Alifold-McCaskill matrices. More...
#include <mcc_matrices.hh>
Public Member Functions | |
McC_ali_matrices_t (vrna_fold_compound_t *vc) | |
Construct from fold compound. | |
virtual | ~McC_ali_matrices_t () |
destruct | |
short | pscore (size_t i, size_t j) const |
Access matrix pscore. | |
short | S (size_t s, size_t i) const |
Read access to sequence encoding S. | |
short | S3 (size_t s, size_t i) const |
Read access to sequence encoding S3. | |
short | S5 (size_t s, size_t i) const |
Read access to sequence encoding S5. | |
short | a2s (size_t s, size_t i) const |
Read access to a2s. | |
char * | Ss (size_t s) const |
Alifold-McCaskill matrices.
LocARNA::McC_ali_matrices_t::McC_ali_matrices_t | ( | vrna_fold_compound_t * | vc | ) | [explicit] |
Construct from fold compound.
vc | vrna fold compound (alignment) |
short LocARNA::McC_ali_matrices_t::a2s | ( | size_t | s, |
size_t | i | ||
) | const [inline] |
Read access to a2s.
s | sequence index |
i | base index |
short LocARNA::McC_ali_matrices_t::pscore | ( | size_t | i, |
size_t | j | ||
) | const [inline] |
Access matrix pscore.
i | first index |
j | second index |
short LocARNA::McC_ali_matrices_t::S | ( | size_t | s, |
size_t | i | ||
) | const [inline] |
Read access to sequence encoding S.
s | sequence index |
i | base index |
short LocARNA::McC_ali_matrices_t::S3 | ( | size_t | s, |
size_t | i | ||
) | const [inline] |
Read access to sequence encoding S3.
s | sequence index |
i | base index |
short LocARNA::McC_ali_matrices_t::S5 | ( | size_t | s, |
size_t | i | ||
) | const [inline] |
Read access to sequence encoding S5.
s | sequence index |
i | base index |