Class for storing MS run data with peptide and protein identifications. More...

#include <OpenMS/METADATA/AnnotatedMSRun.h>

Collaboration diagram for AnnotatedMSRun:

Classes
struct	PairIterator
	Iterator for pairs of spectra and peptide identifications. More...

Public Types
using	SpectrumIdRef = std::pair< MSSpectrum &, PeptideIdentification & >

using	ConstSpectrumIdRef = std::pair< const MSSpectrum &, const PeptideIdentification & >

using	SpectrumType = MSExperiment::SpectrumType

using	ChromatogramType = MSExperiment::ChromatogramType

typedef AnnotatedMSRun::PairIterator< std::vector< MSSpectrum >::iterator, std::vector< PeptideIdentification >::iterator >	Iterator

typedef AnnotatedMSRun::PairIterator< std::vector< MSSpectrum >::const_iterator, std::vector< PeptideIdentification >::const_iterator >	ConstIterator

Public Member Functions
	AnnotatedMSRun ()=default
	Default constructor. More...

	AnnotatedMSRun (MSExperiment &&experiment)
	Move constructor for efficiently loading a MSExperiment without a deep copy. More...

	AnnotatedMSRun (AnnotatedMSRun &&)=default
	Move constructor. More...

	AnnotatedMSRun (const AnnotatedMSRun &)=default
	Copy constructor. More...

AnnotatedMSRun &	operator= (const AnnotatedMSRun &)=default

AnnotatedMSRun &	operator= (AnnotatedMSRun &&)=default

	~AnnotatedMSRun ()=default
	Destructor. More...

std::vector< ProteinIdentification > &	getProteinIdentifications ()
	Get the protein identification. More...

const std::vector< ProteinIdentification > &	getProteinIdentifications () const
	Get the protein identification (const version) More...

std::vector< PeptideIdentification > &	getPeptideIdentifications ()
	Get all peptide identifications for all spectra. More...

const std::vector< PeptideIdentification > &	getPeptideIdentifications () const
	Get all peptide identifications for all spectra (const version) More...

void	setPeptideIdentifications (std::vector< PeptideIdentification > &&ids)
	Set all peptide identifications for all spectra. More...

void	setPeptideIdentifications (const std::vector< PeptideIdentification > &ids)
	Set all peptide identifications for all spectra. More...

MSExperiment &	getMSExperiment ()
	Get the MSExperiment. More...

const MSExperiment &	getMSExperiment () const
	Get the MSExperiment (const version) More...

void	setMSExperiment (MSExperiment &&experiment)
	Set the MSExperiment. More...

void	setMSExperiment (const MSExperiment &experiment)
	Set the MSExperiment. More...

auto	cbegin () const
	Get a const iterator to the beginning of the data. More...

auto	begin ()
	Get an iterator to the beginning of the data. More...

auto	begin () const
	Get a const iterator to the beginning of the data. More...

auto	end ()
	Get an iterator to the end of the data. More...

auto	end () const
	Get a const iterator to the end of the data. More...

auto	cend () const
	Get a const iterator to the end of the data. More...

SpectrumIdRef	operator[] (size_t idx)
	Access a spectrum and its associated peptide identification. More...

ConstSpectrumIdRef	operator[] (size_t idx) const
	Access a spectrum and its associated peptide identification (const version) More...

Private Member Functions
void	checkPeptideIdSize_ (const char *function_name) const

Private Attributes
std::vector< PeptideIdentification >	peptide_ids_

std::vector< ProteinIdentification >	protein_ids_

MSExperiment	data

Detailed Description

Class for storing MS run data with peptide and protein identifications.

This class stores an MSExperiment (containing spectra) along with peptide and protein identifications. Each spectrum in the MSExperiment is associated with a single PeptideIdentification object.

The class provides methods to access and modify these identifications, as well as iterators to traverse the spectra and their associated identifications together.

Member Typedef Documentation

◆ ChromatogramType

using ChromatogramType = MSExperiment::ChromatogramType

◆ ConstIterator

typedef AnnotatedMSRun::PairIterator<std::vector<MSSpectrum>::const_iterator, std::vector<PeptideIdentification>::const_iterator> ConstIterator

◆ ConstSpectrumIdRef

using ConstSpectrumIdRef = std::pair<const MSSpectrum&, const PeptideIdentification&>

◆ Iterator

typedef AnnotatedMSRun::PairIterator<std::vector<MSSpectrum>::iterator, std::vector<PeptideIdentification>::iterator> Iterator

◆ SpectrumIdRef

using SpectrumIdRef = std::pair<MSSpectrum&, PeptideIdentification&>

◆ SpectrumType

using SpectrumType = MSExperiment::SpectrumType

Constructor & Destructor Documentation

◆ AnnotatedMSRun() [1/4]

AnnotatedMSRun ( )

default

Default constructor.

◆ AnnotatedMSRun() [2/4]

AnnotatedMSRun ( MSExperiment && experiment )

inlineexplicit

Move constructor for efficiently loading a MSExperiment without a deep copy.

Parameters

experiment The MSExperiment to move into this object

◆ AnnotatedMSRun() [3/4]

AnnotatedMSRun ( AnnotatedMSRun && )

default

Move constructor.

◆ AnnotatedMSRun() [4/4]

AnnotatedMSRun ( const AnnotatedMSRun & )

default

Copy constructor.

