#include <timsframebase.h>

Inheritance diagram for pappso::TimsFrameBase:

Public Member Functions
	TimsFrameBase (std::size_t timsId, quint32 scanNum)
	constructor for binary independant tims frame More...

	TimsFrameBase (const TimsFrameBase &other)

	~TimsFrameBase ()

virtual std::size_t	getNbrPeaks (std::size_t scanNum) const

virtual MassSpectrumSPtr	getMassSpectrumSPtr (std::size_t scanNum) const

virtual Trace	cumulateScanToTrace (std::size_t scanNumBegin, std::size_t scanNumEnd) const

bool	checkScanNum (std::size_t scanNum) const

void	setAccumulationTime (double accumulation_time_ms)

void	setMzCalibration (double temperature_correction, double digitizerTimebase, double digitizerDelay, double C0, double C1, double C2, double C3)

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...

double	getMzFromTof (double tof) const
	get m/z from time of flight More...

quint32	getRawIndexFromMz (double mz) const
	get raw index of a given m/z More...

double	getVoltageTransformation (std::size_t scanNum) const

double	getTofFromIndex (quint32 index) const
	get time of flight from raw index More...

double	getTofFromIndex (double index) const
	get time of flight from double index More...

Protected Attributes
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...

double	m_digitizerTimebase = 0

double	m_digitizerDelay = 0

std::vector< double >	m_mzCalibrationArr
	MZ calibration parameters. 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

Detailed Description

Todo:: write docs

Definition at line 62 of file timsframebase.h.

Constructor & Destructor Documentation

◆ TimsFrameBase() [1/2]

pappso::TimsFrameBase::TimsFrameBase	(	std::size_t	timsId,
		quint32	scanNum
	)

constructor for binary independant tims frame

Parameters

timsId	tims frame identifier in the database
scanNum	the total number of scans contained in this frame

Definition at line 53 of file timsframebase.cpp.

 {
   m_accumulationTime = accumulation_time_ms;
 }
  
  

References m_accumulationTime.

◆ TimsFrameBase() [2/2]

pappso::TimsFrameBase::TimsFrameBase ( const TimsFrameBase & other )

Copy constructor

Parameters

other TODO

Definition at line 61 of file timsframebase.cpp.

68 {

◆ ~TimsFrameBase()

pappso::TimsFrameBase::~TimsFrameBase ( )

Destructor

Definition at line 65 of file timsframebase.cpp.

68 {

Member Function Documentation

◆ checkScanNum()

bool pappso::TimsFrameBase::checkScanNum ( std::size_t scanNum ) const

Definition at line 100 of file timsframebase.cpp.

 {
   throw PappsoException(
     QObject::tr(
       "ERROR unable to get number of peaks in TimsFrameBase for scan number %1")
       .arg(scanNum));
 }
  
 MassSpectrumSPtr
 TimsFrameBase::getMassSpectrumSPtr(std::size_t scanNum) const
 {
   throw PappsoException(
     QObject::tr(
       "ERROR unable to getMassSpectrumSPtr in TimsFrameBase for scan number %1")

◆ cumulateScanToTrace()

Trace pappso::TimsFrameBase::cumulateScanToTrace	(	std::size_t	scanNumBegin,
		std::size_t	scanNumEnd
	)		const

virtual

Reimplemented in pappso::TimsFrame.

Definition at line 135 of file timsframebase.cpp.

 {
   // mz calibration
   return ((double)index * m_digitizerTimebase) + m_digitizerDelay;
 }
 double
 TimsFrameBase::getMzFromTof(double tof) const
 {
   // http://www.alglib.net/equations/polynomial.php

References m_digitizerDelay, and m_digitizerTimebase.

◆ getDriftTime()

double pappso::TimsFrameBase::getDriftTime ( std::size_t scanNum ) const

get drift time of a scan number in milliseconds

Parameters

scanNum the scan number

Returns: time in milliseconds of mobility delay (drift time)

Definition at line 377 of file timsframebase.cpp.

◆ getId()

std::size_t pappso::TimsFrameBase::getId ( ) const

Definition at line 319 of file timsframebase.cpp.

