bio 1.4.3.0001 → 1.5.0

data/lib/bio/appl/sosui/report.rb

@@ -5,7 +5,6 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id:$
 #
 # == Example
 #
@@ -60,7 +59,7 @@ module Bio
           if /NUMBER OF TM HELIX = (\d+)/ =~ line
             @tms = $1
           elsif /TM (\d+) +(\d+)- *(\d+) (\w+) +(\w+)/ =~ line
-            tmh  = $1.to_i
+            #tmh  = $1.to_i
             range = Range.new($2.to_i, $3.to_i)
             grade = $4
             seq   = $5

data/lib/bio/command.rb

@@ -6,7 +6,6 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-#  $Id:$
 #
 
 require 'open3'
@@ -856,7 +855,7 @@ module Command
         end.join('&')
       end
     when String
-      data = URI.escape(params.strip)
+      raise TypeError, 'Bio::Command.make_cgi_params no longer accepts a single String as a form'
     end
     return data
   end
@@ -882,6 +881,67 @@ module Command
     return result
   end
 
+  # Same as:
+  #  http = Net::HTTP.new(...); http.post(path, data, header)
+  # and 
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  # In addition, +header+ can be set.
+  # (Default Content-Type is application/octet-stream.
+  # Content-Length is automatically set by default.)
+  # +uri+ must be a URI object, +params+ must be a hash, and
+  # +header+ must be a hash.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _http_: Net::HTTP object or compatible object
+  # * (required) _path_: String
+  # * (required) _data_: String containing data
+  # * (optional) _header_: Hash containing header strings
+  # *Returns*:: (same as Net::HTTP::post)
+  def http_post(http, path, data, header = {})
+    hash = {
+      'Content-Type'   => 'application/octet-stream',
+      'Content-Length' => data.length.to_s
+    }
+    hash.update(header)
+
+    http.post(path, data, hash)
+  end
+
+  # Same as:
+  # Net::HTTP.post(uri, params)
+  # and 
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  # In addition, +header+ can be set.
+  # (Default Content-Type is application/octet-stream.
+  # Content-Length is automatically set by default.)
+  # +uri+ must be a URI object, +data+ must be a String, and
+  # +header+ must be a hash.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _uri_: URI object or String
+  # * (optional) _data_: String containing data
+  # * (optional) _header_: Hash containing header strings
+  # *Returns*:: (same as Net::HTTP::post)
+  def post(uri, data, header = {})
+    unless uri.is_a?(URI)
+      uri = URI.parse(uri)
+    end
+
+    hash = {
+      'Content-Type'   => 'application/octet-stream',
+      'Content-Length' => data.length.to_s
+    }
+    hash.update(header)
+
+    start_http(uri.host, uri.port) do |http|
+      http.post(uri.path, data, hash)
+    end
+  end
+
 end # module Command
 end # module Bio
 

data/lib/bio/data/aa.rb

@@ -108,23 +108,21 @@ class AminoAcid
     }
 
     def weight(x = nil)
-      if x
-        if x.length > 1
-          total = 0.0
-          x.each_byte do |byte|
-            aa = byte.chr.upcase
-            if WEIGHT[aa]
-              total += WEIGHT[aa]
-            else
-              raise "Error: invalid amino acid '#{aa}'"
-            end
+      return WEIGHT unless x
+
+      if x.length > 1
+        total = 0.0
+        x.each_byte do |byte|
+          aa = byte.chr.upcase
+          if WEIGHT[aa]
+            total += WEIGHT[aa]
+          else
+            raise "Error: invalid amino acid '#{aa}'"
           end
-          total -= NucleicAcid.weight[:water] * (x.length - 1)
-        else
-          WEIGHT[x]
         end
+        total -= NucleicAcid.weight[:water] * (x.length - 1)
       else
-        WEIGHT
+        WEIGHT[x]
       end
     end
 
@@ -237,11 +235,7 @@ class AminoAcid
 
 
     def reverse
-      hash = Hash.new
-      NAMES.each do |k, v|
-        hash[v] = k
-      end
-      hash
+      @reverse ||= NAMES.invert
     end
 
   end
@@ -254,18 +248,6 @@ class AminoAcid
   extend Data
 
 
-  private
-
-
-  # override when used as an instance method to improve performance
-  alias orig_reverse reverse
-  def reverse
-    unless @reverse
-      @reverse = orig_reverse
-    end
-    @reverse
-  end
-
 end
 
 end # module Bio

data/lib/bio/data/codontable.rb

@@ -5,7 +5,6 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-# $Id:$
 #
 # == Data source
 #
@@ -127,7 +126,7 @@ class CodonTable
   #   table.revtrans("A")	# => ["gcg", "gct", "gca", "gcc"]
   #
   def revtrans(aa)
-    unless @reverse
+    unless (defined? @reverse) && @reverse
       @reverse = {}
       @table.each do |k, v|
         @reverse[v] ||= []

data/lib/bio/db/biosql/biosql_to_biosequence.rb

@@ -11,6 +11,7 @@
 
 require 'bio/sequence'
 require 'bio/sequence/adapter'
+require 'bio/sequence/dblink'
 
 # Internal use only. Normal users should not use this module.
 #

data/lib/bio/db/biosql/sequence.rb

@@ -371,7 +371,7 @@ module Bio
         #probably would be better to d a class refrence to collect these informations
         @entry.bioentry_references.collect do |bio_ref|
           hash = Hash.new
-          hash['authors'] = bio_ref.reference.authors.gsub(/\.\s/, "\.\s\|").split(/\|/)
+          hash['authors'] = bio_ref.reference.authors.gsub(/\.\s/, "\.\s\|").split(/\|/) if (bio_ref.reference and bio_ref.reference.authors)
 
           hash['sequence_position'] = "#{bio_ref.start_pos}-#{bio_ref.end_pos}" if (bio_ref.start_pos and bio_ref.end_pos)
           hash['title'] = bio_ref.reference.title

data/lib/bio/db/embl/common.rb

@@ -149,7 +149,7 @@ module Common
     unless @data['OS']
       os = Array.new
       fetch('OS').split(/, and|, /).each do |tmp|
-        if tmp =~ /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d])/
+        if tmp =~ /([A-Z][a-z]* *[\w \:\'\+\-]+\w)/
           org = $1
           tmp =~ /(\(.+\))/ 
           os.push({'name' => $1, 'os' => org})

data/lib/bio/db/embl/embl.rb

@@ -267,9 +267,10 @@ class EMBL < EMBLDB
     unless @data['OS']
       os = Array.new
       tmp = fetch('OS')
-      if /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d]) *\(([\w\d ]+)\)\s*\z/ =~ tmp
+      if /([A-Z][a-z]* *[\w \:\'\+\-]+\w) *\(([\w ]+)\)\s*\z/ =~ tmp
         org = $1
-        os.push({'name' => $2, 'os' => $1})
+        name = $2
+        os.push({'name' => name, 'os' => org})
       else
         os.push({'name' => nil, 'os' => tmp})
       end
@@ -340,7 +341,7 @@ class EMBL < EMBLDB
       @orig['FT'].each_line do |line|
         next if line =~ /^FEATURES/
 
