The representation of a 1D spectrum. More...

#include <OpenMS/KERNEL/MSSpectrum.h>

Inheritance diagram for MSSpectrum:

Collaboration diagram for MSSpectrum:

Classes
struct	Chunk
	Used to remember what subsets in a spectrum are sorted already to allow faster sorting of the spectrum. More...

struct	Chunks

struct	IMLess
	Comparator for the ion mobility. More...

struct	RTLess
	Comparator for the retention time. More...

Public Types
Base type definitions
typedef OpenMS::Peak1D	PeakType
	Peak type. More...

typedef PeakType::CoordinateType	CoordinateType
	Coordinate (m/z) type. More...

typedef std::vector< PeakType >	ContainerType
	Spectrum base type. More...

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

typedef RangeManager< RangeMZ, RangeIntensity, RangeMobility >	RangeManagerType

typedef OpenMS::DataArrays::FloatDataArray	FloatDataArray
	Float data array vector type. More...

typedef std::vector< FloatDataArray >	FloatDataArrays

typedef OpenMS::DataArrays::StringDataArray	StringDataArray
	String data array vector type. More...

typedef std::vector< StringDataArray >	StringDataArrays

typedef OpenMS::DataArrays::IntegerDataArray	IntegerDataArray
	Integer data array vector type. More...

typedef std::vector< IntegerDataArray >	IntegerDataArrays

Peak container iterator type definitions
typedef ContainerType::iterator	Iterator
	Mutable iterator. More...

typedef ContainerType::const_iterator	ConstIterator
	Non-mutable iterator. More...

typedef ContainerType::reverse_iterator	ReverseIterator
	Mutable reverse iterator. More...

typedef ContainerType::const_reverse_iterator	ConstReverseIterator
	Non-mutable reverse iterator. More...

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

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

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

Public Member Functions
Export methods from std::vector<Peak1D>
	MSSpectrum ()
	Constructor. More...

	MSSpectrum (const std::initializer_list< Peak1D > &init)
	Constructor from a list of Peak1D, e.g. MSSpectrum spec{ {mz1, int1}, {mz2, int2}, ... };. More...

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

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

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

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

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

MSSpectrum &	operator= (const SpectrumSettings &source)
	Assignment operator. More...

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

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

void	updateRanges () override

Accessors for meta information
Returns the absolute retention time (in seconds)
double	getRT () const

void	setRT (double rt)
	Sets the absolute retention time (in seconds) More...

double	getDriftTime () const
	Returns the ion mobility drift time (IMTypes::DRIFTTIME_NOT_SET means it is not set) More...

void	setDriftTime (double dt)
	Sets the ion mobility drift time. More...

DriftTimeUnit	getDriftTimeUnit () const
	Returns the ion mobility drift time unit. More...

String	getDriftTimeUnitAsString () const
	returns the ion mobility drift time unit as string More...

void	setDriftTimeUnit (DriftTimeUnit dt)
	Sets the ion mobility drift time unit. More...

UInt	getMSLevel () const
	Returns the MS level. More...

void	setMSLevel (UInt ms_level)
	Sets the MS level. More...

const String &	getName () const
	Returns the name. More...

void	setName (const String &name)
	Sets the name. More...

Peak data array methods
These methods are used to annotate each peak in a spectrum with meta information. It is an intermediate way between storing the information in the peak's MetaInfoInterface and deriving a new peak type with members for this information. These statements should help you chose which approach to use Access to meta info arrays is slower than to a member variable Access to meta info arrays is faster than to a MetaInfoInterface Meta info arrays are stored when using mzML format for storing
const FloatDataArrays &	getFloatDataArrays () const
	Returns a const reference to the float meta data arrays. More...

FloatDataArrays &	getFloatDataArrays ()
	Returns a mutable reference to the float meta data arrays. More...

void	setFloatDataArrays (const FloatDataArrays &fda)
	Sets the float meta data arrays. More...

const StringDataArrays &	getStringDataArrays () const
	Returns a const reference to the string meta data arrays. More...

