text_alignment 0.2.9 → 0.3.9
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- checksums.yaml +4 -4
- data/bin/align_annotations +190 -39
- data/lib/text_alignment/anchor_finder.rb +149 -0
- data/lib/text_alignment/approximate_fit.rb +50 -52
- data/lib/text_alignment/find_divisions.rb +198 -200
- data/lib/text_alignment/glcs_alignment.rb +297 -297
- data/lib/text_alignment/glcs_alignment_fast.rb +94 -94
- data/lib/text_alignment/glcs_required.rb +50 -50
- data/lib/text_alignment/lcs_alignment.rb +115 -115
- data/lib/text_alignment/lcs_cdiff.rb +46 -48
- data/lib/text_alignment/lcs_comparison.rb +53 -53
- data/lib/text_alignment/lcs_min.rb +144 -138
- data/lib/text_alignment/mappings.rb +68 -69
- data/lib/text_alignment/mixed_alignment.rb +193 -0
- data/lib/text_alignment/text_alignment.rb +232 -174
- data/lib/text_alignment/version.rb +1 -1
- data/text_alignment.gemspec +1 -1
- metadata +5 -13
- data/spec/spec_helper.rb +0 -1
- data/spec/text_alignment/glcs_alignment_spec.rb +0 -302
- data/spec/text_alignment/lcs_alignment_spec.rb +0 -98
- data/spec/text_alignment/lcs_comparision_spec.rb +0 -322
- data/spec/text_alignment/text_alignment_spec.rb +0 -302
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@@ -12,103 +12,103 @@ module TextAlignment; end unless defined? TextAlignment
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TextAlignment::SIGNATURE_NGRAM = 5 unless defined? TextAlignment::SIGNATURE_NGRAM
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class TextAlignment::GLCSTextAlignment
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attr_reader :position_map_begin, :position_map_end
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attr_reader :common_elements, :mapped_elements
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attr_reader :similarity
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attr_reader :str1_match_initial, :str1_match_final, :str2_match_initial, :str2_match_final
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def initialize(str1, str2, mappings = [], lcs = nil, sdiff = nil)
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raise ArgumentError, "nil string" if str1.nil? || str2.nil?
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raise ArgumentError, "nil mappings" if mappings.nil?
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_glcs_alignment_fast(str1, str2, mapptings, lcs, sdiff)
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end
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private
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def _glcs_alignment_fast(str1, str2, mappings, lcs, sdiff)
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sdiff = TextAlignment::LCSMin.new(str1, str2).sdiff if sdiff.nil?
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posmap_begin, posmap_end = {}, {}
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@common_elements, @mapped_elements = [], []
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addition, deletion = [], []
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sdiff.each do |h|
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case h.action
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when '='
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p1, p2 = h.old_position, h.new_position
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@common_elements << [str1[p1], str2[p2]]
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posmap_begin[p1], posmap_end[p1] = p2, p2
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if !addition.empty? && deletion.empty?
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posmap_end[p1] = p2 - addition.length unless p1 == 0
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elsif addition.empty? && !deletion.empty?
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deletion.each{|p| posmap_begin[p], posmap_end[p] = p2, p2}
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elsif !addition.empty? && !deletion.empty?
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if addition.length > 1 || deletion.length > 1
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galign = TextAlignment::GLCSAlignment.new(str1[deletion[0] .. deletion[-1]], str2[addition[0] .. addition[-1]], mappings)
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galign.position_map_begin.each {|k, v| posmap_begin[k + deletion[0]] = v.nil? ? nil : v + addition[0]}
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galign.position_map_end.each {|k, v| posmap_end[k + deletion[0]] = v.nil? ? nil : v + addition[0]}
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posmap_begin[p1], posmap_end[p1] = p2, p2
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@common_elements += galign.common_elements
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@mapped_elements += galign.mapped_elements
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else
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posmap_begin[deletion[0]], posmap_end[deletion[0]] = addition[0], addition[0]
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deletion[1..-1].each{|p| posmap_begin[p], posmap_end[p] = nil, nil}
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@mapped_elements << [str1[deletion[0], deletion.length], str2[addition[0], addition.length]]
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end
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end
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addition.clear; deletion.clear
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when '!'
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deletion << h.old_position
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addition << h.new_position
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when '-'
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deletion << h.old_position
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when '+'
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addition << h.new_position
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end
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end
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p1, p2 = str1.length, str2.length
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posmap_begin[p1], posmap_end[p1] = p2, p2
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if !addition.empty? && deletion.empty?
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posmap_end[p1] = p2 - addition.length unless p1 == 0
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elsif addition.empty? && !deletion.empty?
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deletion.each{|p| posmap_begin[p], posmap_end[p] = p2, p2}
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elsif !addition.empty? && !deletion.empty?
