40 #ifndef _MVAFREQUENCIESSET_H_ 41 #define _MVAFREQUENCIESSET_H_ 44 #include "../Protein/Coala.h" 67 #ifndef NO_VIRTUAL_COV 105 void setFrequencies(
const std::vector<double>& frequencies)
throw (DimensionException, Exception);
123 #endif // _MVAFREQUENCIESSET_H_ void computeCoordsFirstSpacePCA(std::vector< double > &tmpFreqs, std::vector< double > &freqs)
void fireParameterChanged(const ParameterList ¶meters)
RowMatrix< double > tPpalAxes_
MvaFrequenciesSet * clone() const
void setVectorOfColumnWeights(const std::vector< double > &cw)
RowMatrix< double > rowCoords_
void computeReverseCOA(const std::vector< double > &positions, std::vector< double > &tmpFreqs)
void setNbrOfAxes(const size_t &nAxes)
MvaFrequenciesSet(const ProteicAlphabet *alpha)
Constructor.
void computeCoordsFirstSpaceCOA(std::vector< double > &tmpFreqs, std::vector< double > &freqs)
const Alphabet * getAlphabet() const
std::map< std::string, std::string > paramValues_
Parametrize a set of state frequencies for proteins.
void computeReversePCA(const std::vector< double > &positions, std::vector< double > &tmpFreqs)
const ProteicAlphabet * getAlphabet() const
void setModelName(const std::string &modelName)
void setParamValues(std::map< std::string, std::string > &valuesSettings)
MvaFrequenciesSet & operator=(const MvaFrequenciesSet &mfs)
void initSet(CoalaCore *coala)
std::vector< double > columnWeights_
void setFrequencies(const std::vector< double > &frequencies)
Set the parameters in order to match a given set of frequencies.
void setTransposeMatrixOfPpalAxes(const RowMatrix< double > &matrix)
A frequencies set used to estimate frequencies at the root with the COaLA model. Frequencies at the r...
void setMatrixOfRowCoords(const RowMatrix< double > &matrix)
AbstractFrequenciesSet & operator=(const AbstractFrequenciesSet &af)
This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid...
Basic implementation of the FrequenciesSet interface.