, 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 | |