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// $Id: amino.cpp 2414 2007-10-08 14:34:42Z adist $
#include "amino.h"
//VVint amino::_relation;
amino::amino() {
_relation.resize(24); // relation should realy be an allocted, two dimentional array, not a vector.
for (int i=0; i < _relation.size(); ++i) { // this implementation would be much faster. with some c-tricks, this checkup could be done with one access only.
_relation[i].resize(20);
}
for (int k=-2;k<=21;++k){
for (int j=0;j<20;++j){
_relation[k+2][j]=relations_internal(k,j);
}
}
}
int amino::fromChar(const char s) const{
switch (s) {
case 'A' : case'a' : return 0 ; break;
case 'R' : case'r' : return 1 ; break;
case 'N' : case'n' : return 2 ; break;
case 'D' : case'd' : return 3 ; break;
case 'C' : case'c' : return 4 ; break;
case 'Q' : case'q' : return 5 ; break;
case 'E' : case'e' : return 6 ; break;
case 'G' : case'g' : return 7 ; break;
case 'H' : case'h' : return 8 ; break;
case 'I' : case'i' : return 9 ; break;
case 'L' : case'l' : return 10; break;
case 'K' : case'k' : return 11; break;
case 'M' : case'm' : return 12; break;
case 'F' : case'f' : return 13; break;
case 'P' : case'p' : return 14; break;
case 'S' : case's' : return 15; break;
case 'T' : case't' : return 16; break;
case 'W' : case'w' : return 17; break;
case 'Y' : case'y' : return 18; break;
case 'V' : case'v' : return 19; break;
case 'B' : case'b' : return 20 ; break; // aspartate(D) or asparagine(N)
case 'Z' : case'z' : return 21 ; break; // glutamate (E) or glutamine(Q)
case '-' : case'_' : return -1; break;
case '?' : case'*' : return -2; break;
case 'x' : case'X' : return -2; break;
case '.' : return -3; break;
default:
vector<string> err;
err.push_back(" The amino-acid sequences contained the character: ");
err[0]+=s;
err.push_back(" Amino acid was not one of the following: ");
err.push_back(" A, B, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V, X, Z, -, ?");
err.push_back(" a, b, r, n, d, c, q, e, g, h, i, l, k, m, f, p, s, t, w, y, v, x, z, _, *");
errorMsg::reportError(err);
}// end of switch
return -99; // never suppose to be here.
}// end of function
vector<int> amino::fromString(const string &str) const {
vector<int> vec;
for (int i=0;i<str.size();i++)
vec.push_back(fromChar(str[i]));
return vec;
}
string amino::fromInt(const int in_id) const{
char res = 0;
switch (in_id) {
case 0 : res = 'A' ; break;
case 1 : res = 'R' ; break;
case 2 : res = 'N' ; break;
case 3 : res = 'D' ; break;
case 4 : res = 'C' ; break;
case 5 : res = 'Q' ; break;
case 6 : res = 'E' ; break;
case 7 : res = 'G' ; break;
case 8 : res = 'H' ; break;
case 9 : res = 'I' ; break;
case 10: res = 'L' ; break;
case 11: res = 'K' ; break;
case 12: res = 'M' ; break;
case 13: res = 'F' ; break;
case 14: res = 'P' ; break;
case 15: res = 'S' ; break;
case 16: res = 'T' ; break;
case 17: res = 'W' ; break;
case 18: res = 'Y' ; break;
case 19: res = 'V' ; break;
case 20: res = 'B' ; break;
case 21: res = 'Z' ; break;
case -1: res = '-' ; break;
case -2: res = 'X' ; break;
case -3: res = '.' ; break;
default:
vector<string> err;
err.push_back(" unable to print amino ac_id. amino ac_id was not one of the following: ");
err.push_back("A, B, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V, Z, -, ?");
err.push_back("a, b, r, n, d, c, q, e, g, h, i, l, k, m, f, p, s, t, w, y, v, z, _, *");
errorMsg::reportError(err);
}//end of switch
string vRes;
vRes.append(1,res);
return vRes;
}// end of function
int amino::relations(const int charInSeq, const int charToCheck) const{
if (charInSeq == -1) {
errorMsg::reportError("gaps in the sequences. Either change gaps to ? or remove gap positions");
}
return _relation[charInSeq+2][charToCheck];// <-MATAN, HERE YOU SWITHCED THE ORDER...
}
int amino::fromChar(const string& str, const int pos) const{
return fromChar(str[pos]);
}
int amino::relations_internal(const int charInSeq, const int charToCheck) const{
if (charInSeq == charToCheck) return 1;
else if (charInSeq == fromChar('?')) return 1;
else if ((charInSeq == fromChar('B')) &&
((charToCheck == fromChar('N')) ||
(charToCheck == fromChar('D')))) return 1; // B is either N or D
else if ((charInSeq == fromChar('Z')) &&
((charToCheck == fromChar('Q')) ||
(charToCheck == fromChar('E')))) return 1; // Z is either E or Q
return 0;
}
vector<int> aminoUtility::codonOf(const int a, codon &cod){
vector<int> codons;
amino amin;
string strAmino=amin.fromInt(a);
map <string, string> genCode=cod.geneticCode();
map <string, string>::iterator it=genCode.begin();
int tmp2=genCode.size();
while (it!=genCode.end()){
string tmp=(*it).second;
if ((*it).second==strAmino){
string strCodon=(*it).first;
int c=cod.fromChar(strCodon,0);
codons.push_back(c);
}
it++;
}
if (codons.empty()){
cout<<tmp2<<" amino is = "<<a<<endl;
errorMsg::reportError("error in function aminoUtility::codonOf: no codon found for amino acid");
}
return codons;
}
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