| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Protected Attributes | Private Member Functions | List of all members
MSExperiment Class Reference
Kernel

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

`#include <OpenMS/KERNEL/MSExperiment.h>`

Inheritance diagram for MSExperiment:

## Classes

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

## Public Types

typedef Peak1D | PeakT
typedef ChromatogramPeak | ChromatogramPeakT
Base type definitions
typedef PeakT | PeakType
| Peak type. More...
typedef ChromatogramPeakT | ChromatogramPeakType
| Chromatogram peak type. More...
typedef 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 | SpectrumType
| Spectrum Type. More...
typedef MSChromatogram | ChromatogramType
| Chromatogram type. More...
typedef std::vector< SpectrumType > | Base
| STL base class type. More...
Iterator type definitions
typedef std::vector< SpectrumType >::iterator | Iterator
| Mutable iterator. More...
typedef std::vector< SpectrumType >::const_iterator | ConstIterator
| Non-mutable iterator. More...
typedef Internal::AreaIterator< PeakT, PeakT &, PeakT *, Iterator, SpectrumType::Iterator > | AreaIterator
| Mutable area iterator type (for traversal of a rectangular subset of the peaks) More...
typedef Internal::AreaIterator< const PeakT, const PeakT &, const PeakT *, ConstIterator, SpectrumType::ConstIterator > | ConstAreaIterator
| Immutable area iterator type (for traversal of a rectangular subset of the peaks) More...
Public Types inherited from 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...
| MSExperiment (MSExperiment &&)=default
| Move constructor. More...
MSExperiment & | operator= (const MSExperiment &source)
| Assignment operator. More...
MSExperiment & | operator= (MSExperiment &&) &=default
| Move assignment operator. More...
MSExperiment & | operator= (const ExperimentalSettings &source)
| Assignment operator. More...
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 ExperimentalSettings & | getExperimentalSettings () const
| returns the meta information of this experiment (const access) More...
ExperimentalSettings & | getExperimentalSettings ()
| returns the meta information of this experiment (mutable access) More...
void | getPrimaryMSRunPath (StringList &toFill) const
| get the file path to the first MS run More...
ConstIterator | getPrecursorSpectrum (ConstIterator iterator) const
| Returns the precursor spectrum of the scan pointed to by `iterator`. More...
void | swap (MSExperiment &from)
| Swaps the content of this map with the content of `from`. More...
void | setSpectra (const std::vector< MSSpectrum > &spectra)
| sets the spectrum list More...
void | addSpectrum (const MSSpectrum &spectrum)
| adds a spectrum to the list More...
void | addSpectrum (MSSpectrum &&spectrum)
const std::vector< MSSpectrum > & | getSpectra () const
| returns the spectrum list More...
std::vector< MSSpectrum > & | getSpectra ()
| returns the spectrum list (mutable) More...
void | setChromatograms (const std::vector< MSChromatogram > &chromatograms)
| sets the chromatogram list More...
void | addChromatogram (const MSChromatogram &chromatogram)
| adds a chromatogram to the list More...
void | addChromatogram (MSChromatogram &&chrom)
const std::vector< MSChromatogram > & | getChromatograms () const
| returns the chromatogram list More...
std::vector< MSChromatogram > & | getChromatograms ()
| returns the chromatogram list (mutable) More...
const MSChromatogram | getTIC (float rt_bin_size=0) const
| Compute Total Ion Count per MS1 spectrum and applies the resampling algorithm, if a bin size in RT seconds greater than 0 is given. 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<class Container >
void | set2DData (const Container &container, const StringList &store_metadata_names)
| Assignment of a data container with RT and MZ to an MSExperiment. More...
template<bool add_mass_traces, class Container >
void | set2DData (const Container &container)
| Assignment of a data container with RT and MZ to an MSExperiment. More...
Iterating ranges and areas
AreaIterator | areaBegin (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz)
| 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!

