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MSQuantifications Class Reference

#include <OpenMS/METADATA/MSQuantifications.h>

Inheritance diagram for MSQuantifications:
ExperimentalSettings MetaInfoInterface DocumentIdentifier

Classes

struct  AnalysisSummary
 
struct  Assay
 

Public Member Functions

 MSQuantifications ()
 Constructor. More...
 
 ~MSQuantifications ()
 Destructor. More...
 
 MSQuantifications (const MSQuantifications &source)
 Copy constructor. More...
 
MSQuantificationsoperator= (const MSQuantifications &source)
 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 (MSExperiment< Peak1D > &exp, std::vector< std::vector< std::pair< String, DoubleReal > > > labels)
 
- Public Member Functions inherited from ExperimentalSettings
 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...
 

Private Attributes

AnalysisSummary analysis_summary_
 
std::vector< MetaInfobibliographic_reference_
 
std::vector< ConsensusMapconsensus_maps_
 
std::vector< FeatureMap<> > feature_maps_
 
std::vector< Assayassays_
 
std::vector< DataProcessingdata_processings_
 

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]
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 retuns 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
< ProteinIdentification
protein_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

typedef docu

Member Enumeration Documentation

Enumerator
MS1LABEL 
MS2LABEL 
LABELFREE 
SIZE_OF_QUANT_TYPES 

Constructor & Destructor Documentation

Constructor.

Destructor.

MSQuantifications ( const MSQuantifications source)

Copy constructor.

Member Function Documentation

void addConsensusMap ( ConsensusMap m)
void assignUIDs ( )
const AnalysisSummary& getAnalysisSummary ( ) const
AnalysisSummary& getAnalysisSummary ( )
const std::vector<Assay>& getAssays ( ) const
std::vector<Assay>& getAssays ( )
const std::vector<ConsensusMap>& getConsensusMaps ( ) const
std::vector<ConsensusMap>& getConsensusMaps ( )
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 linebreaks
Exceptions
Exception::FileNotFoundis thrown if the file could not be opened.

TODO : implement

const std::vector<FeatureMap<> >& getFeatureMaps ( ) const
bool operator!= ( const MSQuantifications rhs) const

Equality operator.

MSQuantifications& operator= ( const MSQuantifications source)

Assignment operator.

bool operator== ( const MSQuantifications rhs) const

Equality operator.

void registerExperiment ( MSExperiment< Peak1D > &  exp,
std::vector< std::vector< std::pair< String, DoubleReal > > >  labels 
)
void setAnalysisSummaryQuantType ( QUANT_TYPES  r)
void setConsensusMaps ( const std::vector< ConsensusMap > &  )
void setDataProcessingList ( std::vector< DataProcessing > &  dpl)

Member Data Documentation

AnalysisSummary analysis_summary_
private
std::vector<Assay> assays_
private
std::vector<MetaInfo> bibliographic_reference_
private
std::vector<ConsensusMap> consensus_maps_
private
std::vector<DataProcessing> data_processings_
private
std::vector<FeatureMap<> > feature_maps_
private
const std::string NamesOfQuantTypes[SIZE_OF_QUANT_TYPES]
static

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5