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ChromatogramSettings Class Reference

Representation of chromatogram settings, e.g. SRM/MRM chromatograms. More...

#include <OpenMS/METADATA/ChromatogramSettings.h>

Inheritance diagram for ChromatogramSettings:
MetaInfoInterface MSChromatogram< ChromatogramPeakType > MSChromatogram< PeakT >

Public Types

enum  ChromatogramType {
  MASS_CHROMATOGRAM = 0, TOTAL_ION_CURRENT_CHROMATOGRAM, SELECTED_ION_CURRENT_CHROMATOGRAM, BASEPEAK_CHROMATOGRAM,
  SELECTED_ION_MONITORING_CHROMATOGRAM, SELECTED_REACTION_MONITORING_CHROMATOGRAM, ELECTROMAGNETIC_RADIATION_CHROMATOGRAM, ABSORPTION_CHROMATOGRAM,
  EMISSION_CHROMATOGRAM, SIZE_OF_CHROMATOGRAM_TYPE
}
 

Public Member Functions

 ChromatogramSettings ()
 Constructor. More...
 
 ChromatogramSettings (const ChromatogramSettings &source)
 Copy constructor. More...
 
virtual ~ChromatogramSettings ()
 Destructor. More...
 
ChromatogramSettingsoperator= (const ChromatogramSettings &source)
 
bool operator== (const ChromatogramSettings &rhs) const
 Equality operator. More...
 
bool operator!= (const ChromatogramSettings &rhs) const
 Equality operator. 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 PrecursorgetPrecursor () const
 returns a const reference to the precursors More...
 
PrecursorgetPrecursor ()
 returns a mutable reference to the precursors More...
 
void setPrecursor (const Precursor &precursor)
 sets the precursors More...
 
const ProductgetProduct () const
 returns a const reference to the products More...
 
ProductgetProduct ()
 returns a mutable reference to the products More...
 
void setProduct (const Product &product)
 sets the products 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...
 
ChromatogramType getChromatogramType () const
 returns the chromatogram type, e.g. a SRM chromatogram More...
 
void setChromatogramType (ChromatogramType type)
 sets the chromatogram type More...
 
- Public Member Functions inherited from MetaInfoInterface
 MetaInfoInterface ()
 constructor More...
 
 MetaInfoInterface (const MetaInfoInterface &rhs)
 copy constructor More...
 
 ~MetaInfoInterface ()
 destructor More...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (const String &name) const
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (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 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< DataProcessingdata_processing_
 
ChromatogramType type_
 
- 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 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.

Constructor & Destructor Documentation

Copy constructor.

virtual ~ChromatogramSettings ( )
virtual

Destructor.

Member Function Documentation

const AcquisitionInfo& getAcquisitionInfo ( ) const

returns a const reference to the acquisition info

AcquisitionInfo& getAcquisitionInfo ( )

returns a mutable reference to the acquisition info

ChromatogramType getChromatogramType ( ) const

returns the chromatogram type, e.g. a SRM chromatogram

Referenced by MzMLHandler< MapType >::writeChromatogram_().

const String& getComment ( ) const

returns the free-text comment

const std::vector<DataProcessing>& getDataProcessing ( ) const

returns a const reference to the description of the applied processing

Referenced by TOPPBase::addDataProcessing_(), MSDataWritingConsumer::consumeChromatogram(), and ChromatogramExtractor::return_chromatogram().

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

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<> >::populateChromatogramsWithData_(), and MzMLHandler< MapType >::writeChromatogram_().

const Precursor& getPrecursor ( ) const

returns a const reference to the precursors

Referenced by MzMLHandler< MapType >::writeChromatogram_().

Precursor& getPrecursor ( )

returns a mutable reference to the precursors

const Product& getProduct ( ) const

returns a const reference to the products

Referenced by MSChromatogram< ChromatogramPeakType >::getMZ(), and MzMLHandler< MapType >::writeChromatogram_().

Product& getProduct ( )

returns a mutable reference to the products

const SourceFile& getSourceFile ( ) const

returns a const reference to the source file

SourceFile& getSourceFile ( )

returns a mutable reference to the source file

bool operator!= ( const ChromatogramSettings rhs) const

Equality operator.

ChromatogramSettings& operator= ( const ChromatogramSettings source)
bool operator== ( const ChromatogramSettings rhs) const

Equality operator.

Referenced by MSChromatogram< ChromatogramPeakType >::operator==().

void setAcquisitionInfo ( const AcquisitionInfo acquisition_info)

sets the acquisition info

Referenced by ChromatogramExtractor::return_chromatogram().

void setChromatogramType ( ChromatogramType  type)

sets the chromatogram type

Referenced by ChromatogramExtractor::return_chromatogram().

void setComment ( const String comment)

sets the free-text comment

void setDataProcessing ( const std::vector< DataProcessing > &  data_processing)

sets the description of the applied processing

void setInstrumentSettings ( const InstrumentSettings instrument_settings)

sets the instrument settings of the current spectrum

Referenced by ChromatogramExtractor::return_chromatogram().

void setNativeID ( const String native_id)

sets the native identifier for the spectrum, used by the acquisition software.

Referenced by ChromatogramExtractor::return_chromatogram().

void setPrecursor ( const Precursor precursor)

sets the precursors

Referenced by ChromatogramExtractor::return_chromatogram().

void setProduct ( const Product product)

sets the products

Referenced by ChromatogramExtractor::return_chromatogram().

void setSourceFile ( const SourceFile source_file)

sets the source file

Referenced by ChromatogramExtractor::return_chromatogram().

Member Data Documentation

AcquisitionInfo acquisition_info_
protected
const char* const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]
static

Names of chromatogram types corresponding to enum ChromatogramType.

String comment_
protected
std::vector<DataProcessing> data_processing_
protected
InstrumentSettings instrument_settings_
protected
String native_id_
protected
Precursor precursor_
protected
Product product_
protected
SourceFile source_file_
protected
ChromatogramType type_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:33 using doxygen 1.8.9.1