41 #ifndef _NUCLEOTIDEFREQUENCIESSET_H_ 42 #define _NUCLEOTIDEFREQUENCIESSET_H_ 45 #include <Bpp/Seq/Alphabet/NucleicAlphabet.h> 56 #ifndef NO_VIRTUAL_COV 74 addParameter_(
new Parameter(
"GC.theta", 0.5, &Parameter::PROP_CONSTRAINT_IN));
81 addParameter_(
new Parameter(
"GC.theta", theta, &Parameter::PROP_CONSTRAINT_IN));
86 #ifndef NO_VIRTUAL_COV 94 #ifndef NO_VIRTUAL_COV 135 FullNucleotideFrequenciesSet(
const NucleicAlphabet* alphabet,
double theta,
double theta1,
double theta2,
bool allowNullFreqs =
false,
const std::string& name =
"Full");
137 #ifndef NO_VIRTUAL_COV 145 #ifndef NO_VIRTUAL_COV 179 #ifndef NO_VIRTUAL_COV 186 #ifndef NO_VIRTUAL_COV 197 #endif // _NUCLEOTIDEFREQUENCIESSET_H_ const NucleicAlphabet * getAlphabet() const
void fireParameterChanged(const ParameterList ¶meters)
void fireParameterChanged(const ParameterList ¶meters)
FrequenciesSet useful for homogeneous and stationary models.
This class implements a state map where all resolved states are modeled.
FixedNucleotideFrequenciesSet(const NucleicAlphabet *alphabet, const std::string &name="Fixed")
Construction with uniform frequencies on the letters of the alphabet.
Parametrize a set of state frequencies for nucleotides.
const NucleicAlphabet * getAlphabet() const
Parametrize a set of state frequencies.
FullNucleotideFrequenciesSet(const NucleicAlphabet *alphabet, bool allowNullFreqs=false, const std::string &name="Full")
const NucleicAlphabet * getAlphabet() const
GCFrequenciesSet(const NucleicAlphabet *alphabet, double theta)
FixedNucleotideFrequenciesSet * clone() const
Nucleotide FrequenciesSet using three independent parameters (theta, theta1, theta2) to modelize the ...
GCFrequenciesSet * clone() const
const Alphabet * getAlphabet() const
NucleotideFrequenciesSet * clone() const =0
double & getFreq_(size_t i)
void setFrequencies(const std::vector< double > &frequencies)
Set the parameters in order to match a given set of frequencies.
FrequenciesSet useful for homogeneous and stationary models, nucleotide implementation.
FullNucleotideFrequenciesSet * clone() const
void setFrequencies(const std::vector< double > &frequencies)
Set the parameters in order to match a given set of frequencies.
const NucleicAlphabet * getAlphabet() const =0
Nucleotide FrequenciesSet using only one parameter, the GC content.
GCFrequenciesSet(const NucleicAlphabet *alphabet)
FixedNucleotideFrequenciesSet(const NucleicAlphabet *alphabet, const std::vector< double > &initFreqs, const std::string &name="Fixed")
Basic implementation of the FrequenciesSet interface.