-        head = line[0,20].strip  # feature key (source, CDS, ...)
+        #head = line[0,20].strip  # feature key (source, CDS, ...)
         body = line[20,60].chomp # feature value (position, /qualifier=)
         if line =~ /^FT {3}(\S+)/
           ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
@@ -491,7 +492,7 @@ class EMBL < EMBLDB
   def parse_release_version(str)
     return [ nil, nil ] unless str
     a = str.split(/[\(\,\)]/)
-    dstr = a.shift
+    a.shift #date string e.g. "14-OCT-2006"
     rel = nil
     ver = nil
     a.each do |x|

data/lib/bio/db/embl/format_embl.rb

@@ -126,9 +126,9 @@ module Bio::Sequence::Format::NucFormatter
     def mol_type_embl
       if mt = molecule_type then
         mt
-      elsif f = (features or []).find { |f| f.feature == 'source' } and
-          q = f.qualifiers.find { |q| q.qualifier == 'mol_type' } then
-        q.value
+      elsif fe = (features or []).find { |f| f.feature == 'source' } and
+          qu = fe.qualifiers.find { |q| q.qualifier == 'mol_type' } then
+        qu.value
       else
         'NA'
       end

data/lib/bio/db/embl/sptr.rb

@@ -1,1455 +1,20 @@
 #
-# = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
+# = bio/db/embl/sptr.rb - Bio::SPTR is an alias of Bio::UniProtKB
 # 
-# Copyright::   Copyright (C) 2001-2006  Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::   Copyright (C) 2013 BioRuby Project
 # License::     The Ruby License
 #
-# $Id:$
-#
-# == Description
-# 
-# Shared methods for UniProtKB/SwissProt and TrEMBL classes.
-#
-# See the SWISS-PROT document file SPECLIST.TXT or UniProtKB/SwissProt 
-# user manual.
-# 
-# == Examples
-#
-#   str = File.read("p53_human.swiss")
-#   obj = Bio::SPTR.new(str)
-#   obj.entry_id #=> "P53_HUMAN"
-# 
-# == References
-# 
-# * Swiss-Prot Protein knowledgebase. TrEMBL Computer-annotated supplement 
-#   to Swiss-Prot	
-#   http://au.expasy.org/sprot/
-#
-# * UniProt
-#   http://uniprot.org/
-#
-# * The UniProtKB/SwissProt/TrEMBL User Manual
-#   http://www.expasy.org/sprot/userman.html
-#
-
 
-require 'bio/db'
-require 'bio/db/embl/common'
+warn "Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future." if $VERBOSE
 
