34#include "../../xic/xic.h"
35#include "../../msrun/xiccoord/xiccoordtims.h"
80 virtual std::size_t
getNbrPeaks(std::size_t scanNum)
const override;
88 std::size_t scanNumEnd)
const override;
110 std::size_t mzindex_merge_window,
111 std::size_t scanNumBegin,
112 std::size_t scanNumEnd,
113 quint32 &mz_minimum_index,
114 quint32 &mz_maximum_index)
const override;
138 std::size_t mz_index_merge_window,
139 double mz_range_begin,
141 std::size_t mobility_scan_begin,
142 std::size_t mobility_scan_end,
143 quint32 &mz_minimum_index_out,
144 quint32 &mz_maximum_index_out)
const override;
152 std::size_t scanNumBegin,
153 std::size_t scanNumEnd)
const override;
171 std::size_t mz_index_merge_window,
172 double mz_range_begin,
174 quint32 &mz_minimum_index_out,
175 quint32 &mz_maximum_index_out)
const override;
182 std::size_t scanNumEnd)
const override;
187 virtual std::vector<quint32>
193 virtual std::vector<quint32>
208 virtual std::vector<RawValuePair>
210 quint32 accepted_tof_index_range_begin,
211 quint32 accepted_tof_index_range_end)
const;
218 TimsFrame(std::size_t timsId, quint32 scanNum);
221 std::vector<XicCoordTims *>::iterator &itXicListbegin,
222 std::vector<XicCoordTims *>::iterator &itXicListend,
236 quint32 accepted_tof_index_range_begin,
237 quint32 accepted_tof_index_range_end)
const;
QByteArray m_timsDataFrame
virtual std::vector< quint32 > getScanIndexList(std::size_t scanNum) const override
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
virtual std::size_t getNbrPeaks(std::size_t scanNum) const override
get the number of peaks in this spectrum need the binary file
virtual Trace cumulateScansToTraceMzDownResolution(std::size_t mzindex_merge_window, std::size_t scanNumBegin, std::size_t scanNumEnd, quint32 &mz_minimum_index, quint32 &mz_maximum_index) const override
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
virtual quint64 cumulateScansIntensities(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
...
virtual Trace cumulateScansToTraceMzDownResolution2(std::size_t mz_index_merge_window, double mz_range_begin, double mz_range_end, std::size_t mobility_scan_begin, std::size_t mobility_scan_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const override
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
virtual Trace cumulateScansToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace
virtual std::vector< RawValuePair > getRawValuePairList(std::size_t scanNum, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end) const
get the raw index tof_index and intensities (normalized)
friend TimsDirectXicExtractor
virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const override
get Mass spectrum with peaks for this scan number need the binary file
virtual quint64 cumulateSingleScanIntensities(std::size_t scanNum) const override
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const override
get raw intensities without transformation from one scan it needs intensity normalization
void unshufflePacket(const char *src)
unshuffle data packet of tims compression type 2
virtual Trace getMobilityScan(std::size_t scanNum, std::size_t mz_index_merge_window, double mz_range_begin, double mz_range_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const override
get a single mobility scan m/z + intensities
virtual void cumulateScan(std::size_t scanNum, TimsDataFastMap &accumulate_into) const
cumulate a scan into a map
virtual void cumulateScan2(std::size_t scanNum, TimsDataFastMap &accumulate_into, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end) const
std::size_t getScanOffset(std::size_t scanNum) const
get offset for this spectrum in the binary file
virtual void cumulateScansInRawMap(TimsDataFastMap &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace into a raw spectrum map
void extractTimsXicListInRtRange(std::vector< XicCoordTims * >::iterator &itXicListbegin, std::vector< XicCoordTims * >::iterator &itXicListend, XicExtractMethod method) const
virtual pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const
get the raw index tof_index and intensities (normalized)
A simple container of DataPoint instances.
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< TimsFrame > TimsFrameSPtr
std::shared_ptr< Trace > TraceSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
std::size_t mobilityIndexBegin
std::size_t mzIndexUpperBound
std::size_t mzIndexLowerBound
std::size_t mobilityIndexEnd
coordinates of the XIC to extract and the resulting XIC after extraction
handle a single Bruker's TimsTof frame without binary data