biodiversity 0.5.15 → 0.5.16

data/.gitignore

@@ -11,3 +11,4 @@ biodiversity*.gem
 tmp
 .DS_Store
 spec/parser/test_data_new.txt
+t

data/Rakefile

@@ -36,8 +36,24 @@ rescue LoadError
 end
 
 task :tt do
-  system("tt #{dir}/lib/biodiversity/parser/scientific_name_clean.treetop")
-  system("tt #{dir}/lib/biodiversity/parser/scientific_name_dirty.treetop")
-  system("tt #{dir}/lib/biodiversity/parser/scientific_name_canonical.treetop")
+  ['scientific_name_clean', 'scientific_name_dirty', 'scientific_name_canonical'].each do |f|
+    system("tt #{dir}/lib/biodiversity/parser/#{f}.treetop")
+    rf = "#{dir}/lib/biodiversity/parser/#{f}.rb"
+    rfn = open(rf + ".tmp", 'w')
+    skip_head = false
+    f = open(rf)
+    f.each_with_index do |l, i|
+      skip_head = l.match(/^# Autogenerated/) if i == 0
+      if skip_head && (l.strip == '' || l.match(/^# Autogenerated/))
+        next  
+      else
+        skip_head = false
+        rfn.write(l)
+      end
+    end
+    rfn.close
+    f.close
+    `mv #{rf}.tmp #{rf}`
+  end
 end
 

data/VERSION

@@ -1 +1 @@
-0.5.15
+0.5.16

data/bin/nnparse

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 require 'rubygems'
-gem 'dimus-biodiversity' rescue gem 'biodiversity' rescue nil
+gem 'biodiversity' rescue nil
 
 $LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__) + "/../lib"))
 require 'biodiversity'
@@ -31,7 +31,7 @@ IO.foreach(input) do |line|
       $KCODE = 'NONE'
     end
     p.parse(name) 
-    parsed_data = p.parsed.all_json rescue {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}.to_json
+    parsed_data = p.parsed.all_json rescue {'scientificName' => {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}}.to_json
     if ruby_min_version < 19
       $KCODE = old_kcode
     end

data/biodiversity.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{biodiversity}
-  s.version = "0.5.15"
+  s.version = "0.5.16"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dmitry Mozzherin"]
-  s.date = %q{2010-03-24}
+  s.date = %q{2010-04-08}
   s.default_executable = %q{nnparse}
   s.description = %q{Tools for biodiversity informatics}
   s.email = %q{dmozzherin@gmail.com}
@@ -72,13 +72,16 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<treetop>, [">= 0"])
+      s.add_runtime_dependency(%q<json>, [">= 0"])
       s.add_development_dependency(%q<rspec>, [">= 0"])
     else
       s.add_dependency(%q<treetop>, [">= 0"])
+      s.add_dependency(%q<json>, [">= 0"])
       s.add_dependency(%q<rspec>, [">= 0"])
     end
   else
     s.add_dependency(%q<treetop>, [">= 0"])
+    s.add_dependency(%q<json>, [">= 0"])
     s.add_dependency(%q<rspec>, [">= 0"])
   end
 end

data/lib/biodiversity/parser.rb

@@ -34,6 +34,7 @@ class ScientificNameParser
           :canonical => self.canonical,
           :hybrid => hybrid,
           :details => self.details,
+          :parser_run => self.parser_run,
           :positions => self.pos
           })
       else

data/lib/biodiversity/parser/scientific_name_canonical.rb

@@ -6,8 +6,6 @@ module ScientificNameCanonical
     @root || :root
   end
 
-  include ScientificNameClean
-
   include ScientificNameDirty
 
   module Root0
@@ -18,6 +16,10 @@ module ScientificNameCanonical
     def details
       [super]
     end
+
+    def parser_run
+      3
+    end
   end
 
   module Root1
@@ -28,13 +30,20 @@ module ScientificNameCanonical
     def details
       [super]
     end
+
+    def parser_run
+      3
+    end
   end
 
   def _nt_root
     start_index = index
     if node_cache[:root].has_key?(index)
       cached = node_cache[:root][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -64,7 +73,7 @@ module ScientificNameCanonical
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -72,7 +81,7 @@ module ScientificNameCanonical
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -179,7 +188,10 @@ module ScientificNameCanonical
     start_index = index
     if node_cache[:multinomial_with_garbage].has_key?(index)
       cached = node_cache[:multinomial_with_garbage][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -313,7 +325,10 @@ module ScientificNameCanonical
     start_index = index
     if node_cache[:uninomial_with_garbage].has_key?(index)
       cached = node_cache[:uninomial_with_garbage][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -339,11 +354,11 @@ module ScientificNameCanonical
   end
 
   module Garbage0
-    def space
+    def space1
       elements[0]
     end
 
-    def space
+    def space2
       elements[2]
     end
 
@@ -360,7 +375,10 @@ module ScientificNameCanonical
     start_index = index
     if node_cache[:garbage].has_key?(index)
       cached = node_cache[:garbage][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -370,7 +388,7 @@ module ScientificNameCanonical
     s1 << r2
     if r2
       if has_terminal?('\G["\',.]', true, index)
-        r3 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r3 = true
         @index += 1
       else
         r3 = nil
@@ -383,7 +401,7 @@ module ScientificNameCanonical
           s5, i5 = [], index
           loop do
             if has_terminal?('\G[^щ]', true, index)
-              r6 = instantiate_node(SyntaxNode,input, index...(index + 1))
+              r6 = true
               @index += 1
             else
               r6 = nil
@@ -416,7 +434,7 @@ module ScientificNameCanonical
         s9, i9 = [], index
         loop do
           if has_terminal?('\G[^ш]', true, index)
-            r10 = instantiate_node(SyntaxNode,input, index...(index + 1))
+            r10 = true
             @index += 1
           else
             r10 = nil
@@ -460,3 +478,4 @@ end
 class ScientificNameCanonicalParser < Treetop::Runtime::CompiledParser
   include ScientificNameCanonical
 end
+

data/lib/biodiversity/parser/scientific_name_canonical.treetop

@@ -1,6 +1,5 @@
 # encoding: UTF-8
 grammar ScientificNameCanonical
-  include ScientificNameClean
   include ScientificNameDirty
 
