bpp::DataSet Member List

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

addAlleleInfoByLocusName(const std::string &locus_name, const AlleleInfo &allele)	bpp::DataSet
addAlleleInfoByLocusPosition(size_t locus_position, const AlleleInfo &allele)	bpp::DataSet
addEmptyGroup(size_t group_id)	bpp::DataSet
addEmptyIndividualToGroup(size_t groupPosition, const std::string &individual_id)	bpp::DataSet
addGroup(const Group &group)	bpp::DataSet
addIndividualSequenceInGroup(size_t groupPosition, size_t individualPosition, size_t sequencePosition, std::unique_ptr< Sequence > &sequence)	bpp::DataSet
addIndividualToGroup(size_t groupPosition, const Individual &individual)	bpp::DataSet
addLocality(const Locality< double > &locality)	bpp::DataSet
alphabet() const	bpp::DataSet	inline
analyzedLoci() const	bpp::DataSet	inline
analyzedLoci_	bpp::DataSet	private
DataSet()	bpp::DataSet	inline
DataSet(const DataSet &ds)	bpp::DataSet
deleteAnalyzedLoci()	bpp::DataSet	inline
deleteGroupAtPosition(size_t groupPosition)	bpp::DataSet
deleteIndividualAtPositionFromGroup(size_t groupPosition, size_t individualPosition)	bpp::DataSet
deleteIndividualByIdFromGroup(size_t groupPosition, const std::string &individualId)	bpp::DataSet
deleteIndividualGenotypeInGroup(size_t groupPosition, size_t individualPosition)	bpp::DataSet
deleteIndividualSequenceAtPositionInGroup(size_t groupPosition, size_t individualPosition, size_t sequencePosition)	bpp::DataSet
deleteIndividualSequenceByNameInGroup(size_t groupPosition, size_t individualPosition, const std::string &sequenceName)	bpp::DataSet
deleteLocalityAtPosition(size_t localityPosition)	bpp::DataSet
deleteLocalityByName(const std::string &name)	bpp::DataSet
getAlphabet() const	bpp::DataSet	inline
getAlphabetType() const	bpp::DataSet	inline
getGroupAtPosition(size_t groupPosition) const	bpp::DataSet
getGroupById(size_t group_id) const	bpp::DataSet
getGroupName(size_t group_id) const	bpp::DataSet
getGroupPosition(size_t group_id) const	bpp::DataSet
getIndividualAtPositionFromGroup(size_t groupPosition, size_t individualPosition) const	bpp::DataSet
getIndividualByIdFromGroup(size_t groupPosition, const std::string &individualId) const	bpp::DataSet
getIndividualLocalityInGroup(size_t groupPosition, size_t individualPosition) const	bpp::DataSet
getIndividualMonolocusGenotypeInGroup(size_t groupPosition, size_t individualPosition, size_t locusPosition) const	bpp::DataSet
getIndividualNumberOfSequencesInGroup(size_t groupPosition, size_t individualPosition) const	bpp::DataSet
getIndividualPositionInGroup(size_t groupPosition, const std::string &individual_id) const	bpp::DataSet
getIndividualSequenceAtPositionInGroup(size_t groupPosition, size_t individualPosition, size_t sequencePosition) const	bpp::DataSet
getIndividualSequenceByNameInGroup(size_t groupPosition, size_t individualPosition, const std::string &sequenceName) const	bpp::DataSet
getIndividualSequencePositionInGroup(size_t groupPosition, size_t individualPosition, const std::string &sequenceName) const	bpp::DataSet
getIndividualSequencesNamesInGroup(size_t groupPosition, size_t individualPosition) const	bpp::DataSet
getIndividualSexInGroup(size_t groupPosition, size_t individualPosition) const	bpp::DataSet
getLocalityAtPosition(size_t localityPosition) const	bpp::DataSet
