[BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb, 1.12, 1.13 mafft.rb, 1.12, 1.13 sim4.rb, 1.7, 1.8

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv14019/lib/bio/appl

Modified Files:
	clustalw.rb mafft.rb sim4.rb 
Log Message:
forggoten to change @option into @options


Index: sim4.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** sim4.rb	14 Dec 2006 14:54:50 -0000	1.7
--- sim4.rb	14 Dec 2006 15:56:22 -0000	1.8
***************
*** 108,112 ****
      # If <tt>filename2</tt> is not specified, using <tt>self.database</tt>.
      def exec_local(filename1, filename2 = nil)
!       @command = [ @program, filename1, (filename2 or @database), *@option ]
        @output = nil
        @report = nil
--- 108,112 ----
      # If <tt>filename2</tt> is not specified, using <tt>self.database</tt>.
      def exec_local(filename1, filename2 = nil)
!       @command = [ @program, filename1, (filename2 or @database), *@options ]
        @output = nil
        @report = nil

Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** clustalw.rb	14 Dec 2006 14:54:50 -0000	1.12
--- clustalw.rb	14 Dec 2006 15:56:22 -0000	1.13
***************
*** 83,87 ****
          query_align(seqs)
        else
!         exec_local(@option)
        end
      end
--- 83,87 ----
          query_align(seqs)
        else
!         exec_local(@options)
        end
      end
***************
*** 135,139 ****
        ]
        opt << "-type=#{seqtype}" if seqtype
!       opt.concat(@option)
        exec_local(opt)
        tf_out.open
--- 135,139 ----
        ]
        opt << "-type=#{seqtype}" if seqtype
!       opt.concat(@options)
        exec_local(opt)
        tf_out.open

Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** mafft.rb	14 Dec 2006 14:54:50 -0000	1.12
--- mafft.rb	14 Dec 2006 15:56:22 -0000	1.13
***************
*** 159,163 ****
          query_align(seqs)
        else
!         exec_local(@option)
        end
      end
--- 159,163 ----
          query_align(seqs)
        else
!         exec_local(@options)
        end
      end
***************
*** 188,192 ****
      # Performs alignment of sequences in the file named +fn+.
      def query_by_filename(fn, seqtype = nil)
!       opt = @option + [ fn ]
        exec_local(opt)
        @report = Report.new(@output, seqtype)
--- 188,192 ----
      # Performs alignment of sequences in the file named +fn+.
      def query_by_filename(fn, seqtype = nil)
!       opt = @options + [ fn ]
        exec_local(opt)
        @report = Report.new(@output, seqtype)