   rule root
@@ -12,6 +11,10 @@ grammar ScientificNameCanonical
       def details
         [super]
       end
+
+      def parser_run
+        3
+      end
     }
     /
     uninomial_with_garbage {
@@ -22,6 +25,10 @@ grammar ScientificNameCanonical
       def details
         [super]
       end
+
+      def parser_run
+        3
+      end
     }
   end
   

data/lib/biodiversity/parser/scientific_name_clean.rb

@@ -7,7 +7,7 @@ module ScientificNameClean
   end
 
   module Root0
-    def space
+    def space1
       elements[0]
     end
 
@@ -15,7 +15,7 @@ module ScientificNameClean
       elements[1]
     end
 
-    def space
+    def space2
       elements[2]
     end
   end
@@ -40,13 +40,20 @@ module ScientificNameClean
     def details
       a.details.class == Array ? a.details : [a.details]
     end
+
+    def parser_run
+      1
+    end
   end
 
   def _nt_root
     start_index = index
     if node_cache[:root].has_key?(index)
       cached = node_cache[:root][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -80,7 +87,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -88,7 +95,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -123,7 +130,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:scientific_name_5].has_key?(index)
       cached = node_cache[:scientific_name_5][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -177,7 +187,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -185,7 +195,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -221,7 +231,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -229,7 +239,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -261,7 +271,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:scientific_name_4].has_key?(index)
       cached = node_cache[:scientific_name_4][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -310,7 +323,7 @@ module ScientificNameClean
             s7 << r11
             if r11
               if has_terminal?('\G[\\?]', true, index)
-                r13 = instantiate_node(SyntaxNode,input, index...(index + 1))
+                r13 = true
                 @index += 1
               else
                 r13 = nil
@@ -391,7 +404,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:scientific_name_3].has_key?(index)
       cached = node_cache[:scientific_name_3][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -472,7 +488,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:scientific_name_2].has_key?(index)
       cached = node_cache[:scientific_name_2][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -517,7 +536,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:scientific_name_1].has_key?(index)
       cached = node_cache[:scientific_name_1][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -567,7 +589,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:status_part].has_key?(index)
       cached = node_cache[:status_part][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -628,7 +653,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:status_word].has_key?(index)
       cached = node_cache[:status_word][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -637,7 +665,7 @@ module ScientificNameClean
     s0 << r1
     if r1
       if has_terminal?('\G[\\.]', true, index)
-        r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r2 = true
         @index += 1
       else
         r2 = nil
@@ -663,7 +691,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -671,11 +699,11 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
-    def space
+    def space3
       elements[5]
     end
 
@@ -719,7 +747,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -727,11 +755,11 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
-    def space
+    def space3
       elements[5]
     end
 
@@ -767,11 +795,11 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -815,11 +843,11 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -854,7 +882,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:multinomial_name].has_key?(index)
       cached = node_cache[:multinomial_name][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -1087,7 +1118,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:infraspecies_mult].has_key?(index)
       cached = node_cache[:infraspecies_mult][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -1165,7 +1199,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:infraspecies].has_key?(index)
       cached = node_cache[:infraspecies][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -1206,7 +1243,7 @@ module ScientificNameClean
     r0
   end
 
-  module Infraspeciesstring0
+  module InfraspeciesString0
     def sel
       elements[0]
     end
@@ -1220,7 +1257,7 @@ module ScientificNameClean
     end
   end
 
-  module Infraspeciesstring1
+  module InfraspeciesString1
     def value 
       sel.apply(a)
     end
@@ -1237,14 +1274,14 @@ module ScientificNameClean
     end
   end
 
-  module Infraspeciesstring2
+  module InfraspeciesString2
     def species_word
       elements[0]
     end
 
   end
 
-  module Infraspeciesstring3
+  module InfraspeciesString3
     def value
       text_value
     end
@@ -1266,7 +1303,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:infraspecies_string].has_key?(index)
       cached = node_cache[:infraspecies_string][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -1284,8 +1324,8 @@ module ScientificNameClean
     end
     if s1.last
       r1 = instantiate_node(SyntaxNode,input, i1...index, s1)
-      r1.extend(Infraspeciesstring0)
-      r1.extend(Infraspeciesstring1)
+      r1.extend(InfraspeciesString0)
+      r1.extend(InfraspeciesString1)
     else
       @index = i1
       r1 = nil
@@ -1299,7 +1339,7 @@ module ScientificNameClean
       if r6
         i7 = index
         if has_terminal?('\G[\\.]', true, index)
-          r8 = instantiate_node(SyntaxNode,input, index...(index + 1))
+          r8 = true
           @index += 1
         else
           r8 = nil
@@ -1314,8 +1354,8 @@ module ScientificNameClean
       end
       if s5.last
         r5 = instantiate_node(SyntaxNode,input, i5...index, s5)
-        r5.extend(Infraspeciesstring2)
-        r5.extend(Infraspeciesstring3)
+        r5.extend(InfraspeciesString2)
+        r5.extend(InfraspeciesString3)
       else
         @index = i5
         r5 = nil
@@ -1349,7 +1389,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:taxon_concept_rank].has_key?(index)
       cached = node_cache[:taxon_concept_rank][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -1408,7 +1451,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:rank].has_key?(index)
       cached = node_cache[:rank][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -1872,7 +1918,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:rank_forma].has_key?(index)
       cached = node_cache[:rank_forma][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -1973,7 +2022,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:species].has_key?(index)
       cached = node_cache[:species][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -2014,8 +2066,8 @@ module ScientificNameClean
     r0
   end
 
-  module Speciesstring0
-    def space_hard
+  module SpeciesString0
+    def space_hard1
       elements[0]
     end
 
@@ -2023,19 +2075,19 @@ module ScientificNameClean
       elements[1]
     end
 
-    def space_hard
+    def space_hard2
       elements[2]
     end
   end
 
-  module Speciesstring1
+  module SpeciesString1
     def a
       elements[0]
     end
 
   end
 
-  module Speciesstring2
+  module SpeciesString2
     def value 
       a.value
     end
@@ -2057,7 +2109,7 @@ module ScientificNameClean
     end
   end
 