 module Bio
 
-# Parser class for UniProtKB/SwissProt and TrEMBL database entry.
-class SPTR < EMBLDB
-  include Bio::EMBLDB::Common
-    
-  @@entry_regrexp = /[A-Z0-9]{1,4}_[A-Z0-9]{1,5}/
-  @@data_class = ["STANDARD", "PRELIMINARY"]
-
-  # returns a Hash of the ID line.
-  #
-  # returns a content (Int or String) of the ID line by a given key.
-  # Hash keys: ['ENTRY_NAME', 'DATA_CLASS', 'MODECULE_TYPE', 'SEQUENCE_LENGTH']
-  #
-  # === ID Line (since UniProtKB release 9.0 of 31-Oct-2006)
-  #   ID   P53_HUMAN               Reviewed;         393 AA.
-  #   #"ID  #{ENTRY_NAME} #{DATA_CLASS}; #{SEQUENCE_LENGTH}."
-  #
-  # === Examples
-  #   obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"Reviewed", 
-  #                     "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>nil}
-  #
-  #   obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"
-  #
-  # 
-  # === ID Line (older style)
-  #   ID   P53_HUMAN      STANDARD;      PRT;   393 AA.
-  #   #"ID  #{ENTRY_NAME} #{DATA_CLASS}; #{MOLECULE_TYPE}; #{SEQUENCE_LENGTH}."
-  #
-  # === Examples
-  #   obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"STANDARD", 
-  #                     "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>"PRT"}
-  #
-  #   obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"
-  #
-  def id_line(key = nil)
-    return id_line[key] if key
-    return @data['ID'] if @data['ID']
-
-    part = @orig['ID'].split(/ +/)         
-    if part[4].to_s.chomp == 'AA.' then
-      # after UniProtKB release 9.0 of 31-Oct-2006
-      # (http://www.uniprot.org/docs/sp_news.htm)
-      molecule_type   = nil
-      sequence_length = part[3].to_i
-    else
-      molecule_type   = part[3].sub(/;/,'')
-      sequence_length = part[4].to_i
-    end
-    @data['ID'] = {
-      'ENTRY_NAME'      => part[1],
-      'DATA_CLASS'      => part[2].sub(/;/,''),
-      'MOLECULE_TYPE'   => molecule_type,
-      'SEQUENCE_LENGTH' => sequence_length
-    }
-  end
-
-
-  # returns a ENTRY_NAME in the ID line. 
-  #
-  def entry_id
-    id_line('ENTRY_NAME')
-  end
-  alias entry_name entry_id
-  alias entry entry_id
-
-
-  # returns a MOLECULE_TYPE in the ID line.
-  #
-  # A short-cut for Bio::SPTR#id_line('MOLECULE_TYPE').
-  def molecule
-    id_line('MOLECULE_TYPE')
-  end
-  alias molecule_type molecule
-
-
-  # returns a SEQUENCE_LENGTH in the ID line.
-  # 
-  # A short-cut for Bio::SPTR#id_line('SEQUENCE_LENGHT').
-  def sequence_length
-    id_line('SEQUENCE_LENGTH')
-  end
-  alias aalen sequence_length
-
-
-  # Bio::EMBLDB::Common#ac  -> ary
-  #                  #accessions  -> ary
-  #                  #accession  -> String (accessions.first)
-  @@ac_regrexp = /[OPQ][0-9][A-Z0-9]{3}[0-9]/ 
-
-
-
-  # returns a Hash of information in the DT lines.
-  #  hash keys: 
-  #    ['created', 'sequence', 'annotation']
-  #--
-  #  also Symbols acceptable (ASAP):
-  #    [:created, :sequence, :annotation]
-  #++
-  #
-  # Since UniProtKB release 7.0 of 07-Feb-2006, the DT line format is
-  # changed, and the word "annotation" is no longer used in DT lines.
-  # Despite the change, the word "annotation" is still used for keeping
-  # compatibility.
-  #
-  # returns a String of information in the DT lines by a given key.
-  #
-  # === DT Line; date (3/entry)
-  #   DT DD-MMM-YYY (integrated into UniProtKB/XXXXX.)
-  #   DT DD-MMM-YYY (sequence version NN)
-  #   DT DD-MMM-YYY (entry version NN)
-  #
-  # The format have been changed in UniProtKB release 7.0 of 07-Feb-2006.
-  # Below is the older format.
-  #
-  # === Old format of DT Line; date (3/entry)
-  #   DT DD-MMM-YYY (rel. NN, Created)
-  #   DT DD-MMM-YYY (rel. NN, Last sequence update)
-  #   DT DD-MMM-YYY (rel. NN, Last annotation update)
-  def dt(key = nil)
-    return dt[key] if key
-    return @data['DT'] if @data['DT']
-
-    part = self.get('DT').split(/\n/)
-    @data['DT'] = {
-      'created'    => part[0].sub(/\w{2}   /,'').strip,
-      'sequence'   => part[1].sub(/\w{2}   /,'').strip,
-      'annotation' => part[2].sub(/\w{2}   /,'').strip
-    }
-  end
-
-
-  # (private) parses DE line (description lines)
-  # since UniProtKB release 14.0 of 22-Jul-2008
-  #
-  # Return array containing array.
-  #
-  # http://www.uniprot.org/docs/sp_news.htm
-  def parse_DE_line_rel14(str)
-    # Retruns if it is not the new format since Rel.14
-    return nil unless /^DE   (RecName|AltName|SubName)\: / =~ str
-    ret = []
-    cur = nil
-    str.each_line do |line|
-      case line
-      when /^DE   (Includes|Contains)\: *$/
-        cur = [ $1 ]
-        ret.push cur
-        cur = nil
-        #subcat_and_desc = nil
-        next
-      when /^DE   *(RecName|AltName|SubName)\: +(.*)/
-        category = $1
-        subcat_and_desc = $2
-        cur = [ category ]
-        ret.push cur
-      when /^DE   *(Flags)\: +(.*)/
-        category = $1
-        desc = $2
-        flags = desc.strip.split(/\s*\;\s*/) || []
-        cur = [ category, flags ]
-        ret.push cur
-        cur = nil
-        #subcat_and_desc = nil
-        next
-      when /^DE   *(.*)/
-        subcat_and_desc = $1
-      else
-        warn "Warning: skipped DE line in unknown format: #{line.inspect}"
-        #subcat_and_desc = nil
-        next
-      end
-      case subcat_and_desc
-      when nil
-        # does nothing
-      when /\A([^\=]+)\=(.*)/
-        subcat = $1
-        desc = $2
-        desc.sub!(/\;\s*\z/, '')
-        unless cur
-          warn "Warning: unknown category in DE line: #{line.inspect}"
-          cur = [ '' ]
-          ret.push cur
-        end
-        cur.push [ subcat, desc ]
-      else
-        warn "Warning: skipped DE line description in unknown format: #{line.inspect}"
-      end
-    end
-    ret
-  end
-  private :parse_DE_line_rel14
-
-  # returns the proposed official name of the protein.
-  # Returns a String.
-  #
-  # Since UniProtKB release 14.0 of 22-Jul-2008, the DE line format have
-  # been changed. The method returns the full name which is taken from
-  # "RecName: Full=" or "SubName: Full=" line normally in the beginning of
-  # the DE lines. 
-  # Unlike parser for old format, no special treatments for fragment or
-  # precursor.
-  #
-  # For old format, the method parses the DE lines and returns the protein
-  # name as a String.
-  # 
-  # === DE Line; description (>=1)
-  #  "DE #{OFFICIAL_NAME} (#{SYNONYM})"
-  #  "DE #{OFFICIAL_NAME} (#{SYNONYM}) [CONTEINS: #1; #2]."
-  #  OFFICIAL_NAME  1/entry
-  #  SYNONYM        >=0
-  #  CONTEINS       >=0
-  def protein_name
-    @data['DE'] ||= parse_DE_line_rel14(get('DE'))
-    parsed_de_line = @data['DE']
-    if parsed_de_line then
-      # since UniProtKB release 14.0 of 22-Jul-2008
-      name = nil
-      parsed_de_line.each do |a|
-        case a[0]
-        when 'RecName', 'SubName'
-          if name_pair = a[1..-1].find { |b| b[0] == 'Full' } then
-            name = name_pair[1]
-            break
-          end
-        end
-      end
-      name = name.to_s
-    else
-      # old format (before Rel. 13.x)
-      name = ""
-      if de_line = fetch('DE') then
-        str = de_line[/^[^\[]*/] # everything preceding the first [ (the "contains" part)
-        name = str[/^[^(]*/].strip
-        name << ' (Fragment)' if str =~ /fragment/i
-      end
-    end
-    return name
-  end
-
-
-  # returns synonyms (unofficial and/or alternative names).
-  # Returns an Array containing String objects.
-  #
-  # Since UniProtKB release 14.0 of 22-Jul-2008, the DE line format have
-  # been changed. The method returns the full or short names which are
-  # taken from "RecName: Short=", "RecName: EC=", and AltName lines,
-  # except after "Contains:" or "Includes:".
-  # For keeping compatibility with old format parser, "RecName: EC=N.N.N.N"
-  # is reported as "EC N.N.N.N".
-  # In addition, to prevent confusion, "Allergen=" and "CD_antigen=" 
-  # prefixes are added for the corresponding fields.
-  #
-  # For old format, the method parses the DE lines and returns synonyms.
