ChromatogramSettings Class Reference

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.
	ChromatogramSettings (const ChromatogramSettings &)=default
	Copy constructor.
	ChromatogramSettings (ChromatogramSettings &&)=default
	Move constructor.
virtual	~ChromatogramSettings ()
	Destructor.
ChromatogramSettings &	operator= (const ChromatogramSettings &)=default
ChromatogramSettings &	operator= (ChromatogramSettings &&) &=default
	Move assignment operator.
bool	operator== (const ChromatogramSettings &rhs) const
	Equality operator.
bool	operator!= (const ChromatogramSettings &rhs) const
	Equality operator.
const String &	getNativeID () const
	returns the native identifier for the spectrum, used by the acquisition software.
void	setNativeID (const String &native_id)
	sets the native identifier for the spectrum, used by the acquisition software.
const String &	getComment () const
	returns the free-text comment
void	setComment (const String &comment)
	sets the free-text comment
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
void	setInstrumentSettings (const InstrumentSettings &instrument_settings)
	sets the instrument settings of the current spectrum
const AcquisitionInfo &	getAcquisitionInfo () const
	returns a const reference to the acquisition info
AcquisitionInfo &	getAcquisitionInfo ()
	returns a mutable reference to the acquisition info
void	setAcquisitionInfo (const AcquisitionInfo &acquisition_info)
	sets the acquisition info
const SourceFile &	getSourceFile () const
	returns a const reference to the source file
SourceFile &	getSourceFile ()
	returns a mutable reference to the source file
void	setSourceFile (const SourceFile &source_file)
	sets the source file
const Precursor &	getPrecursor () const
	returns a const reference to the precursors
Precursor &	getPrecursor ()
	returns a mutable reference to the precursors
void	setPrecursor (const Precursor &precursor)
	sets the precursors
const Product &	getProduct () const
	returns a const reference to the products
Product &	getProduct ()
	returns a mutable reference to the products
void	setProduct (const Product &product)
	sets the products
ChromatogramType	getChromatogramType () const
	returns the chromatogram type, e.g. a SRM chromatogram
void	setChromatogramType (ChromatogramType type)
	sets the chromatogram type
void	setDataProcessing (const std::vector< DataProcessingPtr > &data_processing)
	sets the description of the applied processing
std::vector< DataProcessingPtr > &	getDataProcessing ()
	returns a mutable reference to the description of the applied processing
const std::vector< std::shared_ptr< const DataProcessing > >	getDataProcessing () const
	returns a const reference to the description of the applied processing
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.
	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.
	~MetaInfoInterface ()
	Destructor.
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator.
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.
void	swap (MetaInfoInterface &rhs)
	Swap contents.
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator.
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator.
const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found.
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
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.
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
bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists.
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name.
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.
void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to name if it exists.
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists.
void	addMetaValues (const MetaInfoInterface &from)
void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.
void	clearMetaInfo ()
	Removes all meta values.

Static Public Attributes
static const char *const	ChromatogramNames [SIZE_OF_CHROMATOGRAM_TYPE+1]
	Names of chromatogram types corresponding to enum ChromatogramType.

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_ = nullptr
	Pointer to the MetaInfo object.

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry.
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.

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< std::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

)

sets the precursors

Referenced by 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