40 #ifndef _SIMPLESCORE_H_ 41 #define _SIMPLESCORE_H_ 47 #include "../Alphabet/Alphabet.h" 48 #include "../Alphabet/AlphabetExceptions.h" 49 #include <Bpp/Exceptions.h> 50 #include <Bpp/Numeric/Matrix/Matrix.h> 105 #endif // _SIMPLESCORE_H_
An alphabet exception thrown when trying to specify a bad char to the alphabet.
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
LinearMatrix< double > * getIndexMatrix() const
This alphabet is used to deal NumericAlphabet.
SimpleScore(const Alphabet *alphabet, double match, double mismatch)
Build a new simpleScore object.
const Alphabet * alphabet_
SimpleScore * clone() const
SimpleScore & operator=(const SimpleScore &sc)
Two dimensionnal alphabet index interface.
Simple Substitution Matrix, with match and mismatch penalties.
An alphabet exception thrown when trying to specify a bad int to the alphabet.
SimpleScore(const SimpleScore &sc)
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.
LinearMatrix< double > distanceMatrix_