LocARNA::AlignerPParams Member List

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

AlignerP (defined in LocARNA::AlignerPParams)	LocARNA::AlignerPParams	[friend]
AlignerParams()	LocARNA::AlignerParams	[inline, protected]
AlignerPParams()	LocARNA::AlignerPParams	[inline, protected]
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::AlignerPParams	[inline]
min_am_prob_	LocARNA::AlignerPParams	[protected]
min_bm_prob(double min_bm_prob)	LocARNA::AlignerPParams	[inline]
min_bm_prob_	LocARNA::AlignerPParams	[protected]
no_lonely_pairs(bool no_lonely_pairs)	LocARNA::AlignerParams	[inline]
no_lonely_pairs_	LocARNA::AlignerParams	[protected]
pf_scale(pf_score_t pf_scale)	LocARNA::AlignerPParams	[inline]
pf_scale_	LocARNA::AlignerPParams	[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]
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]
~AlignerParams() (defined in LocARNA::AlignerParams)	LocARNA::AlignerParams	[virtual]
~AlignerPParams() (defined in LocARNA::AlignerPParams)	LocARNA::AlignerPParams	[inline]