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MSExperiment< PeakT, ChromatogramPeakT > Class Template Reference

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

#include <OpenMS/KERNEL/MSExperiment.h>

Inheritance diagram for MSExperiment< PeakT, ChromatogramPeakT >:
RangeManager< 2 > ExperimentalSettings MetaInfoInterface DocumentIdentifier

Classes

struct  ContainerAdd_
 Helper class to add either general data points in set2DData or use mass traces from meta values. More...
 
struct  ContainerAdd_< ContainerIterator, false >
 
struct  ContainerAdd_< ContainerIterator, true >
 

Public Types

Base type definitions
typedef PeakT PeakType
 Peak type. More...
 
typedef ChromatogramPeakT ChromatogramPeakType
 Chromatogram peak type. More...
 
typedef DRange< 2 > AreaType
 Area type. More...
 
typedef PeakType::CoordinateType CoordinateType
 Coordinate type of peak positions. More...
 
typedef PeakType::IntensityType IntensityType
 Intensity type of peaks. More...
 
typedef RangeManager< 2 > RangeManagerType
 RangeManager type. More...
 
typedef MSSpectrum< PeakTypeSpectrumType
 Spectrum Type. More...
 
typedef MSChromatogram< ChromatogramPeakTypeChromatogramType
 Chromatogram type. More...
 
typedef std::vector< SpectrumTypeBase
 STL base class type. More...
 
Iterator type definitions
typedef std::vector< SpectrumType >::iterator Iterator
 Mutable iterator. More...
 
typedef std::vector< SpectrumType >::const_iterator ConstIterator
 Non-mutable iterator. More...
 
typedef Internal::AreaIterator< PeakT, PeakT &, PeakT *, Iterator, typename SpectrumType::IteratorAreaIterator
 Mutable area iterator type (for traversal of a rectangular subset of the peaks) More...
 
typedef Internal::AreaIterator< const PeakT, const PeakT &, const PeakT *, ConstIterator, typename SpectrumType::ConstIteratorConstAreaIterator
 Immutable area iterator type (for traversal of a rectangular subset of the peaks) More...
 
- Public Types inherited from RangeManager< 2 >
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 Member Functions

void reserveSpaceSpectra (Size s)
 
void reserveSpaceChromatograms (Size s)
 
 MSExperiment ()
 Constructor. More...
 
 MSExperiment (const MSExperiment &source)
 Copy constructor. More...
 
MSExperimentoperator= (const MSExperiment &source)
 Assignment operator. More...
 
MSExperimentoperator= (const ExperimentalSettings &source)
 Assignment operator. More...
 
bool operator== (const MSExperiment &rhs) const
 Equality operator. More...
 
bool operator!= (const MSExperiment &rhs) const
 Equality operator. More...
 
void reset ()
 Resets all internal values. More...
 
bool clearMetaDataArrays ()
 Clears the meta data arrays of all contained spectra (float, integer and string arrays) More...
 
const ExperimentalSettingsgetExperimentalSettings () const
 returns the meta information of this experiment (const access) More...
 
ExperimentalSettingsgetExperimentalSettings ()
 returns the meta information of this experiment (mutable access) More...
 
ConstIterator getPrecursorSpectrum (ConstIterator iterator) const
 Returns the precursor spectrum of the scan pointed to by iterator. More...
 
void swap (MSExperiment &from)
 Swaps the content of this map with the content of from. More...
 
void setSpectra (const std::vector< MSSpectrum< PeakT > > &spectra)
 sets the spectra list More...
 
void addSpectrum (const MSSpectrum< PeakT > &spectrum)
 adds a spectra to the list More...
 
const std::vector< MSSpectrum< PeakT > > & getSpectra () const
 returns the spectra list More...
 
std::vector< MSSpectrum< PeakT > > & getSpectra ()
 returns the spectra list More...
 
void setChromatograms (const std::vector< MSChromatogram< ChromatogramPeakType > > &chromatograms)
 sets the chromatogram list More...
 
void addChromatogram (const MSChromatogram< ChromatogramPeakType > &chromatogram)
 adds a chromatogram to the list More...
 
const std::vector< MSChromatogram< ChromatogramPeakType > > & getChromatograms () const
 returns the chromatogram list More...
 
const MSChromatogram< ChromatogramPeakTypegetTIC () const
 returns the total ion chromatogram (TIC) More...
 
void clear (bool clear_meta_data)
 Clears all data and meta data. More...
 
