/usr/include/libphylo/amino.h is in rate4site 3.0.0-5.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | // $Id: amino.h 1901 2007-03-15 13:21:06Z nimrodru $
#ifndef ____AMINO
#define ____AMINO
#include "definitions.h"
#include "errorMsg.h"
#include "alphabet.h"
#include "geneticCodeHolder.h"
#include "codon.h"
//utility of amino acid
class aminoUtility {
public:
static vector<int> codonOf(const int a, codon &cod); //returns vector of codons that code to a under a specific genetic code.
};
//based on the amino-acid list found in http://www.dur.ac.uk/~dbl0www/Bioinformatics/aminoacids.htm
class amino : public alphabet {
public:
explicit amino();
virtual ~amino() {}
virtual alphabet* clone() const { return new amino(*this); }
int unknown() const {return -2;}
int gap() const {return -1;}
int size() const {return 20;}
int stringSize() const {return 1;} // one letter code.
int relations(const int charInSeq, const int charToCheck) const;
int fromChar(const string& str, const int pos) const;
int fromChar(const char s) const;
string fromInt(const int in_id) const;
vector<int> fromString(const string& str) const;
// "specific" here is not unknown, nor ambiguity, nor gap (for example, for nucleotides it will true for A,C,G, or T).
bool isSpecific(const int id) const {return (id>=0 && id < size());}
private:
int relations_internal(const int charInSeq, const int charToCheck) const;
VVint _relation;
};//end of class
#endif
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