41#include "../trace/maptrace.h"
47#include "../massspectrum/qualifiedmassspectrum.h"
48#include "../msfile/msfilereader.h"
49#include "../exportinmportconfig.h"
84 bool want_binary_data =
true)
const = 0;
118 unsigned int ms_level) = 0;
127 virtual std::size_t scanNumber2SpectrumIndex(std::size_t scan_number);
133 virtual bool hasScanNumbers()
const;
152 virtual std::vector<double> getRetentionTimeLine();
163 virtual Trace getTicChromatogram();
170 void setMonoThread(
bool is_mono_thread);
172 bool isMonoThread()
const;
184 virtual bool accept(
const QString &file_name)
const = 0;
187 bool m_isMonoThread =
false;
provides a multimap to find quickly spectrum index from scan number
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index)=0
virtual std::size_t spectrumListSize() const =0
get the totat number of spectrum conained in the MSrun data file
MsRunIdCstSPtr mcsp_msRunId
virtual bool acquireDevice()=0
acquire data back end device
virtual bool accept(const QString &file_name) const =0
tells if the reader is able to handle this file must be implemented by private MS run reader,...
virtual XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, PrecisionPtr precision) const =0
get a xic coordinate object from a given spectrum index
virtual bool releaseDevice()=0
release data back end device if a the data back end is released, the developper has to use acquireDev...
virtual void initialize()=0
virtual XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const QualifiedMassSpectrum &mass_spectrum, PrecisionPtr precision) const =0
get a xic coordinate object from a given spectrum
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)=0
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index)=0
get a MassSpectrumSPtr class given its spectrum index
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler)=0
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const =0
get a QualifiedMassSpectrum class given its scan number
virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)=0
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
A simple container of DataPoint instances.
Q_DECLARE_METATYPE(pappso::MsRunReaderSPtr)
int msRunReaderSPtrMetaTypeId
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< MsRunReader > MsRunReaderSPtr
std::shared_ptr< const MsRunReader > MsRunReaderCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< XicCoord > XicCoordSPtr