-  module Speciesstring3
+  module SpeciesString3
     def canonical
       value
     end
@@ -2079,7 +2131,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:species_string].has_key?(index)
       cached = node_cache[:species_string][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -2102,7 +2157,7 @@ module ScientificNameClean
       end
       if s4.last
         r4 = instantiate_node(SyntaxNode,input, i4...index, s4)
-        r4.extend(Speciesstring0)
+        r4.extend(SpeciesString0)
       else
         @index = i4
         r4 = nil
@@ -2117,8 +2172,8 @@ module ScientificNameClean
     end
     if s1.last
       r1 = instantiate_node(SyntaxNode,input, i1...index, s1)
-      r1.extend(Speciesstring1)
-      r1.extend(Speciesstring2)
+      r1.extend(SpeciesString1)
+      r1.extend(SpeciesString2)
     else
       @index = i1
       r1 = nil
@@ -2127,7 +2182,7 @@ module ScientificNameClean
       r0 = r1
     else
       r8 = _nt_species_word
-      r8.extend(Speciesstring3)
+      r8.extend(SpeciesString3)
       if r8
         r0 = r8
       else
@@ -2151,7 +2206,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -2159,7 +2214,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -2190,7 +2245,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:infragenus].has_key?(index)
       cached = node_cache[:infragenus][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -2228,7 +2286,7 @@ module ScientificNameClean
   end
 
   module Genus0
-    def space_hard
+    def space_hard1
       elements[0]
     end
 
@@ -2236,7 +2294,7 @@ module ScientificNameClean
       elements[1]
     end
 
-    def space_hard
+    def space_hard2
       elements[2]
     end
 
@@ -2274,44 +2332,59 @@ module ScientificNameClean
     start_index = index
     if node_cache[:genus].has_key?(index)
       cached = node_cache[:genus][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
     i0, s0 = index, []
-    r1 = _nt_cap_latin_word
+    i1 = index
+    r2 = _nt_cap_latin_word_pair
+    if r2
+      r1 = r2
+    else
+      r3 = _nt_cap_latin_word
+      if r3
+        r1 = r3
+      else
+        @index = i1
+        r1 = nil
+      end
+    end
     s0 << r1
     if r1
-      i2 = index
-      i3, s3 = index, []
-      r4 = _nt_space_hard
-      s3 << r4
-      if r4
-        r5 = _nt_author_prefix_word
-        s3 << r5
-        if r5
-          r6 = _nt_space_hard
-          s3 << r6
-          if r6
-            r7 = _nt_author_word
-            s3 << r7
+      i4 = index
+      i5, s5 = index, []
+      r6 = _nt_space_hard
+      s5 << r6
+      if r6
+        r7 = _nt_author_prefix_word
+        s5 << r7
+        if r7
+          r8 = _nt_space_hard
+          s5 << r8
+          if r8
+            r9 = _nt_author_word
+            s5 << r9
           end
         end
       end
-      if s3.last
-        r3 = instantiate_node(SyntaxNode,input, i3...index, s3)
-        r3.extend(Genus0)
+      if s5.last
+        r5 = instantiate_node(SyntaxNode,input, i5...index, s5)
+        r5.extend(Genus0)
       else
-        @index = i3
-        r3 = nil
+        @index = i5
+        r5 = nil
       end
-      if r3
-        r2 = nil
+      if r5
+        r4 = nil
       else
-        @index = i2
-        r2 = instantiate_node(SyntaxNode,input, index...index)
+        @index = i4
+        r4 = instantiate_node(SyntaxNode,input, index...index)
       end
-      s0 << r2
+      s0 << r4
     end
     if s0.last
       r0 = instantiate_node(SyntaxNode,input, i0...index, s0)
@@ -2367,7 +2440,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:uninomial_name].has_key?(index)
       cached = node_cache[:uninomial_name][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -2408,7 +2484,7 @@ module ScientificNameClean
     r0
   end
 
-  module Uninomialstring0
+  module UninomialString0
     def canonical
       value
     end
@@ -2430,12 +2506,28 @@ module ScientificNameClean
     start_index = index
     if node_cache[:uninomial_string].has_key?(index)
       cached = node_cache[:uninomial_string][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
-    r0 = _nt_cap_latin_word
-    r0.extend(Uninomialstring0)
+    i0 = index
+    r1 = _nt_cap_latin_word_pair
+    if r1
+      r0 = r1
+      r0.extend(UninomialString0)
+    else
+      r2 = _nt_cap_latin_word
+      if r2
+        r0 = r2
+        r0.extend(UninomialString0)
+      else
+        @index = i0
+        r0 = nil
+      end
+    end
 
     node_cache[:uninomial_string][start_index] = r0
 
@@ -2447,7 +2539,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -2455,7 +2547,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[4]
     end
 
@@ -2543,7 +2635,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:authorship].has_key?(index)
       cached = node_cache[:authorship][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -2678,7 +2773,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -2686,7 +2781,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -2694,11 +2789,11 @@ module ScientificNameClean
       elements[4]
     end
 
-    def space
+    def space3
       elements[5]
     end
 
-    def space
+    def space4
       elements[7]
     end
 
@@ -2728,7 +2823,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -2736,7 +2831,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[4]
     end
 
@@ -2744,7 +2839,7 @@ module ScientificNameClean
       elements[5]
     end
 
-    def space
+    def space3
       elements[6]
     end
 
@@ -2775,7 +2870,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -2783,7 +2878,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -2813,7 +2908,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -2821,7 +2916,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -2848,7 +2943,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:basionym_authorship_with_parenthesis].has_key?(index)
       cached = node_cache[:basionym_authorship_with_parenthesis][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -2873,7 +2971,7 @@ module ScientificNameClean
               s1 << r7
               if r7
                 if has_terminal?('\G[,]', true, index)
-                  r9 = instantiate_node(SyntaxNode,input, index...(index + 1))
+                  r9 = true
                   @index += 1
                 else
                   r9 = nil
@@ -3073,7 +3171,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:ex_authorship].has_key?(index)
       cached = node_cache[:ex_authorship][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -3107,11 +3208,11 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -3119,11 +3220,11 @@ module ScientificNameClean
       elements[4]
     end
 