-  # synonyms are each placed in () following the official name on the DE line.
-  def synonyms
-    ary = Array.new
-    @data['DE'] ||= parse_DE_line_rel14(get('DE'))
-    parsed_de_line = @data['DE']
-    if parsed_de_line then
-      # since UniProtKB release 14.0 of 22-Jul-2008
-      parsed_de_line.each do |a|
-        case a[0]
-        when 'Includes', 'Contains'
-          break #the each loop
-        when 'RecName', 'SubName', 'AltName'
-          a[1..-1].each do |b|
-            if name = b[1] and b[1] != self.protein_name then
-              case b[0]
-              when 'EC'
-                name = "EC " + b[1]
-              when 'Allergen', 'CD_antigen'
-                name = b[0] + '=' + b[1]
-              else
-                name = b[1]
-              end
-              ary.push name
-            end
-          end
-        end #case a[0]
-      end #parsed_de_line.each
-    else
-      # old format (before Rel. 13.x)
-      if de_line = fetch('DE') then
-        line = de_line.sub(/\[.*\]/,'') # ignore stuff between [ and ].  That's the "contains" part
-      line.scan(/\([^)]+/) do |synonym| 
-        unless synonym =~ /fragment/i then 
-          ary << synonym[1..-1].strip # index to remove the leading (  
-        end
-        end
-      end
-    end
-    return ary
-  end
-
-
-  # returns gene names in the GN line.
-  #
-  # New UniProt/SwissProt format:
-  # * Bio::SPTR#gn -> [ <gene record>* ]
-  # where <gene record> is:
-  #                    { :name => '...', 
-  #                      :synonyms => [ 's1', 's2', ... ],
-  #                      :loci   => [ 'l1', 'l2', ... ],
-  #                      :orfs     => [ 'o1', 'o2', ... ] 
-  #                    }
-  #
-  # Old format:
-  # * Bio::SPTR#gn -> Array      # AND 
-  # * Bio::SPTR#gn[0] -> Array   # OR
-  #
-  # === GN Line: Gene name(s) (>=0, optional)
-  def gn
-    unless @data['GN']
-      case fetch('GN')
-      when /Name=/,/ORFNames=/,/OrderedLocusNames=/,/Synonyms=/
-        @data['GN'] = gn_uniprot_parser
-      else
-        @data['GN'] = gn_old_parser
-      end
-    end
-    @data['GN']
-  end
-
-
-  # returns contents in the old style GN line.
-  # === GN Line: Gene name(s) (>=0, optional)
-  #  GN   HNS OR DRDX OR OSMZ OR BGLY.
-  #  GN   CECA1 AND CECA2.
-  #  GN   CECA1 AND (HOGE OR FUGA).
-  #
-  #  GN NAME1 [(AND|OR) NAME]+.
-  #
-  # Bio::SPTR#gn -> Array      # AND 
-  #          #gn[0] -> Array   # OR
-  #          #gene_names -> Array
-  def gn_old_parser
-    names = Array.new
-    if get('GN').size > 0
-      names = fetch('GN').sub(/\.$/,'').split(/ AND /)
-      names.map! { |synonyms|
-        synonyms = synonyms.gsub(/\(|\)/,'').split(/ OR /).map { |e|
-          e.strip 
-        }
-      }
-    end
-    @data['GN'] = names
-  end
-  private :gn_old_parser
-
-  # returns contents in the structured GN line.
-  # The new format of the GN line is:
-  #  GN   Name=; Synonyms=[, ...]; OrderedLocusNames=[, ...];
-  #  GN   ORFNames=[, ...];
-  #
-  # * Bio::SPTR#gn -> [ <gene record>* ]
-  # where <gene record> is:
-  #                    { :name => '...', 
-  #                      :synonyms => [ 's1', 's2', ... ],
-  #                      :loci   => [ 'l1', 'l2', ... ],
-  #                      :orfs     => [ 'o1', 'o2', ... ] 
-  #                    }
-  def gn_uniprot_parser
-    @data['GN'] = Array.new
-    gn_line = fetch('GN').strip
-    records = gn_line.split(/\s*and\s*/)
-    records.each do |record|
-      gene_hash = {:name => '', :synonyms => [], :loci => [], :orfs => []}
-      record.each_line(';') do |element|
-        case element
-        when /Name=/ then
-          gene_hash[:name] = $'[0..-2]
-        when /Synonyms=/ then
-          gene_hash[:synonyms] = $'[0..-2].split(/\s*,\s*/)
-        when /OrderedLocusNames=/ then
-          gene_hash[:loci] = $'[0..-2].split(/\s*,\s*/)
-        when /ORFNames=/ then
-          gene_hash[:orfs] = $'[0..-2].split(/\s*,\s*/)
-        end
-      end
-      @data['GN'] << gene_hash
-    end
-    return @data['GN']
-  end
-  private :gn_uniprot_parser
-
-
-  # returns a Array of gene names in the GN line.
-  def gene_names
-    gn # set @data['GN'] if it hasn't been already done
-    if @data['GN'].first.class == Hash then
-      @data['GN'].collect { |element| element[:name] }
-    else
-      @data['GN'].first
-    end
-  end
-
-
-  # returns a String of the first gene name in the GN line.
-  def gene_name
-    gene_names.first
-  end
-
-
-  # returns a Array of Hashs or a String of the OS line when a key given.
-  # * Bio::EMBLDB#os  -> Array
-  #  [{'name' => '(Human)', 'os' => 'Homo sapiens'}, 
-  #   {'name' => '(Rat)', 'os' => 'Rattus norveticus'}]
-  # * Bio::EPTR#os[0] -> Hash 
-  #  {'name' => "(Human)", 'os' => 'Homo sapiens'}
-  # * Bio::SPTR#os[0]['name'] -> "(Human)"
-  # * Bio::EPTR#os(0) -> "Homo sapiens (Human)"
-  # 
-  # === OS Line; organism species (>=1)
-  #  OS   Genus species (name).
-  #  OS   Genus species (name0) (name1).
-  #  OS   Genus species (name0) (name1).
-  #  OS   Genus species (name0), G s0 (name0), and G s (name0) (name1).
-  #  OS   Homo sapiens (Human), and Rarrus norveticus (Rat)
-  #  OS   Hippotis sp. Clark and Watts 825.
-  #  OS   unknown cyperaceous sp.
-  def os(num = nil)
-    unless @data['OS']
-      os = Array.new
-      fetch('OS').split(/, and|, /).each do |tmp|
-        if tmp =~ /(\w+ *[\w\d \:\'\+\-\.]+[\w\d\.])/
-          org = $1
-          tmp =~ /(\(.+\))/ 
-          os.push({'name' => $1, 'os' => org})
-        else
-          raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n"
-        end
-      end
-      @data['OS'] = os
-    end
-
-    if num
-      # EX. "Trifolium repens (white clover)"
-      return "#{@data['OS'][num]['os']} #{@data['OS'][num]['name']}"
-    else
-      return @data['OS']
-    end
-  end
-  
-
-  # Bio::EMBLDB::Common#og -> Array
-  # OG Line; organella (0 or 1/entry)
-  # ["MITOCHONDRION", "CHLOROPLAST", "Cyanelle", "Plasmid"]
-  #  or a plasmid name (e.g. "Plasmid pBR322").  
-
-
-  # Bio::EMBLDB::Common#oc -> Array
-  # OC Line; organism classification (>=1)
-  # "OC   Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae;"
-  # "OC   Theileria."
-
-
-
-  # returns a Hash of oraganism taxonomy cross-references.
-  # * Bio::SPTR#ox -> Hash
-  #    {'NCBI_TaxID' => ['1234','2345','3456','4567'], ...}
-  #
-  # === OX Line; organism taxonomy cross-reference (>=1 per entry)
-  #  OX   NCBI_TaxID=1234;
-  #  OX   NCBI_TaxID=1234, 2345, 3456, 4567;
-  def ox
-    unless @data['OX']
-      tmp = fetch('OX').sub(/\.$/,'').split(/;/).map { |e| e.strip }
-      hsh = Hash.new
-      tmp.each do |e|
-        db,refs = e.split(/=/)
-        hsh[db] = refs.split(/, */)
-      end
-      @data['OX'] = hsh
-    end
-    return @data['OX']
-  end
-
-  # === The OH Line;  
-  #
-  # OH   NCBI_TaxID=TaxID; HostName.
-  # http://br.expasy.org/sprot/userman.html#OH_line
-  def oh
-    unless @data['OH']
-      @data['OH'] = fetch('OH').split("\. ").map {|x|
-        if x =~ /NCBI_TaxID=(\d+);/
-          taxid = $1
-        else
-          raise ArgumentError, ["Error: Invalid OH line format (#{self.entry_id}):",
-                                $!, "\n", get('OH'), "\n"].join
-          
-        end
-        if x =~ /NCBI_TaxID=\d+; (.+)/ 
-          host_name = $1
-          host_name.sub!(/\.$/, '')
-        else
-          host_name = nil
-        end
-        {'NCBI_TaxID' => taxid, 'HostName' => host_name}
-      }
-    end
-    @data['OH']
-  end
-
-
-  
-  # Bio::EMBLDB::Common#ref -> Array
-  # R Lines
-  # RN RC RP RX RA RT RL
-
-  # returns contents in the R lines.
-  # * Bio::EMBLDB::Common#ref -> [ <refernece information Hash>* ]
-  # where <reference information Hash> is:
-  #  {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 
-  #   'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
-  # 
-  # R Lines
-  # * RN RC RP RX RA RT RL RG
-  def ref
-    unless @data['R']
-      @data['R'] = [get('R').split(/\nRN   /)].flatten.map { |str|
-        hash = {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 
