Representation of chromatogram settings, e.g. SRM/MRM chromatograms. More...
#include <OpenMS/METADATA/ChromatogramSettings.h>
Public Member Functions | |
| ChromatogramSettings () | |
| Constructor. More... | |
| ChromatogramSettings (const ChromatogramSettings &source) | |
| Copy constructor. More... | |
| virtual | ~ChromatogramSettings () |
| Destructor. More... | |
| ChromatogramSettings & | operator= (const ChromatogramSettings &source) |
| bool | operator== (const ChromatogramSettings &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const ChromatogramSettings &rhs) const |
| Equality operator. 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 Precursor & | getPrecursor () const |
| returns a const reference to the precursors More... | |
| Precursor & | getPrecursor () |
| returns a mutable reference to the precursors More... | |
| void | setPrecursor (const Precursor &precursor) |
| sets the precursors More... | |
| const Product & | getProduct () const |
| returns a const reference to the products More... | |
| Product & | getProduct () |
| returns a mutable reference to the products More... | |
| void | setProduct (const Product &product) |
| sets the products More... | |
| ChromatogramType | getChromatogramType () const |
| returns the chromatogram type, e.g. a SRM chromatogram More... | |
| void | setChromatogramType (ChromatogramType type) |
| sets the chromatogram type 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 () | |
| 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 (or DataValue::EMPTY if not found) More... | |
| const DataValue & | getMetaValue (UInt index) const |
| Returns the value corresponding to an index (or 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 char *const | ChromatogramNames [SIZE_OF_CHROMATOGRAM_TYPE+1] |
| Names of chromatogram types corresponding to enum ChromatogramType. More... | |
Protected Attributes | |
| String | native_id_ |
| String | comment_ |
| InstrumentSettings | instrument_settings_ |
| SourceFile | source_file_ |
| AcquisitionInfo | acquisition_info_ |
| Precursor | precursor_ |
| Product | product_ |
| std::vector< DataProcessingPtr > | data_processing_ |
| ChromatogramType | type_ |
| 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 chromatogram settings, e.g. SRM/MRM chromatograms.
It contains the metadata about chromatogram specific instrument settings, acquisition settings, description of the meta values used in the peaks and precursor info.
Member Enumeration Documentation
◆ ChromatogramType
| enum ChromatogramType |
List of chromatogram names, e.g., SELECTED_REACTION_MONITORING_CHROMATOGRAM. Actual names can be accessed using the ChromatogramNames[] array
Constructor & Destructor Documentation
◆ ChromatogramSettings() [1/2]
Constructor.
◆ ChromatogramSettings() [2/2]
| ChromatogramSettings | ( | const ChromatogramSettings & | source | ) |
Copy constructor.
◆ ~ChromatogramSettings()
|
virtual |
Destructor.
Member Function Documentation
◆ getAcquisitionInfo() [1/2]
| const AcquisitionInfo& getAcquisitionInfo | ( | ) | const |
returns a const reference to the acquisition info
◆ getAcquisitionInfo() [2/2]
| AcquisitionInfo& getAcquisitionInfo | ( | ) |
returns a mutable reference to the acquisition info
◆ getChromatogramType()
| ChromatogramType getChromatogramType | ( | ) | const |
returns the chromatogram type, e.g. a SRM 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 TOPPBase::addDataProcessing_(), and 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
◆ 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 MRMTransitionGroup< SpectrumT, TransitionT >::chromatogramIdsMatch(), and MRMTransitionGroupPicker::pickTransitionGroup().
◆ getPrecursor() [1/2]
| const Precursor& getPrecursor | ( | ) | const |
returns a const reference to the precursors
◆ getPrecursor() [2/2]
| Precursor& getPrecursor | ( | ) |
returns a mutable reference to the precursors
◆ getProduct() [1/2]
| const Product& getProduct | ( | ) | const |
returns a const reference to the products
◆ getProduct() [2/2]
| Product& getProduct | ( | ) |
returns a mutable reference to the products
◆ getSourceFile() [1/2]
| const SourceFile& getSourceFile | ( | ) | const |
returns a const reference to the source file
◆ getSourceFile() [2/2]
| SourceFile& getSourceFile | ( | ) |
returns a mutable reference to the source file
◆ operator!=()
| bool operator!= | ( | const ChromatogramSettings & | rhs | ) | const |
Equality operator.
◆ operator=()
| ChromatogramSettings& operator= | ( | const ChromatogramSettings & | source | ) |
◆ operator==()
| bool operator== | ( | const ChromatogramSettings & | rhs | ) | const |
Equality operator.
◆ setAcquisitionInfo()
| void setAcquisitionInfo | ( | const AcquisitionInfo & | acquisition_info | ) |
sets the acquisition info
Referenced by ChromatogramExtractor::return_chromatogram().
◆ setChromatogramType()
| void setChromatogramType | ( | ChromatogramType | type | ) |
sets the chromatogram type
Referenced by ChromatogramExtractor::return_chromatogram().
◆ setComment()
| void setComment | ( | const String & | comment | ) |
sets the free-text comment
◆ setDataProcessing()
| void setDataProcessing | ( | const std::vector< DataProcessingPtr > & | data_processing | ) |
sets the description of the applied processing
◆ setInstrumentSettings()
| void setInstrumentSettings | ( | const InstrumentSettings & | instrument_settings | ) |
sets the instrument settings of the current spectrum
Referenced by ChromatogramExtractor::return_chromatogram().
◆ setNativeID()
| void setNativeID | ( | const String & | native_id | ) |
sets the native identifier for the spectrum, used by the acquisition software.
Referenced by ChromatogramExtractor::return_chromatogram().
◆ setPrecursor()
| void setPrecursor | ( | const Precursor & | precursor | ) |
sets the precursors
Referenced by ChromatogramTools::convertSpectraToChromatograms(), and ChromatogramExtractor::return_chromatogram().
◆ setProduct()
| void setProduct | ( | const Product & | product | ) |
sets the products
Referenced by ChromatogramExtractor::return_chromatogram().
◆ setSourceFile()
| void setSourceFile | ( | const SourceFile & | source_file | ) |
sets the source file
Referenced by ChromatogramExtractor::return_chromatogram().
Member Data Documentation
◆ acquisition_info_
|
protected |
◆ ChromatogramNames
|
static |
Names of chromatogram types corresponding to enum ChromatogramType.
◆ comment_
|
protected |
◆ data_processing_
|
protected |
◆ instrument_settings_
|
protected |
◆ native_id_
|
protected |
◆ precursor_
|
protected |
◆ product_
|
protected |
◆ source_file_
|
protected |
◆ type_
|
protected |