ProteoWizard
Public Member Functions | Private Attributes | List of all members
pwiz::analysis::SpectrumList_ChargeFromIsotope Class Reference

SpectrumList implementation that assigns (probable) charge states to tandem mass spectra. More...

#include <SpectrumList_ChargeFromIsotope.hpp>

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

Public Member Functions

 SpectrumList_ChargeFromIsotope (const msdata::MSData &msd, int maxCharge=3, int minCharge=1, int parentsBefore=2, int parentsAfter=0, double isolationWindow=1.25, int defaultChargeMax=0, int defaultChargeMin=0)
 
virtual msdata::SpectrumPtr spectrum (size_t index, bool getBinaryData=true) const
 retrieve a spectrum by index More...
 
void getMS1RetentionTimes ()
 
void simulateSSE (const int, const int)
 
void simulateKL (const double, const int, const int)
 
void simulateTotIntensity (const int)
 
void getParentIndices (const SpectrumPtr, std::vector< int > &) const
 
void getParentPeaks (const SpectrumPtr, const std::vector< int > &, const double, const double, const double, std::vector< std::vector< double > > &, std::vector< std::vector< double > > &) const
 
SpectrumListPtr instantiatePeakPicker (const std::vector< int > &) const
 
SpectrumListPtr instantiatePeakPicker (const std::vector< int > &, const double, const double, const double) const
 
- Public Member Functions inherited from pwiz::msdata::SpectrumListWrapper
 SpectrumListWrapper (const SpectrumListPtr &inner)
 
virtual size_t size () const
 returns the number of spectra More...
 
virtual bool empty () const
 returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL) More...
 
virtual const SpectrumIdentityspectrumIdentity (size_t index) const
 access to a spectrum index More...
 
virtual SpectrumPtr spectrum (size_t index, DetailLevel detailLevel) const
 retrieve a spectrum by index More...
 
virtual const boost::shared_ptr< const DataProcessingdataProcessingPtr () const
 returns the data processing affecting spectra retrieved through this interface More...
 
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) More...
 
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) More...
 
virtual IndexList findNameValue (const std::string &name, const std::string &value) const
 find all spectrum indexes with specified name/value pair More...
 
virtual IndexList findSpotID (const std::string &spotID) const
 find all spectrum indexes with spotID (returns empty vector on failure) More...
 
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 More...
 
virtual void warn_once (const char *msg) const
 issues a warning once per SpectrumList instance (based on string hash) More...
 
virtual ~SpectrumList ()
 

Private Attributes

bool override_
 
int maxCharge_
 
int minCharge_
 
double sigVal_
 
int nChainsCheck_
 
int parentsBefore_
 
int parentsAfter_
 
int defaultChargeMax_
 
int defaultChargeMin_
 
double defaultIsolationWidth_
 
int nSamples
 
int maxIsotopePeaks
 
int minIsotopePeaks
 
int maxNumberPeaks
 
int minNumberPeaks
 
double mzTol
 
double massNeutron
 
double upperLimitPadding
 
std::vector< double > simulatedSSEs
 
std::vector< double > simulatedKLs
 
std::vector< int > simulatedIntensityRankSum
 
std::vector< rtimeMapMS1retentionTimes
 

Additional Inherited Members

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

Detailed Description

SpectrumList implementation that assigns (probable) charge states to tandem mass spectra.

Definition at line 68 of file SpectrumList_ChargeFromIsotope.hpp.

Constructor & Destructor Documentation

§ SpectrumList_ChargeFromIsotope()

pwiz::analysis::SpectrumList_ChargeFromIsotope::SpectrumList_ChargeFromIsotope ( const msdata::MSData msd,
int  maxCharge = 3,
int  minCharge = 1,
int  parentsBefore = 2,
int  parentsAfter = 0,
double  isolationWindow = 1.25,
int  defaultChargeMax = 0,
int  defaultChargeMin = 0 
)

Member Function Documentation

§ spectrum()

virtual msdata::SpectrumPtr pwiz::analysis::SpectrumList_ChargeFromIsotope::spectrum ( size_t  index,
bool  getBinaryData = true 
) 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.

§ getMS1RetentionTimes()

void pwiz::analysis::SpectrumList_ChargeFromIsotope::getMS1RetentionTimes ( )

§ simulateSSE()

void pwiz::analysis::SpectrumList_ChargeFromIsotope::simulateSSE ( const int  ,
const int   
)

§ simulateKL()

void pwiz::analysis::SpectrumList_ChargeFromIsotope::simulateKL ( const double  ,
const int  ,
const int   
)

§ simulateTotIntensity()

void pwiz::analysis::SpectrumList_ChargeFromIsotope::simulateTotIntensity ( const int  )

§ getParentIndices()

void pwiz::analysis::SpectrumList_ChargeFromIsotope::getParentIndices ( const SpectrumPtr  ,
std::vector< int > &   
) const

§ getParentPeaks()

void pwiz::analysis::SpectrumList_ChargeFromIsotope::getParentPeaks ( const SpectrumPtr  ,
const std::vector< int > &  ,
const double  ,
const double  ,
const double  ,
std::vector< std::vector< double > > &  ,
std::vector< std::vector< double > > &   
) const

§ instantiatePeakPicker() [1/2]

SpectrumListPtr pwiz::analysis::SpectrumList_ChargeFromIsotope::instantiatePeakPicker ( const std::vector< int > &  ) const

§ instantiatePeakPicker() [2/2]

SpectrumListPtr pwiz::analysis::SpectrumList_ChargeFromIsotope::instantiatePeakPicker ( const std::vector< int > &  ,
const double  ,
const double  ,
const double   
) const

Member Data Documentation

§ override_

bool pwiz::analysis::SpectrumList_ChargeFromIsotope::override_
private

Definition at line 93 of file SpectrumList_ChargeFromIsotope.hpp.

