[BioRuby-cvs] bioruby/lib/bio/shell/plugin codon.rb,1.6,1.7

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv9794/bio/shell/plugin

Modified Files:
	codon.rb 
Log Message:
* codon_usage_table command is integrated to codontable method


Index: codon.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** codon.rb	27 Nov 2005 15:01:17 -0000	1.6
--- codon.rb	28 Nov 2005 07:12:03 -0000	1.7
***************
*** 56,65 ****
      }
  
!     def initialize(number, color = true, cuhash = nil)
        @aacode = Bio::AminoAcid.names
        @table  = Bio::CodonTable[number]
        @number = number
        @cuhash = cuhash
!       if color
          generate_colored_text
        else
--- 56,65 ----
      }
  
!     def initialize(number, cuhash = nil)
        @aacode = Bio::AminoAcid.names
        @table  = Bio::CodonTable[number]
        @number = number
        @cuhash = cuhash
!       if Bio::Shell.config[:color]
          generate_colored_text
        else
***************
*** 186,197 ****
    private
  
!   def codon_usage_table(num = 1, codon_usage = nil)
!     ColoredCodonTable.new(num, Bio::Shell.config(:color), codon_usage)
!   end    
! 
!   def codontable(num = 1)
!     cct = codon_usage_table(num)
!     display cct.output
!     return cct.table
    end
  
--- 186,193 ----
    private
  
!   def codontable(num = 1, codon_usage = nil)
!     cct = ColoredCodonTable.new(num, codon_usage)
!     display cct.output unless codon_usage
!     return cct
    end