libpappsomspp
Library for mass spectrometry
|
#include <timsframe.h>
Classes | |
struct | XicComputeStructure |
Public Member Functions | |
TimsFrame (std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len) | |
TimsFrame (const TimsFrame &other) | |
~TimsFrame () | |
virtual std::size_t | getNbrPeaks (std::size_t scanNum) const override |
virtual Trace | cumulateScanToTrace (std::size_t scanNumBegin, std::size_t scanNumEnd) const override |
cumulate scan list into a trace More... | |
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 More... | |
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 More... | |
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 More... | |
std::vector< quint32 > | getScanIntensities (std::size_t scanNum) const |
get raw intensities without transformation from one scan it needs intensity normalization More... | |
pappso::MassSpectrumCstSPtr | getMassSpectrumCstSPtr (std::size_t scanNum) const |
get the mass spectrum corresponding to a scan number More... | |
virtual pappso::MassSpectrumSPtr | getMassSpectrumSPtr (std::size_t scanNum) const override |
![]() | |
TimsFrameBase (std::size_t timsId, quint32 scanNum) | |
constructor for binary independant tims frame More... | |
TimsFrameBase (const TimsFrameBase &other) | |
~TimsFrameBase () | |
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 between frames More... | |
bool | checkScanNum (std::size_t scanNum) const |
void | setAccumulationTime (double accumulation_time_ms) |
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 | 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) |
void | setTime (double time) |
void | setMsMsType (quint8 type) |
unsigned int | getMsLevel () const |
double | getTime () const |
std::size_t | getId () const |
double | getDriftTime (std::size_t scanNum) const |
get drift time of a scan number in milliseconds More... | |
double | getOneOverK0Transformation (std::size_t scanNum) const |
get 1/K0 value of a given scan (mobility value) More... | |
std::size_t | getScanNumFromOneOverK0 (double one_over_k0) const |
get the scan number from a given 1/Ko mobility value More... | |
double | getVoltageTransformation (std::size_t scanNum) const |
pappso::Trace | getTraceFromCumulatedScans (std::map< quint32, quint32 > &accumulated_scans) const |
transform accumulation of raw scans into a real mass spectrum More... | |
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 More... | |
virtual const MzCalibrationInterfaceSPtr & | getMzCalibrationInterfaceSPtr () const final |
get the MzCalibration model to compute mz and TOF for this frame More... | |
void | setMzCalibrationInterfaceSPtr (MzCalibrationInterfaceSPtr mzCalibration) |
Protected Member Functions | |
void | extractTimsXicListInRtRange (std::vector< TimsXicStructure >::iterator &itXicListbegin, std::vector< TimsXicStructure >::iterator &itXicListend, XicExtractMethod method) const |
Private Member Functions | |
void | unshufflePacket (const char *src) |
std::size_t | getScanOffset (std::size_t scanNum) const |
void | cumulateScan (std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into) const |
cumulate a scan into a map More... | |
pappso::TraceSPtr | getRawTraceSPtr (std::size_t scanNum) const |
Private Attributes | |
friend | TimsDirectXicExtractor |
QByteArray | m_timsDataFrame |
Additional Inherited Members | |
![]() | |
quint32 | m_scanNumber |
total number of scans contained in this frame More... | |
std::size_t | m_timsId |
Tims frame database id (the SQL identifier of this frame) More... | |
double | m_accumulationTime = 0 |
accumulation time in milliseconds More... | |
quint8 | m_msMsType = 0 |
double | m_time = 0 |
retention time More... | |
double | m_timsDvStart = 0 |
double | m_timsSlope |
double | m_timsTtrans = 0 |
double | m_timsNdelay = 0 |
double | m_timsVmin = 0 |
double | m_timsVmax = 0 |
double | m_timsC6 = 0 |
double | m_timsC7 = 0 |
MzCalibrationInterfaceSPtr | msp_mzCalibration = nullptr |
Definition at line 52 of file timsframe.h.
pappso::TimsFrame::TimsFrame | ( | std::size_t | timsId, |
quint32 | scanNum, | ||
char * | p_bytes, | ||
std::size_t | len | ||
) |
Default constructor
Definition at line 57 of file timsframe.cpp.