void | updateRanges () override
| 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 AreaType & | getDataRange () 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 & | getChromatogram (Size id)
| returns a single chromatogram More...
MSSpectrum & | getSpectrum (Size id)
| returns a single spectrum More...
Size | getNrSpectra () const
| get the total number of spectra available More...
Size | getNrChromatograms () const
| get the total number of chromatograms available More...
Public Member Functions inherited from RangeManager< 2 >
| 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 ExperimentalSettings
| ExperimentalSettings ()=default
| Constructor. More...
| ExperimentalSettings (const ExperimentalSettings &)=default
| Copy constructor. More...
| ExperimentalSettings (ExperimentalSettings &&)=default
| Move constructor. More...
| ~ExperimentalSettings () override
| Destructor. More...
ExperimentalSettings & | operator= (const ExperimentalSettings &)=default
| Assignment operator. More...
ExperimentalSettings & | operator= (ExperimentalSettings &&) &=default
| Move assignment operator. More...
bool | operator== (const ExperimentalSettings &rhs) const
| Equality operator. More...
bool | operator!= (const ExperimentalSettings &rhs) const
| Equality operator. More...
const Sample & | getSample () const
| returns a const reference to the sample description More...
Sample & | getSample ()
| returns a mutable reference to the sample description More...
void | setSample (const Sample &sample)
| sets the sample description More...
const std::vector< SourceFile > & | getSourceFiles () const
| returns a const reference to the source data file More...
std::vector< SourceFile > & | getSourceFiles ()
| returns a mutable reference to the source data file More...
void | setSourceFiles (const std::vector< SourceFile > &source_files)
| sets the source data file More...
const std::vector< ContactPerson > & | getContacts () const
| returns a const reference to the list of contact persons More...
std::vector< ContactPerson > & | getContacts ()
| returns a mutable reference to the list of contact persons More...
void | setContacts (const std::vector< ContactPerson > &contacts)
| sets the list of contact persons More...
const Instrument & | getInstrument () const
| returns a const reference to the MS instrument description More...
Instrument & | getInstrument ()
| returns a mutable reference to the MS instrument description More...
void | setInstrument (const Instrument &instrument)
| sets the MS instrument description More...
const HPLC & | getHPLC () const
| returns a const reference to the description of the HPLC run More...
HPLC & | getHPLC ()
| returns a mutable reference to the description of the HPLC run More...
void | setHPLC (const HPLC &hplc)
| sets the description of the HPLC run More...
const DateTime & | getDateTime () const
| returns the date the experiment was performed More...
void | setDateTime (const DateTime &date)
| sets the date the experiment was performed More...
const String & | getComment () const
| returns the free-text comment More...
void | setComment (const String &comment)
| sets the free-text comment More...
const std::vector< ProteinIdentification > & | getProteinIdentifications () const
| returns a const reference to the protein ProteinIdentification vector More...
std::vector< ProteinIdentification > & | getProteinIdentifications ()
| returns a mutable reference to the protein ProteinIdentification vector More...
void | setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications)
| sets the protein ProteinIdentification vector More...
const String & | getFractionIdentifier () const
| returns fraction identifier More...
void | setFractionIdentifier (const String &fraction_identifier)
| sets the fraction identifier More...
Public Member Functions inherited from MetaInfoInterface
| MetaInfoInterface ()
| Constructor. More...
| MetaInfoInterface (const MetaInfoInterface &rhs)
| Copy constructor. More...
| MetaInfoInterface (MetaInfoInterface &&) noexcept
| Move constructor. More...
| ~MetaInfoInterface ()
| Destructor. More...
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs)
| Assignment operator. More...
MetaInfoInterface & | operator= (MetaInfoInterface &&) noexcept
| Move assignment operator. More...
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 | getKeys (std::vector< String > &keys) const
| Fills the given vector with a list of all keys for which a value is set. More...
void | getKeys (std::vector< UInt > &keys) const
| Fills the given vector with a list of all keys for which a value is set. More...
bool | isMetaEmpty () const
| Returns if the MetaInfo is empty. More...
void | clearMetaInfo ()
| Removes all meta values. More...
Public Member Functions inherited from DocumentIdentifier
| DocumentIdentifier ()
| Default constructor. More...
| DocumentIdentifier (const DocumentIdentifier &)=default
| Copy constructor. More...
| DocumentIdentifier (DocumentIdentifier &&)=default
| Move constructor. More...
virtual | ~DocumentIdentifier ()
| Destructor. More...
DocumentIdentifier & | operator= (const DocumentIdentifier &)=default
| Assignment operator. More...
DocumentIdentifier & | operator= (DocumentIdentifier &&) &=default
| Move assignment operator. More...
bool | operator== (const DocumentIdentifier &rhs) const
| Equality operator. More...
void | setIdentifier (const String &id)
| set document identifier (e.g. an LSID) More...
const String & | getIdentifier () const
| retrieve document identifier (e.g. an LSID) More...
void | swap (DocumentIdentifier &from)
| exchange content with `from` More...
void | setLoadedFilePath (const String &file_name)
| set the file_name_ according to absolute path of the file loaded from preferably done whilst loading More...
const String & | getLoadedFilePath () const
| get the file_name_ which is the absolute path to the file loaded from More...
void | setLoadedFileType (const String &file_name)
| set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably done whilst loading More...
const FileTypes::Type & | getLoadedFileType () const
| get the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, ...) of the file loaded from More...

