bpp-seq3  3.0.0
bpp::VectorSiteContainer Member List

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

AbstractSequenceContainer(const Alphabet *alpha)bpp::AbstractSequenceContainerinline
AbstractSequenceContainer(const AbstractSequenceContainer &sc)bpp::AbstractSequenceContainerinline
AbstractSequenceContainer(const SequenceContainer &sc)bpp::AbstractSequenceContainerinline
AbstractValuesContainer(const Alphabet *alpha)bpp::AbstractValuesContainerinline
AbstractValuesContainer(const Comments &comments, const Alphabet *alpha)bpp::AbstractValuesContainerinline
AbstractValuesContainer(const AbstractValuesContainer &sc)bpp::AbstractValuesContainerinline
VectorPositionedContainer< Site >::addObject(std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false)bpp::VectorPositionedContainer< Site >inlineprotected
VectorMappedContainer< Sequence >::addObject(std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false)bpp::VectorMappedContainer< Sequence >inlineprotected
VectorMappedContainer< Sequence >::bpp::PositionedNamedContainer::addObject(std::shared_ptr< T > object, size_t objectIndex, const std::string &name, bool check=false)=0bpp::PositionedNamedContainer< T >protectedpure virtual
VectorMappedContainer< Sequence >::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
VectorPositionedContainer< Site >::addObject_(std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false) constbpp::VectorPositionedContainer< Site >inlineprotected
VectorMappedContainer< Sequence >::addObject_(std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false) constbpp::VectorMappedContainer< Sequence >inlineprotected
VectorMappedContainer< Sequence >::bpp::MappedNamedContainer::addObject_(std::shared_ptr< T > object, const std::string &name, bool checkName=false) constbpp::MappedNamedContainer< T >inlineprotected
bpp::VectorPositionedContainer::addObject_(std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false) constbpp::VectorPositionedContainer< T >inlineprotected
addSequence(const Sequence &sequence, bool checkName=true)bpp::VectorSiteContainervirtual
addSequence(const Sequence &sequence, size_t sequenceIndex, bool checkName=true)bpp::VectorSiteContainer
addSite(const Site &site, bool checkPosition=true)bpp::VectorSiteContainervirtual
addSite(const Site &site, int position, bool checkPosition=true)bpp::VectorSiteContainervirtual
addSite(const Site &site, size_t siteIndex, bool checkPosition=true)bpp::VectorSiteContainervirtual
addSite(const Site &site, size_t siteIndex, int position, bool checkPosition=true)bpp::VectorSiteContainervirtual
AlignedValuesContainer()bpp::AlignedValuesContainerinline
alphabet_bpp::AbstractValuesContainerprotected
VectorPositionedContainer< Site >::appendObject(std::shared_ptr< Site > object)bpp::VectorPositionedContainer< Site >inlineprotected
VectorMappedContainer< Sequence >::appendObject(std::shared_ptr< Sequence > object, const std::string &name, bool check=true)bpp::VectorMappedContainer< Sequence >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::VectorSiteContainervirtual
clearComments()bpp::Commentableinline
clone() constbpp::VectorSiteContainerinlinevirtual
Commentable()bpp::Commentableinline
Commentable(const Comments &comments)bpp::Commentableinline
Commentable(const Commentable &com)bpp::Commentableinline
comments_bpp::Commentableprotected
createEmptyContainer() constbpp::VectorSiteContainervirtual
bpp::deleteGeneralComments()=0bpp::SequencedValuesContainerpure virtual
bpp::AbstractValuesContainer::deleteGeneralComments()bpp::AbstractValuesContainerinlinevirtual
VectorPositionedContainer< Site >::deleteObject(size_t objectIndex)bpp::VectorPositionedContainer< Site >inlineprotectedvirtual
VectorMappedContainer< Sequence >::deleteObject(size_t objectIndex)bpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
VectorMappedContainer< Sequence >::deleteObject(const std::string &name)bpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
VectorPositionedContainer< Site >::deleteObjects(size_t objectIndex, size_t length)bpp::VectorPositionedContainer< Site >inlineprotected
VectorMappedContainer< Sequence >::deleteObjects(size_t objectIndex, size_t length)bpp::VectorPositionedContainer< T >inlineprotected
deleteSite(size_t siteIndex)bpp::VectorSiteContainerinlinevirtual
deleteSites(size_t siteIndex, size_t length)bpp::VectorSiteContainerinlinevirtual
bpp::getAlphabet() const =0bpp::SequencedValuesContainerpure virtual
