Representation of a mass spectrometry experiment. More...

#include <OpenMS/KERNEL/MSExperiment.h>

Inheritance diagram for MSExperiment< PeakT, ChromatogramPeakT >:

Public Types
Base type definitions

typedef PeakT	PeakType
	Peak type.
typedef ChromatogramPeakT	ChromatogramPeakType
	Chromatogram peak type.
typedef DRange< 2 >	AreaType
	Area type.
typedef PeakType::CoordinateType	CoordinateType
	Coordinate type of peak positions.
typedef PeakType::IntensityType	IntensityType
	Intenstiy type of peaks.
typedef RangeManager< 2 >	RangeManagerType
	RangeManager type.
typedef MSSpectrum< PeakType >	SpectrumType
	Spectrum Type.
typedef MSChromatogram < ChromatogramPeakType >	ChromatogramType
	Chromatogram type.
typedef std::vector< SpectrumType >	Base
	STL base class type.
Iterator type definitions

typedef std::vector < SpectrumType >::iterator	Iterator
	Mutable iterator.
typedef std::vector < SpectrumType > ::const_iterator	ConstIterator
	Non-mutable iterator.
typedef Internal::AreaIterator < PeakT, PeakT &, PeakT *, Iterator, typename SpectrumType::Iterator >	AreaIterator
	Mutable area iterator type (for traversal of a rectangular subset of the peaks).
typedef Internal::AreaIterator < const PeakT, const PeakT &, const PeakT *, ConstIterator, typename SpectrumType::ConstIterator >	ConstAreaIterator
	Immutable area iterator type (for traversal of a rectangular subset of the peaks).
Public Member Functions
	MSExperiment ()
	Constructor.
	MSExperiment (const MSExperiment &source)
	Copy constructor.
MSExperiment &	operator= (const MSExperiment &source)
	Assignment operator.
MSExperiment &	operator= (const ExperimentalSettings &source)
	Assignment operator.
bool	operator== (const MSExperiment &rhs) const
	Equality operator.
bool	operator!= (const MSExperiment &rhs) const
	Equality operator.
void	reset ()
	Resets all internal values.
bool	clearMetaDataArrays ()
	Clears the meta data arrays of all contained spectra (float, integer and string arrays).
const ExperimentalSettings &	getExperimentalSettings () const
	returns the meta information of this experiment (const access)
ExperimentalSettings &	getExperimentalSettings ()
	returns the meta information of this experiment (mutable access)
ConstIterator	getPrecursorSpectrum (ConstIterator iterator) const
	Returns the precursor spectrum of the scan pointed to by `iterator`.
void	swap (MSExperiment &from)
	Swaps the content of this map with the content of `from`.
void	setChromatograms (const std::vector< MSChromatogram< ChromatogramPeakType > > &chromatograms)
	sets the chromatogram list
void	addChromatogram (const MSChromatogram< ChromatogramPeakType > &chromatogram)
	adds a chromatogram to the list
const std::vector < MSChromatogram < ChromatogramPeakType > > &	getChromatograms () const
	returns the chromatogram list
const MSChromatogram < ChromatogramPeakType >	getTIC () const
	returns the total ion chromatogram (TIC)
void	clear (bool clear_meta_data)
	Clears all data and meta data.
Conversion to/from 2D data

template<class Container >
void	get2DData (Container &cont) const
	Reads out a 2D Spectrum.
template<class Container >
void	set2DData (const Container &cont)
	Assignment of a 2D spectrum to MSExperiment.
Iterating ranges and areas

