libpappsomspp
Library for mass spectrometry
pappso::TimsMsRunReaderMs2 Class Reference

#include <timsmsrunreaderms2.h>

Inheritance diagram for pappso::TimsMsRunReaderMs2:
pappso::MsRunReader pappso::TimsMsRunReaderMs2Selected

Public Member Functions

 TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp)
 
virtual ~TimsMsRunReaderMs2 ()
 
virtual MassSpectrumSPtr massSpectrumSPtr (std::size_t spectrum_index) override
 get a MassSpectrumSPtr class given its spectrum index More...
 
virtual MassSpectrumCstSPtr massSpectrumCstSPtr (std::size_t spectrum_index) override
 
virtual QualifiedMassSpectrum qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const override
 get a QualifiedMassSpectrum class given its scan number More...
 
virtual void readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More...
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum index More...
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum More...
 
virtual void readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels More...
 
virtual std::size_t spectrumListSize () const override
 get the totat number of spectrum conained in the MSrun data file More...
 
virtual bool hasScanNumbers () const override
 tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided functions can check if scan numbers are available in the current file More...
 
void setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)
 
void setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)
 
void setMs2BuiltinCentroid (bool centroid)
 enable or disable simple centroid filter on raw tims data for MS2 More...
 
virtual std::vector< std::size_t > getPrecursorsIDFromMzRt (int charge, double mz_val, double rt_sec, double k0)
 Get all the precursors id which match the values. More...
 
virtual bool releaseDevice () override
 release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object More...
 
virtual bool acquireDevice () override
 acquire data back end device More...
 
virtual TimsDataSp getTimsDataSPtr ()
 give an access to the underlying raw data pointer More...
 
virtual std::vector< double > getRetentionTimeLine () override
 retention timeline get retention times along the MSrun in seconds More...
 
virtual Trace getTicChromatogram () override
 get a TIC chromatogram More...
 
- Public Member Functions inherited from pappso::MsRunReader
 MsRunReader (MsRunIdCstSPtr &ms_run_id)
 
 MsRunReader (const MsRunReader &other)
 
virtual ~MsRunReader ()
 
const MsRunIdCstSPtrgetMsRunId () const
 
virtual MassSpectrumSPtr massSpectrumSPtr (std::size_t spectrum_index)=0
 get a MassSpectrumSPtr class given its spectrum index More...
 
virtual MassSpectrumCstSPtr massSpectrumCstSPtr (std::size_t spectrum_index)=0
 
virtual QualifiedMassSpectrum qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const =0
 get a QualifiedMassSpectrum class given its scan number More...
 
virtual XicCoordSPtr newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, PrecisionPtr precision) const =0
 get a xic coordinate object from a given spectrum index More...
 
virtual XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum (const QualifiedMassSpectrum &mass_spectrum, PrecisionPtr precision) const =0
 get a xic coordinate object from a given spectrum More...
 
virtual std::size_t spectrumListSize () const =0
 get the totat number of spectrum conained in the MSrun data file More...
 
virtual void readSpectrumCollection (SpectrumCollectionHandlerInterface &handler)=0
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More...
 
virtual void readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)=0
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels More...
 
virtual std::size_t scanNumber2SpectrumIndex (std::size_t scan_number)
 if possible, converts a scan number into a spectrum index This is a convenient function to help transition from the old scan number (not implemented by all vendors) to more secure spectrum index (not vendor dependant). It is better to not rely on this function. More...
 
virtual bool hasScanNumbers () const
 tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided functions can check if scan numbers are available in the current file More...
 
virtual bool releaseDevice ()=0
 release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object More...
 
virtual bool acquireDevice ()=0
 acquire data back end device More...
 
virtual std::vector< double > getRetentionTimeLine ()
 retention timeline get retention times along the MSrun in seconds More...
 
virtual Trace getTicChromatogram ()
 get a TIC chromatogram More...
 
void setMonoThread (bool is_mono_thread)
 set only one is_mono_thread to true More...
 
bool isMonoThread () const
 

Protected Member Functions

virtual void initialize () override
 
virtual bool accept (const QString &file_name) const override
 tells if the reader is able to handle this file must be implemented by private MS run reader, specific of one or more file format More...
 
virtual void initialize ()=0
 
virtual bool accept (const QString &file_name) const =0
 tells if the reader is able to handle this file must be implemented by private MS run reader, specific of one or more file format More...
 

