40 #ifndef _DEFAULTNUCLEOTIDESCORE_H_ 41 #define _DEFAULTNUCLEOTIDESCORE_H_ 47 #include "../Alphabet/NucleicAlphabet.h" 48 #include "../Alphabet/AlphabetExceptions.h" 49 #include <Bpp/Exceptions.h> 50 #include <Bpp/Numeric/Matrix/Matrix.h> 108 #endif // _DEFAULTNUCLEOTIDESCORE_H_ DefaultNucleotideScore(const DefaultNucleotideScore &dns)
An alphabet exception thrown when trying to specify a bad char to the alphabet.
DefaultNucleotideScore * clone() const
DefaultNucleotideScore & operator=(const DefaultNucleotideScore &dns)
This alphabet is used to deal NumericAlphabet.
DefaultNucleotideScore(const NucleicAlphabet *alphabet)
Build a new DefaultNucleotideScore object.
LinearMatrix< double > * getIndexMatrix() const
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.
Default Substitution Matrix for nucleotide alignments.
LinearMatrix< double > distanceMatrix_
Two dimensionnal alphabet index interface.
virtual ~DefaultNucleotideScore()
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
An alphabet exception thrown when trying to specify a bad int to the alphabet.
const NucleicAlphabet * alpha_
The abstract base class for nucleic alphabets.