LocARNA-1.8.11
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McCaskill matrices. More...
#include <mcc_matrices.hh>
Public Member Functions | |
McC_matrices_t (vrna_fold_compound_t *vc) | |
Construct from fold compound. More... | |
virtual | ~McC_matrices_t () |
destruct, optionally free local copy | |
char | ptype (size_t i, size_t j) const |
Access matrix ptype. More... | |
char | rev_ptype (size_t i, size_t j) const |
Reverse ptype. More... | |
short | S1 (size_t i) const |
Read access to sequence encoding S1. More... | |
char * | sequence () const |
Public Member Functions inherited from LocARNA::McC_matrices_base | |
virtual | ~McC_matrices_base () |
Destructor. More... | |
size_t | iidx (size_t i, size_t j) const |
index in triagonal matrix | |
size_t | jidx (size_t i, size_t j) const |
index in triagonal matrix | |
FLT_OR_DBL | bppm (size_t i, size_t j) const |
Read access matrix bppm. More... | |
FLT_OR_DBL | qb (size_t i, size_t j) const |
Read access matrix qb. More... | |
FLT_OR_DBL | qm (size_t i, size_t j) const |
Read access matrix qm. More... | |
vrna_exp_param_t * | exp_params () const |
exp params | |
FLT_OR_DBL | scale (size_t i) const |
scale More... | |
FLT_OR_DBL | expMLbase (size_t i) const |
expMLbase More... | |
FLT_OR_DBL | kT () const |
kT More... | |
FLT_OR_DBL | q1k (size_t k) const |
Read access matrix q1k. More... | |
FLT_OR_DBL | qln (size_t l) const |
Read access matrix qln. More... | |
int | pair (size_t c, size_t d) const |
Read access matrix pair. More... | |
Additional Inherited Members | |
Protected Member Functions inherited from LocARNA::McC_matrices_base | |
McC_matrices_base (vrna_fold_compound_t *vc) | |
construct empty | |
Protected Attributes inherited from LocARNA::McC_matrices_base | |
vrna_fold_compound_t * | vc_ |
vrna fold compound More... | |
McCaskill matrices.
Holds vrna fold compound with DP matrices
LocARNA::McC_matrices_t::McC_matrices_t | ( | vrna_fold_compound_t * | vc | ) |
Construct from fold compound.
vc | vrna fold compound (single) |
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inline |
Access matrix ptype.
i | first index |
j | second index |
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inline |
Reverse ptype.
i | first index |
j | second index |
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inline |
Read access to sequence encoding S1.
i | index |