bpp::CodonFromIndependentFrequenciesSet Member List

This is the complete list of members for bpp::CodonFromIndependentFrequenciesSet, 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
AbstractWordFrequenciesSet(StateMap *stateMap, const std::string &prefix="", const std::string &name="")	bpp::AbstractWordFrequenciesSet
AbstractWordFrequenciesSet(const AbstractWordFrequenciesSet &af)	bpp::AbstractWordFrequenciesSet	inline
clone() const	bpp::CodonFromIndependentFrequenciesSet	inlinevirtual
CodonFromIndependentFrequenciesSet(const GeneticCode *gCode, const std::vector< FrequenciesSet *> &freqvector, const std::string &name="Codon", const std::string &mgmtStopFreq="quadratic")	bpp::CodonFromIndependentFrequenciesSet
CodonFromIndependentFrequenciesSet(const CodonFromIndependentFrequenciesSet &iwfs)	bpp::CodonFromIndependentFrequenciesSet
F0	bpp::CodonFrequenciesSet	static
F1X4	bpp::CodonFrequenciesSet	static
F3X4	bpp::CodonFrequenciesSet	static
F61	bpp::CodonFrequenciesSet	static
fireParameterChanged(const ParameterList &pl)	bpp::WordFromIndependentFrequenciesSet
FREQUENCE_CONSTRAINT_MILLI	bpp::FrequenciesSet	static
FREQUENCE_CONSTRAINT_SMALL	bpp::FrequenciesSet	static
getAlphabet() const	bpp::CodonFromIndependentFrequenciesSet	virtual
bpp::getAlphabetStatesFrequencies() const =0	bpp::FrequenciesSet	pure virtual
bpp::WordFromIndependentFrequenciesSet::bpp::AbstractFrequenciesSet::getAlphabetStatesFrequencies() const	bpp::AbstractFrequenciesSet	virtual
getDescription() const	bpp::WordFromIndependentFrequenciesSet
getFreq_(size_t i)	bpp::AbstractFrequenciesSet	inlineprotected
getFreq_(size_t i) const	bpp::AbstractFrequenciesSet	inlineprotected
bpp::getFrequencies() const =0	bpp::FrequenciesSet	pure virtual
bpp::WordFromIndependentFrequenciesSet::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
getFrequenciesSetForLetter(size_t i) const	bpp::WordFromIndependentFrequenciesSet	inlinevirtual
getGeneticCode() const	bpp::CodonFromIndependentFrequenciesSet	inlinevirtual
getLength() const	bpp::WordFromIndependentFrequenciesSet	virtual
bpp::getName() const =0	bpp::FrequenciesSet	pure virtual
bpp::WordFromIndependentFrequenciesSet::bpp::AbstractFrequenciesSet::getName() const	bpp::AbstractFrequenciesSet	inlinevirtual
bpp::getNumberOfFrequencies() const =0	bpp::FrequenciesSet	pure virtual
bpp::WordFromIndependentFrequenciesSet::bpp::AbstractFrequenciesSet::getNumberOfFrequencies() const	bpp::AbstractFrequenciesSet	inlinevirtual
getSizeFromVector(const std::vector< FrequenciesSet *> &freqVector)	bpp::AbstractWordFrequenciesSet	protectedvirtual
bpp::getStateMap() const =0	bpp::FrequenciesSet	pure virtual
bpp::WordFromIndependentFrequenciesSet::bpp::AbstractFrequenciesSet::getStateMap() const	bpp::AbstractFrequenciesSet	inlinevirtual
mgmtStopFreq_	bpp::CodonFromIndependentFrequenciesSet	private
mStopNeigh_	bpp::CodonFromIndependentFrequenciesSet	private
normalize()	bpp::AbstractFrequenciesSet	inline
operator=(const CodonFromIndependentFrequenciesSet &iwfs)	bpp::CodonFromIndependentFrequenciesSet
bpp::WordFromIndependentFrequenciesSet::operator=(const WordFromIndependentFrequenciesSet &iwfs)	bpp::WordFromIndependentFrequenciesSet
bpp::AbstractWordFrequenciesSet::operator=(const AbstractWordFrequenciesSet &af)	bpp::AbstractWordFrequenciesSet	inline
bpp::AbstractFrequenciesSet::operator=(const AbstractFrequenciesSet &af)	bpp::AbstractFrequenciesSet	inline
pgc_	bpp::CodonFromIndependentFrequenciesSet	private
bpp::setFrequencies(const std::vector< double > &frequencies)=0	bpp::FrequenciesSet	pure virtual
bpp::WordFromIndependentFrequenciesSet::setFrequencies(const std::vector< double > &frequencies)	bpp::WordFromIndependentFrequenciesSet	virtual
setFrequencies_(const std::vector< double > &frequencies)	bpp::AbstractFrequenciesSet	inlineprotected
bpp::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)=0	bpp::FrequenciesSet	pure virtual
bpp::WordFromIndependentFrequenciesSet::bpp::AbstractFrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)	bpp::AbstractFrequenciesSet	virtual
setNamespace(const std::string &prefix)	bpp::WordFromIndependentFrequenciesSet
updateFrequencies()	bpp::CodonFromIndependentFrequenciesSet	virtual
vFreq_	bpp::WordFromIndependentFrequenciesSet	protected
vNestedPrefix_	bpp::WordFromIndependentFrequenciesSet	protected
WordFromIndependentFrequenciesSet(const WordAlphabet *pWA, const std::vector< FrequenciesSet *> &freqVector, const std::string &prefix="", const std::string &name="WordFromIndependent")	bpp::WordFromIndependentFrequenciesSet
WordFromIndependentFrequenciesSet(const WordFromIndependentFrequenciesSet &iwfs)	bpp::WordFromIndependentFrequenciesSet
~AbstractWordFrequenciesSet()	bpp::AbstractWordFrequenciesSet	virtual
~CodonFromIndependentFrequenciesSet()	bpp::CodonFromIndependentFrequenciesSet	inlinevirtual
~WordFromIndependentFrequenciesSet()	bpp::WordFromIndependentFrequenciesSet