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

#include <OpenMS/METADATA/ChromatogramSettings.h>

Inheritance diagram for ChromatogramSettings:

Collaboration diagram for ChromatogramSettings:

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...

ChromatogramSettings &	operator= (const ChromatogramSettings &)=default

ChromatogramSettings &	operator= (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 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 (MetaInfoInterface &&) noexcept
	Move constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...

MetaInfoInterface &	operator= (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 DataValue &	getMetaValue (const String &name, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...

const DataValue &	getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to an index, or a default value (default: 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< 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

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]

ChromatogramSettings ( )

Constructor.

◆ ChromatogramSettings() [2/3]

ChromatogramSettings ( const ChromatogramSettings & )

default

Copy constructor.

◆ ChromatogramSettings() [3/3]

ChromatogramSettings ( ChromatogramSettings && )

default

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

◆ 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 )

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_

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

Public Types

Public Member Functions

Static Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ChromatogramType

Constructor & Destructor Documentation

◆ ChromatogramSettings() [1/3]

◆ ChromatogramSettings() [2/3]

◆ ChromatogramSettings() [3/3]

◆ ~ChromatogramSettings()

Member Function Documentation

◆ getAcquisitionInfo() [1/2]

◆ getAcquisitionInfo() [2/2]

◆ getChromatogramType()

◆ getComment()

◆ getDataProcessing() [1/2]

◆ getDataProcessing() [2/2]

◆ getInstrumentSettings() [1/2]

◆ getInstrumentSettings() [2/2]

◆ getNativeID()

◆ getPrecursor() [1/2]

◆ getPrecursor() [2/2]

◆ getProduct() [1/2]

◆ getProduct() [2/2]

◆ getSourceFile() [1/2]

◆ getSourceFile() [2/2]

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setAcquisitionInfo()

◆ setChromatogramType()

◆ setComment()

◆ setDataProcessing()

◆ setInstrumentSettings()

◆ setNativeID()

◆ setPrecursor()

◆ setProduct()

◆ setSourceFile()

Member Data Documentation

◆ acquisition_info_

◆ ChromatogramNames

◆ comment_

◆ data_processing_

◆ instrument_settings_

◆ native_id_

◆ precursor_

◆ product_

◆ source_file_

◆ type_