annotate weblogolib/colorscheme.py @ 11:4b38580a8b97

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author davidmurphy
date Thu, 16 Feb 2012 21:15:10 -0500
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1
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2 # Copyright (c) 2003-2005 The Regents of the University of California.
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3 # Copyright (c) 2005 Gavin E. Crooks
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4
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5 # This software is distributed under the MIT Open Source License.
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6 # <http://www.opensource.org/licenses/mit-license.html>
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7 #
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8 # Permission is hereby granted, free of charge, to any person obtaining a
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9 # copy of this software and associated documentation files (the "Software"),
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10 # to deal in the Software without restriction, including without limitation
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11 # the rights to use, copy, modify, merge, publish, distribute, sublicense,
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12 # and/or sell copies of the Software, and to permit persons to whom the
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13 # Software is furnished to do so, subject to the following conditions:
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14 #
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15 # The above copyright notice and this permission notice shall be included
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16 # in all copies or substantial portions of the Software.
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17 #
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18 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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19 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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20 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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21 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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22 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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23 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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24 # THE SOFTWARE.
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25
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davidmurphy
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26 """ Popular color codings for nucleic and amino acids.
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27
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28 Classes:
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29 ColorScheme -- A color scheme
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30 ColorGroup
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31
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32
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33 Generic
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34 monochrome
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35
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36 Nucleotides
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37 nucleotide
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38 base pairing
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39
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40 Amino Acid
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41 hydrophobicity
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42 chemistry
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43 charge
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44 taylor
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45
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46 Status : Beta - Needs documentation.
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47
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48 """
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49 # Good online references include bioruby and the JalView alignment editor.
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50 # Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),
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51 # "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7
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52 # http://www.jalview.org
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53
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54 import sys
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55
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56 from corebio import seq
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57 from color import Color
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58 codon_alphabetU=['AAA', 'AAU', 'AAC', 'AAG', 'AUA', 'AUU', 'AUC', 'AUG', 'ACA', 'ACU', 'ACC', 'ACG', 'AGA', 'AGU', 'AGC', 'AGG', 'UAA', 'UAU', 'UAC', 'UAG', 'UUA', 'UUU', 'UUC', 'UUG', 'UCA', 'UCU', 'UCC', 'UCG', 'UGA', 'UGU', 'UGC', 'UGG', 'CAA', 'CAU', 'CAC', 'CAG', 'CUA', 'CUU', 'CUC', 'CUG', 'CCA', 'CCU', 'CCC', 'CCG', 'CGA', 'CGU', 'CGC', 'CGG', 'GAA', 'GAU', 'GAC', 'GAG', 'GUA', 'GUU', 'GUC', 'GUG', 'GCA', 'GCU', 'GCC', 'GCG', 'GGA', 'GGU', 'GGC', 'GGG']
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59 codon_alphabetT=['AAA', 'AAT', 'AAC', 'AAG', 'ATA', 'ATT', 'ATC', 'ATG', 'ACA', 'ACT', 'ACC', 'ACG', 'AGA', 'AGT', 'AGC', 'AGG', 'TAA', 'TAT', 'TAC', 'TAG', 'TTA', 'TTT', 'TTC', 'TTG', 'TCA', 'TCT', 'TCC', 'TCG', 'TGA', 'TGT', 'TGC', 'TGG', 'CAA', 'CAT', 'CAC', 'CAG', 'CTA', 'CTT', 'CTC', 'CTG', 'CCA', 'CCT', 'CCC', 'CCG', 'CGA', 'CGT', 'CGC', 'CGG', 'GAA', 'GAT', 'GAC', 'GAG', 'GTA', 'GTT', 'GTC', 'GTG', 'GCA', 'GCT', 'GCC', 'GCG', 'GGA', 'GGT', 'GGC', 'GGG']
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60
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61 class ColorScheme(object):
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62 """ A coloring of an alphabet.
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63
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64 title : string -- A human readable description
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65 defualt_color : Color --
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66 groups : list of color groups
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67 alphabet : string -- The set of colored symbols
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68 color -- A map between a symbol and a Coloring
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69
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70
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71 """
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72
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73 def __init__(self,
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74 groups = [],
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75 title = "",
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76 description = "",
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77 default_color = "black",
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78 alphabet = seq.generic_alphabet) :
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79 """ """
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80 self.title= title
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81 self.description = description
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82 self.default_color = Color.from_string(default_color)
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83 self.groups = groups
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84 self.alphabet = alphabet
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85 #print >> sys.stderr, groups
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86 altype="codons"
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87 #print >> sys.stderr,altype
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88 #if(alphabet==codon_alphabet):
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89 #print >> sys.stderr,"haleyulia it works"
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90
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91 color = {}
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92 #print >> sys.stderr, groups
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93 if(alphabet!=codon_alphabetT and alphabet!=codon_alphabetU):
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94 for cg in groups :
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95 #print >> sys.stderr, cg
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96 for s in cg.symbols :
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97 color[s] = cg.color
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98 #print >> sys.stderr, s
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99 #print >> sys.stderr, cg
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100 if s not in alphabet :
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101 raise KeyError("Colored symbol does not exist in alphabet.")
