Parameters for partition folding. More...
#include <pfold_params.hh>
Public Member Functions | |
PFoldParams (bool noLP, bool stacking, int max_bp_span, int dangling) | |
const vrna_md_t & | model_details () const |
get ViennaRNA model details structure | |
bool | noLP () const |
Check no LP flag. | |
bool | stacking () const |
Check stacking flag. | |
size_t | max_bp_span () const |
Get maximum base pair span. | |
int | dangling () const |
Get dangling value. |
Parameters for partition folding.
Describes certain parameters for the partition folding of a sequence or alignment.
This is used to store and pass model details for RNA folding. Works as wrapper for the ViennaRNA model details structure.
LocARNA::PFoldParams::PFoldParams | ( | bool | noLP, |
bool | stacking, | ||
int | max_bp_span, | ||
int | dangling | ||
) |
Construct with all parameters
noLP | forbid lonely base pairs |
stacking | calculate stacking probabilities |
max_bp_span | maximum base pair span |
dangling | ViennaRNA dangling end type |
int LocARNA::PFoldParams::dangling | ( | ) | const [inline] |
Get dangling value.
size_t LocARNA::PFoldParams::max_bp_span | ( | ) | const [inline] |
Get maximum base pair span.
const vrna_md_t& LocARNA::PFoldParams::model_details | ( | ) | const [inline] |
get ViennaRNA model details structure
The structure is set to the values of this object for maintained values; some further values are set explicitly, e.g. alifold parameters. All other values are set to the ViennaRNA default values.
bool LocARNA::PFoldParams::noLP | ( | ) | const [inline] |
Check no LP flag.
bool LocARNA::PFoldParams::stacking | ( | ) | const [inline] |
Check stacking flag.