libpappsomspp
Library for mass spectrometry
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29 #include "../../exception/exceptionnotimplemented.h"
51 mpa_timsData =
new TimsData(mcsp_msRunId.get()->getFileName());
58 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__ <<
" "
68 QObject::tr(
"Not yet implemented in TimsMsRunReader %1.\n").arg(__LINE__));
82 bool want_binary_data)
const
112 qDebug() <<
"The spectrum list has size:" << spectrum_list_size;
121 for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
128 qDebug() <<
"The operation was cancelled. Breaking the loop.";
133 bool get_data = want_binary_data;
TimsMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtrByRawIndex(std::size_t raw_index)
get a mass spectrum given its spectrum index
virtual void spectrumListHasSize(std::size_t size)
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
virtual ~TimsMsRunReader()
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
virtual bool shouldStop()
unsigned int getMsLevelBySpectrumIndex(std::size_t spectrum_index)
virtual bool acquireDevice() override
acquire data back end device
virtual void loadingEnded()
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
const MsRunIdCstSPtr & getMsRunId() const
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
virtual void initialize() override
Class representing a fully specified mass spectrum.
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
QualifiedMassSpectrum getQualifiedMassSpectrumByRawIndex(std::size_t spectrum_index, bool want_binary_data)
MSrun file reader for native Bruker TimsTOF raw data.
virtual bool needPeakList() const =0
tells if we need the peak list (if we want the binary data) for each spectrum
void setMassSpectrumId(const MassSpectrumId &iD)
Set the MassSpectrumId.
virtual bool needMsLevelPeakList(unsigned int ms_level) const final
tells if we need the peak list (if we want the binary data) for each spectrum, given an MS level
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
std::size_t getTotalNumberOfScans() const
get the total number of scans
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,...
void setMsRunId(MsRunIdCstSPtr other)
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
interface to collect spectrums from the MsRunReader class
std::shared_ptr< MassSpectrum > MassSpectrumSPtr