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Precursor Class Reference

Precursor meta information. More...

#include <OpenMS/METADATA/Precursor.h>

Inheritance diagram for Precursor:
CVTermList Peak1D MetaInfoInterface

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...
 
Precursoroperator= (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...
 
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...
 
CVTermListoperator= (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...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (const String &name) const
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (UInt index) const
 returns the value corresponding to an index More...
 
bool metaValueExists (const String &name) const
 returns if this MetaInfo is set More...
 
bool metaValueExists (UInt index) const
 returns if this MetaInfo is set 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
Peak1Doperator= (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...
 
PositionTypegetPosition ()
 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...
 

Protected Attributes

std::set< ActivationMethodactivation_methods_
 
double activation_energy_
 
double window_low_
 
double window_up_
 
Int charge_
 
std::vector< Intpossible_charge_states_
 
- Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > > cv_terms_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 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 MetaInfoRegistrymetaRegistry ()
 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:

Constructor & Destructor Documentation

Precursor ( )

Constructor.

Precursor ( const Precursor source)

Copy constructor.

virtual ~Precursor ( )
virtual

Destructor.

Member Function Documentation

double getActivationEnergy ( ) const

returns the activation energy (in electronvolt)

Referenced by MzMLHandler< MapType >::writePrecursor_(), and MzDataHandler< MapType >::writeTo().

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

returns a const reference to the activation methods

Referenced by MzMLHandler< MapType >::writePrecursor_(), and MzDataHandler< MapType >::writeTo().

std::set<ActivationMethod>& getActivationMethods ( )

returns a mutable reference to the activation methods

Int getCharge ( ) const
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 MzMLHandler< MapType >::writePrecursor_(), and MzXMLHandler< MapType >::writeTo().

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 MzMLHandler< MapType >::writePrecursor_(), and MzXMLHandler< MapType >::writeTo().

std::vector<Int>& getPossibleChargeStates ( )

Mutable access to possible charge states.

Referenced by MzMLHandler< MapType >::writePrecursor_().

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

Non-mutable access to possible charge states.

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.

bool operator!= ( const Precursor rhs) const

Equality operator.

Precursor& operator= ( const Precursor source)

Assignment operator.

bool operator== ( const Precursor rhs) const

Equality operator.

void setActivationEnergy ( double  activation_energy)

sets the activation energy (in electronvolt)

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

sets the activation methods

void setCharge ( Int  charge)
void setIsolationWindowLowerOffset ( double  bound)

sets the lower offset from the target m/z

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

void setIsolationWindowUpperOffset ( double  bound)

sets the upper offset from the target m/z

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

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

Sets the possible charge states.

Member Data Documentation

double activation_energy_
protected
std::set<ActivationMethod> activation_methods_
protected
Int charge_
protected
const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
static

Names of activation methods.

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

std::vector<Int> possible_charge_states_
protected
double window_low_
protected
double window_up_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:14:02 using doxygen 1.8.9.1