Representation of a nucleic acid sequence. More...

#include <OpenMS/CHEMISTRY/NASequence.h>

Classes
class	ConstIterator
	ConstIterator of NASequence class. More...

class	Iterator
	Iterator of NASequence class. More...

Public Types
enum	NASFragmentType { Full = 0 , Internal , FivePrime , ThreePrime , AIon , BIon , CIon , XIon , YIon , ZIon , Precursor , BIonMinusH20 , YIonMinusH20 , BIonMinusNH3 , YIonMinusNH3 , NonIdentified , Unannotated , WIon , AminusB , DIon , SizeOfNASFragmentType }
	an enum of all possible fragment ion types More...

using	ConstRibonucleotidePtr = const Ribonucleotide *

Public Member Functions
	NASequence ()=default

	NASequence (const NASequence &)=default
	default constructor

	NASequence (NASequence &&)=default
	Move constructor.

NASequence &	operator= (const NASequence &) &=default
	Copy assignment operator.

NASequence &	operator= (NASequence &&) &=default
	Move assignment operator.

	NASequence (std::vector< const Ribonucleotide * > s, const RibonucleotideChainEnd five_prime, const RibonucleotideChainEnd three_prime)
	full constructor

virtual	~NASequence ()=default

bool	operator== (const NASequence &rhs) const
	destructor

bool	operator!= (const NASequence &rhs) const
	not quality

bool	operator< (const NASequence &rhs) const
	less operator

void	setSequence (const std::vector< const Ribonucleotide * > &seq)
	getter / setter for sequence

const std::vector< const Ribonucleotide * > &	getSequence () const

std::vector< const Ribonucleotide * > &	getSequence ()

void	set (size_t index, const Ribonucleotide *r)
	getter / setter for ribonucleotide elements (easily wrapped using pyOpenMS)

const Ribonucleotide *	get (size_t index)

const Ribonucleotide *&	operator[] (size_t index)
	getter / setter for sequence elements (C++ container style)

const Ribonucleotide *const &	operator[] (size_t index) const

bool	empty () const

size_t	size () const

void	clear ()

bool	hasFivePrimeMod () const
	5' and 3' modifications

void	setFivePrimeMod (const RibonucleotideChainEnd *r)

const RibonucleotideChainEnd *	getFivePrimeMod () const

bool	hasThreePrimeMod () const

void	setThreePrimeMod (const RibonucleotideChainEnd *r)

const RibonucleotideChainEnd *	getThreePrimeMod () const

Iterator	begin ()
	iterators

ConstIterator	begin () const

Iterator	end ()

ConstIterator	end () const

ConstIterator	cbegin () const

ConstIterator	cend () const

double	getMonoWeight (NASFragmentType type=Full, Int charge=0) const
	utility functions

double	getAverageWeight (NASFragmentType type=Full, Int charge=0) const
	Get the Average Weight of a NASequence. NB returns the uncharged mass + or - proton masses to match the charge param.

EmpiricalFormula	getFormula (NASFragmentType type=Full, Int charge=0) const
	Get the formula for a NASequence.

NASequence	getPrefix (Size length) const
	Return sequence prefix of the given length (not end index!)

NASequence	getSuffix (Size length) const
	Return sequence suffix of the given length (not start index!)

NASequence	getSubsequence (Size start=0, Size length=Size(-1)) const
	Return subsequence with given starting position and length.

NASequence	getReversed (bool keep_five_prime=false, bool keep_three_prime=false) const
	Return a reversed copy of this sequence.

NASequence	getShuffled (Math::RandomShuffler &shuffler, double identity_threshold=0.5, int max_attempts=30, bool keep_five_prime=false, bool keep_three_prime=false) const
	Return a shuffled copy of this sequence with identity quality control.

float	getSequenceIdentity (const NASequence &other) const
	Calculate sequence identity between this and another NASequence.

Static Public Member Functions
static NASequence	fromString (const std::string &s)
	create NASequence object by parsing an OpenMS string

Stream operators
writes a NASequence to an output stream
std::vector< const Ribonucleotide * >	seq_

const RibonucleotideChainEnd *	five_prime_ = nullptr

const RibonucleotideChainEnd *	three_prime_ = nullptr

std::string	toString () const

static NASequence	fromString (const char *s)
	create NASequence object by parsing a C string (character array)

std::ostream &	operator<< (std::ostream &os, const NASequence &seq)

static void	parseString_ (const std::string &s, NASequence &nas)

static std::string::const_iterator	parseMod_ (const std::string::const_iterator str_it, const std::string &str, NASequence &nas)
	Parses modifications in square brackets.