Private Attributes

TimsDataSp msp_timsData = nullptr
 
pappso::FilterInterfaceCstSPtr msp_ms1Filter
 
pappso::FilterInterfaceCstSPtr msp_ms2Filter
 
bool m_builtinMs2Centroid = true
 enable builtin centroid on raw tims integers by default More...
 

Friends

class MsFileAccessor
 

Additional Inherited Members

- Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr mcsp_msRunId
 
MsRunReaderScanNumberMultiMapmpa_multiMapScanNumber = nullptr
 

Detailed Description

Definition at line 39 of file timsmsrunreaderms2.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderMs2()

TimsMsRunReaderMs2::TimsMsRunReaderMs2 ( MsRunIdCstSPtr msrun_id_csp)
Todo:
write docs

Definition at line 37 of file timsmsrunreaderms2.cpp.

38 : MsRunReader(msrun_id_csp)
39{
40 initialize();
41}
MsRunReader(MsRunIdCstSPtr &ms_run_id)
virtual void initialize() override

References initialize().

◆ ~TimsMsRunReaderMs2()

TimsMsRunReaderMs2::~TimsMsRunReaderMs2 ( )
virtual

Definition at line 43 of file timsmsrunreaderms2.cpp.

44{
45 if(msp_timsData != nullptr)
46 {
47 msp_timsData = nullptr;
48 }
49}

References msp_timsData.

Member Function Documentation

◆ accept()

bool TimsMsRunReaderMs2::accept ( const QString &  file_name) const
overrideprotectedvirtual

tells if the reader is able to handle this file must be implemented by private MS run reader, specific of one or more file format

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 113 of file timsmsrunreaderms2.cpp.

114{
115 qDebug() << file_name;
116 return true;
117}

◆ acquireDevice()

bool TimsMsRunReaderMs2::acquireDevice ( )
overridevirtual

acquire data back end device

Returns
bool true if done

Implements pappso::MsRunReader.

Definition at line 255 of file timsmsrunreaderms2.cpp.

256{
257 if(msp_timsData == nullptr)
258 {
259 initialize();
260 msp_timsData->setMs2BuiltinCentroid(m_builtinMs2Centroid);
261 msp_timsData->setMs1FilterCstSPtr(msp_ms1Filter);
262 msp_timsData->setMs2FilterCstSPtr(msp_ms2Filter);
263 }
264 return true;
265}
pappso::FilterInterfaceCstSPtr msp_ms2Filter
pappso::FilterInterfaceCstSPtr msp_ms1Filter
bool m_builtinMs2Centroid
enable builtin centroid on raw tims integers by default

References initialize(), m_builtinMs2Centroid, msp_ms1Filter, msp_ms2Filter, and msp_timsData.

Referenced by getTicChromatogram().

◆ getPrecursorsIDFromMzRt()

std::vector< std::size_t > pappso::TimsMsRunReaderMs2::getPrecursorsIDFromMzRt ( int  charge,
double  mz_val,
double  rt_sec,
double  k0 
)
virtual

Get all the precursors id which match the values.

Returns
list of precursors Ids

Definition at line 268 of file timsmsrunreaderms2.cpp.

272{
273 return msp_timsData->getPrecursorsFromMzRtCharge(charge, mz_val, rt_sec, k0);
274}

◆ getRetentionTimeLine()

std::vector< double > pappso::TimsMsRunReaderMs2::getRetentionTimeLine ( )
overridevirtual

retention timeline get retention times along the MSrun in seconds

Returns
vector of retention times (seconds)

Reimplemented from pappso::MsRunReader.

Definition at line 312 of file timsmsrunreaderms2.cpp.

313{
314 return msp_timsData.get()->getRetentionTimeLine();
315}

◆ getTicChromatogram()

Trace TimsMsRunReaderMs2::getTicChromatogram ( )
overridevirtual

get a TIC chromatogram

for each retention time, computes the sum of all intensities. For IM-MS, combines the mobility spectra

Returns
a trace (x=rt, y=intensities)

Reimplemented from pappso::MsRunReader.