## Protected Attributes

std::vector< UInt > | ms_levels_
| MS levels of the data. More...
UInt64 | total_size_
| Number of all data points. More...
std::vector< MSChromatogram > | chromatograms_
| chromatograms More...
std::vector< SpectrumType > | spectra_
| spectra More...
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< SourceFile > | source_files_
std::vector< ContactPerson > | contacts_
Instrument | instrument_
HPLC | hplc_
DateTime | datetime_
String | comment_
std::vector< ProteinIdentification > | protein_identifications_
String | fraction_identifier_
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) More...
Protected Attributes inherited from DocumentIdentifier
String | id_
| the ID (e.g. LSID) More...
String | file_path_
| the path to the loaded file More...
FileTypes::Type | file_type_
| the type of the loaded file More...

## Private Member Functions

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

## 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)
SpectrumType & | operator[] (Size n)
const SpectrumType & | operator[] (Size n) const
Iterator | begin ()
ConstIterator | begin () const
Iterator | end ()
ConstIterator | end () const

## Additional Inherited Members

Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry & | metaRegistry ()
| Returns a reference to the MetaInfoRegistry. More...
Protected Member Functions inherited from RangeManager< 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

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 getChromatogram 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

## ◆ AreaIterator

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

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

## ◆ AreaType

typedef DRange<2> AreaType

Area type.

## ◆ Base

typedef std::vector<SpectrumType> Base

STL base class type.

## ◆ ChromatogramPeakT

typedef ChromatogramPeak ChromatogramPeakT

## ◆ ChromatogramPeakType

typedef ChromatogramPeakT ChromatogramPeakType

Chromatogram peak type.

## ◆ ChromatogramType

typedef MSChromatogram ChromatogramType

Chromatogram type.

## ◆ const_iterator

typedef Base::const_iterator const_iterator

## ◆ ConstAreaIterator

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

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

## ◆ ConstIterator

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

Non-mutable iterator.

## ◆ CoordinateType

typedef PeakType::CoordinateType CoordinateType

Coordinate type of peak positions.

## ◆ IntensityType

typedef PeakType::IntensityType IntensityType

Intensity type of peaks.

## ◆ Iterator

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

Mutable iterator.

## ◆ iterator

typedef Base::iterator iterator

## ◆ PeakT

typedef Peak1D PeakT

## ◆ PeakType

typedef PeakT PeakType

Peak type.

## ◆ RangeManagerType

typedef RangeManager<2> RangeManagerType

RangeManager type.

## ◆ SpectrumType

typedef MSSpectrum SpectrumType

Spectrum Type.