-    def space
+    def space3
       elements[6]
     end
 
-    def space
+    def space4
       elements[8]
     end
 
@@ -3131,11 +3232,11 @@ module ScientificNameClean
       elements[9]
     end
 
-    def space
+    def space5
       elements[10]
     end
 
-    def space
+    def space6
       elements[12]
     end
 
@@ -3171,11 +3272,11 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -3226,7 +3327,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:simple_authorship].has_key?(index)
       cached = node_cache[:simple_authorship][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -3239,7 +3343,7 @@ module ScientificNameClean
       s1 << r3
       if r3
         if has_terminal?('\G[,]', true, index)
-          r5 = instantiate_node(SyntaxNode,input, index...(index + 1))
+          r5 = true
           @index += 1
         else
           r5 = nil
@@ -3263,7 +3367,7 @@ module ScientificNameClean
             s1 << r7
             if r7
               if has_terminal?('\G[,]', true, index)
-                r10 = instantiate_node(SyntaxNode,input, index...(index + 1))
+                r10 = true
                 @index += 1
               else
                 r10 = nil
@@ -3297,7 +3401,7 @@ module ScientificNameClean
                         s1 << r15
                         if r15
                           if has_terminal?('\G[,]', true, index)
-                            r17 = instantiate_node(SyntaxNode,input, index...(index + 1))
+                            r17 = true
                             @index += 1
                           else
                             r17 = nil
@@ -3346,7 +3450,7 @@ module ScientificNameClean
         s20 << r22
         if r22
           if has_terminal?('\G[,]', true, index)
-            r24 = instantiate_node(SyntaxNode,input, index...(index + 1))
+            r24 = true
             @index += 1
           else
             r24 = nil
@@ -3399,7 +3503,7 @@ module ScientificNameClean
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -3407,7 +3511,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -3434,7 +3538,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:authors_names].has_key?(index)
       cached = node_cache[:authors_names][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -3506,7 +3613,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:unknown_auth].has_key?(index)
       cached = node_cache[:unknown_auth][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -3574,7 +3684,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:ex_sep].has_key?(index)
       cached = node_cache[:ex_sep][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -3608,7 +3721,7 @@ module ScientificNameClean
     if r1
       i4 = index
       if has_terminal?('\G[\\s]', true, index)
-        r5 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r5 = true
         @index += 1
       else
         r5 = nil
@@ -3654,7 +3767,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:author_separator].has_key?(index)
       cached = node_cache[:author_separator][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -3716,7 +3832,7 @@ module ScientificNameClean
   end
 
   module AuthorName0
-    def space
+    def space1
       elements[0]
     end
 
@@ -3724,7 +3840,7 @@ module ScientificNameClean
       elements[1]
     end
 
-    def space
+    def space2
       elements[2]
     end
 
@@ -3732,7 +3848,7 @@ module ScientificNameClean
       elements[3]
     end
 
-    def space
+    def space3
       elements[4]
     end
   end
@@ -3752,7 +3868,7 @@ module ScientificNameClean
   end
 
   module AuthorName2
-    def space
+    def space1
       elements[0]
     end
 
@@ -3760,7 +3876,7 @@ module ScientificNameClean
       elements[1]
     end
 
-    def space
+    def space2
       elements[2]
     end
 
@@ -3768,7 +3884,7 @@ module ScientificNameClean
       elements[3]
     end
 
-    def space
+    def space3
       elements[4]
     end
   end
@@ -3791,7 +3907,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:author_name].has_key?(index)
       cached = node_cache[:author_name][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -3938,7 +4057,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:author_word].has_key?(index)
       cached = node_cache[:author_word][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -4119,7 +4241,7 @@ module ScientificNameClean
                                 r7 = r19
                               else
                                 if has_terminal?('\G[A-W]', true, index)
-                                  r20 = instantiate_node(SyntaxNode,input, index...(index + 1))
+                                  r20 = true
                                   @index += 1
                                 else
                                   r20 = nil
@@ -4128,7 +4250,7 @@ module ScientificNameClean
                                   r7 = r20
                                 else
                                   if has_terminal?('\G[Y-Z]', true, index)
-                                    r21 = instantiate_node(SyntaxNode,input, index...(index + 1))
+                                    r21 = true
                                     @index += 1
                                   else
                                     r21 = nil
@@ -4157,7 +4279,7 @@ module ScientificNameClean
           s22, i22 = [], index
           loop do
             if has_terminal?('\G[^0-9\\[\\]\\(\\)\\s&,]', true, index)
-              r23 = instantiate_node(SyntaxNode,input, index...(index + 1))
+              r23 = true
               @index += 1
             else
               r23 = nil
@@ -4195,7 +4317,7 @@ module ScientificNameClean
             s26, i26 = [], index
             loop do
               if has_terminal?('\G[^0-9\\[\\]\\(\\)\\s&,]', true, index)
-                r27 = instantiate_node(SyntaxNode,input, index...(index + 1))
+                r27 = true
                 @index += 1
               else
                 r27 = nil
@@ -4264,7 +4386,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:author_prefix_word].has_key?(index)
       cached = node_cache[:author_prefix_word][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -4456,6 +4581,64 @@ module ScientificNameClean
     r0
   end
 
+  module CapLatinWordPair0
+    def a
+      elements[0]
+    end
+
+    def b
+      elements[2]
+    end
+  end
+
+  module CapLatinWordPair1
+    def value
+      a.value + b.value.downcase
+    end
+  end
+
+  def _nt_cap_latin_word_pair
+    start_index = index
+    if node_cache[:cap_latin_word_pair].has_key?(index)
+      cached = node_cache[:cap_latin_word_pair][index]
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
+      return cached
+    end
+
+    i0, s0 = index, []
+    r1 = _nt_cap_latin_word
+    s0 << r1
+    if r1
+      if has_terminal?("-", false, index)
+        r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        @index += 1
+      else
+        terminal_parse_failure("-")
+        r2 = nil
+      end
+      s0 << r2
+      if r2
+        r3 = _nt_cap_latin_word
+        s0 << r3
+      end
+    end
+    if s0.last
+      r0 = instantiate_node(SyntaxNode,input, i0...index, s0)
+      r0.extend(CapLatinWordPair0)
+      r0.extend(CapLatinWordPair1)
+    else
+      @index = i0
+      r0 = nil
+    end
+
+    node_cache[:cap_latin_word_pair][start_index] = r0
+
+    r0
+  end
+
   module CapLatinWord0
     def a
       elements[0]
@@ -4490,6 +4673,22 @@ module ScientificNameClean
   end
 
