In-Memory representation of a mass spectrometry run. More...

#include <OpenMS/KERNEL/MSExperiment.h>

Inheritance diagram for MSExperiment:

Collaboration diagram for MSExperiment:

Classes
struct	ContainerAdd_
	Helper class to add either general data points in set2DData or use mass traces from meta values. More...

struct	ContainerAdd_< ContainerValueType, false >

struct	ContainerAdd_< ContainerValueType, true >

Public Types
typedef Peak1D	PeakT

typedef ChromatogramPeak	ChromatogramPeakT

Base type definitions
typedef PeakT	PeakType
	Peak type. More...

typedef ChromatogramPeakT	ChromatogramPeakType
	Chromatogram peak type. More...

typedef PeakType::CoordinateType	CoordinateType
	Coordinate type of peak positions. More...

typedef PeakType::IntensityType	IntensityType
	Intensity type of peaks. More...

typedef RangeManager< RangeRT, RangeMZ, RangeIntensity, RangeMobility >	RangeManagerType
	RangeManager type. More...

typedef RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity, RangeMobility >	RangeManagerContainerType
	RangeManager type. More...

typedef MSSpectrum	SpectrumType
	Spectrum Type. More...

typedef MSChromatogram	ChromatogramType
	Chromatogram type. More...

typedef std::vector< SpectrumType >	Base
	STL base class type. More...

Iterator type definitions
typedef std::vector< SpectrumType >::iterator	Iterator
	Mutable iterator. More...

typedef std::vector< SpectrumType >::const_iterator	ConstIterator
	Non-mutable iterator. More...

typedef Internal::AreaIterator< PeakT, PeakT &, PeakT *, Iterator, SpectrumType::Iterator >	AreaIterator
	Mutable area iterator type (for traversal of a rectangular subset of the peaks) More...

typedef Internal::AreaIterator< const PeakT, const PeakT &, const PeakT *, ConstIterator, SpectrumType::ConstIterator >	ConstAreaIterator
	Immutable area iterator type (for traversal of a rectangular subset of the peaks) More...

Public Types inherited from RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity, RangeMobility >
using	ThisRangeType = typename RangeManager< RangeBases... >::ThisRangeType

Public Types inherited from RangeManager< RangeBases... >
using	ThisRangeType = RangeManager< RangeBases... >

Public Member Functions
UInt64	getSqlRunID () const

void	setSqlRunID (UInt64 id)
	sets the run-ID which is used when storing an sqMass file More...

Conversion to/from 2D data
template<class Container >
void	get2DData (Container &cont) const
	Reads out a 2D Spectrum. More...

template<class Container >
void	set2DData (const Container &container)
	Assignment of a data container with RT and MZ to an MSExperiment. More...

template<class Container >
void	set2DData (const Container &container, const StringList &store_metadata_names)
	Assignment of a data container with RT and MZ to an MSExperiment. More...

template<bool add_mass_traces, class Container >
void	set2DData (const Container &container)
	Assignment of a data container with RT and MZ to an MSExperiment. More...

Iterating ranges and areas
AreaIterator	areaBegin (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz, UInt ms_level=1)
	Returns an area iterator for `area`. More...

AreaIterator	areaBegin (const RangeManagerType &range, UInt ms_level=1)
	Returns a area iterator for all peaks in `range`. If a dimension is empty(), it is ignored (i.e. does not restrict the area) More...

AreaIterator	areaEnd ()
	Returns an invalid area iterator marking the end of an area. More...

ConstAreaIterator	areaBeginConst (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz, UInt ms_level=1) const
	Returns a non-mutable area iterator for `area`. More...

ConstAreaIterator	areaBeginConst (const RangeManagerType &range, UInt ms_level=1) const
	Returns a non-mutable area iterator for all peaks in `range`. If a dimension is empty(), it is ignored (i.e. does not restrict the area) More...

ConstAreaIterator	areaEndConst () const
	Returns an non-mutable invalid area iterator marking the end of an area. More...

void	get2DPeakData (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz, std::vector< float > &rt, std::vector< std::vector< float >> &mz, std::vector< std::vector< float >> &intensity) const

void	get2DPeakData (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz, std::vector< float > &rt, std::vector< std::vector< float >> &mz, std::vector< std::vector< float >> &intensity, std::vector< std::vector< float >> &ion_mobility) const

void	get2DPeakData (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz, std::vector< float > &rt, std::vector< float > &mz, std::vector< float > &intensity) const

void	get2DPeakDataIon (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz, std::vector< float > &rt, std::vector< float > &mz, std::vector< float > &intensity, std::vector< float > &ion_mobility) const

ConstIterator	RTBegin (CoordinateType rt) const
	Fast search for spectrum range begin. More...

ConstIterator	RTEnd (CoordinateType rt) const
	Fast search for spectrum range end (returns the past-the-end iterator) More...

Iterator	RTBegin (CoordinateType rt)
	Fast search for spectrum range begin. More...

Iterator	RTEnd (CoordinateType rt)
	Fast search for spectrum range end (returns the past-the-end iterator) More...

ConstIterator	IMBegin (CoordinateType im) const
	Fast search for spectrum range begin. More...

