LocARNA::PFoldParams Class Reference

Parameters for partition folding. More...

#include <pfold_params.hh>

Classes
struct	args

Public Member Functions
template<typename... Args>
	PFoldParams (Args... argpack)
	PFoldParams (const PFoldParams &pfoldparams)
const vrna_md_t &	model_details () const
	get ViennaRNA model details structure More...
bool	noLP () const
	Check no LP flag. More...
bool	stacking () const
	Check stacking flag. More...
size_t	max_bp_span () const
	Get maximum base pair span. More...
int	dangling () const
	Get dangling value. More...

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

PFoldParams() [1/2]

template<typename... Args>

LocARNA::PFoldParams::PFoldParams ( Args...  argpack )

inline

Construct with all parameters

Parameters

noLP	forbid lonely base pairs
stacking	calculate stacking probabilities
max_bp_span	maximum base pair span
dangling	ViennaRNA dangling end type

PFoldParams() [2/2]

LocARNA::PFoldParams::PFoldParams ( const PFoldParams &  pfoldparams )

inline

copy constructor

Member Function Documentation

dangling()

int LocARNA::PFoldParams::dangling ( ) const

inline

Get dangling value.

Returns

value of dangling

max_bp_span()

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)

model_details()

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.

noLP()

bool LocARNA::PFoldParams::noLP ( ) const

inline

Check no LP flag.

Returns

value of flag

stacking()

bool LocARNA::PFoldParams::stacking ( ) const

inline

Check stacking flag.

Returns

value of flag

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

• src/LocARNA/pfold_params.hh