entropy 0.0.2

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  1. data/.gitignore +4 -0
  2. data/Gemfile +4 -0
  3. data/LICENSE.txt +674 -0
  4. data/README.txt +48 -0
  5. data/Rakefile +22 -0
  6. data/doc/rdocs/Entropy.html +234 -0
  7. data/doc/rdocs/Entropy/Dict.html +311 -0
  8. data/doc/rdocs/Entropy/ProbabilityMetricSpace.html +544 -0
  9. data/doc/rdocs/Entropy/ProbabilitySpace.html +473 -0
  10. data/doc/rdocs/Entropy/Stream.html +281 -0
  11. data/doc/rdocs/LICENSE_txt.html +834 -0
  12. data/doc/rdocs/README_txt.html +138 -0
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  34. data/doc/rdocs/index.html +155 -0
  35. data/doc/rdocs/js/darkfish.js +116 -0
  36. data/doc/rdocs/js/jquery.js +32 -0
  37. data/doc/rdocs/js/quicksearch.js +114 -0
  38. data/doc/rdocs/js/thickbox-compressed.js +10 -0
  39. data/doc/rdocs/lib/entropy/dict_rb.html +56 -0
  40. data/doc/rdocs/lib/entropy/metric_space_rb.html +54 -0
  41. data/doc/rdocs/lib/entropy/probability_space_rb.html +52 -0
  42. data/doc/rdocs/lib/entropy/stream_rb.html +52 -0
  43. data/doc/rdocs/lib/entropy/version_rb.html +52 -0
  44. data/doc/rdocs/lib/entropy_rb.html +62 -0
  45. data/doc/rdocs/rdoc.css +763 -0
  46. data/entropy.gemspec +24 -0
  47. data/example/metric_prob_space.rb +42 -0
  48. data/example/prob_space.rb +31 -0
  49. data/lib/entropy.rb +13 -0
  50. data/lib/entropy/dict.rb +30 -0
  51. data/lib/entropy/metric_space.rb +116 -0
  52. data/lib/entropy/probability_space.rb +91 -0
  53. data/lib/entropy/stream.rb +37 -0
  54. data/lib/entropy/version.rb +3 -0
  55. data/test/stream0.txt +1 -0
  56. data/test/stream1.txt +1 -0
  57. data/test/stream2.txt +1 -0
  58. data/test/stream_random.bin +2 -0
  59. data/test/test_entropy_def.rb +10 -0
  60. data/test/test_entropy_metr.rb +36 -0
  61. data/test/test_entropy_prob.rb +64 -0
  62. data/test/test_entropy_stream.rb +29 -0
  63. metadata +127 -0
data/README.txt ADDED
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+ = entropy-gem
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+
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+ This small gem provides methods to calculate the
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+ entropy (and cardinality and diversity) of a probability
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+ space and of a probability metric space.
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+
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+ A probability space is defined by a probability
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+ vector [p1, p2, ..., pn]. A probability metric space
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+ is defined by a probability vector and a metric function.
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+ The metric function defines the "distance" between the point
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+ i and the point j along with a distance matrix D where
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+ D[i, j] = distance between i and j.
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+
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+ Most of the code is derived from:
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+ http://golem.ph.utexas.edu/category/2008/10/entropy_diversity_and_cardinal.html
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+ and
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+ http://golem.ph.utexas.edu/category/2008/11/entropy_diversity_and_cardinal_1.html
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+
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+ In order to define a probability space, you can use the function add_stream to
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+ add a stream of chars (or bit). The method compute the probability
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+ vector using the frequency of each element of the stream. Otherwise
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+ you could supply directly a probability vector as an array of reals.
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+
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+ For a probability metric space you should also define the distance metric,
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+ either passing your function as a block to define_distance, or passing
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+ a matrix to the same define_distance.
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+
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+ The example files show a basic usage of the classes.
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+
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+ NOTE: requires ruby >= 1.9
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+
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+ == Copyright
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+
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+ Copyright (c) 2011 hiraedd@hiraedd.com. See LICENSE.txt for further details.
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+
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+ This program is free software: you can redistribute it and/or modify
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+ it under the terms of the GNU General Public License as published by
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+ the Free Software Foundation, either version 3 of the License, or
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+ (at your option) any later version.
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+
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+ This program is distributed in the hope that it will be useful,
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+ but WITHOUT ANY WARRANTY; without even the implied warranty of
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+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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+ GNU General Public License for more details.
