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#ifndef CODONS_H
#define CODONS_H
#include "GBase.h"
#include <ctype.h>
unsigned short packCodon(char n1, char n2, char n3);
//assumes n1,n2,n3 are UPPERCASE!
struct Codon {
char nuc[3];
Codon(char* str=NULL) {
if (str==NULL) {
nuc[0]='N';
nuc[1]='N';
nuc[2]='N';
}
else {
nuc[0]=toupper(str[0]);
nuc[1]=toupper(str[1]);
nuc[2]=toupper(str[2]);
}
}
Codon(char s1, char s2, char s3) {
nuc[0]=toupper(s1);
nuc[1]=toupper(s2);
nuc[2]=toupper(s3);
}
char& operator[](int idx) {
if (idx<0 || idx>2)
GError("Error: Codon index out of bounds!\n");
return nuc[idx];
}
char operator[](int idx) const {
if (idx<0 || idx>2)
GError("Error: Codon index out of bounds!\n");
return nuc[idx];
}
char translate();
};
//simple 1st frame forward translation of a given DNA string
//will allocated memory for the translation -- the caller is
// responsible for freeing the returned string!
char* translateDNA(const char* dnastr, int& aalen, int dnalen=0);
char translateCodon(const char* dna); //returns the aminoacid code for the 1st codon at dna
bool codonTableInit();
#endif
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