| OpenMS 2.5.0

Classes | Public Member Functions | Private Attributes | List of all members
MSQuantifications Class Reference

`#include <OpenMS/METADATA/MSQuantifications.h>`

Inheritance diagram for MSQuantifications:

## Classes

struct | AnalysisSummary
struct | Assay

## Public Member Functions

| 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...
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 (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 > > >()))
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...
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 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 DataValue & | getMetaValue (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 | 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...

## Private Attributes

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_

## 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 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 | ( | 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]

MSQuantifications | ( | MSQuantifications && |  | ) |

default

Move constructor.

## ◆ ~MSQuantifications()

~MSQuantifications | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ addConsensusMap()

void addConsensusMap | ( | ConsensusMap & | m | ) |

## ◆ assignUIDs()

void assignUIDs | ( |  | ) |

## ◆ getAnalysisSummary() [1/2]

const AnalysisSummary& getAnalysisSummary | ( |  | ) | const

## ◆ getAnalysisSummary() [2/2]

AnalysisSummary& getAnalysisSummary | ( |  | ) |

## ◆ getAssays() [1/2]

const std::vector<Assay>& getAssays | ( |  | ) | const

## ◆ getAssays() [2/2]

std::vector<Assay>& getAssays | ( |  | ) |

## ◆ getConsensusMaps() [1/2]

const std::vector<ConsensusMap>& getConsensusMaps | ( |  | ) | const

## ◆ getConsensusMaps() [2/2]

std::vector<ConsensusMap>& getConsensusMaps | ( |  | ) |

## ◆ 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 linebreaks

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

## ◆ registerExperiment() [2/2]

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 > > >())`
| ) |  |

## ◆ 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