[BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb, 1.16, 1.17 mafft.rb, 1.14, 1.15

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv14222

Modified Files:
	clustalw.rb mafft.rb 
Log Message:
Changed to use output_fasta instead of to_fasta and options are changed.
A mistake is fixed in clustalw.rb


Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** clustalw.rb	14 Dec 2006 16:05:59 -0000	1.16
--- clustalw.rb	14 Dec 2006 16:08:46 -0000	1.17
***************
*** 102,106 ****
          break if seqtype
        end
!       query_string(seqs.output_fasta(70, :avoid_same_name => true), seqtype)
      end
  
--- 102,107 ----
          break if seqtype
        end
!       query_string(seqs.output_fasta(:width => 70,
!                                      :avoid_same_name => true), seqtype)
      end
  
***************
*** 170,174 ****
          io.close_write
          @log = io.read
-         t.join
        end
        @log
--- 171,174 ----

Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** mafft.rb	14 Dec 2006 15:59:21 -0000	1.14
--- mafft.rb	14 Dec 2006 16:08:46 -0000	1.15
***************
*** 169,173 ****
          seqs = Bio::Alignment.new(seqs, *arg)
        end
!       query_string(seqs.to_fasta(70))
      end
  
--- 169,173 ----
          seqs = Bio::Alignment.new(seqs, *arg)
        end
!       query_string(seqs.output_fasta(:width => 70))
      end