DataProcessing Class Reference

Description of the applied preprocessing steps. More...

#include <OpenMS/METADATA/DataProcessing.h>

Inheritance diagram for DataProcessing:

Collaboration diagram for DataProcessing:

Public Types
enum	ProcessingAction {   DATA_PROCESSING , CHARGE_DECONVOLUTION , DEISOTOPING , SMOOTHING ,   CHARGE_CALCULATION , PRECURSOR_RECALCULATION , BASELINE_REDUCTION , PEAK_PICKING ,   ALIGNMENT , CALIBRATION , NORMALIZATION , FILTERING ,   QUANTITATION , FEATURE_GROUPING , IDENTIFICATION_MAPPING , FORMAT_CONVERSION ,   CONVERSION_MZDATA , CONVERSION_MZML , CONVERSION_MZXML , CONVERSION_DTA ,   IDENTIFICATION , ION_MOBILITY_BINNING , SIZE_OF_PROCESSINGACTION }

Public Member Functions
	DataProcessing ()=default
	Constructor. More...
	DataProcessing (const DataProcessing &)=default
	Copy constructor. More...
	DataProcessing (DataProcessing &&) noexcept
	Move constructor. More...
	~DataProcessing ()
	Destructor. More...
DataProcessing &	operator= (const DataProcessing &)=default
	Assignment operator. More...
DataProcessing &	operator= (DataProcessing &&) &=default
	Move assignment operator. More...
bool	operator== (const DataProcessing &rhs) const
	Equality operator. More...
bool	operator!= (const DataProcessing &rhs) const
	Equality operator. More...
const Software &	getSoftware () const
	returns a const reference to the software used for processing More...
Software &	getSoftware ()
	returns a mutable reference to the software used for processing More...
void	setSoftware (const Software &software)
	sets the software used for processing More...
const std::set< ProcessingAction > &	getProcessingActions () const
	returns a const reference to the applied processing actions More...
std::set< ProcessingAction > &	getProcessingActions ()
	returns a mutable reference to the description of the applied processing More...
void	setProcessingActions (const std::set< ProcessingAction > &actions)
	sets the description of the applied processing More...
const DateTime &	getCompletionTime () const
	returns the time of completion of the processing More...
void	setCompletionTime (const DateTime &completion_time)
	sets the time of completion taking a DateTime object 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
	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 DataValue &	getMetaValue (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)
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 Member Functions
static StringList	getAllNamesOfProcessingAction ()
	returns all processing action names known to OpenMS More...
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

Static Public Attributes
static const std::string	NamesOfProcessingAction [SIZE_OF_PROCESSINGACTION]
	Names of inlet types. More...

Protected Attributes
Software	software_
std::set< ProcessingAction >	processing_actions_
DateTime	completion_time_
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Additional Inherited Members
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Detailed Description

Description of the applied preprocessing steps.

Member Enumeration Documentation

ProcessingAction

enum ProcessingAction

Enumerator
DATA_PROCESSING	General data processing (if no other term applies)
CHARGE_DECONVOLUTION	Charge deconvolution.
DEISOTOPING	Deisotoping.
SMOOTHING	Smoothing of the signal to reduce noise.
CHARGE_CALCULATION	Determination of the peak charge.
PRECURSOR_RECALCULATION	Recalculation of precursor m/z.
BASELINE_REDUCTION	Baseline reduction.
PEAK_PICKING	Peak picking (conversion from raw to peak data)
ALIGNMENT	Retention time alignment of different maps.
CALIBRATION	Calibration of m/z positions.
NORMALIZATION	Normalization of intensity values.
FILTERING	Data filtering or extraction.
QUANTITATION	Quantitation.
FEATURE_GROUPING	Feature grouping
IDENTIFICATION_MAPPING	Identification mapping
FORMAT_CONVERSION	General file format conversion (if no other term applies)
CONVERSION_MZDATA	Conversion to mzData format.
CONVERSION_MZML	Conversion to mzML format.
CONVERSION_MZXML	Conversion to mzXML format.
CONVERSION_DTA	Conversion to DTA format.
IDENTIFICATION	Identification.
ION_MOBILITY_BINNING	Ion mobility binning (merging of spectra with similar IM values)
SIZE_OF_PROCESSINGACTION

Constructor & Destructor Documentation

DataProcessing() [1/3]

DataProcessing ( )

default

Constructor.

DataProcessing() [2/3]

DataProcessing ( const DataProcessing &  )

default

Copy constructor.

DataProcessing() [3/3]

DataProcessing ( DataProcessing &&  )

noexcept

Move constructor.

~DataProcessing()

~DataProcessing

(

)

Destructor.

Member Function Documentation

getAllNamesOfProcessingAction()

static StringList getAllNamesOfProcessingAction ( )

static

returns all processing action names known to OpenMS

getCompletionTime()

const DateTime& getCompletionTime

(

)

const

returns the time of completion of the processing

getProcessingActions() [1/2]

std::set<ProcessingAction>& getProcessingActions

(

)

returns a mutable reference to the description of the applied processing

getProcessingActions() [2/2]

const std::set<ProcessingAction>& getProcessingActions

(

)

const

returns a const reference to the applied processing actions

getSoftware() [1/2]

Software& getSoftware

(

)

returns a mutable reference to the software used for processing

getSoftware() [2/2]

const Software& getSoftware

(

)

const

returns a const reference to the software used for processing

operator!=()

bool operator!=

(

const DataProcessing &

rhs

)

const

Equality operator.

operator=() [1/2]

DataProcessing& operator= ( const DataProcessing &  )

default

Assignment operator.

operator=() [2/2]

DataProcessing& operator= ( DataProcessing &&  ) &

default

Move assignment operator.

operator==()

bool operator==

(

const DataProcessing &

rhs

)

const

Equality operator.

setCompletionTime()

void setCompletionTime

(

const DateTime &

completion_time

)

sets the time of completion taking a DateTime object

Referenced by XMassFile::load().

setProcessingActions()

void setProcessingActions

(

const std::set< ProcessingAction > &

actions

)

sets the description of the applied processing

Referenced by XMassFile::load().

setSoftware()

void setSoftware

(

const Software &

software

)

sets the software used for processing

Referenced by XMassFile::load().

Member Data Documentation

completion_time_

DateTime completion_time_

protected

NamesOfProcessingAction

const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION]

static

Names of inlet types.

processing_actions_

std::set<ProcessingAction> processing_actions_

protected

software_

Software software_

protected