StringDataArrays &	getStringDataArrays ()
	Returns a mutable reference to the string meta data arrays. More...

void	setStringDataArrays (const StringDataArrays &sda)
	Sets the string meta data arrays. More...

const IntegerDataArrays &	getIntegerDataArrays () const
	Returns a const reference to the integer meta data arrays. More...

IntegerDataArrays &	getIntegerDataArrays ()
	Returns a mutable reference to the integer meta data arrays. More...

void	setIntegerDataArrays (const IntegerDataArrays &ida)
	Sets the integer meta data arrays. More...

Sorting peaks
void	sortByIntensity (bool reverse=false)
	Lexicographically sorts the peaks by their intensity. More...

void	sortByPosition ()
	Lexicographically sorts the peaks by their position. More...

void	sortByIonMobility ()
	Sorts the m/z peaks by their ion mobility value (and the accociated IM data arrays accordingly). More...

void	sortByPositionPresorted (const std::vector< Chunk > &chunks)
	Sort the spectrum, but uses the fact, that certain chunks are presorted. More...

bool	isSorted () const
	Checks if all peaks are sorted with respect to ascending m/z. More...

bool	isSortedByIM () const

template<class Predicate >
bool	isSorted (const Predicate &lambda) const

template<class Predicate >
void	sort (const Predicate &lambda)

Public Member Functions inherited from RangeManagerContainer< 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 SpectrumSettings
	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...

Searching a peak or peak range
double	retention_time_ = -1
	Retention time. More...

double	drift_time_ = -1
	Drift time. More...

DriftTimeUnit	drift_time_unit_ = DriftTimeUnit::NONE
	Drift time unit. More...

UInt	ms_level_ = 1
	MS level. More...

String	name_
	Name. More...

FloatDataArrays	float_data_arrays_
	Float data arrays. More...

StringDataArrays	string_data_arrays_
	String data arrays. More...

IntegerDataArrays	integer_data_arrays_
	Integer data arrays. More...

Size	findNearest (CoordinateType mz) const
	Binary search for the peak nearest to a specific m/z. More...

Int	findNearest (CoordinateType mz, CoordinateType tolerance) const
	Binary search for the peak nearest to a specific m/z given a +/- tolerance windows in Th. More...

Int	findNearest (CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const
	Search for the peak nearest to a specific m/z given two +/- tolerance windows in Th. More...

Int	findHighestInWindow (CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const
	Search for the peak with highest intensity among the peaks near to a specific m/z given two +/- tolerance windows in Th. More...

Iterator	MZBegin (CoordinateType mz)
	Binary search for peak range begin. More...

Iterator	MZBegin (Iterator begin, CoordinateType mz, Iterator end)
	Binary search for peak range begin. More...

Iterator	MZEnd (CoordinateType mz)
	Binary search for peak range end (returns the past-the-end iterator) More...

Iterator	MZEnd (Iterator begin, CoordinateType mz, Iterator end)
	Binary search for peak range end (returns the past-the-end iterator) More...

ConstIterator	MZBegin (CoordinateType mz) const
	Binary search for peak range begin. More...

ConstIterator	MZBegin (ConstIterator begin, CoordinateType mz, ConstIterator end) const
	Binary search for peak range begin. More...

ConstIterator	MZEnd (CoordinateType mz) const
	Binary search for peak range end (returns the past-the-end iterator) More...

ConstIterator	MZEnd (ConstIterator begin, CoordinateType mz, ConstIterator end) const
	Binary search for peak range end (returns the past-the-end iterator) More...

Iterator	PosBegin (CoordinateType mz)
	Binary search for peak range begin. More...

Iterator	PosBegin (Iterator begin, CoordinateType mz, Iterator end)
	Binary search for peak range begin. More...

