[BioRuby-cvs] bioruby/lib/bio alignment.rb,1.14,1.15

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv22964

Modified Files:
	alignment.rb 
Log Message:
changed Bio::Sequence to Bio::Sequence::NA or Bio::Sequence::AA
due to the change of Bio::Sequence.


Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** alignment.rb	2 Dec 2005 12:01:28 -0000	1.14
--- alignment.rb	24 Jan 2006 14:16:59 -0000	1.15
***************
*** 818,827 ****
        alias slice alignment_slice
  
!       # For each sequence, the 'subseq' method (Bio::Seqeunce#subseq is
        # expected) is executed, and returns a new alignment as
        # a Bio::Alignment::SequenceArray object.
        #
        # All sequences in the alignment are expected to be kind of
!       # Bio::Sequence objects.
        #
        # Unlike alignment_window method, the result alignment
--- 818,827 ----
        alias slice alignment_slice
  
!       # For each sequence, the 'subseq' method (Bio::Seqeunce::Common#subseq is
        # expected) is executed, and returns a new alignment as
        # a Bio::Alignment::SequenceArray object.
        #
        # All sequences in the alignment are expected to be kind of
!       # Bio::Sequence::NA or Bio::Sequence::AA objects.
        #
        # Unlike alignment_window method, the result alignment
***************
*** 1178,1182 ****
        def extract_seq(obj)
          seq = nil
!         if obj.is_a?(Bio::Sequence) then
            seq = obj
          else
--- 1178,1182 ----
        def extract_seq(obj)
          seq = nil
!         if obj.is_a?(Bio::Sequence::NA) or obj.is_a?(Bio::Sequence::AA) then
            seq = obj
          else
***************
*** 1603,1607 ****
        def add_seq(seq, key = nil)
          #(BioPerl) AlignI::add_seq like method
!         unless seq.is_a?(Bio::Sequence) then
            s =   extract_seq(seq)
            key = extract_key(seq) unless key
--- 1603,1607 ----
        def add_seq(seq, key = nil)
          #(BioPerl) AlignI::add_seq like method
!         unless seq.is_a?(Bio::Sequence::NA) or seq.is_a?(Bio::Sequence::AA)
            s =   extract_seq(seq)
            key = extract_key(seq) unless key