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MassAnalyzer Class Reference

Description of a mass analyzer (part of a MS Instrument) More...

#include <OpenMS/METADATA/MassAnalyzer.h>

Inheritance diagram for MassAnalyzer:
MetaInfoInterface

Public Types

enum  AnalyzerType {
  ANALYZERNULL, QUADRUPOLE, PAULIONTRAP, RADIALEJECTIONLINEARIONTRAP,
  AXIALEJECTIONLINEARIONTRAP, TOF, SECTOR, FOURIERTRANSFORM,
  IONSTORAGE, ESA, IT, SWIFT,
  CYCLOTRON, ORBITRAP, LIT, SIZE_OF_ANALYZERTYPE
}
 analyzer type More...
 
enum  ResolutionMethod {
  RESMETHNULL, FWHM, TENPERCENTVALLEY, BASELINE,
  SIZE_OF_RESOLUTIONMETHOD
}
 resolution method More...
 
enum  ResolutionType { RESTYPENULL, CONSTANT, PROPORTIONAL, SIZE_OF_RESOLUTIONTYPE }
 Resolution type. More...
 
enum  ScanDirection { SCANDIRNULL, UP, DOWN, SIZE_OF_SCANDIRECTION }
 direction of scanning More...
 
enum  ScanLaw {
  SCANLAWNULL, EXPONENTIAL, LINEAR, QUADRATIC,
  SIZE_OF_SCANLAW
}
 Scan law. More...
 
enum  ReflectronState {
  REFLSTATENULL, ON, OFF, NONE,
  SIZE_OF_REFLECTRONSTATE
}
 Reflectron state. More...
 

Public Member Functions

 MassAnalyzer ()
 Constructor. More...
 
 MassAnalyzer (const MassAnalyzer &source)
 Copy constructor. More...
 
 ~MassAnalyzer ()
 Destructor. More...
 
MassAnalyzeroperator= (const MassAnalyzer &source)
 Assignment operator. More...
 
bool operator== (const MassAnalyzer &rhs) const
 Equality operator. More...
 
bool operator!= (const MassAnalyzer &rhs) const
 Equality operator. More...
 
AnalyzerType getType () const
 returns the analyzer type More...
 
void setType (AnalyzerType type)
 sets the analyzer type More...
 
ResolutionMethod getResolutionMethod () const
 returns the method used for determination of the resolution More...
 
void setResolutionMethod (ResolutionMethod resolution_method)
 sets the method used for determination of the resolution More...
 
ResolutionType getResolutionType () const
 returns the resolution type More...
 
void setResolutionType (ResolutionType resolution_type)
 sets the resolution type More...
 
ScanDirection getScanDirection () const
 returns the direction of scanning More...
 
void setScanDirection (ScanDirection scan_direction)
 sets the direction of scanning More...
 
ScanLaw getScanLaw () const
 returns the scan law More...
 
void setScanLaw (ScanLaw scan_law)
 sets the scan law More...
 
ReflectronState getReflectronState () const
 returns the reflectron state (for TOF) More...
 
void setReflectronState (ReflectronState reflecton_state)
 sets the reflectron state (for TOF) More...
 
double getResolution () const
 returns the resolution More...
 
void setResolution (double resolution)
 sets the resolution More...
 
double getAccuracy () const
 returns the mass accuracy i.e. how much the theoretical mass may differ from the measured mass (in ppm) More...
 
void setAccuracy (double accuracy)
 sets the accuracy i.e. how much the theoretical mass may differ from the measured mass (in ppm) More...
 
double getScanRate () const
 returns the scan rate (in s) More...
 
void setScanRate (double scan_rate)
 sets the scan rate (in s) More...
 
double getScanTime () const
 returns the scan time for a single scan (in s) More...
 
void setScanTime (double scan_time)
 sets the scan time for a single scan (in s) More...
 
double getTOFTotalPathLength () const
 returns the path length for a TOF mass analyzer (in meter) More...
 
void setTOFTotalPathLength (double TOF_total_path_length)
 sets the path length for a TOF mass analyzer (in meter) More...
 
double getIsolationWidth () const
 returns the isolation width i.e. in which m/z range the precursor ion is selected for MS to the n (in m/z) More...
 
void setIsolationWidth (double isolation_width)
 sets the isolation width i.e. in which m/z range the precursor ion is selected for MS to the n (in m/z) More...
 