ConstIterator	PosBegin (CoordinateType mz) const
	Binary search for peak range begin. More...

ConstIterator	PosBegin (ConstIterator begin, CoordinateType mz, ConstIterator end) const
	Binary search for peak range begin. More...

Iterator	PosEnd (CoordinateType mz)
	Binary search for peak range end (returns the past-the-end iterator) More...

Iterator	PosEnd (Iterator begin, CoordinateType mz, Iterator end)
	Binary search for peak range end (returns the past-the-end iterator) More...

ConstIterator	PosEnd (CoordinateType mz) const
	Binary search for peak range end (returns the past-the-end iterator) More...

ConstIterator	PosEnd (ConstIterator begin, CoordinateType mz, ConstIterator end) const
	Binary search for peak range end (returns the past-the-end iterator) More...

bool	containsIMData () const

std::pair< Size, DriftTimeUnit >	getIMData () const
	Get the Ion mobility data array's `index` and its associated `unit`. More...

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

MSSpectrum &	select (const std::vector< Size > &indices)

SpectrumSettings::SpectrumType	getType (const bool query_data) const
	Determine if spectrum is profile or centroided using up to three layers of information. More...

ConstIterator	getBasePeak () const

Iterator	getBasePeak ()

PeakType::IntensityType	calculateTIC () const
	compute the total ion count (sum of all peak intensities) More...

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

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

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

Detailed Description

The representation of a 1D spectrum.

It contains peak data and metadata about specific instrument settings, acquisition settings, description of the meta values used in the peaks and precursor info (SpectrumSettings).

Several MSSpectrum instances are contained in a peak map (MSExperiment), which is essentially a vector of spectra with additional information about the experiment.

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

Note: For range operations, see RangeUtils module!

Member Typedef Documentation

◆ ConstIterator

typedef ContainerType::const_iterator ConstIterator

Non-mutable iterator.

◆ ConstReverseIterator

typedef ContainerType::const_reverse_iterator ConstReverseIterator

Non-mutable reverse iterator.

◆ ContainerType

typedef std::vector<PeakType> ContainerType

Spectrum base type.

◆ CoordinateType

typedef PeakType::CoordinateType CoordinateType

Coordinate (m/z) type.

◆ FloatDataArray

typedef OpenMS::DataArrays::FloatDataArray FloatDataArray

Float data array vector type.

◆ FloatDataArrays

typedef std::vector<FloatDataArray> FloatDataArrays

◆ IntegerDataArray

typedef OpenMS::DataArrays::IntegerDataArray IntegerDataArray

Integer data array vector type.

◆ IntegerDataArrays

typedef std::vector<IntegerDataArray> IntegerDataArrays

◆ Iterator

typedef ContainerType::iterator Iterator

Mutable iterator.

◆ PeakType

typedef OpenMS::Peak1D PeakType

Peak type.

◆ RangeManagerContainerType

typedef RangeManagerContainer<RangeMZ, RangeIntensity, RangeMobility> RangeManagerContainerType

RangeManager.

◆ RangeManagerType

typedef RangeManager<RangeMZ, RangeIntensity, RangeMobility> RangeManagerType

◆ ReverseIterator

typedef ContainerType::reverse_iterator ReverseIterator

Mutable reverse iterator.

◆ StringDataArray

typedef OpenMS::DataArrays::StringDataArray StringDataArray

String data array vector type.

◆ StringDataArrays

typedef std::vector<StringDataArray> StringDataArrays

Constructor & Destructor Documentation

◆ MSSpectrum() [1/4]

MSSpectrum ( )

Constructor.

◆ MSSpectrum() [2/4]

MSSpectrum ( const std::initializer_list< Peak1D > & init )

Constructor from a list of Peak1D, e.g. MSSpectrum spec{ {mz1, int1}, {mz2, int2}, ... };.

◆ MSSpectrum() [3/4]

MSSpectrum ( const MSSpectrum & source )

Copy constructor.

