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

appName_	bpp::BppApplication	protected
BppApplication(int argc, char *argv[], const std::string &name, bool verbose=true, int warningLevel=1)	bpp::BppApplication
BppPhylogeneticsApplication(int argc, char *argv[], const std::string &name)	bpp::BppPhylogeneticsApplication	inline
BppSequenceApplication(int argc, char *argv[], const std::string &name)	bpp::BppSequenceApplication
displayParameters(const PhyloLikelihoodInterface &tl, bool displaylL=true) const	bpp::BppPhylogeneticsApplication	virtual
done()	bpp::BppApplication	virtual
fixLikelihood(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, std::shared_ptr< PhyloLikelihoodInterface > phylolik, const std::string &suffix="", bool suffixIsOptional=true) const	bpp::BppPhylogeneticsApplication	virtual
getAlignmentsMap(std::shared_ptr< const Alphabet > &alphabet, bool changeGapsToUnknownCharacters=true, bool optionalData=false, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const	bpp::BppSequenceApplication	virtual
getAlphabet(const string &suffix="", bool suffixIsOptional=true, bool allowGeneric=false) const	bpp::BppSequenceApplication	virtual
getCollection(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface > > &mSites, const std::map< size_t, std::shared_ptr< PhyloTree > > &mpTree, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const	bpp::BppPhylogeneticsApplication	virtual
getCollection(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface > > &mSites, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const	bpp::BppPhylogeneticsApplication	virtual
getConstAlignmentsMap(std::shared_ptr< const Alphabet > &alphabet, bool changeGapsToUnknownCharacters=true, bool optionalData=false, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const	bpp::BppSequenceApplication	virtual
getGeneticCode(std::shared_ptr< const Alphabet > &alphabet, const string &suffix="", bool suffixIsOptional=true) const	bpp::BppSequenceApplication	virtual
getParam(const std::string &name) const	bpp::BppApplication	virtual
getParam(const std::string &name)	bpp::BppApplication	virtual
getParams() const	bpp::BppApplication	virtual
getParams()	bpp::BppApplication	virtual
getPhyloLikelihoods(Context &context, std::map< size_t, std::shared_ptr< SequenceEvolution > > mSeqEvol, std::shared_ptr< SubstitutionProcessCollection > collection, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface > > &mSites, const std::string &suffix="", bool suffixIsOptional=true) const	bpp::BppPhylogeneticsApplication	virtual
getPhyloTreesMap(const std::map< size_t, std::shared_ptr< const AlignmentDataInterface > > &mSites, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const	bpp::BppPhylogeneticsApplication	virtual
getProcesses(std::shared_ptr< SubstitutionProcessCollection > collection, std::map< std::string, std::string > &unparsedParams, const std::string &suffix="", bool suffixIsOptional=true) const	bpp::BppPhylogeneticsApplication	virtual
getWarningLevel() const	bpp::BppApplication	virtual
help(const std::string &program) const	bpp::BppApplication	virtual
isVerbose() const	bpp::BppApplication	virtual
params_	bpp::BppApplication	protected
startTimer()	bpp::BppApplication	virtual
timerStarted_	bpp::BppApplication	protected
verbose_	bpp::BppApplication	protected
warn_	bpp::BppApplication	protected
~BppApplication()	bpp::BppApplication	virtual