bpp::SequenceWithQuality Member List

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

AbstractCoreSequence(const std::string &name)	bpp::AbstractCoreSequence	inline
AbstractCoreSequence(const std::string &name, const Comments &comments)	bpp::AbstractCoreSequence	inline
AbstractCoreSequence()	bpp::AbstractCoreSequence	inline
AbstractCoreSequence(const AbstractCoreSequence &s)	bpp::AbstractCoreSequence	inline
AbstractCoreSequence(const CoreSequenceInterface &s)	bpp::AbstractCoreSequence	inline
AbstractTemplateEventDrivenSymbolList(std::shared_ptr< const Alphabet > alpha)	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
AbstractTemplateEventDrivenSymbolList(const std::vector< int > &list, std::shared_ptr< const Alphabet > alpha)	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
AbstractTemplateEventDrivenSymbolList(const TemplateCoreSymbolListInterface< int > &list)	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
AbstractTemplateEventDrivenSymbolList(const AbstractTemplateEventDrivenSymbolList< int > &list)	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
AbstractTemplateSymbolList(std::shared_ptr< const Alphabet > alpha)	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateSymbolList(const std::vector< int > &list, std::shared_ptr< const Alphabet > alpha)	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateSymbolList(const AbstractTemplateSymbolList< int > &list)	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateSymbolList(const TemplateCoreSymbolListInterface< int > &list)	bpp::AbstractTemplateSymbolList< int >	inline
addAnnotation(std::shared_ptr< SequenceAnnotation > anno)	bpp::SequenceWithAnnotation	inlinevirtual
addCoreSymbolListListener(std::shared_ptr< CoreSymbolListListener< int >> listener) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::addCoreSymbolListListener(std::shared_ptr< CoreSymbolListListener< T >> listener)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	pure virtual
addElement(const std::string &c, int q)	bpp::SequenceWithQuality	inline
addElement(size_t pos, const std::string &c, int q)	bpp::SequenceWithQuality	inline
addElement(int v, int q)	bpp::SequenceWithQuality	inline
addElement(size_t pos, int v, int q)	bpp::SequenceWithQuality	inline
addElement(const T &c)=0	bpp::SequenceWithQuality
addElement(size_t pos, const T &c)=0	bpp::SequenceWithQuality
addElement(const std::string &c) override	bpp::SequenceWithQuality
addElement(size_t pos, const std::string &c) override	bpp::SequenceWithQuality
bpp::SequenceWithAnnotation::addElement(const std::string &c)=0	bpp::IntSymbolListInterface	pure virtual
bpp::SequenceWithAnnotation::addElement(size_t pos, const std::string &c)=0	bpp::IntSymbolListInterface	pure virtual
bpp::TemplateCoreSymbolListInterface::addElement(const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::TemplateCoreSymbolListInterface::addElement(size_t pos, const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::SequenceWithAnnotation::addElement(const std::string &c) override	bpp::EventDrivenIntSymbolList	virtual
bpp::EventDrivenIntSymbolList::addElement(size_t pos, const std::string &c) override	bpp::EventDrivenIntSymbolList	virtual
bpp::AbstractTemplateSymbolList< int >::addElement(const int &c) override	bpp::AbstractTemplateSymbolList< int >	inline
bpp::AbstractTemplateSymbolList< int >::addElement(size_t pos, const int &c) override	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateEventDrivenSymbolList< int >::addElement(const int &c) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
AbstractTemplateEventDrivenSymbolList< int >::addElement(size_t pos, const int &c) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
addIntSymbolListListener(std::shared_ptr< IntSymbolListListener > listener)	bpp::EventDrivenIntSymbolList	inline
afterSequenceChanged(const IntSymbolListEditionEvent &event) override	bpp::EventDrivenIntSymbolList	inlineprotectedvirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::afterSequenceChanged(const CoreSymbolListEditionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
afterSequenceDeleted(const IntSymbolListDeletionEvent &event) override	bpp::EventDrivenIntSymbolList	inlineprotectedvirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::afterSequenceDeleted(const CoreSymbolListDeletionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
afterSequenceInserted(const IntSymbolListInsertionEvent &event) override	bpp::EventDrivenIntSymbolList	inlineprotectedvirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::afterSequenceInserted(const CoreSymbolListInsertionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
