#ifndef ___GAIN_LOSS_ALPH
#define ___GAIN_LOSS_ALPH

#include "alphabet.h"
#include "errorMsg.h"

class gainLossAlphabet : public alphabet {
public:
	explicit gainLossAlphabet(); 
	virtual ~gainLossAlphabet() {}
	virtual alphabet* clone() const { return new gainLossAlphabet(*this); }
	int unknown() const  {return -2;}
	int gap() const  {errorMsg::reportError("The method indel::gap() is used"); return -1;} // What is it for ? I don't need this !!!
	int size() const {return 2;} // presence or absence only
	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;
	bool isSpecific(const int id) const {return (id>=0 && id < size());}

};

#endif