LocARNA::AlignerN Member List

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

align()	LocARNA::AlignerN
align_D()	LocARNA::AlignerN	[protected]
AlignerN(const AlignerN &a)	LocARNA::AlignerN
AlignerN(const AlignerParams &ap)	LocARNA::AlignerN
alignment	LocARNA::AlignerN	[protected]
Arc typedef	LocARNA::AlignerN
arc_matches	LocARNA::AlignerN	[protected]
ArcIdx typedef	LocARNA::AlignerN
ArcIdxVec typedef	LocARNA::AlignerN
bpsA	LocARNA::AlignerN	[protected]
bpsB	LocARNA::AlignerN	[protected]
compute_E_entry(index_t al, matidx_t i_index, matidx_t j_index, seq_pos_t i_seq_pos, seq_pos_t i_prev_seq_pos, ScoringView sv)	LocARNA::AlignerN	[protected]
compute_F_entry(index_t bl, matidx_t i_index, matidx_t j_index, seq_pos_t i_seq_pos, seq_pos_t i_prev_seq_pos, ScoringView sv)	LocARNA::AlignerN	[protected]
compute_IX(pos_type xl, const Arc &arcY, pos_type i, ScoringView sv)	LocARNA::AlignerN	[protected]
compute_M_entry(index_t al, index_t bl, matidx_t index_i, matidx_t index_j, ScoringView sv)	LocARNA::AlignerN	[protected]
create()	LocARNA::AlignerN	[inline, static]
D(const ArcMatch &am)	LocARNA::AlignerN	[inline, protected]
D(const Arc &arcX, const Arc &arcY)	LocARNA::AlignerN	[inline, protected]
D(const Arc &arcA, const Arc &arcB)	LocARNA::AlignerN	[inline, protected]
D_created	LocARNA::AlignerN	[protected]
def_scoring_view	LocARNA::AlignerN	[protected]
Dmat	LocARNA::AlignerN	[protected]
Emat	LocARNA::AlignerN	[protected]
fill_D_entries(pos_type al, pos_type bl)	LocARNA::AlignerN	[protected]
fill_IA_entries(pos_type al, Arc arcB, pos_type max_ar)	LocARNA::AlignerN	[protected]
fill_IB_entries(Arc arcA, pos_type bl, pos_type max_br)	LocARNA::AlignerN	[protected]
fill_M_entries(pos_type al, pos_type ar, pos_type bl, pos_type br)	LocARNA::AlignerN	[protected]
Fmat	LocARNA::AlignerN	[protected]
gapCostMatA	LocARNA::AlignerN	[protected]
gapCostMatB	LocARNA::AlignerN	[protected]
get_alignment() const	LocARNA::AlignerN	[inline]
getGapCostBetween(pos_type leftSide, pos_type rightSide)	LocARNA::AlignerN	[inline, protected]
IA(const pos_type i, const Arc &b)	LocARNA::AlignerN	[inline, protected]
IADmat	LocARNA::AlignerN	[protected]
IAmat	LocARNA::AlignerN	[protected]
IB(const Arc &a, const pos_type k)	LocARNA::AlignerN	[inline, protected]
IBDmat	LocARNA::AlignerN	[protected]
IBmat	LocARNA::AlignerN	[protected]
index_t typedef	LocARNA::AlignerN
init_M_E_F(pos_type al, pos_type ar, pos_type bl, pos_type br, ScoringView sv)	LocARNA::AlignerN	[protected]
initGapCostMat(ScoringView sv)	LocARNA::AlignerN	[protected]
IX(const pos_type i, const Arc &arc)	LocARNA::AlignerN	[inline, protected]
IXD(const Arc &arc1, const Arc &arc2)	LocARNA::AlignerN	[inline, protected]
M	LocARNA::AlignerN	[protected]
M_matrix_t typedef	LocARNA::AlignerN
mapperA	LocARNA::AlignerN	[protected]
mapperB	LocARNA::AlignerN	[protected]
matidx_t typedef	LocARNA::AlignerN
max_i	LocARNA::AlignerN	[protected]
max_j	LocARNA::AlignerN	[protected]
min_i	LocARNA::AlignerN	[protected]
min_j	LocARNA::AlignerN	[protected]
mod_scoring	LocARNA::AlignerN	[protected]
mod_scoring_view	LocARNA::AlignerN	[protected]
params	LocARNA::AlignerN	[protected]
r	LocARNA::AlignerN	[protected]
scoring	LocARNA::AlignerN	[protected]
seq_pos_t typedef	LocARNA::AlignerN
seqA	LocARNA::AlignerN	[protected]
seqB	LocARNA::AlignerN	[protected]
trace(ScoringView sv)	LocARNA::AlignerN	[protected]
trace()	LocARNA::AlignerN
trace_D(const Arc &arcA, const Arc &arcB, ScoringView sv)	LocARNA::AlignerN	[protected]
trace_E(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool top_level, ScoringView sv)	LocARNA::AlignerN	[protected]
trace_F(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool top_level, ScoringView sv)	LocARNA::AlignerN	[protected]
trace_IX(pos_type xl, pos_type i, const Arc &arcY, ScoringView sv)	LocARNA::AlignerN	[protected]
trace_IXD(const Arc &arcA, const Arc &arcB, ScoringView sv)	LocARNA::AlignerN	[protected]
trace_M(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool tl, ScoringView sv)	LocARNA::AlignerN	[protected]
trace_M_noex(pos_type al, pos_type i, pos_type bl, pos_type j, bool top_level, ScoringView sv)	LocARNA::AlignerN	[protected]
~AlignerN()	LocARNA::AlignerN