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+
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+ You should have received a copy of the GNU General Public License
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+ along with this program. If not, see <http://www.gnu.org/licenses/>.
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+
data/Rakefile ADDED
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+ require "bundler/gem_tasks"
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+ require 'rake/testtask'
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+ require 'rdoc/task'
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+
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+
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+ Rake::TestTask.new(:test) do |t|
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+ #t.pattern = "test/**/test*.rb"
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+ t.test_files = Dir.glob("test/**/test*.rb")
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+ t.verbose = true
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+ t.warning = true
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+ end
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+
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+ desc 'generate API documentation to doc/rdocs/index.html'
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+ RDoc::Task.new do |rdoc|
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+ rdoc.main = 'README.txt'
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+ rdoc.rdoc_dir = 'doc/rdocs'
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+ rdoc.rdoc_files.include("README.txt", "LICENSE.txt", "lib/**/*.rb")
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+ end
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+
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+ desc "Run tests"
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+ task :default => :test
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+
data/doc/rdocs/Entropy.html ADDED
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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+
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+ <title>Module: Entropy</title>
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+
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+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
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+
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+ <script src="./js/jquery.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="./js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="./js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="./js/darkfish.js" type="text/javascript" charset="utf-8"></script>
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+
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+ </head>
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+ <body id="top" class="module">
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+
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+ <div id="metadata">
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+ <div id="home-metadata">
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+ <div id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="./index.html">Home</a>
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+ <a href="./index.html#classes">Classes</a>
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+ <a href="./index.html#methods">Methods</a>
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+ </h3>
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+ </div>
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+ </div>
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+
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+ <div id="file-metadata">
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+ <div id="file-list-section" class="section">
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+ <h3 class="section-header">In Files</h3>
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+ <div class="section-body">
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+ <ul>
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+
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+ <li><a href="./lib/entropy_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/entropy.rb">lib/entropy.rb</a></li>
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+
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+ <li><a href="./lib/entropy/stream_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/entropy/stream.rb">lib/entropy/stream.rb</a></li>
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+
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+ <li><a href="./lib/entropy/probability_space_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/entropy/probability_space.rb">lib/entropy/probability_space.rb</a></li>
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+
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+ <li><a href="./lib/entropy/version_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/entropy/version.rb">lib/entropy/version.rb</a></li>
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+
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+ <li><a href="./lib/entropy/dict_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/entropy/dict.rb">lib/entropy/dict.rb</a></li>
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+
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+ <li><a href="./lib/entropy/metric_space_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/entropy/metric_space.rb">lib/entropy/metric_space.rb</a></li>
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+
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+ </ul>
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+ </div>
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+ </div>
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+
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+
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+ </div>
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+
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+ <div id="class-metadata">
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+
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+
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+
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+
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+
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+ <!-- Namespace Contents -->
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+ <div id="namespace-list-section" class="section">
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+ <h3 class="section-header">Namespace</h3>
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+ <ul class="link-list">
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+
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+ <li><span class="type">CLASS</span> <a href="Entropy/Dict.html">Entropy::Dict</a></li>
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+
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+ <li><span class="type">CLASS</span> <a href="Entropy/ProbabilityMetricSpace.html">Entropy::ProbabilityMetricSpace</a></li>
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+
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+ <li><span class="type">CLASS</span> <a href="Entropy/ProbabilitySpace.html">Entropy::ProbabilitySpace</a></li>
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+
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+ <li><span class="type">CLASS</span> <a href="Entropy/Stream.html">Entropy::Stream</a></li>
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+
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+ </ul>
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+ </div>
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+
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+
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+
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+ <!-- Method Quickref -->
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+ <div id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+ <ul class="link-list">
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+
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+ <li><a href="#method-c-version_string">::version_string</a></li>
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+
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+ </ul>
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+ </div>
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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 id="project-metadata">
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+
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+
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+ <div id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Files</h3>
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+ <ul>
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+
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+ <li class="file"><a href="./LICENSE_txt.html">LICENSE.txt</a></li>
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+
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+ <li class="file"><a href="./README_txt.html">README.txt</a></li>
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+
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+ </ul>
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+ </div>
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+
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+
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class/Module Index
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+ <span class="search-toggle"><img src="./images/find.png"
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+ height="16" width="16" alt="[+]"
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+ title="show/hide quicksearch" /></span></h3>
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+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
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+ <fieldset>
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+ <legend>Quicksearch</legend>
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+ <input type="text" name="quicksearch" value=""
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+ class="quicksearch-field" />
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+ </fieldset>
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+ </form>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="./Entropy.html">Entropy</a></li>
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+
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+ <li><a href="./Entropy/Dict.html">Entropy::Dict</a></li>
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+
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+ <li><a href="./Entropy/ProbabilityMetricSpace.html">Entropy::ProbabilityMetricSpace</a></li>
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+
