bpp-seq3  3.0.0
YeastMitochondrialGeneticCode.cpp
Go to the documentation of this file.
1 // SPDX-FileCopyrightText: The Bio++ Development Group
2 //
3 // SPDX-License-Identifier: CECILL-2.1
4 
6 
7 using namespace bpp;
8 
9 #include <iostream>
10 
11 using namespace std;
12 
14 {
15  tlnTable_[0] = 11; // AAA -> K
16  tlnTable_[1] = 2; // AAC -> N
17  tlnTable_[2] = 11; // AAG -> K
18  tlnTable_[3] = 2; // AAT -> N
19  tlnTable_[4] = 16; // ACA -> T
20  tlnTable_[5] = 16; // ACC -> T
21  tlnTable_[6] = 16; // ACG -> T
22  tlnTable_[7] = 16; // ACT -> T
23  tlnTable_[8] = 15; // AGA -> S
24  tlnTable_[9] = 15; // AGC -> S
25  tlnTable_[10] = 15; // AGG -> S
26  tlnTable_[11] = 15; // AGT -> S
27  tlnTable_[12] = 12; // ATA -> M
28  tlnTable_[13] = 9; // ATC -> I
29  tlnTable_[14] = 12; // ATG -> M
30  tlnTable_[15] = 9; // ATT -> I
31  tlnTable_[16] = 5; // CAA -> Q
32  tlnTable_[17] = 8; // CAC -> H
33  tlnTable_[18] = 5; // CAG -> Q
34  tlnTable_[19] = 8; // CAT -> H
35  tlnTable_[20] = 14; // CCA -> P
36  tlnTable_[21] = 14; // CCC -> P
37  tlnTable_[22] = 14; // CCG -> P
38  tlnTable_[23] = 14; // CCT -> P
39  tlnTable_[24] = 1; // CGA -> R
40  tlnTable_[25] = 1; // CGC -> R
41  tlnTable_[26] = 1; // CGG -> R
42  tlnTable_[27] = 1; // CGT -> R
43  tlnTable_[28] = 16; // CTA -> T
44  tlnTable_[29] = 16; // CTC -> T
45  tlnTable_[30] = 16; // CTG -> T
46  tlnTable_[31] = 16; // CTT -> T
47  tlnTable_[32] = 6; // GAA -> E
48  tlnTable_[33] = 3; // GAC -> D
49  tlnTable_[34] = 6; // GAG -> E
50  tlnTable_[35] = 3; // GAT -> D
51  tlnTable_[36] = 0; // GCA -> A
52  tlnTable_[37] = 0; // GCC -> A
53  tlnTable_[38] = 0; // GCG -> A
54  tlnTable_[39] = 0; // GCT -> A
55  tlnTable_[40] = 7; // GGA -> G
56  tlnTable_[41] = 7; // GGC -> G
57  tlnTable_[42] = 7; // GGG -> G
58  tlnTable_[43] = 7; // GGT -> G
59  tlnTable_[44] = 19; // GTA -> V
60  tlnTable_[45] = 19; // GTC -> V
61  tlnTable_[46] = 19; // GTG -> V
62  tlnTable_[47] = 19; // GTT -> V
63  tlnTable_[48] = -99; // TAA -> STOP
64  tlnTable_[49] = 18; // TAC -> Y
65  tlnTable_[50] = -99; // TAG -> STOP
66  tlnTable_[51] = 18; // TAT -> Y
67  tlnTable_[52] = 15; // TCA -> S
68  tlnTable_[53] = 15; // TCC -> S
69  tlnTable_[54] = 15; // TCG -> S
70  tlnTable_[55] = 15; // TCT -> S
71  tlnTable_[56] = 17; // TGA -> W
72  tlnTable_[57] = 4; // TGC -> C
73  tlnTable_[58] = 17; // TGG -> W
74  tlnTable_[59] = 4; // TGT -> C
75  tlnTable_[60] = 10; // TTA -> L
76  tlnTable_[61] = 13; // TTC -> F
77  tlnTable_[62] = 10; // TTG -> L
78  tlnTable_[63] = 13; // TTT -> F
79  tlnTable_[codonAlphabet_->getUnknownCharacterCode()] = proteicAlphabet_->getUnknownCharacterCode();
80 }
This alphabet is used to deal NumericAlphabet.