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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 ()
 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...
 

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

List of chromatogram names, e.g., SELECTED_REACTION_MONITORING_CHROMATOGRAM. Actual names can be accessed using the ChromatogramNames[] array

Enumerator
MASS_CHROMATOGRAM 
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 

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

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< 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

void setChromatogramType ( ChromatogramType  type)

sets the chromatogram type

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

void setNativeID ( const String native_id)

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

void setPrecursor ( const Precursor precursor)

sets the precursors

void setProduct ( const Product product)

sets the products

void setSourceFile ( const SourceFile source_file)

sets the source file

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 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:32 using doxygen 1.8.5