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... | |
|  Public Member Functions inherited from MetaInfoInterface | |
| 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 nameif it exists.  More... | |
| void | removeMetaValue (UInt index) | 
| Removes the DataValue corresponding to indexif 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_ | 
|  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 () | 
| retuns 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.
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 >::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 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 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 FeatureFinderAlgorithmSH< PeakType, FeatureType >::run(), 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 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 >::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 MzMLHandler< MapType >::writeSpectrum_().
| SourceFile& getSourceFile | ( | ) | 
returns a mutable reference to the source file
| SpectrumType getType | ( | ) | const | 
returns the spectrum type
Referenced by 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 XMassFile::load(), and TOPPRNPxl::main_().
| void setDataProcessing | ( | const std::vector< DataProcessing > & | 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 XMassFile::load().
| 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(), 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 PeakPickerHiRes::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)
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Names of spectrum types.
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |