MSQuantifications Class Reference

#include <OpenMS/METADATA/MSQuantifications.h>

Inheritance diagram for MSQuantifications:

Collaboration diagram for MSQuantifications:

Classes
struct	AnalysisSummary
struct	Assay

Base type definitions
enum	QUANT_TYPES { MS1LABEL = 0 , MS2LABEL , LABELFREE , SIZE_OF_QUANT_TYPES }
typedef CVTermList	ParamGroupList
	typedef docu More...
static const std::string	NamesOfQuantTypes [SIZE_OF_QUANT_TYPES]
AnalysisSummary	analysis_summary_
std::vector< MetaInfo >	bibliographic_reference_
std::vector< ConsensusMap >	consensus_maps_
std::vector< FeatureMap >	feature_maps_
std::vector< Assay >	assays_
std::vector< DataProcessing >	data_processings_
	MSQuantifications ()=default
	Constructor. More...
	MSQuantifications (const FeatureMap &fm, ExperimentalSettings &es, std::vector< DataProcessing > &dps, std::vector< std::vector< std::pair< String, double >>> labels={})
	Detailed Constructor. More...
	MSQuantifications (const MSQuantifications &source)=default
	Copy constructor. More...
	MSQuantifications (MSQuantifications &&)=default
	Move constructor. More...
	~MSQuantifications () override
	Destructor. More...
MSQuantifications &	operator= (const MSQuantifications &source)=default
	Assignment operator. More...
MSQuantifications &	operator= (MSQuantifications &&) &=default
	Move assignment operator. More...
bool	operator== (const MSQuantifications &rhs) const
	Equality operator. More...
bool	operator!= (const MSQuantifications &rhs) const
	Equality operator. More...
const std::vector< DataProcessing >	getDataProcessingList () const
	Loads data from a text file. More...
const std::vector< Assay > &	getAssays () const
std::vector< Assay > &	getAssays ()
const std::vector< ConsensusMap > &	getConsensusMaps () const
std::vector< ConsensusMap > &	getConsensusMaps ()
void	setConsensusMaps (const std::vector< ConsensusMap > &)
const std::vector< FeatureMap > &	getFeatureMaps () const
const AnalysisSummary &	getAnalysisSummary () const
AnalysisSummary &	getAnalysisSummary ()
void	setDataProcessingList (const std::vector< DataProcessing > &dpl)
void	setAnalysisSummaryQuantType (QUANT_TYPES r)
void	addConsensusMap (ConsensusMap &m)
void	assignUIDs ()
void	registerExperiment (PeakMap &exp, std::vector< std::vector< std::pair< String, double > > > labels)
void	registerExperiment (ExperimentalSettings &es, std::vector< DataProcessing > &dp, std::vector< std::vector< std::pair< String, double > > > labels=(std::vector< std::vector< std::pair< String, double > > >()))

Additional Inherited Members
Public Member Functions inherited from ExperimentalSettings
	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...
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...
Protected Attributes inherited from ExperimentalSettings
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...

Member Typedef Documentation

ParamGroupList

typedef CVTermList ParamGroupList

typedef docu

Member Enumeration Documentation

QUANT_TYPES

enum QUANT_TYPES

Enumerator
MS1LABEL
MS2LABEL
LABELFREE
SIZE_OF_QUANT_TYPES

Constructor & Destructor Documentation

MSQuantifications() [1/4]

MSQuantifications ( )

default

Constructor.

MSQuantifications() [2/4]

MSQuantifications	(	const FeatureMap &	fm,
		ExperimentalSettings &	es,
		std::vector< DataProcessing > &	dps,
		std::vector< std::vector< std::pair< String, double >>>	labels = {}
	)

Detailed Constructor.

MSQuantifications() [3/4]

MSQuantifications ( const MSQuantifications &  source )

default

Copy constructor.

MSQuantifications() [4/4]

MSQuantifications ( MSQuantifications &&  )

default

Move constructor.

~MSQuantifications()

~MSQuantifications ( )

override

Destructor.

Member Function Documentation

addConsensusMap()

void addConsensusMap

(

ConsensusMap &

m

)

assignUIDs()

void assignUIDs

(

)

getAnalysisSummary() [1/2]

AnalysisSummary& getAnalysisSummary

(

)

getAnalysisSummary() [2/2]

const AnalysisSummary& getAnalysisSummary

(

)

const

getAssays() [1/2]

std::vector<Assay>& getAssays

(

)

getAssays() [2/2]

const std::vector<Assay>& getAssays

(

)

const

getConsensusMaps() [1/2]

std::vector<ConsensusMap>& getConsensusMaps

(

)

getConsensusMaps() [2/2]

const std::vector<ConsensusMap>& getConsensusMaps

(

)

const

getDataProcessingList()

const std::vector<DataProcessing> getDataProcessingList

(

)

const

Loads data from a text file.

Parameters

filename	The input file name.
trim_lines	Whether or not the lines are trimmed when reading them from file.
first_n	If set, only first_n lines the lines from the beginning of the file are read.

Note

this function uses unix-style line breaks

Exceptions

Exception::FileNotFound

is thrown if the file could not be opened.

TODO : implement

getFeatureMaps()

const std::vector<FeatureMap >& getFeatureMaps

(

)

const

operator!=()

bool operator!=

(

const MSQuantifications &

rhs

)

const

Equality operator.

operator=() [1/2]

MSQuantifications& operator= ( const MSQuantifications &  source )

default

Assignment operator.

operator=() [2/2]

MSQuantifications& operator= ( MSQuantifications &&  ) &

default

Move assignment operator.

operator==()

bool operator==

(

const MSQuantifications &

rhs

)

const

Equality operator.

registerExperiment() [1/2]

void registerExperiment	(	ExperimentalSettings &	es,
		std::vector< DataProcessing > &	dp,
		std::vector< std::vector< std::pair< String, double > > >	labels = (std::vector< std::vector< std::pair< String, double > > >())
	)

registerExperiment() [2/2]

void registerExperiment	(	PeakMap &	exp,
		std::vector< std::vector< std::pair< String, double > > >	labels
	)

setAnalysisSummaryQuantType()

void setAnalysisSummaryQuantType

(

QUANT_TYPES

r

)

setConsensusMaps()

void setConsensusMaps

(

const std::vector< ConsensusMap > &

)

setDataProcessingList()

void setDataProcessingList

(

const std::vector< DataProcessing > &

dpl

)

Member Data Documentation

analysis_summary_

AnalysisSummary analysis_summary_

private

assays_

std::vector<Assay> assays_

private

bibliographic_reference_

std::vector<MetaInfo> bibliographic_reference_

private

consensus_maps_

std::vector<ConsensusMap> consensus_maps_

private

data_processings_

std::vector<DataProcessing> data_processings_

private

feature_maps_

std::vector<FeatureMap > feature_maps_

private

NamesOfQuantTypes

const std::string NamesOfQuantTypes[SIZE_OF_QUANT_TYPES]

static