text_alignment 0.2.0

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checksums.yaml ADDED
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data/.gitignore ADDED
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+ doc/*
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+ ruby '2.3.4'
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+
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+ # Specify your gem's dependencies in *.gemspec
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+ #gemspec
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+
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+ gem 'ruby-dictionary', '~>1.1', '>=1.1.1'
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+
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+ group :test do
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+ gem 'rspec', '~>3.0'
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+ end
data/Gemfile.lock ADDED
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+ GEM
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+ remote: https://rubygems.org/
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+ specs:
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+ diff-lcs (1.2.5)
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+ rspec (3.0.0)
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+ rspec-core (~> 3.0.0)
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+ rspec-expectations (~> 3.0.0)
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+ rspec-mocks (~> 3.0.0)
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+ rspec-core (3.0.4)
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+ rspec-support (~> 3.0.0)
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+ rspec-expectations (3.0.4)
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+ diff-lcs (>= 1.2.0, < 2.0)
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+ rspec-support (~> 3.0.0)
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+ rspec-mocks (3.0.4)
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+ rspec-support (~> 3.0.0)
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+ rspec-support (3.0.4)
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+ ruby-dictionary (1.1.1)
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+
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+ PLATFORMS
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+ ruby
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+
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+ DEPENDENCIES
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+ rspec (~> 3.0)
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+ ruby-dictionary (~> 1.1, >= 1.1.1)
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+
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+ RUBY VERSION
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+ ruby 2.3.4p301
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+
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+ BUNDLED WITH
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+ 1.17.3
data/LICENSE.txt ADDED
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+ Copyright (c) 2014 Jin-Dong Kim
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+
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+ MIT License
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
data/README.md ADDED
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+ # SequenceAlignment
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+
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+ It allows to get an optimal alignemnt of two character sequences, e.g., text.
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+
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+
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+ ## Installation
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+
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+ Add this line to your application's Gemfile:
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+
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+ gem 'sequence_alignment'
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+
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+ And then execute:
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+
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+ $ bundle
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+
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+ Or install it yourself as:
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+
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+ $ gem install sequence_alignment
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+
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+
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+ ## Contributing
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+
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+ 1. Fork it
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+ 2. Create your feature branch (`git checkout -b my-new-feature`)
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+ 3. Commit your changes (`git commit -am 'Add some feature'`)
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+ 4. Push to the branch (`git push origin my-new-feature`)
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+ 5. Create new Pull Request
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+ require 'text_alignment/text_alignment'
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+ #!/usr/bin/env ruby
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+ module TextAlignment; end unless defined? TextAlignment
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+
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+ # approximate the location of str1 in str2
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+ module TextAlignment
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+ SIGNATURE_NGRAM = 5
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+ MIN_LENGTH_FOR_APPROXIMATION = 50
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+ BUFFER_RATE = 0.2
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+ end
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+
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+ class << TextAlignment
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+
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+ # If finds an approximate region of str2 that contains str1
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+ def approximate_fit(str1, str2)
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+ raise ArgumentError, 'nil string' if str1.nil? || str2.nil?
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+ return 0, str2.length if str2.length < TextAlignment::MIN_LENGTH_FOR_APPROXIMATION
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+
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+ ngram1 = (0 .. str1.length - TextAlignment::SIGNATURE_NGRAM).collect{|i| str1[i, TextAlignment::SIGNATURE_NGRAM]}
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+ ngram2 = (0 .. str2.length - TextAlignment::SIGNATURE_NGRAM).collect{|i| str2[i, TextAlignment::SIGNATURE_NGRAM]}
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+ ngram_shared = ngram1 & ngram2
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+
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+ # If there is no shared n-gram found, it may mean there is no serious overlap between the two strings
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+ return nil, nil if ngram_shared.empty?