getLocalityByName(const std::string &name) const	bpp::DataSet
getLocalityPosition(const std::string &name) const	bpp::DataSet
getLocusInfoAtPosition(size_t locus_position) const	bpp::DataSet
getLocusInfoByName(const std::string &locus_name) const	bpp::DataSet
getNumberOfGroups() const	bpp::DataSet
getNumberOfIndividualsInGroup(size_t groupPosition) const	bpp::DataSet
getNumberOfLocalities() const	bpp::DataSet	inline
getNumberOfLoci() const	bpp::DataSet
getPloidyByLocusName(const std::string &locus_name) const	bpp::DataSet
getPloidyByLocusPosition(size_t locus_position) const	bpp::DataSet
getPolymorphismMultiGContainer() const	bpp::DataSet
getPolymorphismMultiGContainer(const std::map< size_t, std::vector< size_t >> &selection) const	bpp::DataSet
getPolymorphismSequenceContainer(const std::map< size_t, std::vector< size_t >> &selection, size_t sequence_position) const	bpp::DataSet
groups_	bpp::DataSet	private
hasAlleleicData() const	bpp::DataSet	inline
hasLocality() const	bpp::DataSet	inline
hasSequenceData() const	bpp::DataSet	inline
individualCoordInGroup(size_t groupPosition, size_t individualPosition) const	bpp::DataSet
individualDateInGroup(size_t groupPosition, size_t individualPosition) const	bpp::DataSet
initAnalyzedLoci(size_t numberOfLoci)	bpp::DataSet	inline
initIndividualGenotypeInGroup(size_t groupPosition, size_t individualPosition)	bpp::DataSet
localities_	bpp::DataSet	private
localityAtPosition(size_t localityPosition) const	bpp::DataSet
localityByName(const std::string &name) const	bpp::DataSet
mergeGroups(std::vector< size_t > &group_ids)	bpp::DataSet
mergeTwoGroups(size_t source_id, size_t target_id)	bpp::DataSet
operator=(const DataSet &ds)	bpp::DataSet
sequenceAlphabet_	bpp::DataSet	private
setAlphabet(std::shared_ptr< const Alphabet > alpha)	bpp::DataSet	inline
setAlphabet(const std::string &alphaType)	bpp::DataSet
setAnalyzedLoci(const AnalyzedLoci &analyzedLoci)	bpp::DataSet	inline
setGroupName(size_t group_id, const std::string &group_name) const	bpp::DataSet
setIndividualCoordInGroup(size_t groupPosition, size_t individualPosition, const Point2D< double > &coord)	bpp::DataSet
setIndividualDateInGroup(size_t groupPosition, size_t individualPosition, const Date &date)	bpp::DataSet
setIndividualGenotypeInGroup(size_t groupPosition, size_t individualPosition, const MultilocusGenotype &genotype)	bpp::DataSet
setIndividualLocalityInGroupByName(size_t groupPosition, size_t individualPosition, const std::string &localityName)	bpp::DataSet
setIndividualMonolocusGenotypeByAlleleIdInGroup(size_t groupPosition, size_t individualPosition, size_t locusPosition, const std::vector< std::string > alleleId)	bpp::DataSet
setIndividualMonolocusGenotypeByAlleleKeyInGroup(size_t groupPosition, size_t individualPosition, size_t locusPosition, const std::vector< size_t > alleleKeys)	bpp::DataSet
setIndividualMonolocusGenotypeInGroup(size_t groupPosition, size_t individualPosition, size_t locusPosition, const MonolocusGenotypeInterface &monogen)	bpp::DataSet
setIndividualSexInGroup(size_t groupPosition, size_t individualPosition, const unsigned short sex)	bpp::DataSet
setLocusInfo(size_t locus_position, const LocusInfo &locus)	bpp::DataSet
splitGroup(size_t group_id, std::vector< size_t > individuals_selection)	bpp::DataSet
~DataSet()=default	bpp::DataSet	virtual