References pappso::TimsFrameBase::m_scanNumber, m_timsDataFrame, pappso::TimsFrameBase::m_timsId, and unshufflePacket().
pappso::TimsFrame::TimsFrame | ( | const TimsFrame & | other | ) |
pappso::TimsFrame::~TimsFrame | ( | ) |
|
private |
cumulate a scan into a map
Definition at line 216 of file timsframe.cpp.
References getNbrPeaks(), getScanOffset(), m_timsDataFrame, and pappso::y.
Referenced by cumulateScansInRawMap(), and cumulateScanToTrace().
void pappso::TimsFrame::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
scanNumBegin | first scan to cumulate |
scanNumEnd | last scan to cumulate |
accumulate_into | map of x and y integer values |
|
overridevirtual |
cumulate scan list into a trace into a raw spectrum map
rawSpectrum | simple map of integers to cumulate raw counts |
scanNumBegin | first scan to cumulate |
scanNumEnd | last scan to cumulate |
Reimplemented from pappso::TimsFrameBase.
Definition at line 310 of file timsframe.cpp.
References cumulateScan(), and m_timsDataFrame.
|
overridevirtual |
cumulate scan list into a trace
scanNumBegin | first scan to cumulate |
scanNumEnd | last scan to cumulate |
Reimplemented from pappso::TimsFrameBase.
Definition at line 254 of file timsframe.cpp.
References cumulateScan(), pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), pappso::TimsFrameBase::m_accumulationTime, m_timsDataFrame, pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.
|
protected |
Definition at line 404 of file timsframe.cpp.
References getRawTraceSPtr(), pappso::TimsFrameBase::m_time, and pappso::sum.
pappso::MassSpectrumCstSPtr pappso::TimsFrame::getMassSpectrumCstSPtr | ( | std::size_t | scanNum | ) | const |
get the mass spectrum corresponding to a scan number
scanNum | the scan number to retrieve |
Definition at line 344 of file timsframe.cpp.
References getMassSpectrumSPtr().
|
overridevirtual |
Reimplemented from pappso::TimsFrameBase.
Definition at line 351 of file timsframe.cpp.
References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), getNbrPeaks(), getScanOffset(), pappso::TimsFrameBase::m_accumulationTime, m_timsDataFrame, pappso::DataPoint::x, and pappso::DataPoint::y.
Referenced by getMassSpectrumCstSPtr().
|
overridevirtual |
Reimplemented from pappso::TimsFrameBase.
Definition at line 125 of file timsframe.cpp.
References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::m_scanNumber, and m_timsDataFrame.
Referenced by cumulateScan(), getMassSpectrumSPtr(), getRawTraceSPtr(), getScanIndexList(), and getScanIntensities().
|
private |
Definition at line 476 of file timsframe.cpp.
References getNbrPeaks(), getScanOffset(), pappso::TimsFrameBase::m_accumulationTime, m_timsDataFrame, pappso::DataPoint::x, and pappso::DataPoint::y.
Referenced by extractTimsXicListInRtRange().
std::vector< quint32 > pappso::TimsFrame::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
Definition at line 167 of file timsframe.cpp.
References pappso::TimsFrameBase::checkScanNum(), getNbrPeaks(), getScanOffset(), and m_timsDataFrame.
std::vector< quint32 > pappso::TimsFrame::getScanIntensities | ( | std::size_t | scanNum | ) | const |
get raw intensities without transformation from one scan it needs intensity normalization
Definition at line 192 of file timsframe.cpp.
References pappso::TimsFrameBase::checkScanNum(), getNbrPeaks(), getScanOffset(), and m_timsDataFrame.
|
private |
Definition at line 155 of file timsframe.cpp.
References m_timsDataFrame.
Referenced by cumulateScan(), getMassSpectrumSPtr(), getRawTraceSPtr(), getScanIndexList(), and getScanIntensities().
|
private |
|
private |
Definition at line 158 of file timsframe.h.
Referenced by TimsFrame(), cumulateScan(), cumulateScansInRawMap(), cumulateScanToTrace(), getMassSpectrumSPtr(), getNbrPeaks(), getRawTraceSPtr(), getScanIndexList(), getScanIntensities(), getScanOffset(), and unshufflePacket().
|
private |
Definition at line 54 of file timsframe.h.