OpenMS  2.7.0
Classes | List of all members
MSQuantifications Class Reference

#include <OpenMS/METADATA/MSQuantifications.h>

Inheritance diagram for MSQuantifications:
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Collaboration diagram for MSQuantifications:
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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< MetaInfobibliographic_reference_
 
std::vector< ConsensusMapconsensus_maps_
 
std::vector< FeatureMapfeature_maps_
 
std::vector< Assayassays_
 
std::vector< DataProcessingdata_processings_
 
 MSQuantifications ()=default
 Constructor. More...
 
 MSQuantifications (FeatureMap fm, ExperimentalSettings &es, std::vector< DataProcessing > &dps, std::vector< std::vector< std::pair< String, double > > > labels=(std::vector< std::vector< std::pair< String, double > > >()))
 Detailed Constructor. More...
 
 MSQuantifications (const MSQuantifications &source)=default
 Copy constructor. More...
 
 MSQuantifications (MSQuantifications &&)=default
 Move constructor. More...
 
 ~MSQuantifications () override
 Destructor. More...
 
MSQuantificationsoperator= (const MSQuantifications &source)=default
 Assignment operator. More...
 
MSQuantificationsoperator= (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< DataProcessinggetDataProcessingList () 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 AnalysisSummarygetAnalysisSummary () const
 
AnalysisSummarygetAnalysisSummary ()
 
void setDataProcessingList (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...
 
ExperimentalSettingsoperator= (const ExperimentalSettings &)=default
 Assignment operator. More...
 
ExperimentalSettingsoperator= (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 SamplegetSample () const
 returns a const reference to the sample description More...
 
SamplegetSample ()
 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 InstrumentgetInstrument () const
 returns a const reference to the MS instrument description More...
 
InstrumentgetInstrument ()
 returns a mutable reference to the MS instrument description More...
 
void setInstrument (const Instrument &instrument)
 sets the MS instrument description More...
 
const HPLCgetHPLC () const
 returns a const reference to the description of the HPLC run More...
 
HPLCgetHPLC ()
 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 DateTimegetDateTime () const
 returns the date the experiment was performed More...
 
void setDateTime (const DateTime &date)
 sets the date the experiment was performed More...
 
const StringgetComment () 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 StringgetFractionIdentifier () 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...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (MetaInfoInterface &&) noexcept
 Move assignment operator. 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 DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
 
const DataValuegetMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to an index, or a default value (default: 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...
 
DocumentIdentifieroperator= (const DocumentIdentifier &)=default
 Assignment operator. More...
 
DocumentIdentifieroperator= (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 StringgetIdentifier () 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 StringgetLoadedFilePath () 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::TypegetLoadedFileType () 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 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...
 
- Protected Attributes inherited from ExperimentalSettings
Sample sample_
 
std::vector< SourceFilesource_files_
 
std::vector< ContactPersoncontacts_
 
Instrument instrument_
 
HPLC hplc_
 
DateTime datetime_
 
String comment_
 
std::vector< ProteinIdentificationprotein_identifications_
 
String fraction_identifier_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 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 docu

Member Enumeration Documentation

◆ QUANT_TYPES

Enumerator
MS1LABEL 
MS2LABEL 
LABELFREE 
SIZE_OF_QUANT_TYPES 

Constructor & Destructor Documentation

◆ MSQuantifications() [1/4]

MSQuantifications ( )
default

Constructor.

◆ MSQuantifications() [2/4]

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

Detailed Constructor.

◆ MSQuantifications() [3/4]

MSQuantifications ( const MSQuantifications source)
default

Copy constructor.

◆ MSQuantifications() [4/4]

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
filenameThe input file name.
trim_linesWhether or not the lines are trimmed when reading them from file.
first_nIf 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::FileNotFoundis 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 ( 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