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
121 qDebug() <<
"The spectrum list has size:" << spectrum_list_size;
130 for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
132 unsigned int current_ms_level =
139 qDebug() <<
"The operation was cancelled. Breaking the loop.";
145 if(ms_level != current_ms_level)
150 bool get_data = want_binary_data;
void setMsRunId(MsRunIdCstSPtr other)
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.
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
void setMassSpectrumId(const MassSpectrumId &iD)
Set the MassSpectrumId.
interface to collect spectrums from the MsRunReader class
virtual bool shouldStop()
virtual bool needPeakList() const =0
tells if we need the peak list (if we want the binary data) for each spectrum
virtual void loadingEnded()
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
virtual void spectrumListHasSize(std::size_t size)
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0
QualifiedMassSpectrum getQualifiedMassSpectrumByRawIndex(std::size_t spectrum_index, bool want_binary_data)
unsigned int getMsLevelBySpectrumIndex(std::size_t spectrum_index)
std::size_t getTotalNumberOfScans() const
get the total number of scans
pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtrByRawIndex(std::size_t raw_index)
get a mass spectrum given its spectrum index
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 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 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 ~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< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
MSrun file reader for native Bruker TimsTOF raw data.