[BioRuby-cvs] bioruby/lib/bio/db fasta.rb,1.22,1.23

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv14493/lib/bio/db

Modified Files:
	fasta.rb 
Log Message:
* changed Bio::Sequence.new to Bio::Sequence::Generic.new (temporary change)
* changed Lisence to Ruby's


Index: fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fasta.rb,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** fasta.rb	28 Jan 2006 10:48:59 -0000	1.22
--- fasta.rb	9 Feb 2006 03:28:48 -0000	1.23
***************
*** 5,9 ****
  #              GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>,
  #              KATAYAMA Toshiaki <k at bioruby.org>
! # Lisence::    LGPL
  #
  # $Id$
--- 5,9 ----
  #              GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>,
  #              KATAYAMA Toshiaki <k at bioruby.org>
! # Lisence::    Ruby's
  #
  # $Id$
***************
*** 63,84 ****
  #   http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
  #
- #--
- #
- #  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
- #
- #++
- #
  
  require 'bio/db'
--- 63,66 ----
***************
*** 209,213 ****
        unless defined?(@seq)
          unless /\A\s*^\#/ =~ @data then
!           @seq = Sequence.new(@data.tr(" \t\r\n0-9", '')) # lazy clean up
          else
            a = @data.split(/(^\#.*$)/)
--- 191,195 ----
        unless defined?(@seq)
          unless /\A\s*^\#/ =~ @data then
!           @seq = Sequence::Generic.new(@data.tr(" \t\r\n0-9", '')) # lazy clean up
          else
            a = @data.split(/(^\#.*$)/)
***************
*** 225,229 ****
            end
            @comment = cmnt
!           @seq = Bio::Sequence.new(s.join(''))
          end
        end
--- 207,211 ----
            end
            @comment = cmnt
!           @seq = Bio::Sequence::Generic.new(s.join(''))
          end
        end