[BioRuby-cvs] bioruby/lib/bio/io/flatfile indexer.rb,1.22,1.23

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/io/flatfile
In directory pub.open-bio.org:/tmp/cvs-serv32755/lib/bio/io/flatfile

Modified Files:
	indexer.rb 
Log Message:
changes were made due to the Bio::FlatFile internal change


Index: indexer.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/indexer.rb,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** indexer.rb	29 Jan 2006 06:54:14 -0000	1.22
--- indexer.rb	22 Feb 2006 08:41:03 -0000	1.23
***************
*** 1,20 ****
  # 
! # bio/io/flatfile/indexer.rb - OBDA flatfile indexer
! # 
! #   Copyright (C) 2002 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp> 
! # 
! #  This library is free software; you can redistribute it and/or 
! #  modify it under the terms of the GNU Lesser General Public 
! #  License as published by the Free Software Foundation; either 
! #  version 2 of the License, or (at your option) any later version. 
! # 
! #  This library is distributed in the hope that it will be useful, 
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of 
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU 
! #  Lesser General Public License for more details. 
  # 
! #  You should have received a copy of the GNU Lesser General Public 
! #  License along with this library; if not, write to the Free Software 
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA 
  # 
  #  $Id$ 
--- 1,7 ----
  # 
! # = bio/io/flatfile/indexer.rb - OBDA flatfile indexer
  # 
! # Copyright:: Copyright (C) 2002 GOTO Naohisa <ng at bioruby.org> 
! # License::   Ruby's
  # 
  #  $Id$ 
***************
*** 133,140 ****
  
            def each
-             pos = @flatfile.pos
              @flatfile.each do |x|
                @entry = x
!               len = @flatfile.entry_raw.length
                begin
                  yield pos, len
--- 120,127 ----
  
            def each
              @flatfile.each do |x|
                @entry = x
!               pos = @flatfile.entry_start_pos
!               len = @flatfile.entry_ended_pos - @flatfile.entry_start_pos
                begin
                  yield pos, len
***************
*** 153,157 ****
                  end
                end #rescue
-               pos = @flatfile.pos
              end
            end
--- 140,143 ----
***************
*** 206,218 ****
              end
              self.add_secondary_namespaces(*sec_names)
-           end
-           def open_flatfile(fileid, file)
-             super
-             @flatfile.pos = 0
-             begin
-               pos = @flatfile.pos
-               line = @flatfile.gets
-             end until (!line or line =~ /^LOCUS /)
-             @flatfile.pos = pos
            end
          end #class GenBankParser
--- 192,195 ----