-               'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
-        str = 'RN   ' + str unless /^RN   / =~ str
-
-        str.split("\n").each do |line|
-          if /^(R[NPXARLCTG])   (.+)/ =~ line
-            hash[$1] += $2 + ' '
-          else
-            raise "Invalid format in R lines, \n[#{line}]\n"
-          end
-        end
-
-        hash['RN'] = set_RN(hash['RN'])
-        hash['RC'] = set_RC(hash['RC'])
-        hash['RP'] = set_RP(hash['RP'])
-        hash['RX'] = set_RX(hash['RX'])
-        hash['RA'] = set_RA(hash['RA'])
-        hash['RT'] = set_RT(hash['RT'])
-        hash['RL'] = set_RL(hash['RL'])
-        hash['RG'] = set_RG(hash['RG'])
-
-        hash
-      }
-
-    end
-    @data['R']
-  end
-
-  def set_RN(data)
-    data.strip
-  end
-
-  def set_RC(data)
-    data.scan(/([STP]\w+)=(.+);/).map { |comment|
-      [comment[1].split(/, and |, /)].flatten.map { |text|
-        {'Token' => comment[0], 'Text' => text}
-      }
-    }.flatten
-  end
-  private :set_RC
-
-  def set_RP(data)
-    data = data.strip
-    data = data.sub(/\.$/, '')
-    data.split(/, AND |, /i).map {|x| 
-      x = x.strip
-      x = x.gsub('  ', ' ')
-    }
-  end
-  private :set_RP
-
-  def set_RX(data)
-    rx = {'MEDLINE' => nil, 'PubMed' => nil, 'DOI' => nil}
-    if data =~ /MEDLINE=(.+?);/
-      rx['MEDLINE'] = $1
-    end
-    if data =~ /PubMed=(.+?);/
-      rx['PubMed'] = $1
-    end
-    if data =~ /DOI=(.+?);/
-      rx['DOI'] = $1
-    end
-    rx
-  end
-  private :set_RX
-
-  def set_RA(data)
-    data = data.sub(/; *$/, '')
-  end
-  private :set_RA
-
-  def set_RT(data)
-    data = data.sub(/; *$/, '')
-    data = data.gsub(/(^"|"$)/, '')
-  end
-  private :set_RT
-
-  def set_RL(data)
-    data = data.strip
-  end
-  private :set_RL
-
-  def set_RG(data)
-    data = data.split('; ')
-  end
-  private :set_RG
-
-
-
-  # returns Bio::Reference object from Bio::EMBLDB::Common#ref.
-  # * Bio::EMBLDB::Common#ref -> Bio::References
-  def references
-    unless @data['references']
-      ary = self.ref.map {|ent|
-        hash = Hash.new('')
-        ent.each {|key, value|
-          case key
-          when 'RA'
-            hash['authors'] = value.split(/, /)
-          when 'RT'
-            hash['title'] = value
-          when 'RL'
-            if value =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
-              hash['journal'] = $1
-              hash['volume']  = $2
-              hash['issue']   = $3
-              hash['pages']   = $4
-              hash['year']    = $5
-            else
-              hash['journal'] = value
-            end
-          when 'RX'  # PUBMED, MEDLINE, DOI
-            value.each do |tag, xref|
-              hash[ tag.downcase ]  = xref
-            end
-          end
-        }
-        Reference.new(hash)
-      }
-      @data['references'] = References.new(ary)
-    end
-    @data['references']
-  end
-
-
-
-
-
-
-  # === The HI line
-  # Bio::SPTR#hi #=> hash
-  def hi
-    unless @data['HI']
-      @data['HI'] = []
-      fetch('HI').split(/\. /).each do |hlist|
-        hash = {'Category' => '',  'Keywords' => [], 'Keyword' => ''}
-        hash['Category'], hash['Keywords'] = hlist.split(': ')
-        hash['Keywords'] = hash['Keywords'].split('; ')
-        hash['Keyword'] = hash['Keywords'].pop
-        hash['Keyword'].sub!(/\.$/, '')
-        @data['HI'] << hash
-      end
-    end
-    @data['HI']
-  end
-
-
-  @@cc_topics = ['PHARMACEUTICAL',
-                 'BIOTECHNOLOGY',
-                 'TOXIC DOSE', 
-                 'ALLERGEN',   
-                 'RNA EDITING',
-                 'POLYMORPHISM',
-                 'BIOPHYSICOCHEMICAL PROPERTIES',
-                 'MASS SPECTROMETRY',
-                 'WEB RESOURCE', 
-                 'ENZYME REGULATION',
-                 'DISEASE',
-                 'INTERACTION',
-                 'DEVELOPMENTAL STAGE',
-                 'INDUCTION',
-                 'CAUTION',
-                 'ALTERNATIVE PRODUCTS',
-                 'DOMAIN',
-                 'PTM',
-                 'MISCELLANEOUS',
-                 'TISSUE SPECIFICITY',
-                 'COFACTOR',
-                 'PATHWAY',
-                 'SUBUNIT',
-                 'CATALYTIC ACTIVITY',
-                 'SUBCELLULAR LOCATION',
-                 'FUNCTION',
-                 'SIMILARITY']
-  # returns contents in the CC lines.
-  # * Bio::SPTR#cc -> Hash
-  #
-  # returns an object of contents in the TOPIC.
-  # * Bio::SPTR#cc(TOPIC) -> Array w/in Hash, Hash
-  #
-  # returns contents of the "ALTERNATIVE PRODUCTS".
-  # * Bio::SPTR#cc('ALTERNATIVE PRODUCTS') -> Hash
-  #    {'Event' => str, 
-  #     'Named isoforms' => int,  
-  #     'Comment' => str,
-  #     'Variants'=>[{'Name' => str, 'Synonyms' => str, 'IsoId' => str, 'Sequence' => []}]}
-  # 
-  #    CC   -!- ALTERNATIVE PRODUCTS:
-  #    CC       Event=Alternative splicing; Named isoforms=15;
-  #    ...
-  #    CC         placentae isoforms. All tissues differentially splice exon 13;
-  #    CC       Name=A; Synonyms=no del;
-  #    CC         IsoId=P15529-1; Sequence=Displayed;
-  #
-  # returns contents of the "DATABASE".
-  # * Bio::SPTR#cc('DATABASE') -> Array
-  #    [{'NAME'=>str,'NOTE'=>str, 'WWW'=>URI,'FTP'=>URI}, ...]
-  #
-  #    CC   -!- DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].
-  #
-  # returns contents of the "MASS SPECTROMETRY".
-  # * Bio::SPTR#cc('MASS SPECTROMETRY') -> Array
-  #    [{'MW"=>float,'MW_ERR'=>float, 'METHOD'=>str,'RANGE'=>str}, ...]
-  #
-  #    CC   -!- MASS SPECTROMETRY: MW=XXX[; MW_ERR=XX][; METHOD=XX][;RANGE=XX-XX].
-  #
-  # === CC lines (>=0, optional)
-  #   CC   -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT
-  #   CC       IN LIVER, KIDNEY, LUNG AND BRAIN.
-  # 
-  #   CC   -!- TOPIC: FIRST LINE OF A COMMENT BLOCK;
-  #   CC       SECOND AND SUBSEQUENT LINES OF A COMMENT BLOCK.
-  #
-  # See also http://www.expasy.org/sprot/userman.html#CC_line
-  #
-  def cc(topic = nil)
-    unless @data['CC']
-      cc  = Hash.new
-      comment_border= '-' * (77 - 4 + 1)
-      dlm = /-!- /
-
-      # 12KD_MYCSM has no CC lines.
-      return cc if get('CC').size == 0
-      
-      cc_raw = fetch('CC')
-
-      # Removing the copyright statement.
-      cc_raw.sub!(/ *---.+---/m, '')
-
-      # Not any CC Lines without the copyright statement.
-      return cc if cc_raw == ''
-
-      begin
-        cc_raw, copyright = cc_raw.split(/#{comment_border}/)[0]
-        cc_raw = cc_raw.sub(dlm,'')
-        cc_raw.split(dlm).each do |tmp|
-          tmp = tmp.strip
-
-          if /(^[A-Z ]+[A-Z]): (.+)/ =~ tmp
-            key  = $1
-            body = $2
-            body.gsub!(/- (?!AND)/,'-')
-            body.strip!
-            unless cc[key]
-              cc[key] = [body]
-            else
-              cc[key].push(body)
-            end
-          else
-            raise ["Error: [#{entry_id}]: CC Lines", '"', tmp, '"',
-                   '', get('CC'),''].join("\n")
-          end
-        end
-      rescue NameError
-        if fetch('CC') == ''
-          return {}
-        else
-          raise ["Error: Invalid CC Lines: [#{entry_id}]: ",
-                 "\n'#{self.get('CC')}'\n", "(#{$!})"].join
-        end
-      rescue NoMethodError
-      end
-      
-      @data['CC'] = cc
-    end
-
-
-    case topic
-    when 'ALLERGEN'
-      return @data['CC'][topic]
-    when 'ALTERNATIVE PRODUCTS'
-      return cc_alternative_products(@data['CC'][topic])
-    when 'BIOPHYSICOCHEMICAL PROPERTIES'
-      return cc_biophysiochemical_properties(@data['CC'][topic])
-    when 'BIOTECHNOLOGY'
-      return @data['CC'][topic]
-    when 'CATALITIC ACTIVITY'
-      return cc_catalytic_activity(@data['CC'][topic])
-    when 'CAUTION'
-      return cc_caution(@data['CC'][topic])
-    when 'COFACTOR'
-      return @data['CC'][topic]
-    when 'DEVELOPMENTAL STAGE'
-      return @data['CC'][topic].join('')
-    when 'DISEASE'
-      return @data['CC'][topic].join('')
-    when 'DOMAIN'