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+
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+ # approximate the beginning of the fit
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+ signature_ngram = ngram_shared.detect{|g| ngram2.count(g) == 1}
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+
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+ return nil, nil if signature_ngram.nil? #raise "no signature ngram"
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+ offset = str1.index(signature_ngram)
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+ fit_begin = str2.index(signature_ngram) - offset - (offset * TextAlignment::BUFFER_RATE).to_i
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+ fit_begin = 0 if fit_begin < 0
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+
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+ # to change the order according to ngram2
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+ ngram_shared = ngram2 & ngram1
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+
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+ # approximate the end of the fit
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+ ngram_shared_reverse = ngram_shared.reverse
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+ ngram2_reverse = ngram2.reverse
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+ signature_ngram = ngram_shared_reverse.detect{|g| ngram2_reverse.count(g) == 1}
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+ return nil, nil if signature_ngram.nil? # raise "no signature ngram"
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+ offset = str1.length - str1.rindex(signature_ngram)
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+ fit_end = str2.rindex(signature_ngram) + offset + (offset * TextAlignment::BUFFER_RATE).to_i
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+ fit_end = str2.length if fit_end > str2.length
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+
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+ return nil, nil if fit_begin >= fit_end
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+ return fit_begin, fit_end
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+ end
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+ end
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+
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+ if __FILE__ == $0
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+ require 'json'
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+
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+ if ARGV.length == 2
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+ str1 = JSON.parse(File.read(ARGV[0]).strip)["text"]
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+ str2 = JSON.parse(File.read(ARGV[1]).strip)["text"]
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+
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+ loc = TextAlignment::approximate_fit(str1, str2)
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+ p loc
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+ puts str2[loc[0]...loc[1]]
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+ end
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+ end
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+ #!/usr/bin/env ruby
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+ require 'text_alignment/approximate_fit'
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+ require 'text_alignment/lcs_comparison'
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+
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+ module TextAlignment; end unless defined? TextAlignment
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+
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+ # to work on the hash representation of denotations
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+ # to assume that there is no bag representation to this method
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+
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+ module TextAlignment
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+ TextAlignment::SIMILARITY_THRESHOLD = 0.8
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+ end
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+
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+ class << TextAlignment
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+
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+ # It finds, among the sources, the right divisions for the taraget text to fit in.
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+ def find_divisions(target, sources, mappings = [])
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+ raise ArgumentError, "nil target" if target == nil
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+ raise ArgumentError, "nil or empty sources" if sources == nil || sources.empty?
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+ raise ArgumentError, "nil mappings" if mappings == nil
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+
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+ character_mappings = mappings.select{|m| m[0].length == 1 && m[1].length == 1}
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+ mappings.delete_if{|m| m[0].length == 1 && m[1].length == 1}
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+ characters_from = character_mappings.collect{|m| m[0]}.join
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+ characters_to = character_mappings.collect{|m| m[1]}.join
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+ characters_to.gsub!(/-/, '\-')
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+
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+ target.tr!(characters_from, characters_to)
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+ sources.each{|source| source[:text].tr!(characters_from, characters_to)}
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+
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+ sources.sort!{|s1, s2| s1[:text].size <=> s2[:text].size}
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+
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+ TextAlignment._find_divisions(target, sources)
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+ end
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+
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+ def _find_divisions(target, sources)
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+ mode, m, c, offset_begin = nil, nil, nil, nil
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+
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+ sources.each_with_index do |source, i|
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+ if target.size < source[:text].size
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+ mode = :t_in_s
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+ str1 = target
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+ str2 = source[:text]
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+ else
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+ mode = :s_in_t
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+ str1 = source[:text]
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+ str2 = target
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+ end
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+
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+ len1 = str1.length
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+ len2 = str2.length
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+
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+ offset_begin, offset_end = 0, -1
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+ offset_begin, offset_end = approximate_fit(str1, str2) if (len2 - len1) > len1 * (1 - TextAlignment::SIMILARITY_THRESHOLD)
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+
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+ unless offset_begin.nil?
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+ c = TextAlignment::LCSComparison.new(str1, str2[offset_begin .. offset_end])
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+ if (c.similarity > TextAlignment::SIMILARITY_THRESHOLD) && ((len1 - (c.str1_match_final - c.str1_match_initial + 1)) < len1 * (1 - TextAlignment::SIMILARITY_THRESHOLD))
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+ m = i
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+ break
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+ end
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+ end
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+ end
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+
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+ # return remaining target and sources if m.nil?
