OpenMS
ChromatogramSettings Class Reference

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

#include <OpenMS/METADATA/ChromatogramSettings.h>

Inheritance diagram for ChromatogramSettings:
[legend]
Collaboration diagram for ChromatogramSettings:
[legend]

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 &)=default
 Copy constructor. More...
 
 ChromatogramSettings (ChromatogramSettings &&)=default
 Move constructor. More...
 
virtual ~ChromatogramSettings ()
 Destructor. More...
 
ChromatogramSettingsoperator= (const ChromatogramSettings &)=default
 
ChromatogramSettingsoperator= (ChromatogramSettings &&) &=default
 Move assignment operator. More...
 
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...
 
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 (MetaInfoInterface &&) noexcept
 Move constructor. More...
 
 ~MetaInfoInterface ()
 Destructor. More...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (MetaInfoInterface &&) noexcept
 Move assignment operator. More...
 
void swap (MetaInfoInterface &rhs)
 Swap contents. 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, or DataValue::EMPTY if not found. More...
 
DataValue getMetaValue (const String &name, const DataValue &default_value) const
 Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found. More...
 
const DataValuegetMetaValue (UInt index) const
 Returns the value corresponding to the index, or DataValue::EMPTY if not found. More...
 
DataValue getMetaValue (UInt index, const DataValue &default_value) const
 Returns the value corresponding to the index, or a default value (e.g.: 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 addMetaValues (const MetaInfoInterface &from)
 function to copy all meta values from one object to this one 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< DataProcessingPtrdata_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.

Member Enumeration Documentation

◆ ChromatogramType

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

◆ ChromatogramSettings() [1/3]

Constructor.

◆ ChromatogramSettings() [2/3]

Copy constructor.

◆ ChromatogramSettings() [3/3]

Move constructor.

◆ ~ChromatogramSettings()

virtual ~ChromatogramSettings ( )
virtual

Destructor.

Member Function Documentation

◆ getAcquisitionInfo() [1/2]

AcquisitionInfo& getAcquisitionInfo ( )

returns a mutable reference to the acquisition info

◆ getAcquisitionInfo() [2/2]

const AcquisitionInfo& getAcquisitionInfo ( ) const

returns a const 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 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]

InstrumentSettings& getInstrumentSettings ( )

returns a mutable reference to the instrument settings of the current spectrum

◆ getInstrumentSettings() [2/2]

const InstrumentSettings& getInstrumentSettings ( ) const

returns a const 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< ChromatogramType, TransitionType >::chromatogramIdsMatch(), and MRMTransitionGroupPicker::pickTransitionGroup().

◆ getPrecursor() [1/2]

Precursor& getPrecursor ( )

returns a mutable reference to the precursors

◆ getPrecursor() [2/2]

const Precursor& getPrecursor ( ) const

returns a const reference to the precursors

Referenced by DimMZ::map().

◆ getProduct() [1/2]

Product& getProduct ( )

returns a mutable reference to the products

◆ getProduct() [2/2]

const Product& getProduct ( ) const

returns a const reference to the products

◆ getSourceFile() [1/2]

SourceFile& getSourceFile ( )

returns a mutable reference to the source file

◆ getSourceFile() [2/2]

const SourceFile& getSourceFile ( ) const

returns a const reference to the source file

◆ operator!=()

bool operator!= ( const ChromatogramSettings rhs) const

Equality operator.

◆ operator=() [1/2]

ChromatogramSettings& operator= ( ChromatogramSettings &&  ) &
default

Move assignment operator.

◆ operator=() [2/2]

ChromatogramSettings& operator= ( const ChromatogramSettings )
default

◆ 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 MRMTransitionGroupPicker::pickTransitionGroup(), and ChromatogramExtractor::return_chromatogram().

◆ setPrecursor()

void setPrecursor ( const Precursor precursor)

◆ 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_

AcquisitionInfo acquisition_info_
protected

◆ ChromatogramNames

const char* const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]
static

Names of chromatogram types corresponding to enum ChromatogramType.

◆ comment_

String comment_
protected

◆ data_processing_

std::vector< DataProcessingPtr > data_processing_
protected

◆ instrument_settings_

InstrumentSettings instrument_settings_
protected

◆ native_id_

String native_id_
protected

◆ precursor_

Precursor precursor_
protected

◆ product_

Product product_
protected

◆ source_file_

SourceFile source_file_
protected

◆ type_

ChromatogramType type_
protected