   module CapLatinWord4
+    def a
+      elements[0]
+    end
+
+    def b
+      elements[1]
+    end
+  end
+
+  module CapLatinWord5
+    def value
+      a.text_value[0..0] + 'e' + b.value
+    end
+  end
+
+  module CapLatinWord6
     def value
       text_value
     end
@@ -4499,7 +4698,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:cap_latin_word].has_key?(index)
       cached = node_cache[:cap_latin_word][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -4507,7 +4709,7 @@ module ScientificNameClean
     i1, s1 = index, []
     i2 = index
     if has_terminal?('\G[A-Z]', true, index)
-      r3 = instantiate_node(SyntaxNode,input, index...(index + 1))
+      r3 = true
       @index += 1
     else
       r3 = nil
@@ -4552,7 +4754,7 @@ module ScientificNameClean
       i7, s7 = index, []
       i8 = index
       if has_terminal?('\G[A-Z]', true, index)
-        r9 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r9 = true
         @index += 1
       else
         r9 = nil
@@ -4584,218 +4786,261 @@ module ScientificNameClean
       if r7
         r0 = r7
       else
-        i12 = index
-        if has_terminal?("Ca", false, index)
-          r13 = instantiate_node(SyntaxNode,input, index...(index + 2))
+        i12, s12 = index, []
+        i13 = index
+        if has_terminal?("AE", false, index)
+          r14 = instantiate_node(SyntaxNode,input, index...(index + 2))
           @index += 2
         else
-          terminal_parse_failure("Ca")
-          r13 = nil
+          terminal_parse_failure("AE")
+          r14 = nil
+        end
+        if r14
+          r13 = r14
+        else
+          if has_terminal?("OE", false, index)
+            r15 = instantiate_node(SyntaxNode,input, index...(index + 2))
+            @index += 2
+          else
+            terminal_parse_failure("OE")
+            r15 = nil
+          end
+          if r15
+            r13 = r15
+          else
+            @index = i13
+            r13 = nil
+          end
         end
+        s12 << r13
         if r13
-          r12 = r13
+          r16 = _nt_latin_word
+          s12 << r16
+        end
+        if s12.last
+          r12 = instantiate_node(SyntaxNode,input, i12...index, s12)
           r12.extend(CapLatinWord4)
+          r12.extend(CapLatinWord5)
         else
-          if has_terminal?("Ea", false, index)
-            r14 = instantiate_node(SyntaxNode,input, index...(index + 2))
+          @index = i12
+          r12 = nil
+        end
+        if r12
+          r0 = r12
+        else
+          i17 = index
+          if has_terminal?("Ca", false, index)
+            r18 = instantiate_node(SyntaxNode,input, index...(index + 2))
             @index += 2
           else
-            terminal_parse_failure("Ea")
-            r14 = nil
+            terminal_parse_failure("Ca")
+            r18 = nil
           end
-          if r14
-            r12 = r14
-            r12.extend(CapLatinWord4)
+          if r18
+            r17 = r18
+            r17.extend(CapLatinWord6)
           else
-            if has_terminal?("Ge", false, index)
-              r15 = instantiate_node(SyntaxNode,input, index...(index + 2))
+            if has_terminal?("Ea", false, index)
+              r19 = instantiate_node(SyntaxNode,input, index...(index + 2))
               @index += 2
             else
-              terminal_parse_failure("Ge")
-              r15 = nil
+              terminal_parse_failure("Ea")
+              r19 = nil
             end
-            if r15
-              r12 = r15
-              r12.extend(CapLatinWord4)
+            if r19
+              r17 = r19
+              r17.extend(CapLatinWord6)
             else
-              if has_terminal?("Ia", false, index)
-                r16 = instantiate_node(SyntaxNode,input, index...(index + 2))
+              if has_terminal?("Ge", false, index)
+                r20 = instantiate_node(SyntaxNode,input, index...(index + 2))
                 @index += 2
               else
-                terminal_parse_failure("Ia")
-                r16 = nil
+                terminal_parse_failure("Ge")
+                r20 = nil
               end
-              if r16
-                r12 = r16
-                r12.extend(CapLatinWord4)
+              if r20
+                r17 = r20
+                r17.extend(CapLatinWord6)
               else
-                if has_terminal?("Io", false, index)
-                  r17 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                if has_terminal?("Ia", false, index)
+                  r21 = instantiate_node(SyntaxNode,input, index...(index + 2))
                   @index += 2
                 else
-                  terminal_parse_failure("Io")
-                  r17 = nil
+                  terminal_parse_failure("Ia")
+                  r21 = nil
                 end
-                if r17
-                  r12 = r17
-                  r12.extend(CapLatinWord4)
+                if r21
+                  r17 = r21
+                  r17.extend(CapLatinWord6)
                 else
                   if has_terminal?("Io", false, index)
-                    r18 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                    r22 = instantiate_node(SyntaxNode,input, index...(index + 2))
                     @index += 2
                   else
                     terminal_parse_failure("Io")
-                    r18 = nil
+                    r22 = nil
                   end
-                  if r18
-                    r12 = r18
-                    r12.extend(CapLatinWord4)
+                  if r22
+                    r17 = r22
+                    r17.extend(CapLatinWord6)
                   else
-                    if has_terminal?("Ix", false, index)
-                      r19 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                    if has_terminal?("Io", false, index)
+                      r23 = instantiate_node(SyntaxNode,input, index...(index + 2))
                       @index += 2
                     else
-                      terminal_parse_failure("Ix")
-                      r19 = nil
+                      terminal_parse_failure("Io")
+                      r23 = nil
                     end
-                    if r19
-                      r12 = r19
-                      r12.extend(CapLatinWord4)
+                    if r23
+                      r17 = r23
+                      r17.extend(CapLatinWord6)
                     else
-                      if has_terminal?("Lo", false, index)
-                        r20 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                      if has_terminal?("Ix", false, index)
+                        r24 = instantiate_node(SyntaxNode,input, index...(index + 2))
                         @index += 2
                       else
-                        terminal_parse_failure("Lo")
-                        r20 = nil
+                        terminal_parse_failure("Ix")
+                        r24 = nil
                       end
-                      if r20
-                        r12 = r20
-                        r12.extend(CapLatinWord4)
+                      if r24
+                        r17 = r24
+                        r17.extend(CapLatinWord6)
                       else
-                        if has_terminal?("Oa", false, index)
-                          r21 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                        if has_terminal?("Lo", false, index)
+                          r25 = instantiate_node(SyntaxNode,input, index...(index + 2))
                           @index += 2
                         else
-                          terminal_parse_failure("Oa")
-                          r21 = nil
+                          terminal_parse_failure("Lo")
+                          r25 = nil
                         end
-                        if r21
-                          r12 = r21
-                          r12.extend(CapLatinWord4)
+                        if r25
+                          r17 = r25
+                          r17.extend(CapLatinWord6)
                         else
-                          if has_terminal?("Ra", false, index)
-                            r22 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                          if has_terminal?("Oa", false, index)
+                            r26 = instantiate_node(SyntaxNode,input, index...(index + 2))
                             @index += 2
                           else
-                            terminal_parse_failure("Ra")
-                            r22 = nil
+                            terminal_parse_failure("Oa")
+                            r26 = nil
                           end
-                          if r22
-                            r12 = r22
-                            r12.extend(CapLatinWord4)
+                          if r26
+                            r17 = r26
+                            r17.extend(CapLatinWord6)
                           else
-                            if has_terminal?("Ty", false, index)
-                              r23 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                            if has_terminal?("Ra", false, index)
+                              r27 = instantiate_node(SyntaxNode,input, index...(index + 2))
                               @index += 2
                             else
-                              terminal_parse_failure("Ty")
-                              r23 = nil
+                              terminal_parse_failure("Ra")
+                              r27 = nil
                             end
-                            if r23
-                              r12 = r23
-                              r12.extend(CapLatinWord4)
+                            if r27
+                              r17 = r27
+                              r17.extend(CapLatinWord6)
                             else
-                              if has_terminal?("Ua", false, index)
-                                r24 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                              if has_terminal?("Ty", false, index)
+                                r28 = instantiate_node(SyntaxNode,input, index...(index + 2))
                                 @index += 2
                               else
-                                terminal_parse_failure("Ua")
-                                r24 = nil
