libpappsomspp
Library for mass spectrometry
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32 #include "../../types.h"
33 #include "../../msfile/msfileaccessor.h"
34 #include "../../msfile/msfilereader.h"
35 #include "../../vendors/tims/timsdata.h"
42 friend class MsFileAccessor;
48 virtual ~TimsMsRunReaderMs2();
51 massSpectrumSPtr(std::size_t spectrum_index)
override;
53 massSpectrumCstSPtr(std::size_t spectrum_index)
override;
55 virtual QualifiedMassSpectrum
56 qualifiedMassSpectrum(std::size_t spectrum_index,
57 bool want_binary_data =
true)
const override;
62 virtual std::size_t spectrumListSize()
const override;
64 virtual bool hasScanNumbers()
const override;
71 void setMs2BuiltinCentroid(
bool centroid);
76 virtual std::vector<std::size_t>
77 getPrecursorsIDFromMzRt(
int charge,
double mz_val,
double rt_sec,
double k0);
80 virtual bool releaseDevice()
override;
82 virtual bool acquireDevice()
override;
89 virtual void initialize()
override;
90 virtual bool accept(
const QString &file_name)
const override;
99 bool m_builtinMs2Centroid =
true;
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
std::shared_ptr< TimsData > TimsDataSp
shared pointer on a TimsData object
class PMSPP_LIB_DECL MsRunReader
interface to collect spectrums from the MsRunReader class
std::shared_ptr< MassSpectrum > MassSpectrumSPtr