Precursor Class Reference

Precursor meta information. More...

#include <OpenMS/METADATA/Precursor.h>

Inheritance diagram for Precursor:

Collaboration diagram for Precursor:

Public Types
enum class	ActivationMethod {   CID , PSD , PD , SID ,   BIRD , ECD , IMD , SORI ,   HCID , LCID , PHD , ETD ,   ETciD , EThcD , PQD , TRAP ,   HCD , INSOURCE , LIFT , SIZE_OF_ACTIVATIONMETHOD }
	Method of activation. More...
Public Types inherited from Peak1D
enum	{ DIMENSION = 1 }
using	IntensityType = float
	Intensity type.
using	PositionType = DPosition< 1 >
	Position type.
using	CoordinateType = double
	Coordinate type.

Public Member Functions
	Precursor ()=default
	Constructor.
	Precursor (const Precursor &)=default
	Copy constructor.
	Precursor (Precursor &&) noexcept
	Move constructor.
	~Precursor () override=default
	Destructor.
Precursor &	operator= (const Precursor &)=default
	Assignment operator.
Precursor &	operator= (Precursor &&) &=default
	Move assignment operator.
bool	operator== (const Precursor &rhs) const
	Equality operator.
bool	operator!= (const Precursor &rhs) const
	Equality operator.
const std::set< ActivationMethod > &	getActivationMethods () const
	returns a const reference to the activation methods
std::set< ActivationMethod > &	getActivationMethods ()
	returns a mutable reference to the activation methods
StringList	getActivationMethodsAsString () const
	Returns the full names (e.g., "Collision-induced dissociation") of the activation methods set on this instance.
StringList	getActivationMethodsAsShortString () const
	Returns the abbreviations (e.g., "CID") of the activation methods set on this instance.
void	setActivationMethods (const std::set< ActivationMethod > &activation_methods)
	sets the activation methods
double	getActivationEnergy () const
	returns the activation energy (in electronvolt)
void	setActivationEnergy (double activation_energy)
	sets the activation energy (in electronvolt)
double	getIsolationWindowLowerOffset () const
	Returns the lower offset from the target m/z.
void	setIsolationWindowLowerOffset (double bound)
	sets the lower offset from the target m/z
double	getIsolationWindowUpperOffset () const
	Returns the upper offset from the target m/z.
void	setIsolationWindowUpperOffset (double bound)
	sets the upper offset from the target m/z
double	getDriftTime () const
	Returns the ion mobility drift time in milliseconds (-1 means it is not set)
void	setDriftTime (double drift_time)
	sets the ion mobility drift time in milliseconds
DriftTimeUnit	getDriftTimeUnit () const
	Returns the ion mobility drift time unit.
void	setDriftTimeUnit (DriftTimeUnit dt)
	Sets the ion mobility drift time unit.
double	getDriftTimeWindowLowerOffset () const
	Returns the lower offset from the target ion mobility in milliseconds.
void	setDriftTimeWindowLowerOffset (double drift_time)
	sets the lower offset from the target ion mobility
double	getDriftTimeWindowUpperOffset () const
	Returns the upper offset from the target ion mobility in milliseconds.
void	setDriftTimeWindowUpperOffset (double drift_time)
	sets the upper offset from the target ion mobility
Int	getCharge () const
	Non-mutable access to the charge.
void	setCharge (Int charge)
	Mutable access to the charge.
std::vector< Int > &	getPossibleChargeStates ()
	Mutable access to possible charge states.
const std::vector< Int > &	getPossibleChargeStates () const
	Non-mutable access to possible charge states.
void	setPossibleChargeStates (const std::vector< Int > &possible_charge_states)
	Sets the possible charge states.
double	getUnchargedMass () const
	Returns the uncharged mass of the precursor, if charge is unknown, i.e. 0, our best guess is doubly charged.
Public Member Functions inherited from CVTermList
	CVTermList ()=default
	Defaults constructor.
	CVTermList (const CVTermList &)=default
	Copy constructor.
	CVTermList (CVTermList &&) noexcept
	Move constructor.
virtual	~CVTermList ()
	Destructor.
CVTermList &	operator= (const CVTermList &rhs) &=default
	Assignment operator.
CVTermList &	operator= (CVTermList &&) &=default
	Move assignment operator.
void	setCVTerms (const std::vector< CVTerm > &terms)
	sets the CV terms
void	replaceCVTerm (const CVTerm &cv_term)
	replaces the specified CV term
void	replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession)
	replaces the specified CV terms using the given accession number
void	replaceCVTerms (const std::map< String, std::vector< CVTerm > > &cv_term_map)
	replaces all cv terms with a map (can be obtained via getCVTerms)
void	consumeCVTerms (const std::map< String, std::vector< CVTerm > > &cv_term_map)
	merges the given map into the member map, no duplicate checking
const std::map< String, std::vector< CVTerm > > &	getCVTerms () const
	returns the accession string of the term
void	addCVTerm (const CVTerm &term)
	adds a CV term
bool	operator== (const CVTermList &cv_term_list) const
	equality operator
bool	operator!= (const CVTermList &cv_term_list) const
	inequality operator
bool	hasCVTerm (const String &accession) const
	checks whether the term has a value
bool	empty () const
	return true if no terms are available
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.
	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.
	~MetaInfoInterface ()
	Destructor.
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator.
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.
void	swap (MetaInfoInterface &rhs)
	Swap contents.
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator.
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator.
const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found.
DataValue	getMetaValue (const String &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.
DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found
bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists.
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name.
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.
void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to name if it exists.
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists.
void	addMetaValues (const MetaInfoInterface &from)
void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.
void	clearMetaInfo ()
	Removes all meta values.
Public Member Functions inherited from Peak1D
bool	operator== (const Peak1D &rhs) const =default
	Equality operator.
bool	operator!= (const Peak1D &rhs) const
	Equality operator.
	Peak1D ()=default
	Peak1D (PositionType a, IntensityType b)
	construct with position and intensity
	Peak1D (const Peak1D &p)=default
	Copy constructor.
	Peak1D (Peak1D &&) noexcept=default
Peak1D &	operator= (const Peak1D &rhs)=default
	Assignment operator.
Peak1D &	operator= (Peak1D &&) noexcept=default
	Move assignment operator.
	~Peak1D ()=default
	Destructor.
IntensityType	getIntensity () const
void	setIntensity (IntensityType intensity)
	Mutable access to the data point intensity (height)
CoordinateType	getMZ () const
	Non-mutable access to m/z.
void	setMZ (CoordinateType mz)
	Mutable access to m/z.
CoordinateType	getPos () const
	Alias for getMZ()
void	setPos (CoordinateType pos)
	Alias for setMZ()
PositionType const &	getPosition () const
	Non-mutable access to the position.
PositionType &	getPosition ()
	Mutable access to the position.
void	setPosition (PositionType const &position)
	Mutable access to the position.

Static Public Member Functions
static StringList	getAllNamesOfActivationMethods ()
	returns all activation method full names (e.g., "Collision-induced dissociation") known to OpenMS
static StringList	getAllShortNamesOfActivationMethods ()
	returns all activation method abbreviations (e.g., "CID") known to OpenMS
static const std::string &	activationMethodToString (ActivationMethod m)
static const std::string &	activationMethodToShortString (ActivationMethod m)
static ActivationMethod	toActivationMethod (const std::string &name)
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry.

Static Public Attributes
static const std::string	NamesOfActivationMethod [static_cast< size_t >(ActivationMethod::SIZE_OF_ACTIVATIONMETHOD)]
	Names of activation methods.
static const std::string	NamesOfActivationMethodShort [static_cast< size_t >(ActivationMethod::SIZE_OF_ACTIVATIONMETHOD)]

Protected Attributes
std::set< ActivationMethod >	activation_methods_
double	activation_energy_ {}
double	window_low_ {}
double	window_up_ {}
double	drift_time_ {-1}
double	drift_window_low_ {}
double	drift_window_up_ {}
DriftTimeUnit	drift_time_unit_ {DriftTimeUnit::NONE}
Int	charge_ {}
std::vector< Int >	possible_charge_states_
Protected Attributes inherited from CVTermList
std::map< String, std::vector< CVTerm > >	cv_terms_
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_ = nullptr
	Pointer to the MetaInfo object.
Protected Attributes inherited from Peak1D
PositionType	position_
	The data point position.
IntensityType	intensity_ = 0.0
	The data point intensity.

