LocARNA-1.9.2
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Public Member Functions
LocARNA::PFoldParams Class Reference

Parameters for partition folding. More...

#include <pfold_params.hh>

List of all members.

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.

Detailed Description

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.

See also:
RnaEnsemble

Constructor & Destructor Documentation

LocARNA::PFoldParams::PFoldParams ( bool  noLP,
bool  stacking,
int  max_bp_span,
int  dangling 
)

Construct with all parameters

Parameters:
noLPforbid lonely base pairs
stackingcalculate stacking probabilities
max_bp_spanmaximum base pair span
danglingViennaRNA dangling end type

Member Function Documentation

int LocARNA::PFoldParams::dangling ( ) const [inline]

Get dangling value.

Returns:
value of dangling
size_t LocARNA::PFoldParams::max_bp_span ( ) const [inline]

Get maximum base pair span.

Note:
in vrna_md_s, a value of -1 indicates no restriction for distant base pairs; in this case, return the maximum value of size_t
Returns:
maximum allowed base pair span (returns maximum size_t value if unrestricted)
const vrna_md_t& LocARNA::PFoldParams::model_details ( ) const [inline]

get ViennaRNA model details structure

Returns:
initialized md 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.

Returns:
value of flag
bool LocARNA::PFoldParams::stacking ( ) const [inline]

Check stacking flag.

Returns:
value of flag

The documentation for this class was generated from the following files:
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