bpp::AbstractValuesContainer::getAlphabet() constbpp::AbstractValuesContainerinlinevirtual
getComments(const std::string &name) constbpp::AbstractSequenceContainerinlinevirtual
getComments(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
bpp::OrderedSequenceContainer::getComments(size_t sequenceIndex) const=0bpp::OrderedSequenceContainer
bpp::Commentable::getComments() constbpp::Commentableinline
bpp::getGeneralComments() const =0bpp::SequencedValuesContainerpure virtual
bpp::AbstractValuesContainer::getGeneralComments() constbpp::AbstractValuesContainerinlinevirtual
getName(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
getNumberOfObjects() constbpp::VectorMappedContainer< Sequence >inlineprotected
getNumberOfSequences() constbpp::VectorSiteContainerinlinevirtual
getNumberOfSites() constbpp::VectorSiteContainerinlinevirtual
VectorPositionedContainer< Site >::getObject(size_t objectIndex) constbpp::VectorPositionedContainer< Site >inlineprotectedvirtual
VectorPositionedContainer< Site >::getObject(size_t objectIndex)bpp::VectorPositionedContainer< Site >inlineprotectedvirtual
VectorMappedContainer< Sequence >::getObject(size_t objectIndex) constbpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
VectorMappedContainer< Sequence >::getObject(size_t objectIndex)bpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
VectorMappedContainer< Sequence >::getObject(const std::string &name) constbpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
VectorMappedContainer< Sequence >::getObject(const std::string &name)bpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
VectorPositionedContainer< Site >::getObject_(size_t objectIndex) constbpp::VectorPositionedContainer< Site >inlineprotected
VectorMappedContainer< Sequence >::getObject_(size_t objectIndex) constbpp::VectorPositionedContainer< T >inlineprotected
getObjectName(size_t objectIndex) constbpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
getObjectNames() constbpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
getObjectPosition(const std::string &name) constbpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
getSequence(size_t sequenceIndex) constbpp::VectorSiteContainervirtual
getSequence(const std::string &name) constbpp::VectorSiteContainervirtual
bpp::AbstractSequenceContainer::getSequence(const std::string &name) const=0bpp::OrderedSequenceContainer
getSequenceNames() constbpp::VectorSiteContainerinlinevirtual
getSequencePosition(const std::string &name) constbpp::VectorSiteContainerinlinevirtual
getSite(size_t siteIndex) constbpp::VectorSiteContainerinlinevirtual
getSite(size_t siteIndex)bpp::VectorSiteContainerinlinevirtual
getSitePositions() constbpp::VectorSiteContainervirtual
VectorPositionedContainer< Site >::getSize() constbpp::VectorPositionedContainer< Site >inlinevirtual
VectorMappedContainer< Sequence >::getSize() constbpp::VectorMappedContainer< Sequence >inlinevirtual
getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) constbpp::VectorSiteContainerinlinevirtual
getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) constbpp::VectorSiteContainerinlinevirtual
bpp::OrderedValuesContainer::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const=0bpp::OrderedValuesContainer
getSymbolListSite(size_t siteIndex) constbpp::VectorSiteContainerinlinevirtual
getSymbolListSite(size_t siteIndex)bpp::VectorSiteContainerinlinevirtual
hasObject(const std::string &name) constbpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
hasSequence(const std::string &name) constbpp::VectorSiteContainerinlinevirtual
VectorPositionedContainer< Site >::insertObject(std::shared_ptr< Site > object, size_t objectIndex)bpp::VectorPositionedContainer< Site >inlineprotected
VectorMappedContainer< Sequence >::insertObject(std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name)bpp::VectorMappedContainer< Sequence >inlineprotected
VectorMappedContainer< Sequence >::bpp::PositionedNamedContainer::insertObject(std::shared_ptr< T > object, size_t objectIndex, const std::string &name)=0bpp::PositionedNamedContainer< T >protectedpure virtual
bpp::VectorPositionedContainer::insertObject(std::shared_ptr< T > object, size_t objectIndex)bpp::VectorPositionedContainer< T >inlineprotected
isAvailableName(std::string objectName) constbpp::MappedNamedContainer< T >inline
VectorPositionedContainer< Site >::isAvailablePosition(size_t objectIndex) constbpp::VectorPositionedContainer< Site >inline