afterSequenceSubstituted(const IntSymbolListSubstitutionEvent &event) override	bpp::EventDrivenIntSymbolList	inlineprotectedvirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::afterSequenceSubstituted(const CoreSymbolListSubstitutionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
bpp::alphabet() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::AbstractTemplateSymbolList< int >::alphabet() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
alphabet_	bpp::AbstractTemplateSymbolList< int >	private
annotation(const std::string &type) const	bpp::SequenceWithAnnotation	inlinevirtual
annotation(const std::string &type)	bpp::SequenceWithAnnotation	inlinevirtual
append(const std::vector< int > &content, const std::vector< int > &qualities)	bpp::SequenceWithQuality	inlinevirtual
append(const std::vector< std::string > &content, const std::vector< int > &qualities)	bpp::SequenceWithQuality	inlinevirtual
append(const std::string &content, const std::vector< int > &qualities)	bpp::SequenceWithQuality	inlinevirtual
append(const SequenceInterface &seq) override	bpp::SequenceWithQuality
append(const std::vector< int > &content) override	bpp::SequenceWithQuality
append(const std::vector< std::string > &content) override	bpp::SequenceWithQuality
append(const std::string &content) override	bpp::SequenceWithQuality
bpp::SequenceWithAnnotation::append(const SequenceInterface &seq) override	bpp::SequenceWithAnnotation	virtual
bpp::SequenceWithAnnotation::append(const std::vector< int > &content) override	bpp::SequenceWithAnnotation	virtual
bpp::SequenceWithAnnotation::append(const std::vector< std::string > &content) override	bpp::SequenceWithAnnotation	virtual
bpp::SequenceWithAnnotation::append(const std::string &content) override	bpp::SequenceWithAnnotation	virtual
beforeSequenceChanged(const IntSymbolListEditionEvent &event) override	bpp::EventDrivenIntSymbolList	inlineprotectedvirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::beforeSequenceChanged(const CoreSymbolListEditionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
beforeSequenceDeleted(const IntSymbolListDeletionEvent &event) override	bpp::EventDrivenIntSymbolList	inlineprotectedvirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::beforeSequenceDeleted(const CoreSymbolListDeletionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
beforeSequenceInserted(const IntSymbolListInsertionEvent &event) override	bpp::EventDrivenIntSymbolList	inlineprotectedvirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::beforeSequenceInserted(const CoreSymbolListInsertionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
beforeSequenceSubstituted(const IntSymbolListSubstitutionEvent &event) override	bpp::EventDrivenIntSymbolList	inlineprotectedvirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::beforeSequenceSubstituted(const CoreSymbolListSubstitutionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
bpp::clearComments()=0	bpp::Commentable	pure virtual
bpp::AbstractCoreSequence::bpp::SimpleCommentable::clearComments() override	bpp::SimpleCommentable	inlinevirtual
clone() const override	bpp::SequenceWithQuality	inlinevirtual
Commentable()	bpp::Commentable	inline
comments_	bpp::SimpleCommentable	protected
content_	bpp::AbstractTemplateSymbolList< int >	protected
CoreSequenceInterface()	bpp::CoreSequenceInterface	inline
bpp::deleteElement(size_t pos)=0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::bpp::AbstractTemplateSymbolList< int >::deleteElement(size_t pos) override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
bpp::EventDrivenIntSymbolList::AbstractTemplateEventDrivenSymbolList< int >::deleteElement(size_t pos) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
bpp::deleteElements(size_t pos, size_t len)=0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::bpp::AbstractTemplateSymbolList< int >::deleteElements(size_t pos, size_t len) override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
bpp::EventDrivenIntSymbolList::AbstractTemplateEventDrivenSymbolList< int >::deleteElements(size_t pos, size_t len) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
ElementType typedef	bpp::SequenceInterface
EventDrivenIntSymbolList(std::shared_ptr< const Alphabet > alpha)	bpp::EventDrivenIntSymbolList	inline
EventDrivenIntSymbolList(const std::vector< std::string > &list, std::shared_ptr< const Alphabet > alpha)	bpp::EventDrivenIntSymbolList	inline
EventDrivenIntSymbolList(const std::vector< int > &list, std::shared_ptr< const Alphabet > alpha)	bpp::EventDrivenIntSymbolList	inline
EventDrivenIntSymbolList(const IntSymbolList &list)	bpp::EventDrivenIntSymbolList	inline
EventDrivenIntSymbolList(const EventDrivenIntSymbolList &list)	bpp::EventDrivenIntSymbolList	inline
