[BioRuby-cvs] bioruby/lib/bio/appl/clustalw report.rb,1.10,1.11

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/clustalw
In directory dev.open-bio.org:/tmp/cvs-serv13804/lib/bio/appl/clustalw

Modified Files:
	report.rb 
Log Message:
Bio::(ClustalW|MAFFT)::Report#algin is deprecated.
Instead, please use #alignment method.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw/report.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** report.rb	30 Apr 2006 05:50:19 -0000	1.10
--- report.rb	14 Dec 2006 15:22:05 -0000	1.11
***************
*** 82,95 ****
        # Gets an multiple alignment.
        # Returns a Bio::Alignment object.
!       def align
          do_parse() unless @align
          @align
        end
!       alias alignment align
  
        # Gets an fasta-format string of the sequences.
        # Returns a string.
        def to_fasta(*arg)
!         align.to_fasta(*arg)
        end
  
--- 82,103 ----
        # Gets an multiple alignment.
        # Returns a Bio::Alignment object.
!       def alignment
          do_parse() unless @align
          @align
        end
! 
!       # This will be deprecated. Instead, please use alignment.
!       #
!       # Gets an multiple alignment.
!       # Returns a Bio::Alignment object.
!       def align
!         warn "align method will be deprecated. Please use \'alignment\'."
!         alignment
!       end
  
        # Gets an fasta-format string of the sequences.
        # Returns a string.
        def to_fasta(*arg)
!         alignment.to_fasta(*arg)
        end
  
***************
*** 97,101 ****
        # Returns an array of Bio::FastaFormat objects.
        def to_a
!         align.to_fastaformat_array
        end
  
--- 105,109 ----
        # Returns an array of Bio::FastaFormat objects.
        def to_a
!         alignment.to_fastaformat_array
        end