44 #include "../AbstractSubstitutionModel.h" 45 #include "../FrequenciesSet/ProteinFrequenciesSet.h" 48 #include <Bpp/Seq/Alphabet/ProteicAlphabet.h> 79 JTT92(
const ProteicAlphabet* alpha);
92 AbstractParameterAliasable(model),
100 AbstractParameterAliasable::operator=(model);
110 #ifndef NO_VIRTUAL_COV 120 if (
freqSet_->getNamespace().find(
"JTT92+F.")!=std::string::npos)
128 freqSet_->matchParametersValues(parameters);
138 addParameters_(
freqSet_->getParameters());
143 void setFreqFromData(
const SequenceContainer& data,
double pseudoCount = 0);
virtual void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
ProteinFrequenciesSet * freqSet_
void setFreqFromData(const SequenceContainer &data, double pseudoCount=0)
Set equilibrium frequencies equal to the frequencies estimated from the data.
Specialized interface for protein substitution model.
virtual const std::vector< double > getFrequencies() const =0
Vdouble freq_
The vector of equilibrium frequencies.
Parametrize a set of state frequencies.
ProteinFrequenciesSet * clone() const =0
JTT92(const JTT92 &model)
AbstractSubstitutionModel & operator=(const AbstractSubstitutionModel &model)
Partial implementation of the ReversibleSubstitutionModel interface.
Parametrize a set of state frequencies for proteins.
JTT92(const ProteicAlphabet *alpha)
Build a simple JTT92 model, with original equilibrium frequencies.
The Jones, Taylor and Thornton substitution model for proteins.
JTT92 & operator=(const JTT92 &model)
void setFrequenciesSet(const ProteinFrequenciesSet &freqSet)
std::string getName() const
Get the name of the model.
const FrequenciesSet * getFrequenciesSet() const
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.