| AbstractTemplateSequenceContainer(std::shared_ptr< const Alphabet > alphabet) | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inline |
| AbstractTemplateSequenceContainer(std::shared_ptr< const Alphabet > alphabet, const Comments &comments) | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inline |
| AbstractTemplateSequenceContainer(const AbstractTemplateSequenceContainer< SequenceType, HashType > &sc) | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inline |
| AbstractTemplateSequenceContainer(const TemplateSequenceContainerInterface< SequenceType, HashType > &sc) | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inline |
| addSequence(const HashType &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| alphabet() const override | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inlinevirtual |
| alphabet_ | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | protected |
| clear()=0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| bpp::clearComments()=0 | bpp::Commentable | pure virtual |
| bpp::SimpleCommentable::clearComments() override | bpp::SimpleCommentable | inlinevirtual |
| clone() const override=0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| Commentable() | bpp::Commentable | inline |
| comments_ | bpp::SimpleCommentable | protected |
| createEmptyContainer() const override=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| deleteSequence(const HashType &sequenceKey)=0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| deleteSequence(size_t sequencePosition)=0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| getAlphabet() const override | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inlinevirtual |
| bpp::getComments() const =0 | bpp::Commentable | pure virtual |
| bpp::SimpleCommentable::getComments() const override | bpp::SimpleCommentable | inlinevirtual |
| getNumberOfSequences() const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| getSequenceComments() const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| getSequenceKeys() const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| getSequenceNames() const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| getSequencePosition(const HashType &sequenceKey) const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| getStateValueAt(size_t sitePosition, const HashType &sequenceKey, int state) const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| getStateValueAt(size_t sitePosition, size_t sequencePosition, int state) const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| hasSequence(const HashType &sequenceKey) const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| insertSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const HashType &sequenceKey)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| operator()(size_t sitePosition, const HashType &sequenceKey, int state) const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| operator()(size_t sitePosition, size_t sequencePosition, int state) const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| operator=(const AbstractTemplateSequenceContainer< SequenceType, HashType > &sc) | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inline |
| operator=(const TemplateSequenceContainerInterface< SequenceType, HashType > &sc) | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inline |
| bpp::SimpleCommentable::operator=(const SimpleCommentable &com) | bpp::SimpleCommentable | inline |
| removeSequence(const HashType &sequenceKey)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| removeSequence(size_t sequencePosition)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| sequence(const HashType &sequenceKey) const override=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| sequence(size_t sequencePosition) const override=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| sequenceKey(size_t sequencePosition) const =0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| bpp::setComments(const Comments &comments)=0 | bpp::Commentable | pure virtual |
| bpp::SimpleCommentable::setComments(const Comments &comments) override | bpp::SimpleCommentable | inlinevirtual |
| setSequence(const HashType &sequenceKey, std::unique_ptr< SequenceType > &sequencePtr)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| setSequence(size_t sequencePosition, std::unique_ptr< SequenceType > &sequencePtr, const HashType &sequenceKey)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| setSequenceKeys(const std::vector< HashType > &sequenceKeys)=0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| setSequenceNames(const std::vector< std::string > &names, bool updateKeys)=0 | bpp::TemplateSequenceDataInterface< HashType > | pure virtual |
| SimpleCommentable() | bpp::SimpleCommentable | inline |
| SimpleCommentable(const Comments &comments) | bpp::SimpleCommentable | inline |
| SimpleCommentable(const SimpleCommentable &com) | bpp::SimpleCommentable | inline |
| TemplateSequenceContainerInterface() | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | inline |
| TemplateSequenceDataInterface() | bpp::TemplateSequenceDataInterface< HashType > | inline |
| valueAt(const HashType &sequenceKey, size_t sitePosition) const =0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| valueAt(const HashType &sequenceKey, size_t sitePosition)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| valueAt(size_t sequencePosition, size_t sitePosition) const =0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| valueAt(size_t sequencePosition, size_t sitePosition)=0 | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | pure virtual |
| ~AbstractTemplateSequenceContainer() | bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > | inlinevirtual |
| ~Commentable() | bpp::Commentable | inlinevirtual |
| ~SimpleCommentable() | bpp::SimpleCommentable | inlinevirtual |
| ~TemplateSequenceContainerInterface() | bpp::TemplateSequenceContainerInterface< SequenceType, HashType > | inlinevirtual |
| ~TemplateSequenceDataInterface() | bpp::TemplateSequenceDataInterface< HashType > | inlinevirtual |
1.8.13