class Bio::FlatFileIndex::Flat_1::FlatMappingFile

    # File lib/bio/io/flatfile/index.rb
923 def self.external_merge_proc(sort_program =  [ '/usr/bin/env', 
924                                                'LC_ALL=C',
925                                                '/usr/bin/sort' ])
926   Proc.new do |out, in1, *files|
927     # files (and in1) must be sorted
928     cmd = sort_program + [ '-m', '-o', out, in1, *files ]
929     system(*cmd)
930   end
931 end

    # File lib/bio/io/flatfile/index.rb
900 def self.external_merge_sort_proc(sort_program = [ '/usr/bin/env', 
901                                                    'LC_ALL=C',
902                                                    '/usr/bin/sort' ])
903   Proc.new do |out, in1, *files|
904     # (in1 may be sorted)
905     tf_all = []
906     tfn_all = []
907     files.each do |fn|
908       tf = Tempfile.open('sort')
909       tf.close(false)
910       cmd = sort_program + [ '-o', tf.path, fn ]
911       system(*cmd)
912       tf_all << tf
913       tfn_all << tf.path
914     end
915     cmd_fin = sort_program + [ '-m', '-o', out, in1, *tfn_all ]
916     system(*cmd_fin)
917     tf_all.each do |tf|
918       tf.close(true)
919     end
920   end
921 end

    # File lib/bio/io/flatfile/index.rb
891 def self.external_sort_proc(sort_program = [ '/usr/bin/env', 
892                                              'LC_ALL=C',
893                                              '/usr/bin/sort' ])
894   Proc.new do |out, in1, *files|
895     cmd = sort_program + [ '-o', out, in1, *files ]
896     system(*cmd)
897   end
898 end

    # File lib/bio/io/flatfile/index.rb
933 def self.internal_sort_proc
934   Proc.new do |out, in1, *files|
935     a = IO.readlines(in1)
936     files.each do |fn|
937       IO.foreach(fn) do |x|
938         a << x
939       end
940     end
941     a.sort!
942     of = File.open(out, 'w')
943     a.each { |x| of << x }
944     of.close
945   end
946 end

    # File lib/bio/io/flatfile/index.rb
734 def initialize(filename, mode = 'rb')
735   @filename = filename
736   @mode = mode
737   @file = nil
738   #@file = File.open(filename, mode)
739   @record_size = nil
740   @records = nil
741 end

    # File lib/bio/io/flatfile/index.rb
730 def self.open(*arg)
731   self.new(*arg)
732 end

    # File lib/bio/io/flatfile/index.rb
806 def add_record(str)
807   n = records
808   rs = record_size
809   @file.seek(0, IO::SEEK_END)
810   write_record(str)
811   @records += 1
812 end

    # File lib/bio/io/flatfile/index.rb
755 def close
756   if @file then
757     DEBUG.print "FlatMappingFile: close #{@filename}\n"
758     @file.close
759     @file = nil
760   end
761   nil
762 end

    # File lib/bio/io/flatfile/index.rb
841 def each
842   n = records
843   seek(0)
844   (0...n).each do |i|
845     yield Record.new(get_record(i))
846   end
847   self
848 end

    # File lib/bio/io/flatfile/index.rb
850 def export_tsv(stream)
851   self.each do |x|
852     stream << "#{x.to_s}\n"
853   end
854   stream
855 end

    # File lib/bio/io/flatfile/index.rb
776 def get_record(i)
777   rs = record_size
778   seek(i)
779   str = @file.read(rs)
780   #DEBUG.print "get_record(#{i})=#{str.inspect}\n"
781   str
782 end

    # File lib/bio/io/flatfile/index.rb
948 def import_tsv_files(flag_primary, mode, sort_proc, *files)
949   require 'tempfile'
950 
951   tmpfile1 = Tempfile.open('flat')
952   self.export_tsv(tmpfile1) unless mode == :new
953   tmpfile1.close(false)
954 
955   tmpfile0 = Tempfile.open('sorted')
956   tmpfile0.close(false)
957 
958   sort_proc.call(tmpfile0.path, tmpfile1.path, *files)
959 
960   tmpmap = self.class.new(self.filename + ".#{$$}.tmp~", 'wb+')
961   tmpmap.init_with_sorted_tsv_file(tmpfile0.path, flag_primary)
962   tmpmap.close
963   self.close
964 
965   begin
966     File.rename(self.filename, self.filename + ".#{$$}.bak~")
967   rescue Errno::ENOENT
968   end
969   File.rename(tmpmap.filename, self.filename)
970   begin
971     File.delete(self.filename + ".#{$$}.bak~")
972   rescue Errno::ENOENT
973   end
974 
975   tmpfile0.close(true)
976   tmpfile1.close(true)
977   self
978 end

