Representation of 1D spectrum settings. More...

#include <OpenMS/METADATA/SpectrumSettings.h>

Inheritance diagram for SpectrumSettings:

Collaboration diagram for SpectrumSettings:

Public Types
enum	SpectrumType { UNKNOWN , CENTROID , PROFILE , SIZE_OF_SPECTRUMTYPE }
	Spectrum peak type. More...

Public Member Functions
	SpectrumSettings ()
	Constructor. More...

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

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

	~SpectrumSettings ()
	Destructor. More...

SpectrumSettings &	operator= (const SpectrumSettings &)=default

SpectrumSettings &	operator= (SpectrumSettings &&) &=default
	Move assignment operator. More...

bool	operator== (const SpectrumSettings &rhs) const
	Equality operator. More...

bool	operator!= (const SpectrumSettings &rhs) const
	Equality operator. More...

void	unify (const SpectrumSettings &rhs)
	merge another spectrum setting into this one (data is usually appended, except for spectrum type which needs to be unambiguous to be kept) More...

SpectrumType	getType () const
	returns the spectrum type (centroided (PEAKS) or profile data (RAW)) More...

void	setType (SpectrumType type)
	sets the spectrum type More...

const String &	getNativeID () const
	returns the native identifier for the spectrum, used by the acquisition software. More...

void	setNativeID (const String &native_id)
	sets the native identifier for the spectrum, used by the acquisition software. More...

const String &	getComment () const
	returns the free-text comment More...

void	setComment (const String &comment)
	sets the free-text comment More...

const InstrumentSettings &	getInstrumentSettings () const
	returns a const reference to the instrument settings of the current spectrum More...

InstrumentSettings &	getInstrumentSettings ()
	returns a mutable reference to the instrument settings of the current spectrum More...

void	setInstrumentSettings (const InstrumentSettings &instrument_settings)
	sets the instrument settings of the current spectrum More...

const AcquisitionInfo &	getAcquisitionInfo () const
	returns a const reference to the acquisition info More...

AcquisitionInfo &	getAcquisitionInfo ()
	returns a mutable reference to the acquisition info More...

void	setAcquisitionInfo (const AcquisitionInfo &acquisition_info)
	sets the acquisition info More...

const SourceFile &	getSourceFile () const
	returns a const reference to the source file More...

SourceFile &	getSourceFile ()
	returns a mutable reference to the source file More...

void	setSourceFile (const SourceFile &source_file)
	sets the source file More...

const std::vector< Precursor > &	getPrecursors () const
	returns a const reference to the precursors More...

std::vector< Precursor > &	getPrecursors ()
	returns a mutable reference to the precursors More...

void	setPrecursors (const std::vector< Precursor > &precursors)
	sets the precursors More...

const std::vector< Product > &	getProducts () const
	returns a const reference to the products More...

std::vector< Product > &	getProducts ()
	returns a mutable reference to the products More...

void	setProducts (const std::vector< Product > &products)
	sets the products More...

const std::vector< PeptideIdentification > &	getPeptideIdentifications () const
	returns a const reference to the PeptideIdentification vector More...

std::vector< PeptideIdentification > &	getPeptideIdentifications ()
	returns a mutable reference to the PeptideIdentification vector More...

void	setPeptideIdentifications (const std::vector< PeptideIdentification > &identifications)
	sets the PeptideIdentification vector More...

void	setDataProcessing (const std::vector< DataProcessingPtr > &data_processing)
	sets the description of the applied processing More...

std::vector< DataProcessingPtr > &	getDataProcessing ()
	returns a mutable reference to the description of the applied processing More...

const std::vector< boost::shared_ptr< const DataProcessing > >	getDataProcessing () const
	returns a const reference to the description of the applied processing More...

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...

	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...

MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator. More...

void	swap (MetaInfoInterface &rhs)
	Swap contents. More...

bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...

bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...

const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found. More...

DataValue	getMetaValue (const String &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found More...

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found. More...

DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found More...

bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...

bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...

void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...

void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...

void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to `name` if it exists. More...

void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to `index` if it exists. More...

void	addMetaValues (const MetaInfoInterface &from)
	function to copy all meta values from one object to this one More...

void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...

void	clearMetaInfo ()
	Removes all meta values. More...

Static Public Attributes
static const std::string	NamesOfSpectrumType [SIZE_OF_SPECTRUMTYPE]
	Names of spectrum types. More...

Protected Attributes
SpectrumType	type_

String	native_id_

String	comment_

InstrumentSettings	instrument_settings_

SourceFile	source_file_

AcquisitionInfo	acquisition_info_

std::vector< Precursor >	precursors_

std::vector< Product >	products_

std::vector< PeptideIdentification >	identification_

std::vector< DataProcessingPtr >	data_processing_

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Detailed Description

Representation of 1D spectrum settings.