Int getFinalMSExponent () const
 returns the final MS exponent More...
 
void setFinalMSExponent (Int final_MS_exponent)
 sets the final MS exponent More...
 
double getMagneticFieldStrength () const
 returns the strength of the magnetic field (in T) More...
 
void setMagneticFieldStrength (double magnetic_field_strength)
 sets the strength of the magnetic field (in T) More...
 
Int getOrder () const
 returns the position of this part in the whole Instrument. More...
 
void setOrder (Int order)
 sets the order 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...
 

Static Public Attributes

static const std::string NamesOfAnalyzerType [SIZE_OF_ANALYZERTYPE]
 Names of the analyzer types. More...
 
static const std::string NamesOfResolutionMethod [SIZE_OF_RESOLUTIONMETHOD]
 Names of resolution methods. More...
 
static const std::string NamesOfResolutionType [SIZE_OF_RESOLUTIONTYPE]
 Names of resolution type. More...
 
static const std::string NamesOfScanDirection [SIZE_OF_SCANDIRECTION]
 Names of direction of scanning. More...
 
static const std::string NamesOfScanLaw [SIZE_OF_SCANLAW]
 Names of scan laws. More...
 
static const std::string NamesOfReflectronState [SIZE_OF_REFLECTRONSTATE]
 Names of reflectron states. More...
 

Protected Attributes

AnalyzerType type_
 
ResolutionMethod resolution_method_
 
ResolutionType resolution_type_
 
ScanDirection scan_direction_
 
ScanLaw scan_law_
 
ReflectronState reflectron_state_
 
double resolution_
 
double accuracy_
 
double scan_rate_
 
double scan_time_
 
double TOF_total_path_length_
 
double isolation_width_
 
Int final_MS_exponent_
 
double magnetic_field_strength_
 
Int order_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 pointer to the MetaInfo object. 0 by default 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

Description of a mass analyzer (part of a MS Instrument)

Member Enumeration Documentation

analyzer type

Enumerator
ANALYZERNULL 

Unknown.

QUADRUPOLE 

Quadrupole.

PAULIONTRAP 

Quadrupole ion trap / Paul ion trap.

RADIALEJECTIONLINEARIONTRAP 

Radial ejection linear ion trap.

AXIALEJECTIONLINEARIONTRAP 

Axial ejection linear ion trap.

TOF 

Time-of-flight.

SECTOR 

Magnetic sector.

FOURIERTRANSFORM 

Fourier transform ion cyclotron resonance mass spectrometer.

IONSTORAGE 

Ion storage.

ESA 

Electrostatic energy analyzer.

IT 

Ion trap.

SWIFT 

Stored waveform inverse fourier transform.

CYCLOTRON 

Cyclotron.

ORBITRAP 

Orbitrap.

LIT 

Linear ion trap.

SIZE_OF_ANALYZERTYPE 

Reflectron state.

Enumerator
REFLSTATENULL 

Unknown.

ON 

On.

OFF 

Off.

NONE 

None.

SIZE_OF_REFLECTRONSTATE 

resolution method

Which of the available standard measures is used to define whether two peaks are separate

Enumerator
RESMETHNULL 

Unknown.

FWHM 

Full width at half max.

TENPERCENTVALLEY 

Ten percent valley.

BASELINE 

Baseline.

SIZE_OF_RESOLUTIONMETHOD 

Resolution type.

Enumerator
RESTYPENULL 

Unknown.

CONSTANT 

Constant.

PROPORTIONAL 

Proportional.

SIZE_OF_RESOLUTIONTYPE 

direction of scanning

Enumerator
SCANDIRNULL 

Unknown.

UP 

Up.

DOWN 

Down.

SIZE_OF_SCANDIRECTION 
enum ScanLaw

Scan law.

Enumerator
SCANLAWNULL 

Unknown.

EXPONENTIAL 

Unknown.

LINEAR 

Linear.

QUADRATIC 

Quadratic.

SIZE_OF_SCANLAW 

Constructor & Destructor Documentation

Constructor.

MassAnalyzer ( const MassAnalyzer source)

Copy constructor.

Destructor.

Member Function Documentation

double getAccuracy ( ) const

returns the mass accuracy i.e. how much the theoretical mass may differ from the measured mass (in ppm)

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

Int getFinalMSExponent ( ) const

returns the final MS exponent

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

double getIsolationWidth ( ) const

returns the isolation width i.e. in which m/z range the precursor ion is selected for MS to the n (in m/z)

Referenced by MzDataHandler< MapType >::writeTo().

double getMagneticFieldStrength ( ) const

returns the strength of the magnetic field (in T)

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

Int getOrder ( ) const

returns the position of this part in the whole Instrument.