+                                terminal_parse_failure("Ty")
+                                r28 = nil
                               end
-                              if r24
-                                r12 = r24
-                                r12.extend(CapLatinWord4)
+                              if r28
+                                r17 = r28
+                                r17.extend(CapLatinWord6)
                               else
-                                if has_terminal?("Aa", false, index)
-                                  r25 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                if has_terminal?("Ua", false, index)
+                                  r29 = instantiate_node(SyntaxNode,input, index...(index + 2))
                                   @index += 2
                                 else
-                                  terminal_parse_failure("Aa")
-                                  r25 = nil
+                                  terminal_parse_failure("Ua")
+                                  r29 = nil
                                 end
-                                if r25
-                                  r12 = r25
-                                  r12.extend(CapLatinWord4)
+                                if r29
+                                  r17 = r29
+                                  r17.extend(CapLatinWord6)
                                 else
-                                  if has_terminal?("Ja", false, index)
-                                    r26 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                  if has_terminal?("Aa", false, index)
+                                    r30 = instantiate_node(SyntaxNode,input, index...(index + 2))
                                     @index += 2
                                   else
-                                    terminal_parse_failure("Ja")
-                                    r26 = nil
+                                    terminal_parse_failure("Aa")
+                                    r30 = nil
                                   end
-                                  if r26
-                                    r12 = r26
-                                    r12.extend(CapLatinWord4)
+                                  if r30
+                                    r17 = r30
+                                    r17.extend(CapLatinWord6)
                                   else
-                                    if has_terminal?("Zu", false, index)
-                                      r27 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                    if has_terminal?("Ja", false, index)
+                                      r31 = instantiate_node(SyntaxNode,input, index...(index + 2))
                                       @index += 2
                                     else
-                                      terminal_parse_failure("Zu")
-                                      r27 = nil
+                                      terminal_parse_failure("Ja")
+                                      r31 = nil
                                     end
-                                    if r27
-                                      r12 = r27
-                                      r12.extend(CapLatinWord4)
+                                    if r31
+                                      r17 = r31
+                                      r17.extend(CapLatinWord6)
                                     else
-                                      if has_terminal?("La", false, index)
-                                        r28 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                      if has_terminal?("Zu", false, index)
+                                        r32 = instantiate_node(SyntaxNode,input, index...(index + 2))
                                         @index += 2
                                       else
-                                        terminal_parse_failure("La")
-                                        r28 = nil
+                                        terminal_parse_failure("Zu")
+                                        r32 = nil
                                       end
-                                      if r28
-                                        r12 = r28
-                                        r12.extend(CapLatinWord4)
+                                      if r32
+                                        r17 = r32
+                                        r17.extend(CapLatinWord6)
                                       else
-                                        if has_terminal?("Qu", false, index)
-                                          r29 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                        if has_terminal?("La", false, index)
+                                          r33 = instantiate_node(SyntaxNode,input, index...(index + 2))
                                           @index += 2
                                         else
-                                          terminal_parse_failure("Qu")
-                                          r29 = nil
+                                          terminal_parse_failure("La")
+                                          r33 = nil
                                         end
-                                        if r29
-                                          r12 = r29
-                                          r12.extend(CapLatinWord4)
+                                        if r33
+                                          r17 = r33
+                                          r17.extend(CapLatinWord6)
                                         else
-                                          if has_terminal?("As", false, index)
-                                            r30 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                          if has_terminal?("Qu", false, index)
+                                            r34 = instantiate_node(SyntaxNode,input, index...(index + 2))
                                             @index += 2
                                           else
-                                            terminal_parse_failure("As")
-                                            r30 = nil
+                                            terminal_parse_failure("Qu")
+                                            r34 = nil
                                           end
-                                          if r30
-                                            r12 = r30
-                                            r12.extend(CapLatinWord4)
+                                          if r34
+                                            r17 = r34
+                                            r17.extend(CapLatinWord6)
                                           else
-                                            if has_terminal?("Ba", false, index)
-                                              r31 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                            if has_terminal?("As", false, index)
+                                              r35 = instantiate_node(SyntaxNode,input, index...(index + 2))
                                               @index += 2
                                             else
-                                              terminal_parse_failure("Ba")
-                                              r31 = nil
+                                              terminal_parse_failure("As")
+                                              r35 = nil
                                             end
-                                            if r31
-                                              r12 = r31
-                                              r12.extend(CapLatinWord4)
+                                            if r35
+                                              r17 = r35
+                                              r17.extend(CapLatinWord6)
                                             else
-                                              @index = i12
-                                              r12 = nil
+                                              if has_terminal?("Ba", false, index)
+                                                r36 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                                @index += 2
+                                              else
+                                                terminal_parse_failure("Ba")
+                                                r36 = nil
+                                              end
+                                              if r36
+                                                r17 = r36
+                                                r17.extend(CapLatinWord6)
+                                              else
+                                                @index = i17
+                                                r17 = nil
+                                              end
                                             end
                                           end
                                         end
@@ -4814,12 +5059,12 @@ module ScientificNameClean
               end
             end
           end
-        end
-        if r12
-          r0 = r12
-        else
-          @index = i0
-          r0 = nil
+          if r17
+            r0 = r17
+          else
+            @index = i0
+            r0 = nil
+          end
         end
       end
     end
@@ -4941,7 +5186,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:species_word_hybrid].has_key?(index)
       cached = node_cache[:species_word_hybrid][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5042,7 +5290,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:species_prefix].has_key?(index)
       cached = node_cache[:species_prefix][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5128,7 +5379,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:species_word].has_key?(index)
       cached = node_cache[:species_word][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5137,7 +5391,7 @@ module ScientificNameClean
     s2, i2 = [], index
     loop do
       if has_terminal?('\G[0-9]', true, index)
-        r3 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r3 = true
         @index += 1
       else
         r3 = nil
@@ -5211,23 +5465,10 @@ module ScientificNameClean
 
