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

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv5141/lib/bio/appl

Modified Files:
	mafft.rb 
Log Message:
Incompatible change: Bio::MAFFT#output is changed to return
a string of multi-fasta formmatted text. To get an array of
Bio::FastaFormat objects (as of 1.0 or before), please use
report.data instead.


Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** mafft.rb	14 Dec 2006 16:08:46 -0000	1.15
--- mafft.rb	2 Apr 2007 12:55:26 -0000	1.16
***************
*** 143,149 ****
  
      # Shows latest raw alignment result.
!     # Since a result of MAFFT is simply a multiple-fasta format,
!     # it returns an array of Bio::FastaFormat instances
!     # instead of raw string.
      attr_reader :output
  
--- 143,150 ----
  
      # Shows latest raw alignment result.
!     # Return a string. (Changed in bioruby-1.1.0).
!     # Compatibility note:
!     # If you want an array of Bio::FastaFormat instances,
!     # you should use report.data instead.
      attr_reader :output
  
***************
*** 202,207 ****
        Bio::Command.call_command(@command) do |io|
          io.close_write
!         ff = Bio::FlatFile.new(Bio::FastaFormat, io)
!         @output = ff.to_a
        end
      end
--- 203,207 ----
        Bio::Command.call_command(@command) do |io|
          io.close_write
!         @output = io.read
        end
      end