Additional Inherited Members
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.

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 class ActivationMethod

strong

Method of activation.

Enumerator
CID	Collision-induced dissociation (MS:1000133) (also CAD; parent term, but unless otherwise stated often used as synonym for trap-type CID)
PSD	Post-source decay.
PD	Plasma desorption.
SID	Surface-induced dissociation.
BIRD	Blackbody infrared radiative dissociation.
ECD	Electron capture dissociation (MS:1000250)
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.
ETciD	Electron transfer and collision-induced dissociation (MS:1003182)
EThcD	Electron transfer and higher-energy collision dissociation (MS:1002631)
PQD	Pulsed q dissociation (MS:1000599)
TRAP	trap-type collision-induced dissociation (MS:1002472)
HCD	beam-type collision-induced dissociation (MS:1000422)
INSOURCE	in-source collision-induced dissociation (MS:1001880)
LIFT	Bruker proprietary method (MS:1002000)
SIZE_OF_ACTIVATIONMETHOD

Constructor & Destructor Documentation

Precursor() [1/3]

Precursor ( )

default

Constructor.

Precursor() [2/3]

Precursor ( const Precursor &  )

default

Copy constructor.

Precursor() [3/3]

Precursor ( Precursor &&  )

noexcept

Move constructor.

~Precursor()

~Precursor ( )

overridedefault

Destructor.

Member Function Documentation

activationMethodToShortString()

static const std::string & activationMethodToShortString ( ActivationMethod  m )

static

convert an ActivationMethod enum to its short (abbreviated) name string

Exceptions

Exception::InvalidValue

if m is SIZE_OF_ACTIVATIONMETHOD

activationMethodToString()

static const std::string & activationMethodToString ( ActivationMethod  m )

static

convert an ActivationMethod enum to its full name string

Exceptions

Exception::InvalidValue

if m is SIZE_OF_ACTIVATIONMETHOD

getActivationEnergy()

double getActivationEnergy

(

)

const

returns the activation energy (in electronvolt)

getActivationMethods() [1/2]

std::set< ActivationMethod > & getActivationMethods

(

)

returns a mutable reference to the activation methods

getActivationMethods() [2/2]

const std::set< ActivationMethod > & getActivationMethods

(

)

const

returns a const reference to the activation methods

getActivationMethodsAsShortString()

StringList getActivationMethodsAsShortString

(

)

const

Returns the abbreviations (e.g., "CID") of the activation methods set on this instance.

getActivationMethodsAsString()

StringList getActivationMethodsAsString

(

)

const

Returns the full names (e.g., "Collision-induced dissociation") of the activation methods set on this instance.

getAllNamesOfActivationMethods()

static StringList getAllNamesOfActivationMethods ( )

static

returns all activation method full names (e.g., "Collision-induced dissociation") known to OpenMS

getAllShortNamesOfActivationMethods()

static StringList getAllShortNamesOfActivationMethods ( )

static

returns all activation method abbreviations (e.g., "CID") known to OpenMS

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

Referenced by TOPPViewBase::showCurrentPeaksAsDIA().

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

Referenced by TOPPViewBase::showCurrentPeaksAsDIA().

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, our best guess is doubly charged.

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_(), and ChromatogramExtractor::return_chromatogram().

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.

toActivationMethod()

static ActivationMethod toActivationMethod ( const std::string &  name )

static

convert a string (full name or short name) to an ActivationMethod enum

Exceptions

Exception::InvalidValue

if name is not found in NamesOfActivationMethod or NamesOfActivationMethodShort

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_ {-1}

protected

drift_time_unit_

DriftTimeUnit drift_time_unit_ {DriftTimeUnit::NONE}

protected

drift_window_low_

double drift_window_low_ {}

protected

drift_window_up_

double drift_window_up_ {}

protected

NamesOfActivationMethod

const std::string NamesOfActivationMethod[static_cast< size_t >(ActivationMethod::SIZE_OF_ACTIVATIONMETHOD)]

static

Names of activation methods.

Referenced by HasActivationMethod< SpectrumType >::operator()().

NamesOfActivationMethodShort

const std::string NamesOfActivationMethodShort[static_cast< size_t >(ActivationMethod::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