◆ MSSpectrum() [4/4]

MSSpectrum ( MSSpectrum && )

default

Move constructor.

◆ ~MSSpectrum()

~MSSpectrum ( )

default

Destructor.

Member Function Documentation

◆ calculateTIC()

PeakType::IntensityType calculateTIC ( ) const

compute the total ion count (sum of all peak intensities)

◆ clear()

void clear ( bool clear_meta_data )

Clears all data and meta data.

Will delete (clear) all peaks contained in the spectrum as well as any associated data arrays (FloatDataArrays, IntegerDataArrays, StringDataArrays) by default. If clear_meta_data is true, then also all meta data (such as RT, drift time, ms level etc) will be deleted.

Parameters

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

Referenced by SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), MzMLSwathFileConsumer::consumeSwathSpectrum_(), ChromatogramTools::convertSpectraToChromatograms(), NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_(), WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), MS2File::load(), DTA2DFile::load(), XMassFile::load(), DTAFile::load(), and SpectraMerger::mergeSpectra_().

◆ containsIMData()

bool containsIMData ( ) const

do the names of internal float metadata arrays contain any hint of ion mobility data, i.e. they are a child of 'MS:1002893 ! ion mobility array'? (for spectra which represent an IM-frame)

Referenced by MSExperiment::get2DPeakData(), and MSExperiment::get2DPeakDataIon().

◆ findHighestInWindow()

Int findHighestInWindow	(	CoordinateType	mz,
		CoordinateType	tolerance_left,
		CoordinateType	tolerance_right
	)		const

Search for the peak with highest intensity among the peaks near to a specific m/z given two +/- tolerance windows in Th.

Parameters

mz	The searched for mass-to-charge ratio searched
tolerance_left	The non-negative tolerance applied left of mz
tolerance_right	The non-negative tolerance applied right of mz

Returns: Returns the index of the peak or -1 if no peak present in tolerance window or if spectrum is empty

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.; Peaks exactly on borders are considered in tolerance window.

◆ findNearest() [1/3]

Size findNearest ( CoordinateType mz ) const

Binary search for the peak nearest to a specific m/z.

Parameters

mz	The searched for mass-to-charge ratio searched

Returns: Returns the index of the peak.

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

Exceptions

Exception::Precondition is thrown if the spectrum is empty (not only in debug mode)

Referenced by NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_().

◆ findNearest() [2/3]

Int findNearest	(	CoordinateType	mz,
		CoordinateType	tolerance
	)		const

Binary search for the peak nearest to a specific m/z given a +/- tolerance windows in Th.

Parameters

mz	The searched for mass-to-charge ratio searched
tolerance	The non-negative tolerance applied to both sides of mz

Returns: Returns the index of the peak or -1 if no peak present in tolerance window or if spectrum is empty

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.; Peaks exactly on borders are considered in tolerance window.

◆ findNearest() [3/3]

Int findNearest	(	CoordinateType	mz,
		CoordinateType	tolerance_left,
		CoordinateType	tolerance_right
	)		const

Search for the peak nearest to a specific m/z given two +/- tolerance windows in Th.

Parameters

mz	The searched for mass-to-charge ratio searched
tolerance_left	The non-negative tolerance applied left of mz
tolerance_right	The non-negative tolerance applied right of mz

Returns: Returns the index of the peak or -1 if no peak present in tolerance window or if spectrum is empty

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.; Peaks exactly on borders are considered in tolerance window.; Search for the left border is done using a binary search followed by a linear scan

◆ getBasePeak() [1/2]

Iterator getBasePeak ( )

return the peak with the highest intensity. If the peak is not unique, the first peak in the container is returned. The function works correctly, even if the spectrum is unsorted.

◆ getBasePeak() [2/2]

ConstIterator getBasePeak ( ) const

return the peak with the highest intensity. If the peak is not unique, the first peak in the container is returned. The function works correctly, even if the spectrum is unsorted.

