LocARNA-1.9.2
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_probLocARNA::AlignerP [protected]
Arc typedefLocARNA::AlignerP
arc_matchesLocARNA::AlignerP [protected]
bm_probLocARNA::AlignerP [protected]
bpsALocARNA::AlignerP [protected]
bpsBLocARNA::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_createdLocARNA::AlignerP [protected]
DmatLocARNA::AlignerP [protected]
DmatprimeLocARNA::AlignerP [protected]
Dprime(const ArcMatch &am)LocARNA::AlignerP [protected]
Dprime(const Arc &arcA, const Arc &arcB)LocARNA::AlignerP [protected]
Dprime_createdLocARNA::AlignerP [protected]
ELocARNA::AlignerP [protected]
EprimeLocARNA::AlignerP [protected]
ErevLocARNA::AlignerP [protected]
Erev_matLocARNA::AlignerP [protected]
FLocARNA::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]
FprimeLocARNA::AlignerP [protected]
freeD()LocARNA::AlignerP [inline]
freeMprime()LocARNA::AlignerP [inline]
FrevLocARNA::AlignerP [protected]
Frev_matLocARNA::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]
MLocARNA::AlignerP [protected]
MprimeLocARNA::AlignerP [protected]
MrevLocARNA::AlignerP [protected]
paramsLocARNA::AlignerP [protected]
partFuncLocARNA::AlignerP [protected]
pf_scaleLocARNA::AlignerP [protected]
rLocARNA::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]
scoringLocARNA::AlignerP [protected]
seqALocARNA::AlignerP [protected]
seqBLocARNA::AlignerP [protected]
size_pair typedefLocARNA::AlignerP
size_type typedefLocARNA::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
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