33#include "../../massspectrum/massspectrum.h"
115 std::size_t scanIndexEnd)
const;
139 std::size_t tof_index_merge_window,
140 std::size_t scanIndexBegin,
141 std::size_t scanIndexEnd,
142 quint32 &minimum_tof_index_out,
143 quint32 &maximum_tof_index_out)
const;
167 std::size_t mz_index_merge_window,
168 double mz_range_begin,
170 std::size_t mobility_scan_begin,
171 std::size_t mobility_scan_end,
172 quint32 &mz_minimum_index_out,
173 quint32 &mz_maximum_index_out)
const;
192 std::size_t tof_index_merge_window,
193 double mz_range_begin,
195 quint32 &mz_minimum_index_out,
196 quint32 &mz_maximum_index_out)
const;
213 std::size_t scan_index_begin,
214 std::size_t scan_index_end)
const;
234 std::size_t scan_index_begin,
235 std::size_t scan_index_end,
236 quint32 tof_index_begin,
237 quint32 tof_index_end)
const;
243 std::size_t scan_index_end)
const;
255 double digitizerTimebase,
256 double digitizerDelay,
282 std::size_t
getId()
const;
329 virtual std::vector<quint32>
335 virtual std::vector<quint32>
348 std::size_t tof_index_end,
350 std::size_t scan_index_begin,
351 std::size_t scan_index_end)
const;
375 virtual std::vector<TofIndexIntensityPair> &
377 std::size_t tof_index_merge_window,
378 std::vector<TofIndexIntensityPair> &spectrum)
const;
double m_rtInSeconds
retention time
double getVoltageTransformation(std::size_t scanNum) const
get voltage for a given scan number
virtual std::size_t getTotalNumberOfScans() const
get the number of scans contained in this frame each scan represents an ion mobility slice
virtual pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t scan_index) const final
get the mass spectrum corresponding to a scan index
MzCalibrationInterfaceSPtr msp_mzCalibration
virtual std::size_t getScanPeakCount(std::size_t scanIndex) const
get the number of peaks in this spectrum need the binary file
double getDriftTimeInMilliseconds(std::size_t scan_index) const
get drift time of a scan number in milliseconds
virtual Trace cumulateScansToTrace(std::size_t scanIndexBegin, std::size_t scanIndexEnd) const
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
virtual std::vector< TofIndexIntensityPair > & downgradeResolutionOfTofIndexIntensityPairList(std::size_t tof_index_merge_window, std::vector< TofIndexIntensityPair > &spectrum) const
Downgrade the TOF index resolution to lower the number of real m/z computations.
std::size_t getScanIndexFromOneOverK0(double one_over_k0) const
get the scan number from a given 1/Ko mobility value
virtual bool hasSameCalibrationData(const TimsFrameBase &other) const
tells if 2 tims frame has the same calibration data Usefull to know if raw data can be handled betwee...
virtual Trace combineScansToTraceWithDowngradedMzResolution(std::size_t tof_index_merge_window, std::size_t scanIndexBegin, std::size_t scanIndexEnd, quint32 &minimum_tof_index_out, quint32 &maximum_tof_index_out) const
cumulate spectrum given a scan index range need the binary file The intensities are normalized with r...
virtual Trace getIonMobilityTraceByTofIndexRange(std::size_t tof_index_begin, std::size_t tof_index_end, XicExtractMethod method, std::size_t scan_index_begin, std::size_t scan_index_end) const
get a mobility trace cumulating intensities inside the given mass index range
double m_acqDurationInMilliseconds
acquisition duration in milliseconds
double getRtInSeconds() const
virtual quint32 getMaximumRawMassIndex() const
get the maximum raw mass index contained in this frame
pappso::Trace getTraceFromTofIndexIntensityMap(TimsDataFastMap &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum
virtual Trace combineScansToTraceWithDowngradedMzResolution2(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
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
unsigned int getMsLevel() const
void setTimsCalibration(int tims_model_type, double C0, double C1, double C2, double C3, double C4, double C5, double C6, double C7, double C8, double C9)
virtual MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scan_index) const
get Mass spectrum with peaks for this scan index need the binary file
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
virtual quint64 cumulateScanRangeIntensities(std::size_t scan_index_begin, std::size_t scan_index_end) const
void setRtInSeconds(double time)
double getOneOverK0Transformation(std::size_t scan_index) const
get 1/K0 value of a given scan (mobility value)
void setMsMsType(quint8 type)
void setMzCalibration(double T1_frame, double T2_frame, double digitizerTimebase, double digitizerDelay, double C0, double C1, double C2, double C3, double C4, double T1_ref, double T2_ref, double dC1, double dC2)
quint32 m_scanCount
total number of scans contained in this frame
std::size_t m_frameId
Tims frame database id (the SQL identifier of this frame)
void setAcqDurationInMilliseconds(double acquisition_duration_ms)
virtual Trace getMobilityScan(std::size_t scan_index, std::size_t tof_index_merge_window, double mz_range_begin, double mz_range_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const
get a single mobility scan m/z + intensities
bool checkScanNum(std::size_t scanNum) const
check that this scan number exists
virtual void combineScansInTofIndexIntensityMap(TimsDataFastMap &tof_index_intensity_map, std::size_t scan_index_begin, std::size_t scan_index_end) const
cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respe...
void setMzCalibrationInterfaceSPtr(MzCalibrationInterfaceSPtr mzCalibration)
virtual std::vector< quint32 > getScanTofIndexList(std::size_t scan_index) const
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
virtual std::vector< quint32 > getScanIntensityList(std::size_t scan_index) const
get raw intensities without transformation from one scan it needs intensity normalization
std::size_t getId() const
virtual quint64 cumulateScanIntensities(std::size_t scan_index) const
A simple container of DataPoint instances.
handles different ways to compute m/z using calibration parameters
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< const TimsFrameBase > TimsFrameBaseCstSPtr
std::shared_ptr< TimsFrameBase > TimsFrameBaseSPtr
std::shared_ptr< MzCalibrationInterface > MzCalibrationInterfaceSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
replacement fot std::map dedicated to tims data for fast computations