◆ getDriftTime()

double getDriftTime ( ) const

Returns the ion mobility drift time (IMTypes::DRIFTTIME_NOT_SET means it is not set)

Note: Drift times may be stored directly as an attribute of the spectrum (if they relate to the spectrum as a whole). In case of ion mobility spectra, the drift time of the spectrum will always be set here while the drift times attribute in the Precursor class may often be unpopulated.

Referenced by DimIM::map().

◆ getDriftTimeUnit()

DriftTimeUnit getDriftTimeUnit ( ) const

Returns the ion mobility drift time unit.

◆ getDriftTimeUnitAsString()

String getDriftTimeUnitAsString ( ) const

returns the ion mobility drift time unit as string

◆ getFloatDataArrays() [1/2]

FloatDataArrays& getFloatDataArrays ( )

inline

Returns a mutable reference to the float meta data arrays.

◆ getFloatDataArrays() [2/2]

const FloatDataArrays& getFloatDataArrays ( ) const

Returns a const reference to the float meta data arrays.

Referenced by MetaDataBrowser::add(), MSExperiment::ContainerAdd_< ContainerValueType, false >::addData_(), MSExperiment::get2DPeakData(), MSExperiment::get2DPeakDataIon(), DataFilters::passes(), and PeakPickerIterative::pick().

◆ getIMData()

std::pair<Size, DriftTimeUnit> getIMData ( ) const

Get the Ion mobility data array's index and its associated unit.

This only works for spectra which represent an IM-frame, i.e. they have a float metadata array which is a child of 'MS:1002893 ! ion mobility array'? Check this first by using containsIMData().

Exceptions

Exception::MissingInformation if IM data is not present

Referenced by MSExperiment::get2DPeakData(), and MSExperiment::get2DPeakDataIon().

◆ getIntegerDataArrays() [1/2]

IntegerDataArrays& getIntegerDataArrays ( )

Returns a mutable reference to the integer meta data arrays.

◆ getIntegerDataArrays() [2/2]

const IntegerDataArrays& getIntegerDataArrays ( ) const

Returns a const reference to the integer meta data arrays.

Referenced by MetaDataBrowser::add(), and DataFilters::passes().

◆ getMSLevel()

UInt getMSLevel ( ) const

Returns the MS level.

For survey scans this is 1, for MS/MS scans 2, ...

Referenced by FullSwathFileConsumer::consumeSpectrum(), InMSLevelRange< SpectrumType >::operator()(), IsInCollisionEnergyRange< SpectrumType >::operator()(), IsInIsolationWindowSizeRange< SpectrumType >::operator()(), and IsInIsolationWindow< SpectrumType >::operator()().

◆ getName()

const String& getName ( ) const

Returns the name.

◆ getRT()

double getRT ( ) const

Referenced by DTA2DFile::load(), NucleicAcidSearchEngine::main_(), DimRT::map(), IDMapper::mapPrecursorsToIdentifications(), SpectraMerger::mergeSpectra_(), InRTRange< SpectrumType >::operator()(), NucleicAcidSearchEngine::postProcessHits_(), and SpectrumLookup::readSpectra().

◆ getStringDataArrays() [1/2]

StringDataArrays& getStringDataArrays ( )

Returns a mutable reference to the string meta data arrays.

◆ getStringDataArrays() [2/2]

const StringDataArrays& getStringDataArrays ( ) const

Returns a const reference to the string meta data arrays.

Referenced by MetaDataBrowser::add().

◆ getType() [1/2]

SpectrumType getType

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

◆ getType() [2/2]

SpectrumSettings::SpectrumType getType ( const bool query_data ) const

Determine if spectrum is profile or centroided using up to three layers of information.

First, the SpectrumSettings are inquired and the type is returned unless it is unknown. Second, all data processing entries are searched for a centroiding step. If that is unsuccessful as well and query_data is true, the data is fed into PeakTypeEstimator().

