libpappsomspp
Library for mass spectrometry
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pappso::TimsMsRunReaderMs2 Class Reference

#include <timsmsrunreaderms2.h>

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

Public Member Functions

 TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp)
 
 TimsMsRunReaderMs2 (const TimsMsRunReaderBase &msrun_reader_base)
 
virtual ~TimsMsRunReaderMs2 ()
 
virtual MassSpectrumSPtr massSpectrumSPtr (std::size_t spectrum_index) override
 get a MassSpectrumSPtr class given its spectrum index
 
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
 
virtual void readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
 
virtual void readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum index
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum
 
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
 
virtual std::size_t spectrumListSize () const override
 get the totat number of spectrum conained in the MSrun data file
 
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
 
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
 
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.
 
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
 
virtual bool acquireDevice () override
 acquire data back end device
 
virtual TimsDataSp getTimsDataSPtr ()
 give an access to the underlying raw data pointer
 
virtual std::vector< double > getRetentionTimeLine () override
 retention timeline get retention times along the MSrun in seconds
 
virtual Trace getTicChromatogram () override
 get a TIC chromatogram
 
- Public Member Functions inherited from pappso::TimsMsRunReaderBase
 TimsMsRunReaderBase (MsRunIdCstSPtr &msrun_id_csp)
 
 TimsMsRunReaderBase (const TimsMsRunReaderBase &msrun_reader_base)
 
virtual ~TimsMsRunReaderBase ()
 
- Public Member Functions inherited from pappso::MsRunReader
 MsRunReader (const MsRunIdCstSPtr &ms_run_id)
 
 MsRunReader (const MsRunReader &other)
 
virtual ~MsRunReader ()
 
const MsRunIdCstSPtrgetMsRunId () const
 
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.
 
void setMonoThread (bool is_mono_thread)
 set only one is_mono_thread to true
 
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
 

Protected Attributes

TimsDdaPrecursorsmp_timsDdaPrecursors = nullptr
 
- Protected Attributes inherited from pappso::TimsMsRunReaderBase
TimsDataSp msp_timsData = nullptr
 
- Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr mcsp_msRunId
 
MsRunReaderScanNumberMultiMapmpa_multiMapScanNumber = nullptr
 

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
 

Friends

class MsFileAccessor
 

Detailed Description

Definition at line 38 of file timsmsrunreaderms2.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderMs2() [1/2]

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

Definition at line 38 of file timsmsrunreaderms2.cpp.

References initialize().

◆ TimsMsRunReaderMs2() [2/2]

TimsMsRunReaderMs2::TimsMsRunReaderMs2 ( const TimsMsRunReaderBase msrun_reader_base)

Definition at line 44 of file timsmsrunreaderms2.cpp.

45 : TimsMsRunReaderBase(msrun_reader_base)
46{
47 initialize();
48}

References initialize().

◆ ~TimsMsRunReaderMs2()

TimsMsRunReaderMs2::~TimsMsRunReaderMs2 ( )
virtual

Definition at line 50 of file timsmsrunreaderms2.cpp.

51{
52 if(msp_timsData != nullptr)
53 {
54 msp_timsData = nullptr;
55 }
56}

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

Reimplemented from pappso::TimsMsRunReaderBase.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 125 of file timsmsrunreaderms2.cpp.

126{
127 // qDebug() << file_name;
128 return true;
129}

◆ acquireDevice()

bool TimsMsRunReaderMs2::acquireDevice ( )
overridevirtual

acquire data back end device

Returns
bool true if done

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 275 of file timsmsrunreaderms2.cpp.

276{
277 if(msp_timsData == nullptr)
278 {
279 initialize();
283 }
284 return true;
285}
void setMs2BuiltinCentroid(bool centroid)
enable or disable simple centroid filter on raw tims data for MS2
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter)
filter interface to apply just after raw MS2 specturm extraction the filter can be a list of filters ...
void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter)
filter interface to apply just after raw MS1 specturm extraction the filter can be a list of filters ...
pappso::FilterInterfaceCstSPtr msp_ms2Filter
TimsDdaPrecursors * mp_timsDdaPrecursors
pappso::FilterInterfaceCstSPtr msp_ms1Filter
bool m_builtinMs2Centroid
enable builtin centroid on raw tims integers by default

References initialize(), m_builtinMs2Centroid, mp_timsDdaPrecursors, msp_ms1Filter, msp_ms2Filter, msp_timsData, pappso::TimsDdaPrecursors::setMs1FilterCstSPtr(), pappso::TimsDdaPrecursors::setMs2BuiltinCentroid(), and pappso::TimsDdaPrecursors::setMs2FilterCstSPtr().

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 288 of file timsmsrunreaderms2.cpp.

292{
294 charge, mz_val, rt_sec, k0);
295}
std::vector< std::size_t > getPrecursorsByMzRtCharge(int charge, double mz_val, double rt_sec, double k0)
guess possible precursor ids given a charge, m/z, retention time and k0

◆ 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::TimsMsRunReaderBase.

