Class: Taxamatch::Base

Inherits:
Object
  • Object
show all
Defined in:
lib/taxamatch_rb.rb

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Base

Returns a new instance of Base.



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# File 'lib/taxamatch_rb.rb', line 17

def initialize
  @parser = Taxamatch::Atomizer.new
  @dlm = Taxamatch::DamerauLevenshteinMod.new
end

Instance Method Details

#match_authors(preparsed_1, preparsed_2) ⇒ Object 



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# File 'lib/taxamatch_rb.rb', line 82

def match_authors(preparsed_1, preparsed_2)
  au1 = preparsed_1[:all_authors]
  au2 = preparsed_2[:all_authors]
  yr1 = preparsed_1[:all_years]
  yr2 = preparsed_2[:all_years]
  Taxamatch::Authmatch.authmatch(au1, au2, yr1, yr2)
end

#match_genera(genus1, genus2) ⇒ Object 



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# File 'lib/taxamatch_rb.rb', line 55

def match_genera(genus1, genus2)
  genus1_length = genus1[:normalized].size
  genus2_length = genus2[:normalized].size
  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/[genus1_length, genus2_length].min > 0.2
  return {'edit_distance' => ed, 'phonetic_match' => true, 'match' => true} if genus1[:phonetized] == genus2[:phonetized] 

  match = true if ed <= 3 && ([genus1_length, genus2_length].min > ed * 2) && (ed < 2 || genus1[0] == genus2[0])
  {'edit_distance' => ed, 'match' => match, 'phonetic_match' => false} 
end

#match_matches(genus_match, species_match, infraspecies_matches = []) ⇒ Object 



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# File 'lib/taxamatch_rb.rb', line 90

def match_matches(genus_match, species_match, infraspecies_matches = []) 
  match = species_match
  match['edit_distance'] += genus_match['edit_distance']
  match['match'] = false if match['edit_distance'] > 4
  match['match'] &&= genus_match['match']
  match['phonetic_match'] &&= genus_match['phonetic_match']
  match
end

#match_multinomial(preparsed_1, preparsed_2) ⇒ Object 



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# File 'lib/taxamatch_rb.rb', line 47

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][:epitheton].size + preparsed_2[:genus][:epitheton].size + preparsed_1[:species][:epitheton].size + preparsed_2[:species][:epitheton].size
  match = match_matches(gen_match, sp_match)
  match.merge({'score' => (1 - match['edit_distance']/(total_length/2))})
end

#match_species(sp1, sp2) ⇒ Object 



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# File 'lib/taxamatch_rb.rb', line 67

def match_species(sp1, sp2)
  sp1_length = sp1[:normalized].size
  sp2_length = sp2[:normalized].size
  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) #TODO put block 4
  return {'edit_distance' => ed, 'phonetic_match' => false, 'match' => false} if ed/[sp1_length, sp2_length].min > 0.3334
  #puts 's: %s, %s, %s' % [sp1[:normalized], sp2[:normalized], ed]
  return {'edit_distance' => ed, 'phonetic_match' => true, 'match' => true} if sp1[:phonetized] == sp2[:phonetized]

  match = true if ed <= 4 && ([sp1_length, sp2_length].min >= 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) ⇒ Object 



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# File 'lib/taxamatch_rb.rb', line 43

def match_uninomial(preparsed_1, preparsed_2)
  return false
end

#taxamatch(str1, str2, return_boolean = true) ⇒ Object

takes two scientific names and returns true if names match and false if they don’t



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# File 'lib/taxamatch_rb.rb', line 24

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) ⇒ Object

takes two hashes of parsed scientific names, analyses them and returns back this function is useful when species strings are preparsed.



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# File 'lib/taxamatch_rb.rb', line 33

def taxamatch_preparsed(preparsed_1, preparsed_2)
  result = nil
  result =  match_uninomial(preparsed_1, preparsed_2) if preparsed_1[:uninomial] && preparsed_2[:uninomial] 
  result =  match_multinomial(preparsed_1, preparsed_2) if preparsed_1[:genus] && preparsed_2[:genus]
  if result && result['match']
    result['match'] = match_authors(preparsed_1, preparsed_2) == 0 ? false : true 
  end
  return result
end