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102 else:
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103 for cg in groups :
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104 #print >> sys.stderr, cg
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105 color[cg.symbols] = cg.color
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106 #print >> sys.stderr, cg.symbols
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107 self._color = color
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108
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109 def color(self, symbol) :
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110 if symbol in self._color :
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111 return self._color[symbol]
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112 return self.default_color
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113
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114 class ColorGroup(object) :
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115 """Associate a group of symbols with a color"""
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116 def __init__(self, symbols, color, description=None) :
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117 self.symbols = symbols
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118 self.color = Color.from_string(color)
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119 self.description = description
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120
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121
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122
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123 monochrome = ColorScheme([]) # This list intentionally left blank
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124
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125 # From makelogo
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126 nucleotide = ColorScheme([
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127 ColorGroup("G", "orange"),
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128 ColorGroup("TU", "red"),
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129 ColorGroup("C", "blue"),
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130 ColorGroup("A", "green")
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131 ])
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132
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133 base_pairing = ColorScheme([
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134 ColorGroup("TAU", "darkorange", "Weak (2 Watson-Crick hydrogen bonds)"),
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135 ColorGroup("GC", "blue", "Strong (3 Watson-Crick hydrogen bonds)")],
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136 )
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137
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138
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139 hydrophobicity = ColorScheme([
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140 ColorGroup( "RKDENQ", "black", "hydrophobic"),
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141 ColorGroup( "SGHTAP", "green", "neutral" ),
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142 ColorGroup( "YVMCLFIW", "blue", "hydrophilic") ],
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143 alphabet = seq.unambiguous_protein_alphabet
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144 )
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145
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146 # from makelogo
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147 chemistry = ColorScheme([
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148 ColorGroup( "GSTYC", "green", "polar"),
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149 ColorGroup( "NQ", "purple", "neutral"),
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150 ColorGroup( "KRH", "blue", "basic"),
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151 ColorGroup( "DE", "red", "acidic"),
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152 ColorGroup("PAWFLIMV", "black", "hydrophobic") ],
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153 alphabet = seq.unambiguous_protein_alphabet
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154 )
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155
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156
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157 codonsU = ColorScheme([
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158 ColorGroup( 'CAT', '#00FFFF'),
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159 ColorGroup( 'CAU', '#00FFFF'),
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160 ColorGroup( 'CAC', '#00FFFF'),
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161
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162 ColorGroup( 'AAA', '#00FFFF'),
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163 ColorGroup( 'AAG', '#00FFFF'),
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164
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165 ColorGroup( 'CGT', '#00FFFF'),
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166 ColorGroup( 'CGU', '#00FFFF'),
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167 ColorGroup( 'CGC', '#00FFFF'),
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168 ColorGroup( 'CGA', '#00FFFF'),
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169 ColorGroup( 'CGG', '#00FFFF'),
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170 ColorGroup( 'AGA', '#00FFFF'),
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171 ColorGroup( 'AGG', '#00FFFF'),
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172
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173
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174 ColorGroup( 'GAT', '#FF0000'),
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175 ColorGroup( 'GAU', '#FF0000'),
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176 ColorGroup( 'GAC', '#FF0000'),
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177
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178 ColorGroup( 'GAA', '#FF0000'),
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179 ColorGroup( 'GAG', '#FF0000'),
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180
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181
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182 ColorGroup( 'TCT', '#00FF00'),
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183 ColorGroup( 'UCU', '#00FF00'),
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184 ColorGroup( 'TCC', '#00FF00'),
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185 ColorGroup( 'UCC', '#00FF00'),
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186 ColorGroup( 'TCA', '#00FF00'),
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187 ColorGroup( 'UCA', '#00FF00'),
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188 ColorGroup( 'TCG', '#00FF00'),
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189 ColorGroup( 'UCG', '#00FF00'),
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190 ColorGroup( 'AGT', '#00FF00'),
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191 ColorGroup( 'AGU', '#00FF00'),
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192 ColorGroup( 'AGC', '#00FF00'),
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193
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194 ColorGroup( 'ACT', '#00FF00'),
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195 ColorGroup( 'ACU', '#00FF00'),
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196 ColorGroup( 'ACC', '#00FF00'),
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197 ColorGroup( 'ACA', '#00FF00'),
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parents:
diff changeset
198 ColorGroup( 'ACG', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
199
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
200 ColorGroup( 'CAA', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
201 ColorGroup( 'CAG', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
202
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
203 ColorGroup( 'AAT', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
204 ColorGroup( 'AAU', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
205 ColorGroup( 'AAC', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
206
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
207
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
208 ColorGroup( 'GCT', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
209 ColorGroup( 'GCU', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
210 ColorGroup( 'GCC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
211 ColorGroup( 'GCA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
212 ColorGroup( 'GCG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
