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 group_position, const std::string &individual_id)	bpp::DataSet
addGroup(const Group &group)	bpp::DataSet
addIndividualSequenceInGroup(size_t group_position, size_t individual_position, size_t sequence_position, const Sequence &sequence)	bpp::DataSet
addIndividualToGroup(size_t group_position, const Individual &individual)	bpp::DataSet
addLocality(Locality< double > &locality)	bpp::DataSet
analyzedLoci_	bpp::DataSet	private
analyzedSequences_	bpp::DataSet	private
DataSet()	bpp::DataSet
DataSet(const DataSet &ds)	bpp::DataSet
deleteAnalyzedLoci()	bpp::DataSet
deleteGroupAtPosition(size_t group_position)	bpp::DataSet
deleteIndividualAtPositionFromGroup(size_t group_position, size_t individual_position)	bpp::DataSet
deleteIndividualByIdFromGroup(size_t group_position, const std::string &individual_id)	bpp::DataSet
deleteIndividualGenotypeInGroup(size_t group_position, size_t individual_position)	bpp::DataSet
deleteIndividualSequenceAtPositionInGroup(size_t group_position, size_t individual_position, size_t sequence_position)	bpp::DataSet
deleteIndividualSequenceByNameInGroup(size_t group_position, size_t individual_position, const std::string &sequence_name)	bpp::DataSet
deleteLocalityAtPosition(size_t locality_position)	bpp::DataSet
deleteLocalityByName(const std::string &name)	bpp::DataSet
getAlphabet() const	bpp::DataSet
getAlphabetType() const	bpp::DataSet
getAnalyzedLoci() const	bpp::DataSet
getGroupAtPosition(size_t group_position) 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 group_position, size_t individual_position) const	bpp::DataSet
getIndividualByIdFromGroup(size_t group_position, const std::string &individual_id) const	bpp::DataSet
getIndividualCoordInGroup(size_t group_position, size_t individual_position) const	bpp::DataSet
getIndividualDateInGroup(size_t group_position, size_t individual_position) const	bpp::DataSet
getIndividualLocalityInGroup(size_t group_position, size_t individual_position) const	bpp::DataSet
getIndividualMonolocusGenotypeInGroup(size_t group_position, size_t individual_position, size_t locus_position) const	bpp::DataSet
getIndividualNumberOfSequencesInGroup(size_t group_position, size_t individual_position) const	bpp::DataSet
getIndividualPositionInGroup(size_t group_position, const std::string &individual_id) const	bpp::DataSet
getIndividualSequenceAtPositionInGroup(size_t group_position, size_t individual_position, size_t sequence_position) const	bpp::DataSet
getIndividualSequenceByNameInGroup(size_t group_position, size_t individual_position, const std::string &sequence_name) const	bpp::DataSet
getIndividualSequencePositionInGroup(size_t group_position, size_t individual_position, const std::string &sequence_name) const	bpp::DataSet
getIndividualSequencesNamesInGroup(size_t group_position, size_t individual_position) const	bpp::DataSet
getIndividualSexInGroup(size_t group_position, size_t individual_position) const	bpp::DataSet
getLocalityAtPosition(size_t locality_position) 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 group_position) const	bpp::DataSet
getNumberOfLocalities() const	bpp::DataSet
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
hasLocality() const	bpp::DataSet
hasSequenceData() const	bpp::DataSet
initAnalyzedLoci(size_t number_of_loci)	bpp::DataSet
initIndividualGenotypeInGroup(size_t group_position, size_t individual_position)	bpp::DataSet
localities_	bpp::DataSet	private
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
setAlphabet(const Alphabet *alpha)	bpp::DataSet
setAlphabet(const std::string &alpha_type)	bpp::DataSet
setAnalyzedLoci(const AnalyzedLoci &analyzedLoci)	bpp::DataSet
setGroupName(size_t group_id, const std::string &group_name) const	bpp::DataSet
setIndividualCoordInGroup(size_t group_position, size_t individual_position, const Point2D< double > &coord)	bpp::DataSet
setIndividualDateInGroup(size_t group_position, size_t individual_position, const Date &date)	bpp::DataSet
setIndividualGenotypeInGroup(size_t group_position, size_t individual_position, const MultilocusGenotype &genotype)	bpp::DataSet
setIndividualLocalityInGroupByName(size_t group_position, size_t individual_position, const std::string &locality_name)	bpp::DataSet
setIndividualMonolocusGenotypeByAlleleIdInGroup(size_t group_position, size_t individual_position, size_t locus_position, const std::vector< std::string > allele_id)	bpp::DataSet
setIndividualMonolocusGenotypeByAlleleKeyInGroup(size_t group_position, size_t individual_position, size_t locus_position, const std::vector< size_t > allele_keys)	bpp::DataSet
setIndividualMonolocusGenotypeInGroup(size_t group_position, size_t individual_position, size_t locus_position, const MonolocusGenotype &monogen)	bpp::DataSet
setIndividualSexInGroup(size_t group_position, size_t individual_position, 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()	bpp::DataSet