| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
ChromatogramSettings Class Reference
Metadata

Representation of chromatogram settings, e.g. SRM/MRM chromatograms. More...

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

Inheritance diagram for ChromatogramSettings:

## Public Types

enum | ChromatogramType { MASS_CHROMATOGRAM = 0, TOTAL_ION_CURRENT_CHROMATOGRAM, SELECTED_ION_CURRENT_CHROMATOGRAM, BASEPEAK_CHROMATOGRAM, SELECTED_ION_MONITORING_CHROMATOGRAM, SELECTED_REACTION_MONITORING_CHROMATOGRAM, ELECTROMAGNETIC_RADIATION_CHROMATOGRAM, ABSORPTION_CHROMATOGRAM,
EMISSION_CHROMATOGRAM, SIZE_OF_CHROMATOGRAM_TYPE
}

## Public Member Functions

| ChromatogramSettings ()
| Constructor. More...
| ChromatogramSettings (const ChromatogramSettings &)=default
| Copy constructor. More...
| ChromatogramSettings (ChromatogramSettings &&)=default
| Move constructor. More...
virtual | ~ChromatogramSettings ()
| Destructor. More...
ChromatogramSettings & | operator= (const ChromatogramSettings &)=default
ChromatogramSettings & | operator= (ChromatogramSettings &&) &=default
| Move assignment operator. More...
bool | operator== (const ChromatogramSettings &rhs) const
| Equality operator. More...
bool | operator!= (const ChromatogramSettings &rhs) const
| Equality operator. More...
const String & | getNativeID () const
| returns the native identifier for the spectrum, used by the acquisition software. More...
void | setNativeID (const String &native_id)
| sets the native identifier for the spectrum, used by the acquisition software. More...
const String & | getComment () const
| returns the free-text comment More...
void | setComment (const String &comment)
| sets the free-text comment More...
const InstrumentSettings & | getInstrumentSettings () const
| returns a const reference to the instrument settings of the current spectrum More...
InstrumentSettings & | getInstrumentSettings ()
| returns a mutable reference to the instrument settings of the current spectrum More...
void | setInstrumentSettings (const InstrumentSettings &instrument_settings)
| sets the instrument settings of the current spectrum More...
const AcquisitionInfo & | getAcquisitionInfo () const
| returns a const reference to the acquisition info More...
AcquisitionInfo & | getAcquisitionInfo ()
| returns a mutable reference to the acquisition info More...
void | setAcquisitionInfo (const AcquisitionInfo &acquisition_info)
| sets the acquisition info More...
const SourceFile & | getSourceFile () const
| returns a const reference to the source file More...
SourceFile & | getSourceFile ()
| returns a mutable reference to the source file More...
void | setSourceFile (const SourceFile &source_file)
| sets the source file More...
const Precursor & | getPrecursor () const
| returns a const reference to the precursors More...
Precursor & | getPrecursor ()
| returns a mutable reference to the precursors More...
void | setPrecursor (const Precursor &precursor)
| sets the precursors More...
const Product & | getProduct () const
| returns a const reference to the products More...
Product & | getProduct ()
| returns a mutable reference to the products More...
void | setProduct (const Product &product)
| sets the products More...
ChromatogramType | getChromatogramType () const
| returns the chromatogram type, e.g. a SRM chromatogram More...
void | setChromatogramType (ChromatogramType type)
| sets the chromatogram type More...
void | setDataProcessing (const std::vector< DataProcessingPtr > &data_processing)
| sets the description of the applied processing More...
std::vector< DataProcessingPtr > & | getDataProcessing ()
| returns a mutable reference to the description of the applied processing More...
const std::vector< boost::shared_ptr< const DataProcessing > > | getDataProcessing () const
| returns a const reference to the description of the applied processing 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...

## Static Public Attributes

static const char *const | ChromatogramNames [SIZE_OF_CHROMATOGRAM_TYPE+1]
| Names of chromatogram types corresponding to enum ChromatogramType. More...

## Protected Attributes

String | native_id_
String | comment_
InstrumentSettings | instrument_settings_
SourceFile | source_file_
AcquisitionInfo | acquisition_info_
Precursor | precursor_
Product | product_
std::vector< DataProcessingPtr > | data_processing_
ChromatogramType | type_
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) 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

Representation of chromatogram settings, e.g. SRM/MRM chromatograms.

It contains the metadata about chromatogram specific instrument settings, acquisition settings, description of the meta values used in the peaks and precursor info.

## Member Enumeration Documentation

## ◆ ChromatogramType

enum ChromatogramType

List of chromatogram names, e.g., SELECTED_REACTION_MONITORING_CHROMATOGRAM. Actual names can be accessed using the ChromatogramNames[] array

Enumerator
MASS_CHROMATOGRAM |
TOTAL_ION_CURRENT_CHROMATOGRAM |
SELECTED_ION_CURRENT_CHROMATOGRAM |
BASEPEAK_CHROMATOGRAM |
SELECTED_ION_MONITORING_CHROMATOGRAM |
SELECTED_REACTION_MONITORING_CHROMATOGRAM |
ELECTROMAGNETIC_RADIATION_CHROMATOGRAM |
ABSORPTION_CHROMATOGRAM |
EMISSION_CHROMATOGRAM |
SIZE_OF_CHROMATOGRAM_TYPE |

## Constructor & Destructor Documentation

## ◆ ChromatogramSettings() [1/3]

ChromatogramSettings | ( |  | ) |

Constructor.

