bpp::UserProteinSubstitutionModel Member List

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

AbstractReversibleSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix)	bpp::AbstractReversibleSubstitutionModel	inline
AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix)	bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
bpp::addRateParameter()=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::addRateParameter()	bpp::AbstractSubstitutionModel	virtual
alphabet_	bpp::AbstractSubstitutionModel	protected
clone() const	bpp::UserProteinSubstitutionModel	inlinevirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
d2pijt_	bpp::AbstractSubstitutionModel	mutableprotected
bpp::dPij_dt(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::dPij_dt(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
dpijt_	bpp::AbstractSubstitutionModel	mutableprotected
eigenDecompose_	bpp::AbstractSubstitutionModel	protected
eigenValues_	bpp::AbstractSubstitutionModel	protected
bpp::enableEigenDecomposition(bool yn)=0	bpp::SubstitutionModel	pure virtual
bpp::enableEigenDecomposition()=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::enableEigenDecomposition(bool yn)	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::AbstractReversibleSubstitutionModel::enableEigenDecomposition()	bpp::AbstractSubstitutionModel	inlinevirtual
exchangeability_	bpp::AbstractSubstitutionModel	protected
fireParameterChanged(const ParameterList &parameters)	bpp::UserProteinSubstitutionModel	inlinevirtual
bpp::freq(size_t i) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::freq(size_t i) const	bpp::AbstractSubstitutionModel	inlinevirtual
freq_	bpp::AbstractSubstitutionModel	protected
freqSet_	bpp::UserProteinSubstitutionModel	private
generator_	bpp::AbstractSubstitutionModel	protected
bpp::getAlphabet() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getAlphabet() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStateAsChar(size_t index) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getAlphabetStateAsChar(size_t index) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStateAsInt(size_t index) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getAlphabetStateAsInt(size_t index) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStates() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getAlphabetStates() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getColumnRightEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getColumnRightEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getd2Pij_dt2(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getd2Pij_dt2(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getdPij_dt(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getdPij_dt(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getEigenValues() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getExchangeabilityMatrix() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getExchangeabilityMatrix() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getFrequencies() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getFrequencies() const	bpp::AbstractSubstitutionModel	inlinevirtual
getFrequenciesSet() const	bpp::UserProteinSubstitutionModel	inlinevirtual
bpp::getGenerator() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getGenerator() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getIEigenValues() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getIEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getInitValue(size_t i, int state) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getInitValue(size_t i, int state) const	bpp::AbstractSubstitutionModel	virtual
bpp::getModelStates(int code) const =0	bpp::SubstitutionModel	pure virtual
bpp::getModelStates(const std::string &code) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getModelStates(int code) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::AbstractReversibleSubstitutionModel::getModelStates(const std::string &code) const	bpp::AbstractSubstitutionModel	inlinevirtual
getName() const	bpp::UserProteinSubstitutionModel	virtual
getNumberOfStates() const	bpp::ProteinSubstitutionModel	inlinevirtual
getPath() const	bpp::UserProteinSubstitutionModel	inline
bpp::getPij_t(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getPij_t(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getRate() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getRate() const	bpp::AbstractSubstitutionModel	virtual
bpp::getRowLeftEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getRowLeftEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getScale() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getScale() const	bpp::AbstractSubstitutionModel	virtual
bpp::getStateMap() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::getStateMap() const	bpp::AbstractSubstitutionModel	inlinevirtual
iEigenValues_	bpp::AbstractSubstitutionModel	protected
bpp::isDiagonalizable() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::isDiagonalizable() const	bpp::AbstractSubstitutionModel	inlinevirtual
isDiagonalizable_	bpp::AbstractSubstitutionModel	protected
bpp::isNonSingular() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::isNonSingular() const	bpp::AbstractSubstitutionModel	inlinevirtual
isNonSingular_	bpp::AbstractSubstitutionModel	protected
leftEigenVectors_	bpp::AbstractSubstitutionModel	protected
operator=(const UserProteinSubstitutionModel &model)	bpp::UserProteinSubstitutionModel	inline
bpp::AbstractReversibleSubstitutionModel::operator=(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
path_	bpp::UserProteinSubstitutionModel	private
bpp::Pij_t(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::Pij_t(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
pijt_	bpp::AbstractSubstitutionModel	mutableprotected
bpp::Qij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::Qij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
rate_	bpp::AbstractSubstitutionModel	protected
readFromFile()	bpp::UserProteinSubstitutionModel	protected
ReversibleSubstitutionModel()	bpp::ReversibleSubstitutionModel	inline
rightEigenVectors_	bpp::AbstractSubstitutionModel	protected
bpp::setFreq(std::map< int, double > &frequencies)	bpp::SubstitutionModel	inlinevirtual
bpp::AbstractReversibleSubstitutionModel::setFreq(std::map< int, double > &)	bpp::AbstractSubstitutionModel	virtual
setFreqFromData(const SequenceContainer &data, double pseudoCount=0)	bpp::UserProteinSubstitutionModel	virtual
setFrequenciesSet(const ProteinFrequenciesSet &freqSet)	bpp::UserProteinSubstitutionModel	inline
bpp::setRate(double rate)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::setRate(double rate)	bpp::AbstractSubstitutionModel	virtual
bpp::setScale(double scale)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::setScale(double scale)	bpp::AbstractSubstitutionModel	virtual
bpp::Sij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractReversibleSubstitutionModel::Sij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
size_	bpp::AbstractSubstitutionModel	protected
stateMap_	bpp::AbstractSubstitutionModel	protected
SubstitutionModel()	bpp::SubstitutionModel	inline
tmpMat_	bpp::AbstractSubstitutionModel	mutableprotected
updateMatrices()	bpp::AbstractReversibleSubstitutionModel	protectedvirtual
UserProteinSubstitutionModel(const ProteicAlphabet *alpha, const std::string &path, const std::string &prefix)	bpp::UserProteinSubstitutionModel
UserProteinSubstitutionModel(const ProteicAlphabet *alpha, const std::string &path, ProteinFrequenciesSet *freqSet, const std::string &prefix, bool initFreqs=false)	bpp::UserProteinSubstitutionModel
UserProteinSubstitutionModel(const UserProteinSubstitutionModel &model)	bpp::UserProteinSubstitutionModel	inline
vPowGen_	bpp::AbstractSubstitutionModel	protected
~AbstractReversibleSubstitutionModel()	bpp::AbstractReversibleSubstitutionModel	inlinevirtual
~AbstractSubstitutionModel()	bpp::AbstractSubstitutionModel	inlinevirtual
~ProteinSubstitutionModel()	bpp::ProteinSubstitutionModel	inlinevirtual
~ReversibleSubstitutionModel()	bpp::ReversibleSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual
~UserProteinSubstitutionModel()	bpp::UserProteinSubstitutionModel	inlinevirtual