| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
SpectrumSettings Class Reference
Metadata

Representation of 1D spectrum settings. More...

`#include <OpenMS/METADATA/SpectrumSettings.h>`

Inheritance diagram for SpectrumSettings:

## Public Types

enum | SpectrumType { UNKNOWN, CENTROID, PROFILE, SIZE_OF_SPECTRUMTYPE }
| Spectrum peak type. More...

## Public Member Functions

| 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 | 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...

## Static Public Attributes

static const std::string | NamesOfSpectrumType [SIZE_OF_SPECTRUMTYPE]
| Names of spectrum types. More...

## Protected Attributes

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...

## 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 MetaInfoInterface
void | createIfNotExists_ ()
| Creates the MetaInfo object if it does not exist. More...

## Detailed Description

Representation of 1D spectrum settings.

It contains the metadata about spectrum specific instrument settings, acquisition settings, description of the meta values used in the peaks and precursor info.

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

## Member Enumeration Documentation

## ◆ SpectrumType

enum SpectrumType

Spectrum peak type.

Enumerator
UNKNOWN | Unknown spectrum type.
CENTROID | centroid data or stick data
PROFILE | profile data
SIZE_OF_SPECTRUMTYPE |

## Constructor & Destructor Documentation

## ◆ SpectrumSettings() [1/3]

SpectrumSettings | ( |  | ) |

Constructor.

## ◆ SpectrumSettings() [2/3]

SpectrumSettings | ( | const SpectrumSettings & |  | ) |

default

Copy constructor.

## ◆ SpectrumSettings() [3/3]

SpectrumSettings | ( | SpectrumSettings && |  | ) |

default

Move constructor.

## ◆ ~SpectrumSettings()

~SpectrumSettings | ( |  | ) |

Destructor.

## Member Function Documentation

## ◆ getAcquisitionInfo() [1/2]

const AcquisitionInfo& getAcquisitionInfo | ( |  | ) | const

returns a const reference to the acquisition info

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ getAcquisitionInfo() [2/2]

AcquisitionInfo& getAcquisitionInfo | ( |  | ) |

returns a mutable reference to the acquisition info

## ◆ getComment()

const String& getComment | ( |  | ) | const

returns the free-text comment

## ◆ getDataProcessing() [1/2]

std::vector< DataProcessingPtr >& getDataProcessing | ( |  | ) |

returns a mutable reference to the description of the applied processing

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ getDataProcessing() [2/2]

const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing | ( |  | ) | const

returns a const reference to the description of the applied processing

## ◆ getInstrumentSettings() [1/2]

const InstrumentSettings& getInstrumentSettings | ( |  | ) | const

returns a const reference to the instrument settings of the current spectrum

Referenced by HasScanMode< SpectrumType >::operator()(), HasScanPolarity< SpectrumType >::operator()(), IsZoomSpectrum< SpectrumType >::operator()(), and ChromatogramExtractor::return_chromatogram().

## ◆ getInstrumentSettings() [2/2]

InstrumentSettings& getInstrumentSettings | ( |  | ) |

returns a mutable reference to the instrument settings of the current spectrum

## ◆ getNativeID()

const String& getNativeID | ( |  | ) | const

returns the native identifier for the spectrum, used by the acquisition software.

Referenced by MascotGenericFile::getNextSpectrum_(), NucleicAcidSearchEngine::postProcessHits_(), NucleicAcidSearchEngine::preprocessSpectra_(), and SpectrumLookup::readSpectra().

## ◆ getPeptideIdentifications() [1/2]

const std::vector<PeptideIdentification>& getPeptideIdentifications | ( |  | ) | const

returns a const reference to the PeptideIdentification vector

## ◆ getPeptideIdentifications() [2/2]

std::vector<PeptideIdentification>& getPeptideIdentifications | ( |  | ) |

returns a mutable reference to the PeptideIdentification vector

## ◆ getPrecursors() [1/2]

const std::vector<Precursor>& getPrecursors | ( |  | ) | const

returns a const reference to the precursors

Referenced by ComplementFilter::apply(), ComplementMarker::apply(), IntensityBalanceFilter::apply(), FullSwathFileConsumer::consumeSpectrum(), ChromatogramTools::convertChromatogramsToSpectra(), ParentPeakMower::filterSpectrum(), IsobaricChannelExtractor::getActivationMethod_(), MascotGenericFile::getNextSpectrum_(), MS2File::load(), DTAFile::load(), MascotInfile::load(), MascotGenericFile::load(), IDMapper::mapPrecursorsToIdentifications(), SpectraMerger::mergeSpectra_(), PrecursorMassComparator::operator()(), HasActivationMethod< SpectrumType >::operator()(), InPrecursorMZRange< SpectrumType >::operator()(), HasPrecursorCharge< SpectrumType >::operator()(), IsInCollisionEnergyRange< SpectrumType >::operator()(), IsInIsolationWindowSizeRange< SpectrumType >::operator()(), IsInIsolationWindow< SpectrumType >::operator()(), NucleicAcidSearchEngine::postProcessHits_(), NucleicAcidSearchEngine::preprocessSpectra_(), ChromatogramExtractor::return_chromatogram(), TOPPViewBase::showCurrentPeaksAsDIA(), and DTAFile::store().