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if addition.length > 1 && deletion.length > 1
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galign = TextAlignment::GLCSAlignment.new(str1[deletion[0] .. deletion[-1]], str2[addition[0] .. addition[-1]], mappings)
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galign.position_map_begin.each {|k, v| posmap_begin[k + deletion[0]] = v.nil? ? nil : v + addition[0]}
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galign.position_map_end.each {|k, v| posmap_end[k + deletion[0]] = v.nil? ? nil : v + addition[0]}
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posmap_begin[p1], posmap_end[p1] = p2, p2
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@mapped_elements += galign.common_elements + galign.mapped_elements
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else
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posmap_begin[deletion[0]], posmap_end[deletion[0]] = addition[0], addition[0]
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deletion[1..-1].each{|p| posmap_begin[p], posmap_end[p] = nil, nil}
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@mapped_elements << [str1[deletion[0], deletion.length], str2[addition[0], addition.length]]
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end
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end
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@position_map_begin = posmap_begin.sort.to_h
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@position_map_end = posmap_end.sort.to_h
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end
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end
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if __FILE__ == $0
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str1 = '-βκ-'
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str2 = '-betakappa-'
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# anns1 = JSON.parse File.read(ARGV[0]), :symbolize_names => true
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# anns2 = JSON.parse File.read(ARGV[1]), :symbolize_names => true
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dictionary = [["β", "beta"]]
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# align = TextAlignment::TextAlignment.new(str1, str2)
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align = TextAlignment::TextAlignment.new(str1, str2, TextAlignment::MAPPINGS)
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p align.common_elements
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p align.mapped_elements
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end
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module TextAlignment; end unless defined? TextAlignment
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class << TextAlignment
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def glcs_required?(str1, mappings = [])
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raise ArgumentError, "nil string" if str1.nil?
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raise ArgumentError, "nil mappings" if mappings.nil?
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# character mappings can be safely applied to the strings withoug changing the position of other characters
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character_mappings = mappings.select{|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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str1.tr!(characters_from, characters_to)
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str1 =~/([^\p{ASCII}][^\p{ASCII}])/
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$1
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end
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end
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if __FILE__ == $0
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dictionary = [
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["×", "x"], #U+00D7 (multiplication sign)
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["•", "*"], #U+2022 (bullet)
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["Δ", "delta"], #U+0394 (greek capital letter delta)
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["Φ", "phi"], #U+03A6 (greek capital letter phi)
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["α", "alpha"], #U+03B1 (greek small letter alpha)
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["β", "beta"], #U+03B2 (greek small letter beta)
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["γ", "gamma"], #U+03B3 (greek small letter gamma)
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["δ", "delta"], #U+03B4 (greek small letter delta)
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["ε", "epsilon"], #U+03B5 (greek small letter epsilon)
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["κ", "kappa"], #U+03BA (greek small letter kappa)
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["λ", "lambda"], #U+03BB (greek small letter lambda)
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["μ", "mu"], #U+03BC (greek small letter mu)
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["χ", "chi"], #U+03C7 (greek small letter chi)
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["ϕ", "phi"], #U+03D5 (greek phi symbol)
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[" ", " "], #U+2009 (thin space)
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[" ", " "], #U+200A (hair space)
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[" ", " "], #U+00A0 (no-break space)
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[" ", " "], #U+3000 (ideographic space)
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["−", "-"], #U+2212 (minus sign)
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["–", "-"], #U+2013 (en dash)
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["′", "'"], #U+2032 (prime)
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["‘", "'"], #U+2018 (left single quotation mark)
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["’", "'"], #U+2019 (right single quotation mark)
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["“", '"'], #U+201C (left double quotation mark)
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["”", '"'] #U+201D (right double quotation mark)
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]
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str = "TGF-β–induced"
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# from_text = "TGF-beta-induced"
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# to_text = "TGF-β–induced"
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# from_text = "TGF-β–β induced"
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# to_text = "TGF-beta-beta induced"
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# str = "-βκ-"
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if ARGV.length == 1
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str = File.read(ARGV[0])
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end
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# anns2 = JSON.parse File.read(ARGV[1]), :symbolize_names => true
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p TextAlignment.glcs_required?(str, dictionary)
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end
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require 'text_alignment/lcs_min'
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class TextAlignment::LCSAlignment
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41
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-
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42
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-
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43
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-
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44
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-
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45
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-
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46
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-
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47
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-
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48
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-
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49
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-
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50
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-
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51
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-
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52
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-
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53
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-
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54
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-
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55
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-
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56
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-
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57
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-
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58
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-
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59
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-
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60
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-
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61
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-
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62
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-
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63
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-
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64
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-
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65
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-
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66
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-
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67
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-
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68
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-
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69
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-
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70
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-
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71
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-
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72
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-
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73
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-
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5
|
+
attr_reader :position_map_begin, :position_map_end
|
|
6
|
+
attr_reader :common_elements, :mapped_elements
|
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7
|
+
|
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8
|
+
# It initializes the LCS table for the given two strings, str1 and str2.
|
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9
|
+
# Exception is raised when nil given passed to either str1, str2 or dictionary
|
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10
|
+
def initialize(str1, str2, lcs = nil, sdiff = nil)
|
|
11
|
+
raise ArgumentError, "nil string" if str1 == nil || str2 == nil
|
|
12
|
+
sdiff = TextAlignment::LCSMin.new(str1, str2).sdiff if sdiff.nil?