Definition at line 318 of file timsmsrunreaderms2.cpp.

319{
320 // Use the Sqlite database to fetch the total ion current chromatogram (TIC
321 // chromatogram).
322
324
325 return msp_timsData->getTicChromatogram();
326}
virtual bool acquireDevice() override
acquire data back end device

References acquireDevice(), and msp_timsData.

◆ getTimsDataSPtr()

pappso::TimsDataSp pappso::TimsMsRunReaderMs2::getTimsDataSPtr ( )
virtual

give an access to the underlying raw data pointer

Definition at line 277 of file timsmsrunreaderms2.cpp.

278{
280 return msp_timsData;
281}

Referenced by pappso::TimsXicExtractorInterface::TimsXicExtractorInterface().

◆ hasScanNumbers()

bool TimsMsRunReaderMs2::hasScanNumbers ( ) const
overridevirtual

tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided functions can check if scan numbers are available in the current file

Reimplemented from pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 241 of file timsmsrunreaderms2.cpp.

242{
243 return false;
244}

◆ initialize()

void pappso::TimsMsRunReaderMs2::initialize ( )
overrideprotectedvirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 52 of file timsmsrunreaderms2.cpp.

53{
54 msp_timsData = std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
55 if(msp_timsData == nullptr)
56 {
57 throw PappsoException(
58 QObject::tr("ERROR in TimsMsRunReaderMs2::initialize "
59 "msp_timsData is null for MsRunId %1")
60 .arg(mcsp_msRunId.get()->toString()));
61 }
62}
MsRunIdCstSPtr mcsp_msRunId
Definition: msrunreader.h:298

Referenced by TimsMsRunReaderMs2(), and acquireDevice().

◆ massSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr TimsMsRunReaderMs2::massSpectrumCstSPtr ( std::size_t  spectrum_index)
overridevirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 130 of file timsmsrunreaderms2.cpp.

131{
132 QualifiedMassSpectrum mass_spectrum =
133 qualifiedMassSpectrum(spectrum_index, true);
134 return mass_spectrum.getMassSpectrumSPtr();
135}
Class representing a fully specified mass spectrum.
MassSpectrumSPtr getMassSpectrumSPtr() const
Get the MassSpectrumSPtr.
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number

References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().

◆ massSpectrumSPtr()

pappso::MassSpectrumSPtr TimsMsRunReaderMs2::massSpectrumSPtr ( std::size_t  spectrum_index)
overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 121 of file timsmsrunreaderms2.cpp.

122{
123 QualifiedMassSpectrum mass_spectrum =
124 qualifiedMassSpectrum(spectrum_index, true);
125 return mass_spectrum.getMassSpectrumSPtr();
126}

References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

pappso::XicCoordSPtr TimsMsRunReaderMs2::newXicCoordSPtrFromQualifiedMassSpectrum ( const pappso::QualifiedMassSpectrum mass_spectrum,
pappso::PrecisionPtr  precision 
) const
overridevirtual

get a xic coordinate object from a given spectrum

Implements pappso::MsRunReader.

Definition at line 303 of file timsmsrunreaderms2.cpp.

306{
308 mass_spectrum.getMassSpectrumId().getSpectrumIndex(), precision);
309}
std::size_t getSpectrumIndex() const
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index

References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getSpectrumIndex(), and newXicCoordSPtrFromSpectrumIndex().

◆ newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex ( std::size_t  spectrum_index,
pappso::PrecisionPtr  precision 
) const
overridevirtual

get a xic coordinate object from a given spectrum index

Implements pappso::MsRunReader.

Definition at line 285 of file timsmsrunreaderms2.cpp.

287{
288 XicCoordTimsSPtr xic_coord = std::make_shared<XicCoordTims>();
289 std::size_t precursor_index = (spectrum_index / 2) + 1;
290 auto xic = this->msp_timsData.get()->getXicCoordTimsFromPrecursorId(
291 precursor_index, precision);
292
293 xic_coord.get()->mzRange = xic.mzRange;
294 xic_coord.get()->rtTarget = xic.rtTarget;
295 xic_coord.get()->scanNumBegin = xic.scanNumBegin;
296 xic_coord.get()->scanNumEnd = xic.scanNumEnd;
297
298
299 return xic_coord;
300}
std::shared_ptr< XicCoordTims > XicCoordTimsSPtr
Definition: xiccoordtims.h:40

References msp_timsData.

