MSSpectrum Class Reference

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	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 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 RangeManager< 1 >
enum
	Dimension of the position range. More...
typedef DRange< D >	PositionRangeType
	Position range type. More...
typedef DPosition< D >	PositionType
	Position Type. More...
typedef DRange< 1 >	IntensityRangeType
	Intensity range type. More...
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 MSSpectrum &source)
	Copy constructor. More...
	MSSpectrum (MSSpectrum &&)=default
	Move constructor. More...
	~MSSpectrum () override
	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
	Updates minimum and maximum position/intensity. More...
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 (MSSpectrum::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	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...
template<class Predicate >
bool	isSorted (const Predicate &lambda) const
template<class Predicate >
void	sort (const Predicate &lambda)
Public Member Functions inherited from RangeManager< 1 >
	RangeManager ()
	Default constructor. More...
	RangeManager (const RangeManager &rhs)
	Copy constructor. More...
	RangeManager (RangeManager &&) noexcept=default
	Move constructor. More...
virtual	~RangeManager ()
	Destructor. More...
RangeManager &	operator= (const RangeManager &rhs)
	Assignment operator. More...
bool	operator== (const RangeManager &rhs) const
	Equality operator. More...
bool	operator!= (const RangeManager &rhs) const
	Equality operator. More...
const PositionType &	getMin () const
	Returns the minimum position. More...
const PositionType &	getMax () const
	Returns the maximum position. More...
double	getMinInt () const
	Returns the minimum intensity. More...
double	getMaxInt () const
	Returns the maximum intensity. More...
void	clearRanges ()
	Resets the ranges. 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...
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 DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
const DataValue &	getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to an index, or a default value (default: 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_
	Retention time. More...
double	drift_time_
	Drift time. More...
DriftTimeUnit	drift_time_unit_
	Drift time unit. More...
UInt	ms_level_
	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< 1 >
void	updateRanges_ (const PeakIteratorType &begin, const PeakIteratorType &end)
	Updates the range using data points in the iterator range. More...
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...
Protected Attributes inherited from RangeManager< 1 >
IntensityRangeType	int_range_
	Intensity range (1-dimensional) More...
PositionRangeType	pos_range_
	Position range (D-dimensional) 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.

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() [1/3]

MSSpectrum

(

)

Constructor.

MSSpectrum() [2/3]

MSSpectrum

(

const MSSpectrum &

source

)

Copy constructor.

MSSpectrum() [3/3]

MSSpectrum ( MSSpectrum &&  )

default

Move constructor.

~MSSpectrum()

~MSSpectrum ( )

inlineoverride

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.

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(), SpectraMerger::mergeSpectra_(), TwoDOptimization::optimizeRegionsScanwise_(), and PeakPickerIterative::pick().

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)

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	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() [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 (MSSpectrum::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.

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_(), TwoDOptimization::optimizeRegions_(), TwoDOptimization::optimizeRegionsScanwise_(), 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'?

Exceptions

Exception::MissingInformation

if IM data is not present

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(), ParentPeakMower::filterSpectrum(), InMSLevelRange< SpectrumType >::operator()(), IsInCollisionEnergyRange< SpectrumType >::operator()(), IsInIsolationWindowSizeRange< SpectrumType >::operator()(), IsInIsolationWindow< SpectrumType >::operator()(), and PeakPickerIterative::pick().

getName()

const String& getName

(

)

const

Returns the name.

Referenced by PeakPickerIterative::pick().

getRT()

double getRT

(

)

const

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), GaussFilter::filter(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getRT(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), DTA2DFile::load(), IDMapper::mapPrecursorsToIdentifications(), SpectraMerger::mergeSpectra_(), InRTRange< SpectrumType >::operator()(), PeakPickerIterative::pick(), 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)

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.

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

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.

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::MZEnd().

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_(), PeakPickerIterative::pick(), and TOPPViewBase::showCurrentPeaksAsDIA().

setName()

void setName

(

const String &

name

)

Sets the name.

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

setRT()

void setRT

(

double

rt

)

Sets the absolute retention time (in seconds)

Referenced by MascotGenericFile::getNextSpectrum_(), TwoDOptimization::getRegionEndpoints_(), MascotInfile::load(), DTA2DFile::load(), XMassFile::load(), SpectraMerger::mergeSpectra_(), TwoDOptimization::optimize(), and PeakPickerIterative::pick().

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 Scaler::filterSpectrum().

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 ComplementFilter::apply(), IsotopeMarker::apply(), NeutralLossMarker::apply(), ComplementMarker::apply(), NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_(), WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), WindowMower::filterPeakSpectrumForTopNInSlidingWindow(), BernNorm::filterSpectrum(), 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

Updates minimum and maximum position/intensity.

This method is usually implemented by calling clearRanges() and updateRanges_().

Implements RangeManager< 1 >.

Member Data Documentation

drift_time_

double drift_time_

protected

Drift time.

drift_time_unit_

DriftTimeUnit drift_time_unit_

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_

protected

MS level.

name_

String name_

protected

Name.

retention_time_

double retention_time_

protected

Retention time.

string_data_arrays_

StringDataArrays string_data_arrays_

protected

String data arrays.