Definition at line 334 of file timsmsrunreaderms2.cpp.

335{
336 return msp_timsData.get()->getRetentionTimeLineInSeconds();
337}

◆ 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

Note that, formally, a TIC chromatogram is computed only for MS1 spectra.

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

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 340 of file timsmsrunreaderms2.cpp.

341{
342 // Use the Sqlite database to fetch the total ion current chromatogram (TIC
343 // chromatogram).
344
346
347 return msp_timsData->getTicChromatogram();
348}
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

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 298 of file timsmsrunreaderms2.cpp.

299{
301 return msp_timsData;
302}

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::TimsMsRunReaderBase.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 261 of file timsmsrunreaderms2.cpp.

262{
263 return false;
264}

◆ initialize()

void pappso::TimsMsRunReaderMs2::initialize ( )
overrideprotectedvirtual

Reimplemented from pappso::TimsMsRunReaderBase.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 59 of file timsmsrunreaderms2.cpp.

60{
61 if(msp_timsData == nullptr)
63 std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
64
65 if(msp_timsData == nullptr)
66 {
67 throw PappsoException(
68 QObject::tr("ERROR in TimsMsRunReaderMs2::initialize "
69 "msp_timsData is null for MsRunId %1")
70 .arg(mcsp_msRunId.get()->toString()));
71 }
72
73 mp_timsDdaPrecursors = msp_timsData.get()->getTimsDdaPrecursorsPtr();
74}
MsRunIdCstSPtr mcsp_msRunId

Referenced by TimsMsRunReaderMs2(), TimsMsRunReaderMs2(), and acquireDevice().

◆ massSpectrumCstSPtr()

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

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 142 of file timsmsrunreaderms2.cpp.

143{
144 QualifiedMassSpectrum mass_spectrum =
145 qualifiedMassSpectrum(spectrum_index, true);
146 return mass_spectrum.getMassSpectrumSPtr();
147}
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 133 of file timsmsrunreaderms2.cpp.

134{
135 QualifiedMassSpectrum mass_spectrum =
136 qualifiedMassSpectrum(spectrum_index, true);
137 return mass_spectrum.getMassSpectrumSPtr();
138}

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

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 325 of file timsmsrunreaderms2.cpp.

328{
330 mass_spectrum.getMassSpectrumId().getSpectrumIndex(), precision);
331}
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

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 306 of file timsmsrunreaderms2.cpp.

308{
309 XicCoordTimsSPtr xic_coord = std::make_shared<XicCoordTims>();
310 std::size_t precursor_index = (spectrum_index / 2) + 1;
311 auto xic = this->msp_timsData.get()
312 ->getTimsDdaPrecursorsPtr()
313 ->getXicCoordTimsFromPrecursorId(precursor_index, precision);
314
315 xic_coord.get()->mzRange = xic.mzRange;
316 xic_coord.get()->rtTarget = xic.rtTarget;
317 xic_coord.get()->scanNumBegin = xic.scanNumBegin;
318 xic_coord.get()->scanNumEnd = xic.scanNumEnd;
319
320
321 return xic_coord;
322}
std::shared_ptr< XicCoordTims > XicCoordTimsSPtr

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 151 of file timsmsrunreaderms2.cpp.

153{
154
155 std::size_t precursor_index = (spectrum_index / 2) + 1;
157 try
158 {
159 spectrum_descr =
161 }
162 catch(ExceptionNotFound &error)
163 {
164 throw ExceptionNotFound(
165 QObject::tr("spectrum_index %1 NOT FOUND in file %2 : %3")
166 .arg(spectrum_index)
167 .arg(getMsRunId().get()->getFileName())
168 .arg(error.qwhat()));
169 }
170
171 if(spectrum_index % 2 == 0)
172 {
173 // qDebug() << "MS1 spectrum precursor_index=" << precursor_index;
174 // this is an MS1 spectrum
175 QualifiedMassSpectrum mass_spectrum_ms1;
177 getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data);
178 // qDebug(); // << mass_spectrum_ms1.toString();
179
180 // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString();
181 return mass_spectrum_ms1;
182 }
183 else
184 {
185 // qDebug() << "MS2 spectrum precursor_index=" << precursor_index;
186 QualifiedMassSpectrum mass_spectrum_ms2;
187 if(spectrum_descr.ms2_index != spectrum_index)
188 {
189 // qDebug();
190 throw PappsoException(
191 QObject::tr("ERROR in %1 %2 %3 spectrum_descr.ms2_index(%4) != "
192 "spectrum_index(%5)")
193 .arg(__FILE__)
194 .arg(__FUNCTION__)
195 .arg(__LINE__)
196 .arg(spectrum_descr.ms2_index)
197 .arg(spectrum_index));
198 }
199
201 getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data);
202 // qDebug() << mass_spectrum_ms2.toString();
203
204 // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString();
205 return mass_spectrum_ms2;
206 }
207}
const MsRunIdCstSPtr & getMsRunId() const
virtual const QString & qwhat() const
void getQualifiedMs1MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
void getQualifiedMs2MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
TimsDdaPrecursors::SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id) const
get an intermediate structure describing a spectrum

References pappso::MsRunReader::getMsRunId(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getSpectrumDescrWithPrecursorId(), mp_timsDdaPrecursors, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, 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 211 of file timsmsrunreaderms2.cpp.