AreaIterator	areaBegin (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz)
	Returns an area iterator for `area`.
AreaIterator	areaEnd ()
	Returns an invalid area iterator marking the end of an area.
ConstAreaIterator	areaBeginConst (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const
	Returns a non-mutable area iterator for `area`.
ConstAreaIterator	areaEndConst () const
	Returns an non-mutable invalid area iterator marking the end of an area.
ConstIterator	RTBegin (CoordinateType rt) const
	Fast search for spectrum range begin.
ConstIterator	RTEnd (CoordinateType rt) const
	Fast search for spectrum range end (returns the past-the-end iterator).
Iterator	RTBegin (CoordinateType rt)
	Fast search for spectrum range begin.
Iterator	RTEnd (CoordinateType rt)
	Fast search for spectrum range end (returns the past-the-end iterator).
Range methods
Note: The range values (min, max, etc.) are not updated automatically. Call updateRanges() to update the values!
virtual void	updateRanges ()
void	updateRanges (Int ms_level)
	Updates the m/z, intensity, retention time and MS level ranges of all spectra with a certain ms level.
CoordinateType	getMinMZ () const
	returns the minimal m/z value
CoordinateType	getMaxMZ () const
	returns the maximal m/z value
CoordinateType	getMinRT () const
	returns the minimal retention time value
CoordinateType	getMaxRT () const
	returns the maximal retention time value
const AreaType &	getDataRange () const
	Returns RT and m/z range the data lies in.
UInt64	getSize () const
	returns the total number of peaks
const std::vector< UInt > &	getMSLevels () const
	returns an array of MS levels
Sorting spectra and peaks

void	sortSpectra (bool sort_mz=true)
	Sorts the data points by retention time.
void	sortChromatograms (bool sort_rt=true)
	Sorts the data points of the chromatograms by m/z.
bool	isSorted (bool check_mz=true) const
	Checks if all spectra are sorted with respect to ascending RT.
Protected Member Functions
virtual void	clearChildIds_ ()
	Clears the persistence id of all sub-objects.
Protected Attributes
std::vector< UInt >	ms_levels_
	MS levels of the data.
UInt64	total_size_
	Number of all data points.
std::vector< MSChromatogram < ChromatogramPeakType > >	chromatograms_
	chromatograms

Detailed Description

template<typename PeakT = Peak1D, typename ChromatogramPeakT = ChromatogramPeak>
class OpenMS::MSExperiment< PeakT, ChromatogramPeakT >

Representation of a mass spectrometry experiment.

Contains the data and metadata of an experiment performed with an MS (or HPLC and MS).

Be carefull when changing the order of contained MSSpectrum instances, if tandem-MS data is stored in this class. The only way to find a precursor spectrum of MSSpectrum x is to search for the first spectrum before x that has a lower MS-level!

Note:: For range operations, see RangeUtils module!

Member Typedef Documentation

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

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

typedef DRange<2> AreaType

Area type.

typedef std::vector<SpectrumType> Base

STL base class type.

typedef ChromatogramPeakT ChromatogramPeakType

Chromatogram peak type.

typedef MSChromatogram<ChromatogramPeakType> ChromatogramType

Chromatogram type.

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

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

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

Non-mutable iterator.

typedef PeakType::CoordinateType CoordinateType

Coordinate type of peak positions.

typedef PeakType::IntensityType IntensityType

Intenstiy type of peaks.

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

Mutable iterator.

typedef PeakT PeakType

Peak type.

typedef RangeManager<2> RangeManagerType

RangeManager type.

typedef MSSpectrum<PeakType> SpectrumType

Spectrum Type.

Constructor & Destructor Documentation

MSExperiment ( ) [inline]

Constructor.

MSExperiment ( const MSExperiment< PeakT, ChromatogramPeakT > & source ) [inline]

Copy constructor.

Member Function Documentation

void addChromatogram ( const MSChromatogram< ChromatogramPeakType > & chromatogram ) [inline]

adds a chromatogram to the list

AreaIterator areaBegin	(	CoordinateType	min_rt,
		CoordinateType	max_rt,
		CoordinateType	min_mz,
		CoordinateType	max_mz
	)			`[inline]`

Returns an area iterator for area.