ConstIterator	IMEnd (CoordinateType im) const
	Fast search for spectrum range end (returns the past-the-end iterator) More...

Range methods
Note The range values (min, max, etc.) are not updated automatically. Call updateRanges() to update the values!
void	updateRanges () override

void	updateRanges (Int ms_level)
	Updates the m/z, intensity, retention time and MS level ranges of all spectra with a certain ms level. More...

CoordinateType	getMinMZ () const
	returns the minimal m/z value More...

CoordinateType	getMaxMZ () const
	returns the maximal m/z value More...

CoordinateType	getMinRT () const
	returns the minimal retention time value More...

CoordinateType	getMaxRT () const
	returns the maximal retention time value More...

UInt64	getSize () const
	returns the total number of peaks More...

const std::vector< UInt > &	getMSLevels () const
	returns an array of MS levels More...

Sorting spectra and peaks
void	sortSpectra (bool sort_mz=true)
	Sorts the data points by retention time. More...

void	sortChromatograms (bool sort_rt=true)
	Sorts the data points of the chromatograms by m/z. More...

bool	isSorted (bool check_mz=true) const
	Checks if all spectra are sorted with respect to ascending RT. More...

void	reset ()
	Clear all internal data (spectra, ranges, metadata) More...

bool	clearMetaDataArrays ()
	Clears the meta data arrays of all contained spectra (float, integer and string arrays) More...

const ExperimentalSettings &	getExperimentalSettings () const
	returns the meta information of this experiment (const access) More...

ExperimentalSettings &	getExperimentalSettings ()
	returns the meta information of this experiment (mutable access) More...

void	getPrimaryMSRunPath (StringList &toFill) const
	get the file path to the first MS run More...

ConstIterator	getPrecursorSpectrum (ConstIterator iterator) const
	Returns the precursor spectrum of the scan pointed to by `iterator`. More...

int	getPrecursorSpectrum (int zero_based_index) const
	Returns the index of the precursor spectrum for spectrum at index `zero_based_index`. More...

void	swap (MSExperiment &from)
	Swaps the content of this map with the content of `from`. More...

void	setSpectra (const std::vector< MSSpectrum > &spectra)
	sets the spectrum list More...

void	setSpectra (std::vector< MSSpectrum > &&spectra)

void	addSpectrum (const MSSpectrum &spectrum)
	adds a spectrum to the list More...

void	addSpectrum (MSSpectrum &&spectrum)

const std::vector< MSSpectrum > &	getSpectra () const
	returns the spectrum list More...

std::vector< MSSpectrum > &	getSpectra ()
	returns the spectrum list (mutable) More...

void	setChromatograms (const std::vector< MSChromatogram > &chromatograms)
	sets the chromatogram list More...

void	setChromatograms (std::vector< MSChromatogram > &&chromatograms)

void	addChromatogram (const MSChromatogram &chromatogram)
	adds a chromatogram to the list More...

void	addChromatogram (MSChromatogram &&chrom)

const std::vector< MSChromatogram > &	getChromatograms () const
	returns the chromatogram list More...

std::vector< MSChromatogram > &	getChromatograms ()
	returns the chromatogram list (mutable) More...

Public Member Functions inherited from RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity, RangeMobility >
virtual	~RangeManagerContainer ()=default
	D'tor. More...

const ThisRangeType &	getRange () const
	get range of current data (call updateRanges() before to ensure the range is accurate) More...

ThisRangeType &	getRange ()
	get mutable range, provided for efficiency reasons (avoid updateRanges(), if only minor changes were made) More...

Public Member Functions inherited from RangeManager< RangeBases... >
bool	operator== (const RangeManager &rhs) const

bool	operator!= (const RangeManager &rhs) const

bool	assignUnsafe (const RangeManager< RangeBasesOther... > &rhs)

auto &	assign (const RangeManager< RangeBasesOther... > &rhs)

bool	extendUnsafe (const RangeManager< RangeBasesOther... > &rhs)

void	extend (const RangeManager< RangeBasesOther... > &rhs)

void	scaleBy (const double factor)
	calls RangeBase::scale() for each dimension More...

void	minSpanIfSingular (const double min_span)
	If any dimension is a single point, e.g. min==max, then extend this dimension by `min_span` / 2 on either side. More...

bool	pushIntoUnsafe (const RangeManager< RangeBasesOther... > &rhs)

void	pushInto (const RangeManager< RangeBasesOther... > &sandbox)

bool	clampToUnsafe (const RangeManager< RangeBasesOther... > &rhs)

void	clampTo (const RangeManager< RangeBasesOther... > &rhs)

const RangeBase &	getRangeForDim (MSDim dim) const
	obtain a range dimension at runtime using `dim` More...

RangeBase &	getRangeForDim (MSDim dim)
	obtain a range dimension at runtime using `dim` More...

HasRangeType	hasRange () const
	is any/some/all dimension in this range populated? More...

bool	containsAll (const RangeManager< RangeBasesOther... > &rhs) const

void	clearRanges ()
	Resets all ranges. More...

ThisRangeType &	clear (const DIM_UNIT range)

void	printRange (std::ostream &out) const
	print each dimension (base classes) to a stream More...

