bpp-seq  2.2.0
bpp::CompressedVectorSiteContainer Member List

This is the complete list of members for bpp::CompressedVectorSiteContainer, 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::CompressedVectorSiteContainerinlinevirtual
addSequence(const Sequence &sequence, size_t sequenceIndex, bool checkName=true)bpp::CompressedVectorSiteContainerinline
addSite(const Site &site, bool checkPosition=false)bpp::CompressedVectorSiteContainervirtual
addSite(const Site &site, int position, bool checkPosition=false)bpp::CompressedVectorSiteContainerinlinevirtual
addSite(const Site &site, size_t siteIndex, bool checkPosition=false)bpp::CompressedVectorSiteContainervirtual
addSite(const Site &site, size_t siteIndex, int position, bool checkPosition=false)bpp::CompressedVectorSiteContainerinlinevirtual
clear()bpp::CompressedVectorSiteContainervirtual
clone() constbpp::CompressedVectorSiteContainerinlinevirtual
comments_bpp::CompressedVectorSiteContainerprotected
CompressedVectorSiteContainer(const std::vector< const Site *> &vs, const Alphabet *alpha)bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(size_t size, const Alphabet *alpha)bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(const std::vector< std::string > &names, const Alphabet *alpha)bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(const Alphabet *alpha)bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(const CompressedVectorSiteContainer &vsc)bpp::CompressedVectorSiteContainer
CompressedVectorSiteContainer(const SiteContainer &sc)bpp::CompressedVectorSiteContainer
createEmptyContainer() constbpp::CompressedVectorSiteContainervirtual
deleteGeneralComments()bpp::AbstractSequenceContainerinlinevirtual
deleteSequence(size_t sequenceIndex)bpp::CompressedVectorSiteContainerinlinevirtual
deleteSequence(const std::string &name)bpp::CompressedVectorSiteContainerinlinevirtual
deleteSite(size_t siteIndex)bpp::CompressedVectorSiteContainervirtual
deleteSites(size_t siteIndex, size_t length)bpp::CompressedVectorSiteContainervirtual
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::CompressedVectorSiteContainerinlinevirtual
getNumberOfSites() constbpp::CompressedVectorSiteContainerinlinevirtual
getSequence(size_t sequenceIndex) constbpp::CompressedVectorSiteContainervirtual
getSequence(const std::string &name) constbpp::CompressedVectorSiteContainervirtual
getSequencePosition(const std::string &name) constbpp::CompressedVectorSiteContainervirtual
getSequencesNames() constbpp::CompressedVectorSiteContainervirtual
getSite(size_t siteIndex) constbpp::CompressedVectorSiteContainervirtual
getSiteIndex_(const Site &site)bpp::CompressedVectorSiteContainerprotected
getSitePositions() constbpp::CompressedVectorSiteContainervirtual
hasSequence(const std::string &name) constbpp::CompressedVectorSiteContainervirtual
index_bpp::CompressedVectorSiteContainerprotected
names_bpp::CompressedVectorSiteContainerprotected
operator()(const std::string &sequenceName, size_t elementIndex)bpp::CompressedVectorSiteContainerinlinevirtual
operator()(const std::string &sequenceName, size_t elementIndex) constbpp::CompressedVectorSiteContainerinlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex)bpp::CompressedVectorSiteContainerinlinevirtual
operator()(size_t sequenceIndex, size_t elementIndex) constbpp::CompressedVectorSiteContainerinlinevirtual
operator=(const CompressedVectorSiteContainer &vsc)bpp::CompressedVectorSiteContainer
operator=(const SiteContainer &sc)bpp::CompressedVectorSiteContainer
bpp::AbstractSequenceContainer::operator=(const AbstractSequenceContainer &sc)bpp::AbstractSequenceContainerinline
bpp::AbstractSequenceContainer::operator=(const SequenceContainer &sc)bpp::AbstractSequenceContainerinline
OrderedSequenceContainer()bpp::OrderedSequenceContainerinline
reindexSites()bpp::CompressedVectorSiteContainervirtual
removeSequence(size_t sequenceIndex)bpp::CompressedVectorSiteContainerinlinevirtual
removeSequence(const std::string &name)bpp::CompressedVectorSiteContainerinlinevirtual
removeSite(size_t siteIndex)bpp::CompressedVectorSiteContainervirtual
SequenceContainer()bpp::SequenceContainerinline
sequences_bpp::CompressedVectorSiteContainermutableprotected
setComments(size_t sequenceIndex, const Comments &comments)bpp::CompressedVectorSiteContainervirtual
bpp::AbstractSequenceContainer::setComments(const std::string &name, const Comments &comments)bpp::AbstractSequenceContainervirtual
setGeneralComments(const Comments &comments)bpp::AbstractSequenceContainerinlinevirtual
setSequence(const std::string &name, const Sequence &sequence, bool checkName)bpp::CompressedVectorSiteContainerinlinevirtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName)bpp::CompressedVectorSiteContainerinlinevirtual
setSequencesNames(const std::vector< std::string > &names, bool checkNames=true)bpp::CompressedVectorSiteContainervirtual
setSite(size_t siteIndex, const Site &site, bool checkPosition=false)bpp::CompressedVectorSiteContainervirtual
SiteContainer()bpp::SiteContainerinline
sites_bpp::CompressedVectorSiteContainerprotected
toString(const std::string &name) constbpp::AbstractSequenceContainerinlinevirtual
toString(size_t sequenceIndex) constbpp::AbstractSequenceContainerinlinevirtual
valueAt(const std::string &sequenceName, size_t elementIndex)bpp::CompressedVectorSiteContainerinlinevirtual
valueAt(const std::string &sequenceName, size_t elementIndex) constbpp::CompressedVectorSiteContainerinlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex)bpp::CompressedVectorSiteContainerinlinevirtual
valueAt(size_t sequenceIndex, size_t elementIndex) constbpp::CompressedVectorSiteContainerinlinevirtual
~AbstractSequenceContainer()bpp::AbstractSequenceContainerinlinevirtual
~CompressedVectorSiteContainer()bpp::CompressedVectorSiteContainerinlinevirtual
~OrderedSequenceContainer()bpp::OrderedSequenceContainerinlinevirtual
~SequenceContainer()bpp::SequenceContainerinlinevirtual
~SiteContainer()bpp::SiteContainerinlinevirtual