bpp::MvaFrequenciesSet Member List

This is the complete list of members for bpp::MvaFrequenciesSet, including all inherited members.

AbstractFrequenciesSet(StateMap *stateMap, const std::string &prefix, const std::string &name)	bpp::AbstractFrequenciesSet	inline
AbstractFrequenciesSet(const AbstractFrequenciesSet &af)	bpp::AbstractFrequenciesSet	inline
clone() const	bpp::MvaFrequenciesSet	inlinevirtual
columnWeights_	bpp::MvaFrequenciesSet	protected
computeCoordsFirstSpaceCOA(std::vector< double > &tmpFreqs, std::vector< double > &freqs)	bpp::MvaFrequenciesSet
computeCoordsFirstSpacePCA(std::vector< double > &tmpFreqs, std::vector< double > &freqs)	bpp::MvaFrequenciesSet
computeReverseCOA(const std::vector< double > &positions, std::vector< double > &tmpFreqs)	bpp::MvaFrequenciesSet
computeReversePCA(const std::vector< double > &positions, std::vector< double > &tmpFreqs)	bpp::MvaFrequenciesSet
defineParameters()	bpp::MvaFrequenciesSet
fireParameterChanged(const ParameterList &parameters)	bpp::MvaFrequenciesSet
FREQUENCE_CONSTRAINT_MILLI	bpp::FrequenciesSet	static
FREQUENCE_CONSTRAINT_SMALL	bpp::FrequenciesSet	static
getAlphabet() const	bpp::MvaFrequenciesSet	inlinevirtual
bpp::getAlphabetStatesFrequencies() const =0	bpp::FrequenciesSet	pure virtual
bpp::AbstractFrequenciesSet::getAlphabetStatesFrequencies() const	bpp::AbstractFrequenciesSet	virtual
getFreq_(size_t i)	bpp::AbstractFrequenciesSet	inlineprotected
getFreq_(size_t i) const	bpp::AbstractFrequenciesSet	inlineprotected
bpp::getFrequencies() const =0	bpp::FrequenciesSet	pure virtual
bpp::AbstractFrequenciesSet::getFrequencies() const	bpp::AbstractFrequenciesSet	inlinevirtual
getFrequencies_()	bpp::AbstractFrequenciesSet	inlineprotected
bpp::getName() const =0	bpp::FrequenciesSet	pure virtual
bpp::AbstractFrequenciesSet::getName() const	bpp::AbstractFrequenciesSet	inlinevirtual
bpp::getNumberOfFrequencies() const =0	bpp::FrequenciesSet	pure virtual
bpp::AbstractFrequenciesSet::getNumberOfFrequencies() const	bpp::AbstractFrequenciesSet	inlinevirtual
bpp::getStateMap() const =0	bpp::FrequenciesSet	pure virtual
bpp::AbstractFrequenciesSet::getStateMap() const	bpp::AbstractFrequenciesSet	inlinevirtual
initSet(CoalaCore *coala)	bpp::MvaFrequenciesSet
model_	bpp::MvaFrequenciesSet	protected
MvaFrequenciesSet(const ProteicAlphabet *alpha)	bpp::MvaFrequenciesSet
nbrOfAxes_	bpp::MvaFrequenciesSet	protected
normalize()	bpp::AbstractFrequenciesSet	inline
operator=(const MvaFrequenciesSet &mfs)	bpp::MvaFrequenciesSet	inline
bpp::AbstractFrequenciesSet::operator=(const AbstractFrequenciesSet &af)	bpp::AbstractFrequenciesSet	inline
paramValues_	bpp::MvaFrequenciesSet	protected
rowCoords_	bpp::MvaFrequenciesSet	protected
setFrequencies(const std::vector< double > &frequencies)	bpp::MvaFrequenciesSet	virtual
setFrequencies_(const std::vector< double > &frequencies)	bpp::AbstractFrequenciesSet	inlineprotected
bpp::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)=0	bpp::FrequenciesSet	pure virtual
bpp::AbstractFrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)	bpp::AbstractFrequenciesSet	virtual
setMatrixOfRowCoords(const RowMatrix< double > &matrix)	bpp::MvaFrequenciesSet	inline
setModelName(const std::string &modelName)	bpp::MvaFrequenciesSet	inline
setNbrOfAxes(const size_t &nAxes)	bpp::MvaFrequenciesSet	inline
setParamValues(std::map< std::string, std::string > &valuesSettings)	bpp::MvaFrequenciesSet	inline
setTransposeMatrixOfPpalAxes(const RowMatrix< double > &matrix)	bpp::MvaFrequenciesSet	inline
setVectorOfColumnWeights(const std::vector< double > &cw)	bpp::MvaFrequenciesSet	inline
tPpalAxes_	bpp::MvaFrequenciesSet	protected
updateFrequencies()	bpp::MvaFrequenciesSet