Public Member Functions inherited from ExperimentalSettings
	ExperimentalSettings ()=default
	Constructor. More...

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

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

	~ExperimentalSettings () override
	Destructor. More...

ExperimentalSettings &	operator= (const ExperimentalSettings &)=default
	Assignment operator. More...

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

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

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

const Sample &	getSample () const
	returns a const reference to the sample description More...

Sample &	getSample ()
	returns a mutable reference to the sample description More...

void	setSample (const Sample &sample)
	sets the sample description More...

const std::vector< SourceFile > &	getSourceFiles () const
	returns a const reference to the source data file More...

std::vector< SourceFile > &	getSourceFiles ()
	returns a mutable reference to the source data file More...

void	setSourceFiles (const std::vector< SourceFile > &source_files)
	sets the source data file More...

const std::vector< ContactPerson > &	getContacts () const
	returns a const reference to the list of contact persons More...

std::vector< ContactPerson > &	getContacts ()
	returns a mutable reference to the list of contact persons More...

void	setContacts (const std::vector< ContactPerson > &contacts)
	sets the list of contact persons More...

const Instrument &	getInstrument () const
	returns a const reference to the MS instrument description More...

Instrument &	getInstrument ()
	returns a mutable reference to the MS instrument description More...

void	setInstrument (const Instrument &instrument)
	sets the MS instrument description More...

const HPLC &	getHPLC () const
	returns a const reference to the description of the HPLC run More...

HPLC &	getHPLC ()
	returns a mutable reference to the description of the HPLC run More...

void	setHPLC (const HPLC &hplc)
	sets the description of the HPLC run More...

const DateTime &	getDateTime () const
	returns the date the experiment was performed More...

void	setDateTime (const DateTime &date)
	sets the date the experiment was performed More...

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

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

const std::vector< ProteinIdentification > &	getProteinIdentifications () const
	returns a const reference to the protein ProteinIdentification vector More...

std::vector< ProteinIdentification > &	getProteinIdentifications ()
	returns a mutable reference to the protein ProteinIdentification vector More...

void	setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications)
	sets the protein ProteinIdentification vector More...

const String &	getFractionIdentifier () const
	returns fraction identifier More...

void	setFractionIdentifier (const String &fraction_identifier)
	sets the fraction identifier 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...

Public Member Functions inherited from DocumentIdentifier
	DocumentIdentifier ()
	Default constructor. More...

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

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

virtual	~DocumentIdentifier ()
	Destructor. More...

DocumentIdentifier &	operator= (const DocumentIdentifier &)=default
	Assignment operator. More...

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

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

void	setIdentifier (const String &id)
	set document identifier (e.g. an LSID) More...

const String &	getIdentifier () const
	retrieve document identifier (e.g. an LSID) More...

void	swap (DocumentIdentifier &from)
	exchange content with `from` More...

void	setLoadedFilePath (const String &file_name)
	set the file_name_ according to absolute path of the file loaded from preferably done whilst loading More...

const String &	getLoadedFilePath () const
	get the file_name_ which is the absolute path to the file loaded from More...

void	setLoadedFileType (const String &file_name)
	set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably done whilst loading More...

const FileTypes::Type &	getLoadedFileType () const
	get the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, ...) of the file loaded from More...

Delegations of calls to the vector of MSSpectra
typedef Base::value_type	value_type

typedef Base::iterator	iterator

typedef Base::const_iterator	const_iterator

	MSExperiment ()
	Constructor. More...

	MSExperiment (const MSExperiment &source)
	Copy constructor. More...

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

MSExperiment &	operator= (const MSExperiment &source)
	Assignment operator. More...

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

MSExperiment &	operator= (const ExperimentalSettings &source)
	Assignment operator. More...

	~MSExperiment () override
	D'tor. More...

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

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

Size	size () const
	The number of spectra. More...

void	resize (Size n)
	Resize to `n` spectra. More...

bool	empty () const
	Are there any spectra (does not consider chromatograms) More...

void	reserve (Size n)
	Reserve space for `n` spectra. More...

SpectrumType &	operator[] (Size n)
	Random access to `n'th` spectrum. More...

const SpectrumType &	operator[] (Size n) const
	Random access to `n'th` spectrum. More...

Iterator	begin ()

ConstIterator	begin () const

Iterator	end ()

ConstIterator	end () const

void	reserveSpaceSpectra (Size s)

void	reserveSpaceChromatograms (Size s)

Easy Access interface
std::vector< UInt >	ms_levels_
	MS levels of the data. More...

UInt64	total_size_
	Number of all data points. More...

std::vector< MSChromatogram >	chromatograms_
	chromatograms More...

std::vector< SpectrumType >	spectra_
	spectra More...

MSChromatogram &	getChromatogram (Size id)
	returns a single chromatogram More...

MSSpectrum &	getSpectrum (Size id)
	returns a single spectrum More...

Size	getNrSpectra () const
	get the total number of spectra available More...