Parameters

[query_data] If SpectrumSettings and DataProcessing information are not sufficient, should the data be queried? (potentially expensive)

Returns: The spectrum type (centroided, profile or unknown)

◆ isSorted() [1/2]

bool isSorted ( ) const

Checks if all peaks are sorted with respect to ascending m/z.

◆ isSorted() [2/2]

bool isSorted ( const Predicate & lambda ) const

inline

Checks if container is sorted by a certain user-defined property. You can pass any lambda function with [](Size index_1, Size index_2) --> bool which given two indices into MSSpectrum (either for peaks or data arrays) returns a weak-ordering. (you need to capture the MSSpectrum in the lambda and operate on it, based on the indices)

◆ isSortedByIM()

bool isSortedByIM ( ) const

Checks if m/z peaks are sorted by their associated ion mobility value. Requires a binary data array which is a child of 'MS:1002893 ! ion mobility array' (see getIMData())

Exceptions

Exception::MissingInformation if containsIMData() returns false

◆ MZBegin() [1/4]

ConstIterator MZBegin	(	ConstIterator	begin,
		CoordinateType	mz,
		ConstIterator	end
	)		const

Binary search for peak range begin.

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

◆ MZBegin() [2/4]

Iterator MZBegin ( CoordinateType mz )

Binary search for peak range begin.

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

◆ MZBegin() [3/4]

ConstIterator MZBegin ( CoordinateType mz ) const

Binary search for peak range begin.

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

◆ MZBegin() [4/4]

Iterator MZBegin	(	Iterator	begin,
		CoordinateType	mz,
		Iterator	end
	)

Binary search for peak range begin.

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

◆ MZEnd() [1/4]

ConstIterator MZEnd	(	ConstIterator	begin,
		CoordinateType	mz,
		ConstIterator	end
	)		const

Binary search for peak range end (returns the past-the-end iterator)

Note: Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

◆ MZEnd() [2/4]

Iterator MZEnd ( CoordinateType mz )

Binary search for peak range end (returns the past-the-end iterator)

Note: Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

◆ MZEnd() [3/4]

ConstIterator MZEnd ( CoordinateType mz ) const

Binary search for peak range end (returns the past-the-end iterator)

Note: Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

◆ MZEnd() [4/4]

Iterator MZEnd	(	Iterator	begin,
		CoordinateType	mz,
		Iterator	end
	)

Binary search for peak range end (returns the past-the-end iterator)

Note: Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

◆ operator!=()

bool operator!= ( const MSSpectrum & rhs ) const

inline

Equality operator.

References OpenMS::Internal::operator==().

◆ operator=() [1/3]

MSSpectrum& operator= ( const MSSpectrum & source )

Assignment operator.

◆ operator=() [2/3]

MSSpectrum& operator= ( const SpectrumSettings & source )

Assignment operator.

◆ operator=() [3/3]

MSSpectrum& operator= ( MSSpectrum && ) &

default

Move assignment operator.

◆ operator==()

bool operator== ( const MSSpectrum & rhs ) const

Equality operator.

◆ PosBegin() [1/4]

ConstIterator PosBegin	(	ConstIterator	begin,
		CoordinateType	mz,
		ConstIterator	end
	)		const

Binary search for peak range begin.

Alias for MZBegin()

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

◆ PosBegin() [2/4]

Iterator PosBegin ( CoordinateType mz )

Binary search for peak range begin.

Alias for MZBegin()

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

◆ PosBegin() [3/4]

ConstIterator PosBegin ( CoordinateType mz ) const

Binary search for peak range begin.

Alias for MZBegin()

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

◆ PosBegin() [4/4]

Iterator PosBegin	(	Iterator	begin,
		CoordinateType	mz,
		Iterator	end
	)

Binary search for peak range begin.