Detailed Description

Representation of a nucleic acid sequence.

NASequence represents nucleic acid sequences (RNA) in OpenMS. Each NASequence consists of a vector of pointers to Ribonucleotides as well as RibonucleotideChainEnds representing the 5' and 3' ends of the sequence. Each Ribonucleotide has only a single instance. These are accessible through RibonucleotideDB. Modified Ribonucleotides are included in RibonucleotideDB and are expressed as the Modomics Short name surrounded by brackets when converted to string.

Member Typedef Documentation

◆ ConstRibonucleotidePtr

using ConstRibonucleotidePtr = const Ribonucleotide*

Member Enumeration Documentation

◆ NASFragmentType

enum NASFragmentType

an enum of all possible fragment ion types

Enumerator
Full	with N-terminus and C-terminus
Internal	internal, without any termini
FivePrime	only 5' terminus
ThreePrime	only 3' terminus
AIon	MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond.
BIon	MS:1001224 N-terminus up to the peptide bond.
CIon	MS:1001231 N-terminus up to the amide/C-alpha bond.
XIon	MS:1001228 amide/C-alpha bond up to the C-terminus.
YIon	MS:1001220 peptide bond up to the C-terminus.
ZIon	MS:1001230 C-alpha/carbonyl carbon bond.
Precursor	MS:1001523 Precursor ion.
BIonMinusH20	MS:1001222 b ion without water.
YIonMinusH20	MS:1001223 y ion without water.
BIonMinusNH3	MS:1001232 b ion without ammonia.
YIonMinusNH3	MS:1001233 y ion without ammonia.
NonIdentified	MS:1001240 Non-identified ion.
Unannotated	no stored annotation
WIon	W ion, added for nucleic acid support.
AminusB	A ion with base loss, added for nucleic acid support.
DIon	D ion, added for nucleic acid support.
SizeOfNASFragmentType

Constructor & Destructor Documentation

◆ NASequence() [1/4]

NASequence ( )

default

◆ NASequence() [2/4]

NASequence ( const NASequence & )

default

default constructor

Copy constructor

◆ NASequence() [3/4]

NASequence ( NASequence && )

default

Move constructor.

◆ NASequence() [4/4]

NASequence	(	std::vector< const Ribonucleotide * >	s,
		const RibonucleotideChainEnd *	five_prime,
		const RibonucleotideChainEnd *	three_prime
	)

full constructor

◆ ~NASequence()

virtual ~NASequence ( )

virtualdefault

Member Function Documentation

◆ begin() [1/2]

Iterator begin ( )

inline

iterators

◆ begin() [2/2]

ConstIterator begin ( ) const

inline

◆ cbegin()

ConstIterator cbegin ( ) const

inline

Referenced by ModifiedNASequenceGenerator::applyAtMostOneVariableModification_().

◆ cend()

ConstIterator cend ( ) const

inline

Referenced by ModifiedNASequenceGenerator::applyAtMostOneVariableModification_().

◆ clear()

void clear ( )

◆ empty()

bool empty ( ) const

Referenced by NucleicAcidSearchEngine::resolveAmbiguousMods_().

◆ end() [1/2]

Iterator end ( )

inline

◆ end() [2/2]

ConstIterator end ( ) const

inline

◆ fromString() [1/2]

static NASequence fromString ( const char * s )

static

create NASequence object by parsing a C string (character array)

Parameters

[in] s Input string

Exceptions

Exception::ParseError if an invalid string representation of a nucleic acid sequence is passed

◆ fromString() [2/2]

static NASequence fromString ( const std::string & s )

static

create NASequence object by parsing an OpenMS string

Parameters

[in] s Input string

Exceptions

Exception::ParseError if an invalid string representation of a nucleic acid sequence is passed

Referenced by NucleicAcidSearchEngine::main_().

◆ get()

const Ribonucleotide * get ( size_t index )

inline

◆ getAverageWeight()

double getAverageWeight	(	NASFragmentType	type = `Full`,
		Int	charge = `0`
	)		const

Get the Average Weight of a NASequence. NB returns the uncharged mass + or - proton masses to match the charge param.

