# File lib/bio/db/fasta.rb, line 469
    def initialize(str)
      @deflines = []
      @info = {}
      @list_ids = []

      @entry_id = nil

      lines = str.split("\x01")
      lines.each do |line|
        add_defline(line)
      end
    end

# File lib/bio/db/fasta.rb, line 782
    def acc_version
      unless defined?(@acc_version) then
        @acc_version = get_by_type('acc_version')
      end
      @acc_version
    end

# File lib/bio/db/fasta.rb, line 800
    def accession
      unless defined?(@accession) then
        if acc_version then
          @accession = acc_version.split('.')[0]
        else
          @accession = accessions[0]
        end
      end
      @accession
    end

# File lib/bio/db/fasta.rb, line 791
    def accessions
      unless defined?(@accessions) then
        @accessions = get_all_by_type('accession', 'acc_version')
        @accessions.collect! { |x| x.sub(/\..*\z/, '') }
      end
      @accessions
    end

# File lib/bio/db/fasta.rb, line 483
    def add_defline(str)
      case str
      when /^\>?\s*((?:[^\|\s]*\|)+[^\s]+)\s*(.*)$/
        # NSIDs
        # examples:
        # >gi|9910844|sp|Q9UWG2|RL3_METVA 50S ribosomal protein L3P
        #
        # note: regexp (:?) means grouping without backreferences
        i = $1
        d = $2
        tks = i.split('|')
        tks << '' if i[-1,1] == '|'
        a = parse_NSIDs(tks)
        i = a[0].join('|')
        a.unshift('|')
        d = tks.join('|') + ' ' + d unless tks.empty?
        a << d
        this_line = a
        match_EC(d)
        parse_square_brackets(d).each do |x|
          if !match_EC(x, false) and x =~ /\A[A-Z]/ then
            di = [  x ]
            @list_ids << di
            @info['organism'] = x unless @info['organism']
          end
        end

      when /^\>?\s*([a-zA-Z0-9]+\:[^\s]+)\s*(.*)$/
        # examples:
        # >sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
        # >emb:CACDC28 [X80034] C.albicans CDC28 gene 
        i = $1
        d = $2
        a = parse_ColonSepID(i)
        i = a.join(':')
        this_line = [ ':', a , d ]
        match_EC(d)
        parse_square_brackets(d).each do |x|
          if !match_EC(x, false) and x =~ /:/ then
            parse_ColonSepID(x)
          elsif x =~ /\A\s*([A-Z][A-Z0-9_\.]+)\s*\z/ then
            @list_ids << [ $1 ]
          end
        end

      when /^\>?\s*(\S+)(?:\s+(.+))?$/
        # examples:
        # >ABC12345 this is test
        i = $1
        d = $2.to_s
        @list_ids << [ i.chomp('.') ]
        this_line = [  '', [ i ], d ]
        match_EC(d)
      else
        i = str
        d = ''
        match_EC(i)
        this_line = [ '', [ i ], d ]
      end

      @deflines << this_line
      @entry_id = i unless @entry_id
    end

# File lib/bio/db/fasta.rb, line 625
    def description
      @deflines[0].to_a[-1]
    end

# File lib/bio/db/fasta.rb, line 630
    def descriptions
      @deflines.collect do |a|
        a[-1]
      end
    end

# File lib/bio/db/fasta.rb, line 706
    def get(dbname)
      db = dbname.to_s
      r = nil
      unless r = @info[db] then
        di = @list_ids.find { |x| x[0] == db.to_s }
        if di and di.size <= 2 then
          r = di[-1]
        elsif di then
          labels = self.class::NSIDs[db]
          [ 'acc_version', 'entry_id',
            'locus', 'accession', 'number'].each do |x|
            if i = labels.index(x) then
              r = di[i+1]
              break if r
            end
          end
          r = di[1..-1].find { |x| x } unless r
        end
        @info[db] = r if r
      end
      r
    end

# File lib/bio/db/fasta.rb, line 742
    def get_all_by_type(*type_strarg)
      d = []
      @list_ids.each do |x|
        if labels = self.class::NSIDs[x[0]] then
          type_strarg.each do |y|
            if i = labels.index(y) then
              d << x[i+1] if x[i+1]
            end
          end
        end
      end
      d
    end

# File lib/bio/db/fasta.rb, line 730
    def get_by_type(type_str)
      @list_ids.each do |x|
        if labels = self.class::NSIDs[x[0]] then
          if i = labels.index(type_str) then
            return x[i+1]
          end
        end
      end
      nil
    end

# File lib/bio/db/fasta.rb, line 771
    def gi
      unless defined?(@gi) then
        @gi = get_by_type('gi')
      end
      @gi
    end

# File lib/bio/db/fasta.rb, line 638
    def id_strings
      r = []
      @list_ids.each do |a|
        if a.size >= 2 then
          r.concat a[1..-1].find_all { |x| x }
        else
          if a[0].to_s.size > 0 and a[0] =~ /\A[A-Za-z0-9\.\-\_]+\z/
            r << a[0]
          end
        end
      end
      r.concat( words(true, []).find_all do |x|
                 x =~ /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/ or
                   x =~ /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/
               end)
      r
    end

# File lib/bio/db/fasta.rb, line 760
    def locus
      unless defined?(@locus)
        @locus = get_by_type('locus')
      end
      @locus
    end

# File lib/bio/db/fasta.rb, line 811
    def method_missing(name, *args)
      # raise ArgumentError,
      # "wrong # of arguments(#{args.size} for 1)" if args.size >= 2
      r = get(name, *args)
      if !r and !(self.class::NSIDs[name.to_s]) then
        raise "NameError: undefined method `#{name.inspect}'"
      end
      r
    end

# File lib/bio/db/fasta.rb, line 617
    def to_s
      @deflines.collect { |a|
        s = a[0]
        (a[1..-2].collect { |x| x.join(s) }.join(s) + ' ' + a[-1]).strip
      }.join("\x01")
    end

# File lib/bio/db/fasta.rb, line 680
    def words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray,
              kwhash = self.class::KillWordsHash)
      a = descriptions.join(' ').split(/[\.\,\;\:\(\)\[\]\{\}\<\>\"\'\`\~\/\|\?\!\&\@\#\s\x00-\x1f\x7f]+/)
      a.collect! do |x|
        x.sub!(/\A[\$\*\-\+]+/, '')
        x.sub!(/[\$\*\-\=]+\z/, '')
        if x.size <= 1 then
          nil
        elsif kwhash[x.downcase] then
          nil
        else
          if kill_regexp.find { |expr| expr =~ x } then
            nil
          else
            x
          end
        end
      end
      a.compact!
      a.collect! { |x| x.downcase } unless case_sensitive
      a.sort!
      a.uniq!
      a
    end