libpappsomspp
Library for mass spectrometry
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33 #include "../../massspectrum/massspectrum.h"
72 virtual std::size_t
getNbrPeaks(std::size_t scanNum)
const;
75 std::size_t scanNumEnd)
const;
84 std::size_t scanNumBegin,
85 std::size_t scanNumEnd)
const;
93 double digitizerTimebase,
94 double digitizerDelay,
120 std::size_t
getId()
const;
147 std::map<quint32, quint32> &accumulated_scans)
const;
153 std::map<quint32, quint32> &accumulated_scans)
const;
bool checkScanNum(std::size_t scanNum) const
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)
void setMzCalibrationInterfaceSPtr(MzCalibrationInterfaceSPtr mzCalibration)
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)
unsigned int getMsLevel() const
MzCalibrationInterfaceSPtr msp_mzCalibration
handles different ways to compute m/z using calibration parameters
virtual Trace cumulateScanToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
void setAccumulationTime(double accumulation_time_ms)
std::shared_ptr< const TimsFrameBase > TimsFrameBaseCstSPtr
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)
void setTime(double time)
TimsFrameBase(const TimsFrameBase &other)
virtual std::size_t getNbrPeaks(std::size_t scanNum) const
double getDriftTime(std::size_t scanNum) const
get drift time of a scan number in milliseconds
double m_accumulationTime
accumulation time in milliseconds
double m_time
retention time
pappso::Trace getTraceFromCumulatedScansBuiltinCentroid(std::map< quint32, quint32 > &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum with a simple centroid on raw integers
A simple container of DataPoint instances.
double getVoltageTransformation(std::size_t scanNum) const
std::size_t getId() const
std::shared_ptr< MzCalibrationInterface > MzCalibrationInterfaceSPtr
virtual MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const
std::size_t getScanNumFromOneOverK0(double one_over_k0) const
get the scan number from a given 1/Ko mobility value
std::shared_ptr< TimsFrameBase > TimsFrameBaseSPtr
TimsFrameBase(std::size_t timsId, quint32 scanNum)
constructor for binary independant tims frame
void setMsMsType(quint8 type)
virtual void cumulateScansInRawMap(std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const
cumulate scan list into a trace into a raw spectrum map
double getOneOverK0Transformation(std::size_t scanNum) const
get 1/K0 value of a given scan (mobility value)
quint32 m_scanNumber
total number of scans contained in this frame
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
pappso::Trace getTraceFromCumulatedScans(std::map< quint32, quint32 > &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum
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...