29 #include "../../exception/exceptionnotimplemented.h"
48 msp_timsData = std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
49 if(msp_timsData ==
nullptr)
51 throw PappsoException(QObject::tr(
"ERROR in TimsMsRunReader::initialize "
52 "msp_timsData is null for MsRunId %1")
53 .arg(mcsp_msRunId.get()->toString()));
61 qDebug() << file_name;
70 QObject::tr(
"Not yet implemented in TimsMsRunReader %1.\n").arg(__LINE__));
78 return msp_timsData->getMassSpectrumCstSPtrByRawIndex(spectrum_index);
84 bool want_binary_data)
const
90 getMsRunId(), mass_spectrum, spectrum_index, want_binary_data);
111 msp_timsData.get()->rawReaderSpectrumCollectionByMsLevel(
164 [[maybe_unused]])
const
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
const MsRunIdCstSPtr & getMsRunId() const
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
virtual void loadingEnded()
virtual void initialize() override
TimsMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
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 MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
virtual TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
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 QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
virtual bool acquireDevice() override
acquire data back end device
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 std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
virtual ~TimsMsRunReader()
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< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
MSrun file reader for native Bruker TimsTOF raw data.