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+ return [[-1, [target, sources.collect{|s| s[:divid]}]]] if m.nil?
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+
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+ index = if mode == :t_in_s
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+ [sources[m][:divid], [0, target.size]]
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+ else # :s_in_t
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+ [sources[m][:divid], [c.str2_match_initial + offset_begin, c.str2_match_final + offset_begin + 1]]
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+ end
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+
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+ next_target = target[0 ... index[1][0]] + target[index[1][1] .. -1]
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+ sources.delete_at(m)
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+
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+ if next_target.strip.empty? || sources.empty?
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+ return [index]
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+ else
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+ more_index = _find_divisions(next_target, sources)
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+ gap = index[1][1] - index[1][0]
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+ more_index.each do |i|
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+ if (i[0] > -1)
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+ i[1][0] += gap if i[1][0] >= index[1][0]
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+ i[1][1] += gap if i[1][1] > index[1][0]
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+ end
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+ end
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+ return [index] + more_index
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+ end
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+ end
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+ end
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+
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+ if __FILE__ == $0
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+ require 'json'
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+ if ARGV.length == 2
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+ target = JSON.parse File.read(ARGV[0]), :symbolize_names => true
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+ target_text = target[:text].strip
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+
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+ sources = JSON.parse File.read(ARGV[1]), :symbolize_names => true
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+ div_index = TextAlignment::find_divisions(target_text, sources)
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+
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+ # str1 = File.read(ARGV[0]).strip
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+ # str2 = File.read(ARGV[1]).strip
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+ # div_index = TextAlignment::find_divisions(str1, [str2])
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+
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+ puts "target length: #{target_text.length}"
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+ div_index.each do |i|
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+ if i[0] >= 0
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+ puts "[Div: #{i[0]}] (#{i[1][0]}, #{i[1][1]})"
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+ puts target_text[i[1][0] ... i[1][1]]
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+ puts "=========="
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+ else
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+ p i
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+ end
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+ end
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+ end
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+ end
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+ #!/usr/bin/env ruby
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+ require 'ruby-dictionary'
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+
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+ module TextAlignment; end unless defined? TextAlignment
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+
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+ # An instance of this class holds the results of generalized LCS computation for the two strings str1 and str2.
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+ # an optional dictionary is used for generalized suffix comparision.
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+ class TextAlignment::GLCSAlignment
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+ # The mapping function from str1 to str2
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+ attr_reader :position_map_begin, :position_map_end
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+
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+ # The position initial and final position of matching on str1 and str2
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+ attr_reader :str1_match_begin, :str1_match_end, :str2_match_begin, :str2_match_end
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+
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+ # The length of GLCS
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+ attr_reader :length
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+
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+ # the elements that are common in the two strings, str1 and str2
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+ attr_reader :common_elements
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+
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+ # the elements that are mapped to each other in the two strings, str1 and str2
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+ attr_reader :mapped_elements
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+
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+ # the string of non-mapped characters
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+ attr_reader :diff_strings
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+
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+ attr_reader :similarity
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+
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+ # It initializes the GLCS table for the given two strings, str1 and str2.
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+ # When the array, mappings, is given, general suffix comparision is performed based on the mappings.
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+ # Exception is raised when nil given passed to either str1, str2 or dictionary
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+ def initialize(str1, str2, mappings = [])
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+ raise ArgumentError, "nil string" if str1 == nil || str2 == nil
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+ raise ArgumentError, "nil dictionary" if mappings == nil
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+
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+ # index the mappings in hash.
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+ @dic = (mappings + mappings.map{|e| e.reverse}).to_h
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+
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+ # prefix dictionary
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+ @pdic = Dictionary.new(mappings.flatten)
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+
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+ @len1 = str1.length
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+ @len2 = str2.length
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+
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+ # add a final marker to the end of the strings
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+ @str1 = str1 + '_'
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+ @str2 = str2 + '_'
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+
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+ # compute the GLCS table
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+ @glcs = _compute_glcs_table
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+ @length = @glcs[0][0]
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+
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+ _trace_glcs_table
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+ end
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+
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+ # Prints the GLCS table
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+ def show_glcs
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+ puts "\t\t" + @str2.split(//).join("\t")
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+ @glcs.each_with_index do |row, i|
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+ h = (@str1[i].nil?)? '' : @str1[i]
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+ puts i.to_s + "\t" + h + "\t" + row.join("\t")
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+ end
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+ end
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+
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+ # Returns the character-by-character difference
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+ def cdiff
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+ cdiff1, cdiff2 = '', ''
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+ p1, p2 = 0, 0
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+ begin
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+ s1, s2 = _prefix_eq(@str1[p1...@len1], @str2[p2...@len2])
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+ if s1 != nil
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+ l1, l2 = s1.length, s2.length
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+
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+ cdiff1 += s1; cdiff2 += s2
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+ if l1 > l2 then cdiff2 += ' ' * (l1 - l2) else cdiff1 += ' ' * (l2 - l1) end
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+ p1 += s1.length; p2 += s2.length
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+ elsif p2 < @len2 && (p1 == @len1 or @glcs[p1][p2 + 1] > @glcs[p1 + 1][p2])
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+ cdiff1 += ' '
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+ cdiff2 += @str2[p2]
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+ p2 += 1
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+ elsif p1 < @len1 && (p2 == @len2 or @glcs[p1][p2 + 1] <= @glcs[p1 + 1][p2])
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+ cdiff1 += @str1[p1]
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+ cdiff2 += ' '
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+ p1 += 1
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+ end
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+ end until p1 == @len1 && p2 == @len2
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+
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+ return [cdiff1, cdiff2]
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+ end
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+
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+
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+ # Computes the similarity of the two strings
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+ def similarity(cut = false)
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+ c = @length
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+
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+ l1 = c + @diff_strings[0].length
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+ l2 = c + @diff_strings[1].length
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+
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+ if cut
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+ l1 -= front_overflow if front_overflow > 0
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+ l1 -= rear_overflow if rear_overflow > 0
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+ l1 += front_overflow if front_overflow < 0
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+ l1 += rear_overflow if rear_overflow < 0
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+ end
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+
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+ similarity = 2 * c / (l1 + l2).to_f
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+ end
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+
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+ def transform_a_span(span)
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+ {:begin=>@position_map_begin[span[:begin]], :end=>@position_map_end[span[:end]]}
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+ end
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+
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+ def transform_spans(spans)
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+ spans.map{|span| transform_a_span(span)}
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+ end
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+
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+
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+ private
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+
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+ # Computes the GLCS table for the two strings, @str1 and @str2.
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+ # Unlike normal LCS algorithms, the computation is performed from the end to the beginning of the strings.
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+ def _compute_glcs_table
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+ glcs = Array.new(@len1 + 1) { Array.new(@len2 + 1) }
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+
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+ # initialize the final row and the final column
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+ (0..@len1).each {|p| glcs[p][@len2] = 0}
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+ (0..@len2).each {|p| glcs[@len1][p] = 0}
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+
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+ # compute the GLCS table
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+ str1_reverse_iteration = (0...@len1).to_a.reverse
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+ str2_reverse_iteration = (0...@len2).to_a.reverse
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+
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+ str1_reverse_iteration.each do |p1|
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+ str2_reverse_iteration.each do |p2|
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+ s1, s2 = _prefix_eq(@str1[p1...@len1], @str2[p2...@len2])
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+ unless s1 == nil
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+ glcs[p1][p2] = glcs[p1 + s1.length][p2 + s2.length] + 1
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+ else
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+ glcs[p1][p2] = (glcs[p1][p2 + 1] > glcs[p1 + 1][p2])? glcs[p1][p2 + 1] : glcs[p1 + 1][p2]
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+ end
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+ end
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+ end
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+
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+ glcs
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+ end
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+
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+ # Backtrace the GLCS table, computing the mapping function from str1 to str2
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+ # As its side effect, it updates four global variables
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+ # * front_overflow: the length of the front part of str1 that cannot fit in str2.
