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/* -*- c-basic-offset: 4; indent-tabs-mode: nil -*- */
#ifndef _AACODONS_H_
#define _AACODONS_H_
#include <vector>
#include "base/SVector.h"
#include "analysis/DNAVector.h"
// forward declare some classes
// http://stackoverflow.com/questions/2133250/does-not-name-a-type-error-in-c
class DNAVector;
class AAAmb;
class AACodons {
public:
static void init();
static const string & GetBases(char aa, int i);
static char GetCodon(const DNAVector& d, int pos);
static char GetCodon(const char * p);
static int GetCodonCount();
static const string & GetCodon(int i);
static void AminoAcidToBases(char * out, char aa);
static char BasesToAminoAcid(char * b);
private:
static bool initialized;
static svec<int> m_table;
static svec<AAAmb> m_bases;
static svec<char> m_aminoAcids;
static svec<string> m_codonBases;
static void Set(const string & aa, const string & codon, int index);
};
#endif //_AACODONS_H_
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