AbstractFrequenciesSet(StateMap *stateMap, const std::string &prefix, const std::string &name) | bpp::AbstractFrequenciesSet | inline |
AbstractFrequenciesSet(const AbstractFrequenciesSet &af) | bpp::AbstractFrequenciesSet | inline |
clone() const | bpp::FullFrequenciesSet | inlinevirtual |
fireParameterChanged(const ParameterList ¶meters) | bpp::FullFrequenciesSet | protected |
FREQUENCE_CONSTRAINT_MILLI | bpp::FrequenciesSet | static |
FREQUENCE_CONSTRAINT_SMALL | bpp::FrequenciesSet | static |
FullFrequenciesSet(StateMap *stateMap, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full.") | bpp::FullFrequenciesSet | |
FullFrequenciesSet(StateMap *stateMap, const std::vector< double > &initFreqs, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full.") | bpp::FullFrequenciesSet | |
getAlphabet() const | bpp::AbstractFrequenciesSet | inlinevirtual |
getAlphabetStatesFrequencies() const | bpp::AbstractFrequenciesSet | virtual |
getFreq_(size_t i) | bpp::AbstractFrequenciesSet | inlineprotected |
getFreq_(size_t i) const | bpp::AbstractFrequenciesSet | inlineprotected |
getFrequencies() const | bpp::AbstractFrequenciesSet | inlinevirtual |
getFrequencies_() | bpp::AbstractFrequenciesSet | inlineprotected |
getMethod() const | bpp::FullFrequenciesSet | inline |
getName() const | bpp::AbstractFrequenciesSet | inlinevirtual |
getNumberOfFrequencies() const | bpp::AbstractFrequenciesSet | inlinevirtual |
getStateMap() const | bpp::AbstractFrequenciesSet | inlinevirtual |
normalize() | bpp::AbstractFrequenciesSet | inline |
operator=(const AbstractFrequenciesSet &af) | bpp::AbstractFrequenciesSet | inline |
setFrequencies(const std::vector< double > &frequencies) | bpp::FullFrequenciesSet | virtual |
setFrequencies_(const std::vector< double > &frequencies) | bpp::AbstractFrequenciesSet | inlineprotected |
setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies) | bpp::AbstractFrequenciesSet | virtual |
setNamespace(const std::string &nameSpace) | bpp::FullFrequenciesSet | |
sFreq_ | bpp::FullFrequenciesSet | private |
updateFreq_() | bpp::FullFrequenciesSet | private |