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//
// codon.cpp
// Mothur
//
// Created by Sarah Westcott on 5/24/21.
// Copyright © 2021 Schloss Lab. All rights reserved.
//
#include "aminoacid.hpp"
/******************************************************************************************************************/
AminoAcid::AminoAcid() {
try {
m = MothurOut::getInstance();
indexes['A'] = 0; indexes['T'] = 1; indexes['G'] = 2; indexes['C'] = 3; indexes['N'] = 4; indexes['-'] = 5; indexes['.'] = 5;
setAmino('?');
}
catch(exception& e) {
m->errorOut(e, "AminoAcid", "AminoAcid");
exit(1);
}
}
/******************************************************************************************************************/
AminoAcid::AminoAcid(char c) {
try {
m = MothurOut::getInstance();
indexes['A'] = 0; indexes['T'] = 1; indexes['G'] = 2; indexes['C'] = 3; indexes['N'] = 4; indexes['-'] = 5; indexes['.'] = 5;
setAmino(c);
}
catch(exception& e) {
m->errorOut(e, "AminoAcid", "AminoAcid");
exit(1);
}
}
/******************************************************************************************************************/
//requires the codon to be 3 characters long. Only valid characters are a,t,g,c,n.
AminoAcid::AminoAcid(string codon) {
try {
m = MothurOut::getInstance();
indexes['A'] = 0; indexes['T'] = 1; indexes['G'] = 2; indexes['C'] = 3; indexes['N'] = 4; indexes['-'] = 5; indexes['.'] = 5;
char amino = findAmino(codon);
setAmino(amino);
}
catch(exception& e) {
m->errorOut(e, "AminoAcid", "AminoAcid");
exit(1);
}
}
/******************************************************************************************************************/
void AminoAcid::setAmino(char c) {
try {
c = toupper(c);
if (m->validAminoAcids.count(c) != 0) {
aminoBase = c;
getName(); //sets name, number and compressed dna
}else { m->mothurOut("[ERROR]: " + toString(c) + " is an invalid amino acid, please correct.\n"); m->setControl_pressed(true); }
}
catch(exception& e) {
m->errorOut(e, "AminoAcid", "setAmino");
exit(1);
}
}
/******************************************************************************************************************/
char AminoAcid::findAmino(string codon) {
try {
char amino = '?';
if (codon.length() != 3) { m->mothurOut("[ERROR]: " + codon + " is not the correct length. Codons must be 3 characters long, quitting.\n"); m->setControl_pressed(true); return amino; }
int index1 = -1; int index2 = -1; int index3 = -1;
it = indexes.find(codon[0]); if (it != indexes.end()) { index1 = it->second; } else { m->mothurOut("[ERROR]: " + toString(codon[0]) + " is not A, T, G, C, or N, quitting.\n"); m->setControl_pressed(true); return amino; }
it = indexes.find(codon[1]); if (it != indexes.end()) { index2 = it->second; } else { m->mothurOut("[ERROR]: " + toString(codon[1]) + " is not A, T, G, C, or N, quitting.\n"); m->setControl_pressed(true); return amino; }
it = indexes.find(codon[2]); if (it != indexes.end()) { index3 = it->second; } else { m->mothurOut("[ERROR]: " + toString(codon[2]) + " is not A, T, G, C, or N, quitting.\n"); m->setControl_pressed(true); return amino; }
if ((index1 == 5) && (index2 == 5) && (index3 == 5)) { amino = '-'; return amino; }
//if no N's then the set should contain one amino acid. if N's, then try all possible values for N in that position.
