LocARNA::TraceController Member List

This is the complete list of members for LocARNA::TraceController, including all inherited members.

consensus_cost(size_type i, size_type j, const std::vector< TraceRange > &trs) const	LocARNA::TraceRange
get_delta() const	LocARNA::TraceController	inline
idx_vec_t typedef (defined in LocARNA::TraceRange)	LocARNA::TraceRange	protected
is_valid(size_type i, size_type j) const	LocARNA::TraceController	inline
is_valid_match(size_type i, size_type j) const	LocARNA::TraceController	inlinevirtual
lenA_	LocARNA::TraceRange	protected
lenB_	LocARNA::TraceRange	protected
max_col(size_t i) const	LocARNA::TraceRange	inline
max_col_	LocARNA::TraceRange	protected
min_col(size_t i) const	LocARNA::TraceRange	inline
min_col_	LocARNA::TraceRange	protected
print_debug(std::ostream &out=std::cerr) const	LocARNA::TraceRange
remove_common_gaps(const SeqEntry &aliA, const SeqEntry &aliB)	LocARNA::TraceRange	static
restrict_by_anchors(const AnchorConstraints &constraints)	LocARNA::TraceController
restrict_by_trace_probabilities(const TraceProbs &trace_probs, double min_prob)	LocARNA::TraceController
reverse() const	LocARNA::TraceController
rows() const	LocARNA::TraceRange	inline
SeqEntry typedef	LocARNA::TraceRange
seqentry_pair_t typedef	LocARNA::TraceRange
TraceController(const Sequence &seqA, const Sequence &seqB, const MultipleAlignment *ma, int delta, bool relaxed_merging=false)	LocARNA::TraceController
TraceRange(const SeqEntry &pseqA, const SeqEntry &pseqB, const SeqEntry &aliA, const SeqEntry &aliB, size_type delta)	LocARNA::TraceRange
TraceRange(size_type lenA, size_type lenB, const std::vector< TraceRange > &trs, size_type delta)	LocARNA::TraceRange
TraceRange(size_t lenA, size_t lenB)	LocARNA::TraceRange	inlineprotected
~MatchController() (defined in LocARNA::MatchController)	LocARNA::MatchController	virtual
~TraceController()	LocARNA::TraceController	virtual