| AbstractValuesContainer(const Alphabet *alpha) | bpp::AbstractValuesContainer | inline |
| AbstractValuesContainer(const Comments &comments, const Alphabet *alpha) | bpp::AbstractValuesContainer | inline |
| AbstractValuesContainer(const AbstractValuesContainer &sc) | bpp::AbstractValuesContainer | inline |
| addObject(std::shared_ptr< ProbabilisticSequence > object, size_t objectIndex, const std::string &name, bool check=false) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotected |
| bpp::PositionedNamedContainer::addObject(std::shared_ptr< T > object, size_t objectIndex, const std::string &name, bool check=false)=0 | bpp::PositionedNamedContainer< T > | protectedpure virtual |
| bpp::MappedNamedContainer::addObject(std::shared_ptr< T > object, const std::string &name, bool checkName=false) | bpp::MappedNamedContainer< T > | inlineprotected |
| bpp::VectorPositionedContainer::addObject(std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false) | bpp::VectorPositionedContainer< T > | inlineprotected |
| addObject_(std::shared_ptr< ProbabilisticSequence > object, size_t objectIndex, const std::string &name, bool check=false) const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotected |
| bpp::MappedNamedContainer::addObject_(std::shared_ptr< T > object, const std::string &name, bool checkName=false) const | bpp::MappedNamedContainer< T > | inlineprotected |
| bpp::VectorPositionedContainer::addObject_(std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false) const | bpp::VectorPositionedContainer< T > | inlineprotected |
| addSequence(const ProbabilisticSequence &sequence, bool checkName=true) | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| addSequence(const std::shared_ptr< ProbabilisticSequence > sequence, bool checkName=true) | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| addSequence(const ProbabilisticSequence &sequence, size_t sequenceIndex, bool checkName=true) | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| alphabet_ | bpp::AbstractValuesContainer | protected |
| appendObject(std::shared_ptr< ProbabilisticSequence > object, const std::string &name, bool check=true) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotected |
| bpp::VectorPositionedContainer::appendObject(std::shared_ptr< T > object) | bpp::VectorPositionedContainer< T > | inlineprotected |
| changeName(const std::string &okey, const std::string &nkey) | bpp::MappedNamedContainer< T > | inline |
| clear() | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| clearComments() | bpp::Commentable | inline |
| clone() const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| Commentable() | bpp::Commentable | inline |
| Commentable(const Comments &comments) | bpp::Commentable | inline |
| Commentable(const Commentable &com) | bpp::Commentable | inline |
| comments_ | bpp::Commentable | protected |
| createEmptyContainer() const | bpp::VectorProbabilisticSequenceContainer | virtual |
| deleteGeneralComments() | bpp::AbstractValuesContainer | inlinevirtual |
| deleteObject(size_t objectIndex) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| deleteObject(const std::string &name) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| deleteObjects(size_t objectIndex, size_t length) | bpp::VectorPositionedContainer< T > | inlineprotected |
| getAlphabet() const | bpp::AbstractValuesContainer | inlinevirtual |
| getComments(const std::string &name) const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| getComments(size_t sequenceIndex) const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| bpp::OrderedValuesContainer::getComments(const std::string &name) const=0 | bpp::OrderedValuesContainer | |
| bpp::Commentable::getComments() const | bpp::Commentable | inline |
| getGeneralComments() const | bpp::AbstractValuesContainer | inlinevirtual |
| getName(size_t sequenceIndex) const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| getNumberOfObjects() const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotected |
| getNumberOfSequences() const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| getObject(size_t objectIndex) const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| getObject(size_t objectIndex) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| getObject(const std::string &name) const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| getObject(const std::string &name) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| getObject_(size_t objectIndex) const | bpp::VectorPositionedContainer< T > | inlineprotected |
| getObjectName(size_t objectIndex) const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| getObjectNames() const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| getObjectPosition(const std::string &name) const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| getSequence(const std::string &name) const | bpp::VectorProbabilisticSequenceContainer | inline |
| getSequence(size_t sequenceIndex) const | bpp::VectorProbabilisticSequenceContainer | inline |
| getSequence_(size_t i) | bpp::VectorProbabilisticSequenceContainer | inlineprotected |
| getSequence_(const std::string &name) | bpp::VectorProbabilisticSequenceContainer | inlineprotected |
| getSequenceNames() const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| getSequencePosition(const std::string &name) const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| getSize() const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlinevirtual |
| getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const | bpp::VectorProbabilisticSequenceContainer | inlineprotectedvirtual |
| getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) const | bpp::VectorProbabilisticSequenceContainer | inlineprotectedvirtual |
| bpp::AbstractValuesContainer::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const=0 | bpp::OrderedValuesContainer | |
| hasObject(const std::string &name) const | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| hasSequence(const std::string &name) const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| insertObject(std::shared_ptr< ProbabilisticSequence > object, size_t objectIndex, const std::string &name) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotected |
| bpp::PositionedNamedContainer::insertObject(std::shared_ptr< T > object, size_t objectIndex, const std::string &name)=0 | bpp::PositionedNamedContainer< T > | protectedpure virtual |
| bpp::VectorPositionedContainer::insertObject(std::shared_ptr< T > object, size_t objectIndex) | bpp::VectorPositionedContainer< T > | inlineprotected |
| isAvailableName(std::string objectName) const | bpp::MappedNamedContainer< T > | inline |
| isAvailablePosition(size_t objectIndex) const | bpp::VectorPositionedContainer< T > | inline |
| MappedNamedContainer() | bpp::MappedNamedContainer< T > | inline |
| MappedNamedContainer(const std::map< std::string, std::shared_ptr< T > > &ms) | bpp::MappedNamedContainer< T > | inline |
| MappedNamedContainer(const MappedNamedContainer &msc) | bpp::MappedNamedContainer< T > | inline |
| mNames_ | bpp::VectorMappedContainer< ProbabilisticSequence > | private |
| mObjects_ | bpp::MappedNamedContainer< T > | private |
| bpp::NamedContainer() | bpp::NamedContainer< T > | inlineprivate |
| bpp::MappedNamedContainer::NamedContainer() | bpp::NamedContainer< T > | inline |
| nullify() | bpp::VectorPositionedContainer< T > | inline |
| operator()(size_t siteIndex, const std::string &sequenceName, int state) const | bpp::VectorProbabilisticSequenceContainer | inlineprotectedvirtual |
| operator()(size_t siteIndex, size_t sequenceIndex, int state) const | bpp::VectorProbabilisticSequenceContainer | inlineprotectedvirtual |
| operator=(const VectorProbabilisticSequenceContainer &vsc) | bpp::VectorProbabilisticSequenceContainer | |
| bpp::AbstractValuesContainer::operator=(const AbstractValuesContainer &sc) | bpp::AbstractValuesContainer | inline |
| bpp::Commentable::operator=(const Commentable &com) | bpp::Commentable | inline |
| VectorMappedContainer< ProbabilisticSequence >::operator=(const VectorMappedContainer &vsc) | bpp::VectorMappedContainer< ProbabilisticSequence > | inline |
| VectorMappedContainer< ProbabilisticSequence >::bpp::MappedNamedContainer::operator=(const MappedNamedContainer &msc) | bpp::MappedNamedContainer< T > | inline |
| bpp::VectorPositionedContainer::operator=(const VectorPositionedContainer< T > &vsc) | bpp::VectorPositionedContainer< T > | inline |