//for example:ACN -> Threonine (T) because ACA,ACT,ACG,ACC all map to Threonine
// but GAN -> could be Glutamate (E) (for N=A or G) or Aspartate (D) (for N=T or C)
if ((index1 > 3) || (index2 > 3) || (index3 > 3)) { //any position of the codon is an N or gap
set<char> possibleAminoAcids;
if (((index1 > 3) && (index2 > 3)) || ((index1 > 3) && (index3 > 3)) || ((index3 > 3) && (index2 > 3))) { //2 N's or gaps in codon
}else{ //only 1 N
if (index1 > 3) {
possibleAminoAcids.insert(m->codons[0][index2][index3]); possibleAminoAcids.insert(m->codons[1][index2][index3]);
possibleAminoAcids.insert(m->codons[2][index2][index3]); possibleAminoAcids.insert(m->codons[3][index2][index3]);
}else if (index2 > 3) {
possibleAminoAcids.insert(m->codons[index1][0][index3]); possibleAminoAcids.insert(m->codons[index1][1][index3]);
possibleAminoAcids.insert(m->codons[index1][2][index3]); possibleAminoAcids.insert(m->codons[index1][3][index3]);
}else {
possibleAminoAcids.insert(m->codons[index1][index2][0]); possibleAminoAcids.insert(m->codons[index1][index2][1]);
possibleAminoAcids.insert(m->codons[index1][index2][2]); possibleAminoAcids.insert(m->codons[index1][index2][3]);
}
if (possibleAminoAcids.size() == 1) {
amino = (*possibleAminoAcids.begin());
}
}
}else {
amino = m->codons[index1][index2][index3];
}
return amino;
}
catch(exception& e) {
m->errorOut(e, "AminoAcid", "findAmino");
exit(1);
}
}
/******************************************************************************************************************/
//ala(0), arg(1), asn(2), asp(3), cys(4), gln(5), glu(6), gly(7), his(8), ileu(9), leu(10), lys(11), met(12), phe(13), pro(14),
//ser1(15), ser2(16), thr(17), trp(18), tyr(19), val(20), del(21), stop(22), asx(23), glx(24), ser(25), unk(26), quest(27)
string AminoAcid::getName() {
try {
string aminoName = "unknown"; aminoNum = unk;
if (aminoBase == 'A') { aminoName = "Alanine"; aminoNum = ala; } //0
else if (aminoBase == 'R') { aminoName = "Arginine"; aminoNum = arg; } //1
else if (aminoBase == 'N') { aminoName = "Asparagine"; aminoNum = asn; } //2
else if (aminoBase == 'D') { aminoName = "Aspartic"; aminoNum = asp; } //3
else if (aminoBase == 'B') { aminoName = "Asparagine or Aspartic"; aminoNum = asx; } //23
else if (aminoBase == 'C') { aminoName = "Cysteine"; aminoNum = cys; } //4
else if (aminoBase == 'Q') { aminoName = "Glutamine"; aminoNum = gln; } //5
else if (aminoBase == 'E') { aminoName = "Glutamic"; aminoNum = glu; } //6
else if (aminoBase == 'Z') { aminoName = "Glutamine or Glutamic_Acid"; aminoNum = glx; } //24
else if (aminoBase == 'G') { aminoName = "Glycine"; aminoNum = gly; } //7
else if (aminoBase == 'H') { aminoName = "Histidine"; aminoNum = his; } //8
else if (aminoBase == 'I') { aminoName = "Isoleucine"; aminoNum = ileu; } //9
else if (aminoBase == 'L') { aminoName = "Leucine"; aminoNum = leu; } //10
else if (aminoBase == 'K') { aminoName = "Lysine"; aminoNum = lys; } //11
else if (aminoBase == 'M') { aminoName = "Methionine"; aminoNum = met; } //12
else if (aminoBase == 'F') { aminoName = "Phenylalanine"; aminoNum = phe; } //13
else if (aminoBase == 'P') { aminoName = "Proline"; aminoNum = pro; } //14
else if (aminoBase == 'S') { aminoName = "Serine"; aminoNum = ser1; } //15
else if (aminoBase == 'T') { aminoName = "Threonine"; aminoNum = thr; } //17
else if (aminoBase == 'W') { aminoName = "Tryptophan"; aminoNum = trp; } //18
else if (aminoBase == 'Y') { aminoName = "Tyrosine"; aminoNum = tyr; } //19
else if (aminoBase == 'V') { aminoName = "Valine"; aminoNum = val; } //20
else if ((aminoBase == '.') || (aminoBase == '-')) { aminoName = "Gap"; aminoNum = del; } //21
else if ((aminoBase == '*') || (aminoBase == 'X')) { aminoName = "STOP"; aminoNum = stop; } //22
else if (aminoBase == '?') { aminoName = "QUESTION"; aminoNum = quest; } //27
return aminoName;
}
catch(exception& e) {
m->errorOut(e, "AminoAcid", "getName");
exit(1);
}
}
/******************************************************************************************************************/
|
