41 #include "../trace/maptrace.h"
45 #include "../massspectrum/qualifiedmassspectrum.h"
46 #include "../msfile/msfilereader.h"
47 #include "../exportinmportconfig.h"
69 virtual bool needMsLevelPeakList(
unsigned int ms_level)
const final;
73 virtual void setNeedMsLevelPeakList(
unsigned int ms_level,
74 bool want_peak_list)
final;
75 virtual bool shouldStop();
76 virtual void loadingEnded();
77 virtual void spectrumListHasSize(std::size_t size);
83 virtual void setReadAhead(
bool is_read_ahead)
final;
87 virtual bool isReadAhead()
const;
90 bool m_isReadAhead =
false;
92 std::vector<bool> m_needPeakListByMsLevel = {
true,
121 virtual bool needPeakList()
const override;
122 virtual void loadingEnded()
override;
124 unsigned long getMsLevelCount(
unsigned int ms_level)
const;
126 unsigned long getTotalCount()
const;
142 virtual bool needPeakList()
const override;
144 std::size_t getSpectrumIndexFromScanNumber(std::size_t scan_number)
const;
160 virtual bool needPeakList()
const override;
162 const std::vector<double> &getRetentionTimeLine()
const;
173 virtual void setQualifiedMassSpectrum(
175 virtual bool needPeakList()
const override;
177 Trace getTicChromatogram()
const;
213 bool want_binary_data =
true)
const = 0;
244 unsigned int ms_level) = 0;
253 virtual std::size_t scanNumber2SpectrumIndex(std::size_t scan_number);
259 virtual bool hasScanNumbers()
const;
278 virtual std::vector<double> getRetentionTimeLine();
289 virtual Trace getTicChromatogram();
296 void setMonoThread(
bool is_mono_thread);
298 bool isMonoThread()
const;
310 virtual bool accept(
const QString &file_name)
const = 0;
313 bool m_isMonoThread =
false;
collect retention times along MS run
std::vector< double > m_retention_time_list
provides a multimap to find quickly spectrum index from scan number
std::multimap< std::size_t, std::size_t > m_mmap_scan2index
calculate a TIC chromatogram
MapTrace m_ticChromMapTrace
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 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
example of interface to count MS levels of all spectrum in an MSrun
std::vector< unsigned long > m_countMsLevelSpectrum
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
virtual bool needPeakList() const =0
tells if we need the peak list (if we want the binary data) for each spectrum
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0
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
class PMSPP_LIB_DECL MsRunReader
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< XicCoord > XicCoordSPtr