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/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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<span class="method-name">new</span><span
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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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<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>: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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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-comment">#to save</span>
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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-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-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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}
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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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<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">"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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<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">"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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|
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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
|
+
|
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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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|
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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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351
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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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</div>
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|
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|
+
</div><!-- getGroup-method -->
|
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|
+
|
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|
+
|
|
377
|
+
<div id="method-i-getParams" class="method-detail ">
|
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|
+
|
|
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
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+
</div>
|
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384
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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>
|
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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
|
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</div>
|
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431
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+
|
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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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+
|
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445
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+
|
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446
|
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<div class="method-description">
|
|
447
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+
|
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+
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449
|
+
|
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450
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+
|
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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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</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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486
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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>
|
|
493
|
+
<span class="ruby-keyword">end</span>
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|
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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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