OpenMS
DataProcessing Class Reference

Description of the applied preprocessing steps. More...

#include <OpenMS/METADATA/DataProcessing.h>

Inheritance diagram for DataProcessing:
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Collaboration diagram for DataProcessing:
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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...
 
DataProcessingoperator= (const DataProcessing &)=default
 Assignment operator. More...
 
DataProcessingoperator= (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 SoftwaregetSoftware () const
 returns a const reference to the software used for processing More...
 
SoftwaregetSoftware ()
 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 DateTimegetCompletionTime () 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...
 
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 std::string NamesOfProcessingAction [SIZE_OF_PROCESSINGACTION]
 Names of inlet types. More...
 

Protected Attributes

Software software_
 
std::set< ProcessingActionprocessing_actions_
 
DateTime completion_time_
 
- 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

Description of the applied preprocessing steps.

Member Enumeration Documentation

◆ 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()

Destructor.

Member Function Documentation

◆ 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