213{
215}
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().

◆ readSpectrumCollection2()

void TimsMsRunReaderMs2::readSpectrumCollection2 ( const MsRunReadConfig config,
SpectrumCollectionHandlerInterface handler 
)
overridevirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 218 of file timsmsrunreaderms2.cpp.

221{
223}

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 226 of file timsmsrunreaderms2.cpp.

228{
229 // qDebug() << " ms_level=" << ms_level;
230 // We'll need it to perform the looping in the spectrum list.
231 std::size_t spectrum_list_size = spectrumListSize();
232
233 // qDebug() << "The spectrum list has size:" << spectrum_list_size;
234
235 // Inform the handler of the spectrum list so that it can handle feedback to
236 // the user.
237 handler.spectrumListHasSize(spectrum_list_size);
238
240
242 getMsRunId(), handler, ms_level);
243
244 // Now let the loading handler know that the loading of the data has ended.
245 // The handler might need this "signal" to perform additional tasks or to
246 // cleanup cruft.
247
248 // qDebug() << "Loading ended";
249 handler.loadingEnded();
250}
bool isMonoThread() const
void ms2ReaderSpectrumCollectionByMsLevel(const MsRunIdCstSPtr &msrun_id, SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
void setMonoThread(bool is_mono_thread)
set only one is_mono_thread to true
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(), mp_timsDdaPrecursors, pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel(), pappso::TimsDdaPrecursors::setMonoThread(), pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().

Referenced by readSpectrumCollection(), and readSpectrumCollection2().

◆ 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

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 268 of file timsmsrunreaderms2.cpp.

269{
270 msp_timsData = nullptr;
271 return true;
272}

References msp_timsData.

◆ setMs1FilterCstSPtr()

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

Definition at line 109 of file timsmsrunreaderms2.cpp.

110{
111 msp_ms1Filter = filter;
112 if(mp_timsDdaPrecursors != nullptr)
113 {
115 }
116 else
117 {
118 throw PappsoException(
119 QObject::tr("ERROR in TimsMsRunReaderMs2::setMs1FilterCstSPtr "
120 "msp_timsData is null"));
121 }
122}

References mp_timsDdaPrecursors, msp_ms1Filter, and pappso::TimsDdaPrecursors::setMs1FilterCstSPtr().

◆ setMs2BuiltinCentroid()

void TimsMsRunReaderMs2::setMs2BuiltinCentroid ( bool  centroid)

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

Definition at line 77 of file timsmsrunreaderms2.cpp.

78{
79 m_builtinMs2Centroid = centroid;
80 if(mp_timsDdaPrecursors != nullptr)
81 {
83 }
84 else
85 {
86 throw PappsoException(
87 QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2BuiltinCentroid "
88 "mp_timsDdaPrecursors is null"));
89 }
90}

References m_builtinMs2Centroid, mp_timsDdaPrecursors, and pappso::TimsDdaPrecursors::setMs2BuiltinCentroid().

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

◆ setMs2FilterCstSPtr()

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

Definition at line 93 of file timsmsrunreaderms2.cpp.

94{
95 msp_ms2Filter = filter;
96 if(mp_timsDdaPrecursors != nullptr)
97 {
99 }
100 else
101 {
102 throw PappsoException(
103 QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2FilterCstSPtr "
104 "mp_timsDdaPrecursors is null"));
105 }
106}

References mp_timsDdaPrecursors, msp_ms2Filter, and pappso::TimsDdaPrecursors::setMs2FilterCstSPtr().

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 254 of file timsmsrunreaderms2.cpp.

255{
257}
std::size_t getTotalPrecursorCount() const
get the number of precursors analyzed by PASEF

References pappso::TimsDdaPrecursors::getTotalPrecursorCount(), and mp_timsDdaPrecursors.

Referenced by readSpectrumCollectionByMsLevel().

Friends And Related Symbol Documentation

◆ MsFileAccessor

friend class MsFileAccessor
friend

Definition at line 40 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 124 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2BuiltinCentroid().

◆ mp_timsDdaPrecursors

◆ msp_ms1Filter

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

Definition at line 120 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs1FilterCstSPtr().

◆ msp_ms2Filter

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

Definition at line 121 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2FilterCstSPtr().

◆ msp_timsData

TimsDataSp pappso::TimsMsRunReaderMs2::msp_timsData = nullptr
private

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