Description of the experimental settings. More...

#include <OpenMS/METADATA/ExperimentalSettings.h>

Inheritance diagram for ExperimentalSettings:

Collaboration diagram for ExperimentalSettings:

Public Member Functions
	ExperimentalSettings ()=default
	Constructor. More...

	ExperimentalSettings (const ExperimentalSettings &)=default
	Copy constructor. More...

	ExperimentalSettings (ExperimentalSettings &&)=default
	Move constructor. More...

	~ExperimentalSettings () override
	Destructor. More...

ExperimentalSettings &	operator= (const ExperimentalSettings &)=default
	Assignment operator. More...

ExperimentalSettings &	operator= (ExperimentalSettings &&)=default
	Move assignment operator. More...

bool	operator== (const ExperimentalSettings &rhs) const
	Equality operator. More...

bool	operator!= (const ExperimentalSettings &rhs) const
	Equality operator. More...

const Sample &	getSample () const
	returns a const reference to the sample description More...

Sample &	getSample ()
	returns a mutable reference to the sample description More...

void	setSample (const Sample &sample)
	sets the sample description More...

const std::vector< SourceFile > &	getSourceFiles () const
	returns a const reference to the source data file More...

std::vector< SourceFile > &	getSourceFiles ()
	returns a mutable reference to the source data file More...

void	setSourceFiles (const std::vector< SourceFile > &source_files)
	sets the source data file More...

const std::vector< ContactPerson > &	getContacts () const
	returns a const reference to the list of contact persons More...

std::vector< ContactPerson > &	getContacts ()
	returns a mutable reference to the list of contact persons More...

void	setContacts (const std::vector< ContactPerson > &contacts)
	sets the list of contact persons More...

const Instrument &	getInstrument () const
	returns a const reference to the MS instrument description More...

Instrument &	getInstrument ()
	returns a mutable reference to the MS instrument description More...

void	setInstrument (const Instrument &instrument)
	sets the MS instrument description More...

const HPLC &	getHPLC () const
	returns a const reference to the description of the HPLC run More...

HPLC &	getHPLC ()
	returns a mutable reference to the description of the HPLC run More...

void	setHPLC (const HPLC &hplc)
	sets the description of the HPLC run More...

const DateTime &	getDateTime () const
	returns the date the experiment was performed More...

void	setDateTime (const DateTime &date)
	sets the date the experiment was performed More...

const String &	getComment () const
	returns the free-text comment More...

void	setComment (const String &comment)
	sets the free-text comment More...

const std::vector< ProteinIdentification > &	getProteinIdentifications () const
	returns a const reference to the protein ProteinIdentification vector More...

std::vector< ProteinIdentification > &	getProteinIdentifications ()
	returns a mutable reference to the protein ProteinIdentification vector More...

void	setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications)
	sets the protein ProteinIdentification vector More...

const String &	getFractionIdentifier () const
	returns fraction identifier More...

void	setFractionIdentifier (const String &fraction_identifier)
	sets the fraction identifier 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)
	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...

Public Member Functions inherited from DocumentIdentifier
	DocumentIdentifier ()
	Default constructor. More...

	DocumentIdentifier (const DocumentIdentifier &)=default
	Copy constructor. More...

	DocumentIdentifier (DocumentIdentifier &&)=default
	Move constructor. More...

virtual	~DocumentIdentifier ()
	Destructor. More...

DocumentIdentifier &	operator= (const DocumentIdentifier &)=default
	Assignment operator. More...

DocumentIdentifier &	operator= (DocumentIdentifier &&) &=default
	Move assignment operator. More...

bool	operator== (const DocumentIdentifier &rhs) const
	Equality operator. More...

void	setIdentifier (const String &id)
	set document identifier (e.g. an LSID) More...

const String &	getIdentifier () const
	retrieve document identifier (e.g. an LSID) More...

void	swap (DocumentIdentifier &from)
	exchange content with `from` More...

void	setLoadedFilePath (const String &file_name)
	set the file_name_ according to absolute path of the file loaded from preferably done whilst loading More...

const String &	getLoadedFilePath () const
	get the file_name_ which is the absolute path to the file loaded from More...

void	setLoadedFileType (const String &file_name)
	set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably done whilst loading More...

const FileTypes::Type &	getLoadedFileType () const
	get the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, ...) of the file loaded from More...

Protected Attributes
Sample	sample_

std::vector< SourceFile >	source_files_

std::vector< ContactPerson >	contacts_

Instrument	instrument_

HPLC	hplc_

DateTime	datetime_

String	comment_

std::vector< ProteinIdentification >	protein_identifications_

String	fraction_identifier_

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Protected Attributes inherited from DocumentIdentifier
String	id_
	the ID (e.g. LSID) More...

String	file_path_
	the path to the loaded file More...

FileTypes::Type	file_type_
	the type of the loaded file 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

Description of the experimental settings.

These settings are valid for the whole experiment. See SpectrumSettings for settings which are specific to an MSSpectrum. See ChromatogramSettings for settings which are specific to an MSChromatogram.

Constructor & Destructor Documentation

◆ ExperimentalSettings() [1/3]

ExperimentalSettings ( )

default

Constructor.

◆ ExperimentalSettings() [2/3]

ExperimentalSettings ( const ExperimentalSettings & )

default

Copy constructor.

◆ ExperimentalSettings() [3/3]

ExperimentalSettings ( ExperimentalSettings && )

default

Move constructor.