## ◆ value_type

typedef Base::value_type value_type

## Constructor & Destructor Documentation

## ◆ MSExperiment() [1/3]

MSExperiment | ( |  | ) |

Constructor.

## ◆ MSExperiment() [2/3]

MSExperiment | ( | const MSExperiment & | source | ) |

Copy constructor.

## ◆ MSExperiment() [3/3]

MSExperiment | ( | MSExperiment && |  | ) |

default

Move constructor.

## Member Function Documentation

## ◆ addChromatogram() [1/2]

void addChromatogram | ( | const MSChromatogram & | chromatogram | ) |

adds a chromatogram to the list

## ◆ addChromatogram() [2/2]

void addChromatogram | ( | MSChromatogram && | chrom | ) |

inline

## ◆ addSpectrum() [1/2]

void addSpectrum | ( | const MSSpectrum & | spectrum | ) |

adds a spectrum to the list

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

## ◆ addSpectrum() [2/2]

void addSpectrum | ( | MSSpectrum && | spectrum | ) |

inline

## ◆ areaBegin()

AreaIterator areaBegin | ( | CoordinateType | min_rt,
|  | CoordinateType | max_rt,
|  | CoordinateType | min_mz,
|  | CoordinateType | max_mz
| ) |  |

Returns an area iterator for `area`.

## ◆ areaBeginConst()

ConstAreaIterator areaBeginConst | ( | CoordinateType | min_rt,
|  | CoordinateType | max_rt,
|  | CoordinateType | min_mz,
|  | CoordinateType | max_mz
| ) |  | const

Returns a non-mutable area iterator for `area`.

Referenced by MetaProSIPXICExtraction::extractXICs().

## ◆ areaEnd()

AreaIterator areaEnd | ( |  | ) |

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

## ◆ areaEndConst()

ConstAreaIterator areaEndConst | ( |  | ) | const

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

Referenced by MetaProSIPXICExtraction::extractXICs().

## ◆ begin() [1/2]

Iterator begin | ( |  | ) |

inline

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

## ◆ begin() [2/2]

ConstIterator begin | ( |  | ) | const

inline

## ◆ 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 UTILProteomicsLFQ::centroidAndCorrectPrecursors_(), SpectraMerger::mergeSpectra_(), PeakPickerIterative::pickExperiment(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().

## ◆ clearMetaDataArrays()

bool clearMetaDataArrays | ( |  | ) |

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

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

Referenced by UTILProteomicsLFQ::centroidAndCorrectPrecursors_().

## ◆ createSpec_() [1/2]

SpectrumType* createSpec_ | ( | PeakType::CoordinateType | rt | ) |

private

## ◆ createSpec_() [2/2]

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

private

## ◆ empty()

bool empty | ( |  | ) | const

inline

Referenced by UTILProteomicsLFQ::centroidAndCorrectPrecursors_(), OpenMS::collapseIMSpectrum(), OpenMS::determineIMType(), TOPPViewBase::hasPeptideIdentifications(), and TwoDOptimization::optimize().

## ◆ end() [1/2]

Iterator end | ( |  | ) |

inline

Referenced by KDTreeFeatureMaps::addMaps(), SpectraMerger::average(), SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), TOPPViewBase::estimateNoiseFromRandomMS1Scans(), IDFilter::filterHitsByScore(), MapAlignmentAlgorithmIdentification::getRetentionTimes_(), IDFilter::keepHitsMatchingProteins(), IDFilter::keepNBestHits(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraBlockWise(), TwoDOptimization::optimize(), and DTA2DFile::store().

## ◆ end() [2/2]

ConstIterator end | ( |  | ) | const

inline

## ◆ get2DData()

void get2DData | ( | Container & | cont | ) | const

inline

Reads out a 2D Spectrum.

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

## ◆ getChromatogram()

MSChromatogram& getChromatogram | ( | Size | id | ) |

returns a single chromatogram

Referenced by GaussFilter::filterExperiment(), and SavitzkyGolayFilter::filterExperiment().