-      return @data['CC'][topic]
-    when 'ENZYME REGULATION'
-      return @data['CC'][topic].join('')
-    when 'FUNCTION'
-      return @data['CC'][topic].join('')
-    when 'INDUCTION'
-      return @data['CC'][topic].join('')
-    when 'INTERACTION'
-      return cc_interaction(@data['CC'][topic])
-    when 'MASS SPECTROMETRY'
-      return cc_mass_spectrometry(@data['CC'][topic])
-    when 'MISCELLANEOUS'
-      return @data['CC'][topic]
-    when 'PATHWAY'
-      return cc_pathway(@data['CC'][topic])
-    when 'PHARMACEUTICAL'
-      return @data['CC'][topic]
-    when 'POLYMORPHISM'
-      return @data['CC'][topic]
-    when 'PTM'
-      return @data['CC'][topic]
-    when 'RNA EDITING'
-      return cc_rna_editing(@data['CC'][topic])
-    when 'SIMILARITY'
-      return @data['CC'][topic]
-    when 'SUBCELLULAR LOCATION'
-      return cc_subcellular_location(@data['CC'][topic])
-    when 'SUBUNIT'
-      return @data['CC'][topic]
-    when 'TISSUE SPECIFICITY'
-      return @data['CC'][topic]
-    when 'TOXIC DOSE'
-      return @data['CC'][topic]
-    when 'WEB RESOURCE'
-      return cc_web_resource(@data['CC'][topic])
-    when 'DATABASE'
-      # DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].
-      tmp = Array.new
-      db = @data['CC']['DATABASE']
-      return db unless db
-
-      db.each do |e|
-        db = {'NAME' => nil, 'NOTE' => nil, 'WWW' => nil, 'FTP' => nil}
-        e.sub(/.$/,'').split(/;/).each do |line|
-          case line
-          when /NAME=(.+)/
-            db['NAME'] = $1
-          when /NOTE=(.+)/
-            db['NOTE'] = $1
-          when /WWW="(.+)"/
-            db['WWW'] = $1
-          when /FTP="(.+)"/
-            db['FTP'] = $1
-          end 
-        end
-        tmp.push(db)
-      end
-      return tmp
-    when nil
-      return @data['CC']
-    else
-      return @data['CC'][topic]
-    end
-  end
-
-
-  def cc_alternative_products(data)
-    ap = data.join('')
-    return ap unless ap
-
-    # Event, Named isoforms, Comment, [Name, Synonyms, IsoId, Sequnce]+
-    tmp = {'Event' => "", 'Named isoforms' => "", 'Comment' => "", 
-           'Variants'  => []}
-    if /Event=(.+?);/ =~ ap
-      tmp['Event'] = $1
-      tmp['Event'] = tmp['Event'].sub(/;/,'').split(/, /)
-    end
-    if /Named isoforms=(\S+?);/ =~ ap
-      tmp['Named isoforms'] = $1
-    end
-    if /Comment=(.+?);/m =~ ap
-      tmp['Comment'] = $1
-    end
-    ap.scan(/Name=.+?Sequence=.+?;/).each do |ent|
-      tmp['Variants'] << cc_alternative_products_variants(ent)
-    end
-    return tmp
-  end
-  private :cc_alternative_products
-
-  def cc_alternative_products_variants(data)
-    variant = {'Name' => '', 'Synonyms' => [], 'IsoId' => [], 'Sequence' => []}
-    data.split(/; /).map {|x| x.split(/=/) }.each do |e|
-      case e[0]
-      when 'Sequence', 'Synonyms', 'IsoId'
-        e[1] = e[1].sub(/;/,'').split(/, /)
-      end
-      variant[e[0]] = e[1]
-    end
-    variant
-  end
-  private :cc_alternative_products_variants
-
-
-  def cc_biophysiochemical_properties(data)
-    data = data[0]
-
-    hash = {'Absorption' => {}, 
-            'Kinetic parameters' => {},
-            'pH dependence' => "",
-            'Redox potential' => "",
-            'Temperature dependence' => ""}
-    if data =~ /Absorption: Abs\(max\)=(.+?);/
-      hash['Absorption']['Abs(max)'] = $1
-    end
-    if data =~ /Absorption: Abs\(max\)=.+; Note=(.+?);/
-      hash['Absorption']['Note'] = $1
-    end
-    if data =~ /Kinetic parameters: KM=(.+?); Vmax=(.+?);/
-      hash['Kinetic parameters']['KM'] = $1
-      hash['Kinetic parameters']['Vmax'] = $2
-    end
-    if data =~ /Kinetic parameters: KM=.+; Vmax=.+; Note=(.+?);/
-      hash['Kinetic parameters']['Note'] = $1
-    end
-    if data =~ /pH dependence: (.+?);/
-      hash['pH dependence'] = $1
-    end
-    if data =~ /Redox potential: (.+?);/
-      hash['Redox potential'] = $1
-    end
-    if data =~ /Temperature dependence: (.+?);/
-      hash['Temperature dependence'] = $1
-    end
-    hash
-  end
-  private :cc_biophysiochemical_properties
-
-
-  def cc_caution(data)
-    data.join('')
-  end
-  private :cc_caution
-
-
-  # returns conteins in a line of the CC INTERACTION section.
-  #
-  #   CC       P46527:CDKN1B; NbExp=1; IntAct=EBI-359815, EBI-519280;
-  def cc_interaction(data)
-    str = data.join('')
-    it = str.scan(/(.+?); NbExp=(.+?); IntAct=(.+?);/)
-    it.map {|ent|
-      ent.map! {|x| x.strip }
-      if ent[0] =~ /^(.+):(.+)/
-        spac = $1
-        spid = $2.split(' ')[0]
-        optid = nil
-      elsif ent[0] =~ /Self/
-        spac = self.entry_id
-        spid = self.entry_id
-        optid = nil
-      end
-      if ent[0] =~ /^.+:.+ (.+)/
-        optid = $1
-      end
-
-      {'SP_Ac' => spac,
-       'identifier' => spid,
-       'NbExp' => ent[1],
-       'IntAct' => ent[2].split(', '),
-       'optional_identifier' => optid}
-    }
-  end
-  private :cc_interaction
-
-
-  def cc_mass_spectrometry(data)
-    # MASS SPECTROMETRY: MW=XXX[; MW_ERR=XX][; METHOD=XX][;RANGE=XX-XX].
-    return data unless data
-
-    data.map { |m|
-      mass = {'MW' => nil, 'MW_ERR' => nil, 'METHOD' => nil, 'RANGE' => nil,
-              'NOTE' => nil}
-      m.sub(/.$/,'').split(/;/).each do |line|
-        case line
-        when /MW=(.+)/
-          mass['MW'] = $1
-        when /MW_ERR=(.+)/
-          mass['MW_ERR'] = $1
-        when /METHOD=(.+)/
-          mass['METHOD'] = $1
-        when /RANGE=(\d+-\d+)/ 
-          mass['RANGE'] = $1          # RANGE class ? 
-        when /NOTE=(.+)/
-          mass['NOTE'] = $1
-        end 
-      end
-      mass
-    }
-  end
-  private :cc_mass_spectrometry
-
-
-  def cc_pathway(data)
-    data.map {|x| x.sub(/\.$/, '') }.map {|x|
-      x.split(/; | and |: /)
-    }[0]
-  end
-  private :cc_pathway
-
-
-  def cc_rna_editing(data)
-    data = data.join('')
-    entry = {'Modified_positions' => [], 'Note' => ""}
-    if data =~ /Modified_positions=(.+?)(\.|;)/
-      entry['Modified_positions'] = $1.sub(/\.$/, '').split(', ')
-    else
-      raise ArgumentError, "Invarid CC RNA Editing lines (#{self.entry_id}):#{$!}\n#{get('CC')}"
-    end
-    if data =~ /Note=(.+)/
-      entry['Note'] = $1
-    end
-    entry
-  end
-  private :cc_rna_editing
-
-
-  def cc_subcellular_location(data)
-    data.map {|x| 
-      x.split('. ').map {|y| 
-        y.split('; ').map {|z| 
-          z.sub(/\.$/, '') 
-        } 
-      } 
-    }[0]
-  end
-  private :cc_subcellular_location
-
-
-  #--
-  # Since UniProtKB release 12.2 of 11-Sep-2007:
-  # CC   -!- WEB RESOURCE: Name=ResourceName[; Note=FreeText][; URL=WWWAddress].  # Old format:
-  # CC   -!- WEB RESOURCE: NAME=ResourceName[; NOTE=FreeText][; URL=WWWAddress].
-  #++
-
-  def cc_web_resource(data)
-    data.map {|x|
-      entry = {'Name' => nil, 'Note' => nil, 'URL' => nil}
-      x.split(';').each do |y|
-        case y
-        when /(Name|Note)\=(.+)/
-          key = $1
-          val = $2.strip
-          entry[key] = val
-        when /(NAME|NOTE)\=(.+)/
-          key = $1.downcase.capitalize
-          val = $2.strip
-          entry[key] = val
-        when /URL\=\"(.+)\"/
-          entry['URL'] = $1.strip
-        end
-      end
-      entry
-    }
-  end
-  private :cc_web_resource
-
-  # returns databases cross-references in the DR lines.
-  # * Bio::SPTR#dr  -> Hash w/in Array
-  #
-  # === DR Line; defabases cross-reference (>=0)
-  #    DR  database_identifier; primary_identifier; secondary_identifier.
-  #  a cross_ref pre one line
-  @@dr_database_identifier = ['EMBL','CARBBANK','DICTYDB','ECO2DBASE',
-    'ECOGENE',
-    'FLYBASE','GCRDB','HIV','HSC-2DPAGE','HSSP','INTERPRO','MAIZEDB',
-    'MAIZE-2DPAGE','MENDEL','MGD''MIM','PDB','PFAM','PIR','PRINTS',
-    'PROSITE','REBASE','AARHUS/GHENT-2DPAGE','SGD','STYGENE','SUBTILIST',
-    'SWISS-2DPAGE','TIGR','TRANSFAC','TUBERCULIST','WORMPEP','YEPD','ZFIN']
-
-  # Backup Bio::EMBLDB#dr as embl_dr
-  alias :embl_dr :dr 
-
-  # Bio::SPTR#dr
-  def dr(key = nil)
