40 #ifndef _MIYATAAACHEMICALDISTANCE_H_ 41 #define _MIYATAAACHEMICALDISTANCE_H_ 47 #include "../Alphabet/ProteicAlphabet.h" 48 #include "../Alphabet/AlphabetExceptions.h" 49 #include <Bpp/Exceptions.h> 50 #include <Bpp/Numeric/Matrix/Matrix.h> 115 #endif // _MIYATAAACHEMICALDISTANCE_H_ An alphabet exception thrown when trying to specify a bad char to the alphabet.
MiyataAAChemicalDistance & operator=(const MiyataAAChemicalDistance &md)
This alphabet is used to deal NumericAlphabet.
Matrix< double > * getIndexMatrix() const
virtual ~MiyataAAChemicalDistance()
Miyata et al. (1979) Amino-Acid chemical distance.
This alphabet is used to deal with proteins.
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.
const ProteicAlphabet * alpha_
MiyataAAChemicalDistance()
MiyataAAChemicalDistance * clone() const
Two dimensionnal alphabet index interface.
MiyataAAChemicalDistance(const MiyataAAChemicalDistance &md)
void setSymmetric(bool yn)
An alphabet exception thrown when trying to specify a bad int to the alphabet.
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
LinearMatrix< double > distanceMatrix_