lib/bio/shell/plugin/codon.rb in bio-1.0.0 vs lib/bio/shell/plugin/codon.rb in bio-1.1.0

@@ -1,13 +1,13 @@
 #
 # = bio/shell/plugin/codon.rb - plugin for the codon table
 #
 # Copyright::   Copyright (C) 2005
 #               Toshiaki Katayama <[e-mail]>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: codon.rb,v 1.13 2006/02/09 20:48:53 k Exp $
+# $Id: codon.rb,v 1.16 2007/04/05 23:35:41 trevor Exp $
 #
 
 module Bio::Shell
 
   class ColoredCodonTable
@@ -33,28 +33,28 @@
       end
     end
     attr_reader :table
 
     def setup_colors
-      esc_seq = Bio::Shell.esc_seq
+      c = Bio::Shell.colors
 
       @colors = {
-        :text		=> esc_seq[:none],
-        :aa		=> esc_seq[:green],
-        :start		=> esc_seq[:red],
-        :stop		=> esc_seq[:red],
-        :basic		=> esc_seq[:cyan],
-        :polar		=> esc_seq[:blue],
-        :acidic		=> esc_seq[:magenta],
-        :nonpolar	=> esc_seq[:yellow],
+        :text		=> c[:none],
+        :aa		=> c[:green],
+        :start		=> c[:red],
+        :stop		=> c[:red],
+        :basic		=> c[:cyan],
+        :polar		=> c[:blue],
+        :acidic		=> c[:magenta],
+        :nonpolar	=> c[:yellow],
       }
     end
 
     def generate_mono_text
       @table.each do |codon, aa|
         if aa == '*'
-          code = "STOP"
+          code = 'STOP'
           aa = '' unless @cuhash
         else
           code = @aacode[aa]
         end
         if @cuhash
@@ -76,14 +76,22 @@
     def generate_colored_text
       @table.each do |codon, aa|
         property, = @@properties.detect {|key, list| list.include?(aa)}
 
         if aa == '*'
-          color_code = "#{@colors[:stop]}STOP"
           if @cuhash
+            color_code = "#{@colors[:stop]}STOP"
             color_aa = "#{@colors[:stop]}#{aa}"
           else
-            color_aa = ''
+            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
           color_code = "#{@colors[property]}#{@aacode[aa]}"
           if @table.start_codon?(codon)
             if @cuhash