It contains the metadata about spectrum specific instrument settings, acquisition settings, description of the meta values used in the peaks and precursor info.

Precursor info should only be used if this spectrum is a tandem-MS spectrum. The precursor spectrum is the first spectrum before this spectrum, that has a lower MS-level than the current spectrum.

Member Enumeration Documentation

◆ SpectrumType

enum SpectrumType

Spectrum peak type.

Enumerator
UNKNOWN	Unknown spectrum type.
CENTROID	centroid data or stick data
PROFILE	profile data
SIZE_OF_SPECTRUMTYPE

Constructor & Destructor Documentation

◆ SpectrumSettings() [1/3]

SpectrumSettings ( )

Constructor.

◆ SpectrumSettings() [2/3]

SpectrumSettings ( const SpectrumSettings & )

default

Copy constructor.

◆ SpectrumSettings() [3/3]

SpectrumSettings ( SpectrumSettings && )

default

Move constructor.

◆ ~SpectrumSettings()

~SpectrumSettings ( )

Destructor.

Member Function Documentation

◆ getAcquisitionInfo() [1/2]

AcquisitionInfo& getAcquisitionInfo ( )

returns a mutable reference to the acquisition info

◆ getAcquisitionInfo() [2/2]

const AcquisitionInfo& getAcquisitionInfo ( ) const

returns a const reference to the acquisition info

Referenced by ChromatogramExtractor::return_chromatogram().

◆ getComment()

const String& getComment ( ) const

returns the free-text comment

◆ getDataProcessing() [1/2]

std::vector< DataProcessingPtr >& getDataProcessing ( )

returns a mutable reference to the description of the applied processing

Referenced by ChromatogramExtractor::return_chromatogram().

◆ getDataProcessing() [2/2]

const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing ( ) const

returns a const reference to the description of the applied processing

◆ getInstrumentSettings() [1/2]

InstrumentSettings& getInstrumentSettings ( )

returns a mutable reference to the instrument settings of the current spectrum

◆ getInstrumentSettings() [2/2]

const InstrumentSettings& getInstrumentSettings ( ) const

returns a const reference to the instrument settings of the current spectrum

Referenced by HasScanMode< SpectrumType >::operator()(), HasScanPolarity< SpectrumType >::operator()(), IsZoomSpectrum< SpectrumType >::operator()(), and ChromatogramExtractor::return_chromatogram().

◆ getNativeID()

const String& getNativeID ( ) const

returns the native identifier for the spectrum, used by the acquisition software.

Referenced by MascotGenericFile::getNextSpectrum_(), SpectraMerger::mergeSpectra_(), NucleicAcidSearchEngine::postProcessHits_(), NucleicAcidSearchEngine::preprocessSpectra_(), and SpectrumLookup::readSpectra().

◆ getPeptideIdentifications() [1/2]

std::vector<PeptideIdentification>& getPeptideIdentifications ( )

returns a mutable reference to the PeptideIdentification vector

◆ getPeptideIdentifications() [2/2]

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

returns a const reference to the PeptideIdentification vector

◆ getPrecursors() [1/2]

std::vector<Precursor>& getPrecursors ( )

returns a mutable reference to the precursors

◆ getPrecursors() [2/2]

const std::vector<Precursor>& getPrecursors ( ) const

returns a const reference to the precursors

Referenced by FullSwathFileConsumer::consumeSpectrum(), ChromatogramTools::convertChromatogramsToSpectra(), IsobaricChannelExtractor::getActivationMethod_(), MascotGenericFile::getNextSpectrum_(), MascotGenericFile::load(), MascotInfile::load(), MS2File::load(), DTAFile::load(), IDMapper::mapPrecursorsToIdentifications(), SpectraMerger::mergeSpectra_(), PrecursorMassComparator::operator()(), HasActivationMethod< SpectrumType >::operator()(), InPrecursorMZRange< SpectrumType >::operator()(), HasPrecursorCharge< SpectrumType >::operator()(), IsInCollisionEnergyRange< SpectrumType >::operator()(), IsInIsolationWindowSizeRange< SpectrumType >::operator()(), IsInIsolationWindow< SpectrumType >::operator()(), NucleicAcidSearchEngine::postProcessHits_(), NucleicAcidSearchEngine::preprocessSpectra_(), ChromatogramExtractor::return_chromatogram(), and DTAFile::store().

◆ getProducts() [1/2]

std::vector<Product>& getProducts ( )

returns a mutable reference to the products

◆ getProducts() [2/2]

const std::vector<Product>& getProducts ( ) const

returns a const reference to the products

◆ getSourceFile() [1/2]

SourceFile& getSourceFile ( )

returns a mutable reference to the source file

◆ getSourceFile() [2/2]

const SourceFile& getSourceFile ( ) const

returns a const reference to the source file

Referenced by ChromatogramExtractor::return_chromatogram().

