LocARNA::AlignerImpl Member List

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

align()	LocARNA::AlignerImpl
align_D()	LocARNA::AlignerImpl
align_in_arcmatch(pos_type al, pos_type ar, pos_type bl, pos_type br, bool allow_exclusion)	LocARNA::AlignerImpl
align_noex(int state, pos_type al, pos_type bl, pos_type i, pos_type j, ScoringView sv)	LocARNA::AlignerImpl
align_top_level_free_endgaps()	LocARNA::AlignerImpl
align_top_level_locally(ScoringView sv)	LocARNA::AlignerImpl
AlignerImpl(const AlignerImpl &a)	LocARNA::AlignerImpl
AlignerImpl(const Sequence &seqA, const Sequence &seqB, const ArcMatches &arc_matches, const AlignerParams *ap, const Scoring *s)	LocARNA::AlignerImpl
alignment_	LocARNA::AlignerImpl
Arc typedef	LocARNA::AlignerImpl
arc_matches_	LocARNA::AlignerImpl
bpsA_	LocARNA::AlignerImpl
bpsB_	LocARNA::AlignerImpl
D(const ArcMatch &am)	LocARNA::AlignerImpl	[inline]
D(const Arc &arcA, const Arc &arcB)	LocARNA::AlignerImpl	[inline]
D_created_	LocARNA::AlignerImpl
def_scoring_view_	LocARNA::AlignerImpl
Dmat_	LocARNA::AlignerImpl
E_NO_NO enum value (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
E_NO_OP enum value (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
E_NO_X enum value (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
E_OP_NO enum value (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
E_OP_X enum value (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
E_X_NO enum value (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
E_X_OP enum value (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
E_X_X enum value (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
Es_	LocARNA::AlignerImpl
fill_D_entries(pos_type al, pos_type bl)	LocARNA::AlignerImpl
fill_D_entries_noLP(pos_type al, pos_type bl)	LocARNA::AlignerImpl
free_endgaps_ (defined in LocARNA::AlignerImpl)	LocARNA::AlignerImpl
Fs_	LocARNA::AlignerImpl
init_state(int state, pos_type al, pos_type ar, pos_type bl, pos_type br, bool globalA, bool exclA, bool globalB, bool exclB, ScoringView sv)	LocARNA::AlignerImpl
M_matrix_t typedef	LocARNA::AlignerImpl
max_i_	LocARNA::AlignerImpl
max_j_	LocARNA::AlignerImpl
min_i_	LocARNA::AlignerImpl
min_j_	LocARNA::AlignerImpl
mod_scoring_	LocARNA::AlignerImpl
mod_scoring_view_	LocARNA::AlignerImpl
Ms_	LocARNA::AlignerImpl
params_	LocARNA::AlignerImpl
r_	LocARNA::AlignerImpl
scoring_	LocARNA::AlignerImpl
seqA_	LocARNA::AlignerImpl
seqB_	LocARNA::AlignerImpl
trace(ScoringView sv)	LocARNA::AlignerImpl
trace_arcmatch(const ArcMatch &am)	LocARNA::AlignerImpl
trace_arcmatch_noLP(const ArcMatch &am)	LocARNA::AlignerImpl
trace_in_arcmatch(int state, int al, int i, int bl, int j, bool top_level, ScoringView sv)	LocARNA::AlignerImpl
trace_noex(int state, pos_type al, pos_type i, pos_type bl, pos_type j, bool top_level, ScoringView sv)	LocARNA::AlignerImpl
~AlignerImpl()	LocARNA::AlignerImpl