 {
   if(tims_model_type != 2)
     {
       throw pappso::PappsoException(QObject::tr(

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::TimsFrameBase::getMassSpectrumSPtr ( std::size_t scanNum ) const

virtual

Reimplemented in pappso::TimsFrame.

Definition at line 127 of file timsframebase.cpp.

 {
   // mz calibration
   return (index * m_digitizerTimebase) + m_digitizerDelay;
 }

◆ getMsLevel()

unsigned int pappso::TimsFrameBase::getMsLevel ( ) const

Definition at line 305 of file timsframebase.cpp.

319 {

◆ getMzFromTof()

double pappso::TimsFrameBase::getMzFromTof ( double tof ) const

get m/z from time of flight

Parameters

tof	time of flight

Returns: m/z value

Definition at line 157 of file timsframebase.cpp.

                      { 1 + sqrt((10^12)/670) * m2 + 207.775676931964 * (m2^2)
 + 59.2526676368822 * (m2^3) }
 > plot(eq2(1:sqrt(1000)), type='l')
 */
   // How to Factor a Trinomial with Fractions as Coefficients
  
   // formula
   // a = c0 = 1
   // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
   // c = c2, c2 = 207.775676931964  * m
   // d = c3, c3 = 59.2526676368822  * m^1.5  (3/2)
   // double mz = 0;
   std::vector<double> X;
   X.push_back((m_mzCalibrationArr[0] - (double)tof));
   X.push_back(m_mzCalibrationArr[1]);
   if(m_mzCalibrationArr[2] != 0)
     {
       X.push_back(m_mzCalibrationArr[2]);
     }
   if(m_mzCalibrationArr[3] != 0)
     {
       X.push_back(m_mzCalibrationArr[3]);
     }
   else
     {
       qDebug() << m_mzCalibrationArr[3];
     }
  
   alglib::real_1d_array polynom_array;
   try
     {
       polynom_array.setcontent(X.size(), &(X[0]));
     }
   catch(alglib::ap_error &error)
     {
       // PolynomialSolve: A[N]=0
       throw pappso::PappsoException(
         QObject::tr("ERROR in alglib::polynom_array.setcontent :\n%1")
           .arg(error.msg.c_str()));
     }
  
  
   /*
   alglib::polynomialsolve(
 real_1d_array a,
 ae_int_t n,
 complex_1d_array& x,
 polynomialsolverreport& rep,
 const xparams _params = alglib::xdefault);
 */
   alglib::complex_1d_array m;
   alglib::polynomialsolverreport rep;
   // qDebug();
   try
     {
       alglib::polynomialsolve(polynom_array, X.size() - 1, m, rep);
     }
   catch(alglib::ap_error &error)
     {
       qDebug() << " X.size() - 1 = " << X.size() - 1;
       qDebug() << m_mzCalibrationArr[0];
       qDebug() << m_mzCalibrationArr[1];
       qDebug() << m_mzCalibrationArr[2];
       qDebug() << m_mzCalibrationArr[3];
  
       // PolynomialSolve: A[N]=0
       throw pappso::PappsoException(
         QObject::tr("ERROR in alglib::polynomialsolve :\n%1")
           .arg(error.msg.c_str()));
     }
  
  
   // qDebug();
  
   if(m.length() == 0)
     {
       throw pappso::PappsoException(
         QObject::tr("ERROR in TimsFrame::getMzFromTof m.size() == 0"));
     }
   // qDebug();
   if(m[0].y != 0)
     {
       throw pappso::PappsoException(
         QObject::tr("ERROR in TimsFrame::getMzFromTof m[0].y!= 0"));
     }
  
   return pow(m[0].x, 2);
 }
  
 quint32
 TimsFrameBase::getRawIndexFromMz(double mz) const
 {
   // formula
   // a = c0 = 1
   // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
   // c = c2, c2 = 207.775676931964  * m
   // d = c3, c3 = 59.2526676368822  * m^1.5  (3/2)
   qDebug() << "mz=" << mz;
  
   double tof = m_mzCalibrationArr[0];
   qDebug() << "tof ( m_mzCalibrationArr[0])=" << tof;
   // TODO cache value of  std::sqrt((std::pow(10, 12) / m_mzCalibrationArr[1]))
   tof += m_mzCalibrationArr[1] * std::sqrt(mz);
   qDebug() << "tof=" << tof;

References m_mzCalibrationArr.

