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 and changes multichar...
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