ConstAreaIterator areaBeginConst	(	CoordinateType	min_rt,
		CoordinateType	max_rt,
		CoordinateType	min_mz,
		CoordinateType	max_mz
	)			const `[inline]`

Returns a non-mutable area iterator for area.

Referenced by TOPPRNPxlXICFilter::filterByFoldChange(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

AreaIterator areaEnd ( ) [inline]

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

ConstAreaIterator areaEndConst ( ) const [inline]

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

Referenced by TOPPRNPxlXICFilter::filterByFoldChange(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

void clear ( bool clear_meta_data ) [inline]

Clears all data and meta data.

Parameters:

clear_meta_data

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

Referenced by MSExperiment< SimPointType >::clear(), IDFilter::filterIdentificationsByBestNHits(), IDFilter::filterIdentificationsByProteins(), IDFilter::filterIdentificationsByScores(), IDFilter::filterIdentificationsByThresholds(), TOPPRNPxlXICFilter::main_(), PeakPickerHiRes::pickExperiment(), MSExperiment< SimPointType >::reset(), and CachedmzML::writeMetadata().

virtual void clearChildIds_ ( ) [inline, protected, virtual]

Clears the persistence id of all sub-objects.

Implements PersistentObject.

bool clearMetaDataArrays ( ) [inline]

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.

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()

Referenced by ConsensusMap::convert().

const std::vector<MSChromatogram<ChromatogramPeakType> >& getChromatograms ( ) const [inline]

returns the chromatogram list

Referenced by TOPPBase::addDataProcessing_(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FeatureFinder::run(), FileHandler::storeExperiment(), CachedmzML::writeMemdump(), and CachedmzML::writeMetadata().

const AreaType& getDataRange ( ) const [inline]

Returns RT and m/z range the data lies in.

RT is dimension 0, m/z is dimension 1

const ExperimentalSettings& getExperimentalSettings ( ) const [inline]

returns the meta information of this experiment (const access)

Referenced by XMassFile::importExperimentalSettings().

ExperimentalSettings& getExperimentalSettings ( ) [inline]

returns the meta information of this experiment (mutable access)

CoordinateType getMaxMZ ( ) const [inline]

returns the maximal m/z value

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

CoordinateType getMaxRT ( ) const [inline]

returns the maximal retention time value

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

CoordinateType getMinMZ ( ) const [inline]

returns the minimal m/z value

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

CoordinateType getMinRT ( ) const [inline]

returns the minimal retention time value

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

const std::vector<UInt>& getMSLevels ( ) const [inline]

returns an array of MS levels

Referenced by FeatureFinder::run().

ConstIterator getPrecursorSpectrum ( ConstIterator iterator ) const [inline]

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

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

UInt64 getSize ( ) const [inline]

returns the total number of peaks

Referenced by ConsensusMap::convert(), and FeatureFinder::run().

const MSChromatogram<ChromatogramPeakType> getTIC ( ) const [inline]

returns the total ion chromatogram (TIC)

bool isSorted ( bool check_mz = true ) const [inline]

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

Referenced by FeatureFinder::run().

bool operator!= ( const MSExperiment< PeakT, ChromatogramPeakT > & rhs ) const [inline]

Equality operator.

MSExperiment& operator= ( const ExperimentalSettings & source ) [inline]

Assignment operator.

MSExperiment& operator= ( const MSExperiment< PeakT, ChromatogramPeakT > & source ) [inline]

Assignment operator.

Referenced by MSExperiment< SimPointType >::clear(), MSExperiment< SimPointType >::operator=(), MSExperiment< SimPointType >::reset(), and MSExperiment< SimPointType >::swap().

bool operator== ( const MSExperiment< PeakT, ChromatogramPeakT > & rhs ) const [inline]

Equality operator.

Referenced by MSExperiment< SimPointType >::operator!=(), and MSExperiment< SimPointType >::operator==().

void reset ( ) [inline]

Resets all internal values.

Referenced by InspectOutfile::getExperiment(), and FileHandler::loadExperiment().

