Precursor Class Reference

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...
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 &source)
	Copy constructor. More...
virtual	~Precursor ()
	Destructor. More...
Precursor &	operator= (const Precursor &source)
	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...
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 ()
	Defaults constructor. More...
	CVTermList (const CVTermList &rhs)
	Copy constructor. More...
virtual	~CVTermList ()
	Destructor. More...
CVTermList &	operator= (const CVTermList &rhs)
	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 ()
	Destructor. More...
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	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
	Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to an index (or 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 ()
	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_
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

Constructor & Destructor Documentation

Precursor() [1/2]

Precursor

(

)

Constructor.

Precursor() [2/2]

Precursor

(

const Precursor &

source

)

Copy constructor.

~Precursor()

virtual ~Precursor ( )

virtual

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.

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=()

Precursor& operator=

(

const Precursor &

source

)

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(), TOPPRNPxl::main_(), and TOPPViewBase::showSpectrumGenerationDialog().

setDriftTime()

void setDriftTime

(

double

drift_time

)

sets the ion mobility drift time in milliseconds

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

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