ProteoWizard
|
SpectrumList implementation that assigns (probable) charge states to tandem mass spectra. More...
#include <SpectrumList_ChargeFromIsotope.hpp>
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 |
![]() | |
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 SpectrumIdentity & | spectrumIdentity (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 DataProcessing > | dataProcessingPtr () const |
returns the data processing affecting spectra retrieved through this interface More... | |
SpectrumListPtr | inner () const |
SpectrumListPtr | innermost () const |
![]() | |
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< rtimeMap > | MS1retentionTimes |
Additional Inherited Members | |
![]() | |
SpectrumListPtr | inner_ |
DataProcessingPtr | dp_ |
SpectrumList implementation that assigns (probable) charge states to tandem mass spectra.
Definition at line 68 of file SpectrumList_ChargeFromIsotope.hpp.
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 |
||
) |
|
virtual |
retrieve a spectrum by index
Implements pwiz::msdata::SpectrumListWrapper.
void pwiz::analysis::SpectrumList_ChargeFromIsotope::getMS1RetentionTimes | ( | ) |
void pwiz::analysis::SpectrumList_ChargeFromIsotope::simulateSSE | ( | const int | , |
const int | |||
) |
void pwiz::analysis::SpectrumList_ChargeFromIsotope::simulateKL | ( | const double | , |
const int | , | ||
const int | |||
) |
void pwiz::analysis::SpectrumList_ChargeFromIsotope::simulateTotIntensity | ( | const int | ) |
void pwiz::analysis::SpectrumList_ChargeFromIsotope::getParentIndices | ( | const SpectrumPtr | , |
std::vector< int > & | |||
) | const |
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 |
SpectrumListPtr pwiz::analysis::SpectrumList_ChargeFromIsotope::instantiatePeakPicker | ( | const std::vector< int > & | ) | const |
SpectrumListPtr pwiz::analysis::SpectrumList_ChargeFromIsotope::instantiatePeakPicker | ( | const std::vector< int > & | , |
const double | , | ||
const double | , | ||
const double | |||
) | const |
|
private |
Definition at line 93 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 94 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 95 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 96 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 97 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 98 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 99 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 100 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 101 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 102 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 104 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 105 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 106 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 107 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 108 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 109 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 110 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 111 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 113 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 114 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 115 of file SpectrumList_ChargeFromIsotope.hpp.
|
private |
Definition at line 116 of file SpectrumList_ChargeFromIsotope.hpp.