[BioRuby-cvs] bioruby/lib/bio/shell/plugin codon.rb,1.13,1.14

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory dev.open-bio.org:/tmp/cvs-serv496/lib/bio/shell/plugin

Modified Files:
	codon.rb 
Log Message:
* Pyrrolysine and Selenocysteine are supported in the color mode


Index: codon.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** codon.rb	9 Feb 2006 20:48:53 -0000	1.13
--- codon.rb	19 Sep 2006 06:17:19 -0000	1.14
***************
*** 53,57 ****
        @table.each do |codon, aa|
          if aa == '*'
!           code = "STOP"
            aa = '' unless @cuhash
          else
--- 53,57 ----
        @table.each do |codon, aa|
          if aa == '*'
!           code = 'STOP'
            aa = '' unless @cuhash
          else
***************
*** 79,87 ****
  
          if aa == '*'
-           color_code = "#{@colors[:stop]}STOP"
            if @cuhash
              color_aa = "#{@colors[:stop]}#{aa}"
            else
!             color_aa = ''
            end
          else
--- 79,95 ----
  
          if aa == '*'
            if @cuhash
+             color_code = "#{@colors[:stop]}STOP"
              color_aa = "#{@colors[:stop]}#{aa}"
            else
!             color_code = "#{@colors[:stop]}STP"
!             case codon
!             when 'tga'
!               color_aa = "#{@colors[:text]}U"
!             when 'tag'
!               color_aa = "#{@colors[:text]}O"
!             else
!               color_aa = "#{@colors[:text]}*"
!             end
            end
          else