LocARNA::AlignerNParams Member List

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

AlignerN (defined in LocARNA::AlignerNParams)	LocARNA::AlignerNParams	friend
AlignerNParams()	LocARNA::AlignerNParams	inlineprotected
AlignerParams()	LocARNA::AlignerParams	inlineprotected
arc_matches(const ArcMatches &arc_matches)	LocARNA::AlignerParams	inline
arc_matches_	LocARNA::AlignerParams	protected
constraints(const AnchorConstraints &constraints)	LocARNA::AlignerParams	inline
constraints_	LocARNA::AlignerParams	protected
DO_TRACE(bool DO_TRACE)	LocARNA::AlignerParams	inline
DO_TRACE_	LocARNA::AlignerParams	protected
free_endgaps(const std::string &free_endgaps)	LocARNA::AlignerParams	inline
free_endgaps_	LocARNA::AlignerParams	protected
max_diff_am(int max_diff_am)	LocARNA::AlignerParams	inline
max_diff_am_	LocARNA::AlignerParams	protected
max_diff_at_am(int max_diff_at_am)	LocARNA::AlignerParams	inline
max_diff_at_am_	LocARNA::AlignerParams	protected
min_am_prob(double min_am_prob)	LocARNA::AlignerParams	inline
min_am_prob_	LocARNA::AlignerParams	protected
min_bm_prob(double min_bm_prob)	LocARNA::AlignerParams	inline
min_bm_prob_	LocARNA::AlignerParams	protected
no_lonely_pairs(bool no_lonely_pairs)	LocARNA::AlignerParams	inline
no_lonely_pairs_	LocARNA::AlignerParams	protected
scoring(const Scoring &scoring)	LocARNA::AlignerParams	inline
scoring_	LocARNA::AlignerParams	protected
seqA(const Sequence &seqA)	LocARNA::AlignerParams	inline
seqA_	LocARNA::AlignerParams	protected
seqB(const Sequence &seqB)	LocARNA::AlignerParams	inline
seqB_	LocARNA::AlignerParams	protected
sequ_local(bool sequ_local)	LocARNA::AlignerParams	inline
sequ_local_	LocARNA::AlignerParams	protected
sparsification_mapperA(const SparsificationMapper &sparsification_mapperA)	LocARNA::AlignerNParams	inline
sparsification_mapperA_	LocARNA::AlignerNParams	protected
sparsification_mapperB(const SparsificationMapper &sparsification_mapperB)	LocARNA::AlignerNParams	inline
sparsification_mapperB_	LocARNA::AlignerNParams	protected
stacking(bool stacking)	LocARNA::AlignerParams	inline
stacking_	LocARNA::AlignerParams	protected
struct_local(bool struct_local)	LocARNA::AlignerParams	inline
struct_local_	LocARNA::AlignerParams	protected
trace_controller(const TraceController &trace_controller)	LocARNA::AlignerParams	inline
trace_controller_	LocARNA::AlignerParams	protected
~AlignerNParams() (defined in LocARNA::AlignerNParams)	LocARNA::AlignerNParams	inline
~AlignerParams() (defined in LocARNA::AlignerParams)	LocARNA::AlignerParams	virtual