LocARNA::AlignerP Member List

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

align_D()	LocARNA::AlignerP	[protected]
align_Dprime()	LocARNA::AlignerP	[protected]
align_inside()	LocARNA::AlignerP
align_inside_arcmatch(size_type al, size_type ar, size_type bl, size_type br)	LocARNA::AlignerP	[protected]
align_outside()	LocARNA::AlignerP
align_outside_arcmatch(size_type al, size_type ar, size_type max_ar, size_type bl, size_type br, size_type max_br)	LocARNA::AlignerP	[protected]
align_reverse(size_type al, size_type ar, size_type bl, size_type br, bool copy=false)	LocARNA::AlignerP	[protected]
AlignerP(const AlignerParams &ap)	LocARNA::AlignerP
AlignerP(const AlignerP &p)	LocARNA::AlignerP
alloc_inside_matrices()	LocARNA::AlignerP	[protected]
alloc_outside_matrices()	LocARNA::AlignerP	[protected]
am_prob	LocARNA::AlignerP	[protected]
Arc typedef	LocARNA::AlignerP
arc_matches	LocARNA::AlignerP	[protected]
bm_prob	LocARNA::AlignerP	[protected]
bpsA	LocARNA::AlignerP	[protected]
bpsB	LocARNA::AlignerP	[protected]
comp_E_entry(size_type al, size_type bl, size_type i, size_type j)	LocARNA::AlignerP	[inline, protected]
comp_Eprime_entry(size_type al, size_type bl, size_type i, size_type j)	LocARNA::AlignerP	[inline, protected]
comp_Erev_entry(size_type i, size_type j)	LocARNA::AlignerP	[inline, protected]
comp_F_entry(size_type al, size_type bl, size_type i, size_type j)	LocARNA::AlignerP	[inline, protected]
comp_Fprime_entry(size_type al, size_type bl, size_type i, size_type j)	LocARNA::AlignerP	[inline, protected]
comp_Frev_entry(size_type i, size_type j)	LocARNA::AlignerP	[inline, protected]
comp_M_entry(size_type al, size_type bl, size_type i, size_type j)	LocARNA::AlignerP	[inline, protected]
comp_Mprime_entry(size_type al, size_type bl, size_type i, size_type j, size_type max_ar, size_type max_br)	LocARNA::AlignerP	[inline, protected]
comp_Mrev_entry(size_type i, size_type j, size_type ar, size_type br)	LocARNA::AlignerP	[inline, protected]
compute_arcmatch_probabilities()	LocARNA::AlignerP
compute_basematch_probabilities(bool basematch_probs_include_arcmatch)	LocARNA::AlignerP
compute_fragment_match_prob(size_type i, size_type j, size_type k, size_type l)	LocARNA::AlignerP
create()	LocARNA::AlignerP	[inline, static]
D(const ArcMatch &am)	LocARNA::AlignerP	[protected]
D(const Arc &arcA, const Arc &arcB)	LocARNA::AlignerP	[protected]
D_created	LocARNA::AlignerP	[protected]
Dmat	LocARNA::AlignerP	[protected]
Dmatprime	LocARNA::AlignerP	[protected]
Dprime(const ArcMatch &am)	LocARNA::AlignerP	[protected]
Dprime(const Arc &arcA, const Arc &arcB)	LocARNA::AlignerP	[protected]
Dprime_created	LocARNA::AlignerP	[protected]
E	LocARNA::AlignerP	[protected]
Eprime	LocARNA::AlignerP	[protected]
Erev	LocARNA::AlignerP	[protected]
Erev_mat	LocARNA::AlignerP	[protected]
F	LocARNA::AlignerP	[protected]
fill_D(size_type al, size_type bl, size_type max_ar, size_type max_br)	LocARNA::AlignerP	[protected]
fill_Dprime(size_type al, size_type bl, size_type min_ar, size_type min_br, size_type max_ar, size_type max_br)	LocARNA::AlignerP	[protected]
Fprime	LocARNA::AlignerP	[protected]
freeD()	LocARNA::AlignerP	[inline]
freeMprime()	LocARNA::AlignerP	[inline]
Frev	LocARNA::AlignerP	[protected]
Frev_mat	LocARNA::AlignerP	[protected]
init_E(size_type al, size_type ar, size_type bl, size_type br)	LocARNA::AlignerP	[protected]
init_Erev(size_type al, size_type ar, size_type bl, size_type br)	LocARNA::AlignerP	[protected]
init_M(size_type al, size_type ar, size_type bl, size_type br)	LocARNA::AlignerP	[protected]
init_Mrev(size_type al, size_type ar, size_type bl, size_type br)	LocARNA::AlignerP	[protected]
leftmost_covering_arc(size_type s, const BasePairs &bps, size_type l, size_type r) const	LocARNA::AlignerP	[protected]
leftmost_covering_arcmatch(size_type al, size_type bl, size_type ar, size_type br) const	LocARNA::AlignerP	[protected]
M	LocARNA::AlignerP	[protected]
Mprime	LocARNA::AlignerP	[protected]
Mrev	LocARNA::AlignerP	[protected]
params	LocARNA::AlignerP	[protected]
partFunc	LocARNA::AlignerP	[protected]
pf_scale	LocARNA::AlignerP	[protected]
r	LocARNA::AlignerP	[protected]
rightmost_covering_arc(const BasePairs &bps, size_type l, size_type r, size_type s) const	LocARNA::AlignerP	[protected]
rightmost_covering_arcmatch(size_type al, size_type bl, size_type ar, size_type br) const	LocARNA::AlignerP	[protected]
scoring	LocARNA::AlignerP	[protected]
seqA	LocARNA::AlignerP	[protected]
seqB	LocARNA::AlignerP	[protected]
size_pair typedef	LocARNA::AlignerP
size_type typedef	LocARNA::AlignerP
virtual_Mprime(size_type al, size_type bl, size_type i, size_type j, size_type max_ar, size_type max_br) const	LocARNA::AlignerP
write_arcmatch_probabilities(std::ostream &out)	LocARNA::AlignerP
write_basematch_probabilities(std::ostream &out)	LocARNA::AlignerP
~AlignerP()	LocARNA::AlignerP