   module LatinWord1
     def value
-      a.text_value + b.value
-    end
-  end
-
-  module LatinWord2
-    def a
-      elements[0]
-    end
-
-    def b
-      elements[1]
-    end
-  end
-
-  module LatinWord3
-    def value
-      a.value + b.value
+      l = a.text_value
+      l = 'ae' if l == 'æ'
+      l = 'oe' if l == 'œ'
+      l + b.value
     end
   end
 
@@ -5235,165 +5476,51 @@ module ScientificNameClean
     start_index = index
     if node_cache[:latin_word].has_key?(index)
       cached = node_cache[:latin_word][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
-    i0 = index
-    i1, s1 = index, []
-    if has_terminal?('\G[a-zëüäöïéåóç]', true, index)
-      r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
+    i0, s0 = index, []
+    if has_terminal?('\G[a-zëæœ]', true, index)
+      r1 = true
       @index += 1
     else
-      r2 = nil
-    end
-    s1 << r2
-    if r2
-      r3 = _nt_full_name_letters
-      s1 << r3
-    end
-    if s1.last
-      r1 = instantiate_node(SyntaxNode,input, i1...index, s1)
-      r1.extend(LatinWord0)
-      r1.extend(LatinWord1)
-    else
-      @index = i1
       r1 = nil
     end
+    s0 << r1
     if r1
-      r0 = r1
-    else
-      i4, s4 = index, []
-      r5 = _nt_digraph
-      s4 << r5
-      if r5
-        r6 = _nt_full_name_letters
-        s4 << r6
-      end
-      if s4.last
-        r4 = instantiate_node(SyntaxNode,input, i4...index, s4)
-        r4.extend(LatinWord2)
-        r4.extend(LatinWord3)
-      else
-        @index = i4
-        r4 = nil
-      end
-      if r4
-        r0 = r4
-      else
-        @index = i0
-        r0 = nil
-      end
-    end
-
-    node_cache[:latin_word][start_index] = r0
-
-    r0
-  end
-
-  module FullNameLetters0
-    def a
-      elements[0]
-    end
-
-    def b
-      elements[1]
-    end
-  end
-
-  module FullNameLetters1
-    def value
-      a.value + b.value
-    end
-  end
-
-  module FullNameLetters2
-    def a
-      elements[0]
-    end
-
-    def b
-      elements[1]
-    end
-
-    def c
-      elements[2]
-    end
-  end
-
-  module FullNameLetters3
-    def value
-      a.value + b.value + c.value
-    end
-  end
-
-  def _nt_full_name_letters
-    start_index = index
-    if node_cache[:full_name_letters].has_key?(index)
-      cached = node_cache[:full_name_letters][index]
-      @index = cached.interval.end if cached
-      return cached
-    end
-
-    i0 = index
-    i1, s1 = index, []
-    r2 = _nt_digraph
-    s1 << r2
-    if r2
-      r3 = _nt_full_name_letters
-      s1 << r3
-    end
-    if s1.last
-      r1 = instantiate_node(SyntaxNode,input, i1...index, s1)
-      r1.extend(FullNameLetters0)
-      r1.extend(FullNameLetters1)
-    else
-      @index = i1
-      r1 = nil
+      r2 = _nt_valid_name_letters
+      s0 << r2
     end
-    if r1
-      r0 = r1
+    if s0.last
+      r0 = instantiate_node(SyntaxNode,input, i0...index, s0)
+      r0.extend(LatinWord0)
+      r0.extend(LatinWord1)
     else
-      i4, s4 = index, []
-      r5 = _nt_valid_name_letters
-      s4 << r5
-      if r5
-        r6 = _nt_digraph
-        s4 << r6
-        if r6
-          r7 = _nt_full_name_letters
-          s4 << r7
-        end
-      end
-      if s4.last
-        r4 = instantiate_node(SyntaxNode,input, i4...index, s4)
-        r4.extend(FullNameLetters2)
-        r4.extend(FullNameLetters3)
-      else
-        @index = i4
-        r4 = nil
-      end
-      if r4
-        r0 = r4
-      else
-        r8 = _nt_valid_name_letters
-        if r8
-          r0 = r8
-        else
-          @index = i0
-          r0 = nil
-        end
-      end
+      @index = i0
+      r0 = nil
     end
 
-    node_cache[:full_name_letters][start_index] = r0
+    node_cache[:latin_word][start_index] = r0
 
     r0
   end
 
   module ValidNameLetters0
     def value
-      text_value
+      res = ''
+      text_value.split('').each do |l|
+        l = 'ae' if l == 'æ'
+        l = 'oe' if l == 'œ'
+        # not sure if we should normalize ë as well. It is legal in botanical code, but it 
+        # might be beneficial to normalize it for the reconsiliation purposes
+        # l = 'e' if l == 'ë' 
+        res << l
+      end
+      res
     end
   end
 