Conversion to/from 2D data
template<class Container >
void get2DData (Container &cont) const
 Reads out a 2D Spectrum. More...
 
template<class Container >
void set2DData (const Container &container)
 Assignment of a data container with RT and MZ to an MSExperiment. More...
 
template<bool add_mass_traces, class Container >
void set2DData (const Container &container)
 Assignment of a data container with RT and MZ to an MSExperiment. More...
 
Iterating ranges and areas
AreaIterator areaBegin (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz)
 Returns an area iterator for area. More...
 
AreaIterator areaEnd ()
 Returns an invalid area iterator marking the end of an area. More...
 
ConstAreaIterator areaBeginConst (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const
 Returns a non-mutable area iterator for area. More...
 
ConstAreaIterator areaEndConst () const
 Returns an non-mutable invalid area iterator marking the end of an area. More...
 
ConstIterator RTBegin (CoordinateType rt) const
 Fast search for spectrum range begin. More...
 
ConstIterator RTEnd (CoordinateType rt) const
 Fast search for spectrum range end (returns the past-the-end iterator) More...
 
Iterator RTBegin (CoordinateType rt)
 Fast search for spectrum range begin. More...
 
Iterator RTEnd (CoordinateType rt)
 Fast search for spectrum range end (returns the past-the-end iterator) More...
 
Range methods
Note
The range values (min, max, etc.) are not updated automatically. Call updateRanges() to update the values!
virtual void updateRanges ()
 Updates minimum and maximum position/intensity. More...
 
void updateRanges (Int ms_level)
 Updates the m/z, intensity, retention time and MS level ranges of all spectra with a certain ms level. More...
 
CoordinateType getMinMZ () const
 returns the minimal m/z value More...
 
CoordinateType getMaxMZ () const
 returns the maximal m/z value More...
 
CoordinateType getMinRT () const
 returns the minimal retention time value More...
 
CoordinateType getMaxRT () const
 returns the maximal retention time value More...
 
const AreaTypegetDataRange () const
 Returns RT and m/z range the data lies in. More...
 
UInt64 getSize () const
 returns the total number of peaks More...
 
const std::vector< UInt > & getMSLevels () const
 returns an array of MS levels More...
 
Sorting spectra and peaks
void sortSpectra (bool sort_mz=true)
 Sorts the data points by retention time. More...
 
void sortChromatograms (bool sort_rt=true)
 Sorts the data points of the chromatograms by m/z. More...
 
bool isSorted (bool check_mz=true) const
 Checks if all spectra are sorted with respect to ascending RT. More...
 
Easy Access interface
MSChromatogram< ChromatogramPeakType > & getChromatogram (Size id)
 returns a single chromatogram More...
 
MSSpectrum< PeakT > & getSpectrum (Size id)
 returns a single spectrum More...
 
Size getNrSpectra () const
 get the total number of spectra available More...
 
Size getNrChromatograms () const
 get the total number of chromatograms available More...
 
- Public Member Functions inherited from RangeManager< 2 >
 RangeManager ()
 Default constructor. More...
 
 RangeManager (const RangeManager &rhs)
 Copy constructor. More...
 
virtual ~RangeManager ()
 Destructor. More...
 
RangeManageroperator= (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 PositionTypegetMin () const
 Returns the minimum position. More...
 
const PositionTypegetMax () 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 ExperimentalSettings
 ExperimentalSettings ()
 Constructor. More...
 
 ExperimentalSettings (const ExperimentalSettings &source)
 Copy constructor. More...
 
 ~ExperimentalSettings ()
 Destructor. More...
 
ExperimentalSettingsoperator= (const ExperimentalSettings &source)
 Assignment operator. More...
 
bool operator== (const ExperimentalSettings &rhs) const
 Equality operator. More...
 
bool operator!= (const ExperimentalSettings &rhs) const
 Equality operator. More...
 
const SamplegetSample () const
 returns a const reference to the sample description More...
 