|
|
13
|
+
_compute_position_map(str1, str2, sdiff)
|
|
14
|
+
end
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|
15
|
+
|
|
16
|
+
private
|
|
17
|
+
|
|
18
|
+
def _compute_position_map(str1, str2, sdiff)
|
|
19
|
+
posmap_begin, posmap_end = {}, {}
|
|
20
|
+
@common_elements, @mapped_elements = [], []
|
|
21
|
+
|
|
22
|
+
addition, deletion = [], []
|
|
23
|
+
|
|
24
|
+
sdiff.each do |h|
|
|
25
|
+
case h.action
|
|
26
|
+
when '='
|
|
27
|
+
p1, p2 = h.old_position, h.new_position
|
|
28
|
+
|
|
29
|
+
@common_elements << [str1[p1], str2[p2]]
|
|
30
|
+
posmap_begin[p1], posmap_end[p1] = p2, p2
|
|
31
|
+
|
|
32
|
+
if !addition.empty? && deletion.empty?
|
|
33
|
+
# correct the position for end
|
|
34
|
+
posmap_end[p1] = p2 - addition.length unless p1 == 0
|
|
35
|
+
elsif addition.empty? && !deletion.empty?
|
|
36
|
+
deletion.each{|p| posmap_begin[p], posmap_end[p] = p2, p2}
|
|
37
|
+
elsif !addition.empty? && !deletion.empty?
|
|
38
|
+
@mapped_elements << [str1[deletion[0], deletion.length], str2[addition[0], addition.length]]
|
|
39
|
+
|
|
40
|
+
posmap_begin[deletion[0]], posmap_end[deletion[0]] = addition[0], addition[0]
|
|
41
|
+
deletion[1..-1].each{|p| posmap_begin[p], posmap_end[p] = nil, nil}
|
|
42
|
+
end
|
|
43
|
+
|
|
44
|
+
addition.clear; deletion.clear
|
|
45
|
+
|
|
46
|
+
when '!'
|
|
47
|
+
deletion << h.old_position
|
|
48
|
+
addition << h.new_position
|
|
49
|
+
when '-'
|
|
50
|
+
deletion << h.old_position
|
|
51
|
+
when '+'
|
|
52
|
+
addition << h.new_position
|
|
53
|
+
end
|
|
54
|
+
end
|
|
55
|
+
|
|
56
|
+
p1, p2 = str1.length, str2.length
|
|
57
|
+
posmap_begin[p1], posmap_end[p1] = p2, p2
|
|
58
|
+
|
|
59
|
+
if !addition.empty? && deletion.empty?
|
|
60
|
+
# correct the position for end
|
|
61
|
+
posmap_end[p1] = p2 - addition.length unless p1 == 0
|
|
62
|
+
elsif addition.empty? && !deletion.empty?
|
|
63
|
+
deletion.each{|p| posmap_begin[p], posmap_end[p] = p2, p2}
|
|
64
|
+
elsif !addition.empty? && !deletion.empty?
