| OpenMS 2.5.0

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

Precursor meta information. More...

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

Inheritance diagram for Precursor:

## Public Types

enum | ActivationMethod { CID, PSD, PD, SID, BIRD, ECD, IMD, SORI, HCID, LCID, PHD, ETD, PQD, SIZE_OF_ACTIVATIONMETHOD
}
| Method of activation. More...
enum | DriftTimeUnit { NONE, MILLISECOND, VSSC, SIZE_OF_DRIFTTIMEUNIT }
| Drift time unit. More...
Public Types inherited from Peak1D
enum | { DIMENSION = 1 }
typedef float | IntensityType
| Intensity type. More...
typedef DPosition< 1 > | PositionType
| Position type. More...
typedef double | CoordinateType
| Coordinate type. More...

## Public Member Functions

| Precursor ()
| Constructor. More...
| Precursor (const Precursor &)=default
| Copy constructor. More...
| Precursor (Precursor &&) noexcept
| Move constructor. More...
| ~Precursor () override
| Destructor. More...
Precursor & | operator= (const Precursor &)=default
| Assignment operator. More...
Precursor & | operator= (Precursor &&) &=default
| Move assignment operator. More...
bool | operator== (const Precursor &rhs) const
| Equality operator. More...
bool | operator!= (const Precursor &rhs) const
| Equality operator. More...
const std::set< ActivationMethod > & | getActivationMethods () const
| returns a const reference to the activation methods More...
std::set< ActivationMethod > & | getActivationMethods ()
| returns a mutable reference to the activation methods More...
void | setActivationMethods (const std::set< ActivationMethod > &activation_methods)
| sets the activation methods More...
double | getActivationEnergy () const
| returns the activation energy (in electronvolt) More...
void | setActivationEnergy (double activation_energy)
| sets the activation energy (in electronvolt) More...
double | getIsolationWindowLowerOffset () const
| Returns the lower offset from the target m/z. More...
void | setIsolationWindowLowerOffset (double bound)
| sets the lower offset from the target m/z More...
double | getIsolationWindowUpperOffset () const
| Returns the upper offset from the target m/z. More...
void | setIsolationWindowUpperOffset (double bound)
| sets the upper offset from the target m/z More...
double | getDriftTime () const
| Returns the ion mobility drift time in milliseconds (-1 means it is not set) More...
void | setDriftTime (double drift_time)
| sets the ion mobility drift time in milliseconds More...
DriftTimeUnit | getDriftTimeUnit () const
| Returns the ion mobility drift time unit. More...
void | setDriftTimeUnit (DriftTimeUnit dt)
| Sets the ion mobility drift time unit. More...
double | getDriftTimeWindowLowerOffset () const
| Returns the lower offset from the target ion mobility in milliseconds. More...
void | setDriftTimeWindowLowerOffset (double drift_time)
| sets the lower offset from the target ion mobility More...
double | getDriftTimeWindowUpperOffset () const
| Returns the upper offset from the target ion mobility in milliseconds. More...
void | setDriftTimeWindowUpperOffset (double drift_time)
| sets the upper offset from the target ion mobility More...
Int | getCharge () const
| Non-mutable access to the charge. More...
void | setCharge (Int charge)
| Mutable access to the charge. More...
std::vector< Int > & | getPossibleChargeStates ()
| Mutable access to possible charge states. More...
const std::vector< Int > & | getPossibleChargeStates () const
| Non-mutable access to possible charge states. More...
void | setPossibleChargeStates (const std::vector< Int > &possible_charge_states)
| Sets the possible charge states. More...
double | getUnchargedMass () const
| Returns the uncharged mass of the precursor, if charge is unknown, i.e. 0 best guess is its doubly charged. More...
Public Member Functions inherited from CVTermList
| CVTermList ()=default
| Defaults constructor. More...
| CVTermList (const CVTermList &)=default
| Copy constructor. More...
| CVTermList (CVTermList &&) noexcept
| Move constructor. More...
virtual | ~CVTermList ()
| Destructor. More...
CVTermList & | operator= (const CVTermList &rhs) &=default
| Assignment operator. More...
CVTermList & | operator= (CVTermList &&) &=default
| Move assignment operator. More...
void | setCVTerms (const std::vector< CVTerm > &terms)
| sets the CV terms More...
void | replaceCVTerm (const CVTerm &cv_term)
| replaces the specified CV term More...
void | replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession)
| replaces the specified CV terms using the given accession number More...
void | replaceCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
| replaces all cv terms with a map (can be obtained via getCVTerms) More...
void | consumeCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
| merges the given map into the member map, no duplicate checking More...
const Map< String, std::vector< CVTerm > > & | getCVTerms () const
| returns the accession string of the term More...
void | addCVTerm (const CVTerm &term)
| adds a CV term More...
bool | operator== (const CVTermList &cv_term_list) const
| equality operator More...
bool | operator!= (const CVTermList &cv_term_list) const
| inequality operator More...
bool | hasCVTerm (const String &accession) const
| checks whether the term has a value More...
bool | empty () const
| return true if no terms are available 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 Peak1D
Peak1D & | operator= (const Peak1D &rhs)
| Assignment operator. More...
bool | operator== (const Peak1D &rhs) const
| Equality operator. More...
bool | operator!= (const Peak1D &rhs) const
| Equality operator. More...
| Peak1D ()
| Peak1D (PositionType a, IntensityType b)
| construct with position and intensity More...
| Peak1D (const Peak1D &p)
| Copy constructor. More...
| Peak1D (Peak1D &&) noexcept=default
| ~Peak1D ()
| Destructor. More...
IntensityType | getIntensity () const
void | setIntensity (IntensityType intensity)
| Mutable access to the data point intensity (height) More...
CoordinateType | getMZ () const
| Non-mutable access to m/z. More...
void | setMZ (CoordinateType mz)
| Mutable access to m/z. More...
CoordinateType | getPos () const
| Alias for getMZ() More...
void | setPos (CoordinateType pos)
| Alias for setMZ() More...
PositionType const & | getPosition () const
| Non-mutable access to the position. More...
PositionType & | getPosition ()
| Mutable access to the position. More...
void | setPosition (PositionType const &position)
| Mutable access to the position. More...