## ◆ getChromatograms() [1/2]

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

returns the chromatogram list

Referenced by GaussFilter::filterExperiment(), and SavitzkyGolayFilter::filterExperiment().

## ◆ getChromatograms() [2/2]

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

returns the chromatogram list (mutable)

## ◆ getDataRange()

const AreaType& getDataRange | ( |  | ) | const

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

RT is dimension 0, m/z is dimension 1

## ◆ getExperimentalSettings() [1/2]

const ExperimentalSettings& getExperimentalSettings | ( |  | ) | const

returns the meta information of this experiment (const access)

Referenced by XMassFile::importExperimentalSettings().

## ◆ getExperimentalSettings() [2/2]

ExperimentalSettings& getExperimentalSettings | ( |  | ) |

returns the meta information of this experiment (mutable access)

## ◆ getMaxMZ()

CoordinateType getMaxMZ | ( |  | ) | const

returns the maximal m/z value

## ◆ getMaxRT()

CoordinateType getMaxRT | ( |  | ) | const

returns the maximal retention time value

## ◆ getMinMZ()

CoordinateType getMinMZ | ( |  | ) | const

returns the minimal m/z value

## ◆ getMinRT()

CoordinateType getMinRT | ( |  | ) | const

returns the minimal retention time value

## ◆ getMSLevels()

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

returns an array of MS levels

## ◆ getNrChromatograms()

Size getNrChromatograms | ( |  | ) | const

get the total number of chromatograms available

## ◆ getNrSpectra()

Size getNrSpectra | ( |  | ) | const

get the total number of spectra available

Referenced by NucleicAcidSearchEngine::main_().

## ◆ getPrecursorSpectrum()

ConstIterator getPrecursorSpectrum | ( | ConstIterator | iterator | ) | const

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

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

## ◆ getPrimaryMSRunPath()

void getPrimaryMSRunPath | ( | StringList & | toFill | ) | const

get the file path to the first MS run

Referenced by NucleicAcidSearchEngine::main_().

## ◆ getSize()

UInt64 getSize | ( |  | ) | const

returns the total number of peaks

## ◆ getSpectra() [1/2]

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

returns the spectrum list

Referenced by SpectraMerger::mergeSpectra_().

## ◆ getSpectra() [2/2]

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

returns the spectrum list (mutable)

## ◆ getSpectrum()

MSSpectrum& getSpectrum | ( | Size | id | ) |

returns a single spectrum

## ◆ getTIC()

const MSChromatogram getTIC | ( | float | rt_bin_size = `0` | ) | const

Compute Total Ion Count per MS1 spectrum and applies the resampling algorithm, if a bin size in RT seconds greater than 0 is given.

By default, each MS1 spectrum's intensity just gets summed up. Regular RT bins can be obtained by specifying `rt_bin_size`.

Parameters

  bin_size | RT bin size in seconds

Returns
  TIC Chromatogram

Referenced by DTA2DFile::storeTIC().

## ◆ isSorted()

bool isSorted | ( | bool | check_mz = `true` | ) | const

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

Parameters

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

## ◆ operator!=()

bool operator!= | ( | const MSExperiment & | rhs | ) | const

Equality operator.

## ◆ operator=() [1/3]

MSExperiment& operator= | ( | const MSExperiment & | source | ) |

Assignment operator.

## ◆ operator=() [2/3]

MSExperiment& operator= | ( | MSExperiment && |  | ) | &

default

Move assignment operator.

## ◆ operator=() [3/3]

MSExperiment& operator= | ( | const ExperimentalSettings & | source | ) |

Assignment operator.

## ◆ operator==()

bool operator== | ( | const MSExperiment & | rhs | ) | const

Equality operator.

