44 #include "../AbstractSubstitutionModel.h" 45 #include "../FrequenciesSet/ProteinFrequenciesSet.h" 48 #include <Bpp/Seq/Alphabet/ProteicAlphabet.h> 84 WAG01(
const ProteicAlphabet* alpha);
97 AbstractParameterAliasable(model),
105 AbstractParameterAliasable::operator=(model);
115 #ifndef NO_VIRTUAL_COV 125 if (
freqSet_->getNamespace().find(
"WAG01+F.")!=std::string::npos)
133 freqSet_->matchParametersValues(parameters);
143 addParameters_(
freqSet_->getParameters());
148 void setFreqFromData(
const SequenceContainer& data,
double pseudoCount = 0);
virtual void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
The Whelan and Goldman substitution model for proteins.
void setFrequenciesSet(const ProteinFrequenciesSet &freqSet)
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
AbstractSubstitutionModel & operator=(const AbstractSubstitutionModel &model)
Partial implementation of the ReversibleSubstitutionModel interface.
WAG01 & operator=(const WAG01 &model)
Parametrize a set of state frequencies for proteins.
void setFreqFromData(const SequenceContainer &data, double pseudoCount=0)
Set equilibrium frequencies equal to the frequencies estimated from the data.
WAG01(const ProteicAlphabet *alpha)
Build a simple WAG01 model, with original equilibrium frequencies.
ProteinFrequenciesSet * freqSet_
void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
const FrequenciesSet * getFrequenciesSet() const
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
std::string getName() const
Get the name of the model.
WAG01(const WAG01 &model)