40 #ifndef _USERPROTEINSUBSTITUTIONMODEL_H_ 41 #define _USERPROTEINSUBSTITUTIONMODEL_H_ 44 #include "../AbstractSubstitutionModel.h" 45 #include "../FrequenciesSet/ProteinFrequenciesSet.h" 48 #include <Bpp/Seq/Alphabet/ProteicAlphabet.h> 81 const ProteicAlphabet* alpha,
82 const std::string& path,
83 const std::string& prefix);
96 const ProteicAlphabet* alpha,
97 const std::string& path,
99 const std::string& prefix,
100 bool initFreqs =
false 104 AbstractParameterAliasable(model),
113 AbstractParameterAliasable::operator=(model);
123 #ifndef NO_VIRTUAL_COV 136 freqSet_->matchParametersValues(parameters);
146 addParameters_(
freqSet_->getParameters());
151 void setFreqFromData(
const SequenceContainer& data,
double pseudoCount = 0);
160 #endif //_USERPROTEINSUBSTITUTIONMODEL_H_ std::string getName() const
Get the name of the model.
ProteinFrequenciesSet * freqSet_
virtual void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
void setFrequenciesSet(const ProteinFrequenciesSet &freqSet)
virtual ~UserProteinSubstitutionModel()
UserProteinSubstitutionModel & operator=(const UserProteinSubstitutionModel &model)
void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
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)
UserProteinSubstitutionModel(const ProteicAlphabet *alpha, const std::string &path, const std::string &prefix)
Build a protein model from a PAML file, with original equilibrium frequencies.
Partial implementation of the ReversibleSubstitutionModel interface.
Parametrize a set of state frequencies for proteins.
const FrequenciesSet * getFrequenciesSet() const
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
UserProteinSubstitutionModel * clone() const
const std::string & getPath() const
UserProteinSubstitutionModel(const UserProteinSubstitutionModel &model)
void setFreqFromData(const SequenceContainer &data, double pseudoCount=0)
Set equilibrium frequencies equal to the frequencies estimated from the data.
Build an empirical protein substitution model from a file.