## ◆ operator[]() [1/2]

SpectrumType& operator[] | ( | Size | n | ) |

inline

## ◆ operator[]() [2/2]

const SpectrumType& operator[] | ( | Size | n | ) | const

inline

## ◆ reserve()

void reserve | ( | Size | s | ) |

inline

## ◆ reserveSpaceChromatograms()

void reserveSpaceChromatograms | ( | Size | s | ) |

## ◆ reserveSpaceSpectra()

void reserveSpaceSpectra | ( | Size | s | ) |

## ◆ reset()

void reset | ( |  | ) |

Resets all internal values.

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

## ◆ resize()

void resize | ( | Size | s | ) |

inline

Referenced by PeakPickerIterative::pickExperiment().

## ◆ RTBegin() [1/2]

ConstIterator RTBegin | ( | CoordinateType | rt | ) | const

Fast search for spectrum range begin.

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

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

Referenced by MetaProSIPXICExtraction::extractXICs(), and TwoDOptimization::getRegionEndpoints_().

## ◆ RTBegin() [2/2]

Iterator RTBegin | ( | CoordinateType | rt | ) |

Fast search for spectrum range begin.

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

## ◆ RTEnd() [1/2]

ConstIterator RTEnd | ( | CoordinateType | rt | ) | const

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

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

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

## ◆ RTEnd() [2/2]

Iterator RTEnd | ( | CoordinateType | rt | ) |

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

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

## ◆ set2DData() [1/3]

void set2DData | ( | const Container & | container | ) |

inline

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

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

Parameters

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

Exceptions

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

## ◆ set2DData() [2/3]

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

inline

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

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

Parameters

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

Exceptions

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

## ◆ set2DData() [3/3]

void set2DData | ( | const Container & | container | ) |

inline

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

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

Parameters

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

Exceptions

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

## ◆ setChromatograms()

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

sets the chromatogram list

## ◆ setSpectra()

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

sets the spectrum list

## ◆ size()

Size size | ( |  | ) | const

inline

Referenced by SpectrumCanvas::addDataProcessing_(), UTILProteomicsLFQ::centroidAndCorrectPrecursors_(), OpenSwathHelper::checkSwathMapAndSelectTransitions(), OpenMS::collapseIMSpectrum(), TOPPViewBase::containsMS1Scans(), OpenMS::determineIMType(), TOPPViewBase::estimateNoiseFromRandomMS1Scans(), GaussFilter::filterExperiment(), SavitzkyGolayFilter::filterExperiment(), MorphologicalFilter::filterExperiment(), TwoDOptimization::getRegionEndpoints_(), TOPPViewBase::hasMS1Zeros(), TOPPViewBase::hasPeptideIdentifications(), NucleicAcidSearchEngine::main_(), IDMapper::mapPrecursorsToIdentifications(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraPrecursors(), TwoDOptimization::optimize(), PeakPickerIterative::pickExperiment(), NucleicAcidSearchEngine::preprocessSpectra_(), LinearResampler::rasterExperiment(), DTA2DFile::store(), DTA2DFile::storeTIC(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().

## ◆ sortChromatograms()

void sortChromatograms | ( | bool | sort_rt = `true` | ) |

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

Parameters

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

## ◆ sortSpectra()

void sortSpectra | ( | bool | sort_mz = `true` | ) |

Sorts the data points by retention time.

Parameters

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

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

## ◆ swap()

void swap | ( | MSExperiment & | from | ) |

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

Referenced by UTILProteomicsLFQ::quantifyFraction_().

## ◆ updateRanges() [1/2]

void updateRanges | ( |  | ) |

override virtual

Updates minimum and maximum position/intensity.

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

Implements RangeManager< 2 >.

## ◆ updateRanges() [2/2]

void updateRanges | ( | Int | ms_level | ) |

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

Parameters

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

## Member Data Documentation

## ◆ chromatograms_

std::vector<MSChromatogram > chromatograms_

protected

chromatograms

## ◆ ms_levels_

std::vector<UInt> ms_levels_

protected

MS levels of the data.

## ◆ spectra_

std::vector<SpectrumType> spectra_

protected

spectra

## ◆ total_size_

UInt64 total_size_

protected

Number of all data points.