41 #ifndef _PROTEINFREQUENCIESSET_H_ 42 #define _PROTEINFREQUENCIESSET_H_ 44 #include <Bpp/Seq/Alphabet/ProteicAlphabet.h> 56 #ifndef NO_VIRTUAL_COV 79 FullProteinFrequenciesSet(
const ProteicAlphabet* alphabet,
bool allowNullFreqs =
false,
unsigned short method = 1,
const std::string& name =
"Full") :
81 FullProteinFrequenciesSet(
const ProteicAlphabet* alphabet,
const std::vector<double>& initFreqs,
bool allowNullFreqs =
false,
unsigned short method = 1,
const std::string& name =
"Full") :
84 #ifndef NO_VIRTUAL_COV 92 #ifndef NO_VIRTUAL_COV 120 #ifndef NO_VIRTUAL_COV 127 #ifndef NO_VIRTUAL_COV 138 #endif // _PROTEINFREQUENCIESSET_H_ FixedProteinFrequenciesSet(const ProteicAlphabet *alphabet, const std::string &name="Fixed")
Construction with uniform frequencies on the letters of the alphabet.
FixedProteinFrequenciesSet * clone() const
FrequenciesSet useful for homogeneous and stationary models.
const ProteicAlphabet * getAlphabet() const
FullProteinFrequenciesSet * clone() const
This class implements a state map where all resolved states are modeled.
FixedProteinFrequenciesSet(const ProteicAlphabet *alphabet, const std::vector< double > &initFreqs, const std::string &name="Fixed")
FrequenciesSet useful for homogeneous and stationary models, protein implementation.
Parametrize a set of state frequencies.
ProteinFrequenciesSet * clone() const =0
A generic FrequenciesSet allowing for the estimation of all frequencies.
Protein FrequenciesSet using 19 independent parameters to model the 20 frequencies.
const Alphabet * getAlphabet() const
FullProteinFrequenciesSet(const ProteicAlphabet *alphabet, const std::vector< double > &initFreqs, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full")
Parametrize a set of state frequencies for proteins.
const ProteicAlphabet * getAlphabet() const
FullProteinFrequenciesSet(const ProteicAlphabet *alphabet, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full")
const ProteicAlphabet * getAlphabet() const =0