## ◆ getPrecursors() [2/2]

std::vector<Precursor>& getPrecursors | ( |  | ) |

returns a mutable reference to the precursors

## ◆ getProducts() [1/2]

const std::vector<Product>& getProducts | ( |  | ) | const

returns a const reference to the products

## ◆ getProducts() [2/2]

std::vector<Product>& getProducts | ( |  | ) |

returns a mutable reference to the products

## ◆ getSourceFile() [1/2]

const SourceFile& getSourceFile | ( |  | ) | const

returns a const reference to the source file

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ getSourceFile() [2/2]

SourceFile& getSourceFile | ( |  | ) |

returns a mutable reference to the source file

## ◆ getType()

SpectrumType getType | ( |  | ) | const

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

## ◆ operator!=()

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

Equality operator.

## ◆ operator=() [1/2]

SpectrumSettings& operator= | ( | const SpectrumSettings & |  | ) |

default

## ◆ operator=() [2/2]

SpectrumSettings& operator= | ( | SpectrumSettings && |  | ) | &

default

Move assignment operator.

## ◆ operator==()

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

Equality operator.

## ◆ setAcquisitionInfo()

void setAcquisitionInfo | ( | const AcquisitionInfo & | acquisition_info | ) |

sets the acquisition info

Referenced by XMassFile::load().

## ◆ setComment()

void setComment | ( | const String & | comment | ) |

sets the free-text comment

Referenced by XMassFile::load().

## ◆ setDataProcessing()

void setDataProcessing | ( | const std::vector< DataProcessingPtr > & | data_processing | ) |

sets the description of the applied processing

Referenced by XMassFile::load().

## ◆ setInstrumentSettings()

void setInstrumentSettings | ( | const InstrumentSettings & | instrument_settings | ) |

sets the instrument settings of the current spectrum

Referenced by XMassFile::load().

## ◆ setNativeID()

void setNativeID | ( | const String & | native_id | ) |

sets the native identifier for the spectrum, used by the acquisition software.

Referenced by MascotGenericFile::getNextSpectrum_(), MS2File::load(), XMassFile::load(), and DTA2DFile::load().

## ◆ setPeptideIdentifications()

void setPeptideIdentifications | ( | const std::vector< PeptideIdentification > & | identifications | ) |

sets the PeptideIdentification vector

## ◆ setPrecursors()

void setPrecursors | ( | const std::vector< Precursor > & | precursors | ) |

sets the precursors

Referenced by SpectraMerger::mergeSpectra_(), NucleicAcidSearchEngine::preprocessSpectra_(), and TOPPViewBase::showSpectrumGenerationDialog().

## ◆ setProducts()

void setProducts | ( | const std::vector< Product > & | products | ) |

sets the products

## ◆ setSourceFile()

void setSourceFile | ( | const SourceFile & | source_file | ) |

sets the source file

Referenced by XMassFile::load().

## ◆ setType()

void setType | ( | SpectrumType | type | ) |

sets the spectrum type

Referenced by GaussFilter::filter(), MorphologicalFilter::filter(), XMassFile::load(), and PeakPickerIterative::pick().

## ◆ unify()

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)

Referenced by SpectraMerger::mergeSpectra_().

## Member Data Documentation

## ◆ acquisition_info_

AcquisitionInfo acquisition_info_

protected

## ◆ comment_

String comment_

protected

## ◆ data_processing_

std::vector< DataProcessingPtr > data_processing_

protected

## ◆ identification_

std::vector<PeptideIdentification> identification_

protected

## ◆ instrument_settings_

InstrumentSettings instrument_settings_

protected

## ◆ NamesOfSpectrumType

const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE]

static

Names of spectrum types.

## ◆ native_id_

String native_id_

protected

## ◆ precursors_

std::vector<Precursor> precursors_

protected

## ◆ products_

std::vector<Product> products_

protected

## ◆ source_file_

SourceFile source_file_

protected

## ◆ type_

SpectrumType type_

protected