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pwiz::analysis::SpectrumList_IonMobility Class Reference

SpectrumList implementation that provides access to vendor-specific ion mobility functions. More...

#include <SpectrumList_IonMobility.hpp>

Inheritance diagram for pwiz::analysis::SpectrumList_IonMobility:
pwiz::msdata::SpectrumListWrapper pwiz::msdata::SpectrumList

Public Types

enum class  IonMobilityUnits { none , drift_time_msec , inverse_reduced_ion_mobility_Vsec_per_cm2 , compensation_V }
 

Public Member Functions

 SpectrumList_IonMobility (const msdata::SpectrumListPtr &inner)
 
virtual msdata::SpectrumPtr spectrum (size_t index, bool getBinaryData=false) const
 retrieve a spectrum by index
 
virtual IonMobilityUnits getIonMobilityUnits () const
 
virtual bool canConvertIonMobilityAndCCS (IonMobilityUnits units) const
 returns true if file in question contains necessary information for CCS/IonMobility handling (as with Drift Time in Agilent)
 
virtual double ionMobilityToCCS (double ionMobility, double mz, int charge) const
 returns collisional cross-section associated with the ion mobility (units depend on IonMobilityEquipment)
 
virtual double ccsToIonMobility (double ccs, double mz, int charge) const
 returns the ion mobility (units depend on IonMobilityEquipment) associated with the given collisional cross-section
 
virtual std::pair< int, int > sonarMzToDriftBinRange (int function, float precursorMz, float precursorTolerance) const
 for Waters SONAR data, given a (0-based) function number, a precursor m/z, and a tolerance, return the corresponding start and end "drift" bins
 
- Public Member Functions inherited from pwiz::msdata::SpectrumListWrapper
 SpectrumListWrapper (const SpectrumListPtr &inner)
 
virtual size_t size () const
 returns the number of spectra
 
virtual bool empty () const
 returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL)
 
virtual const SpectrumIdentityspectrumIdentity (size_t index) const
 access to a spectrum index
 
virtual SpectrumPtr spectrum (size_t index, DetailLevel detailLevel) const
 retrieve a spectrum by index
 
virtual const boost::shared_ptr< const DataProcessingdataProcessingPtr () const
 returns the data processing affecting spectra retrieved through this interface
 
SpectrumListPtr inner () const
 
SpectrumListPtr innermost () const
 
- Public Member Functions inherited from pwiz::msdata::SpectrumList
virtual size_t find (const std::string &id) const
 find id in the spectrum index (returns size() on failure)
 
virtual size_t findAbbreviated (const std::string &abbreviatedId, char delimiter='.') const
 find an abbreviated id (e.g. "1.1.123.2" for "sample=1 period=1 cycle=123 experiment=2") in the spectrum index (returns size() on failure)
 
virtual IndexList findNameValue (const std::string &name, const std::string &value) const
 find all spectrum indexes with specified name/value pair
 
virtual IndexList findSpotID (const std::string &spotID) const
 find all spectrum indexes with spotID (returns empty vector on failure)
 
virtual SpectrumPtr spectrum (const SpectrumPtr &seed, bool getBinaryData) const
 get a copy of the seed spectrum, optionally with its binary data populated this is useful for formats like mzML that can delay loading of binary data
 
virtual void warn_once (const char *msg) const
 issues a warning once per SpectrumList instance (based on string hash)
 
virtual ~SpectrumList ()
 

Static Public Member Functions

static bool accept (const msdata::SpectrumListPtr &inner)
 

Private Types

enum class  IonMobilityEquipment {
  None , AgilentDrift , WatersDrift , WatersSonar ,
  BrukerTIMS , ThermoFAIMS
}
 

Private Attributes

IonMobilityEquipment equipment_
 
IonMobilityUnits units_
 
msdata::SpectrumListIonMobilityBasesl_
 

Additional Inherited Members

- Protected Attributes inherited from pwiz::msdata::SpectrumListWrapper
SpectrumListPtr inner_
 
DataProcessingPtr dp_
 

Detailed Description

SpectrumList implementation that provides access to vendor-specific ion mobility functions.

Definition at line 35 of file SpectrumList_IonMobility.hpp.

Member Enumeration Documentation

◆ IonMobilityUnits

◆ IonMobilityEquipment

Constructor & Destructor Documentation

◆ SpectrumList_IonMobility()

pwiz::analysis::SpectrumList_IonMobility::SpectrumList_IonMobility ( const msdata::SpectrumListPtr inner)

Member Function Documentation

◆ accept()

static bool pwiz::analysis::SpectrumList_IonMobility::accept ( const msdata::SpectrumListPtr inner)
static

◆ spectrum()

virtual msdata::SpectrumPtr pwiz::analysis::SpectrumList_IonMobility::spectrum ( size_t  index,
bool  getBinaryData = false 
) const
virtual

retrieve a spectrum by index

  • binary data arrays will be provided if (getBinaryData == true);
  • client may assume the underlying Spectrum* is valid

Implements pwiz::msdata::SpectrumListWrapper.

◆ getIonMobilityUnits()

virtual IonMobilityUnits pwiz::analysis::SpectrumList_IonMobility::getIonMobilityUnits ( ) const
virtual

Referenced by test().

◆ canConvertIonMobilityAndCCS()

virtual bool pwiz::analysis::SpectrumList_IonMobility::canConvertIonMobilityAndCCS ( IonMobilityUnits  units) const
virtual

returns true if file in question contains necessary information for CCS/IonMobility handling (as with Drift Time in Agilent)

Referenced by test().

◆ ionMobilityToCCS()

virtual double pwiz::analysis::SpectrumList_IonMobility::ionMobilityToCCS ( double  ionMobility,
double  mz,
int  charge 
) const
virtual

returns collisional cross-section associated with the ion mobility (units depend on IonMobilityEquipment)

Referenced by test().

◆ ccsToIonMobility()

virtual double pwiz::analysis::SpectrumList_IonMobility::ccsToIonMobility ( double  ccs,
double  mz,
int  charge 
) const
virtual

returns the ion mobility (units depend on IonMobilityEquipment) associated with the given collisional cross-section

Referenced by test().

◆ sonarMzToDriftBinRange()

virtual std::pair< int, int > pwiz::analysis::SpectrumList_IonMobility::sonarMzToDriftBinRange ( int  function,
float  precursorMz,
float  precursorTolerance 
) const
virtual

for Waters SONAR data, given a (0-based) function number, a precursor m/z, and a tolerance, return the corresponding start and end "drift" bins

Member Data Documentation

◆ equipment_

IonMobilityEquipment pwiz::analysis::SpectrumList_IonMobility::equipment_
private

Definition at line 64 of file SpectrumList_IonMobility.hpp.

◆ units_

IonMobilityUnits pwiz::analysis::SpectrumList_IonMobility::units_
private

Definition at line 65 of file SpectrumList_IonMobility.hpp.

◆ sl_

msdata::SpectrumListIonMobilityBase* pwiz::analysis::SpectrumList_IonMobility::sl_
private

Definition at line 66 of file SpectrumList_IonMobility.hpp.


The documentation for this class was generated from the following file: