[BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb, 1.13, 1.14 mafft.rb, 1.13, 1.14 sim4.rb, 1.8, 1.9

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv14091/lib/bio/appl

Modified Files:
	clustalw.rb mafft.rb sim4.rb 
Log Message:
forgotten to change *@command to @command.


Index: sim4.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** sim4.rb	14 Dec 2006 15:56:22 -0000	1.8
--- sim4.rb	14 Dec 2006 15:59:21 -0000	1.9
***************
*** 111,115 ****
        @output = nil
        @report = nil
!       Bio::Command.call_command(*@command) do |io|
          io.close_write
          @output = io.read
--- 111,115 ----
        @output = nil
        @report = nil
!       Bio::Command.call_command(@command) do |io|
          io.close_write
          @output = io.read

Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** clustalw.rb	14 Dec 2006 15:56:22 -0000	1.13
--- clustalw.rb	14 Dec 2006 15:59:21 -0000	1.14
***************
*** 167,171 ****
        @log = nil
  
!       Bio::Command.call_command(*@command) do |io|
          io.close_write
          @log = dout.read
--- 167,171 ----
        @log = nil
  
!       Bio::Command.call_command(@command) do |io|
          io.close_write
          @log = dout.read

Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** mafft.rb	14 Dec 2006 15:56:22 -0000	1.13
--- mafft.rb	14 Dec 2006 15:59:21 -0000	1.14
***************
*** 200,204 ****
        #STDERR.print "DEBUG: ", @command.join(" "), "\n"
        @output = nil
!       Bio::Command.call_command(*@command) do |io|
          io.close_write
          ff = Bio::FlatFile.new(Bio::FastaFormat, io)
--- 200,204 ----
        #STDERR.print "DEBUG: ", @command.join(" "), "\n"
        @output = nil
!       Bio::Command.call_command(@command) do |io|
          io.close_write
          ff = Bio::FlatFile.new(Bio::FastaFormat, io)