bpp::FullCodonFrequenciesSet Member List

This is the complete list of members for bpp::FullCodonFrequenciesSet, 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::FullCodonFrequenciesSet	inlinevirtual
F0	bpp::CodonFrequenciesSet	static
F1X4	bpp::CodonFrequenciesSet	static
F3X4	bpp::CodonFrequenciesSet	static
F61	bpp::CodonFrequenciesSet	static
fireParameterChanged(const ParameterList &parameters)	bpp::FullCodonFrequenciesSet	protected
FREQUENCE_CONSTRAINT_MILLI	bpp::FrequenciesSet	static
FREQUENCE_CONSTRAINT_SMALL	bpp::FrequenciesSet	static
FullCodonFrequenciesSet(const GeneticCode *gCode, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full")	bpp::FullCodonFrequenciesSet
FullCodonFrequenciesSet(const GeneticCode *gCode, const std::vector< double > &initFreqs, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full")	bpp::FullCodonFrequenciesSet
FullCodonFrequenciesSet(const FullCodonFrequenciesSet &fcfs)	bpp::FullCodonFrequenciesSet
getAlphabet() const	bpp::FullCodonFrequenciesSet	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
getFrequenciesSetForCodons(short option, const GeneticCode *gCode, const std::string &mgmtStopFreq="quadratic", unsigned short method=1)	bpp::CodonFrequenciesSet	static
getGeneticCode() const	bpp::FullCodonFrequenciesSet	inlinevirtual
getMethod() const	bpp::FullCodonFrequenciesSet	inline
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
normalize()	bpp::AbstractFrequenciesSet	inline
operator=(const FullCodonFrequenciesSet &fcfs)	bpp::FullCodonFrequenciesSet
bpp::AbstractFrequenciesSet::operator=(const AbstractFrequenciesSet &af)	bpp::AbstractFrequenciesSet	inline
pgc_	bpp::FullCodonFrequenciesSet	protected
setFrequencies(const std::vector< double > &frequencies)	bpp::FullCodonFrequenciesSet	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
setNamespace(const std::string &nameSpace)	bpp::FullCodonFrequenciesSet
sFreq_	bpp::FullCodonFrequenciesSet	private
updateFreq_()	bpp::FullCodonFrequenciesSet	protected