ConstIterator RTBegin ( CoordinateType rt ) const [inline]

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.

Referenced by MSExperiment< SimPointType >::areaBegin(), MSExperiment< SimPointType >::areaBeginConst(), InternalCalibration::calibrateMapGlobally(), OfflinePrecursorIonSelection::getMassRanges(), TwoDOptimization::getRegionEndpoints_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), and FeatureFinder::run().

Iterator RTBegin ( CoordinateType rt ) [inline]

Fast search for spectrum range begin.

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

ConstIterator RTEnd ( CoordinateType rt ) const [inline]

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.

Referenced by MSExperiment< SimPointType >::areaBegin(), MSExperiment< SimPointType >::areaBeginConst(), and OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap().

Iterator RTEnd ( CoordinateType rt ) [inline]

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.

void set2DData ( const Container & cont ) [inline]

Assignment of a 2D spectrum to MSExperiment.

Container can be a PeakArray or an STL container of peaks.

Exceptions:

Exception::Precondition

is thrown if the container is not sorted according to retention time (not only in debug mode)

void setChromatograms ( const std::vector< MSChromatogram< ChromatogramPeakType > > & chromatograms ) [inline]

sets the chromatogram list

Referenced by TOPPBase::addDataProcessing_(), CachedmzML::readMemdump(), and CachedmzML::writeMetadata().

void sortChromatograms ( bool sort_rt = true ) [inline]

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

Parameters:

sort_rt

if true, chromatograms are sorted by rt position as well

Referenced by FeatureFinder::run().

void sortSpectra ( bool sort_mz = true ) [inline]

Sorts the data points by retention time.

Parameters:

sort_mz

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

Referenced by FeatureFinder::run().

void swap ( MSExperiment< PeakT, ChromatogramPeakT > & from ) [inline]

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

Referenced by MSExperiment< SimPointType >::swap().

virtual void updateRanges ( ) [inline, virtual]

Referenced by ConsensusMap::convert(), and MSExperiment< SimPointType >::updateRanges().

void updateRanges ( Int ms_level ) [inline]

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

std::vector<MSChromatogram<ChromatogramPeakType> > chromatograms_ [protected]

chromatograms

Referenced by MSExperiment< SimPointType >::addChromatogram(), MSExperiment< SimPointType >::clear(), MSExperiment< SimPointType >::getChromatograms(), MSExperiment< SimPointType >::operator=(), MSExperiment< SimPointType >::operator==(), MSExperiment< SimPointType >::setChromatograms(), MSExperiment< SimPointType >::sortChromatograms(), MSExperiment< SimPointType >::swap(), and MSExperiment< SimPointType >::updateRanges().

std::vector<UInt> ms_levels_ [protected]

MS levels of the data.

Referenced by MSExperiment< SimPointType >::clear(), MSExperiment< SimPointType >::getMSLevels(), MSExperiment< SimPointType >::operator=(), MSExperiment< SimPointType >::swap(), and MSExperiment< SimPointType >::updateRanges().

UInt64 total_size_ [protected]

Number of all data points.

Referenced by MSExperiment< SimPointType >::clear(), MSExperiment< SimPointType >::getSize(), MSExperiment< SimPointType >::operator=(), MSExperiment< SimPointType >::swap(), and MSExperiment< SimPointType >::updateRanges().

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:55 using doxygen 1.7.1

MSExperiment< PeakT, ChromatogramPeakT > Class Template Reference [Kernel]

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<typename PeakT = Peak1D, typename ChromatogramPeakT = ChromatogramPeak> class OpenMS::MSExperiment< PeakT, ChromatogramPeakT >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

MSExperiment< PeakT, ChromatogramPeakT > Class Template Reference
[Kernel]

template<typename PeakT = Peak1D, typename ChromatogramPeakT = ChromatogramPeak>
class OpenMS::MSExperiment< PeakT, ChromatogramPeakT >