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+ <li><a href="./Entropy/ProbabilitySpace.html">Entropy::ProbabilitySpace</a></li>
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+
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+ <li><a href="./Entropy/Stream.html">Entropy::Stream</a></li>
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+
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+ </ul>
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+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
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+ </div>
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="documentation">
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+ <h1 class="module">Entropy</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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+
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+
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+
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+
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+ <div id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+
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+
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+ <!-- Constants -->
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+ <div id="constants-list" class="section">
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+ <h3 class="section-header">Constants</h3>
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+ <dl>
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+
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+ <dt><a name="VERSION">VERSION</a></dt>
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+
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+ <dd class="description"></dd>
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+
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+
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+ </dl>
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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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+ <!-- Methods -->
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+
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+ <div id="public-class-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+
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+
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+ <div id="version_string-method" class="method-detail ">
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+ <a name="method-c-version_string"></a>
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+
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+
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+ <div class="method-heading">
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+ <span class="method-name">version_string</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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+
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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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+
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+
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+ <div class="method-source-code" id="version_string-source">
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+ <pre>
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+ <span class="ruby-comment"># File lib/entropy.rb, line 9</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">version_string</span>
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+ <span class="ruby-node">&quot;Entropy version #{Entropy::VERSION}&quot;</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- version_string-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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+
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+ </div><!-- version_string-method -->
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+
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+
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+ </div><!-- public-class-method-details -->
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+
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+ </div><!-- 5Buntitled-5D -->
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+
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+
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+ </div><!-- documentation -->
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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+ Rdoc Generator</a> 2</small>.</p>
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+ </div>
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+
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+ </body>
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+ </html>
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+
data/doc/rdocs/Entropy/Dict.html ADDED
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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+
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+ <title>Class: Entropy::Dict</title>
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+
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+ <link rel="stylesheet" href="../rdoc.css" type="text/css" media="screen" />
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+
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+ <script src="../js/jquery.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/darkfish.js" type="text/javascript" charset="utf-8"></script>
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+
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+ </head>
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+ <body id="top" class="class">
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+
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+ <div id="metadata">
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+ <div id="home-metadata">
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+ <div id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../index.html">Home</a>
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+ <a href="../index.html#classes">Classes</a>
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+ <a href="../index.html#methods">Methods</a>
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+ </h3>
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+ </div>
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+ </div>
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+
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+ <div id="file-metadata">
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+ <div id="file-list-section" class="section">
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+ <h3 class="section-header">In Files</h3>
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+ <div class="section-body">
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+ <ul>
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+
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+ <li><a href="../lib/entropy/dict_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/entropy/dict.rb">lib/entropy/dict.rb</a></li>
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+
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+ </ul>
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+ </div>
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+ </div>
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+
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+
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+ </div>
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+
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+ <div id="class-metadata">
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+
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+ <!-- Parent Class -->
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+ <div id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+
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+ <p class="link">Object</p>
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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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+
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+
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+ <!-- Method Quickref -->
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+ <div id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+ <ul class="link-list">
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+
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+ <li><a href="#method-c-new">::new</a></li>
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+
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+ <li><a href="#method-i-freq">#freq</a></li>
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+
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+ <li><a href="#method-i-scan_keys">#scan_keys</a></li>
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+
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+ <li><a href="#method-i-upd">#upd</a></li>
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+
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+ </ul>
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+ </div>
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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 id="project-metadata">
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+
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+
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+ <div id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Files</h3>
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+ <ul>
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+
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+ <li class="file"><a href="../LICENSE_txt.html">LICENSE.txt</a></li>
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+
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+ <li class="file"><a href="../README_txt.html">README.txt</a></li>
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+
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+ </ul>
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+ </div>
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+
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+
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class/Module Index
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+ <span class="search-toggle"><img src="../images/find.png"
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+ height="16" width="16" alt="[+]"
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+ title="show/hide quicksearch" /></span></h3>
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+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
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+ <fieldset>
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+ <legend>Quicksearch</legend>
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+ <input type="text" name="quicksearch" value=""
