bpp-seq  2.2.0
VertebrateMitochondrialGeneticCode.cpp
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1 //
2 // File: VertebrateMitochondrialGeneticCode.cpp
3 // Created by: Eric Bazin
4 // Created on: wen mar 2 16:01:59 CET 2005
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
9 
10 This software is a computer program whose purpose is to provide classes
11 for sequences analysis.
12 
13 This software is governed by the CeCILL license under French law and
14 abiding by the rules of distribution of free software. You can use,
15 modify and/ or redistribute the software under the terms of the CeCILL
16 license as circulated by CEA, CNRS and INRIA at the following URL
17 "http://www.cecill.info".
18 
19 As a counterpart to the access to the source code and rights to copy,
20 modify and redistribute granted by the license, users are provided only
21 with a limited warranty and the software's author, the holder of the
22 economic rights, and the successive licensors have only limited
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25 In this respect, the user's attention is drawn to the risks associated
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27 software by the user in light of its specific status of free software,
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35 
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38 */
39 
41 
42 using namespace bpp;
43 
44 #include <iostream>
45 
46 using namespace std;
47 
49  GeneticCode(alphabet)
50 {
51  tlnTable_[0] = 11; //AAA -> K
52  tlnTable_[1] = 2; //AAC -> N
53  tlnTable_[2] = 11; //AAG -> K
54  tlnTable_[3] = 2; //AAT -> N
55  tlnTable_[4] = 16; //ACA -> T
56  tlnTable_[5] = 16; //ACC -> T
57  tlnTable_[6] = 16; //ACG -> T
58  tlnTable_[7] = 16; //ACT -> T
59  tlnTable_[8] = -99; //AGA -> STOP
60  tlnTable_[9] = 15; //AGC -> S
61  tlnTable_[10] = -99; //AGG -> STOP
62  tlnTable_[11] = 15; //AGT -> S
63  tlnTable_[12] = 12; //ATA -> M
64  tlnTable_[13] = 9; //ATC -> I
65  tlnTable_[14] = 12; //ATG -> M
66  tlnTable_[15] = 9; //ATT -> I
67  tlnTable_[16] = 5; //CAA -> Q
68  tlnTable_[17] = 8; //CAC -> H
69  tlnTable_[18] = 5; //CAG -> Q
70  tlnTable_[19] = 8; //CAT -> H
71  tlnTable_[20] = 14; //CCA -> P
72  tlnTable_[21] = 14; //CCC -> P
73  tlnTable_[22] = 14; //CCG -> P
74  tlnTable_[23] = 14; //CCT -> P
75  tlnTable_[24] = 1; //CGA -> R
76  tlnTable_[25] = 1; //CGC -> R
77  tlnTable_[26] = 1; //CGG -> R
78  tlnTable_[27] = 1; //CGT -> R
79  tlnTable_[28] = 10; //CTA -> L
80  tlnTable_[29] = 10; //CTC -> L
81  tlnTable_[30] = 10; //CTG -> L
82  tlnTable_[31] = 10; //CTT -> L
83  tlnTable_[32] = 6; //GAA -> E
84  tlnTable_[33] = 3; //GAC -> D
85  tlnTable_[34] = 6; //GAG -> E
86  tlnTable_[35] = 3; //GAT -> D
87  tlnTable_[36] = 0; //GCA -> A
88  tlnTable_[37] = 0; //GCC -> A
89  tlnTable_[38] = 0; //GCG -> A
90  tlnTable_[39] = 0; //GCT -> A
91  tlnTable_[40] = 7; //GGA -> G
92  tlnTable_[41] = 7; //GGC -> G
93  tlnTable_[42] = 7; //GGG -> G
94  tlnTable_[43] = 7; //GGT -> G
95  tlnTable_[44] = 19; //GTA -> V
96  tlnTable_[45] = 19; //GTC -> V
97  tlnTable_[46] = 19; //GTG -> V
98  tlnTable_[47] = 19; //GTT -> V
99  tlnTable_[48] = -99; //TAA -> STOP
100  tlnTable_[49] = 18; //TAC -> Y
101  tlnTable_[50] = -99; //TAG -> STOP
102  tlnTable_[51] = 18; //TAT -> Y
103  tlnTable_[52] = 15; //TCA -> S
104  tlnTable_[53] = 15; //TCC -> S
105  tlnTable_[54] = 15; //TCG -> S
106  tlnTable_[55] = 15; //TCT -> S
107  tlnTable_[56] = 17; //TGA -> W
108  tlnTable_[57] = 4; //TGC -> C
109  tlnTable_[58] = 17; //TGG -> W
110  tlnTable_[59] = 4; //TGT -> C
111  tlnTable_[60] = 10; //TTA -> L
112  tlnTable_[61] = 13; //TTC -> F
113  tlnTable_[62] = 10; //TTG -> L
114  tlnTable_[63] = 13; //TTT -> F
116 }
117 
This alphabet is used to deal NumericAlphabet.
ProteicAlphabet proteicAlphabet_
Definition: GeneticCode.h:85
STL namespace.
CodonAlphabet codonAlphabet_
Definition: GeneticCode.h:84
int getUnknownCharacterCode() const
VertebrateMitochondrialGeneticCode(const NucleicAlphabet *alphabet)
int getUnknownCharacterCode() const
Definition: WordAlphabet.h:173
std::map< int, int > tlnTable_
Definition: GeneticCode.h:86
Partial implementation of the Transliterator interface for genetic code object.
Definition: GeneticCode.h:79
The abstract base class for nucleic alphabets.