Order can be ignored, as long the instrument has this default setup:

  • one ion source
  • one or many mass analyzers
  • one ion detector

For more complex instruments, the order should be defined.

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

ReflectronState getReflectronState ( ) const

returns the reflectron state (for TOF)

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

double getResolution ( ) const

returns the resolution

The maximum m/z value at which two peaks can be resolved, according to one of the standard measures

Referenced by MzDataHandler< MapType >::writeTo().

ResolutionMethod getResolutionMethod ( ) const

returns the method used for determination of the resolution

Referenced by MzDataHandler< MapType >::writeTo().

ResolutionType getResolutionType ( ) const

returns the resolution type

Referenced by MzDataHandler< MapType >::writeTo().

ScanDirection getScanDirection ( ) const

returns the direction of scanning

Referenced by MzDataHandler< MapType >::writeTo().

ScanLaw getScanLaw ( ) const

returns the scan law

Referenced by MzDataHandler< MapType >::writeTo().

double getScanRate ( ) const

returns the scan rate (in s)

Referenced by MzDataHandler< MapType >::writeTo().

double getScanTime ( ) const

returns the scan time for a single scan (in s)

Referenced by MzDataHandler< MapType >::writeTo().

double getTOFTotalPathLength ( ) const

returns the path length for a TOF mass analyzer (in meter)

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

AnalyzerType getType ( ) const

returns the analyzer type

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

bool operator!= ( const MassAnalyzer rhs) const

Equality operator.

MassAnalyzer& operator= ( const MassAnalyzer source)

Assignment operator.

bool operator== ( const MassAnalyzer rhs) const

Equality operator.

void setAccuracy ( double  accuracy)

sets the accuracy i.e. how much the theoretical mass may differ from the measured mass (in ppm)

void setFinalMSExponent ( Int  final_MS_exponent)

sets the final MS exponent

void setIsolationWidth ( double  isolation_width)

sets the isolation width i.e. in which m/z range the precursor ion is selected for MS to the n (in m/z)

void setMagneticFieldStrength ( double  magnetic_field_strength)

sets the strength of the magnetic field (in T)

void setOrder ( Int  order)

sets the order

void setReflectronState ( ReflectronState  reflecton_state)

sets the reflectron state (for TOF)

void setResolution ( double  resolution)

sets the resolution

void setResolutionMethod ( ResolutionMethod  resolution_method)

sets the method used for determination of the resolution

void setResolutionType ( ResolutionType  resolution_type)

sets the resolution type

void setScanDirection ( ScanDirection  scan_direction)

sets the direction of scanning

void setScanLaw ( ScanLaw  scan_law)

sets the scan law

void setScanRate ( double  scan_rate)

sets the scan rate (in s)

void setScanTime ( double  scan_time)

sets the scan time for a single scan (in s)

void setTOFTotalPathLength ( double  TOF_total_path_length)

sets the path length for a TOF mass analyzer (in meter)

void setType ( AnalyzerType  type)

sets the analyzer type

Member Data Documentation

double accuracy_
protected
Int final_MS_exponent_
protected
double isolation_width_
protected
double magnetic_field_strength_
protected
const std::string NamesOfAnalyzerType[SIZE_OF_ANALYZERTYPE]
static

Names of the analyzer types.

const std::string NamesOfReflectronState[SIZE_OF_REFLECTRONSTATE]
static

Names of reflectron states.

const std::string NamesOfResolutionMethod[SIZE_OF_RESOLUTIONMETHOD]
static

Names of resolution methods.

const std::string NamesOfResolutionType[SIZE_OF_RESOLUTIONTYPE]
static

Names of resolution type.

const std::string NamesOfScanDirection[SIZE_OF_SCANDIRECTION]
static

Names of direction of scanning.

const std::string NamesOfScanLaw[SIZE_OF_SCANLAW]
static

Names of scan laws.

Int order_
protected
ReflectronState reflectron_state_
protected
double resolution_
protected
ResolutionMethod resolution_method_
protected
ResolutionType resolution_type_
protected
ScanDirection scan_direction_
protected
ScanLaw scan_law_
protected
double scan_rate_
protected
double scan_time_
protected
double TOF_total_path_length_
protected
AnalyzerType type_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:28 using doxygen 1.8.11