bpp::SequenceWithQuality Member List

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

addAnnotation(SequenceAnnotation *anno)	bpp::SequenceWithAnnotation	inlinevirtual
addElement(const std::string &c)	bpp::SequenceWithQuality	inlinevirtual
addElement(const std::string &c, int q)	bpp::SequenceWithQuality	inline
addElement(size_t pos, const std::string &c)	bpp::SequenceWithQuality	inlinevirtual
addElement(size_t pos, const std::string &c, int q)	bpp::SequenceWithQuality	inline
addElement(int v)	bpp::SequenceWithQuality	inlinevirtual
addElement(int v, int q)	bpp::SequenceWithQuality	inline
addElement(size_t pos, int v)	bpp::SequenceWithQuality	inlinevirtual
addElement(size_t pos, int v, int q)	bpp::SequenceWithQuality	inline
addSymbolListListener(SymbolListListener *listener)	bpp::EdSymbolList	inlinevirtual
afterSequenceChanged(const SymbolListEditionEvent &event)	bpp::EdSymbolList	inlineprotectedvirtual
afterSequenceDeleted(const SymbolListDeletionEvent &event)	bpp::EdSymbolList	inlineprotectedvirtual
afterSequenceInserted(const SymbolListInsertionEvent &event)	bpp::EdSymbolList	inlineprotectedvirtual
afterSequenceSubstituted(const SymbolListSubstitutionEvent &event)	bpp::EdSymbolList	inlineprotectedvirtual
append(const std::vector< int > &content)	bpp::SequenceWithQuality	inlinevirtual
append(const std::vector< int > &content, const std::vector< int > &qualities)	bpp::SequenceWithQuality	inline
append(const std::vector< std::string > &content)	bpp::SequenceWithQuality	inlinevirtual
append(const std::vector< std::string > &content, const std::vector< int > &qualities)	bpp::SequenceWithQuality	inline
append(const std::string &content)	bpp::SequenceWithQuality	inlinevirtual
append(const std::string &content, const std::vector< int > &qualities)	bpp::SequenceWithQuality	inline
beforeSequenceChanged(const SymbolListEditionEvent &event)	bpp::EdSymbolList	inlineprotectedvirtual
beforeSequenceDeleted(const SymbolListDeletionEvent &event)	bpp::EdSymbolList	inlineprotectedvirtual
beforeSequenceInserted(const SymbolListInsertionEvent &event)	bpp::EdSymbolList	inlineprotectedvirtual
beforeSequenceSubstituted(const SymbolListSubstitutionEvent &event)	bpp::EdSymbolList	inlineprotectedvirtual
clone() const	bpp::SequenceWithQuality	inlinevirtual
content_	bpp::EdSymbolList	protected
bpp::deleteElement(size_t pos)=0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::deleteElement(size_t pos)	bpp::EdSymbolList	virtual
bpp::deleteElements(size_t pos, size_t len)=0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::deleteElements(size_t pos, size_t len)	bpp::EdSymbolList	virtual
EdSymbolList(const Alphabet *alpha)	bpp::EdSymbolList	inline
EdSymbolList(const std::vector< std::string > &list, const Alphabet *alpha)	bpp::EdSymbolList
EdSymbolList(const std::vector< int > &list, const Alphabet *alpha)	bpp::EdSymbolList
EdSymbolList(const SymbolList &list)	bpp::EdSymbolList
EdSymbolList(const EdSymbolList &list)	bpp::EdSymbolList
fireAfterSequenceChanged(const SymbolListEditionEvent &event)	bpp::EdSymbolList	inlineprotected
fireAfterSequenceDeleted(const SymbolListDeletionEvent &event)	bpp::EdSymbolList	inlineprotected
fireAfterSequenceInserted(const SymbolListInsertionEvent &event)	bpp::EdSymbolList	inlineprotected
fireAfterSequenceSubstituted(const SymbolListSubstitutionEvent &event)	bpp::EdSymbolList	inlineprotected
fireBeforeSequenceChanged(const SymbolListEditionEvent &event)	bpp::EdSymbolList	inlineprotected
fireBeforeSequenceDeleted(const SymbolListDeletionEvent &event)	bpp::EdSymbolList	inlineprotected
fireBeforeSequenceInserted(const SymbolListInsertionEvent &event)	bpp::EdSymbolList	inlineprotected
fireBeforeSequenceSubstituted(const SymbolListSubstitutionEvent &event)	bpp::EdSymbolList	inlineprotected
bpp::getAlphabet() const =0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::getAlphabet() const	bpp::EdSymbolList	inlinevirtual
getAnnotation(const std::string &type) const	bpp::SequenceWithAnnotation	inlinevirtual
getAnnotation(const std::string &type)	bpp::SequenceWithAnnotation	inlinevirtual
getAnnotationTypes() const	bpp::SequenceWithAnnotation	virtual
bpp::getChar(size_t pos) const =0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::getChar(size_t pos) const	bpp::EdSymbolList	virtual
getComments() const	bpp::SequenceWithAnnotation	inlinevirtual
bpp::getContent() const =0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::getContent() const	bpp::EdSymbolList	inlinevirtual
getListener(size_t i) const	bpp::EdSymbolList	inlinevirtual
getListener(size_t i)	bpp::EdSymbolList	inlinevirtual
getName() const	bpp::SequenceWithAnnotation	inlinevirtual
getNumberOfListeners() const	bpp::EdSymbolList	inlinevirtual
getQualities() const	bpp::SequenceWithQuality	inline
getQuality(size_t pos) const	bpp::SequenceWithQuality	inline
bpp::getValue(size_t pos) const =0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::getValue(size_t pos) const	bpp::EdSymbolList	virtual
