bpp-seq  2.2.0
EchinodermMitochondrialGeneticCode.cpp
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1 //
2 // File: EchinodermMitochondrialGeneticCode.cpp
3 // Created by: Eric Bazin
4 // Created on: 14 11:31:27 CET 2005
5 
6 /*
7 Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
8 
9 This software is a computer program whose purpose is to provide classes
10 for sequences analysis.
11 
12 This software is governed by the CeCILL license under French law and
13 abiding by the rules of distribution of free software. You can use,
14 modify and/ or redistribute the software under the terms of the CeCILL
15 license as circulated by CEA, CNRS and INRIA at the following URL
16 "http://www.cecill.info".
17 
18 As a counterpart to the access to the source code and rights to copy,
19 modify and redistribute granted by the license, users are provided only
20 with a limited warranty and the software's author, the holder of the
21 economic rights, and the successive licensors have only limited
22 liability.
23 
24 In this respect, the user's attention is drawn to the risks associated
25 with loading, using, modifying and/or developing or reproducing the
26 software by the user in light of its specific status of free software,
27 that may mean that it is complicated to manipulate, and that also
28 therefore means that it is reserved for developers and experienced
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33 same conditions as regards security.
34 
35 The fact that you are presently reading this means that you have had
36 knowledge of the CeCILL license and that you accept its terms.
37 */
38 
40 
41 using namespace bpp;
42 
43 #include <iostream>
44 
45 using namespace std;
46 
48  GeneticCode(alphabet)
49 {
50  tlnTable_[0] = 2; //AAA -> N
51  tlnTable_[1] = 2; //AAC -> N
52  tlnTable_[2] = 11; //AAG -> K
53  tlnTable_[3] = 2; //AAT -> N
54  tlnTable_[4] = 16; //ACA -> T
55  tlnTable_[5] = 16; //ACC -> T
56  tlnTable_[6] = 16; //ACG -> T
57  tlnTable_[7] = 16; //ACT -> T
58  tlnTable_[8] = 15; //AGA -> S
59  tlnTable_[9] = 15; //AGC -> S
60  tlnTable_[10] = 15; //AGG -> S
61  tlnTable_[11] = 15; //AGT -> S
62  tlnTable_[12] = 9; //ATA -> I
63  tlnTable_[13] = 9; //ATC -> I
64  tlnTable_[14] = 12; //ATG -> M
65  tlnTable_[15] = 9; //ATT -> I
66  tlnTable_[16] = 5; //CAA -> Q
67  tlnTable_[17] = 8; //CAC -> H
68  tlnTable_[18] = 5; //CAG -> Q
69  tlnTable_[19] = 8; //CAT -> H
70  tlnTable_[20] = 14; //CCA -> P
71  tlnTable_[21] = 14; //CCC -> P
72  tlnTable_[22] = 14; //CCG -> P
73  tlnTable_[23] = 14; //CCT -> P
74  tlnTable_[24] = 1; //CGA -> R
75  tlnTable_[25] = 1; //CGC -> R
76  tlnTable_[26] = 1; //CGG -> R
77  tlnTable_[27] = 1; //CGT -> R
78  tlnTable_[28] = 10; //CTA -> L
79  tlnTable_[29] = 10; //CTC -> L
80  tlnTable_[30] = 10; //CTG -> L
81  tlnTable_[31] = 10; //CTT -> L
82  tlnTable_[32] = 6; //GAA -> E
83  tlnTable_[33] = 3; //GAC -> D
84  tlnTable_[34] = 6; //GAG -> E
85  tlnTable_[35] = 3; //GAT -> D
86  tlnTable_[36] = 0; //GCA -> A
87  tlnTable_[37] = 0; //GCC -> A
88  tlnTable_[38] = 0; //GCG -> A
89  tlnTable_[39] = 0; //GCT -> A
90  tlnTable_[40] = 7; //GGA -> G
91  tlnTable_[41] = 7; //GGC -> G
92  tlnTable_[42] = 7; //GGG -> G
93  tlnTable_[43] = 7; //GGT -> G
94  tlnTable_[44] = 19; //GTA -> V
95  tlnTable_[45] = 19; //GTC -> V
96  tlnTable_[46] = 19; //GTG -> V
97  tlnTable_[47] = 19; //GTT -> V
98  tlnTable_[48] = -99; //TAA -> STOP
99  tlnTable_[49] = 18; //TAC -> Y
100  tlnTable_[50] = -99; //TAG -> STOP
101  tlnTable_[51] = 18; //TAT -> Y
102  tlnTable_[52] = 15; //TCA -> S
103  tlnTable_[53] = 15; //TCC -> S
104  tlnTable_[54] = 15; //TCG -> S
105  tlnTable_[55] = 15; //TCT -> S
106  tlnTable_[56] = 17; //TGA -> W
107  tlnTable_[57] = 4; //TGC -> C
108  tlnTable_[58] = 17; //TGG -> W
109  tlnTable_[59] = 4; //TGT -> C
110  tlnTable_[60] = 10; //TTA -> L
111  tlnTable_[61] = 13; //TTC -> F
112  tlnTable_[62] = 10; //TTG -> L
113  tlnTable_[63] = 13; //TTT -> F
115 }
116 
This alphabet is used to deal NumericAlphabet.
ProteicAlphabet proteicAlphabet_
Definition: GeneticCode.h:85
STL namespace.
CodonAlphabet codonAlphabet_
Definition: GeneticCode.h:84
EchinodermMitochondrialGeneticCode(const NucleicAlphabet *alphabet)
int getUnknownCharacterCode() const
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.