§ maxCharge_

int pwiz::analysis::SpectrumList_ChargeFromIsotope::maxCharge_
private

Definition at line 94 of file SpectrumList_ChargeFromIsotope.hpp.

§ minCharge_

int pwiz::analysis::SpectrumList_ChargeFromIsotope::minCharge_
private

Definition at line 95 of file SpectrumList_ChargeFromIsotope.hpp.

§ sigVal_

double pwiz::analysis::SpectrumList_ChargeFromIsotope::sigVal_
private

Definition at line 96 of file SpectrumList_ChargeFromIsotope.hpp.

§ nChainsCheck_

int pwiz::analysis::SpectrumList_ChargeFromIsotope::nChainsCheck_
private

Definition at line 97 of file SpectrumList_ChargeFromIsotope.hpp.

§ parentsBefore_

int pwiz::analysis::SpectrumList_ChargeFromIsotope::parentsBefore_
private

Definition at line 98 of file SpectrumList_ChargeFromIsotope.hpp.

§ parentsAfter_

int pwiz::analysis::SpectrumList_ChargeFromIsotope::parentsAfter_
private

Definition at line 99 of file SpectrumList_ChargeFromIsotope.hpp.

§ defaultChargeMax_

int pwiz::analysis::SpectrumList_ChargeFromIsotope::defaultChargeMax_
private

Definition at line 100 of file SpectrumList_ChargeFromIsotope.hpp.

§ defaultChargeMin_

int pwiz::analysis::SpectrumList_ChargeFromIsotope::defaultChargeMin_
private

Definition at line 101 of file SpectrumList_ChargeFromIsotope.hpp.

§ defaultIsolationWidth_

double pwiz::analysis::SpectrumList_ChargeFromIsotope::defaultIsolationWidth_
private

Definition at line 102 of file SpectrumList_ChargeFromIsotope.hpp.

§ nSamples

int pwiz::analysis::SpectrumList_ChargeFromIsotope::nSamples
private

Definition at line 104 of file SpectrumList_ChargeFromIsotope.hpp.

§ maxIsotopePeaks

int pwiz::analysis::SpectrumList_ChargeFromIsotope::maxIsotopePeaks
private

Definition at line 105 of file SpectrumList_ChargeFromIsotope.hpp.

§ minIsotopePeaks

int pwiz::analysis::SpectrumList_ChargeFromIsotope::minIsotopePeaks
private

Definition at line 106 of file SpectrumList_ChargeFromIsotope.hpp.

§ maxNumberPeaks

int pwiz::analysis::SpectrumList_ChargeFromIsotope::maxNumberPeaks
private

Definition at line 107 of file SpectrumList_ChargeFromIsotope.hpp.

§ minNumberPeaks

int pwiz::analysis::SpectrumList_ChargeFromIsotope::minNumberPeaks
private

Definition at line 108 of file SpectrumList_ChargeFromIsotope.hpp.

§ mzTol

double pwiz::analysis::SpectrumList_ChargeFromIsotope::mzTol
private

Definition at line 109 of file SpectrumList_ChargeFromIsotope.hpp.

§ massNeutron

double pwiz::analysis::SpectrumList_ChargeFromIsotope::massNeutron
private

Definition at line 110 of file SpectrumList_ChargeFromIsotope.hpp.

§ upperLimitPadding

double pwiz::analysis::SpectrumList_ChargeFromIsotope::upperLimitPadding
private

Definition at line 111 of file SpectrumList_ChargeFromIsotope.hpp.

§ simulatedSSEs

std::vector<double> pwiz::analysis::SpectrumList_ChargeFromIsotope::simulatedSSEs
private

Definition at line 113 of file SpectrumList_ChargeFromIsotope.hpp.

§ simulatedKLs

std::vector<double> pwiz::analysis::SpectrumList_ChargeFromIsotope::simulatedKLs
private

Definition at line 114 of file SpectrumList_ChargeFromIsotope.hpp.

§ simulatedIntensityRankSum

std::vector<int> pwiz::analysis::SpectrumList_ChargeFromIsotope::simulatedIntensityRankSum
private

Definition at line 115 of file SpectrumList_ChargeFromIsotope.hpp.

§ MS1retentionTimes

std::vector<rtimeMap> pwiz::analysis::SpectrumList_ChargeFromIsotope::MS1retentionTimes
private

Definition at line 116 of file SpectrumList_ChargeFromIsotope.hpp.


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