213
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
214 ColorGroup( 'GTT', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
215 ColorGroup( 'GUU', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
216 ColorGroup( 'GTC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
217 ColorGroup( 'GUC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
218 ColorGroup( 'GTA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
219 ColorGroup( 'GUA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
220 ColorGroup( 'GTG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
221 ColorGroup( 'GUG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
222
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
223 ColorGroup( 'CTT', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
224 ColorGroup( 'CUU', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
225 ColorGroup( 'CTC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
226 ColorGroup( 'CUC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
227 ColorGroup( 'CTA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
228 ColorGroup( 'CUA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
229 ColorGroup( 'CTG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
230 ColorGroup( 'CUG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
231 ColorGroup( 'TTA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
232 ColorGroup( 'UUA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
233 ColorGroup( 'TTG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
234 ColorGroup( 'UUG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
235
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
236 ColorGroup( 'ATT', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
237 ColorGroup( 'AUU', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
238 ColorGroup( 'ATC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
239 ColorGroup( 'AUC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
240 ColorGroup( 'ATA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
241 ColorGroup( 'AUA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
242
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
243 ColorGroup( 'ATG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
244 ColorGroup( 'AUG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
245
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
246
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
247 ColorGroup( 'TTT', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
248 ColorGroup( 'UUU', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
249 ColorGroup( 'TTC', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
250 ColorGroup( 'UUC', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
251
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
252 ColorGroup( 'TAT', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
253 ColorGroup( 'UAU', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
254 ColorGroup( 'TAC', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
255 ColorGroup( 'UAC', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
256
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
257 ColorGroup( 'TGG', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
258 ColorGroup( 'UGG', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
259
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
260
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
261 ColorGroup( 'GGT', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
262 ColorGroup( 'GGU', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
263 ColorGroup( 'GGC', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
264 ColorGroup( 'GGA', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
265 ColorGroup( 'GGG', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
266
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
267 ColorGroup( 'CCT', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
268 ColorGroup( 'CCU', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
269 ColorGroup( 'CCC', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
270 ColorGroup( 'CCA', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
271 ColorGroup( 'CCG', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
272
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
273
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
274 ColorGroup( 'TGT', '#FFFF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
275 ColorGroup( 'UGU', '#FFFF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
276 ColorGroup( 'TGC', '#FFFF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
277 ColorGroup( 'UGC', '#FFFF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
278
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
279 ColorGroup( 'TAA', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
280 ColorGroup( 'UAA', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
281 ColorGroup( 'TAG', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
282 ColorGroup( 'UAG', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
283 ColorGroup( 'TGA', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
284 ColorGroup( 'UGA', '#000000')],
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
285 alphabet = codon_alphabetU
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
286 )
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
287 codonsT = ColorScheme([
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
288 ColorGroup( 'CAT', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
289 ColorGroup( 'CAU', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
290 ColorGroup( 'CAC', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
291
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
292 ColorGroup( 'AAA', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
293 ColorGroup( 'AAG', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
294
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
295 ColorGroup( 'CGT', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
296 ColorGroup( 'CGU', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
297 ColorGroup( 'CGC', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
298 ColorGroup( 'CGA', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
299 ColorGroup( 'CGG', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
300 ColorGroup( 'AGA', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
301 ColorGroup( 'AGG', '#00FFFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
302
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
303
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
304 ColorGroup( 'GAT', '#FF0000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
305 ColorGroup( 'GAU', '#FF0000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
306 ColorGroup( 'GAC', '#FF0000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
307
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
308 ColorGroup( 'GAA', '#FF0000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
309 ColorGroup( 'GAG', '#FF0000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
310
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
311
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
312 ColorGroup( 'TCT', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
313 ColorGroup( 'UCU', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
314 ColorGroup( 'TCC', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
315 ColorGroup( 'UCC', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
316 ColorGroup( 'TCA', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
317 ColorGroup( 'UCA', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
318 ColorGroup( 'TCG', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
319 ColorGroup( 'UCG', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
320 ColorGroup( 'AGT', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
321 ColorGroup( 'AGU', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
322 ColorGroup( 'AGC', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
323
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
324 ColorGroup( 'ACT', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
325 ColorGroup( 'ACU', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
326 ColorGroup( 'ACC', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
327 ColorGroup( 'ACA', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
328 ColorGroup( 'ACG', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
329
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
330 ColorGroup( 'CAA', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
331 ColorGroup( 'CAG', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
332
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
333 ColorGroup( 'AAT', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
334 ColorGroup( 'AAU', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
335 ColorGroup( 'AAC', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
