bpp-seq3  3.0.0
bpp::MapSequenceContainer Member List

This is the complete list of members for bpp::MapSequenceContainer, 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
addSequence(const std::string &key, const Sequence &sequence, bool checkNames=true)bpp::MapSequenceContainer
addSequence(const Sequence &sequence, bool checkNames=true)bpp::MapSequenceContainerinlinevirtual
alphabet_bpp::AbstractValuesContainerprotected
clear()bpp::MapSequenceContainervirtual
clearComments()bpp::Commentableinline
clone() constbpp::MapSequenceContainerinlinevirtual
Commentable()bpp::Commentableinline
Commentable(const Comments &comments)bpp::Commentableinline
Commentable(const Commentable &com)bpp::Commentableinline
comments_bpp::Commentableprotected
createEmptyContainer() constbpp::MapSequenceContainervirtual
bpp::deleteGeneralComments()=0bpp::SequencedValuesContainerpure virtual
bpp::AbstractValuesContainer::deleteGeneralComments()bpp::AbstractValuesContainerinlinevirtual
deleteSequence(const std::string &name)bpp::MapSequenceContainer
deleteSequence(size_t sequenceIndex)bpp::MapSequenceContainer
deleteSequenceByKey(const std::string &key)bpp::MapSequenceContainer
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
getKey(size_t pos) constbpp::MapSequenceContainer
getKey(const std::string &name) constbpp::MapSequenceContainer
getKeys() constbpp::MapSequenceContainer
getName(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
getNumberOfSequences() constbpp::MapSequenceContainerinlinevirtual
getSequence(const std::string &name) constbpp::MapSequenceContainervirtual
getSequence(size_t sequenceIndex) constbpp::MapSequenceContainervirtual
getSequence_(size_t i)bpp::MapSequenceContainer
getSequence_(const std::string &name)bpp::MapSequenceContainer
getSequenceByKey(const std::string &key) constbpp::MapSequenceContainer
getSequencePosition(const std::string &name) constbpp::MapSequenceContainervirtual
getSequencesNames() constbpp::MapSequenceContainervirtual
getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) constbpp::MapSequenceContainerinlinevirtual
getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) constbpp::MapSequenceContainerinlinevirtual
bpp::OrderedValuesContainer::getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const=0bpp::OrderedValuesContainer
hasSequence(const std::string &name) constbpp::MapSequenceContainervirtual
MapSequenceContainer(const std::map< std::string, Sequence * > &ms, const Alphabet *alpha)bpp::MapSequenceContainer
MapSequenceContainer(const Alphabet *alpha)bpp::MapSequenceContainerinline
MapSequenceContainer(const MapSequenceContainer &msc)bpp::MapSequenceContainer
operator()(const std::string &sequenceName, size_t elementIndex)bpp::MapSequenceContainerinlinevirtual
operator()(const std::string &sequenceName, size_t elementIndex) constbpp::MapSequenceContainerinlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex)bpp::MapSequenceContainerinlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex) constbpp::MapSequenceContainerinlinevirtual
operator()(size_t siteIndex, const std::string &sequenceName, int state) constbpp::MapSequenceContainerinlinevirtual
operator()(size_t siteIndex, size_t sequenceIndex, int state) constbpp::MapSequenceContainerinlinevirtual
operator=(const MapSequenceContainer &msc)bpp::MapSequenceContainer
bpp::AbstractSequenceContainer::operator=(const AbstractSequenceContainer &sc)bpp::AbstractSequenceContainerinline
bpp::AbstractSequenceContainer::operator=(const SequenceContainer &sc)bpp::AbstractSequenceContainerinline
bpp::AbstractValuesContainer::operator=(const AbstractValuesContainer &sc)bpp::AbstractValuesContainerinline
bpp::Commentable::operator=(const Commentable &com)bpp::Commentableinline
OrderedSequenceContainer()bpp::OrderedSequenceContainerinline
OrderedValuesContainer()bpp::OrderedValuesContainerinline
removeSequence(const std::string &name)bpp::MapSequenceContainervirtual
removeSequence(size_t sequenceIndex)bpp::MapSequenceContainervirtual
removeSequenceByKey(const std::string &key)bpp::MapSequenceContainer
SequenceContainer()bpp::SequenceContainerinline
SequencedValuesContainer()bpp::SequencedValuesContainerinline
sequences_bpp::MapSequenceContainerprivate
setComments(size_t sequenceIndex, const Comments &comments)bpp::MapSequenceContainervirtual
bpp::AbstractSequenceContainer::setComments(const std::string &name, const Comments &comments)bpp::AbstractSequenceContainerinlinevirtual
bpp::OrderedSequenceContainer::setComments(size_t sequenceIndex, const Comments &comments)=0bpp::OrderedSequenceContainer
bpp::Commentable::setComments(const Comments &comments)bpp::Commentableinline
bpp::setGeneralComments(const Comments &comments)=0bpp::SequencedValuesContainerpure virtual
bpp::AbstractValuesContainer::setGeneralComments(const Comments &comments)bpp::AbstractValuesContainerinlinevirtual
setSequence(const std::string &name, const Sequence &sequence, bool checkName=true)bpp::MapSequenceContainervirtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName=true)bpp::MapSequenceContainervirtual
setSequenceByKey(const std::string &key, const Sequence &sequence, bool checkNames=true)bpp::MapSequenceContainer
setSequencesNames(const std::vector< std::string > &names, bool checkNames)bpp::MapSequenceContainervirtual
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::MapSequenceContainerinlinevirtual
valueAt(const std::string &sequenceName, size_t elementIndex) constbpp::MapSequenceContainerinlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex)bpp::MapSequenceContainerinlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex) constbpp::MapSequenceContainerinlinevirtual
~AbstractSequenceContainer()bpp::AbstractSequenceContainerinlinevirtual
~AbstractValuesContainer()bpp::AbstractValuesContainerinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~Commentable()bpp::Commentableinlinevirtual
~MapSequenceContainer()bpp::MapSequenceContainervirtual
~OrderedSequenceContainer()bpp::OrderedSequenceContainerinlinevirtual
~OrderedValuesContainer()bpp::OrderedValuesContainerinlinevirtual
~SequenceContainer()bpp::SequenceContainerinlinevirtual
~SequencedValuesContainer()bpp::SequencedValuesContainerinlinevirtual