class Taxamatch::Base
Public Class Methods
new()
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# File lib/taxamatch_rb/base.rb, line 3 def initialize @parser = Taxamatch::Atomizer.new @dlm = DamerauLevenshtein end
Public Instance Methods
match_genera(genus1, genus2, opts = {})
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# File lib/taxamatch_rb/base.rb, line 67 def match_genera(genus1, genus2, opts = {}) genus1_length = genus1[:normalized].size genus2_length = genus2[:normalized].size opts = { with_phonetic_match: true }.merge(opts) min_length = [genus1_length, genus2_length].min unless opts[:with_phonetic_match] genus1[:phonetized] = 'A' genus2[:phonetized] = 'B' end match = false ed = @dlm.distance(genus1[:normalized], genus2[:normalized], 1, 3) #TODO put block = 2 return { 'edit_distance' => ed, 'phonetic_match' => false, 'match' => false } if ed/min_length.to_f > 0.2 return { 'edit_distance' => ed, 'phonetic_match' => true, 'match' => true } if genus1[:phonetized] == genus2[:phonetized] match = true if ed <= 3 && (min_length > ed * 2) && (ed < 2 || genus1[0] == genus2[0]) { 'edit_distance' => ed, 'match' => match, 'phonetic_match' => false } end
match_matches(genus_match, species_match, infraspecies_match = nil)
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# File lib/taxamatch_rb/base.rb, line 141 def match_matches(genus_match, species_match, infraspecies_match = nil) match = species_match if infraspecies_match match['edit_distance'] += infraspecies_match['edit_distance'] match['match'] &&= infraspecies_match['match'] match['phonetic_match'] &&= infraspecies_match['phonetic_match'] end match['edit_distance'] += genus_match['edit_distance'] if match['edit_distance'] > (infraspecies_match ? 6 : 4) match['match'] = false end match['match'] &&= genus_match['match'] match['phonetic_match'] &&= genus_match['phonetic_match'] match end
match_multinomial(preparsed_1, preparsed_2)
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# File lib/taxamatch_rb/base.rb, line 38 def match_multinomial(preparsed_1, preparsed_2) gen_match = match_genera(preparsed_1[:genus], preparsed_2[:genus]) sp_match = match_species(preparsed_1[:species], preparsed_2[:species]) total_length = preparsed_1[:genus][:string].size + preparsed_2[:genus][:string].size + preparsed_1[:species][:string].size + preparsed_2[:species][:string].size if preparsed_1[:infraspecies] && preparsed_2[:infraspecies] infrasp_match = match_species(preparsed_1[:infraspecies][0], preparsed_2[:infraspecies][0]) total_length += preparsed_1[:infraspecies][0][:string].size + preparsed_2[:infraspecies][0][:string].size match_hash = match_matches(gen_match, sp_match, infrasp_match) elsif (preparsed_1[:infraspecies] && !preparsed_2[:infraspecies]) || (!preparsed_1[:infraspecies] && preparsed_2[:infraspecies]) match_hash = { 'match' => false, 'edit_distance' => 5, 'phonetic_match' => false } total_length += preparsed_1[:infraspecies] ? preparsed_1[:infraspecies][0][:string].size : preparsed_2[:infraspecies][0][:string].size else match_hash = match_matches(gen_match, sp_match) end match_hash.merge({ 'score' => (1 - match_hash['edit_distance']/(total_length/2)) }) match_hash end
match_species(sp1, sp2, opts = {})
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# File lib/taxamatch_rb/base.rb, line 91 def match_species(sp1, sp2, opts = {}) sp1_length = sp1[:normalized].size sp2_length = sp2[:normalized].size opts = { with_phonetic_match: true }.merge(opts) min_length = [sp1_length, sp2_length].min unless opts[:with_phonetic_match] sp1[:phonetized] = 'A' sp2[:phonetized] = 'B' end sp1[:phonetized] = Taxamatch::Phonetizer.normalize_ending sp1[:phonetized] sp2[:phonetized] = Taxamatch::Phonetizer.normalize_ending sp2[:phonetized] match = false ed = @dlm.distance(sp1[:normalized], sp2[:normalized], 1, 4) return { 'edit_distance' => ed, 'phonetic_match' => false, 'match' => false } if ed/min_length.to_f > 0.3334 return {'edit_distance' => ed, 'phonetic_match' => true, 'match' => true} if sp1[:phonetized] == sp2[:phonetized] match = true if ed <= 4 && (min_length >= ed * 2) && (ed < 2 || sp1[:normalized][0] == sp2[:normalized][0]) && (ed < 4 || sp1[:normalized][0...3] == sp2[:normalized][0...3]) { 'edit_distance' => ed, 'match' => match, 'phonetic_match' => false } end
match_uninomial(preparsed_1, preparsed_2)
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# File lib/taxamatch_rb/base.rb, line 34 def match_uninomial(preparsed_1, preparsed_2) match_genera(preparsed_1[:uninomial], preparsed_2[:uninomial]) end
taxamatch(str1, str2, return_boolean = true)
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takes two scientific names and returns true if names match and false if they don't
# File lib/taxamatch_rb/base.rb, line 10 def taxamatch(str1, str2, return_boolean = true) preparsed_1 = @parser.parse(str1) preparsed_2 = @parser.parse(str2) match = taxamatch_preparsed(preparsed_1, preparsed_2) rescue nil return_boolean ? (!!match && match['match']) : match end
taxamatch_preparsed(preparsed_1, preparsed_2)
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takes two hashes of parsed scientific names, analyses them and returns back this function is useful when species strings are preparsed.
# File lib/taxamatch_rb/base.rb, line 19 def taxamatch_preparsed(preparsed_1, preparsed_2) result = nil if preparsed_1[:uninomial] && preparsed_2[:uninomial] result = match_uninomial(preparsed_1, preparsed_2) end if preparsed_1[:genus] && preparsed_2[:genus] result = match_multinomial(preparsed_1, preparsed_2) end if result && result['match'] result['match'] = match_authors(preparsed_1, preparsed_2) == -1 ? false : true end return result end