bpp-seq  2.2.0
bpp::SiteContainer Member List

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

addSequence(const Sequence &sequence, bool checkName)=0bpp::SequenceContainerpure virtual
addSite(const Site &site, bool checkPosition)=0bpp::SiteContainerpure virtual
addSite(const Site &site, int position, bool checkPosition)=0bpp::SiteContainerpure virtual
addSite(const Site &site, size_t siteIndex, bool checkPosition)=0bpp::SiteContainerpure virtual
addSite(const Site &site, size_t siteIndex, int position, bool checkPosition)=0bpp::SiteContainerpure virtual
clear()=0bpp::SequenceContainerpure virtual
clone() const =0bpp::SiteContainerpure virtual
createEmptyContainer() const =0bpp::SequenceContainerpure virtual
deleteGeneralComments()=0bpp::SequenceContainerpure virtual
deleteSequence(size_t sequenceIndex)=0bpp::OrderedSequenceContainerpure virtual
deleteSequence(const std::string &name)=0bpp::OrderedSequenceContainerpure virtual
deleteSite(size_t siteIndex)=0bpp::SiteContainerpure virtual
deleteSites(size_t siteIndex, size_t length)=0bpp::SiteContainerpure virtual
getAlphabet() const =0bpp::SequenceContainerpure virtual
getComments(size_t sequenceIndex) const =0bpp::OrderedSequenceContainerpure virtual
getComments(const std::string &name) const =0bpp::OrderedSequenceContainerpure virtual
getContent(size_t sequenceIndex) const =0bpp::OrderedSequenceContainerpure virtual
getContent(const std::string &name) const =0bpp::OrderedSequenceContainerpure virtual
getGeneralComments() const =0bpp::SequenceContainerpure virtual
getName(size_t sequenceIndex) const =0bpp::OrderedSequenceContainerpure virtual
getNumberOfSequences() const =0bpp::OrderedSequenceContainerpure virtual
getNumberOfSites() const =0bpp::SiteContainerpure virtual
getSequence(size_t sequenceIndex) const =0bpp::OrderedSequenceContainerpure virtual
getSequence(const std::string &name) const =0bpp::OrderedSequenceContainerpure virtual
getSequencePosition(const std::string &name) const =0bpp::OrderedSequenceContainerpure virtual
getSequencesNames() const =0bpp::OrderedSequenceContainerpure virtual
getSite(size_t siteIndex) const =0bpp::SiteContainerpure virtual
getSitePositions() const =0bpp::SiteContainerpure virtual
hasSequence(const std::string &name) const =0bpp::SequenceContainerpure virtual
operator()(size_t sequenceIndex, size_t elementIndex)=0bpp::OrderedSequenceContainerpure virtual
operator()(size_t sequenceIndex, size_t elementIndex) const =0bpp::OrderedSequenceContainerpure virtual
bpp::SequenceContainer::operator()(const std::string &sequenceName, size_t elementIndex)=0bpp::SequenceContainerpure virtual
bpp::SequenceContainer::operator()(const std::string &sequenceName, size_t elementIndex) const =0bpp::SequenceContainerpure virtual
OrderedSequenceContainer()bpp::OrderedSequenceContainerinline
reindexSites()=0bpp::SiteContainerpure virtual
removeSequence(size_t sequenceIndex)=0bpp::OrderedSequenceContainerpure virtual
removeSequence(const std::string &name)=0bpp::OrderedSequenceContainerpure virtual
removeSite(size_t siteIndex)=0bpp::SiteContainerpure virtual
SequenceContainer()bpp::SequenceContainerinline
setComments(size_t sequenceIndex, const Comments &comments)=0bpp::OrderedSequenceContainerpure virtual
setComments(const std::string &name, const Comments &comments)=0bpp::OrderedSequenceContainerpure virtual
setGeneralComments(const Comments &comments)=0bpp::SequenceContainerpure virtual
setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName)=0bpp::OrderedSequenceContainerpure virtual
setSequence(const std::string &name, const Sequence &sequence, bool checkName)=0bpp::OrderedSequenceContainerpure virtual
setSequencesNames(const std::vector< std::string > &names, bool checkNames)=0bpp::OrderedSequenceContainerpure virtual
setSite(size_t siteIndex, const Site &site, bool checkPosition)=0bpp::SiteContainerpure virtual
SiteContainer()bpp::SiteContainerinline
toString(size_t sequenceIndex) const =0bpp::OrderedSequenceContainerpure virtual
toString(const std::string &name) const =0bpp::OrderedSequenceContainerpure virtual
valueAt(const std::string &sequenceName, size_t elementIndex)=0bpp::OrderedSequenceContainerpure virtual
valueAt(const std::string &sequenceName, size_t elementIndex) const =0bpp::OrderedSequenceContainerpure virtual
valueAt(size_t sequenceIndex, size_t elementIndex)=0bpp::OrderedSequenceContainerpure virtual
valueAt(size_t sequenceIndex, size_t elementIndex) const =0bpp::OrderedSequenceContainerpure virtual
~OrderedSequenceContainer()bpp::OrderedSequenceContainerinlinevirtual
~SequenceContainer()bpp::SequenceContainerinlinevirtual
~SiteContainer()bpp::SiteContainerinlinevirtual