SamplegetSample ()
 returns a mutable reference to the sample description More...
 
void setSample (const Sample &sample)
 sets the sample description More...
 
const std::vector< SourceFile > & getSourceFiles () const
 returns a const reference to the source data file More...
 
std::vector< SourceFile > & getSourceFiles ()
 returns a mutable reference to the source data file More...
 
void setSourceFiles (const std::vector< SourceFile > &source_files)
 sets the source data file More...
 
const std::vector< ContactPerson > & getContacts () const
 returns a const reference to the list of contact persons More...
 
std::vector< ContactPerson > & getContacts ()
 returns a mutable reference to the list of contact persons More...
 
void setContacts (const std::vector< ContactPerson > &contacts)
 sets the list of contact persons More...
 
const InstrumentgetInstrument () const
 returns a const reference to the MS instrument description More...
 
InstrumentgetInstrument ()
 returns a mutable reference to the MS instrument description More...
 
void setInstrument (const Instrument &instrument)
 sets the MS instrument description More...
 
const HPLCgetHPLC () const
 returns a const reference to the description of the HPLC run More...
 
HPLCgetHPLC ()
 returns a mutable reference to the description of the HPLC run More...
 
void setHPLC (const HPLC &hplc)
 sets the description of the HPLC run More...
 
const DateTimegetDateTime () const
 returns the date the experiment was performed More...
 
void setDateTime (const DateTime &date)
 sets the date the experiment was performed More...
 
const StringgetComment () const
 returns the free-text comment More...
 
void setComment (const String &comment)
 sets the free-text comment More...
 
const std::vector< ProteinIdentification > & getProteinIdentifications () const
 returns a const reference to the protein ProteinIdentification vector More...
 
std::vector< ProteinIdentification > & getProteinIdentifications ()
 returns a mutable reference to the protein ProteinIdentification vector More...
 
void setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications)
 sets the protein ProteinIdentification vector More...
 
const StringgetFractionIdentifier () const
 returns fraction identifier More...
 
void setFractionIdentifier (const String &fraction_identifier)
 sets the fraction identifier More...
 
- Public Member Functions inherited from MetaInfoInterface
 MetaInfoInterface ()
 constructor More...
 
 MetaInfoInterface (const MetaInfoInterface &rhs)
 copy constructor More...
 
 ~MetaInfoInterface ()
 destructor More...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 assignment operator More...
 
bool operator== (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
bool operator!= (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
const DataValuegetMetaValue (const String &name) const
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (UInt index) const
 returns the value corresponding to an index More...
 
bool metaValueExists (const String &name) const
 returns if this MetaInfo is set More...
 
bool metaValueExists (UInt index) const
 returns if this MetaInfo is set 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 getKeys (std::vector< String > &keys) const
 fills the given vector with a list of all keys for which a value is set More...
 
void getKeys (std::vector< UInt > &keys) const
 fills the given vector with a list of all keys for which a value is set More...
 
bool isMetaEmpty () const
 returns if the MetaInfo is empty More...
 
void clearMetaInfo ()
 removes all meta values More...
 
- Public Member Functions inherited from DocumentIdentifier
 DocumentIdentifier ()
 default constructor More...
 
 DocumentIdentifier (const DocumentIdentifier &source)
 Copy constructor. More...
 
DocumentIdentifieroperator= (const DocumentIdentifier &source)
 Assignment operator. More...
 
bool operator== (const DocumentIdentifier &rhs) const
 Equality operator. More...
 
virtual ~DocumentIdentifier ()
 destructor More...
 
void setIdentifier (const String &id)
 set document identifier (e.g. an LSID) More...
 
const StringgetIdentifier () const
 retrieve document identifier (e.g. an LSID) More...
 
void swap (DocumentIdentifier &from)
 exchange content with from More...
 
void setLoadedFilePath (const String &file_name)
 set the file_name_ according to absolute path of the file loaded from preferably done whilst loading More...
 
const StringgetLoadedFilePath () const
 get the file_name_ which is the absolute path to the file loaded from More...
 
void setLoadedFileType (const String &file_name)
 set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably done whilst loading More...
 
const FileTypes::TypegetLoadedFileType () const
 get the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, ...) of the file loaded from More...
 

Protected Attributes

std::vector< UIntms_levels_
 MS levels of the data. More...
 
UInt64 total_size_
 Number of all data points. More...
 
std::vector< MSChromatogram< ChromatogramPeakType > > chromatograms_
 chromatograms More...
 
std::vector< SpectrumTypespectra_
 spectra More...
 
