|
+
|
|
439
|
+
<div class="method-heading">
|
|
440
|
+
<span class="method-name">save</span><span
|
|
441
|
+
class="method-args">()</span>
|
|
442
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
443
|
+
</div>
|
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444
|
+
|
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445
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+
|
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446
|
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<div class="method-description">
|
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447
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+
|
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448
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+
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449
|
+
|
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450
|
+
|
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451
|
+
|
|
452
|
+
<div class="method-source-code" id="save-source">
|
|
453
|
+
<pre><span class="ruby-comment"># File lib/bar_chart/bar_chart.rb, line 125</span>
|
|
454
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">save</span>
|
|
455
|
+
<span class="ruby-keyword">begin</span>
|
|
456
|
+
<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>
|
|
457
|
+
<span class="ruby-identifier">a</span>.<span class="ruby-identifier">save_bar</span>(<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getGroup</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getValue</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getParams</span>)
|
|
458
|
+
<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">ex</span>
|
|
459
|
+
<span class="ruby-keyword">end</span>
|
|
460
|
+
<span class="ruby-keyword">end</span></pre>
|
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461
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+
</div><!-- save-source -->
|
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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><!-- save-method -->
|
|
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|
+
|
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470
|
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|
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471
|
+
<div id="method-i-view" class="method-detail ">
|
|
472
|
+
|
|
473
|
+
<div class="method-heading">
|
|
474
|
+
<span class="method-name">view</span><span
|
|
475
|
+
class="method-args">()</span>
|
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476
|
+
<span class="method-click-advice">click to toggle source</span>
|
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477
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</div>
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|
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<div class="method-source-code" id="view-source">
|
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487
|
+
<pre><span class="ruby-comment"># File lib/bar_chart/bar_chart.rb, line 132</span>
|
|
488
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">view</span>
|
|
489
|
+
<span class="ruby-keyword">begin</span>
|
|
490
|
+
<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>
|
|
491
|
+
<span class="ruby-identifier">a</span>.<span class="ruby-identifier">view_bar</span>(<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getGroup</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getValue</span>,<span class="ruby-keyword">self</span>.<span class="ruby-identifier">getParams</span>)
|
|
492
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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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493
|
+
<span class="ruby-keyword">end</span>
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494
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495
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|
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496
|
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<span class="ruby-keyword">end</span></pre>
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</div><!-- view-source -->
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</div>
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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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