# File lib/bio/shell/plugin/codon.rb, line 23
23:     def initialize(number, cuhash = nil)
24:       @aacode = Bio::AminoAcid.names
25:       @table  = Bio::CodonTable[number]
26:       @number = number
27:       @cuhash = cuhash
28:       setup_colors
29:       if Bio::Shell.config[:color]
30:         generate_colored_text
31:       else
32:         generate_mono_text
33:       end
34:     end

     # File lib/bio/shell/plugin/codon.rb, line 76
 76:     def generate_colored_text
 77:       @table.each do |codon, aa|
 78:         property, = @@properties.detect {|key, list| list.include?(aa)}
 79: 
 80:         if aa == '*'
 81:           if @cuhash
 82:             color_code = "#{@colors[:stop]}STOP"
 83:             color_aa = "#{@colors[:stop]}#{aa}"
 84:           else
 85:             color_code = "#{@colors[:stop]}STP"
 86:             case codon
 87:             when 'tga'
 88:               color_aa = "#{@colors[:text]}U"
 89:             when 'tag'
 90:               color_aa = "#{@colors[:text]}O"
 91:             else
 92:               color_aa = "#{@colors[:text]}*"
 93:             end
 94:           end
 95:         else
 96:           color_code = "#{@colors[property]}#{@aacode[aa]}"
 97:           if @table.start_codon?(codon)
 98:             if @cuhash
 99:               color_aa = "#{@colors[:aa]}#{aa}"
100:             else
101:               color_aa = "#{@colors[:start]}#{aa}"
102:             end
103:           else
104:             if @cuhash
105:               color_aa = "#{@colors[property]}#{aa}"
106:             else
107:               color_aa = "#{@colors[:aa]}#{aa}"
108:             end
109:           end
110:         end
111: 
112:         if @cuhash
113:           percent = @cuhash[codon].to_s.rjust(6)
114:           eval("@#{codon} = '#{color_aa}#{@colors[:text]}#{percent}'")
115:         else
116:           eval("@#{codon} = ' #{color_code} #{color_aa}#{@colors[:text]} '")
117:         end
118:       end
119: 
120:       @hydrophilic = [
121:         "#{@colors[:basic]}basic#{@colors[:text]},",
122:         "#{@colors[:polar]}polar#{@colors[:text]},",
123:         "#{@colors[:acidic]}acidic#{@colors[:text]}"
124:       ].join(" ")
125:       @hydrophobic = "#{@colors[:nonpolar]}nonpolar"
126:     end

    # File lib/bio/shell/plugin/codon.rb, line 52
52:     def generate_mono_text
53:       @table.each do |codon, aa|
54:         if aa == '*'
55:           code = 'STOP'
56:           aa = '' unless @cuhash
57:         else
58:           code = @aacode[aa]
59:         end
60:         if @cuhash
61:           percent = @cuhash[codon].to_s.rjust(6)
62:           eval("@#{codon} = '#{aa}#{percent}'")
63:         else
64:           eval("@#{codon} = ' #{code} #{aa} '")
65:         end
66:       end
67: 
68:       @hydrophilic = [
69:         @@properties[:basic].join(" "), "(basic),",
70:         @@properties[:polar].join(" "), "(polar),",
71:         @@properties[:acidic].join(" "), "(acidic)",
72:       ].join(" ")
73:       @hydrophobic = @@properties[:nonpolar].join(" ") + " (nonpolar)"
74:     end

     # File lib/bio/shell/plugin/codon.rb, line 128
128:     def output
129:       header = "#\n# = Codon table \#{@number} : \#{@table.definition}\n#\n#   hydrophilic: \#{@hydrophilic}\n#   hydrophobic: \#{@hydrophobic}\n"
130:       table = "#\n# *---------------------------------------------*\n# |       |              2nd              |     |\n# |  1st  |-------------------------------| 3rd |\n# |       |  U    |  C    |  A    |  G    |     |\n# |-------+-------+-------+-------+-------+-----|\n# | U   U |\#{@ttt}|\#{@tct}|\#{@tat}|\#{@tgt}|  u  |\n# | U   U |\#{@ttc}|\#{@tcc}|\#{@tac}|\#{@tgc}|  c  |\n# | U   U |\#{@tta}|\#{@tca}|\#{@taa}|\#{@tga}|  a  |\n# |  UUU  |\#{@ttg}|\#{@tcg}|\#{@tag}|\#{@tgg}|  g  |\n# |-------+-------+-------+-------+-------+-----|\n# |  CCCC |\#{@ctt}|\#{@cct}|\#{@cat}|\#{@cgt}|  u  |\n# | C     |\#{@ctc}|\#{@ccc}|\#{@cac}|\#{@cgc}|  c  |\n# | C     |\#{@cta}|\#{@cca}|\#{@caa}|\#{@cga}|  a  |\n# |  CCCC |\#{@ctg}|\#{@ccg}|\#{@cag}|\#{@cgg}|  g  |\n# |-------+-------+-------+-------+-------+-----|\n# |   A   |\#{@att}|\#{@act}|\#{@aat}|\#{@agt}|  u  |\n# |  A A  |\#{@atc}|\#{@acc}|\#{@aac}|\#{@agc}|  c  |\n# | AAAAA |\#{@ata}|\#{@aca}|\#{@aaa}|\#{@aga}|  a  |\n# | A   A |\#{@atg}|\#{@acg}|\#{@aag}|\#{@agg}|  g  |\n# |-------+-------+-------+-------+-------+-----|\n# |  GGGG |\#{@gtt}|\#{@gct}|\#{@gat}|\#{@ggt}|  u  |\n# | G     |\#{@gtc}|\#{@gcc}|\#{@gac}|\#{@ggc}|  c  |\n# | G GGG |\#{@gta}|\#{@gca}|\#{@gaa}|\#{@gga}|  a  |\n# |  GG G |\#{@gtg}|\#{@gcg}|\#{@gag}|\#{@ggg}|  g  |\n# *---------------------------------------------*\n#\n"
131:       if @cuhash
132:         text = table
133:       else
134:         text = header + table
135:       end
136:       if Bio::Shell.config[:color]
137:         text.gsub(/^\s+#/, @colors[:text])
138:       else
139:         text.gsub(/^\s+#/, '')
140:       end
141:     end

    # File lib/bio/shell/plugin/codon.rb, line 37
37:     def setup_colors
38:       c = Bio::Shell.colors
39: 
40:       @colors = {
41:         :text           => c[:none],
42:         :aa             => c[:green],
43:         :start          => c[:red],
44:         :stop           => c[:red],
45:         :basic          => c[:cyan],
46:         :polar          => c[:blue],
47:         :acidic         => c[:magenta],
48:         :nonpolar       => c[:yellow],
49:       }
50:     end