## ◆ ChromatogramSettings() [2/3]

ChromatogramSettings | ( | const ChromatogramSettings & |  | ) |

default

Copy constructor.

## ◆ ChromatogramSettings() [3/3]

ChromatogramSettings | ( | ChromatogramSettings && |  | ) |

default

Move constructor.

## ◆ ~ChromatogramSettings()

virtual ~ChromatogramSettings | ( |  | ) |

virtual

Destructor.

## Member Function Documentation

## ◆ getAcquisitionInfo() [1/2]

const AcquisitionInfo& getAcquisitionInfo | ( |  | ) | const

returns a const reference to the acquisition info

## ◆ getAcquisitionInfo() [2/2]

AcquisitionInfo& getAcquisitionInfo | ( |  | ) |

returns a mutable reference to the acquisition info

## ◆ getChromatogramType()

ChromatogramType getChromatogramType | ( |  | ) | const

returns the chromatogram type, e.g. a SRM chromatogram

## ◆ getComment()

const String& getComment | ( |  | ) | const

returns the free-text comment

## ◆ getDataProcessing() [1/2]

std::vector< DataProcessingPtr >& getDataProcessing | ( |  | ) |

returns a mutable reference to the description of the applied processing

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ getDataProcessing() [2/2]

const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing | ( |  | ) | const

returns a const reference to the description of the applied processing

## ◆ getInstrumentSettings() [1/2]

const InstrumentSettings& getInstrumentSettings | ( |  | ) | const

returns a const reference to the instrument settings of the current spectrum

## ◆ getInstrumentSettings() [2/2]

InstrumentSettings& getInstrumentSettings | ( |  | ) |

returns a mutable reference to the instrument settings of the current spectrum

## ◆ getNativeID()

const String& getNativeID | ( |  | ) | const

returns the native identifier for the spectrum, used by the acquisition software.

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::chromatogramIdsMatch(), and MRMTransitionGroupPicker::pickTransitionGroup().

## ◆ getPrecursor() [1/2]

const Precursor& getPrecursor | ( |  | ) | const

returns a const reference to the precursors

## ◆ getPrecursor() [2/2]

Precursor& getPrecursor | ( |  | ) |

returns a mutable reference to the precursors

## ◆ getProduct() [1/2]

const Product& getProduct | ( |  | ) | const

returns a const reference to the products

## ◆ getProduct() [2/2]

Product& getProduct | ( |  | ) |

returns a mutable reference to the products

## ◆ getSourceFile() [1/2]

const SourceFile& getSourceFile | ( |  | ) | const

returns a const reference to the source file

## ◆ getSourceFile() [2/2]

SourceFile& getSourceFile | ( |  | ) |

returns a mutable reference to the source file

## ◆ operator!=()

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

Equality operator.

## ◆ operator=() [1/2]

ChromatogramSettings& operator= | ( | const ChromatogramSettings & |  | ) |

default

## ◆ operator=() [2/2]

ChromatogramSettings& operator= | ( | ChromatogramSettings && |  | ) | &

default

Move assignment operator.

## ◆ operator==()

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

Equality operator.

## ◆ setAcquisitionInfo()

void setAcquisitionInfo | ( | const AcquisitionInfo & | acquisition_info | ) |

sets the acquisition info

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ setChromatogramType()

void setChromatogramType | ( | ChromatogramType | type | ) |

sets the chromatogram type

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ setComment()

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

sets the free-text comment

## ◆ setDataProcessing()

void setDataProcessing | ( | const std::vector< DataProcessingPtr > & | data_processing | ) |

sets the description of the applied processing

## ◆ setInstrumentSettings()

void setInstrumentSettings | ( | const InstrumentSettings & | instrument_settings | ) |

sets the instrument settings of the current spectrum

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ setNativeID()

void setNativeID | ( | const String & | native_id | ) |

sets the native identifier for the spectrum, used by the acquisition software.

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ setPrecursor()

void setPrecursor | ( | const Precursor & | precursor | ) |

sets the precursors

Referenced by ChromatogramTools::convertSpectraToChromatograms(), and ChromatogramExtractor::return_chromatogram().

## ◆ setProduct()

void setProduct | ( | const Product & | product | ) |

sets the products

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ setSourceFile()

void setSourceFile | ( | const SourceFile & | source_file | ) |

sets the source file

Referenced by ChromatogramExtractor::return_chromatogram().

## Member Data Documentation

## ◆ acquisition_info_

AcquisitionInfo acquisition_info_

protected

## ◆ ChromatogramNames

const char* const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]

static

Names of chromatogram types corresponding to enum ChromatogramType.

## ◆ comment_

String comment_

protected

## ◆ data_processing_

std::vector< DataProcessingPtr > data_processing_

protected

## ◆ instrument_settings_

InstrumentSettings instrument_settings_

protected

## ◆ native_id_

String native_id_

protected

## ◆ precursor_

Precursor precursor_

protected

## ◆ product_

Product product_

protected

## ◆ source_file_

SourceFile source_file_

protected

## ◆ type_

ChromatogramType type_

protected