Representation of 1D spectrum settings. More...
#include <OpenMS/METADATA/SpectrumSettings.h>
Public Types | |
enum | SpectrumType { UNKNOWN, PEAKS, RAWDATA, SIZE_OF_SPECTRUMTYPE } |
Spectrum peak type. More... | |
Public Member Functions | |
SpectrumSettings () | |
Constructor. More... | |
SpectrumSettings (const SpectrumSettings &source) | |
Copy constructor. More... | |
~SpectrumSettings () | |
Destructor. More... | |
SpectrumSettings & | operator= (const SpectrumSettings &source) |
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 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... | |
const std::vector< DataProcessing > & | getDataProcessing () const |
returns a const reference to the description of the applied processing More... | |
std::vector< DataProcessing > & | getDataProcessing () |
returns a mutable reference to the description of the applied processing More... | |
void | setDataProcessing (const std::vector< DataProcessing > &data_processing) |
sets the description of the applied processing More... | |
![]() | |
MetaInfoInterface () | |
constructor More... | |
MetaInfoInterface (const MetaInfoInterface &rhs) | |
copy constructor More... | |
~MetaInfoInterface () | |
destructor More... | |
MetaInfoInterface & | operator= (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 DataValue & | getMetaValue (const String &name) const |
returns the value corresponding to a string More... | |
const DataValue & | getMetaValue (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... | |
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< DataProcessing > | data_processing_ |
![]() | |
MetaInfo * | meta_ |
pointer to the MetaInfo object. 0 by default More... | |
Additional Inherited Members | |
![]() | |
static MetaInfoRegistry & | metaRegistry () |
returns a reference to the MetaInfoRegistry More... | |
![]() | |
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.
Referenced by MSSpectrum< RichPeak1D >::clear().
SpectrumSettings | ( | const SpectrumSettings & | source | ) |
Copy constructor.
~SpectrumSettings | ( | ) |
Destructor.
const AcquisitionInfo& getAcquisitionInfo | ( | ) | const |
returns a const reference to the acquisition info
Referenced by MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), ChromatogramExtractor::return_chromatogram(), MzDataHandler< MapType >::startElement(), MzMLHandler< MapType >::startElement(), MzMLHandler< MapType >::writeSpectrum_(), and MzDataHandler< MapType >::writeTo().
AcquisitionInfo& getAcquisitionInfo | ( | ) |
returns a mutable reference to the acquisition info
const String& getComment | ( | ) | const |
returns the free-text comment
Referenced by MzXMLHandler< MapType >::writeTo().
const std::vector<DataProcessing>& getDataProcessing | ( | ) | const |
returns a const reference to the description of the applied processing
Referenced by MSDataWritingConsumer::consumeSpectrum(), ChromatogramExtractor::return_chromatogram(), MzDataHandler< MapType >::startElement(), and MzMLHandler< MapType >::writeSpectrum_().
std::vector<DataProcessing>& getDataProcessing | ( | ) |
returns a mutable reference to the description of the applied processing
const InstrumentSettings& getInstrumentSettings | ( | ) | const |
returns a const reference to the instrument settings of the current spectrum
Referenced by MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), ChromatogramExtractor::return_chromatogram(), MzDataHandler< MapType >::startElement(), MzMLHandler< MapType >::startElement(), MzMLHandler< MapType >::writeSpectrum_(), MzDataHandler< MapType >::writeTo(), and MzXMLHandler< MapType >::writeTo().
InstrumentSettings& getInstrumentSettings | ( | ) |
returns a mutable reference to the instrument settings of the current spectrum
const String& getNativeID | ( | ) | const |
returns the native identifier for the spectrum, used by the acquisition software.
Referenced by MzMLHandler< MSExperiment<> >::populateSpectraWithData_(), MzMLHandler< MapType >::writeSpectrum_(), MzDataHandler< MapType >::writeTo(), and MzXMLHandler< MapType >::writeTo().
const std::vector<PeptideIdentification>& getPeptideIdentifications | ( | ) | const |
returns a const reference to the PeptideIdentification vector
std::vector<PeptideIdentification>& getPeptideIdentifications | ( | ) |
returns a mutable reference to the PeptideIdentification vector
const std::vector<Precursor>& getPrecursors | ( | ) | const |
returns a const reference to the precursors
Referenced by FullSwathFileConsumer::consumeSpectrum(), SwathFile::countScansInSwath_(), MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), MS2File::load(), MascotInfile::load(), MascotGenericFile::load(), SimpleSearchEngine::main_(), SpectraMerger::mergeSpectra_(), PrecursorMassComparator::operator()(), ChromatogramExtractor::return_chromatogram(), MzDataHandler< MapType >::startElement(), MzMLHandler< MapType >::startElement(), MzMLHandler< MapType >::writeSpectrum_(), MzDataHandler< MapType >::writeTo(), and MzXMLHandler< MapType >::writeTo().
std::vector<Precursor>& getPrecursors | ( | ) |
returns a mutable reference to the precursors
const std::vector<Product>& getProducts | ( | ) | const |
returns a const reference to the products
Referenced by MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), MzMLHandler< MapType >::startElement(), and MzMLHandler< MapType >::writeSpectrum_().
std::vector<Product>& getProducts | ( | ) |
returns a mutable reference to the products
const SourceFile& getSourceFile | ( | ) | const |
returns a const reference to the source file
Referenced by ChromatogramExtractor::return_chromatogram(), and MzMLHandler< MapType >::writeSpectrum_().
SourceFile& getSourceFile | ( | ) |
returns a mutable reference to the source file
SpectrumType getType | ( | ) | const |
returns the spectrum type
Referenced by PeakPickerHiRes::pickExperiment(), MzMLHandler< MapType >::writeSpectrum_(), and MzDataHandler< MapType >::writeTo().
bool operator!= | ( | const SpectrumSettings & | rhs | ) | const |
Equality operator.
SpectrumSettings& operator= | ( | const SpectrumSettings & | source | ) |
Referenced by MSSpectrum< RichPeak1D >::clear(), and MSSpectrum< RichPeak1D >::operator=().
bool operator== | ( | const SpectrumSettings & | rhs | ) | const |
Equality operator.
Referenced by MSSpectrum< RichPeak1D >::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 MzDataHandler< MapType >::characters(), XMassFile::load(), and TOPPRNPxl::main_().
void setDataProcessing | ( | const std::vector< DataProcessing > & | data_processing | ) |
sets the description of the applied processing
Referenced by XMassFile::load(), and MzMLHandler< MapType >::startElement().
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 MS2File::load(), XMassFile::load(), DTA2DFile::load(), MzDataHandler< MapType >::startElement(), and MzMLHandler< MapType >::startElement().
void setPeptideIdentifications | ( | const std::vector< PeptideIdentification > & | identifications | ) |
sets the PeptideIdentification vector
void setPrecursors | ( | const std::vector< Precursor > & | precursors | ) |
sets the precursors
Referenced by TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), SpectraMerger::mergeSpectra_(), 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(), and MzMLHandler< MapType >::startElement().
void setType | ( | SpectrumType | type | ) |
sets the spectrum type
Referenced by GaussFilter::filter(), MorphologicalFilter::filter(), MzMLHandler< MapType >::handleCVParam_(), XMassFile::load(), PeakPickerHiRes::pick(), PeakPickerIterative::pick(), and MzDataHandler< MapType >::startElement().
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_().
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
static |
Names of spectrum types.
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |