61 if(msp_timsData ==
nullptr)
63 std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
65 if(msp_timsData ==
nullptr)
68 QObject::tr(
"ERROR in TimsMsRunReaderMs2::initialize "
69 "msp_timsData is null for MsRunId %1")
70 .arg(mcsp_msRunId.get()->toString()));
73 mp_timsDdaPrecursors = msp_timsData.get()->getTimsDdaPrecursorsPtr();
87 QObject::tr(
"ERROR in TimsMsRunReaderMs2::setMs2BuiltinCentroid "
88 "mp_timsDdaPrecursors is null"));
103 QObject::tr(
"ERROR in TimsMsRunReaderMs2::setMs2FilterCstSPtr "
104 "mp_timsDdaPrecursors is null"));
119 QObject::tr(
"ERROR in TimsMsRunReaderMs2::setMs1FilterCstSPtr "
120 "msp_timsData is null"));
152 bool want_binary_data)
const
155 std::size_t precursor_index = (spectrum_index / 2) + 1;
165 QObject::tr(
"spectrum_index %1 NOT FOUND in file %2 : %3")
168 .arg(error.
qwhat()));
171 if(spectrum_index % 2 == 0)
177 getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data);
181 return mass_spectrum_ms1;
187 if(spectrum_descr.
ms2_index != spectrum_index)
191 QObject::tr(
"ERROR in %1 %2 %3 spectrum_descr.ms2_index(%4) != "
192 "spectrum_index(%5)")
197 .arg(spectrum_index));
201 getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data);
205 return mass_spectrum_ms2;
287std::vector<std::size_t>
293 return mp_timsDdaPrecursors->getPrecursorsByMzRtCharge(
294 charge, mz_val, rt_sec, k0);
310 std::size_t precursor_index = (spectrum_index / 2) + 1;
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;
336 return msp_timsData.get()->getRetentionTimeLineInSeconds();
std::size_t getSpectrumIndex() const
bool isMonoThread() const
const MsRunIdCstSPtr & getMsRunId() const
virtual const QString & qwhat() const
Class representing a fully specified mass spectrum.
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
MassSpectrumSPtr getMassSpectrumSPtr() const
Get the MassSpectrumSPtr.
interface to collect spectrums from the MsRunReader class
virtual void loadingEnded()
virtual void spectrumListHasSize(std::size_t size)
Trace getTicChromatogram() const
TimsDdaPrecursors * getTimsDdaPrecursorsPtr() const
void getQualifiedMs1MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
void setMs2BuiltinCentroid(bool centroid)
enable or disable simple centroid filter on raw tims data for MS2
void getQualifiedMs2MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
XicCoordTims getXicCoordTimsFromPrecursorId(std::size_t precursor_id, PrecisionPtr precision_ptr)
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter)
filter interface to apply just after raw MS2 specturm extraction the filter can be a list of filters ...
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 setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter)
filter interface to apply just after raw MS1 specturm extraction the filter can be a list of filters ...
TimsDdaPrecursors::SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id) const
get an intermediate structure describing a spectrum
void setMonoThread(bool is_mono_thread)
set only one is_mono_thread to true
std::size_t getTotalPrecursorCount() const
get the number of precursors analyzed by PASEF
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter)
void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter)
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
TimsMsRunReaderMs2(MsRunIdCstSPtr &msrun_id_csp)
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 MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
pappso::FilterInterfaceCstSPtr msp_ms2Filter
TimsDdaPrecursors * mp_timsDdaPrecursors
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
pappso::FilterInterfaceCstSPtr msp_ms1Filter
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
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 void initialize() override
virtual std::vector< double > getRetentionTimeLine() override
retention timeline get retention times along the MSrun in seconds
bool m_builtinMs2Centroid
enable builtin centroid on raw tims integers by default
virtual Trace getTicChromatogram() override
get a TIC chromatogram
void setMs2BuiltinCentroid(bool centroid)
enable or disable simple centroid filter on raw tims data for MS2
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
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 bool acquireDevice() override
acquire data back end device
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
virtual ~TimsMsRunReaderMs2()
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
virtual TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
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,...
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
A simple container of DataPoint instances.
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
std::shared_ptr< TimsData > TimsDataSp
shared pointer on a TimsData object
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< XicCoordTims > XicCoordTimsSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
handle specific data for DDA MS runs
MSrun file reader for native Bruker TimsTOF specialized for MS2 purpose.
XIC coordinate in a Tims MSrun.