Referenced by newXicCoordSPtrFromQualifiedMassSpectrum().

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum TimsMsRunReaderMs2::qualifiedMassSpectrum ( std::size_t  spectrum_index,
bool  want_binary_data = true 
) const
overridevirtual

get a QualifiedMassSpectrum class given its scan number

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 139 of file timsmsrunreaderms2.cpp.

141{
142
143 std::size_t precursor_index = (spectrum_index / 2) + 1;
144 TimsData::SpectrumDescr spectrum_descr;
145 try
146 {
147 spectrum_descr =
148 msp_timsData.get()->getSpectrumDescrWithPrecursorId(precursor_index);
149 }
150 catch(ExceptionNotFound &error)
151 {
152 throw ExceptionNotFound(
153 QObject::tr("spectrum_index %1 NOT FOUND in file %2 : %3")
154 .arg(spectrum_index)
155 .arg(getMsRunId().get()->getFileName())
156 .arg(error.qwhat()));
157 }
158
159 if(spectrum_index % 2 == 0)
160 {
161 qDebug() << "MS1 spectrum precursor_index=" << precursor_index;
162 // this is an MS1 spectrum
163 QualifiedMassSpectrum mass_spectrum_ms1;
164 msp_timsData->getQualifiedMs1MassSpectrumByPrecursorId(
165 getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data);
166 qDebug(); // << mass_spectrum_ms1.toString();
167
168 // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString();
169 return mass_spectrum_ms1;
170 }
171 else
172 {
173 qDebug() << "MS2 spectrum precursor_index=" << precursor_index;
174 QualifiedMassSpectrum mass_spectrum_ms2;
175 if(spectrum_descr.ms2_index != spectrum_index)
176 {
177 qDebug();
178 throw PappsoException(
179 QObject::tr("ERROR in %1 %2 %3 spectrum_descr.ms2_index(%4) != "
180 "spectrum_index(%5)")
181 .arg(__FILE__)
182 .arg(__FUNCTION__)
183 .arg(__LINE__)
184 .arg(spectrum_descr.ms2_index)
185 .arg(spectrum_index));
186 }
187
188 msp_timsData->getQualifiedMs2MassSpectrumByPrecursorId(
189 getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data);
190 qDebug(); // << mass_spectrum_ms2.toString();
191
192 // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString();
193 return mass_spectrum_ms2;
194 }
195}
const MsRunIdCstSPtr & getMsRunId() const
virtual const QString & qwhat() const

References pappso::MsRunReader::getMsRunId(), pappso::TimsData::SpectrumDescr::ms2_index, msp_timsData, and pappso::PappsoException::qwhat().

Referenced by massSpectrumCstSPtr(), and massSpectrumSPtr().

◆ readSpectrumCollection()

void TimsMsRunReaderMs2::readSpectrumCollection ( SpectrumCollectionHandlerInterface handler)
overridevirtual

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 199 of file timsmsrunreaderms2.cpp.

201{
203}
virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

References readSpectrumCollectionByMsLevel().

◆ readSpectrumCollectionByMsLevel()

void TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel ( SpectrumCollectionHandlerInterface handler,
unsigned int  ms_level 
)
overridevirtual

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

Implements pappso::MsRunReader.

Definition at line 206 of file timsmsrunreaderms2.cpp.

208{
209 qDebug() << " ms_level=" << ms_level;
210 // We'll need it to perform the looping in the spectrum list.
211 std::size_t spectrum_list_size = spectrumListSize();
212
213 // qDebug() << "The spectrum list has size:" << spectrum_list_size;
214
215 // Inform the handler of the spectrum list so that it can handle feedback to
216 // the user.
217 handler.spectrumListHasSize(spectrum_list_size);
218
219
220 msp_timsData.get()->setMonoThread(isMonoThread());
221
222 msp_timsData.get()->ms2ReaderSpectrumCollectionByMsLevel(
223 getMsRunId(), handler, ms_level);
224 // Now let the loading handler know that the loading of the data has ended.
225 // The handler might need this "signal" to perform additional tasks or to
226 // cleanup cruft.
227
228 // qDebug() << "Loading ended";
229 handler.loadingEnded();
230}
bool isMonoThread() const
virtual void spectrumListHasSize(std::size_t size)
Definition: msrunreader.cpp:53
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file

References pappso::MsRunReader::getMsRunId(), pappso::MsRunReader::isMonoThread(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), msp_timsData, pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().