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+ # * rear_overflow: the length of the rear part of str1 that cannot fit in str2.
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+ # * common_elements: an array which stores the common elements in the two strings.
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+ # * mapped_elements: an array which stores the mapped elements in the two strings.
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+ def _trace_glcs_table
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+ @front_overflow, @rear_overflow = 0, 0
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+ @common_elements, @mapped_elements = [], []
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+ diff_string1, diff_string2 = '', ''
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+
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+ @position_map_begin, @position_map_end = {}, {}
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+ addition, deletion = [], []
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+ p1, p2 = 0, 0
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+
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+ while p1 <= @len1 && p2 <= @len2
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+ s1, s2 = _prefix_eq(@str1[p1..@len1], @str2[p2..@len2])
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+ if s1 != nil
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+ l1, l2 = s1.length, s2.length
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+
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+ @position_map_begin[p1], @position_map_end[p1] = p2, p2
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+ (p1 + 1 ... p1 + l1).each{|i| @position_map_begin[i], @position_map_end[i] = nil, nil}
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+
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+ @common_elements << [s1, s2]
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+
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+ if !addition.empty? && deletion.empty?
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+ # If an addition is found in the front or the rear, it is a case of underflow
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+ @str2_match_begin = addition.length if p1 == 0
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+ @str2_match_end = l2 - addition.length if p1 == @len1
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+
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+ if p1 == 0
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+ # leave as it is
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+ elsif p1 == @len1
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+ # retract from the end
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+ @position_map_begin[p1] = p2 - addition.length
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+ @position_map_end[p1] = @position_map_begin[p1]
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+ else
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+ # correct the position for end
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+ @position_map_end[p1] = p2 - addition.length
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+ end
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+ elsif addition.empty? && !deletion.empty?
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+ # If a deletion is found in the front or the rear, it is a case of overflow
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+ @str1_match_begin = deletion.length if p1 == deletion.length
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+ @str1_match_end = l1 - deletion.length if p1 == @len1
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+
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+ deletion.each{|p| @position_map_begin[p], @position_map_end[p] = p2, p2}
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+ elsif !addition.empty? && !deletion.empty?
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+ # If an addition and a deletion are both found in the front or the rear,
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+ # the overflow/underflow is approximated to the difference.
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+ al, dl = addition.length, deletion.length
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+ @front_overflow = dl - al if p1 == dl
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+ @rear_overflow = dl - al if p1 == @len1
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+
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+ @mapped_elements << [@str1[deletion[0], dl], @str2[addition[0], al]]
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+
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+ @position_map_begin[deletion[0]], @position_map_end[deletion[0]] = addition[0], addition[0]
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+ deletion[1..-1].each{|p| @position_map_begin[p], @position_map_end[p] = nil, nil}
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+ end
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+
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+ addition.clear; deletion.clear
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+ p1 += l1; p2 += l2
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+
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+ elsif p2 < @len2 && (p1 == @len1 || @glcs[p1][p2 + 1] > @glcs[p1 + 1][p2])
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+ diff_string2 += @str2[p2]
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+
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+ addition << p2
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+ p2 += 1
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+ elsif p1 < @len1 && (p2 == @len2 || @glcs[p1][p2 + 1] <= @glcs[p1 + 1][p2])
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+ diff_string1 += @str1[p1]
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+
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+ deletion << p1
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+ p1 += 1
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+ end
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+ end
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+
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+ @common_elements.pop
223
+ @diff_strings = [diff_string1, diff_string2]
224
+ end
225
+
226
+ # General prefix comparison is performed based on the dictionary.
227
+ # The pair of matched suffixes are returned when found.
228
+ # Otherwise, the pair of nil values are returned.
229
+ def _prefix_eq(str1, str2)
230
+ return nil, nil if str1.empty? || str2.empty?
