SpectrumSettings Class Reference

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 ()=default
	Constructor.
	SpectrumSettings (const SpectrumSettings &)=default
	Copy constructor.
	SpectrumSettings (SpectrumSettings &&) noexcept=default
	Move constructor.
	~SpectrumSettings () noexcept=default
	Destructor.
SpectrumSettings &	operator= (const SpectrumSettings &)=default
SpectrumSettings &	operator= (SpectrumSettings &&) &=default
	Move assignment operator.
bool	operator== (const SpectrumSettings &rhs) const
	Equality operator.
bool	operator!= (const SpectrumSettings &rhs) const
	Equality operator.
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)
SpectrumType	getType () const
	returns the spectrum type (centroided (PEAKS) or profile data (RAW))
void	setType (SpectrumType type)
	sets the spectrum type
void	setIMFormat (const IMFormat &im_type)
	sets the IMFormat of the spectrum
IMFormat	getIMFormat () const
	returns the IMFormat of the spectrum if set. Otherwise UNKNOWN (default).
const String &	getNativeID () const
	returns the native identifier for the spectrum, used by the acquisition software.
void	setNativeID (const String &native_id)
	sets the native identifier for the spectrum, used by the acquisition software.
const String &	getComment () const
	returns the free-text comment
void	setComment (const String &comment)
	sets the free-text comment
const InstrumentSettings &	getInstrumentSettings () const
	returns a const reference to the instrument settings of the current spectrum
InstrumentSettings &	getInstrumentSettings ()
	returns a mutable reference to the instrument settings of the current spectrum
void	setInstrumentSettings (const InstrumentSettings &instrument_settings)
	sets the instrument settings of the current spectrum
const AcquisitionInfo &	getAcquisitionInfo () const
	returns a const reference to the acquisition info
AcquisitionInfo &	getAcquisitionInfo ()
	returns a mutable reference to the acquisition info
void	setAcquisitionInfo (const AcquisitionInfo &acquisition_info)
	sets the acquisition info
const SourceFile &	getSourceFile () const
	returns a const reference to the source file
SourceFile &	getSourceFile ()
	returns a mutable reference to the source file
void	setSourceFile (const SourceFile &source_file)
	sets the source file
const std::vector< Precursor > &	getPrecursors () const
	returns a const reference to the precursors
std::vector< Precursor > &	getPrecursors ()
	returns a mutable reference to the precursors
void	setPrecursors (const std::vector< Precursor > &precursors)
	sets the precursors
const std::vector< Product > &	getProducts () const
	returns a const reference to the products
std::vector< Product > &	getProducts ()
	returns a mutable reference to the products
void	setProducts (const std::vector< Product > &products)
	sets the products
void	setDataProcessing (const std::vector< DataProcessingPtr > &data_processing)
	sets the description of the applied processing
std::vector< DataProcessingPtr > &	getDataProcessing ()
	returns a mutable reference to the description of the applied processing
const std::vector< std::shared_ptr< const DataProcessing > >	getDataProcessing () const
	returns a const reference to the description of the applied processing
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.
	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.
	~MetaInfoInterface ()
	Destructor.
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator.
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.
void	swap (MetaInfoInterface &rhs)
	Swap contents.
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator.
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator.
const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found.
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
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.
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
bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists.
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name.
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.
void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to name if it exists.
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists.
void	addMetaValues (const MetaInfoInterface &from)
void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.
void	clearMetaInfo ()
	Removes all meta values.

Static Public Member Functions
static StringList	getAllNamesOfSpectrumType ()
	returns all spectrum type names known to OpenMS
static const std::string &	spectrumTypeToString (SpectrumType type)
static SpectrumType	toSpectrumType (const std::string &name)
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry.

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

Protected Attributes
SpectrumType	type_ = UNKNOWN
IMFormat	im_type_ = IMFormat::UNKNOWN
String	native_id_
String	comment_
InstrumentSettings	instrument_settings_
SourceFile	source_file_
AcquisitionInfo	acquisition_info_
std::vector< Precursor >	precursors_
std::vector< Product >	products_
std::vector< DataProcessingPtr >	data_processing_
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_ = nullptr
	Pointer to the MetaInfo object.

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

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 ( )

default

Constructor.

SpectrumSettings() [2/3]

SpectrumSettings ( const SpectrumSettings &  )

default

Copy constructor.

SpectrumSettings() [3/3]

SpectrumSettings ( SpectrumSettings &&  )

defaultnoexcept

Move constructor.

~SpectrumSettings()

~SpectrumSettings ( )

defaultnoexcept

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().

getAllNamesOfSpectrumType()

static StringList getAllNamesOfSpectrumType ( )

static

returns all spectrum type names known to OpenMS

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< std::shared_ptr< const DataProcessing > > getDataProcessing

(

)

const

returns a const reference to the description of the applied processing

getIMFormat()

IMFormat getIMFormat

(

)

const

returns the IMFormat of the spectrum if set. Otherwise UNKNOWN (default).

Note: If UNKNOWN, use IMFormat::determineIMFormat to determine the IMFormat based on the data.

Returns

IMFormat of the spectrum

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().

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(), IsobaricChannelExtractor::getActivationMethod_(), MascotGenericFile::getNextSpectrum_(), MascotGenericFile::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().

setIMFormat()

void setIMFormat

(

const IMFormat &

im_type

)

sets the IMFormat of the spectrum

Parameters

[in]

im_type

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_().

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().

spectrumTypeToString()

static const std::string & spectrumTypeToString ( SpectrumType  type )

static

Convert a SpectrumType enum to String

Exceptions

Exception::InvalidValue

if type is SIZE_OF_SPECTRUMTYPE

toSpectrumType()

static SpectrumType toSpectrumType ( const std::string &  name )

static

Convert an entry in NamesOfSpectrumType[] to SpectrumType enum

Exceptions

Exception::InvalidValue

if name is not contained in NamesOfSpectrumType[]

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

im_type_

IMFormat im_type_ = IMFormat::UNKNOWN

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_ = UNKNOWN

protected