◆ ~AnnotatedMSRun()

~AnnotatedMSRun ( )

default

Destructor.

Member Function Documentation

◆ begin() [1/2]

auto begin ( )

inline

Get an iterator to the beginning of the data.

Returns: An iterator to the beginning

◆ begin() [2/2]

auto begin ( ) const

inline

Get a const iterator to the beginning of the data.

Returns: A const iterator to the beginning

◆ cbegin()

auto cbegin ( ) const

inline

Get a const iterator to the beginning of the data.

Returns: A const iterator to the beginning

◆ cend()

auto cend ( ) const

inline

Get a const iterator to the end of the data.

Returns: A const iterator to the end

◆ checkPeptideIdSize_()

void checkPeptideIdSize_ ( const char * function_name ) const

private

◆ end() [1/2]

auto end ( )

inline

Get an iterator to the end of the data.

Returns: An iterator to the end

◆ end() [2/2]

auto end ( ) const

inline

Get a const iterator to the end of the data.

Returns: A const iterator to the end

◆ getMSExperiment() [1/2]

MSExperiment& getMSExperiment ( )

Get the MSExperiment.

Returns: A reference to the MSExperiment

Referenced by TOPPViewBase::metadataFileDialog().

◆ getMSExperiment() [2/2]

const MSExperiment& getMSExperiment ( ) const

Get the MSExperiment (const version)

Returns: A const reference to the MSExperiment

◆ getPeptideIdentifications() [1/2]

std::vector<PeptideIdentification>& getPeptideIdentifications ( )

Get all peptide identifications for all spectra.

Returns: A reference to the vector of peptide identifications

Referenced by IDFilter::keepHitsMatchingProteins().

◆ getPeptideIdentifications() [2/2]

const std::vector<PeptideIdentification>& getPeptideIdentifications ( ) const

Get all peptide identifications for all spectra (const version)

Returns: A const reference to the vector of peptide identifications

◆ getProteinIdentifications() [1/2]

std::vector<ProteinIdentification>& getProteinIdentifications ( )

inline

Get the protein identification.

Returns: A reference to the protein identification

Referenced by IDFilter::keepHitsMatchingProteins().

◆ getProteinIdentifications() [2/2]

const std::vector<ProteinIdentification>& getProteinIdentifications ( ) const

inline

Get the protein identification (const version)

Returns: A const reference to the protein identification

◆ operator=() [1/2]

AnnotatedMSRun& operator= ( AnnotatedMSRun && )

default

◆ operator=() [2/2]

AnnotatedMSRun& operator= ( const AnnotatedMSRun & )

default

◆ operator[]() [1/2]

SpectrumIdRef operator[] ( size_t idx )

inline

Access a spectrum and its associated peptide identification.

Parameters

idx	The index of the spectrum

Returns: A pair of references to the spectrum and its peptide identification

◆ operator[]() [2/2]

ConstSpectrumIdRef operator[] ( size_t idx ) const

inline

Access a spectrum and its associated peptide identification (const version)

Parameters

idx	The index of the spectrum

Returns: A pair of const references to the spectrum and its peptide identification

◆ setMSExperiment() [1/2]

void setMSExperiment ( const MSExperiment & experiment )

Set the MSExperiment.

Parameters

experiment The MSExperiment to set

◆ setMSExperiment() [2/2]

void setMSExperiment ( MSExperiment && experiment )

Set the MSExperiment.

Parameters

experiment The MSExperiment to set

◆ setPeptideIdentifications() [1/2]

void setPeptideIdentifications ( const std::vector< PeptideIdentification > & ids )

Set all peptide identifications for all spectra.

Parameters

ids	Vector of peptide identifications

◆ setPeptideIdentifications() [2/2]

void setPeptideIdentifications ( std::vector< PeptideIdentification > && ids )

Set all peptide identifications for all spectra.

Parameters

ids	Vector of peptide identifications

Member Data Documentation

◆ data

MSExperiment data

private

◆ peptide_ids_

std::vector<PeptideIdentification> peptide_ids_

private

◆ protein_ids_

std::vector<ProteinIdentification> protein_ids_

private

Classes

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ChromatogramType

◆ ConstIterator

◆ ConstSpectrumIdRef

◆ Iterator

◆ SpectrumIdRef

◆ SpectrumType

Constructor & Destructor Documentation

◆ AnnotatedMSRun() [1/4]

◆ AnnotatedMSRun() [2/4]

◆ AnnotatedMSRun() [3/4]

◆ AnnotatedMSRun() [4/4]

◆ ~AnnotatedMSRun()

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ cbegin()

◆ cend()

◆ checkPeptideIdSize_()

◆ end() [1/2]

◆ end() [2/2]

◆ getMSExperiment() [1/2]

◆ getMSExperiment() [2/2]

◆ getPeptideIdentifications() [1/2]

◆ getPeptideIdentifications() [2/2]

◆ getProteinIdentifications() [1/2]

◆ getProteinIdentifications() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ setMSExperiment() [1/2]

◆ setMSExperiment() [2/2]

◆ setPeptideIdentifications() [1/2]

◆ setPeptideIdentifications() [2/2]

Member Data Documentation

◆ data

◆ peptide_ids_

◆ protein_ids_