Alias for MZBegin()

Note: Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

◆ PosEnd() [1/4]

ConstIterator PosEnd	(	ConstIterator	begin,
		CoordinateType	mz,
		ConstIterator	end
	)		const

Binary search for peak range end (returns the past-the-end iterator)

Alias for MZEnd()

Note: Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

◆ PosEnd() [2/4]

Iterator PosEnd ( CoordinateType mz )

Binary search for peak range end (returns the past-the-end iterator)

Alias for MZEnd()

Note: Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

◆ PosEnd() [3/4]

ConstIterator PosEnd ( CoordinateType mz ) const

Binary search for peak range end (returns the past-the-end iterator)

Alias for MZEnd()

Note: Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

◆ PosEnd() [4/4]

Iterator PosEnd	(	Iterator	begin,
		CoordinateType	mz,
		Iterator	end
	)

Binary search for peak range end (returns the past-the-end iterator)

Alias for MZEnd()

Note: Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

◆ select()

MSSpectrum& select ( const std::vector< Size > & indices )

Referenced by WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), WindowMower::filterPeakSpectrumForTopNInSlidingWindow(), NLargest::filterSpectrum(), and ThresholdMower::filterSpectrum().

◆ setDriftTime()

void setDriftTime ( double dt )

Sets the ion mobility drift time.

◆ setDriftTimeUnit()

void setDriftTimeUnit ( DriftTimeUnit dt )

Sets the ion mobility drift time unit.

◆ setFloatDataArrays()

void setFloatDataArrays ( const FloatDataArrays & fda )

Sets the float meta data arrays.

◆ setIntegerDataArrays()

void setIntegerDataArrays ( const IntegerDataArrays & ida )

Sets the integer meta data arrays.

◆ setMSLevel()

void setMSLevel ( UInt ms_level )

Sets the MS level.

Referenced by MascotGenericFile::load(), MascotInfile::load(), MS2File::load(), XMassFile::load(), DTAFile::load(), SpectraMerger::mergeSpectra_(), and TOPPViewBase::showCurrentPeaksAsDIA().

◆ setName()

void setName ( const String & name )

Sets the name.

Referenced by XMassFile::load(), DTAFile::load(), and NucleicAcidSearchEngine::main_().

◆ setRT()

void setRT ( double rt )

Sets the absolute retention time (in seconds)

Referenced by MascotGenericFile::getNextSpectrum_(), MascotInfile::load(), DTA2DFile::load(), XMassFile::load(), NucleicAcidSearchEngine::main_(), and SpectraMerger::mergeSpectra_().

◆ setStringDataArrays()

void setStringDataArrays ( const StringDataArrays & sda )

Sets the string meta data arrays.

◆ sort()

void sort ( const Predicate & lambda )

inline

Sort by a user-defined property You can pass any lambda function with [](Size index_1, Size index_2) --> bool which given two indices into MSSpectrum (either for peaks or data arrays) returns a weak-ordering. (you need to capture the MSSpectrum in the lambda and operate on it, based on the indices)

◆ sortByIntensity()

void sortByIntensity ( bool reverse = false )

Lexicographically sorts the peaks by their intensity.

Sorts the peaks according to ascending intensity. Meta data arrays will be sorted accordingly.

Referenced by WindowMower::filterPeakSpectrumForTopNInSlidingWindow(), NLargest::filterSpectrum(), and RankScaler::filterSpectrum().

◆ sortByIonMobility()

void sortByIonMobility ( )

Sorts the m/z peaks by their ion mobility value (and the accociated IM data arrays accordingly).

Requires a binary data array which is a child of 'MS:1002893 ! ion mobility array' (see getIMData())

Exceptions

Exception::MissingInformation if containsIMData() returns false

◆ sortByPosition()

void sortByPosition ( )

Lexicographically sorts the peaks by their position.

The spectrum is sorted with respect to position. Meta data arrays will be sorted accordingly.

