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.

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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

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Constructor & Destructor Documentation

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

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

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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

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

• src/LocARNA/pfold_params.hh
• src/LocARNA/pfold_params.cc