## Static Public Attributes

static const std::string | NamesOfActivationMethod [SIZE_OF_ACTIVATIONMETHOD]
| Names of activation methods. More...
static const std::string | NamesOfActivationMethodShort [SIZE_OF_ACTIVATIONMETHOD]

## Protected Attributes

std::set< ActivationMethod > | activation_methods_
double | activation_energy_
double | window_low_
double | window_up_
double | drift_time_
double | drift_window_low_
double | drift_window_up_
DriftTimeUnit | drift_time_unit_
Int | charge_
std::vector< Int > | possible_charge_states_
Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > > | cv_terms_
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) More...
Protected Attributes inherited from Peak1D
PositionType | position_
| The data point position. More...
IntensityType | intensity_
| The data point intensity. 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

Precursor meta information.

This class contains precursor information:

- isolation window
- activation
- selected ion (m/z, intensity, charge, possible charge states)
- ion mobility drift time

## Member Enumeration Documentation

## ◆ ActivationMethod

enum ActivationMethod

Method of activation.

Enumerator
CID | Collision-induced dissociation.
PSD | Post-source decay.
PD | Plasma desorption.
SID | Surface-induced dissociation.
BIRD | Blackbody infrared radiative dissociation.
ECD | Electron capture dissociation.
IMD | Infrared multiphoton dissociation.
SORI | Sustained off-resonance irradiation.
HCID | High-energy collision-induced dissociation.
LCID | Low-energy collision-induced dissociation.
PHD | Photodissociation.
ETD | Electron transfer dissociation.
PQD | Pulsed q dissociation.
SIZE_OF_ACTIVATIONMETHOD |

## ◆ DriftTimeUnit

enum DriftTimeUnit

Drift time unit.

Enumerator
NONE | No unit.
MILLISECOND | milliseconds
VSSC | volt-second per square centimeter
SIZE_OF_DRIFTTIMEUNIT |

## Constructor & Destructor Documentation

## ◆ Precursor() [1/3]

Precursor | ( |  | ) |

Constructor.

## ◆ Precursor() [2/3]

Precursor | ( | const Precursor & |  | ) |

default

Copy constructor.

## ◆ Precursor() [3/3]

Precursor | ( | Precursor && |  | ) |

noexcept

Move constructor.

## ◆ ~Precursor()

~Precursor | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ getActivationEnergy()

double getActivationEnergy | ( |  | ) | const

returns the activation energy (in electronvolt)

## ◆ getActivationMethods() [1/2]

const std::set<ActivationMethod>& getActivationMethods | ( |  | ) | const

returns a const reference to the activation methods

## ◆ getActivationMethods() [2/2]

std::set<ActivationMethod>& getActivationMethods | ( |  | ) |

returns a mutable reference to the activation methods

## ◆ getCharge()

Int getCharge | ( |  | ) | const

Non-mutable access to the charge.

Referenced by DTAFile::store().

## ◆ getDriftTime()

double getDriftTime | ( |  | ) | const

Returns the ion mobility drift time in milliseconds (-1 means it is not set)

Note
  It is possible for the spectrum to not have a Precursor but still have a drift time, please check getDriftTime of MSSpectrum first and only use this function if you need find-grained access to individual precursors.

## ◆ getDriftTimeUnit()

DriftTimeUnit getDriftTimeUnit | ( |  | ) | const

Returns the ion mobility drift time unit.

## ◆ getDriftTimeWindowLowerOffset()

double getDriftTimeWindowLowerOffset | ( |  | ) | const

Returns the lower offset from the target ion mobility in milliseconds.

Note
  This is an offset relative to the target ion mobility. The start of the ion mobility isolation window should thus be computed as:

p.getDriftTime() + p.getDriftTimeWindowLowerOffset()

Returns
  the lower offset from the target ion mobility

## ◆ getDriftTimeWindowUpperOffset()

double getDriftTimeWindowUpperOffset | ( |  | ) | const

Returns the upper offset from the target ion mobility in milliseconds.