◆ getType()

SpectrumType getType ( ) const

returns the spectrum type (centroided (PEAKS) or profile data (RAW))

◆ operator!=()

bool operator!= ( const SpectrumSettings & rhs ) const

Equality operator.

◆ operator=() [1/2]

SpectrumSettings& operator= ( const SpectrumSettings & )

default

◆ operator=() [2/2]

SpectrumSettings& operator= ( SpectrumSettings && ) &

default

Move assignment operator.

◆ operator==()

bool operator== ( const SpectrumSettings & rhs ) const

Equality operator.

◆ setAcquisitionInfo()

void setAcquisitionInfo ( const AcquisitionInfo & acquisition_info )

sets the acquisition info

Referenced by XMassFile::load().

◆ setComment()

void setComment ( const String & comment )

sets the free-text comment

Referenced by XMassFile::load().

◆ setDataProcessing()

void setDataProcessing ( const std::vector< DataProcessingPtr > & data_processing )

sets the description of the applied processing

Referenced by XMassFile::load().

◆ setInstrumentSettings()

void setInstrumentSettings ( const InstrumentSettings & instrument_settings )

sets the instrument settings of the current spectrum

Referenced by XMassFile::load().

◆ setNativeID()

void setNativeID ( const String & native_id )

sets the native identifier for the spectrum, used by the acquisition software.

Referenced by MascotGenericFile::getNextSpectrum_(), MS2File::load(), DTA2DFile::load(), XMassFile::load(), and SpectraMerger::mergeSpectra_().

◆ setPeptideIdentifications()

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

sets the PeptideIdentification vector

◆ setPrecursors()

void setPrecursors ( const std::vector< Precursor > & precursors )

sets the precursors

Referenced by SpectraMerger::mergeSpectra_(), and NucleicAcidSearchEngine::preprocessSpectra_().

◆ setProducts()

void setProducts ( const std::vector< Product > & products )

sets the products

◆ setSourceFile()

void setSourceFile ( const SourceFile & source_file )

sets the source file

Referenced by XMassFile::load().

◆ setType()

void setType ( SpectrumType type )

sets the spectrum type

Referenced by MorphologicalFilter::filter(), MascotGenericFile::load(), XMassFile::load(), and PeakPickerIterative::pick().

◆ unify()

void unify ( const SpectrumSettings & rhs )

merge another spectrum setting into this one (data is usually appended, except for spectrum type which needs to be unambiguous to be kept)

Referenced by SpectraMerger::mergeSpectra_().

Member Data Documentation

◆ acquisition_info_

AcquisitionInfo acquisition_info_

protected

◆ comment_

String comment_

protected

◆ data_processing_

std::vector< DataProcessingPtr > data_processing_

protected

◆ identification_

std::vector<PeptideIdentification> identification_

protected

◆ instrument_settings_

InstrumentSettings instrument_settings_

protected

◆ NamesOfSpectrumType

const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE]

static

Names of spectrum types.

◆ native_id_

String native_id_

protected

◆ precursors_

std::vector<Precursor> precursors_

protected

◆ products_

std::vector<Product> products_

protected

◆ source_file_

SourceFile source_file_

protected

◆ type_

SpectrumType type_

protected

Public Types

Public Member Functions

Static Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ SpectrumType

Constructor & Destructor Documentation

◆ SpectrumSettings() [1/3]

◆ SpectrumSettings() [2/3]

◆ SpectrumSettings() [3/3]

◆ ~SpectrumSettings()

Member Function Documentation

◆ getAcquisitionInfo() [1/2]

◆ getAcquisitionInfo() [2/2]

◆ getComment()

◆ getDataProcessing() [1/2]

◆ getDataProcessing() [2/2]

◆ getInstrumentSettings() [1/2]

◆ getInstrumentSettings() [2/2]

◆ getNativeID()

◆ getPeptideIdentifications() [1/2]

◆ getPeptideIdentifications() [2/2]

◆ getPrecursors() [1/2]

◆ getPrecursors() [2/2]

◆ getProducts() [1/2]

◆ getProducts() [2/2]

◆ getSourceFile() [1/2]

◆ getSourceFile() [2/2]

◆ getType()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setAcquisitionInfo()

◆ setComment()

◆ setDataProcessing()

◆ setInstrumentSettings()

◆ setNativeID()

◆ setPeptideIdentifications()

◆ setPrecursors()

◆ setProducts()

◆ setSourceFile()

◆ setType()

◆ unify()

Member Data Documentation

◆ acquisition_info_

◆ comment_

◆ data_processing_

◆ identification_

◆ instrument_settings_

◆ NamesOfSpectrumType

◆ native_id_

◆ precursors_

◆ products_

◆ source_file_

◆ type_