| OrderedValuesContainer() | bpp::OrderedValuesContainer | inline |
| bpp::PositionedContainer() | bpp::PositionedContainer< T > | inlineprivate |
| bpp::VectorPositionedContainer::PositionedContainer() | bpp::PositionedContainer< T > | inline |
| positions_ | bpp::VectorPositionedContainer< T > | protected |
| removeObject(size_t objectIndex) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| removeObject(const std::string &name) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotectedvirtual |
| removeSequence(const std::string &name) | bpp::VectorProbabilisticSequenceContainer | inline |
| removeSequence(size_t sequenceIndex) | bpp::VectorProbabilisticSequenceContainer | inline |
| setComments(const std::string &name, const Comments &comments) | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| setComments(size_t sequenceIndex, const Comments &comments) | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| bpp::OrderedValuesContainer::setComments(const std::string &name, const Comments &comments)=0 | bpp::OrderedValuesContainer | |
| bpp::Commentable::setComments(const Comments &comments) | bpp::Commentable | inline |
| setGeneralComments(const Comments &comments) | bpp::AbstractValuesContainer | inlinevirtual |
| setObjectName(size_t pos, const std::string &name) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotected |
| setObjectNames(const std::vector< std::string > &names) | bpp::VectorMappedContainer< ProbabilisticSequence > | inlineprotected |
| setSequence(const std::string &name, const ProbabilisticSequence &sequence, bool checkName=true) | bpp::VectorProbabilisticSequenceContainer | inline |
| setSequence(size_t sequenceIndex, const ProbabilisticSequence &sequence, bool checkName=true) | bpp::VectorProbabilisticSequenceContainer | inline |
| setSequenceNames(const std::vector< std::string > &names, bool checkNames=true) | bpp::VectorProbabilisticSequenceContainer | virtual |
| bpp::setSize(size_t size) | bpp::PositionedContainer< T > | inlineprivatevirtual |
| bpp::VectorPositionedContainer::setSize(size_t size) | bpp::VectorPositionedContainer< T > | inlinevirtual |
| toString(const std::string &name) const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| toString(size_t sequenceIndex) const | bpp::VectorProbabilisticSequenceContainer | inlinevirtual |
| bpp::AbstractValuesContainer::toString(const std::string &name) const=0 | bpp::OrderedValuesContainer | |
| VectorMappedContainer() | bpp::VectorMappedContainer< ProbabilisticSequence > | inline |
| VectorMappedContainer(const VectorMappedContainer &vsc) | bpp::VectorMappedContainer< ProbabilisticSequence > | inline |
| VectorPositionedContainer(const std::vector< std::shared_ptr< T > > &vs) | bpp::VectorPositionedContainer< T > | inline |
| VectorPositionedContainer(size_t size=0) | bpp::VectorPositionedContainer< T > | inline |
| VectorPositionedContainer(const VectorPositionedContainer< T > &vsc) | bpp::VectorPositionedContainer< T > | inline |
| VectorProbabilisticSequenceContainer(const std::vector< std::shared_ptr< ProbabilisticSequence >> &vs, const Alphabet *alpha) | bpp::VectorProbabilisticSequenceContainer | |
| VectorProbabilisticSequenceContainer(const Alphabet *alpha) | bpp::VectorProbabilisticSequenceContainer | inline |
| VectorProbabilisticSequenceContainer(const VectorProbabilisticSequenceContainer &vsc) | bpp::VectorProbabilisticSequenceContainer | |
| vNames_ | bpp::VectorMappedContainer< ProbabilisticSequence > | private |
| ~AbstractValuesContainer() | bpp::AbstractValuesContainer | inlinevirtual |
| ~Clonable()=default | bpp::Clonable | virtual |
| ~Commentable() | bpp::Commentable | inlinevirtual |
| ~MappedNamedContainer() | bpp::MappedNamedContainer< T > | inlinevirtual |
| ~NamedContainer() | bpp::NamedContainer< T > | inlineprivatevirtual |
| ~OrderedValuesContainer() | bpp::OrderedValuesContainer | inlinevirtual |
| ~PositionedContainer() | bpp::PositionedContainer< T > | inlineprivatevirtual |
| ~PositionedNamedContainer() | bpp::PositionedNamedContainer< T > | inlinevirtual |
| ~VectorPositionedContainer() | bpp::VectorPositionedContainer< T > | inlinevirtual |
1.9.1