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ExperimentalSettings Class Reference

Description of the experimental settings. More...

#include <OpenMS/METADATA/ExperimentalSettings.h>

Inheritance diagram for ExperimentalSettings:
MetaInfoInterface DocumentIdentifier MSExperiment< OpenMS::Peak1D > MSExperiment< Peak1D > MSExperiment< SimPointType > MSExperiment<> MSExperiment< PeakT, ChromatogramPeakT > MSQuantifications

Public Member Functions

 ExperimentalSettings ()
 Constructor. More...
 
 ExperimentalSettings (const ExperimentalSettings &source)
 Copy constructor. More...
 
 ~ExperimentalSettings ()
 Destructor. More...
 
ExperimentalSettingsoperator= (const ExperimentalSettings &source)
 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 ()
 destructor More...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 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
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (UInt index) const
 returns the value corresponding to an index More...
 
bool metaValueExists (const String &name) const
 returns if this MetaInfo is set More...
 
bool metaValueExists (UInt index) const
 returns if this MetaInfo is set 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 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 &source)
 Copy constructor. More...
 
DocumentIdentifieroperator= (const DocumentIdentifier &source)
 Assignment operator. More...
 
bool operator== (const DocumentIdentifier &rhs) const
 Equality operator. More...
 
virtual ~DocumentIdentifier ()
 destructor 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...
 

Protected Attributes

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...
 

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 experimental settings.

These settings are valid for the whole experiment. See SpectrumSettings for settings which are spectrum specific.

Constructor & Destructor Documentation

Copy constructor.

Destructor.

Member Function Documentation

const String& getComment ( ) const

returns the free-text comment

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

returns a const reference to the list of contact persons

std::vector<ContactPerson>& getContacts ( )

returns a mutable reference to the list of contact persons

const DateTime& getDateTime ( ) const

returns the date the experiment was performed

const String& getFractionIdentifier ( ) const

returns fraction identifier

const HPLC& getHPLC ( ) const

returns a const reference to the description of the HPLC run

HPLC& getHPLC ( )

returns a mutable reference to the description of the HPLC run

const Instrument& getInstrument ( ) const

returns a const reference to the MS instrument description

Instrument& getInstrument ( )

returns a mutable reference to the MS instrument description

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

returns a mutable reference to the protein ProteinIdentification vector

const Sample& getSample ( ) const

returns a const reference to the sample description

Sample& getSample ( )

returns a mutable reference to the sample description

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

returns a const reference to the source data file

Referenced by FileHandler::loadExperiment().

std::vector<SourceFile>& getSourceFiles ( )

returns a mutable reference to the source data file

bool operator!= ( const ExperimentalSettings rhs) const

Equality operator.

ExperimentalSettings& operator= ( const ExperimentalSettings source)
bool operator== ( const ExperimentalSettings rhs) const

Equality operator.

Referenced by MSExperiment< SimPointType >::operator==().

void setComment ( const String comment)

sets the free-text comment

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

sets the list of contact persons

void setDateTime ( const DateTime date)

sets the date the experiment was performed

void setFractionIdentifier ( const String fraction_identifier)

sets the fraction identifier

void setHPLC ( const HPLC hplc)

sets the description of the HPLC run

void setInstrument ( const Instrument instrument)

sets the MS instrument description

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

sets the sample description

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

sets the source data file

Member Data Documentation

String comment_
protected
std::vector<ContactPerson> contacts_
protected
DateTime datetime_
protected
String fraction_identifier_
protected
HPLC hplc_
protected
Instrument instrument_
protected
std::vector<ProteinIdentification> protein_identifications_
protected
Sample sample_
protected
std::vector<SourceFile> source_files_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:34 using doxygen 1.8.9.1