29 #include "../../exception/exceptionnotimplemented.h"
52 throw PappsoException(QObject::tr(
"ERROR in TimsMsRunReader::initialize "
53 "msp_timsData is null for MsRunId %1")
62 qDebug() << file_name;
71 QObject::tr(
"Not yet implemented in TimsMsRunReader %1.\n").arg(__LINE__));
79 return msp_timsData->getMassSpectrumCstSPtrByRawIndex(spectrum_index);
85 bool want_binary_data)
const
91 getMsRunId(), mass_spectrum, spectrum_index, want_binary_data);
112 msp_timsData.get()->rawReaderSpectrumCollectionByMsLevel(
160 [[maybe_unused]])
const
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
MsRunIdCstSPtr mcsp_msRunId
const MsRunIdCstSPtr & getMsRunId() const
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
virtual void loadingEnded()
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 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 TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
virtual void initialize() override
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()
virtual Trace getTicChromatogram() override
get a TIC chromatogram
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< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
MSrun file reader for native Bruker TimsTOF raw data.