| OpenMS 2.5.0

Public Member Functions | Protected Attributes | List of all members
ExperimentalSettings Class Reference
Metadata

Description of the experimental settings. More...

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

Inheritance diagram for ExperimentalSettings:

## Public Member Functions

| 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...

## Protected Attributes

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...

## 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...

## Detailed Description

Description of the experimental settings.

These settings are valid for the whole experiment. See SpectrumSettings for settings which are specific to an MSSpectrum. See ChromatogramSettings for settings which are specific to an MSChromatogram.

## Constructor & Destructor Documentation

## ◆ ExperimentalSettings() [1/3]

ExperimentalSettings | ( |  | ) |

default

Constructor.

## ◆ ExperimentalSettings() [2/3]

ExperimentalSettings | ( | const ExperimentalSettings & |  | ) |

default

Copy constructor.

## ◆ ExperimentalSettings() [3/3]

ExperimentalSettings | ( | ExperimentalSettings && |  | ) |

default

Move constructor.

## ◆ ~ExperimentalSettings()

~ExperimentalSettings | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ getComment()

const String& getComment | ( |  | ) | const

returns the free-text comment

## ◆ getContacts() [1/2]

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

returns a const reference to the list of contact persons

## ◆ getContacts() [2/2]

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

returns a mutable reference to the list of contact persons

## ◆ getDateTime()

const DateTime& getDateTime | ( |  | ) | const

returns the date the experiment was performed

## ◆ getFractionIdentifier()

const String& getFractionIdentifier | ( |  | ) | const

returns fraction identifier

## ◆ getHPLC() [1/2]

const HPLC& getHPLC | ( |  | ) | const

returns a const reference to the description of the HPLC run

## ◆ getHPLC() [2/2]

HPLC& getHPLC | ( |  | ) |

returns a mutable reference to the description of the HPLC run

## ◆ getInstrument() [1/2]

const Instrument& getInstrument | ( |  | ) | const

returns a const reference to the MS instrument description

## ◆ getInstrument() [2/2]

Instrument& getInstrument | ( |  | ) |

returns a mutable reference to the MS instrument description

## ◆ getProteinIdentifications() [1/2]

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

returns a const reference to the protein ProteinIdentification vector

Referenced by IDFilter::filterHitsByScore(), IDFilter::keepBestPerPeptidePerRun(), IDFilter::keepHitsMatchingProteins(), and IDFilter::keepNBestHits().

## ◆ getProteinIdentifications() [2/2]

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

returns a mutable reference to the protein ProteinIdentification vector

## ◆ getSample() [1/2]

const Sample& getSample | ( |  | ) | const

returns a const reference to the sample description

## ◆ getSample() [2/2]

Sample& getSample | ( |  | ) |

returns a mutable reference to the sample description

## ◆ getSourceFiles() [1/2]

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

returns a const reference to the source data file

## ◆ getSourceFiles() [2/2]

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

returns a mutable reference to the source data file

## ◆ operator!=()

bool operator!= | ( | const ExperimentalSettings & | rhs | ) | const

Equality operator.

## ◆ operator=() [1/2]

ExperimentalSettings& operator= | ( | const ExperimentalSettings & |  | ) |

default

Assignment operator.

## ◆ operator=() [2/2]

ExperimentalSettings& operator= | ( | ExperimentalSettings && |  | ) | &

default

Move assignment operator.

## ◆ operator==()

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

Equality operator.

## ◆ setComment()

void setComment | ( | const String & | comment | ) |

sets the free-text comment

## ◆ setContacts()

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

sets the list of contact persons

## ◆ setDateTime()

void setDateTime | ( | const DateTime & | date | ) |

sets the date the experiment was performed

## ◆ setFractionIdentifier()

void setFractionIdentifier | ( | const String & | fraction_identifier | ) |

sets the fraction identifier

## ◆ setHPLC()

void setHPLC | ( | const HPLC & | hplc | ) |

sets the description of the HPLC run

## ◆ setInstrument()

void setInstrument | ( | const Instrument & | instrument | ) |

sets the MS instrument description

## ◆ setProteinIdentifications()

void setProteinIdentifications | ( | const std::vector< ProteinIdentification > & | protein_identifications | ) |

sets the protein ProteinIdentification vector

## ◆ setSample()

void setSample | ( | const Sample & | sample | ) |

sets the sample description

## ◆ setSourceFiles()

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

sets the source data file

## Member Data Documentation

## ◆ comment_

String comment_

protected

## ◆ contacts_

std::vector<ContactPerson> contacts_

protected

## ◆ datetime_

DateTime datetime_

protected

## ◆ fraction_identifier_

String fraction_identifier_

protected

## ◆ hplc_

HPLC hplc_

protected

## ◆ instrument_

Instrument instrument_

protected

## ◆ protein_identifications_

std::vector<ProteinIdentification> protein_identifications_

protected

## ◆ sample_

Sample sample_

protected

## ◆ source_files_

std::vector<SourceFile> source_files_

protected