fireAfterSequenceChanged(const CoreSymbolListEditionEvent< int > &event) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::TemplateEventDrivenCoreSymbolListInterface::fireAfterSequenceChanged(const CoreSymbolListEditionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
fireAfterSequenceDeleted(const CoreSymbolListDeletionEvent< int > &event) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::TemplateEventDrivenCoreSymbolListInterface::fireAfterSequenceDeleted(const CoreSymbolListDeletionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
fireAfterSequenceInserted(const CoreSymbolListInsertionEvent< int > &event) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::TemplateEventDrivenCoreSymbolListInterface::fireAfterSequenceInserted(const CoreSymbolListInsertionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
fireAfterSequenceSubstituted(const CoreSymbolListSubstitutionEvent< int > &event) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::TemplateEventDrivenCoreSymbolListInterface::fireAfterSequenceSubstituted(const CoreSymbolListSubstitutionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
fireBeforeSequenceChanged(const CoreSymbolListEditionEvent< int > &event) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::TemplateEventDrivenCoreSymbolListInterface::fireBeforeSequenceChanged(const CoreSymbolListEditionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
fireBeforeSequenceDeleted(const CoreSymbolListDeletionEvent< int > &event) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::TemplateEventDrivenCoreSymbolListInterface::fireBeforeSequenceDeleted(const CoreSymbolListDeletionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
fireBeforeSequenceInserted(const CoreSymbolListInsertionEvent< int > &event) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::TemplateEventDrivenCoreSymbolListInterface::fireBeforeSequenceInserted(const CoreSymbolListInsertionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
fireBeforeSequenceSubstituted(const CoreSymbolListSubstitutionEvent< int > &event) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::TemplateEventDrivenCoreSymbolListInterface::fireBeforeSequenceSubstituted(const CoreSymbolListSubstitutionEvent< T > &event)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	protectedpure virtual
bpp::getAlphabet() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::AbstractTemplateSymbolList< int >::getAlphabet() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
getAnnotationTypes() const	bpp::SequenceWithAnnotation	virtual
bpp::getChar(size_t pos) const =0	bpp::IntSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::getChar(size_t pos) const override	bpp::EventDrivenIntSymbolList	virtual
bpp::getComments() const =0	bpp::Commentable	pure virtual
bpp::AbstractCoreSequence::bpp::SimpleCommentable::getComments() const override	bpp::SimpleCommentable	inlinevirtual
bpp::getContent() const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::EventDrivenIntSymbolList::AbstractTemplateSymbolList< int >::getContent() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
bpp::getElement(size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::EventDrivenIntSymbolList::AbstractTemplateSymbolList< int >::getElement(size_t pos) const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
getListener(size_t i) const override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
getListener(size_t i) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
bpp::getName() const =0	bpp::CoreSequenceInterface	pure virtual
bpp::AbstractCoreSequence::getName() const override	bpp::AbstractCoreSequence	inlinevirtual
getNumberOfListeners() const override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
getQualities() const	bpp::SequenceWithQuality	inline
getQuality(size_t pos) const	bpp::SequenceWithQuality	inline
bpp::getStateValueAt(size_t position, int state) const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::getStateValueAt(size_t siteIndex, int state) const override	bpp::IntSymbolList	inlinevirtual
bpp::getValue(size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::EventDrivenIntSymbolList::AbstractTemplateSymbolList< int >::getValue(size_t pos) const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
hasAnnotation(const std::string &type) const	bpp::SequenceWithAnnotation	inlinevirtual
IntSymbolList(std::shared_ptr< const Alphabet > alpha)	bpp::IntSymbolList	inline
IntSymbolList(const std::vector< std::string > &list, std::shared_ptr< const Alphabet > alpha)	bpp::IntSymbolList	inline
IntSymbolList(const std::vector< int > &list, std::shared_ptr< const Alphabet > alpha)	bpp::IntSymbolList	inline
