libpappsomspp
Library for mass spectrometry
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33 #include "../../massspectrum/qualifiedmassspectrum.h"
35 #include "../../xic/xic.h"
46 struct TimsXicStructure;
47 class TimsDirectXicExtractor;
52 class TimsFrame :
public TimsFrameBase
77 virtual std::size_t
getNbrPeaks(std::size_t scanNum)
const override;
85 std::size_t scanNumEnd)
const override;
93 std::size_t scanNumBegin,
94 std::size_t scanNumEnd)
const override;
102 std::size_t scanNumEnd,
103 std::map<quint32, quint32> &accumulate_into)
const;
125 std::vector<TimsXicStructure>::iterator &itXicListbegin,
126 std::vector<TimsXicStructure>::iterator &itXicListend,
138 std::map<quint32, quint32> &accumulate_into)
const;
XicComputeStructure(const TimsFrame *fram_p, const TimsXicStructure &xic_struct)
std::vector< quint32 > getScanIntensities(std::size_t scanNum) const
get raw intensities without transformation from one scan it needs intensity normalization
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< TimsFrame > TimsFrameSPtr
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const override
void cumulateScans(std::size_t scanNumBegin, std::size_t scanNumEnd, std::map< quint32, quint32 > &accumulate_into) const
cumulate a scan list into a map of integers
std::size_t mobilityIndexEnd
pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const
std::size_t mzIndexUpperBound
pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t scanNum) const
get the mass spectrum corresponding to a scan number
TimsFrame(std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len)
A simple container of DataPoint instances.
virtual void cumulateScansInRawMap(std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace into a raw spectrum map
QByteArray m_timsDataFrame
void unshufflePacket(const char *src)
std::shared_ptr< Trace > TraceSPtr
virtual std::size_t getNbrPeaks(std::size_t scanNum) const override
handle a single Bruker's TimsTof frame without binary data
std::size_t mzIndexLowerBound
virtual Trace cumulateScanToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace
structure needed to extract XIC from Tims data
std::vector< quint32 > getScanIndexList(std::size_t scanNum) const
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
friend TimsDirectXicExtractor
std::size_t mobilityIndexBegin
std::size_t getScanOffset(std::size_t scanNum) const
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
void cumulateScan(std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into) const
cumulate a scan into a map
void extractTimsXicListInRtRange(std::vector< TimsXicStructure >::iterator &itXicListbegin, std::vector< TimsXicStructure >::iterator &itXicListend, XicExtractMethod method) const
std::shared_ptr< MassSpectrum > MassSpectrumSPtr