OpenMS  2.8.0
Public Types | Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
SpectrumSettings Class Reference

Representation of 1D spectrum settings. More...

#include <OpenMS/METADATA/SpectrumSettings.h>

Inheritance diagram for SpectrumSettings:
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Collaboration diagram for SpectrumSettings:
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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...
 
SpectrumSettingsoperator= (const SpectrumSettings &)=default
 
SpectrumSettingsoperator= (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 StringgetNativeID () 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 StringgetComment () const
 returns the free-text comment More...
 
void setComment (const String &comment)
 sets the free-text comment More...
 
const InstrumentSettingsgetInstrumentSettings () const
 returns a const reference to the instrument settings of the current spectrum More...
 
InstrumentSettingsgetInstrumentSettings ()
 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 AcquisitionInfogetAcquisitionInfo () const
 returns a const reference to the acquisition info More...
 
AcquisitionInfogetAcquisitionInfo ()
 returns a mutable reference to the acquisition info More...
 
void setAcquisitionInfo (const AcquisitionInfo &acquisition_info)
 sets the acquisition info More...
 
const SourceFilegetSourceFile () const
 returns a const reference to the source file More...
 
SourceFilegetSourceFile ()
 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...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (MetaInfoInterface &&) noexcept
 Move assignment operator. More...
 
void swap (MetaInfoInterface &rhs)
 Swap contents. 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 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 DataValuegetMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More...
 
bool metaValueExists (const String &name) const
 Returns whether an entry with the given name exists. More...
 
bool metaValueExists (UInt index) const
 Returns whether an entry with the given index exists. More...
 
void setMetaValue (const String &name, const DataValue &value)
 Sets the DataValue corresponding to a name. More...
 
void setMetaValue (UInt index, const DataValue &value)
 Sets the DataValue corresponding to an index. More...
 
void removeMetaValue (const String &name)
 Removes the DataValue corresponding to name if it exists. More...
 
void removeMetaValue (UInt index)
 Removes the DataValue corresponding to index if it exists. More...
 
void addMetaValues (const MetaInfoInterface &from)
 function to copy all meta values from one object to this one More...
 
void getKeys (std::vector< String > &keys) const
 Fills the given vector with a list of all keys for which a value is set. More...
 
void getKeys (std::vector< UInt > &keys) const
 Fills the given vector with a list of all keys for which a value is set. More...
 
bool isMetaEmpty () const
 Returns if the MetaInfo is empty. More...
 
void clearMetaInfo ()
 Removes all meta values. More...
 

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< Precursorprecursors_
 
std::vector< Productproducts_
 
std::vector< PeptideIdentificationidentification_
 
std::vector< DataProcessingPtrdata_processing_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 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

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]

Constructor.

◆ SpectrumSettings() [2/3]

SpectrumSettings ( const SpectrumSettings )
default

Copy constructor.

◆ SpectrumSettings() [3/3]

Move constructor.

◆ ~SpectrumSettings()

Destructor.

Member Function Documentation

◆ getAcquisitionInfo() [1/2]

AcquisitionInfo& getAcquisitionInfo ( )

returns a mutable reference to the acquisition info

◆ getAcquisitionInfo() [2/2]

const AcquisitionInfo& getAcquisitionInfo ( ) const

returns a const reference to the acquisition info

Referenced by ChromatogramExtractor::return_chromatogram().

◆ 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]

InstrumentSettings& getInstrumentSettings ( )

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

◆ getInstrumentSettings() [2/2]

const InstrumentSettings& getInstrumentSettings ( ) const

◆ 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]

std::vector<PeptideIdentification>& getPeptideIdentifications ( )

returns a mutable reference to the PeptideIdentification vector

◆ getPeptideIdentifications() [2/2]

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

returns a const reference to the PeptideIdentification vector

◆ getPrecursors() [1/2]

std::vector<Precursor>& getPrecursors ( )

returns a mutable reference to the precursors

◆ getPrecursors() [2/2]

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

◆ getProducts() [1/2]

std::vector<Product>& getProducts ( )

returns a mutable reference to the products

◆ getProducts() [2/2]

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

returns a const reference to the products

◆ getSourceFile() [1/2]

SourceFile& getSourceFile ( )

returns a mutable reference to the source file

◆ getSourceFile() [2/2]

const SourceFile& getSourceFile ( ) const

returns a const reference to the source file

Referenced by ChromatogramExtractor::return_chromatogram().

◆ 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(), DTA2DFile::load(), and XMassFile::load().

◆ setPeptideIdentifications()

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

sets the PeptideIdentification vector

◆ setPrecursors()

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

◆ 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)

◆ 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