Size	getNrChromatograms () const
	get the total number of chromatograms available More...

const MSChromatogram	calculateTIC (float rt_bin_size=0, UInt ms_level=1) const
	Computes the total ion chromatogram (TIC) for a given MS level (use ms_level = 0 for all levels). More...

void	clear (bool clear_meta_data)
	Clears all data and meta data. More...

bool	containsScanOfLevel (size_t ms_level) const
	returns true if at least one of the spectra has the specified level More...

bool	hasZeroIntensities (size_t ms_level) const
	returns true if any MS spectra of trthe specified level contain at least one peak with intensity of 0.0 More...

bool	hasPeptideIdentifications () const
	do any of the spectra have a PeptideID? More...

bool	isIMFrame () const
	Are all MSSpectra in this experiment part of an IM Frame? I.e. they all have the same RT, but different drift times. More...

SpectrumType *	createSpec_ (PeakType::CoordinateType rt)

SpectrumType *	createSpec_ (PeakType::CoordinateType rt, const StringList &metadata_names)

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 RangeManager< RangeBases... >
void	for_each_base_ (Visitor &&visitor)
	use fold expression to iterate over all RangeBases of RangeManager and apply a lambda (Visitor) for each one More...

void	for_each_base_ (Visitor &&visitor) const
	.. and a const version More...

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

Static Protected Member Functions inherited from RangeManager< RangeBases... >
static void	static_for_each_base_ (Visitor &&visitor)
	use fold expression to iterate over all RangeBases of RangeManager and apply a lambda (Visitor) for each one (for static members) More...

Protected Attributes inherited from ExperimentalSettings
Sample	sample_

std::vector< SourceFile >	source_files_

std::vector< ContactPerson >	contacts_

Instrument	instrument_

HPLC	hplc_

DateTime	datetime_

String	comment_

std::vector< ProteinIdentification >	protein_identifications_

String	fraction_identifier_

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

Protected Attributes inherited from DocumentIdentifier
String	id_
	the ID (e.g. LSID) More...

String	file_path_
	the path to the loaded file More...

FileTypes::Type	file_type_
	the type of the loaded file More...

Detailed Description

In-Memory representation of a mass spectrometry run.

This representation of an MS run is organized as list of spectra and chromatograms and provides an in-memory representation of popular mass-spectrometric file formats such as mzXML or mzML. The meta-data associated with an experiment is contained in ExperimentalSettings (by inheritance) while the raw data (as well as spectra and chromatogram level meta data) is stored in objects of type MSSpectrum and MSChromatogram, which are accessible through the getSpectrum and getChromatogram functions.

Note: For range operations, see RangeUtils module!; Some of the meta data is associated with the spectra directly (e.g. DataProcessing) and therefore the spectra need to be present to retain this information.; For an on-disc representation of an MS experiment, see OnDiskExperiment.

Member Typedef Documentation

◆ AreaIterator

typedef Internal::AreaIterator<PeakT, PeakT&, PeakT*, Iterator, SpectrumType::Iterator> AreaIterator

Mutable area iterator type (for traversal of a rectangular subset of the peaks)

◆ Base

typedef std::vector<SpectrumType> Base

STL base class type.

◆ ChromatogramPeakT

typedef ChromatogramPeak ChromatogramPeakT

◆ ChromatogramPeakType

typedef ChromatogramPeakT ChromatogramPeakType

Chromatogram peak type.

◆ ChromatogramType

typedef MSChromatogram ChromatogramType

Chromatogram type.

◆ const_iterator

typedef Base::const_iterator const_iterator

◆ ConstAreaIterator

typedef Internal::AreaIterator<const PeakT, const PeakT&, const PeakT*, ConstIterator, SpectrumType::ConstIterator> ConstAreaIterator

Immutable area iterator type (for traversal of a rectangular subset of the peaks)

◆ ConstIterator

typedef std::vector<SpectrumType>::const_iterator ConstIterator

Non-mutable iterator.

◆ CoordinateType

typedef PeakType::CoordinateType CoordinateType

Coordinate type of peak positions.

◆ IntensityType

typedef PeakType::IntensityType IntensityType

Intensity type of peaks.

◆ Iterator

typedef std::vector<SpectrumType>::iterator Iterator

Mutable iterator.

◆ iterator

typedef Base::iterator iterator

◆ PeakT

typedef Peak1D PeakT

◆ PeakType

typedef PeakT PeakType

Peak type.

◆ RangeManagerContainerType

typedef RangeManagerContainer<RangeRT, RangeMZ, RangeIntensity, RangeMobility> RangeManagerContainerType

RangeManager type.

◆ RangeManagerType

typedef RangeManager<RangeRT, RangeMZ, RangeIntensity, RangeMobility> RangeManagerType

RangeManager type.

◆ SpectrumType

typedef MSSpectrum SpectrumType

Spectrum Type.

◆ value_type

typedef Base::value_type value_type

Constructor & Destructor Documentation

◆ MSExperiment() [1/3]

MSExperiment ( )

Constructor.

◆ MSExperiment() [2/3]

MSExperiment ( const MSExperiment & source )

Copy constructor.

◆ MSExperiment() [3/3]

MSExperiment ( MSExperiment && )

default

Move constructor.

◆ ~MSExperiment()

~MSExperiment ( )

override

D'tor.