IntSymbolList(const IntSymbolList &list)	bpp::IntSymbolList	inline
IntSymbolListInterface()	bpp::IntSymbolListInterface	inline
listener(size_t i) const override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
listener(size_t i) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
listeners_	bpp::AbstractTemplateEventDrivenSymbolList< int >	protected
merge(const SequenceWithAnnotation &swa)	bpp::SequenceWithAnnotation	virtual
name_	bpp::AbstractCoreSequence	private
bpp::operator()(size_t position, int state) const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::operator()(size_t siteIndex, int state) const override	bpp::IntSymbolList	inlinevirtual
operator=(const SequenceWithQuality &sequence)	bpp::SequenceWithQuality	inline
bpp::SequenceWithAnnotation::operator=(const Sequence &s)	bpp::SequenceWithAnnotation	inline
bpp::SequenceWithAnnotation::operator=(const SequenceWithAnnotation &s)	bpp::SequenceWithAnnotation	inline
bpp::AbstractCoreSequence::operator=(const AbstractCoreSequence &s)	bpp::AbstractCoreSequence	inline
bpp::AbstractCoreSequence::operator=(const CoreSequenceInterface &s)	bpp::AbstractCoreSequence	inline
bpp::SimpleCommentable::operator=(const SimpleCommentable &com)	bpp::SimpleCommentable	inline
bpp::EventDrivenIntSymbolList::operator=(const IntSymbolList &list)	bpp::EventDrivenIntSymbolList	inline
bpp::EventDrivenIntSymbolList::operator=(const EventDrivenIntSymbolList &list)	bpp::EventDrivenIntSymbolList	inline
bpp::IntSymbolList::operator=(const IntSymbolListInterface &list)	bpp::IntSymbolList
bpp::AbstractTemplateSymbolList< int >::operator=(const TemplateCoreSymbolListInterface< int > &list)	bpp::AbstractTemplateSymbolList< int >	inline
bpp::AbstractTemplateSymbolList< int >::operator=(const AbstractTemplateSymbolList< int > &list)	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateEventDrivenSymbolList< int >::operator=(const TemplateCoreSymbolListInterface< int > &list)	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
AbstractTemplateEventDrivenSymbolList< int >::operator=(const AbstractTemplateEventDrivenSymbolList &list)	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotected
bpp::operator[](size_t pos) const =0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::operator[](size_t pos)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::EventDrivenIntSymbolList::AbstractTemplateSymbolList< int >::operator[](size_t pos) const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
AbstractTemplateSymbolList< int >::operator[](size_t pos) override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
propagateEvents(bool yn) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotectedvirtual
propagateEvents() const override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlineprotectedvirtual
propagateEvents_	bpp::AbstractTemplateEventDrivenSymbolList< int >	private
qualScores_	bpp::SequenceWithQuality	private
removeCoreSymbolListListener(std::shared_ptr< CoreSymbolListListener< int >> listener) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
bpp::TemplateEventDrivenCoreSymbolListInterface::removeCoreSymbolListListener(std::shared_ptr< CoreSymbolListListener< T >> listener)=0	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	pure virtual
SequenceWithAnnotation(std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithAnnotation	inline
SequenceWithAnnotation(const std::string &name, const std::string &sequence, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithAnnotation	inline
SequenceWithAnnotation(const std::string &name, const std::string &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithAnnotation	inline
SequenceWithAnnotation(const std::string &name, const std::vector< std::string > &sequence, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithAnnotation	inline
SequenceWithAnnotation(const std::string &name, const std::vector< std::string > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithAnnotation	inline
SequenceWithAnnotation(const std::string &name, const std::vector< int > &sequence, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithAnnotation	inline
SequenceWithAnnotation(const std::string &name, const std::vector< int > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithAnnotation	inline
SequenceWithAnnotation(const Sequence &s)	bpp::SequenceWithAnnotation	inline
SequenceWithAnnotation(const SequenceWithAnnotation &s)	bpp::SequenceWithAnnotation	inline