◆ ~ExperimentalSettings()

~ExperimentalSettings ( )

override

Destructor.

Member Function Documentation

◆ getComment()

const String& getComment ( ) const

returns the free-text comment

◆ getContacts() [1/2]

std::vector<ContactPerson>& getContacts ( )

returns a mutable reference to the list of contact persons

◆ getContacts() [2/2]

const std::vector<ContactPerson>& getContacts ( ) const

returns a const reference to the list of contact persons

◆ getDateTime()

const DateTime& getDateTime ( ) const

returns the date the experiment was performed

◆ getFractionIdentifier()

const String& getFractionIdentifier ( ) const

returns fraction identifier

◆ getHPLC() [1/2]

HPLC& getHPLC ( )

returns a mutable reference to the description of the HPLC run

◆ getHPLC() [2/2]

const HPLC& getHPLC ( ) const

returns a const reference to the description of the HPLC run

◆ getInstrument() [1/2]

Instrument& getInstrument ( )

returns a mutable reference to the MS instrument description

◆ getInstrument() [2/2]

const Instrument& getInstrument ( ) const

returns a const reference to the MS instrument description

Referenced by XMassFile::importExperimentalSettings().

◆ getProteinIdentifications() [1/2]

std::vector<ProteinIdentification>& getProteinIdentifications ( )

returns a mutable reference to the protein ProteinIdentification vector

◆ getProteinIdentifications() [2/2]

const std::vector<ProteinIdentification>& getProteinIdentifications ( ) const

returns a const reference to the protein ProteinIdentification vector

Referenced by IDFilter::annotateBestPerPeptidePerRun(), IDFilter::filterHitsByScore(), IDFilter::keepHitsMatchingProteins(), and IDFilter::keepNBestHits().

◆ getSample() [1/2]

Sample& getSample ( )

returns a mutable reference to the sample description

◆ getSample() [2/2]

const Sample& getSample ( ) const

returns a const reference to the sample description

◆ getSourceFiles() [1/2]

std::vector<SourceFile>& getSourceFiles ( )

returns a mutable reference to the source data file

◆ getSourceFiles() [2/2]

const std::vector<SourceFile>& getSourceFiles ( ) const

returns a const reference to the source data file

Referenced by TOPPFLASHDeconv::main_().

◆ operator!=()

bool operator!= ( const ExperimentalSettings & rhs ) const

Equality operator.

◆ operator=() [1/2]

ExperimentalSettings& operator= ( const ExperimentalSettings & )

default

Assignment operator.

◆ operator=() [2/2]

ExperimentalSettings& operator= ( ExperimentalSettings && )

default

Move assignment operator.

◆ operator==()

bool operator== ( const ExperimentalSettings & rhs ) const

Equality operator.

◆ setComment()

void setComment ( const String & comment )

sets the free-text comment

◆ setContacts()

void setContacts ( const std::vector< ContactPerson > & contacts )

sets the list of contact persons

◆ setDateTime()

void setDateTime ( const DateTime & date )

sets the date the experiment was performed

Referenced by XMassFile::importExperimentalSettings().

◆ setFractionIdentifier()

void setFractionIdentifier ( const String & fraction_identifier )

sets the fraction identifier

◆ setHPLC()

void setHPLC ( const HPLC & hplc )

sets the description of the HPLC run

◆ setInstrument()

void setInstrument ( const Instrument & instrument )

sets the MS instrument description

◆ setProteinIdentifications()

void setProteinIdentifications ( const std::vector< ProteinIdentification > & protein_identifications )

sets the protein ProteinIdentification vector

◆ setSample()

void setSample ( const Sample & sample )

sets the sample description

◆ setSourceFiles()

void setSourceFiles ( const std::vector< SourceFile > & source_files )

sets the source data file

Member Data Documentation

◆ comment_

String comment_

protected

◆ contacts_

std::vector<ContactPerson> contacts_

protected

◆ datetime_

DateTime datetime_

protected

◆ fraction_identifier_

String fraction_identifier_

protected

◆ hplc_

HPLC hplc_

protected

◆ instrument_

Instrument instrument_

protected

◆ protein_identifications_

std::vector<ProteinIdentification> protein_identifications_

protected

◆ sample_

Sample sample_

protected

◆ source_files_

std::vector<SourceFile> source_files_

protected

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ExperimentalSettings() [1/3]

◆ ExperimentalSettings() [2/3]

◆ ExperimentalSettings() [3/3]

◆ ~ExperimentalSettings()

Member Function Documentation

◆ getComment()

◆ getContacts() [1/2]

◆ getContacts() [2/2]

◆ getDateTime()

◆ getFractionIdentifier()

◆ getHPLC() [1/2]

◆ getHPLC() [2/2]

◆ getInstrument() [1/2]

◆ getInstrument() [2/2]

◆ getProteinIdentifications() [1/2]

◆ getProteinIdentifications() [2/2]

◆ getSample() [1/2]

◆ getSample() [2/2]

◆ getSourceFiles() [1/2]

◆ getSourceFiles() [2/2]

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setComment()

◆ setContacts()

◆ setDateTime()

◆ setFractionIdentifier()

◆ setHPLC()

◆ setInstrument()

◆ setProteinIdentifications()

◆ setSample()

◆ setSourceFiles()

Member Data Documentation

◆ comment_

◆ contacts_

◆ datetime_

◆ fraction_identifier_

◆ hplc_

◆ instrument_

◆ protein_identifications_

◆ sample_

◆ source_files_