- Protected Attributes inherited from RangeManager< 2 >
IntensityRangeType int_range_
 Intensity range (1-dimensional) More...
 
PositionRangeType pos_range_
 Position range (D-dimensional) More...
 
- Protected Attributes inherited from ExperimentalSettings
Sample sample_
 
std::vector< SourceFilesource_files_
 
std::vector< ContactPersoncontacts_
 
Instrument instrument_
 
HPLC hplc_
 
DateTime datetime_
 
String comment_
 
std::vector< ProteinIdentificationprotein_identifications_
 
String fraction_identifier_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 pointer to the MetaInfo object. 0 by default More...
 
- Protected Attributes inherited from DocumentIdentifier
String id_
 the ID (e.g. LSID) More...
 
String file_path_
 the path to the loaded file More...
 
FileTypes::Type file_type_
 the type of the loaded file More...
 

Delegations of calls to the vector of MSSpectra

typedef Base::value_type value_type
 
typedef Base::iterator iterator
 
typedef Base::const_iterator const_iterator
 
Size size () const
 
void resize (Size s)
 
bool empty () const
 
void reserve (Size s)
 
SpectrumTypeoperator[] (Size n)
 
const SpectrumTypeoperator[] (Size n) const
 
Iterator begin ()
 
ConstIterator begin () const
 
Iterator end ()
 
ConstIterator end () const
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 returns a reference to the MetaInfoRegistry More...
 
- Protected Member Functions inherited from RangeManager< 2 >
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...
 

Detailed Description

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

In-Memory representation of a mass spectrometry experiment.

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

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

Member Typedef Documentation

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.

Chromatogram type.

typedef Base::const_iterator const_iterator

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

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

Non-mutable iterator.

Coordinate type of peak positions.

Intensity type of peaks.

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

Mutable iterator.

typedef Base::iterator iterator
typedef PeakT PeakType

Peak type.

RangeManager type.

Spectrum Type.

typedef Base::value_type value_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

Referenced by MSDataWritingConsumer::consumeChromatogram(), and PeakPickerHiRes::pickExperiment().

void addSpectrum ( const MSSpectrum< PeakT > &  spectrum)
inline
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.

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.

Iterator begin ( )
inline
ConstIterator begin ( ) const
inline
void clear ( bool  clear_meta_data)
inline

Clears all data and meta data.

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

Referenced by SpectraMerger::mergeSpectra_(), PeakPickerIterative::pickExperiment(), PeakPickerHiRes::pickExperiment(), MSExperiment< SimPointType >::set2DData(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().

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.
bool empty ( ) const
inline
Iterator end ( )
inline
ConstIterator end ( ) const
inline
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()

MSChromatogram<ChromatogramPeakType>& getChromatogram ( Size  id)
inline
const std::vector<MSChromatogram<ChromatogramPeakType> >& getChromatograms ( ) const
inline
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

CoordinateType getMaxRT ( ) const
inline

returns the maximal retention time value

CoordinateType getMinMZ ( ) const
inline

returns the minimal m/z value

CoordinateType getMinRT ( ) const
inline

returns the minimal retention time value

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

returns an array of MS levels

Size getNrChromatograms ( ) const
inline

get the total number of chromatograms available

Referenced by TOPPBase::addDataProcessing_().

Size getNrSpectra ( ) const
inline

get the total number of spectra available

Referenced by PeakPickerHiRes::pickExperiment().

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

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

returns the spectra list

Referenced by SpectraMerger::mergeSpectra_(), and MSExperiment< SimPointType >::swap().

std::vector<MSSpectrum<PeakT> >& getSpectra ( )
inline

returns the spectra list

MSSpectrum<PeakT>& getSpectrum ( Size  id)
inline

returns a single spectrum

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

Referenced by MSExperiment< SimPointType >::areaBeginConst(), and MSExperiment< SimPointType >::isSorted().

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

Equality operator.

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

Assignment operator.

MSExperiment& operator= ( const ExperimentalSettings source)
inline

Assignment operator.

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

Equality operator.

