Align Member List

This is the complete list of members for Align, including all inherited members.

Align()	Align	[inline]
Align(const std::string &str)	Align
Align(const Sequence &s1, const Sequence &s2, Pair startPos=Pair(0, 0))	Align
FirstPair() const	Align	[inline]
Gaps() const	Align	[inline]
Identity(const Sequence &s1, const Sequence &s2) const (defined in Align)	Align	[inline]
LastPair() const	Align	[inline]
MakeLocal(Sequence &seq1, Sequence &seq2)	Align
MakeLocal(Align &align, Sequence &seq1, Sequence &seq2, long offset=0) const	Align
operator<<(std::ostream &ost, const Align &a)	Align	[friend]
parent_t typedef	Align
Positive(const Sequence &s1, const Sequence &s2, const ScoreMatrix &s) const	Align	[inline]
push_back(const AlignEntry &v)	Align	[inline]
push_back(long i, long j)	Align	[inline]
Score(const Sequence::const_iterator &first_begin, const Sequence::const_iterator &second_begin, const ScoreMatrix &scoreMatrix, int gap_open, int gap_extension, bool local=false) const	Align
Score(const Sequence &s1, const Sequence &s2, const ScoreMatrix &scoreMatrix, int gap_open, int gap_extension, bool local=false) const	Align	[inline]
SeqEnd() const	Align	[inline]
SeqOffset() const	Align	[inline]
SetStartPos(Pair p)	Align