[BioRuby-cvs] bioruby/lib/bio/appl/clustalw report.rb,1.12,1.13

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/clustalw
In directory dev.open-bio.org:/tmp/cvs-serv28056/lib/bio/appl/clustalw

Modified Files:
	report.rb 
Log Message:
changed messages and documents


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw/report.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** report.rb	5 Apr 2007 23:35:39 -0000	1.12
--- report.rb	18 Jul 2007 08:47:39 -0000	1.13
***************
*** 92,105 ****
        # 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
  
        # Gets an array of the sequences.
        # Returns an array of Bio::FastaFormat objects.
--- 92,111 ----
        # Returns a Bio::Alignment object.
        def align
!         warn "Bio::ClustalW#align will be deprecated. Please use \'alignment\'."
          alignment
        end
  
+       # This will be deprecated. Instead, please use alignment.output_fasta.
+       #
        # Gets an fasta-format string of the sequences.
        # Returns a string.
        def to_fasta(*arg)
!         warn "Bio::ClustalW::report#to_fasta is deprecated. Please use \'alignment.output_fasta\'"
!         alignment.output_fasta(*arg)
        end
  
+       # Compatibility note: Behavior of the method will be changed
+       # in the future.
+       #
        # Gets an array of the sequences.
        # Returns an array of Bio::FastaFormat objects.