VectorMappedContainer< Sequence >::isAvailablePosition(size_t objectIndex) constbpp::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< Sequence >private
mObjects_bpp::MappedNamedContainer< T >private
bpp::NamedContainer()bpp::NamedContainer< T >inlineprivate
bpp::MappedNamedContainer::NamedContainer()bpp::NamedContainer< T >inline
VectorPositionedContainer< Site >::nullify()bpp::VectorPositionedContainer< Site >inline
VectorMappedContainer< Sequence >::nullify()bpp::VectorPositionedContainer< T >inline
operator()(const std::string &sequenceName, size_t elementIndex)bpp::VectorSiteContainerinlinevirtual
operator()(const std::string &sequenceName, size_t elementIndex) constbpp::VectorSiteContainerinlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex)bpp::VectorSiteContainerinlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex) constbpp::VectorSiteContainerinlinevirtual
operator()(size_t siteIndex, const std::string &sequenceName, int state) constbpp::VectorSiteContainerinlinevirtual
operator()(size_t siteIndex, size_t sequenceIndex, int state) constbpp::VectorSiteContainerinlinevirtual
operator=(const VectorSiteContainer &vsc)bpp::VectorSiteContainer
operator=(const SiteContainer &sc)bpp::VectorSiteContainer
operator=(const OrderedSequenceContainer &osc)bpp::VectorSiteContainer
operator=(const SequenceContainer &sc)bpp::VectorSiteContainer
bpp::AbstractSequenceContainer::operator=(const AbstractSequenceContainer &sc)bpp::AbstractSequenceContainerinline
bpp::AbstractValuesContainer::operator=(const AbstractValuesContainer &sc)bpp::AbstractValuesContainerinline
bpp::Commentable::operator=(const Commentable &com)bpp::Commentableinline
VectorPositionedContainer< Site >::operator=(const VectorPositionedContainer< Site > &vsc)bpp::VectorPositionedContainer< Site >inline
VectorMappedContainer< Sequence >::operator=(const VectorMappedContainer &vsc)bpp::VectorMappedContainer< Sequence >inline
VectorMappedContainer< Sequence >::bpp::MappedNamedContainer::operator=(const MappedNamedContainer &msc)bpp::MappedNamedContainer< T >inline
bpp::VectorPositionedContainer::operator=(const VectorPositionedContainer< T > &vsc)bpp::VectorPositionedContainer< T >inline
OrderedSequenceContainer()bpp::OrderedSequenceContainerinline
OrderedValuesContainer()bpp::OrderedValuesContainerinline
VectorPositionedContainer< Site >::PositionedContainer()bpp::PositionedContainer< T >inline
VectorMappedContainer< Sequence >::bpp::PositionedContainer()bpp::PositionedContainer< T >inline
VectorPositionedContainer< Site >::positions_bpp::VectorPositionedContainer< Site >protected
VectorMappedContainer< Sequence >::positions_bpp::VectorPositionedContainer< T >protected
realloc(size_t n)bpp::VectorSiteContainerprotected
reindexSites()bpp::VectorSiteContainervirtual
VectorPositionedContainer< Site >::removeObject(size_t objectIndex)bpp::VectorPositionedContainer< Site >inlineprotectedvirtual
VectorMappedContainer< Sequence >::removeObject(size_t objectIndex)bpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
VectorMappedContainer< Sequence >::removeObject(const std::string &name)bpp::VectorMappedContainer< Sequence >inlineprotectedvirtual
removeSequence(size_t sequenceIndex)bpp::VectorSiteContainervirtual
removeSequence(const std::string &name)bpp::VectorSiteContainervirtual
bpp::AbstractSequenceContainer::removeSequence(const std::string &name)=0bpp::OrderedSequenceContainer
removeSite(size_t siteIndex)bpp::VectorSiteContainerinlinevirtual
SequenceContainer()bpp::SequenceContainerinline
setComments(size_t sequenceIndex, const Comments &comments)bpp::VectorSiteContainervirtual
setComments(size_t sequenceIndex, const Comments &comments)=0bpp::VectorSiteContainer
bpp::AbstractSequenceContainer::setComments(const std::string &name, const Comments &comments)bpp::AbstractSequenceContainerinlinevirtual
bpp::Commentable::setComments(const Comments &comments)bpp::Commentableinline
bpp::setGeneralComments(const Comments &comments)=0bpp::SequencedValuesContainerpure virtual
bpp::AbstractValuesContainer::setGeneralComments(const Comments &comments)bpp::AbstractValuesContainerinlinevirtual
setObjectName(size_t pos, const std::string &name)bpp::VectorMappedContainer< Sequence >inlineprotected
setObjectNames(const std::vector< std::string > &names)bpp::VectorMappedContainer< Sequence >inlineprotected
setSequence(const std::string &name, const Sequence &sequence, bool checkName)bpp::VectorSiteContainervirtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName)bpp::VectorSiteContainervirtual