Member Function Documentation

◆ addChromatogram() [1/2]

void addChromatogram ( const MSChromatogram & chromatogram )

adds a chromatogram to the list

◆ addChromatogram() [2/2]

void addChromatogram ( MSChromatogram && chrom )

◆ addSpectrum() [1/2]

void addSpectrum ( const MSSpectrum & spectrum )

adds a spectrum to the list

Referenced by SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), MascotGenericFile::load(), MascotInfile::load(), MS2File::load(), DTA2DFile::load(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectra_(), OPXLDataStructs::PreprocessedPairSpectra::PreprocessedPairSpectra(), and TOPPViewBase::showSpectrumGenerationDialog().

◆ addSpectrum() [2/2]

void addSpectrum ( MSSpectrum && spectrum )

◆ areaBegin() [1/2]

AreaIterator areaBegin	(	const RangeManagerType &	range,
		UInt	ms_level = `1`
	)

Returns a area iterator for all peaks in range. If a dimension is empty(), it is ignored (i.e. does not restrict the area)

◆ areaBegin() [2/2]

AreaIterator areaBegin	(	CoordinateType	min_rt,
		CoordinateType	max_rt,
		CoordinateType	min_mz,
		CoordinateType	max_mz,
		UInt	ms_level = `1`
	)

Returns an area iterator for area.

◆ areaBeginConst() [1/2]

ConstAreaIterator areaBeginConst	(	const RangeManagerType &	range,
		UInt	ms_level = `1`
	)		const

Returns a non-mutable area iterator for all peaks in range. If a dimension is empty(), it is ignored (i.e. does not restrict the area)

◆ areaBeginConst() [2/2]

ConstAreaIterator areaBeginConst	(	CoordinateType	min_rt,
		CoordinateType	max_rt,
		CoordinateType	min_mz,
		CoordinateType	max_mz,
		UInt	ms_level = `1`
	)		const

Returns a non-mutable area iterator for area.

◆ areaEnd()

AreaIterator areaEnd ( )

Returns an invalid area iterator marking the end of an area.

◆ areaEndConst()

ConstAreaIterator areaEndConst ( ) const

Returns an non-mutable invalid area iterator marking the end of an area.

◆ begin() [1/2]

Iterator begin ( )

inline

Referenced by KDTreeFeatureMaps::addMaps(), SpectraMerger::average(), SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), IsotopeWaveletTransform< PeakType >::extendBox_(), IDFilter::filterHitsByScore(), MapAlignmentAlgorithmIdentification::getRetentionTimes_(), IDFilter::keepHitsMatchingProteins(), IDFilter::keepNBestHits(), TOPPFLASHDeconv::main_(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraBlockWise(), and DTA2DFile::store().

◆ begin() [2/2]

ConstIterator begin ( ) const

inline

◆ calculateTIC()

const MSChromatogram calculateTIC	(	float	rt_bin_size = `0`,
		UInt	ms_level = `1`
	)		const

Computes the total ion chromatogram (TIC) for a given MS level (use ms_level = 0 for all levels).

By default, each MS spectrum's intensity just gets summed up. Regular RT bins can be obtained by specifying rt_bin_size. If a bin size in RT seconds greater than 0 is given resampling is used.

Parameters

bin_size	RT bin size in seconds (0 = no resampling)
ms_level	MS level of spectra for calculation (0 = all levels)

Returns: TIC Chromatogram

Referenced by DTA2DFile::storeTIC().

◆ clear()

void clear ( bool clear_meta_data )

Clears all data and meta data.

Parameters

clear_meta_data If true, all meta data is cleared in addition to the data.

Referenced by SpectraMerger::mergeSpectra_(), PeakPickerIterative::pickExperiment(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().

◆ clearMetaDataArrays()

bool clearMetaDataArrays ( )

Clears the meta data arrays of all contained spectra (float, integer and string arrays)

Returns: true if meta data arrays were present and removed. false otherwise.

◆ containsScanOfLevel()

bool containsScanOfLevel ( size_t ms_level ) const

returns true if at least one of the spectra has the specified level

◆ createSpec_() [1/2]

SpectrumType* createSpec_ ( PeakType::CoordinateType rt )

private

◆ createSpec_() [2/2]

SpectrumType* createSpec_	(	PeakType::CoordinateType	rt,
		const StringList &	metadata_names
	)

private

◆ empty()

bool empty ( ) const

inline

Are there any spectra (does not consider chromatograms)

Referenced by OpenSwathHelper::checkSwathMapAndSelectTransitions().

◆ end() [1/2]

Iterator end ( )

inline

Referenced by KDTreeFeatureMaps::addMaps(), SpectraMerger::average(), SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), IDFilter::filterHitsByScore(), MapAlignmentAlgorithmIdentification::getRetentionTimes_(), IDFilter::keepHitsMatchingProteins(), IDFilter::keepNBestHits(), TOPPFLASHDeconv::main_(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraBlockWise(), and DTA2DFile::store().

◆ end() [2/2]

ConstIterator end ( ) const

inline

◆ get2DData()

void get2DData ( Container & cont ) const

inline

Reads out a 2D Spectrum.