hasAnnotation(const std::string &type) const	bpp::SequenceWithAnnotation	inlinevirtual
listeners_	bpp::EdSymbolList	protected
merge(const SequenceWithAnnotation &swa)	bpp::SequenceWithAnnotation	virtual
operator=(const SequenceWithQuality &sequence)	bpp::SequenceWithQuality	inline
bpp::SequenceWithAnnotation::operator=(const Sequence &s)	bpp::SequenceWithAnnotation
bpp::SequenceWithAnnotation::operator=(const SequenceWithAnnotation &s)	bpp::SequenceWithAnnotation
bpp::EdSymbolList::operator=(const SymbolList &list)	bpp::EdSymbolList
bpp::EdSymbolList::operator=(const EdSymbolList &list)	bpp::EdSymbolList
bpp::operator[](size_t i) const =0	bpp::SymbolList	pure virtual
bpp::operator[](size_t i)=0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::operator[](size_t i) const	bpp::EdSymbolList	inlinevirtual
bpp::EdSymbolList::operator[](size_t i)	bpp::EdSymbolList	inlinevirtual
propagateEvents(bool yn)	bpp::EdSymbolList	inlineprotected
propagateEvents() const	bpp::EdSymbolList	inlineprotected
qualScores_	bpp::SequenceWithQuality	private
removeSymbolListListener(SymbolListListener *listener)	bpp::EdSymbolList	inlinevirtual
SequenceWithAnnotation(const Alphabet *alpha)	bpp::SequenceWithAnnotation
SequenceWithAnnotation(const std::string &name, const std::string &sequence, const Alphabet *alpha)	bpp::SequenceWithAnnotation
SequenceWithAnnotation(const std::string &name, const std::string &sequence, const Comments &comments, const Alphabet *alpha)	bpp::SequenceWithAnnotation
SequenceWithAnnotation(const std::string &name, const std::vector< std::string > &sequence, const Alphabet *alpha)	bpp::SequenceWithAnnotation
SequenceWithAnnotation(const std::string &name, const std::vector< std::string > &sequence, const Comments &comments, const Alphabet *alpha)	bpp::SequenceWithAnnotation
SequenceWithAnnotation(const std::string &name, const std::vector< int > &sequence, const Alphabet *alpha)	bpp::SequenceWithAnnotation
SequenceWithAnnotation(const std::string &name, const std::vector< int > &sequence, const Comments &comments, const Alphabet *alpha)	bpp::SequenceWithAnnotation
SequenceWithAnnotation(const Sequence &s)	bpp::SequenceWithAnnotation
SequenceWithAnnotation(const SequenceWithAnnotation &s)	bpp::SequenceWithAnnotation
SequenceWithQuality(const Alphabet *alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::string &sequence, const Alphabet *alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::string &sequence, const Comments &comments, const Alphabet *alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::string &sequence, const std::vector< int > &quality, const Alphabet *alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::string &sequence, const std::vector< int > &quality, const Comments &comments, const Alphabet *alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::vector< int > &sequence, const Alphabet *alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::vector< int > &sequence, const Comments &comments, const Alphabet *alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::vector< int > &sequence, const std::vector< int > &quality, const Alphabet *alpha)	bpp::SequenceWithQuality	inline
SequenceWithQuality(const std::string &name, const std::vector< int > &sequence, const std::vector< int > &quality, const Comments &comments, 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
setComments(const Comments &comments)	bpp::SequenceWithAnnotation	inlinevirtual
setContent(const std::string &sequence)	bpp::SequenceWithAnnotation	virtual
setContent(const std::vector< int > &list)	bpp::SequenceWithAnnotation	inlinevirtual
setContent(const std::vector< std::string > &list)	bpp::SequenceWithAnnotation	inlinevirtual
bpp::setElement(size_t pos, const std::string &c)=0	bpp::SymbolList	pure virtual
bpp::setElement(size_t pos, int v)=0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::setElement(size_t pos, const std::string &c)	bpp::EdSymbolList	virtual
bpp::EdSymbolList::setElement(size_t pos, int v)	bpp::EdSymbolList	virtual
setName(const std::string &name)	bpp::SequenceWithAnnotation	inlinevirtual
setQualities(const std::vector< int > &quality)	bpp::SequenceWithQuality	inline
setQuality(size_t pos, int quality)	bpp::SequenceWithQuality	inline
setToSizeL(size_t newSize)	bpp::SequenceWithAnnotation	virtual
setToSizeR(size_t newSize)	bpp::SequenceWithAnnotation	virtual
bpp::shuffle()=0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::shuffle()	bpp::EdSymbolList	inlinevirtual
bpp::size() const =0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::size() const	bpp::EdSymbolList	inlinevirtual
bpp::toString() const =0	bpp::SymbolList	pure virtual
bpp::EdSymbolList::toString() const	bpp::EdSymbolList	virtual
~EdSymbolList()	bpp::EdSymbolList	inlinevirtual
~Sequence()	bpp::Sequence	inlinevirtual
~SequenceWithAnnotation()	bpp::SequenceWithAnnotation	inlinevirtual
~SequenceWithQuality()	bpp::SequenceWithQuality	inlinevirtual
~SymbolList()	bpp::SymbolList	inlinevirtual