Referenced by readSpectrumCollection().

◆ releaseDevice()

bool TimsMsRunReaderMs2::releaseDevice ( )
overridevirtual

release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object

Returns
bool true if done

Implements pappso::MsRunReader.

Definition at line 248 of file timsmsrunreaderms2.cpp.

249{
250 msp_timsData = nullptr;
251 return true;
252}

References msp_timsData.

◆ setMs1FilterCstSPtr()

void TimsMsRunReaderMs2::setMs1FilterCstSPtr ( pappso::FilterInterfaceCstSPtr  filter)

Definition at line 97 of file timsmsrunreaderms2.cpp.

98{
99 msp_ms1Filter = filter;
100 if(msp_timsData != nullptr)
101 {
102 msp_timsData->setMs1FilterCstSPtr(filter);
103 }
104 else
105 {
106 throw PappsoException(
107 QObject::tr("ERROR in TimsMsRunReaderMs2::setMs1FilterCstSPtr "
108 "msp_timsData is null"));
109 }
110}

References msp_ms1Filter, and msp_timsData.

◆ setMs2BuiltinCentroid()

void TimsMsRunReaderMs2::setMs2BuiltinCentroid ( bool  centroid)

enable or disable simple centroid filter on raw tims data for MS2

Definition at line 65 of file timsmsrunreaderms2.cpp.

66{
67 m_builtinMs2Centroid = centroid;
68 if(msp_timsData != nullptr)
69 {
70 msp_timsData->setMs2BuiltinCentroid(m_builtinMs2Centroid);
71 }
72 else
73 {
74 throw PappsoException(
75 QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2BuiltinCentroid "
76 "msp_timsData is null"));
77 }
78}

References m_builtinMs2Centroid, and msp_timsData.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ setMs2FilterCstSPtr()

void TimsMsRunReaderMs2::setMs2FilterCstSPtr ( pappso::FilterInterfaceCstSPtr  filter)

Definition at line 81 of file timsmsrunreaderms2.cpp.

82{
83 msp_ms2Filter = filter;
84 if(msp_timsData != nullptr)
85 {
86 msp_timsData->setMs2FilterCstSPtr(msp_ms2Filter);
87 }
88 else
89 {
90 throw PappsoException(
91 QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2FilterCstSPtr "
92 "msp_timsData is null"));
93 }
94}

References msp_ms2Filter, and msp_timsData.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ spectrumListSize()

std::size_t TimsMsRunReaderMs2::spectrumListSize ( ) const
overridevirtual

get the totat number of spectrum conained in the MSrun data file

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 234 of file timsmsrunreaderms2.cpp.

235{
236 return (msp_timsData->getTotalNumberOfPrecursors() * 2);
237}

References msp_timsData.

Referenced by readSpectrumCollectionByMsLevel().

Friends And Related Function Documentation

◆ MsFileAccessor

friend class MsFileAccessor
friend

Definition at line 41 of file timsmsrunreaderms2.h.

Member Data Documentation

◆ m_builtinMs2Centroid

bool pappso::TimsMsRunReaderMs2::m_builtinMs2Centroid = true
private

enable builtin centroid on raw tims integers by default

Definition at line 120 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2BuiltinCentroid().

◆ msp_ms1Filter

pappso::FilterInterfaceCstSPtr pappso::TimsMsRunReaderMs2::msp_ms1Filter
private

Definition at line 116 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs1FilterCstSPtr().

◆ msp_ms2Filter

pappso::FilterInterfaceCstSPtr pappso::TimsMsRunReaderMs2::msp_ms2Filter
private

Definition at line 117 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2FilterCstSPtr().

◆ msp_timsData


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