Container can be a PeakArray or an STL container of peaks which supports push_back(), end() and back()

◆ get2DPeakData() [1/3]

void get2DPeakData	(	CoordinateType	min_rt,
		CoordinateType	max_rt,
		CoordinateType	min_mz,
		CoordinateType	max_mz,
		std::vector< float > &	rt,
		std::vector< float > &	mz,
		std::vector< float > &	intensity
	)		const

inline

◆ get2DPeakData() [2/3]

void get2DPeakData	(	CoordinateType	min_rt,
		CoordinateType	max_rt,
		CoordinateType	min_mz,
		CoordinateType	max_mz,
		std::vector< float > &	rt,
		std::vector< std::vector< float >> &	mz,
		std::vector< std::vector< float >> &	intensity
	)		const

inline

◆ get2DPeakData() [3/3]

void get2DPeakData	(	CoordinateType	min_rt,
		CoordinateType	max_rt,
		CoordinateType	min_mz,
		CoordinateType	max_mz,
		std::vector< float > &	rt,
		std::vector< std::vector< float >> &	mz,
		std::vector< std::vector< float >> &	intensity,
		std::vector< std::vector< float >> &	ion_mobility
	)		const

inline

References MSSpectrum::containsIMData(), MSSpectrum::getFloatDataArrays(), and MSSpectrum::getIMData().

◆ get2DPeakDataIon()

void get2DPeakDataIon	(	CoordinateType	min_rt,
		CoordinateType	max_rt,
		CoordinateType	min_mz,
		CoordinateType	max_mz,
		std::vector< float > &	rt,
		std::vector< float > &	mz,
		std::vector< float > &	intensity,
		std::vector< float > &	ion_mobility
	)		const

inline

References MSSpectrum::containsIMData(), MSSpectrum::getFloatDataArrays(), and MSSpectrum::getIMData().

◆ getChromatogram()

MSChromatogram& getChromatogram ( Size id )

returns a single chromatogram

Referenced by SavitzkyGolayFilter::filterExperiment().

◆ getChromatograms() [1/2]

std::vector<MSChromatogram>& getChromatograms ( )

returns the chromatogram list (mutable)

◆ getChromatograms() [2/2]

const std::vector<MSChromatogram>& getChromatograms ( ) const

returns the chromatogram list

Referenced by SavitzkyGolayFilter::filterExperiment().

◆ getExperimentalSettings() [1/2]

ExperimentalSettings& getExperimentalSettings ( )

returns the meta information of this experiment (mutable access)

◆ getExperimentalSettings() [2/2]

const ExperimentalSettings& getExperimentalSettings ( ) const

returns the meta information of this experiment (const access)

Referenced by XMassFile::importExperimentalSettings().

◆ getMaxMZ()

CoordinateType getMaxMZ ( ) const

returns the maximal m/z value

◆ getMaxRT()

CoordinateType getMaxRT ( ) const

returns the maximal retention time value

◆ getMinMZ()

CoordinateType getMinMZ ( ) const

returns the minimal m/z value

◆ getMinRT()

CoordinateType getMinRT ( ) const

returns the minimal retention time value

◆ getMSLevels()

const std::vector<UInt>& getMSLevels ( ) const

returns an array of MS levels

◆ getNrChromatograms()

Size getNrChromatograms ( ) const

get the total number of chromatograms available

◆ getNrSpectra()

Size getNrSpectra ( ) const

get the total number of spectra available

Referenced by NucleicAcidSearchEngine::main_().

◆ getPrecursorSpectrum() [1/2]

ConstIterator getPrecursorSpectrum ( ConstIterator iterator ) const

Returns the precursor spectrum of the scan pointed to by iterator.

If there is no precursor scan the past-the-end iterator is returned.

◆ getPrecursorSpectrum() [2/2]

int getPrecursorSpectrum ( int zero_based_index ) const

Returns the index of the precursor spectrum for spectrum at index zero_based_index.

If there is no precursor scan -1 is returned.

◆ getPrimaryMSRunPath()

void getPrimaryMSRunPath ( StringList & toFill ) const

get the file path to the first MS run

Referenced by NucleicAcidSearchEngine::main_().

◆ getSize()

UInt64 getSize ( ) const

returns the total number of peaks

◆ getSpectra() [1/2]

std::vector<MSSpectrum>& getSpectra ( )

returns the spectrum list (mutable)

◆ getSpectra() [2/2]

const std::vector<MSSpectrum>& getSpectra ( ) const

returns the spectrum list

Referenced by SpectraMerger::mergeSpectra_().

◆ getSpectrum()

MSSpectrum& getSpectrum ( Size id )

returns a single spectrum

◆ getSqlRunID()

UInt64 getSqlRunID ( ) const

If the file is loaded from an sqMass file, this run-ID allows to connect to the corresponding OSW identification file If the run-ID was not stored (older version) or this MSExperiment was not loaded from sqMass, then 0 is returned.

◆ hasPeptideIdentifications()

bool hasPeptideIdentifications ( ) const

do any of the spectra have a PeptideID?

◆ hasZeroIntensities()

bool hasZeroIntensities ( size_t ms_level ) const

returns true if any MS spectra of trthe specified level contain at least one peak with intensity of 0.0

◆ IMBegin()

ConstIterator IMBegin ( CoordinateType im ) const

Fast search for spectrum range begin.

Returns the first scan which has equal or higher (>=) ion mobility than rt.

