bpp-phyl  2.2.0
bpp::MarkovModulatedFrequenciesSet Member List

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

AbstractFrequenciesSet(StateMap *stateMap, const std::string &prefix, const std::string &name)bpp::AbstractFrequenciesSetinline
AbstractFrequenciesSet(const AbstractFrequenciesSet &af)bpp::AbstractFrequenciesSetinline
clone() constbpp::MarkovModulatedFrequenciesSetinlinevirtual
fireParameterChanged(const ParameterList &pl)bpp::MarkovModulatedFrequenciesSetinline
freqSet_bpp::MarkovModulatedFrequenciesSetprivate
FREQUENCE_CONSTRAINT_MILLIbpp::FrequenciesSetstatic
FREQUENCE_CONSTRAINT_SMALLbpp::FrequenciesSetstatic
getAlphabet() constbpp::AbstractFrequenciesSetinlinevirtual
getAlphabetStatesFrequencies() constbpp::AbstractFrequenciesSetvirtual
getFreq_(size_t i)bpp::AbstractFrequenciesSetinlineprotected
getFreq_(size_t i) constbpp::AbstractFrequenciesSetinlineprotected
getFrequencies() constbpp::AbstractFrequenciesSetinlinevirtual
getFrequencies_()bpp::AbstractFrequenciesSetinlineprotected
getName() constbpp::AbstractFrequenciesSetinlinevirtual
getNumberOfFrequencies() constbpp::AbstractFrequenciesSetinlinevirtual
getStateMap() constbpp::AbstractFrequenciesSetinlinevirtual
getStatesFrequenciesSet() constbpp::MarkovModulatedFrequenciesSetinline
MarkovModulatedFrequenciesSet(FrequenciesSet *freqSet, const std::vector< double > &rateFreqs)bpp::MarkovModulatedFrequenciesSet
MarkovModulatedFrequenciesSet(const MarkovModulatedFrequenciesSet &mmfs)bpp::MarkovModulatedFrequenciesSetinline
normalize()bpp::AbstractFrequenciesSetinline
operator=(const MarkovModulatedFrequenciesSet &mmfs)bpp::MarkovModulatedFrequenciesSetinline
bpp::AbstractFrequenciesSet::operator=(const AbstractFrequenciesSet &af)bpp::AbstractFrequenciesSetinline
rateFreqs_bpp::MarkovModulatedFrequenciesSetprivate
setFrequencies(const std::vector< double > &frequencies)bpp::MarkovModulatedFrequenciesSetinlinevirtual
setFrequencies_(const std::vector< double > &frequencies)bpp::AbstractFrequenciesSetinlineprotected
setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)bpp::AbstractFrequenciesSetvirtual
~MarkovModulatedFrequenciesSet()bpp::MarkovModulatedFrequenciesSetinlinevirtual