40 #ifndef _GRANTHAMAACHEMICALDISTANCE_H_ 41 #define _GRANTHAMAACHEMICALDISTANCE_H_ 47 #include "../Alphabet/ProteicAlphabet.h" 48 #include "../Alphabet/AlphabetExceptions.h" 49 #include <Bpp/Exceptions.h> 50 #include <Bpp/Numeric/Matrix/Matrix.h> 157 #endif // _GRANTHAMAACHEMICALDISTANCE_H_ static short int SIGN_ARBITRARY
An alphabet exception thrown when trying to specify a bad char to the alphabet.
This alphabet is used to deal NumericAlphabet.
GranthamAAChemicalDistance & operator=(const GranthamAAChemicalDistance &gd)
const ProteicAlphabet * alpha_
void setSymmetric(bool yn)
static short int SIGN_NONE
Grantham (1974) Amino-Acid chemical distance.
This alphabet is used to deal with proteins.
GranthamAAChemicalDistance(const GranthamAAChemicalDistance &gd)
LinearMatrix< double > distanceMatrix_
Matrix< double > * getIndexMatrix() const
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
GranthamAAChemicalDistance * clone() const
Two dimensionnal alphabet index interface.
An alphabet exception thrown when trying to specify a bad int to the alphabet.
GranthamAAChemicalDistance()
static short int SIGN_PC1
virtual ~GranthamAAChemicalDistance()
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.
void setPC1Sign(bool yn)
The sign of the distance is computed using the coordinate on the first axis of a principal component ...
LinearMatrix< double > signMatrix_