bpp-seq  2.2.0
bpp::AlignedSequenceContainer Member List

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

AbstractSequenceContainer(const Alphabet *alpha)bpp::AbstractSequenceContainerinline
AbstractSequenceContainer(const AbstractSequenceContainer &sc)bpp::AbstractSequenceContainerinline
AbstractSequenceContainer(const SequenceContainer &sc)bpp::AbstractSequenceContainerinline
addSequence(const Sequence &sequence, bool checkName=true)bpp::AlignedSequenceContainervirtual
addSequence(const Sequence &sequence, size_t sequenceIndex, bool checkName=true)bpp::AlignedSequenceContainervirtual
addSite(const Site &site, bool checkPosition=true)bpp::AlignedSequenceContainervirtual
addSite(const Site &site, int position, bool checkPosition=true)bpp::AlignedSequenceContainervirtual
addSite(const Site &site, size_t siteIndex, bool checkPosition=true)bpp::AlignedSequenceContainervirtual
addSite(const Site &site, size_t siteIndex, int position, bool checkPosition=true)bpp::AlignedSequenceContainervirtual
AlignedSequenceContainer(const Alphabet *alpha)bpp::AlignedSequenceContainerinline
AlignedSequenceContainer(const AlignedSequenceContainer &asc)bpp::AlignedSequenceContainerinline
AlignedSequenceContainer(const SiteContainer &sc)bpp::AlignedSequenceContainerinline
AlignedSequenceContainer(const OrderedSequenceContainer &osc)bpp::AlignedSequenceContainer
checkSize_(const Sequence &sequence)bpp::AlignedSequenceContainerinlineprotected
clear()bpp::AlignedSequenceContainervirtual
clone() constbpp::AlignedSequenceContainerinlinevirtual
createEmptyContainer() constbpp::AlignedSequenceContainervirtual
deleteGeneralComments()bpp::AbstractSequenceContainerinlinevirtual
deleteSequence(const std::string &name)bpp::VectorSequenceContainerinlinevirtual
deleteSequence(size_t sequenceIndex)bpp::VectorSequenceContainervirtual
deleteSite(size_t siteIndex)bpp::AlignedSequenceContainervirtual
deleteSites(size_t siteIndex, size_t length)bpp::AlignedSequenceContainervirtual
getAlphabet() constbpp::AbstractSequenceContainerinlinevirtual
getComments(const std::string &name) constbpp::AbstractSequenceContainerinlinevirtual
getComments(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
getContent(const std::string &name) constbpp::AbstractSequenceContainerinlinevirtual
getContent(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
getGeneralComments() constbpp::AbstractSequenceContainerinlinevirtual
getName(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
getNumberOfSequences() constbpp::VectorSequenceContainerinlinevirtual
getNumberOfSites() constbpp::AlignedSequenceContainerinlinevirtual
getSequence(const std::string &name) constbpp::VectorSequenceContainervirtual
getSequence(size_t sequenceIndex) constbpp::VectorSequenceContainervirtual
getSequence_(size_t i)bpp::VectorSequenceContainerprotected
getSequence_(const std::string &name)bpp::VectorSequenceContainerprotected
getSequencePosition(const std::string &name) constbpp::VectorSequenceContainervirtual
getSequencesNames() constbpp::VectorSequenceContainervirtual
getSite(size_t siteIndex) constbpp::AlignedSequenceContainervirtual
getSitePositions() constbpp::AlignedSequenceContainerinlinevirtual
hasSequence(const std::string &name) constbpp::VectorSequenceContainervirtual
length_bpp::AlignedSequenceContainerprivate
operator()(const std::string &sequenceName, size_t elementIndex)bpp::VectorSequenceContainerinlinevirtual
operator()(const std::string &sequenceName, size_t elementIndex) constbpp::VectorSequenceContainerinlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex)bpp::VectorSequenceContainerinlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex) constbpp::VectorSequenceContainerinlinevirtual
operator=(const AlignedSequenceContainer &asc)bpp::AlignedSequenceContainer
operator=(const SiteContainer &sc)bpp::AlignedSequenceContainer
operator=(const OrderedSequenceContainer &osc)bpp::AlignedSequenceContainer
bpp::VectorSequenceContainer::operator=(const VectorSequenceContainer &vsc)bpp::VectorSequenceContainer
bpp::VectorSequenceContainer::operator=(const SequenceContainer &osc)bpp::VectorSequenceContainer
bpp::AbstractSequenceContainer::operator=(const AbstractSequenceContainer &sc)bpp::AbstractSequenceContainerinline
OrderedSequenceContainer()bpp::OrderedSequenceContainerinline
positions_bpp::AlignedSequenceContainerprivate
reindexSites()bpp::AlignedSequenceContainervirtual
removeSequence(const std::string &name)bpp::VectorSequenceContainerinlinevirtual
removeSequence(size_t sequenceIndex)bpp::VectorSequenceContainervirtual
removeSite(size_t siteIndex)bpp::AlignedSequenceContainervirtual
SequenceContainer()bpp::SequenceContainerinline
setComments(const std::string &name, const Comments &comments)bpp::VectorSequenceContainerinlinevirtual
setComments(size_t sequenceIndex, const Comments &comments)bpp::VectorSequenceContainervirtual
setGeneralComments(const Comments &comments)bpp::AbstractSequenceContainerinlinevirtual
setSequence(const std::string &name, const Sequence &sequence, bool checkName=true)bpp::AlignedSequenceContainervirtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName=true)bpp::AlignedSequenceContainervirtual
setSequencesNames(const std::vector< std::string > &names, bool checkNames=true)bpp::VectorSequenceContainervirtual
setSite(size_t siteIndex, const Site &site, bool checkPosition=true)bpp::AlignedSequenceContainervirtual
SiteContainer()bpp::SiteContainerinline
sites_bpp::AlignedSequenceContainermutableprivate
toString(const std::string &name) constbpp::AbstractSequenceContainerinlinevirtual
toString(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
valueAt(const std::string &sequenceName, size_t elementIndex)bpp::VectorSequenceContainerinlinevirtual
valueAt(const std::string &sequenceName, size_t elementIndex) constbpp::VectorSequenceContainerinlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex)bpp::VectorSequenceContainerinlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex) constbpp::VectorSequenceContainerinlinevirtual
VectorSequenceContainer(const std::vector< const Sequence *> &vs, const Alphabet *alpha)bpp::VectorSequenceContainer
VectorSequenceContainer(const Alphabet *alpha)bpp::VectorSequenceContainerinline
VectorSequenceContainer(const VectorSequenceContainer &vsc)bpp::VectorSequenceContainer
VectorSequenceContainer(const OrderedSequenceContainer &osc)bpp::VectorSequenceContainer
VectorSequenceContainer(const SequenceContainer &osc)bpp::VectorSequenceContainer
~AbstractSequenceContainer()bpp::AbstractSequenceContainerinlinevirtual
~AlignedSequenceContainer()bpp::AlignedSequenceContainervirtual
~OrderedSequenceContainer()bpp::OrderedSequenceContainerinlinevirtual
~SequenceContainer()bpp::SequenceContainerinlinevirtual
~SiteContainer()bpp::SiteContainerinlinevirtual
~VectorSequenceContainer()bpp::VectorSequenceContainerinlinevirtual