Note
  This is an offset relative to the target ion mobility. The end of the ion mobility isolation window should thus be computed as:

p.getDriftTime() + p.getDriftTimeWindowUpperOffset()

Returns
  the upper offset from the target ion mobility

## ◆ getIsolationWindowLowerOffset()

double getIsolationWindowLowerOffset | ( |  | ) | const

Returns the lower offset from the target m/z.

Note
  This is an offset relative to the target m/z. The start of the mass isolation window should thus be computed as:

p.getMZ() - p.getIsolationWindowLowerOffset()

Returns
  the lower offset from the target m/z

## ◆ getIsolationWindowUpperOffset()

double getIsolationWindowUpperOffset | ( |  | ) | const

Returns the upper offset from the target m/z.

Note
  This is an offset relative to the target m/z. The end of the mass isolation window should thus be computed as:

p.getMZ() + p.getIsolationWindowUpperOffset()

Returns
  the upper offset from the target m/z

## ◆ getPossibleChargeStates() [1/2]

std::vector<Int>& getPossibleChargeStates | ( |  | ) |

Mutable access to possible charge states.

## ◆ getPossibleChargeStates() [2/2]

const std::vector<Int>& getPossibleChargeStates | ( |  | ) | const

Non-mutable access to possible charge states.

## ◆ getUnchargedMass()

double getUnchargedMass | ( |  | ) | const

inline

Returns the uncharged mass of the precursor, if charge is unknown, i.e. 0 best guess is its doubly charged.

References OpenMS::Constants::c, and OpenMS::Constants::PROTON_MASS_U.

## ◆ operator!=()

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

Equality operator.

## ◆ operator=() [1/2]

Precursor& operator= | ( | const Precursor & |  | ) |

default

Assignment operator.

## ◆ operator=() [2/2]

Precursor& operator= | ( | Precursor && |  | ) | &

default

Move assignment operator.

## ◆ operator==()

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

Equality operator.

## ◆ setActivationEnergy()

void setActivationEnergy | ( | double | activation_energy | ) |

sets the activation energy (in electronvolt)

## ◆ setActivationMethods()

void setActivationMethods | ( | const std::set< ActivationMethod > & | activation_methods | ) |

sets the activation methods

## ◆ setCharge()

void setCharge | ( | Int | charge | ) |

Mutable access to the charge.

Referenced by DTAFile::load(), NucleicAcidSearchEngine::preprocessSpectra_(), ChromatogramExtractor::return_chromatogram(), and TOPPViewBase::showSpectrumGenerationDialog().

## ◆ setDriftTime()

void setDriftTime | ( | double | drift_time | ) |

sets the ion mobility drift time in milliseconds

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ setDriftTimeUnit()

void setDriftTimeUnit | ( | DriftTimeUnit | dt | ) |

Sets the ion mobility drift time unit.

## ◆ setDriftTimeWindowLowerOffset()

void setDriftTimeWindowLowerOffset | ( | double | drift_time | ) |

sets the lower offset from the target ion mobility

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ setDriftTimeWindowUpperOffset()

void setDriftTimeWindowUpperOffset | ( | double | drift_time | ) |

sets the upper offset from the target ion mobility

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ setIsolationWindowLowerOffset()

void setIsolationWindowLowerOffset | ( | double | bound | ) |

sets the lower offset from the target m/z

Referenced by ChromatogramExtractor::prepareSpectra_(), and ChromatogramExtractor::return_chromatogram().

## ◆ setIsolationWindowUpperOffset()

void setIsolationWindowUpperOffset | ( | double | bound | ) |

sets the upper offset from the target m/z

Referenced by ChromatogramExtractor::prepareSpectra_(), and ChromatogramExtractor::return_chromatogram().

## ◆ setPossibleChargeStates()

void setPossibleChargeStates | ( | const std::vector< Int > & | possible_charge_states | ) |

Sets the possible charge states.

## Member Data Documentation

## ◆ activation_energy_

double activation_energy_

protected

## ◆ activation_methods_

std::set<ActivationMethod> activation_methods_

protected

## ◆ charge_

Int charge_

protected

## ◆ drift_time_

double drift_time_

protected

## ◆ drift_time_unit_

DriftTimeUnit drift_time_unit_

protected

## ◆ drift_window_low_

double drift_window_low_

protected

## ◆ drift_window_up_

double drift_window_up_

protected

## ◆ NamesOfActivationMethod

const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]

static

Names of activation methods.

Referenced by IsobaricChannelExtractor::getActivationMethod_(), and HasActivationMethod< SpectrumType >::operator()().

## ◆ NamesOfActivationMethodShort

const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD]

static

## ◆ possible_charge_states_

std::vector<Int> possible_charge_states_

protected

## ◆ window_low_

double window_low_

protected

## ◆ window_up_

double window_up_

protected