Parameters

[in]	type	fragment type to return
[out]	charge	how many protons to add or subtract, NB the mass returned is the UNCHARGED MASS

Returns: double

◆ getFivePrimeMod()

const RibonucleotideChainEnd * getFivePrimeMod ( ) const

◆ getFormula()

EmpiricalFormula getFormula	(	NASFragmentType	type = `Full`,
		Int	charge = `0`
	)		const

Get the formula for a NASequence.

Parameters

[in]	type	fragment type for formula
[out]	charge	how many H to add or subtract

Returns: EmpiricalFormula

◆ getMonoWeight()

double getMonoWeight	(	NASFragmentType	type = `Full`,
		Int	charge = `0`
	)		const

utility functions

Get the Monoisotopic Weight of a NASequence. NB returns the uncharged mass + or - proton masses to match the charge param

Parameters

[in]	type	fragment type to return
[in]	charge	how many protons to add or subtract, NB the mass returned is the UNCHARGED MASS

Returns: double

◆ getPrefix()

NASequence getPrefix ( Size length ) const

Return sequence prefix of the given length (not end index!)

Parameters

[in] length

Returns: NASequence

◆ getReversed()

NASequence getReversed	(	bool	keep_five_prime = `false`,
		bool	keep_three_prime = `false`
	)		const

Return a reversed copy of this sequence.

Reverses the internal ribonucleotide sequence while preserving 5' and 3' terminal modifications in their original positions.

Parameters

[in]	keep_five_prime	If true, preserve the first (5') nucleotide position
[in]	keep_three_prime	If true, preserve the last (3') nucleotide position

Returns: NASequence with reversed internal sequence

Note: Terminal modifications (5' and 3' chain ends) are always preserved. The keep parameters control whether the first/last nucleotides in the internal sequence are kept in place (useful for maintaining RNase cleavage site characteristics in decoy generation).

◆ getSequence() [1/2]

std::vector< const Ribonucleotide * > & getSequence ( )

inline

◆ getSequence() [2/2]

const std::vector< const Ribonucleotide * > & getSequence ( ) const

inline

Referenced by NucleicAcidSearchEngine::reshuffleOligo_().

◆ getSequenceIdentity()

float getSequenceIdentity ( const NASequence & other ) const

Calculate sequence identity between this and another NASequence.

Compares ribonucleotide codes position-by-position. Only considers the internal sequence (ignores 5' and 3' terminal modifications).

Parameters

[in] other Sequence to compare against

Returns: Sequence identity as a fraction (0.0-1.0), where 1.0 means identical

Precondition: Both sequences must have the same length (asserted).

◆ getShuffled()

NASequence getShuffled	(	Math::RandomShuffler &	shuffler,
		double	identity_threshold = `0.5`,
		int	max_attempts = `30`,
		bool	keep_five_prime = `false`,
		bool	keep_three_prime = `false`
	)		const

Return a shuffled copy of this sequence with identity quality control.

Shuffles the internal ribonucleotide sequence while optionally preserving terminal nucleotides. Repeatedly attempts shuffling until the sequence identity with the original falls below the threshold or max_attempts is reached. If max_attempts is exhausted, individual nucleotides are mutated to force a different sequence.

Parameters

[in]	shuffler	Random shuffler to use (seeded externally for reproducibility)
[in]	identity_threshold	Maximum allowed sequence identity with original (0.0-1.0)
[in]	max_attempts	Maximum number of shuffle attempts before mutating
[in]	keep_five_prime	If true, preserve the first (5') nucleotide position
[in]	keep_three_prime	If true, preserve the last (3') nucleotide position

Returns: NASequence with shuffled internal sequence

Note: Terminal modifications (5' and 3' chain ends) are always preserved.

◆ getSubsequence()

NASequence getSubsequence	(	Size	start = `0`,
		Size	length = `Size(-1)`
	)		const

Return subsequence with given starting position and length.

Parameters

[in]	start
[in]	length

Returns: NASequence

◆ getSuffix()

NASequence getSuffix ( Size length ) const

Return sequence suffix of the given length (not start index!)

Parameters

[in] length

Returns: NASequence

◆ getThreePrimeMod()

const RibonucleotideChainEnd * getThreePrimeMod ( ) const

◆ hasFivePrimeMod()

bool hasFivePrimeMod ( ) const

5' and 3' modifications

◆ hasThreePrimeMod()

bool hasThreePrimeMod ( ) const

◆ operator!=()

bool operator!= ( const NASequence & rhs ) const

not quality

◆ operator<()

bool operator< ( const NASequence & rhs ) const

less operator

◆ operator=() [1/2]

NASequence & operator= ( const NASequence & ) &

default

Copy assignment operator.

