| 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::CodonFromUniqueFrequenciesSet | inlinevirtual |
| CodonFromUniqueFrequenciesSet(const GeneticCode *gCode, FrequenciesSet *pfreq, const std::string &name="Codon", const std::string &mgmtStopFreq="quadratic") | bpp::CodonFromUniqueFrequenciesSet | |
| CodonFromUniqueFrequenciesSet(const CodonFromUniqueFrequenciesSet &iwfs) | bpp::CodonFromUniqueFrequenciesSet | |
| F0 | bpp::CodonFrequenciesSet | static |
| F1X4 | bpp::CodonFrequenciesSet | static |
| F3X4 | bpp::CodonFrequenciesSet | static |
| F61 | bpp::CodonFrequenciesSet | static |
| fireParameterChanged(const ParameterList &pl) | bpp::WordFromUniqueFrequenciesSet | virtual |
| FREQUENCE_CONSTRAINT_MILLI | bpp::FrequenciesSet | static |
| FREQUENCE_CONSTRAINT_SMALL | bpp::FrequenciesSet | static |
| getAlphabet() const | bpp::CodonFromUniqueFrequenciesSet | virtual |
| bpp::getAlphabetStatesFrequencies() const =0 | bpp::FrequenciesSet | pure virtual |
| bpp::WordFromUniqueFrequenciesSet::bpp::AbstractFrequenciesSet::getAlphabetStatesFrequencies() const | bpp::AbstractFrequenciesSet | virtual |
| getDescription() const | bpp::WordFromUniqueFrequenciesSet | |
| getFreq_(size_t i) | bpp::AbstractFrequenciesSet | inlineprotected |
| getFreq_(size_t i) const | bpp::AbstractFrequenciesSet | inlineprotected |
| bpp::getFrequencies() const =0 | bpp::FrequenciesSet | pure virtual |
| bpp::WordFromUniqueFrequenciesSet::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::WordFromUniqueFrequenciesSet | inlinevirtual |
| getGeneticCode() const | bpp::CodonFromUniqueFrequenciesSet | inlinevirtual |
| getLength() const | bpp::WordFromUniqueFrequenciesSet | inlinevirtual |
| bpp::getName() const =0 | bpp::FrequenciesSet | pure virtual |
| bpp::WordFromUniqueFrequenciesSet::bpp::AbstractFrequenciesSet::getName() const | bpp::AbstractFrequenciesSet | inlinevirtual |
| bpp::getNumberOfFrequencies() const =0 | bpp::FrequenciesSet | pure virtual |
| bpp::WordFromUniqueFrequenciesSet::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::WordFromUniqueFrequenciesSet::bpp::AbstractFrequenciesSet::getStateMap() const | bpp::AbstractFrequenciesSet | inlinevirtual |
| length_ | bpp::WordFromUniqueFrequenciesSet | protected |
| mgmtStopFreq_ | bpp::CodonFromUniqueFrequenciesSet | private |
| mStopNeigh_ | bpp::CodonFromUniqueFrequenciesSet | private |
| NestedPrefix_ | bpp::WordFromUniqueFrequenciesSet | protected |
| normalize() | bpp::AbstractFrequenciesSet | inline |
| operator=(const CodonFromUniqueFrequenciesSet &iwfs) | bpp::CodonFromUniqueFrequenciesSet | |
| bpp::WordFromUniqueFrequenciesSet::operator=(const WordFromUniqueFrequenciesSet &iwfs) | bpp::WordFromUniqueFrequenciesSet | |
| bpp::AbstractWordFrequenciesSet::operator=(const AbstractWordFrequenciesSet &af) | bpp::AbstractWordFrequenciesSet | inline |
| bpp::AbstractFrequenciesSet::operator=(const AbstractFrequenciesSet &af) | bpp::AbstractFrequenciesSet | inline |
| pFreq_ | bpp::WordFromUniqueFrequenciesSet | protected |
| pgc_ | bpp::CodonFromUniqueFrequenciesSet | private |
| bpp::setFrequencies(const std::vector< double > &frequencies)=0 | bpp::FrequenciesSet | pure virtual |
| bpp::WordFromUniqueFrequenciesSet::setFrequencies(const std::vector< double > &frequencies) | bpp::WordFromUniqueFrequenciesSet | virtual |
| setFrequencies_(const std::vector< double > &frequencies) | bpp::AbstractFrequenciesSet | inlineprotected |
| bpp::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)=0 | bpp::FrequenciesSet | pure virtual |
| bpp::WordFromUniqueFrequenciesSet::bpp::AbstractFrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies) | bpp::AbstractFrequenciesSet | virtual |
| setNamespace(const std::string &prefix) | bpp::WordFromUniqueFrequenciesSet | |
| updateFrequencies() | bpp::CodonFromUniqueFrequenciesSet | virtual |
| WordFromUniqueFrequenciesSet(const WordAlphabet *pWA, FrequenciesSet *pabsfreq, const std::string &prefix="", const std::string &name="WordFromUnique") | bpp::WordFromUniqueFrequenciesSet | |
| WordFromUniqueFrequenciesSet(const WordFromUniqueFrequenciesSet &iwfs) | bpp::WordFromUniqueFrequenciesSet | |
| ~AbstractWordFrequenciesSet() | bpp::AbstractWordFrequenciesSet | virtual |
| ~CodonFromUniqueFrequenciesSet() | bpp::CodonFromUniqueFrequenciesSet | inlinevirtual |
| ~WordFromUniqueFrequenciesSet() | bpp::WordFromUniqueFrequenciesSet | |
1.8.14