@@ -5401,14 +5528,17 @@ module ScientificNameClean
     start_index = index
     if node_cache[:valid_name_letters].has_key?(index)
       cached = node_cache[:valid_name_letters][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
     s0, i0 = [], index
     loop do
-      if has_terminal?('\G[a-z\\-ëüäöïéåóç]', true, index)
-        r1 = instantiate_node(SyntaxNode,input, index...(index + 1))
+      if has_terminal?('\G[a-z\\-ëæœ]', true, index)
+        r1 = true
         @index += 1
       else
         r1 = nil
@@ -5448,7 +5578,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:cap_digraph].has_key?(index)
       cached = node_cache[:cap_digraph][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5485,65 +5618,12 @@ module ScientificNameClean
     r0
   end
 
-  module Digraph0
-    def value
-    'ae'
-    end
-  end
-
-  module Digraph1
-    def value
-    'oe'
-    end
-  end
-
-  def _nt_digraph
-    start_index = index
-    if node_cache[:digraph].has_key?(index)
-      cached = node_cache[:digraph][index]
-      @index = cached.interval.end if cached
-      return cached
-    end
-
-    i0 = index
-    if has_terminal?("æ", false, index)
-      r1 = instantiate_node(SyntaxNode,input, index...(index + 2))
-      r1.extend(Digraph0)
-      @index += 2
-    else
-      terminal_parse_failure("æ")
-      r1 = nil
-    end
-    if r1
-      r0 = r1
-    else
-      if has_terminal?("œ", false, index)
-        r2 = instantiate_node(SyntaxNode,input, index...(index + 2))
-        r2.extend(Digraph1)
-        @index += 2
-      else
-        terminal_parse_failure("œ")
-        r2 = nil
-      end
-      if r2
-        r0 = r2
-      else
-        @index = i0
-        r0 = nil
-      end
-    end
-
-    node_cache[:digraph][start_index] = r0
-
-    r0
-  end
-
   module Year0
     def b
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -5551,7 +5631,7 @@ module ScientificNameClean
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -5578,7 +5658,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:year].has_key?(index)
       cached = node_cache[:year][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5669,7 +5752,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:year_number_with_character].has_key?(index)
       cached = node_cache[:year_number_with_character][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5678,7 +5764,7 @@ module ScientificNameClean
     s0 << r1
     if r1
       if has_terminal?('\G[a-zA-Z]', true, index)
-        r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r2 = true
         @index += 1
       else
         r2 = nil
@@ -5720,13 +5806,16 @@ module ScientificNameClean
     start_index = index
     if node_cache[:year_number].has_key?(index)
       cached = node_cache[:year_number][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
     i0, s0 = index, []
     if has_terminal?('\G[12]', true, index)
-      r1 = instantiate_node(SyntaxNode,input, index...(index + 1))
+      r1 = true
       @index += 1
     else
       r1 = nil
@@ -5734,7 +5823,7 @@ module ScientificNameClean
     s0 << r1
     if r1
       if has_terminal?('\G[7890]', true, index)
-        r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r2 = true
         @index += 1
       else
         r2 = nil
@@ -5742,7 +5831,7 @@ module ScientificNameClean
       s0 << r2
       if r2
         if has_terminal?('\G[0-9]', true, index)
-          r3 = instantiate_node(SyntaxNode,input, index...(index + 1))
+          r3 = true
           @index += 1
         else
           r3 = nil
@@ -5750,7 +5839,7 @@ module ScientificNameClean
         s0 << r3
         if r3
           if has_terminal?('\G[0-9]', true, index)
-            r5 = instantiate_node(SyntaxNode,input, index...(index + 1))
+            r5 = true
             @index += 1
           else
             r5 = nil
@@ -5763,7 +5852,7 @@ module ScientificNameClean
           s0 << r4
           if r4
             if has_terminal?('\G[\\?]', true, index)
-              r7 = instantiate_node(SyntaxNode,input, index...(index + 1))
+              r7 = true
               @index += 1
             else
               r7 = nil
@@ -5796,7 +5885,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:left_paren].has_key?(index)
       cached = node_cache[:left_paren][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5817,7 +5909,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:right_paren].has_key?(index)
       cached = node_cache[:right_paren][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5844,7 +5939,10 @@ module ScientificNameClean
     start_index = index
     if node_cache[:hybrid_character].has_key?(index)
       cached = node_cache[:hybrid_character][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -5895,7 +5993,7 @@ module ScientificNameClean
 
   module MultiplicationSign0
     def value
-      text_value
+      "×"
     end
   end
 
@@ -5903,17 +6001,39 @@ module ScientificNameClean
     start_index = index
     if node_cache[:multiplication_sign].has_key?(index)
       cached = node_cache[:multiplication_sign][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
+    i0 = index
     if has_terminal?("×", false, index)
-      r0 = instantiate_node(SyntaxNode,input, index...(index + 2))
-      r0.extend(MultiplicationSign0)
+      r1 = instantiate_node(SyntaxNode,input, index...(index + 2))
       @index += 2
     else
       terminal_parse_failure("×")
-      r0 = nil
+      r1 = nil
+    end
+    if r1
+      r0 = r1
+      r0.extend(MultiplicationSign0)
+    else
+      if has_terminal?("*", false, index)
+        r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        @index += 1
+      else
+        terminal_parse_failure("*")
+        r2 = nil
+      end
+      if r2
+        r0 = r2
+        r0.extend(MultiplicationSign0)
+      else
+        @index = i0
+        r0 = nil
+      end
     end
 
     node_cache[:multiplication_sign][start_index] = r0
@@ -5925,14 +6045,17 @@ module ScientificNameClean
     start_index = index
     if node_cache[:space].has_key?(index)
       cached = node_cache[:space][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
     s0, i0 = [], index
     loop do
       if has_terminal?('\G[\\s]', true, index)
-        r1 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r1 = true
         @index += 1
       else
         r1 = nil
@@ -5954,14 +6077,17 @@ module ScientificNameClean
     start_index = index
     if node_cache[:space_hard].has_key?(index)
       cached = node_cache[:space_hard][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
     s0, i0 = [], index
     loop do
       if has_terminal?('\G[\\s]', true, index)
-        r1 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r1 = true
         @index += 1
       else
         r1 = nil
@@ -5989,3 +6115,4 @@ end
 class ScientificNameCleanParser < Treetop::Runtime::CompiledParser
   include ScientificNameClean
 end
+