/usr/include/libphylo/gainLossAlphabet.h is in rate4site 3.0.0-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #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
|