libpappsomspp
Library for mass spectrometry
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48 #include "../massspectrum/qualifiedmassspectrum.h"
49 #include "../msfile/msfilereader.h"
50 #include "../exportinmportconfig.h"
72 virtual bool needMsLevelPeakList(
unsigned int ms_level)
const final;
76 virtual void setNeedMsLevelPeakList(
unsigned int ms_level,
77 bool want_peak_list)
final;
78 virtual bool shouldStop();
79 virtual void loadingEnded();
80 virtual void spectrumListHasSize(std::size_t size);
86 virtual void setReadAhead(
bool is_read_ahead)
final;
90 virtual bool isReadAhead()
const;
93 bool m_isReadAhead =
false;
94 std::vector<bool> m_needPeakListByMsLevel = {
true,
123 virtual bool needPeakList()
const override;
124 virtual void loadingEnded()
override;
126 unsigned long getMsLevelCount(
unsigned int ms_level)
const;
128 unsigned long getTotalCount()
const;
144 virtual bool needPeakList()
const override;
146 std::size_t getSpectrumIndexFromScanNumber(std::size_t scan_number)
const;
179 bool want_binary_data =
true)
const = 0;
197 virtual std::size_t scanNumber2SpectrumIndex(std::size_t scan_number);
203 virtual bool hasScanNumbers()
const;
229 virtual bool accept(
const QString &file_name)
const = 0;
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index)=0
get a MassSpectrumSPtr class given its 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...
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index)=0
std::shared_ptr< MsRunReader > MsRunReaderSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
std::multimap< std::size_t, std::size_t > m_mmap_scan2index
virtual std::size_t spectrumListSize() const =0
get the totat number of spectrum conained in the MSrun data file
MsRunIdCstSPtr mcsp_msRunId
Q_DECLARE_METATYPE(pappso::MsRunReaderSPtr)
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
Class representing a fully specified mass spectrum.
virtual bool needPeakList() const =0
tells if we need the peak list (if we want the binary data) for each spectrum
std::shared_ptr< const MsRunReader > MsRunReaderCstSPtr
virtual void initialize()=0
class PMSPP_LIB_DECL MsRunReader
virtual bool acquireDevice()=0
acquire data back end device
provides a multimap to find quickly spectrum index from scan number
std::vector< unsigned long > m_countMsLevelSpectrum
example of interface to count MS levels of all spectrum in an MSrun
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,...
int msRunReaderSPtrMetaTypeId
interface to collect spectrums from the MsRunReader class
std::shared_ptr< MassSpectrum > MassSpectrumSPtr