OpenMS
2.6.0
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Representation of 1D spectrum settings. More...
#include <OpenMS/METADATA/SpectrumSettings.h>
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 | 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< 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... | |
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.
enum SpectrumType |
SpectrumSettings | ( | ) |
Constructor.
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default |
Copy constructor.
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default |
Move constructor.
~SpectrumSettings | ( | ) |
Destructor.
AcquisitionInfo& getAcquisitionInfo | ( | ) |
returns a mutable reference to the acquisition info
const AcquisitionInfo& getAcquisitionInfo | ( | ) | const |
returns a const reference to the acquisition info
Referenced by ChromatogramExtractor::return_chromatogram().
const String& getComment | ( | ) | const |
returns the free-text comment
std::vector< DataProcessingPtr >& getDataProcessing | ( | ) |
returns a mutable reference to the description of the applied processing
Referenced by ChromatogramExtractor::return_chromatogram().
const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing | ( | ) | const |
returns a const reference to the description of the applied processing
InstrumentSettings& getInstrumentSettings | ( | ) |
returns a mutable reference to the instrument settings of the current spectrum
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().
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().
std::vector<PeptideIdentification>& getPeptideIdentifications | ( | ) |
returns a mutable reference to the PeptideIdentification vector
const std::vector<PeptideIdentification>& getPeptideIdentifications | ( | ) | const |
returns a const reference to the PeptideIdentification vector
std::vector<Precursor>& getPrecursors | ( | ) |
returns a mutable reference to the precursors
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().
std::vector<Product>& getProducts | ( | ) |
returns a mutable reference to the products
const std::vector<Product>& getProducts | ( | ) | const |
returns a const reference to the products
SourceFile& getSourceFile | ( | ) |
returns a mutable reference to the source file
const SourceFile& getSourceFile | ( | ) | const |
returns a const reference to the source file
Referenced by ChromatogramExtractor::return_chromatogram().
SpectrumType getType | ( | ) | const |
returns the spectrum type (centroided (PEAKS) or profile data (RAW))
bool operator!= | ( | const SpectrumSettings & | rhs | ) | const |
Equality operator.
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default |
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default |
Move assignment operator.
bool operator== | ( | const SpectrumSettings & | rhs | ) | const |
Equality operator.
void setAcquisitionInfo | ( | const AcquisitionInfo & | acquisition_info | ) |
sets the acquisition info
Referenced by XMassFile::load().
void setComment | ( | const String & | comment | ) |
sets the free-text comment
Referenced by XMassFile::load().
void setDataProcessing | ( | const std::vector< DataProcessingPtr > & | data_processing | ) |
sets the description of the applied processing
Referenced by XMassFile::load().
void setInstrumentSettings | ( | const InstrumentSettings & | instrument_settings | ) |
sets the instrument settings of the current spectrum
Referenced by XMassFile::load().
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().
void setPeptideIdentifications | ( | const std::vector< PeptideIdentification > & | identifications | ) |
sets the PeptideIdentification vector
void setPrecursors | ( | const std::vector< Precursor > & | precursors | ) |
sets the precursors
Referenced by SpectraMerger::mergeSpectra_(), NucleicAcidSearchEngine::preprocessSpectra_(), and TOPPViewBase::showSpectrumGenerationDialog().
void setProducts | ( | const std::vector< Product > & | products | ) |
sets the products
void setSourceFile | ( | const SourceFile & | source_file | ) |
sets the source file
Referenced by XMassFile::load().
void setType | ( | SpectrumType | type | ) |
sets the spectrum type
Referenced by GaussFilter::filter(), MorphologicalFilter::filter(), XMassFile::load(), and PeakPickerIterative::pick().
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_().
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Names of spectrum types.
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