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+ class="quicksearch-field" />
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+ </fieldset>
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+ </form>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="../Entropy.html">Entropy</a></li>
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+
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+ <li><a href="../Entropy/Dict.html">Entropy::Dict</a></li>
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+
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+ <li><a href="../Entropy/ProbabilityMetricSpace.html">Entropy::ProbabilityMetricSpace</a></li>
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+
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+ <li><a href="../Entropy/ProbabilitySpace.html">Entropy::ProbabilitySpace</a></li>
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+
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+ <li><a href="../Entropy/Stream.html">Entropy::Stream</a></li>
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+
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+ </ul>
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+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
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+ </div>
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="documentation">
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+ <h1 class="class">Entropy::Dict</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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+
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+
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+
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+
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+ <div id="5Buntitled-5D" class="documentation-section">
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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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+ <!-- Methods -->
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+
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+ <div id="public-class-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+
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+
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+ <div id="new-method" class="method-detail ">
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+ <a name="method-c-new"></a>
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+
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+
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+ <div class="method-heading">
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+ <span class="method-name">new</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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+
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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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+
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+ <div class="method-source-code" id="new-source">
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+ <pre>
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+ <span class="ruby-comment"># File lib/entropy/dict.rb, line 8</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>
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+ <span class="ruby-ivar">@bucket</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">0</span>)
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+ <span class="ruby-ivar">@space_size</span> = <span class="ruby-value">0</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- new-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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+
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+ </div><!-- new-method -->
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+
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+
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+ </div><!-- public-class-method-details -->
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+
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+ <div id="public-instance-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
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+
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+
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+ <div id="freq-method" class="method-detail ">
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+ <a name="method-i-freq"></a>
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+
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+
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+ <div class="method-heading">
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+ <span class="method-name">freq</span><span
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+ class="method-args">(k)</span>
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+ <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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+ <div class="method-description">
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+
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+ <p>Compute frequency of the element</p>
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+
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+
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+ <div class="method-source-code" id="freq-source">
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+ <pre>
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+ <span class="ruby-comment"># File lib/entropy/dict.rb, line 20</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">freq</span>(<span class="ruby-identifier">k</span>)
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+ (<span class="ruby-ivar">@bucket</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_d</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@space_size</span>)
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- freq-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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+
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+ </div><!-- freq-method -->
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+
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+
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+ <div id="scan_keys-method" class="method-detail ">
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+ <a name="method-i-scan_keys"></a>
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+
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+
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+ <div class="method-heading">
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+ <span class="method-name">scan_keys</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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+
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+
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+ <div class="method-description">
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+
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+ <p>Return all the elements of the space</p>
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+
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+
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+
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+ <div class="method-source-code" id="scan_keys-source">
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+ <pre>
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+ <span class="ruby-comment"># File lib/entropy/dict.rb, line 25</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">scan_keys</span>
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+ <span class="ruby-ivar">@bucket</span>.<span class="ruby-identifier">keys</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- scan_keys-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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+
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+ </div><!-- scan_keys-method -->
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+
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+
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+ <div id="upd-method" class="method-detail ">
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+ <a name="method-i-upd"></a>
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+
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+
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+ <div class="method-heading">
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+ <span class="method-name">upd</span><span
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+ class="method-args">(k)</span>
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+ <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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+ <div class="method-description">
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+
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+ <p>Add an element to the space</p>
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+
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+
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+
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+ <div class="method-source-code" id="upd-source">
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+ <pre>
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+ <span class="ruby-comment"># File lib/entropy/dict.rb, line 14</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">upd</span>(<span class="ruby-identifier">k</span>)
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+ <span class="ruby-ivar">@bucket</span>[<span class="ruby-identifier">k</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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+ <span class="ruby-ivar">@space_size</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- upd-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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+
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+ </div><!-- upd-method -->
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+
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+
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+ </div><!-- public-instance-method-details -->
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+
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+ </div><!-- 5Buntitled-5D -->
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+
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+
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+ </div><!-- documentation -->
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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+ Rdoc Generator</a> 2</small>.</p>
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+ </div>
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+
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+ </body>
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+ </html>
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+