SequenceWithQuality(std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::string &sequence, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::string &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::string &sequence, const std::vector< int > &quality, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::string &sequence, const std::vector< int > &quality, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::vector< int > &sequence, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::vector< int > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::vector< int > &sequence, const std::vector< int > &quality, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::vector< int > &sequence, const std::vector< int > &quality, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const Sequence &s)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const Sequence &s, const std::vector< int > &sc)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const SequenceWithQuality &sequence)	bpp::SequenceWithQuality	inline
bpp::setComments(const Comments &comments)=0	bpp::Commentable	pure virtual
bpp::AbstractCoreSequence::bpp::SimpleCommentable::setComments(const Comments &comments) override	bpp::SimpleCommentable	inlinevirtual
setContent(const std::string &sequence) override	bpp::SequenceWithAnnotation	virtual
setContent(const std::vector< std::string > &list) override	bpp::SequenceWithAnnotation	inlinevirtual
setContent(const std::vector< int > &list) override	bpp::SequenceWithAnnotation	inlinevirtual
bpp::IntSymbolListInterface::setContent(const std::vector< T > &list)=0	bpp::IntSymbolListInterface
bpp::TemplateCoreSymbolListInterface::setContent(const std::vector< T > &list)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::setElement(size_t pos, const std::string &c)=0	bpp::IntSymbolListInterface	pure virtual
bpp::setElement(size_t pos, const T &c)=0	bpp::IntSymbolListInterface
bpp::TemplateCoreSymbolListInterface::setElement(size_t pos, const T &c)=0	bpp::TemplateCoreSymbolListInterface< T >	pure virtual
bpp::EventDrivenIntSymbolList::setElement(size_t pos, const std::string &c) override	bpp::EventDrivenIntSymbolList	virtual
bpp::IntSymbolList::setElement(size_t pos, const T &c) override	bpp::IntSymbolList	inline
bpp::AbstractTemplateSymbolList< int >::setElement(size_t pos, const int &c) override	bpp::AbstractTemplateSymbolList< int >	inline
AbstractTemplateEventDrivenSymbolList< int >::setElement(size_t pos, const int &c) override	bpp::AbstractTemplateEventDrivenSymbolList< int >	inlinevirtual
bpp::setName(const std::string &name)=0	bpp::CoreSequenceInterface	pure virtual
bpp::AbstractCoreSequence::setName(const std::string &name) override	bpp::AbstractCoreSequence	inlinevirtual
setQualities(const std::vector< int > &quality)	bpp::SequenceWithQuality	inline
setQuality(size_t pos, int quality)	bpp::SequenceWithQuality	inline
setToSizeL(size_t newSize) override	bpp::SequenceWithAnnotation	virtual
setToSizeR(size_t newSize) override	bpp::SequenceWithAnnotation	virtual
bpp::shuffle()=0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::AbstractTemplateSymbolList< int >::shuffle() override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
SimpleCommentable()	bpp::SimpleCommentable	inline
SimpleCommentable(const Comments &comments)	bpp::SimpleCommentable	inline
SimpleCommentable(const SimpleCommentable &com)	bpp::SimpleCommentable	inline
bpp::size() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::AbstractTemplateSymbolList< int >::size() const override	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
SymbolType typedef	bpp::IntSymbolListInterface
bpp::toString() const =0	bpp::CruxSymbolListInterface	pure virtual
bpp::EventDrivenIntSymbolList::toString() const override	bpp::EventDrivenIntSymbolList	virtual
~AbstractCoreSequence()	bpp::AbstractCoreSequence	inlinevirtual
~AbstractTemplateEventDrivenSymbolList()=default	bpp::AbstractTemplateEventDrivenSymbolList< int >	protectedvirtual
~AbstractTemplateSymbolList()	bpp::AbstractTemplateSymbolList< int >	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~Commentable()	bpp::Commentable	inlinevirtual
~CoreSequenceInterface()	bpp::CoreSequenceInterface	inlinevirtual
~CruxSymbolListInterface()	bpp::CruxSymbolListInterface	inlinevirtual
~EventDrivenIntSymbolList()	bpp::EventDrivenIntSymbolList	inlinevirtual
~IntSymbolList()	bpp::IntSymbolList	inlinevirtual
~IntSymbolListInterface()	bpp::IntSymbolListInterface	inlinevirtual
~SequenceInterface()	bpp::SequenceInterface	inlinevirtual
~SequenceWithAnnotation()	bpp::SequenceWithAnnotation	inlinevirtual
~SequenceWithQuality()	bpp::SequenceWithQuality	inlinevirtual
~SimpleCommentable()	bpp::SimpleCommentable	inlinevirtual
~TemplateCoreSymbolListInterface()	bpp::TemplateCoreSymbolListInterface< T >	inlinevirtual
~TemplateEventDrivenCoreSymbolListInterface()	bpp::TemplateEventDrivenCoreSymbolListInterface< T >	inlinevirtual