LocARNA::RnaStructure Class Reference

An RNA secondary structure. More...

#include <rna_structure.hh>

Public Types
typedef std::pair< size_t, size_t >	bp_t
	base pair type
typedef std::set< bp_t, std::less< bp_t > >	bps_t
	base pair set type
typedef bps_t::const_iterator	const_iterator
	constant iterator over base pairs

Public Member Functions
	RnaStructure (size_t length=0)
	construct empty
	RnaStructure (const std::string &structure)
	construct from dot-bracket string More...
bool	operator== (const RnaStructure &s) const
	Equality operator. More...
bool	contains (const bp_t &x) const
	Base pair for membership test. More...
size_t	length () const
	sequence length
size_t	size () const
	number of base pairs
void	insert (const bp_t &bp)
	insert base pair More...
void	remove (const bp_t &bp)
	remove base pair More...
void	clear ()
	clear structure set structure to empty
const_iterator	begin () const
	begin of base pair set More...
const_iterator	end () const
	end of base pair set More...
std::string	to_string () const
	convert to dot-bracket string More...
bool	empty () const
	Check for empty structure / class PLAIN. More...
bool	nested () const
	Check for nested structure / class NESTED. More...
bool	crossing () const
	Check for crossing structure / class CROSSING. More...
void	remove_lonely_pairs ()
	remove lonely base pairs More...
void	apply_bpfilter (const BasePairFilter::Filter &filter)
	apply base pair filter More...

Static Public Member Functions
static bool	empty (const bps_t &bps)
	Check base pair set for empty structure / class PLAIN. More...
static bool	nested (const bps_t &bps)
	Check for class NESTED. More...
static bool	crossing (const bps_t &bps)
	Check for class CROSSING. More...

Detailed Description

An RNA secondary structure.

Represents a structure (for a sequence of given length) as set of base pairs. Supports parsing of dot-bracket strings (potentially including pseudoknots) and traversal of base pairs.

Generally, base pairs (i,j) have to be oriented, i.e. i<j; compare private method assert_valid_bp()

Constructor & Destructor Documentation

RnaStructure()

LocARNA::RnaStructure::RnaStructure ( const std::string &  structure )

explicit

construct from dot-bracket string

Parameters

structure

dot-bracket string

We recognize different bracket pairs: (),[],{},<>, and letter pairs Aa, Bb, etc ; the structure string can encode crossing base pairs like in

.(((..[[.AA...)))..]]..aa.

The parser ignores all other symbols ( including _-,:.~ ) such that e.g. Vienna dot-bracket strings and WUSS notation is parsed correctly. Note that the parser is more general than the WUSS-specification, which forbids crossing of different bracket-symbols like [(...]), so that other common pseudoknot specifications are recognized as well.

Member Function Documentation

apply_bpfilter()

void LocARNA::RnaStructure::apply_bpfilter

(

const BasePairFilter::Filter &

filter

)

apply base pair filter

Applies a base pair filter to all base pairs; removes all base pairs that don't pass; in place.

begin()

const_iterator LocARNA::RnaStructure::begin ( ) const

inline

begin of base pair set

Returns

constant iterator at begin

contains()

bool LocARNA::RnaStructure::contains ( const bp_t &  x ) const

inline

Base pair for membership test.

Parameters

x

base pair

Returns

whether structure contains the base pair

crossing() [1/2]

bool LocARNA::RnaStructure::crossing ( ) const

inline

Check for crossing structure / class CROSSING.

Returns

whether structure is in crossing class

crossing() [2/2]

bool LocARNA::RnaStructure::crossing ( const bps_t &  bps )

static

Check for class CROSSING.

Parameters

bps	set of base pairs

Returns

whether structure is in the crossing class (i.e., not in unlimited)

A structure is in the crossing class if no base pairs share common ends.

Note

this does not test for the presence of crossing base pairs. For the latter, use !nested().

empty() [1/2]

bool LocARNA::RnaStructure::empty ( ) const

inline

Check for empty structure / class PLAIN.

Returns

whether structure is empty

empty() [2/2]

bool LocARNA::RnaStructure::empty ( const bps_t &  bps )

static

Check base pair set for empty structure / class PLAIN.

Parameters

bps	set of base pairs

Returns

whether given base pair set represents empty structure

end()

const_iterator LocARNA::RnaStructure::end ( ) const

inline

end of base pair set

Returns

constant iterator at end

insert()

void LocARNA::RnaStructure::insert ( const bp_t &  bp )

inline

insert base pair

Parameters

bp

base pair

nested() [1/2]

bool LocARNA::RnaStructure::nested ( ) const

inline

Check for nested structure / class NESTED.

Returns

whether structure is nested class

nested() [2/2]

bool LocARNA::RnaStructure::nested ( const bps_t &  bps )

static

Check for class NESTED.

Parameters

bps	set of base pairs

Returns

whether structure is in the nested class (i.e., not in classes crossing or unlimited)

A structure is in the class nested if no base pairs cross or share common ends.

See also

in_crossing() for naming

operator==()

bool LocARNA::RnaStructure::operator== ( const RnaStructure &  s ) const

inline

Equality operator.

Parameters

s	rna structure to be compared

Returns

whether equal

remove()

void LocARNA::RnaStructure::remove ( const bp_t &  bp )

inline

remove base pair

Parameters

bp

base pair

remove_lonely_pairs()

void LocARNA::RnaStructure::remove_lonely_pairs

(

)

remove lonely base pairs

Removes the lonely base pairs in the structure; in place

to_string()

std::string LocARNA::RnaStructure::to_string

(

)

const

convert to dot-bracket string

Returns

dot-bracket string

If the structure contains crossing base pairs, such base pairs are encoded using more than one pair of bracket symbols. ( see constructor from dot bracket string ). The use of bracket symbols is greedy from left to right, following the order defined in the class (by constants open_symbols_ and close_symbols_).

Precondition

structure is in crossing class, i.e. not unlimited!

---

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

• src/LocARNA/rna_structure.hh
• src/LocARNA/rna_structure.cc