41 #ifndef _SUBSTITUTIOMODELFACTORY_H_ 42 #define _SUBSTITUTIOMODELFACTORY_H_ 44 #include "../Model/Nucleotide/JCnuc.h" 48 #include <Bpp/Seq/Alphabet/Alphabet.h> 49 #include <Bpp/Seq/Alphabet/AlphabetExceptions.h> 50 #include <Bpp/Seq/GeneticCode/GeneticCode.h> 130 #endif //_SUBSTITUTIOMODELFACTORY_H_ Interface for all substitution models.
const GeneticCode * geneticCode_
static const std::string JUKES_CANTOR
static const std::string KIMURA_2P
static const std::string FELSENSTEIN
virtual ~SubstitutionModelFactory()
SubstitutionModelFactory(const SubstitutionModelFactory &smf)
Utilitary class for creating substitution models.
virtual SubstitutionModel * createModel(const std::string &modelName) const
Get a new dynamically created SubstitutionModel object.
static const std::string LOBRY
static const std::string LE_GASCUEL
const Alphabet * alphabet_
static const std::string HASEGAWA_KISHINO_YANO
static const std::string TAMURA
static const std::string DAYHOFF_SCHWARTZ_ORCUTT
static const std::string WHELAN_AND_GOLDMAN
static const std::string JOHN_TAYLOR_THORNTON
SubstitutionModelFactory(const Alphabet *alphabet, const GeneticCode *geneticCode)
Creates a new factory object with the given alphabet.
static const std::string STRAND_SYMMETRIC_REVERSIBLE
SubstitutionModelFactory & operator=(const SubstitutionModelFactory &smf)
static const std::string GENERAL_TIME_REVERSIBLE
static const std::string TAMURA_NEI