    # File lib/bio/io/flatfile/index.rb
827 def init(rs)
828   unless 0 < rs and rs < 10 ** @@recsize_width then
829     raise 'record size out of range'
830   end
831   open
832   @record_size = rs
833   str = sprintf("%0*d", @@recsize_width, rs)
834   @file.truncate(0)
835   @file.seek(0, IO::SEEK_SET)
836   @file.write(str)
837   @records = 0
838 end

    # File lib/bio/io/flatfile/index.rb
857 def init_with_sorted_tsv_file(filename, flag_primary = false)
858   rec_size = 1
859   f = File.open(filename)
860   f.each do |y|
861     rec_size = y.chomp.length if rec_size < y.chomp.length
862   end
863   self.init(rec_size)
864 
865   prev = nil
866   f.rewind
867   if flag_primary then
868     f.each do |y|
869       x = Record.new(y.chomp, rec_size)
870       if prev then
871         if x.key == prev.key
872           DEBUG.print "Warining: overwrote unique id #{x.key.inspect}\n"
873         else
874           self.add_record(prev.to_s)
875         end
876       end
877       prev = x
878     end
879     self.add_record(prev.to_s) if prev
880   else
881     f.each do |y|
882       x = Record.new(y.chomp, rec_size)
883       self.add_record(x.to_s) if x != prev
884       prev = x
885     end
886   end
887   f.close
888   self
889 end

    # File lib/bio/io/flatfile/index.rb
745 def open
746   unless @file then
747     DEBUG.print "FlatMappingFile: open #{@filename}\n"
748     @file = File.open(@filename, @mode)
749     true
750   else
751     nil
752   end
753 end

    # File lib/bio/io/flatfile/index.rb
814 def put_record(i, str)
815   n = records
816   rs = record_size
817   if i >= n then
818     @file.seek(0, IO::SEEK_END)
819     @file.write(sprintf("%-*s", rs, '') * (i - n))
820     @records = i + 1
821   else
822     seek(i)
823   end
824   write_record(str)
825 end

    # File lib/bio/io/flatfile/index.rb
764 def record_size
765   unless @record_size then
766     open
767     @file.seek(0, IO::SEEK_SET)
768     s = @file.read(@@recsize_width)
769     raise 'strange record size' unless s =~ @@recsize_regex
770     @record_size = s.to_i
771     DEBUG.print "FlatMappingFile: record_size: #{@record_size}\n"
772   end
773   @record_size
774 end

    # File lib/bio/io/flatfile/index.rb
789 def records
790   unless @records then
791     rs = record_size
792     @records = (@file.stat.size - @@recsize_width) / rs
793     DEBUG.print "FlatMappingFile: records: #{@records}\n"
794   end
795   @records
796 end

     # File lib/bio/io/flatfile/index.rb
 982 def search(key)
 983   n = records
 984   return [] if n <= 0
 985   i = n / 2
 986   i_prev = nil
 987   DEBUG.print "binary search starts...\n"
 988   begin
 989     rec = Record.new(get_record(i))
 990     i_prev = i
 991     if key < rec.key then
 992       n = i
 993       i = i / 2
 994     elsif key > rec.key then
 995       i = (i + n) / 2
 996     else # key == rec.key
 997       result = [ rec.val ]
 998       j = i - 1
 999       while j >= 0 and
1000           (rec = Record.new(get_record(j))).key == key
1001         result << rec.val
1002         j = j - 1
1003       end
1004       result.reverse!
1005       j = i + 1
1006       while j < n and
1007           (rec = Record.new(get_record(j))).key == key
1008         result << rec.val
1009         j = j + 1
1010       end
1011       DEBUG.print "#{result.size} hits found!!\n"
1012       return result
1013     end
1014   end until i_prev == i
1015   DEBUG.print "no hits found\n"
1016   #nil
1017   []
1018 end

    # File lib/bio/io/flatfile/index.rb
784 def seek(i)
785   rs = record_size
786   @file.seek(@@recsize_width + rs * i)
787 end

    # File lib/bio/io/flatfile/index.rb
800 def write_record(str)
801   rs = record_size
802   rec = sprintf("%-*s", rs, str)[0..rs]
803   @file.write(rec)
804 end