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

SpectrumType& operator[] ( Size  n)
inline
const SpectrumType& operator[] ( Size  n) const
inline
void reserve ( Size  s)
inline
void reserveSpaceChromatograms ( Size  s)
inline
void reserveSpaceSpectra ( Size  s)
inline
void reset ( )
inline
void resize ( Size  s)
inline
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 >::areaBeginConst(), InternalCalibration::calibrateMapGlobally(), OfflinePrecursorIonSelection::getMassRanges(), TwoDOptimization::getRegionEndpoints_(), and OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap().

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 >::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 &  container)
inline

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

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

Parameters
containerAn iterable type whose elements support getRT(), getMZ() and getIntensity()
Exceptions
Exception::Preconditionis thrown if the container is not sorted according to retention time (in debug AND release mode)
void set2DData ( const Container &  container)
inline

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

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

Parameters
containerAn iterable type whose elements support getRT(), getMZ() and getIntensity()
add_mass_tracesIf true, each container element is searched for the metavalue "num_of_masstraces". If found, "masstrace_intensity_<X>" (X>=0) meta values are added as data points (with 13C spacing). This is useful for, e.g., FF-Metabo output. Note that the actual feature will NOT be added if mass traces are found (since MT0 is usually identical)
Exceptions
Exception::Preconditionis thrown if the container is not sorted according to retention time (in debug AND release mode) OR a "masstrace_intensity_<X>" value is expected but not found
void setChromatograms ( const std::vector< MSChromatogram< ChromatogramPeakType > > &  chromatograms)
inline

sets the chromatogram list

Referenced by OpenSwathWorkflow::performRTNormalization().

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

sets the spectra list

Size size ( ) const
inline

Referenced by TOPPBase::addDataProcessing_(), SpectrumCanvas::addDataProcessing_(), IDMapper::annotate(), OfflinePrecursorIonSelection::calculateXICs_(), TOFCalibration::calibrate(), InternalCalibration::calibrateMapGlobally(), InternalCalibration::calibrateMapSpectrumwise(), OpenSwathHelper::checkSwathMapAndSelectTransitions(), TOPPViewBase::containsMS1Scans(), TOPPViewBase::countMS1Zeros(), PSLPFormulation::createAndSolveCombinedLPForKnownLCMSMapFeatureBased(), PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased(), TOPPViewBase::estimateNoiseFromRandomMS1Scans(), GaussFilter::filterExperiment(), SavitzkyGolayFilter::filterExperiment(), MorphologicalFilter::filterExperiment(), IDFilter::filterIdentificationsByBestNHits(), IDFilter::filterIdentificationsByProteins(), IDFilter::filterIdentificationsByScores(), IDFilter::filterIdentificationsByThresholds(), OfflinePrecursorIonSelection::getMassRanges(), FeaFiModule< PeakType >::getNextMz(), FeaFiModule< PeakType >::getNextRt(), FeaFiModule< PeakType >::getPeakIntensity(), FeaFiModule< PeakType >::getPeakMz(), FeaFiModule< PeakType >::getPeakRt(), FeaFiModule< PeakType >::getPrevMz(), FeaFiModule< PeakType >::getPrevRt(), TwoDOptimization::getRegionEndpoints_(), TOPPViewBase::hasPeptideIdentifications(), TOPPRNPxl::main_(), SimpleSearchEngine::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraPrecursors(), TwoDOptimization::optimize(), PeakPickerIterative::pickExperiment(), PeakPickerHiRes::pickExperiment(), SimpleSearchEngine::preprocessSpectra_(), LinearResampler::rasterExperiment(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().

void sortChromatograms ( bool  sort_rt = true)
inline

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

Parameters
sort_rtif true, chromatograms are sorted by rt position as well
void sortSpectra ( bool  sort_mz = true)
inline

Sorts the data points by retention time.

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

Referenced by SimpleSearchEngine::main_(), SpectraMerger::mergeSpectraBlockWise(), SpectraMerger::mergeSpectraPrecursors(), and SimpleSearchEngine::preprocessSpectra_().

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

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

virtual void updateRanges ( )
inlinevirtual

Updates minimum and maximum position/intensity.

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

Implements RangeManager< 2 >.

Referenced by 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_levelMS 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
std::vector<UInt> ms_levels_
protected
std::vector<SpectrumType> spectra_
protected
UInt64 total_size_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:41 using doxygen 1.8.9.1