Note: Make sure the spectra are sorted with respect to ion mobility! Otherwise the result is undefined.

◆ IMEnd()

ConstIterator IMEnd ( CoordinateType im ) const

Fast search for spectrum range end (returns the past-the-end iterator)

Returns the first scan which has higher (>) ion mobility than im.

Note: Make sure the spectra are sorted with respect to ion mobility! Otherwise the result is undefined.

◆ isIMFrame()

bool isIMFrame ( ) const

Are all MSSpectra in this experiment part of an IM Frame? I.e. they all have the same RT, but different drift times.

◆ isSorted()

bool isSorted ( bool check_mz = true ) const

Checks if all spectra are sorted with respect to ascending RT.

Parameters

check_mz if true, checks if all peaks are sorted with respect to ascending m/z

◆ operator!=()

bool operator!= ( const MSExperiment & rhs ) const

Equality operator.

◆ operator=() [1/3]

MSExperiment& operator= ( const ExperimentalSettings & source )

Assignment operator.

◆ operator=() [2/3]

MSExperiment& operator= ( const MSExperiment & source )

Assignment operator.

◆ operator=() [3/3]

MSExperiment& operator= ( MSExperiment && ) &

default

Move assignment operator.

◆ operator==()

bool operator== ( const MSExperiment & rhs ) const

Equality operator.

◆ operator[]() [1/2]

SpectrumType& operator[] ( Size n )

inline

Random access to n'th spectrum.

◆ operator[]() [2/2]

const SpectrumType& operator[] ( Size n ) const

inline

Random access to n'th spectrum.

◆ reserve()

void reserve ( Size n )

inline

Reserve space for n spectra.

◆ reserveSpaceChromatograms()

void reserveSpaceChromatograms ( Size s )

◆ reserveSpaceSpectra()

void reserveSpaceSpectra ( Size s )

◆ reset()

void reset ( )

Clear all internal data (spectra, ranges, metadata)

Referenced by InspectOutfile::getExperiment(), MascotGenericFile::load(), MascotInfile::load(), MS2File::load(), and DTA2DFile::load().

◆ resize()

void resize ( Size n )

inline

Resize to n spectra.

Referenced by PeakPickerIterative::pickExperiment().

◆ RTBegin() [1/2]

Iterator RTBegin ( CoordinateType rt )

Fast search for spectrum range begin.

Note: Make sure the spectra are sorted with respect to retention time! Otherwise the result is undefined.

◆ RTBegin() [2/2]

ConstIterator RTBegin ( CoordinateType rt ) const

Fast search for spectrum range begin.

Returns the first scan which has equal or higher (>=) RT than rt.

Note: Make sure the spectra are sorted with respect to retention time! Otherwise the result is undefined.

◆ RTEnd() [1/2]

Iterator RTEnd ( CoordinateType rt )

Fast search for spectrum range end (returns the past-the-end iterator)

Note: Make sure the spectra are sorted with respect to retention time! Otherwise the result is undefined.

◆ RTEnd() [2/2]

ConstIterator RTEnd ( CoordinateType rt ) const

Fast search for spectrum range end (returns the past-the-end iterator)

Returns the first scan which has higher (>) RT than rt.

Note: Make sure the spectra are sorted with respect to retention time! Otherwise the result is undefined.

◆ set2DData() [1/3]

void set2DData ( const Container & container )

inline

Assignment of a data container with RT and MZ to an MSExperiment.

Fill MSExperiment with data. Note that all data present (including meta-data) will be deleted prior to adding new data!

Parameters

container An iterable type whose elements support getRT(), getMZ() and getIntensity()

Exceptions

Exception::Precondition is thrown if the container is not sorted according to retention time (in debug AND release mode)

◆ set2DData() [2/3]

void set2DData ( const Container & container )

inline

Assignment of a data container with RT and MZ to an MSExperiment.

Fill MSExperiment with data. Note that all data present (including meta-data) will be deleted prior to adding new data!

Parameters

container	An iterable type whose elements support getRT(), getMZ() and getIntensity()
add_mass_traces	If true, each container element is searched for the metavalue "num_of_masstraces". If found, "masstrace_intensity" (X>=0) meta values are added as data points (with 13C spacing). This is useful for, e.g., FF-Metabo output. Note that the actual feature will NOT be added if mass traces are found (since MT0 is usually identical)

Exceptions

Exception::Precondition is thrown if the container is not sorted according to retention time (in debug AND release mode) OR a "masstrace_intensity" value is expected but not found

◆ set2DData() [3/3]

void set2DData	(	const Container &	container,
		const StringList &	store_metadata_names
	)

inline

Assignment of a data container with RT and MZ to an MSExperiment.

Fill MSExperiment with data. Note that all data present (including meta-data) will be deleted prior to adding new data!

Parameters

container	An iterable type whose elements support getRT(), getMZ() and getIntensity()
store_metadata_names	[MetaInfoInterface input only] Names of metadata arrays which should be created; data is filled from the metainfointerface of each element of the input container. Currently, only float data is supported!