336
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
337
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
338 ColorGroup( 'GCT', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
339 ColorGroup( 'GCU', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
340 ColorGroup( 'GCC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
341 ColorGroup( 'GCA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
342 ColorGroup( 'GCG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
343
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
344 ColorGroup( 'GTT', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
345 ColorGroup( 'GUU', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
346 ColorGroup( 'GTC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
347 ColorGroup( 'GUC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
348 ColorGroup( 'GTA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
349 ColorGroup( 'GUA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
350 ColorGroup( 'GTG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
351 ColorGroup( 'GUG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
352
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
353 ColorGroup( 'CTT', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
354 ColorGroup( 'CUU', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
355 ColorGroup( 'CTC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
356 ColorGroup( 'CUC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
357 ColorGroup( 'CTA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
358 ColorGroup( 'CUA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
359 ColorGroup( 'CTG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
360 ColorGroup( 'CUG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
361 ColorGroup( 'TTA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
362 ColorGroup( 'UUA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
363 ColorGroup( 'TTG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
364 ColorGroup( 'UUG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
365
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
366 ColorGroup( 'ATT', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
367 ColorGroup( 'AUU', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
368 ColorGroup( 'ATC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
369 ColorGroup( 'AUC', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
370 ColorGroup( 'ATA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
371 ColorGroup( 'AUA', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
372
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
373 ColorGroup( 'ATG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
374 ColorGroup( 'AUG', '#5555FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
375
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
376
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
377 ColorGroup( 'TTT', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
378 ColorGroup( 'UUU', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
379 ColorGroup( 'TTC', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
380 ColorGroup( 'UUC', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
381
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
382 ColorGroup( 'TAT', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
383 ColorGroup( 'UAU', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
384 ColorGroup( 'TAC', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
385 ColorGroup( 'UAC', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
386
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
387 ColorGroup( 'TGG', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
388 ColorGroup( 'UGG', '#FF00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
389
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
390
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
391 ColorGroup( 'GGT', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
392 ColorGroup( 'GGU', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
393 ColorGroup( 'GGC', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
394 ColorGroup( 'GGA', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
395 ColorGroup( 'GGG', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
396
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
397 ColorGroup( 'CCT', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
398 ColorGroup( 'CCU', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
399 ColorGroup( 'CCC', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
400 ColorGroup( 'CCA', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
401 ColorGroup( 'CCG', '#996600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
402
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
403
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
404 ColorGroup( 'TGT', '#FFFF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
405 ColorGroup( 'UGU', '#FFFF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
406 ColorGroup( 'TGC', '#FFFF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
407 ColorGroup( 'UGC', '#FFFF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
408
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
409 ColorGroup( 'TAA', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
410 ColorGroup( 'UAA', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
411 ColorGroup( 'TAG', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
412 ColorGroup( 'UAG', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
413 ColorGroup( 'TGA', '#000000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
414 ColorGroup( 'UGA', '#000000')],
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
415 alphabet = codon_alphabetT
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
416 )
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
417
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
418
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
419
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
420
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
421 charge = ColorScheme([
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
422 ColorGroup("KRH", "blue", "Positive" ),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
423 ColorGroup( "DE", "red", "Negative") ],
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
424 alphabet = seq.unambiguous_protein_alphabet
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
425 )
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
426
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
427
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
428 taylor = ColorScheme([
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
429 ColorGroup( 'A', '#CCFF00' ),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
430 ColorGroup( 'C', '#FFFF00' ),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
431 ColorGroup( 'D', '#FF0000'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
432 ColorGroup( 'E', '#FF0066' ),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
433 ColorGroup( 'F', '#00FF66'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
434 ColorGroup( 'G', '#FF9900'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
435 ColorGroup( 'H', '#0066FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
436 ColorGroup( 'I', '#66FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
437 ColorGroup( 'K', '#6600FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
438 ColorGroup( 'L', '#33FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
439 ColorGroup( 'M', '#00FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
440 ColorGroup( 'N', '#CC00FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
441 ColorGroup( 'P', '#FFCC00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
442 ColorGroup( 'Q', '#FF00CC'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
443 ColorGroup( 'R', '#0000FF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
444 ColorGroup( 'S', '#FF3300'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
445 ColorGroup( 'T', '#FF6600'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
446 ColorGroup( 'V', '#99FF00'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
447 ColorGroup( 'W', '#00CCFF'),
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
448 ColorGroup( 'Y', '#00FFCC')],
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
449 title = "Taylor",
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
450 description = "W. Taylor, Protein Engineering, Vol 10 , 743-746 (1997)",
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
451 alphabet = seq.unambiguous_protein_alphabet
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
452 )
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
453
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
454
c55bdc2fb9fa Uploaded
davidmurphy
parents:
diff changeset
455