bpp::AbstractSequenceContainer::setSequence(const std::string &name, const Sequence &sequence, bool checkName)=0bpp::OrderedSequenceContainer
setSequenceNames(const std::vector< std::string > &names, bool checkNames=true)bpp::VectorSiteContainerinlinevirtual
setSite(size_t siteIndex, const Site &site, bool checkPosition=true)bpp::VectorSiteContainervirtual
setSitePositions(Vint vPositions)bpp::VectorSiteContainervirtual
VectorPositionedContainer< Site >::setSize(size_t size)bpp::VectorPositionedContainer< Site >inlinevirtual
VectorMappedContainer< Sequence >::bpp::VectorPositionedContainer::setSize(size_t size)bpp::VectorPositionedContainer< T >inlinevirtual
SiteContainer()bpp::SiteContainerinline
toString(const std::string &name) constbpp::AbstractSequenceContainerinlinevirtual
toString(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
bpp::OrderedSequenceContainer::toString(size_t sequenceIndex) const=0bpp::OrderedSequenceContainer
valueAt(const std::string &sequenceName, size_t elementIndex)bpp::VectorSiteContainerinlinevirtual
valueAt(const std::string &sequenceName, size_t elementIndex) constbpp::VectorSiteContainerinlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex)bpp::VectorSiteContainerinlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex) constbpp::VectorSiteContainerinlinevirtual
VectorMappedContainer()bpp::VectorMappedContainer< Sequence >inline
VectorMappedContainer(const VectorMappedContainer &vsc)bpp::VectorMappedContainer< Sequence >inline
VectorPositionedContainer< Site >::VectorPositionedContainer(const std::vector< std::shared_ptr< Site > > &vs)bpp::VectorPositionedContainer< Site >inline
VectorPositionedContainer< Site >::VectorPositionedContainer(size_t size=0)bpp::VectorPositionedContainer< Site >inline
VectorPositionedContainer< Site >::VectorPositionedContainer(const VectorPositionedContainer< Site > &vsc)bpp::VectorPositionedContainer< Site >inline
VectorMappedContainer< Sequence >::VectorPositionedContainer(const std::vector< std::shared_ptr< T > > &vs)bpp::VectorPositionedContainer< T >inline
VectorMappedContainer< Sequence >::VectorPositionedContainer(size_t size=0)bpp::VectorPositionedContainer< T >inline
VectorMappedContainer< Sequence >::VectorPositionedContainer(const VectorPositionedContainer< T > &vsc)bpp::VectorPositionedContainer< T >inline
VectorSiteContainer(const std::vector< const CruxSymbolListSite * > &vs, const Alphabet *alpha, bool checkPositions=true)bpp::VectorSiteContainer
VectorSiteContainer(const std::vector< const Site * > &vs, const Alphabet *alpha, bool checkPositions=true)bpp::VectorSiteContainer
VectorSiteContainer(size_t size, const Alphabet *alpha)bpp::VectorSiteContainer
VectorSiteContainer(const std::vector< std::string > &names, const Alphabet *alpha)bpp::VectorSiteContainer
VectorSiteContainer(const Alphabet *alpha)bpp::VectorSiteContainer
VectorSiteContainer(const VectorSiteContainer &vsc)bpp::VectorSiteContainer
VectorSiteContainer(const SiteContainer &sc)bpp::VectorSiteContainer
VectorSiteContainer(const OrderedSequenceContainer &osc)bpp::VectorSiteContainer
VectorSiteContainer(const SequenceContainer &sc)bpp::VectorSiteContainer
VectorSiteContainer(const AlignedValuesContainer &avc)bpp::VectorSiteContainer
vNames_bpp::VectorMappedContainer< Sequence >private
~AbstractSequenceContainer()bpp::AbstractSequenceContainerinlinevirtual
~AbstractValuesContainer()bpp::AbstractValuesContainerinlinevirtual
~AlignedValuesContainer()bpp::AlignedValuesContainerinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~Commentable()bpp::Commentableinlinevirtual
~MappedNamedContainer()bpp::MappedNamedContainer< T >inlinevirtual
~NamedContainer()bpp::NamedContainer< T >inlineprivatevirtual
~OrderedSequenceContainer()bpp::OrderedSequenceContainerinlinevirtual
~OrderedValuesContainer()bpp::OrderedValuesContainerinlinevirtual
~PositionedContainer()bpp::PositionedContainer< T >inlinevirtual
~PositionedNamedContainer()bpp::PositionedNamedContainer< T >inlinevirtual
~SequenceContainer()bpp::SequenceContainerinlinevirtual
~SiteContainer()bpp::SiteContainerinlinevirtual
VectorPositionedContainer< Site >::~VectorPositionedContainer()bpp::VectorPositionedContainer< Site >inlinevirtual
VectorMappedContainer< Sequence >::~VectorPositionedContainer()bpp::VectorPositionedContainer< T >inlinevirtual
~VectorSiteContainer()bpp::VectorSiteContainerinlinevirtual