Exceptions

Exception::Precondition is thrown if the container is not sorted according to retention time (in debug AND release mode)

◆ setChromatograms() [1/2]

void setChromatograms ( const std::vector< MSChromatogram > & chromatograms )

sets the chromatogram list

◆ setChromatograms() [2/2]

void setChromatograms ( std::vector< MSChromatogram > && chromatograms )

◆ setSpectra() [1/2]

void setSpectra ( const std::vector< MSSpectrum > & spectra )

sets the spectrum list

◆ setSpectra() [2/2]

void setSpectra ( std::vector< MSSpectrum > && spectra )

◆ setSqlRunID()

void setSqlRunID ( UInt64 id )

sets the run-ID which is used when storing an sqMass file

◆ size()

Size size ( ) const

inline

The number of spectra.

Referenced by PlotCanvas::addDataProcessing_(), IsotopeWaveletTransform< PeakType >::extendBox_(), MorphologicalFilter::filterExperiment(), SavitzkyGolayFilter::filterExperiment(), TOPPFLASHDeconv::main_(), NucleicAcidSearchEngine::main_(), IDMapper::mapPrecursorsToIdentifications(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraPrecursors(), PeakPickerIterative::pickExperiment(), NucleicAcidSearchEngine::preprocessSpectra_(), LinearResampler::rasterExperiment(), DTA2DFile::store(), DTA2DFile::storeTIC(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().

◆ sortChromatograms()

void sortChromatograms ( bool sort_rt = true )

Sorts the data points of the chromatograms by m/z.

Parameters

sort_rt if true, chromatograms are sorted by rt position as well

◆ sortSpectra()

void sortSpectra ( bool sort_mz = true )

Sorts the data points by retention time.

Parameters

sort_mz if true, spectra are sorted by m/z position as well

Referenced by SpectraMerger::average(), TOPPFLASHDeconv::main_(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectraBlockWise(), SpectraMerger::mergeSpectraPrecursors(), and NucleicAcidSearchEngine::preprocessSpectra_().

◆ swap()

void swap ( MSExperiment & from )

Swaps the content of this map with the content of from.

◆ updateRanges() [1/2]

void updateRanges ( )

overridevirtual

implement this function to reflect the underlying data of the derived class (e.g. an MSSpectrum) Usually, call clearRanges() internally and then populate the dimensions.

Implements RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity, RangeMobility >.

◆ updateRanges() [2/2]

void updateRanges ( Int ms_level )

Updates the m/z, intensity, retention time and MS level ranges of all spectra with a certain ms level.

Parameters

ms_level MS level to consider for m/z range , RT range and intensity range (All MS levels if negative)

Member Data Documentation

◆ chromatograms_

std::vector<MSChromatogram > chromatograms_

protected

chromatograms

◆ ms_levels_

std::vector<UInt> ms_levels_

protected

MS levels of the data.

◆ spectra_

std::vector<SpectrumType> spectra_

protected

spectra

◆ total_size_

UInt64 total_size_

protected

Number of all data points.

Classes

Public Types

Public Member Functions

Delegations of calls to the vector of MSSpectra

Easy Access interface

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ AreaIterator

◆ Base

◆ ChromatogramPeakT

◆ ChromatogramPeakType

◆ ChromatogramType

◆ const_iterator

◆ ConstAreaIterator

◆ ConstIterator

◆ CoordinateType

◆ IntensityType

◆ Iterator

◆ iterator

◆ PeakT

◆ PeakType

◆ RangeManagerContainerType

◆ RangeManagerType

◆ SpectrumType

◆ value_type

Constructor & Destructor Documentation

◆ MSExperiment() [1/3]

◆ MSExperiment() [2/3]

◆ MSExperiment() [3/3]

◆ ~MSExperiment()

Member Function Documentation

◆ addChromatogram() [1/2]

◆ addChromatogram() [2/2]

◆ addSpectrum() [1/2]

◆ addSpectrum() [2/2]

◆ areaBegin() [1/2]

◆ areaBegin() [2/2]

◆ areaBeginConst() [1/2]

◆ areaBeginConst() [2/2]

◆ areaEnd()

◆ areaEndConst()

◆ begin() [1/2]

◆ begin() [2/2]

◆ calculateTIC()

◆ clear()

◆ clearMetaDataArrays()

◆ containsScanOfLevel()

◆ createSpec_() [1/2]

◆ createSpec_() [2/2]

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ get2DData()

◆ get2DPeakData() [1/3]

◆ get2DPeakData() [2/3]

◆ get2DPeakData() [3/3]

◆ get2DPeakDataIon()

◆ getChromatogram()

◆ getChromatograms() [1/2]

◆ getChromatograms() [2/2]

◆ getExperimentalSettings() [1/2]

◆ getExperimentalSettings() [2/2]

◆ getMaxMZ()

◆ getMaxRT()

◆ getMinMZ()

◆ getMinRT()

◆ getMSLevels()

◆ getNrChromatograms()

◆ getNrSpectra()

◆ getPrecursorSpectrum() [1/2]

◆ getPrecursorSpectrum() [2/2]

◆ getPrimaryMSRunPath()

◆ getSize()

◆ getSpectra() [1/2]

◆ getSpectra() [2/2]

◆ getSpectrum()

◆ getSqlRunID()

◆ hasPeptideIdentifications()

◆ hasZeroIntensities()