|
|
65
|
+
@mapped_elements << [str1[deletion[0], deletion.length], str2[addition[0], addition.length]]
|
|
66
|
+
|
|
67
|
+
posmap_begin[deletion[0]], posmap_end[deletion[0]] = addition[0], addition[0]
|
|
68
|
+
deletion[1..-1].each{|p| posmap_begin[p], posmap_end[p] = nil, nil}
|
|
69
|
+
end
|
|
70
|
+
|
|
71
|
+
@position_map_begin = posmap_begin.sort.to_h
|
|
72
|
+
@position_map_end = posmap_end.sort.to_h
|
|
73
|
+
end
|
|
74
74
|
|
|
75
75
|
end
|
|
76
76
|
|
|
77
77
|
if __FILE__ == $0
|
|
78
78
|
|
|
79
|
-
|
|
80
|
-
|
|
79
|
+
# from_text = "TGF-β mRNA"
|
|
80
|
+
# to_text = "TGF-beta mRNA"
|
|
81
81
|
|
|
82
|
-
|
|
83
|
-
|
|
82
|
+
# from_text = "TGF-beta mRNA"
|
|
83
|
+
# to_text = "TGF-β mRNA"
|
|
84
84
|
|
|
85
|
-
|
|
86
|
-
|
|
85
|
+
# from_text = "TGF-beta mRNA"
|
|
86
|
+
# to_text = "TGF- mRNA"
|
|
87
87
|
|
|
88
|
-
|
|
89
|
-
|
|
88
|
+
# from_text = "TGF-β–induced"
|
|
89
|
+
# to_text = "TGF-beta-induced"
|
|
90
90
|
|
|
91
|
-
|
|
92
|
-
|
|
91
|
+
from_text = 'abxyzcd'
|
|
92
|
+
to_text = 'abcd'
|
|
93
93
|
|
|
94
|
-
|
|
95
|
-
|
|
94
|
+
# from_text = "TGF-beta-induced"
|
|
95
|
+
# to_text = "TGF-β–induced"
|
|
96
96
|
|
|
97
|
-
|
|
98
|
-
|
|
97
|
+
# from_text = "beta-induced"
|
|
98
|
+
# to_text = "TGF-beta-induced"
|
|
99
99
|
|
|
100
|
-
|
|
101
|
-
|
|
100
|
+
# from_text = "TGF-beta-induced"
|
|
101
|
+
# to_text = "beta-induced"
|
|
102
102
|
|
|
103
|
-
|
|
104
|
-
|
|
103
|
+
# from_text = "TGF-β–β induced"
|
|
104
|
+
# to_text = "TGF-beta-beta induced"
|
|
105
105
|
|
|
106
|
-
|
|
107
|
-
|
|
106
|
+
# from_text = "-βκ-"
|
|
107
|
+
# to_text = "-betakappa-"
|
|
108
108
|
|
|
109
|
-
|
|
110
|
-
|
|
109
|
+
# from_text = "-betakappa-beta-z"
|
|
110
|
+
# to_text = "-βκ-β–z"
|
|
111
111
|
|
|
112
|
-
|
|
113
|
-
|
|
112
|
+
# from_text = "affect C/EBP-β’s ability"
|
|
113
|
+
# to_text = "affect C/EBP-beta's ability"
|
|
114
114
|
|
|
115
|
-
|
|
116
|
-
|
|
115
|
+
# from_text = "12 ± 34"
|
|
116
|
+
# to_text = "12 +/- 34"
|
|
117
117
|
|
|
118
|
-
|
|
119
|
-
|
|
118
|
+
# from_text = "TGF-β–treated"
|
|
119
|
+
# to_text = "TGF-beta-treated"
|
|
120
120
|
|
|
121
|
-
|
|
122
|
-
|
|
121
|
+
# from_text = "in TGF-β–treated cells"
|
|
122
|
+
# to_text = "in TGF-beta-treated cells"
|
|
123
123
|
|
|
124
|
-
|
|
125
|
-
|
|
124
|
+
# from_text = "TGF-β–induced"
|
|
125
|
+
# to_text = "TGF-beta-induced"
|
|
126
126
|
|
|
127
|
-
|
|
128
|
-
|
|
127
|
+
# anns1 = JSON.parse File.read(ARGV[0]), :symbolize_names => true
|
|
128
|
+
# anns2 = JSON.parse File.read(ARGV[1]), :symbolize_names => true
|
|
129
129
|
|
|
130
|
-
|
|
131
|
-
|
|
130
|
+
# aligner = TextAlignment.new(anns1[:text], anns2[:text], [["Δ", "delta"], [" ", " "], ["–", "-"], ["′", "'"]])
|
|
131
|
+
# denotations = aligner.transform_denotations(anns1[:denotations])
|
|
132
132
|
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
133
|
+
denotations_s = <<-'ANN'
|
|
134
|
+
[{"id":"T0", "span":{"begin":1,"end":2}, "category":"Protein"}]
|
|
135
|
+
ANN
|
|
136
136
|
|
|
137
|
-
|
|
137
|
+
# denotations = JSON.parse denotations_s, :symbolize_names => true
|
|
138
138
|
|
|
139
|
-
|
|
140
|
-
|
|
141
|
-
|
|
142
|
-
|
|
143
|
-
|
|
139
|
+
a = TextAlignment::LCSAlignment.new(from_text, to_text)
|
|
140
|
+
p a.position_map_begin
|
|
141
|
+
puts "-----"
|
|
142
|
+
p a.position_map_end
|
|
143
|
+
# aligner = TextAlignment.new(from_text, to_text, [["Δ", "delta"], [" ", " "], ["–", "-"], ["′", "'"], ["β", "beta"]])
|
|
144
144
|
|
|
145
|
-
|
|
145
|
+
# p denotations
|
|
146
146
|
end
|