◆ operator=() [2/2]

NASequence & operator= ( NASequence && ) &

default

Move assignment operator.

◆ operator==()

bool operator== ( const NASequence & rhs ) const

destructor

element-wise equality

◆ operator[]() [1/2]

const Ribonucleotide *& operator[] ( size_t index )

inline

getter / setter for sequence elements (C++ container style)

◆ operator[]() [2/2]

const Ribonucleotide *const & operator[] ( size_t index ) const

inline

◆ parseMod_()

static std::string::const_iterator parseMod_	(	const std::string::const_iterator	str_it,
		const std::string &	str,
		NASequence &	nas
	)

staticprivate

Parses modifications in square brackets.

Parameters

[in]	str_it	Current position in the string to be parsed
[in]	str	Full input string
[in,out]	nas	Current AASequence object (will be modified with the correct ribo added)

Returns: Position at which to continue parsing

◆ parseString_()

static void parseString_	(	const std::string &	s,
		NASequence &	nas
	)

staticprivate

◆ set()

void set	(	size_t	index,
		const Ribonucleotide *	r
	)

getter / setter for ribonucleotide elements (easily wrapped using pyOpenMS)

Referenced by ModifiedNASequenceGenerator::recurseAndGenerateVariableModifiedSequences_().

◆ setFivePrimeMod()

void setFivePrimeMod ( const RibonucleotideChainEnd * r )

Referenced by ModifiedNASequenceGenerator::recurseAndGenerateVariableModifiedSequences_().

◆ setSequence()

void setSequence ( const std::vector< const Ribonucleotide * > & seq )

getter / setter for sequence

Referenced by NucleicAcidSearchEngine::reshuffleOligo_().

◆ setThreePrimeMod()

void setThreePrimeMod ( const RibonucleotideChainEnd * r )

Referenced by ModifiedNASequenceGenerator::recurseAndGenerateVariableModifiedSequences_().

◆ size()

size_t size ( ) const

Referenced by NucleicAcidSearchEngine::calculateFragmentCoverage_(), NucleicAcidSearchEngine::HasInvalidLength::operator()(), NucleicAcidSearchEngine::registerDigestedOligo_(), NucleicAcidSearchEngine::reshuffleOligo_(), and NucleicAcidSearchEngine::resolveAmbiguousMods_().

◆ toString()

std::string toString ( ) const

Referenced by NucleicAcidSearchEngine::main_(), NucleicAcidSearchEngine::postProcessHits_(), and NucleicAcidSearchEngine::reshuffleDecoyIfCollision_().

Friends And Related Symbol Documentation

◆ operator<<

std::ostream & operator<<	(	std::ostream &	os,
		const NASequence &	seq
	)

friend

Member Data Documentation

◆ five_prime_

const RibonucleotideChainEnd* five_prime_ = nullptr

private

◆ seq_

std::vector<const Ribonucleotide*> seq_

private

◆ three_prime_

const RibonucleotideChainEnd* three_prime_ = nullptr

private

Classes

Public Types

Public Member Functions

Static Public Member Functions

Stream operators

Detailed Description

Member Typedef Documentation

◆ ConstRibonucleotidePtr

Member Enumeration Documentation

◆ NASFragmentType

Constructor & Destructor Documentation

◆ NASequence() [1/4]

◆ NASequence() [2/4]

◆ NASequence() [3/4]

◆ NASequence() [4/4]

◆ ~NASequence()

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ cbegin()

◆ cend()

◆ clear()

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ fromString() [1/2]

◆ fromString() [2/2]

◆ get()

◆ getAverageWeight()

◆ getFivePrimeMod()

◆ getFormula()

◆ getMonoWeight()

◆ getPrefix()

◆ getReversed()

◆ getSequence() [1/2]

◆ getSequence() [2/2]

◆ getSequenceIdentity()

◆ getShuffled()

◆ getSubsequence()

◆ getSuffix()

◆ getThreePrimeMod()

◆ hasFivePrimeMod()

◆ hasThreePrimeMod()

◆ operator!=()

◆ operator<()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ parseMod_()

◆ parseString_()

◆ set()

◆ setFivePrimeMod()

◆ setSequence()

◆ setThreePrimeMod()

◆ size()

◆ toString()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ five_prime_

◆ seq_

◆ three_prime_