LocARNA::RnaStructure Class Reference

An RNA secondary structure. More...

#include <rna_structure.hh>

List of all members.

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

---

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()

Todo:

read structure in ct format from stream

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Member Typedef Documentation

typedef bps_t::const_iterator LocARNA::RnaStructure::const_iterator

Check whether a loop contains a position.

Parameters:

k	position
x	loop; (0,length+1) means external loop

Returns:

whether the loop enclosed by x contains k

Definition: the loop enclosed by (i,j) contains k iff i<k<j and there is no base pair (i',j') in the structure, where i<i'<k<j'<j. Note that we don't require (i,j) to be element of the structure.

k can be member of more than one loop unless nested(). constant iterator over base pairs

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Constructor & Destructor Documentation

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

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.

const_iterator LocARNA::RnaStructure::begin

(

)

const [inline]

begin of base pair set

Returns:

constant iterator at begin

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

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().

bool LocARNA::RnaStructure::crossing

(

)

const [inline]

Check for crossing structure / class CROSSING.

Returns:

whether structure is in crossing class

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

bool LocARNA::RnaStructure::empty

(

)

const [inline]

Check for empty structure / class PLAIN.

Returns:

whether structure is empty

const_iterator LocARNA::RnaStructure::end

(

)

const [inline]

end of base pair set

Returns:

constant iterator at end

void LocARNA::RnaStructure::insert

(

const bp_t &

bp

)

[inline]

insert base pair

Parameters:

bp

base pair

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

bool LocARNA::RnaStructure::nested

(

)

const [inline]

Check for nested structure / class NESTED.

Returns:

whether structure is nested class

bool LocARNA::RnaStructure::operator==

(

const RnaStructure &

s

)

const [inline]

Equality operator.

Parameters:

s	rna structure to be compared

Returns:

whether equal

void LocARNA::RnaStructure::remove

(

const bp_t &

bp

)

[inline]

remove base pair

Parameters:

bp

base pair

void LocARNA::RnaStructure::remove_lonely_pairs

(

)

remove lonely base pairs

Removes the lonely base pairs in the structure; in place

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!

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

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