VertebrateMitochondrialGeneticCode.cpp

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