-    unless key
-      embl_dr
-    else
-      (embl_dr[key] or []).map {|x|
-        {'Accession' => x[0],
-         'Version' => x[1],
-         ' ' => x[2],
-         'Molecular Type' => x[3]}
-      }
-    end
-  end
-
-
-  # Bio::EMBLDB::Common#kw - Array
-  #                    #keywords  -> Array
-  #
-  # KW Line; keyword (>=1)
-  # KW   [Keyword;]+
-
-
-  # returns contents in the feature table.
-  #
-  # == Examples
-  #
-  #  sp = Bio::SPTR.new(entry)
-  #  ft = sp.ft
-  #  ft.class #=> Hash
-  #  ft.keys.each do |feature_key|
-  #    ft[feature_key].each do |feature|
-  #      feature['From'] #=> '1'
-  #      feature['To']   #=> '21'
-  #      feature['Description'] #=> ''
-  #      feature['FTId'] #=> ''
-  #      feature['diff'] #=> []
-  #      feature['original'] #=> [feature_key, '1', '21', '', '']
-  #    end
-  #  end
-  #
-  # * Bio::SPTR#ft -> Hash
-  #    {FEATURE_KEY => [{'From' => int, 'To' => int, 
-  #                      'Description' => aStr, 'FTId' => aStr,
-  #                      'diff' => [original_residues, changed_residues],
-  #                      'original' => aAry }],...}
-  #
-  # returns an Array of the information about the feature_name in the feature table.
-  # * Bio::SPTR#ft(feature_name) -> Array of Hash
-  #    [{'From' => str, 'To' => str, 'Description' => str, 'FTId' => str},...]
-  #
-  # == FT Line; feature table data (>=0, optional)
-  #
-  #   Col     Data item
-  #   -----   -----------------
-  #    1- 2   FT
-  #    6-13   Feature name 
-  #   15-20   `FROM' endpoint
-  #   22-27   `TO' endpoint
-  #   35-75   Description (>=0 per key)
-  #   -----   -----------------
-  #
-  # Note: 'FROM' and 'TO' endopoints are allowed to use non-numerial charactors 
-  # including '<', '>' or '?'. (c.f. '<1', '?42')
-  #
-  # See also http://www.expasy.org/sprot/userman.html#FT_line
-  #
-  def ft(feature_key = nil)
-    return ft[feature_key] if feature_key
-    return @data['FT'] if @data['FT']
-
-    table = []
-    begin
-      get('FT').split("\n").each do |line|
-        if line =~ /^FT   \w/
-          feature = line.chomp.ljust(74)
-          table << [feature[ 5..12].strip,   # Feature Name
-                    feature[14..19].strip,   # From
-                    feature[21..26].strip,   # To
-                    feature[34..74].strip ]  # Description
-        else
-          table.last << line.chomp.sub!(/^FT +/, '')
-        end
-      end
-
-      # Joining Description lines
-      table = table.map { |feature| 
-        ftid = feature.pop if feature.last =~ /FTId=/
-        if feature.size > 4
-          feature = [feature[0], 
-                     feature[1], 
-                     feature[2], 
-                     feature[3, feature.size - 3].join(" ")]
-        end
-        feature << if ftid then ftid else '' end
-      }
-
-      hash = {}
-      table.each do |feature|
-        hash[feature[0]] = [] unless hash[feature[0]]
-        hash[feature[0]] << {
-          # Removing '<', '>' or '?' in FROM/TO endopoint.
-          'From' => feature[1].sub(/\D/, '').to_i,  
-          'To'   => feature[2].sub(/\D/, '').to_i, 
-          'Description' => feature[3], 
-          'FTId' => feature[4].to_s.sub(/\/FTId=/, '').sub(/\.$/, ''),
-          'diff' => [],
-          'original' => feature
-        }
-
-        case feature[0]
-        when 'VARSPLIC', 'VARIANT', 'VAR_SEQ', 'CONFLICT'
-          case hash[feature[0]].last['Description']
-          when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
-            original_res = $1
-            changed_res = $2
-            original_res = original_res.gsub(/ /,'').strip
-            chenged_res = changed_res.gsub(/ /,'').strip
-          when /Missing/i
-            original_res = seq.subseq(hash[feature[0]].last['From'],
-                                      hash[feature[0]].last['To'])
-            changed_res = ''
-          end
-          hash[feature[0]].last['diff'] = [original_res, chenged_res]
-        end
-      end
-    rescue
-      raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
-    end
-
-    @data['FT'] = hash
-  end
-
-
-
-  # returns a Hash of conteins in the SQ lines.
-  # * Bio::SPTRL#sq  -> hsh
-  #
-  # returns a value of a key given in the SQ lines.
-  # * Bio::SPTRL#sq(key)  -> int or str
-  # * Keys: ['MW', 'mw', 'molecular', 'weight', 'aalen', 'len', 'length', 
-  #          'CRC64']
-  #
-  # === SQ Line; sequence header (1/entry)
-  #    SQ   SEQUENCE   233 AA;  25630 MW;  146A1B48A1475C86 CRC64;
-  #    SQ   SEQUENCE  \d+ AA; \d+ MW;  [0-9A-Z]+ CRC64;
-  #
-  # MW, Dalton unit.
-  # CRC64 (64-bit Cyclic Redundancy Check, ISO 3309).
-  def sq(key = nil)
-    unless @data['SQ']
-      if fetch('SQ') =~ /(\d+) AA\; (\d+) MW; (.+) CRC64;/
-        @data['SQ'] = { 'aalen' => $1.to_i, 'MW' => $2.to_i, 'CRC64' => $3 }
-      else
-        raise "Invalid SQ Line: \n'#{fetch('SQ')}'"
-      end
-    end
-
-    if key
-      case key
-      when /mw/, /molecular/, /weight/
-        @data['SQ']['MW']
-      when /len/, /length/, /AA/
-        @data['SQ']['aalen']
-      else
-        @data['SQ'][key]
-      end
-    else 
-      @data['SQ']
-    end
-  end
-
-
-  # returns a Bio::Sequence::AA of the amino acid sequence.
-  # * Bio::SPTR#seq -> Bio::Sequence::AA
-  #
-  # blank Line; sequence data (>=1)
-  def seq
-    unless @data['']
-      @data[''] = Sequence::AA.new( fetch('').gsub(/ |\d+/,'') )
-    end
-    return @data['']
-  end
-  alias aaseq seq
-
-end # class SPTR
-
-end # module Bio
-
-
-
-=begin
-
-= Bio::SPTR < Bio::DB
-
-Class for a entry in the SWISS-PROT/TrEMBL database.
-
-  * ((<URL:http://www.ebi.ac.uk/swissprot/>))
-  * ((<URL:http://www.ebi.ac.uk/trembl/>))
-  * ((<URL:http://www.ebi.ac.uk/sprot/userman.html>))
-  
-
---- Bio::SPTR.new(a_sp_entry)
-
-=== ID line (Identification)
-
---- Bio::SPTR#id_line -> {'ENTRY_NAME' => str, 'DATA_CLASS' => str,
-                          'MOLECULE_TYPE' => str, 'SEQUENCE_LENGTH' => int }  
---- Bio::SPTR#id_line(key) -> str
-
-       key = (ENTRY_NAME|MOLECULE_TYPE|DATA_CLASS|SEQUENCE_LENGTH)
-
---- Bio::SPTR#entry_id -> str
---- Bio::SPTR#molecule -> str
---- Bio::SPTR#sequence_length -> int
-    
-
-=== AC lines (Accession number)
-
---- Bio::SPTR#ac -> ary
---- Bio::SPTR#accessions -> ary
---- Bio::SPTR#accession -> accessions.first
-
- 
-=== GN line (Gene name(s))
-
---- Bio::SPTR#gn -> [ary, ...] or [{:name => str, :synonyms => [], :loci => [], :orfs => []}]
---- Bio::SPTR#gene_name -> str
---- Bio::SPTR#gene_names -> [str] or [str]
-
-
-=== DT lines (Date) 
-
---- Bio::SPTR#dt -> {'created' => str, 'sequence' => str, 'annotation' => str}
---- Bio::SPTR#dt(key) -> str
-
-      key := (created|annotation|sequence)
-
-
-=== DE lines (Description)
-
---- Bio::SPTR#de -> str
-             #definition -> str
-
---- Bio::SPTR#protein_name
-
-      Returns the proposed official name of the protein
-
-
---- Bio::SPTR#synonyms
-
-      Returns an array of synonyms (unofficial names)
-
-=== KW lines (Keyword)
-
---- Bio::SPTR#kw -> ary
-
-=== OS lines (Organism species)
-
---- Bio::SPTR#os -> [{'name' => str, 'os' => str}, ...]
-
-=== OC lines (organism classification)
-
---- Bio::SPTR#oc -> ary
-
-=== OG line (Organella)
-
---- Bio::SPTR#og -> ary
-
-=== OX line (Organism taxonomy cross-reference)
-
---- Bio::SPTR#ox -> {'NCBI_TaxID' => [], ...}
-
-=== RN RC RP RX RA RT RL RG lines (Reference)  
-
---- Bio::SPTR#ref -> [{'RN' => int, 'RP' => str, 'RC' => str, 'RX' => str, ''RT' => str, 'RL' => str, 'RA' => str, 'RC' => str, 'RG' => str},...]
-
-=== DR lines (Database cross-reference)
-
---- Bio::SPTR#dr -> {'EMBL' => ary, ...}
-
-=== FT lines (Feature table data)
-
---- Bio::SPTR#ft -> hsh
-
-=== SQ lines (Sequence header and data)
-
---- Bio::SPTR#sq -> {'CRC64' => str, 'MW' => int, 'aalen' => int}
---- Bio::SPTR#sq(key) -> int or str
-
-          key := (aalen|MW|CRC64)
-
---- Bio::EMBL#seq -> Bio::Sequece::AA
-             #aaseq -> Bio::Sequece::AA
-
-=end
+  require "bio/db/embl/uniprotkb" unless const_defined?(:UniProtKB)
 