Referenced by NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_(), WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), WindowMower::filterPeakSpectrumForTopNInSlidingWindow(), SpectraMerger::mergeSpectra_(), PeakPickerIterative::pick(), and NucleicAcidSearchEngine::preprocessSpectra_().

◆ sortByPositionPresorted()

void sortByPositionPresorted ( const std::vector< Chunk > & chunks )

Sort the spectrum, but uses the fact, that certain chunks are presorted.

Parameters

chunks a Chunk is an object that contains the start and end of a sublist of peaks in the spectrum, that is or isn't sorted yet (is_sorted member)

◆ updateRanges()

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< RangeMZ, RangeIntensity, RangeMobility >.

Member Data Documentation

◆ drift_time_

double drift_time_ = -1

protected

Drift time.

◆ drift_time_unit_

DriftTimeUnit drift_time_unit_ = DriftTimeUnit::NONE

protected

Drift time unit.

◆ float_data_arrays_

FloatDataArrays float_data_arrays_

protected

Float data arrays.

◆ integer_data_arrays_

IntegerDataArrays integer_data_arrays_

protected

Integer data arrays.

◆ ms_level_

UInt ms_level_ = 1

protected

MS level.

◆ name_

String name_

protected

Name.

◆ retention_time_

double retention_time_ = -1

protected

Retention time.

◆ string_data_arrays_

StringDataArrays string_data_arrays_

protected

String data arrays.

Classes

Public Types

Public Member Functions

Searching a peak or peak range

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConstIterator

◆ ConstReverseIterator

◆ ContainerType

◆ CoordinateType

◆ FloatDataArray

◆ FloatDataArrays

◆ IntegerDataArray

◆ IntegerDataArrays

◆ Iterator

◆ PeakType

◆ RangeManagerContainerType

◆ RangeManagerType

◆ ReverseIterator

◆ StringDataArray

◆ StringDataArrays

Constructor & Destructor Documentation

◆ MSSpectrum() [1/4]

◆ MSSpectrum() [2/4]

◆ MSSpectrum() [3/4]

◆ MSSpectrum() [4/4]

◆ ~MSSpectrum()

Member Function Documentation

◆ calculateTIC()

◆ clear()

◆ containsIMData()

◆ findHighestInWindow()

◆ findNearest() [1/3]

◆ findNearest() [2/3]

◆ findNearest() [3/3]

◆ getBasePeak() [1/2]

◆ getBasePeak() [2/2]

◆ getDriftTime()

◆ getDriftTimeUnit()

◆ getDriftTimeUnitAsString()

◆ getFloatDataArrays() [1/2]

◆ getFloatDataArrays() [2/2]

◆ getIMData()

◆ getIntegerDataArrays() [1/2]

◆ getIntegerDataArrays() [2/2]

◆ getMSLevel()

◆ getName()

◆ getRT()

◆ getStringDataArrays() [1/2]

◆ getStringDataArrays() [2/2]

◆ getType() [1/2]

◆ getType() [2/2]

◆ isSorted() [1/2]

◆ isSorted() [2/2]

◆ isSortedByIM()

◆ MZBegin() [1/4]

◆ MZBegin() [2/4]

◆ MZBegin() [3/4]

◆ MZBegin() [4/4]

◆ MZEnd() [1/4]

◆ MZEnd() [2/4]

◆ MZEnd() [3/4]

◆ MZEnd() [4/4]

◆ operator!=()

◆ operator=() [1/3]

◆ operator=() [2/3]

◆ operator=() [3/3]

◆ operator==()

◆ PosBegin() [1/4]

◆ PosBegin() [2/4]

◆ PosBegin() [3/4]

◆ PosBegin() [4/4]

◆ PosEnd() [1/4]

◆ PosEnd() [2/4]

◆ PosEnd() [3/4]

◆ PosEnd() [4/4]

◆ select()

◆ setDriftTime()

◆ setDriftTimeUnit()