231
+ prefixes1 = @pdic.prefixes(str1)
232
+ prefixes1.each {|p1| p2 = @dic[p1]; return p1, p2 if str2.start_with?(p2)}
233
+ return str1[0], str2[0] if (str1[0] == str2[0])
234
+ return nil, nil
235
+ end
236
+
237
+ end
238
+
239
+ if __FILE__ == $0
240
+
241
+ dictionary = [
242
+ ["×", "x"], #U+00D7 (multiplication sign)
243
+ ["•", "*"], #U+2022 (bullet)
244
+ ["Δ", "delta"], #U+0394 (greek capital letter delta)
245
+ ["Φ", "phi"], #U+03A6 (greek capital letter phi)
246
+ ["α", "alpha"], #U+03B1 (greek small letter alpha)
247
+ ["β", "beta"], #U+03B2 (greek small letter beta)
248
+ ["γ", "gamma"], #U+03B3 (greek small letter gamma)
249
+ ["δ", "delta"], #U+03B4 (greek small letter delta)
250
+ ["ε", "epsilon"], #U+03B5 (greek small letter epsilon)
251
+ ["κ", "kappa"], #U+03BA (greek small letter kappa)
252
+ ["λ", "lambda"], #U+03BB (greek small letter lambda)
253
+ ["μ", "mu"], #U+03BC (greek small letter mu)
254
+ ["χ", "chi"], #U+03C7 (greek small letter chi)
255
+ ["ϕ", "phi"], #U+03D5 (greek phi symbol)
256
+ [" ", " "], #U+2009 (thin space)
257
+ [" ", " "], #U+200A (hair space)
258
+ [" ", " "], #U+00A0 (no-break space)
259
+ [" ", " "], #U+3000 (ideographic space)
260
+ ["−", "-"], #U+2212 (minus sign)
261
+ ["–", "-"], #U+2013 (en dash)
262
+ ["′", "'"], #U+2032 (prime)
263
+ ["‘", "'"], #U+2018 (left single quotation mark)
264
+ ["’", "'"], #U+2019 (right single quotation mark)
265
+ ["“", '"'], #U+201C (left double quotation mark)
266
+ ["”", '"'] #U+201D (right double quotation mark)
267
+ ]
268
+
269
+ # str1 = "-betakappaxyz-"
270
+ # str2 = "-ijkβκ-"
271
+
272
+ # str1 = "-βκ-β-z-xy"
273
+ # str2 = "abc-betakappa-beta-z"
274
+
275
+ # str1 = "-βκ-z-xy"
276
+ # str2 = "abc-betakappa-z"
277
+
278
+ # str1 = "abc-βκ-β-z"
279
+ # str2 = "-betakappa-beta-z-xyz"
280
+
281
+ # str1 = "-β-"
282
+ # str2 = "-beta-"
283
+
284
+ # str1 = "-κ-"
285
+ # str2 = "-kappa-"
286
+
287
+ # str1 = File.read(ARGV[0]).strip
288
+ # str2 = File.read(ARGV[1]).strip
289
+
290
+ str1 = "beta"
291
+ str2 = "β***"
292
+
293
+ # puts "str1: #{str1}"
294
+ # puts "str2: #{str2}"
295
+ sa = TextAlignment::GLCSAlignment.new(str1, str2, dictionary)
296
+ sa.position_map_begin.each {|h| p h}
297
+ puts '-----'
298
+ sa.position_map_end.each {|h| p h}
299
+ puts '-----'
300
+ puts "common_elements: #{sa.common_elements}"
301
+ puts '-----'
302
+ puts "mapped_elements: #{sa.mapped_elements}"
303
+ puts '-----'
304
+ # puts "diff_string1: #{sa.diff_strings[0]}"
305
+ # puts "diff_string2: #{sa.diff_strings[1]}"
306
+ puts "front_overflow: #{sa.front_overflow}"
307
+ puts "rear_overflow : #{sa.rear_overflow}"
308
+ puts '-----'
309
+ puts "similarity : #{sa.similarity}"
310
+ puts "similarity(cut): #{sa.similarity(true)}"
311
+ end