-  #      Content                      Occurrence in an entry
-  # ---- ---------------------------  --------------------------------
-  # ID - identification               (begins each entry; 1 per entry)
-  # AC - accession number(s)          (>=1 per entry)
-  # DT - date                         (3 per entry)
-  # DE - description                  (>=1 per entry)
-  # GN - gene name(s)                 (>=0 per entry; optional)
-  # OS - organism species             (>=1 per entry)
-  # OG - organelle                    (0 or 1 per entry; optional)
-  # OC - organism classification      (>=1 per entry)
-  # OX - organism taxonomy x-ref      (>=1 per entry)
-  # OH - Organism Host
-  # RN - reference number             (>=1 per entry)
-  # RP - reference positions          (>=1 per entry)
-  # RC - reference comment(s)         (>=0 per entry; optional)
-  # RX - reference cross-reference(s) (>=0 per entry; optional)
-  # RA - reference author(s)          (>=1 per entry)
-  # RT - reference title              (>=0 per entry; optional)
-  # RL - reference location           (>=1 per entry)
-  # RG - reference group(s)
-  # CC - comments or notes            (>=0 per entry; optional)
-  # DR - database cross-references    (>=0 per entry; optional)
-  # KW - keywords                     (>=1 per entry)
-  # FT - feature table data           (>=0 per entry; optional)
-  # SQ - sequence header              (1 per entry)
-  #    - (blanks) The sequence data   (>=1 per entry)
-  # // - termination line             (ends each entry; 1 per entry)
-  # ---- ---------------------------  --------------------------------
+  # Bio::SPTR is changed to an alias of Bio::UniProtKB.
+  # Please use Bio::UniProtKB.
+  # Bio::SPTR may be deprecated in the future.
+  SPTR = UniProtKB
 
+end #module Bio