Referenced by pappso::TimsFrame::getTraceFromCumulatedScans().

◆ getNbrPeaks()

std::size_t pappso::TimsFrameBase::getNbrPeaks ( std::size_t scanNum ) const

virtual

Reimplemented in pappso::TimsFrame.

Definition at line 118 of file timsframebase.cpp.

 {
   throw PappsoException(
     QObject::tr("ERROR unable to cumulateScanToTrace in TimsFrameBase for scan "
                 "number begin %1 end %2")

◆ getOneOverK0Transformation()

double pappso::TimsFrameBase::getOneOverK0Transformation ( std::size_t scanNum ) const

get 1/K0 value of a given scan (mobility value)

Parameters

scanNum the scan number

Definition at line 383 of file timsframebase.cpp.

◆ getRawIndexFromMz()

quint32 pappso::TimsFrameBase::getRawIndexFromMz ( double mz ) const

get raw index of a given m/z

Parameters

mz	the mass to transform

Returns: integer x raw value

Definition at line 265 of file timsframebase.cpp.

 {
   m_time = time;
 }
  
 void
 TimsFrameBase::setMsMsType(quint8 type)
 {
  
   qDebug() << " m_msMsType=" << type;
   m_msMsType = type;
 }
  
 unsigned int

◆ getTime()

double pappso::TimsFrameBase::getTime ( ) const

Definition at line 313 of file timsframebase.cpp.

319 {

◆ getTofFromIndex() [1/2]

double pappso::TimsFrameBase::getTofFromIndex ( double index ) const

get time of flight from double index

Definition at line 145 of file timsframebase.cpp.

◆ getTofFromIndex() [2/2]

double pappso::TimsFrameBase::getTofFromIndex ( quint32 index ) const

get time of flight from raw index

Parameters

index digitizer x raw value

Returns: tof time of flight

Definition at line 151 of file timsframebase.cpp.

                    { 313.577620892277 + (sqrt((10^12)/157424.07710945) *
 sqrt(m)) + (0.000338743021989553 * m)
 + (0 * (m^1.5)) }
 > plot(eq(1:1000), type='l')

Referenced by pappso::TimsFrame::getTraceFromCumulatedScans().

◆ getVoltageTransformation()

double pappso::TimsFrameBase::getVoltageTransformation ( std::size_t scanNum ) const

Definition at line 355 of file timsframebase.cpp.

 {
   return (m_accumulationTime / (double)m_scanNumber) * ((double)scanNum);
 }
  
 double
 TimsFrameBase::getOneOverK0Transformation(std::size_t scanNum) const
 {
   return 1 / (m_timsC6 + (m_timsC7 / getVoltageTransformation(scanNum)));
 }
 } // namespace pappso

◆ setAccumulationTime()

void pappso::TimsFrameBase::setAccumulationTime ( double accumulation_time_ms )

Definition at line 70 of file timsframebase.cpp.

◆ setMsMsType()

void pappso::TimsFrameBase::setMsMsType ( quint8 type )

Definition at line 297 of file timsframebase.cpp.

 {
   return m_time;
 }
  
 std::size_t

References m_time.

◆ setMzCalibration()

void pappso::TimsFrameBase::setMzCalibration	(	double	temperature_correction,
		double	digitizerTimebase,
		double	digitizerDelay,
		double	C0,
		double	C1,
		double	C2,
		double	C3
	)

Definition at line 77 of file timsframebase.cpp.

 {
   if(scanNum < 0)
     {
       throw pappso::ExceptionOutOfRange(
         QObject::tr("Invalid scan number : scanNum%1 < 0").arg(scanNum));
     }
   if(scanNum >= m_scanNumber)
     {
       throw pappso::ExceptionOutOfRange(
         QObject::tr("Invalid scan number : scanNum%1  > m_scanNumber")
           .arg(scanNum));
     }
  

◆ setTime()

void pappso::TimsFrameBase::setTime ( double time )

Definition at line 291 of file timsframebase.cpp.

◆ setTimsCalibration()

void pappso::TimsFrameBase::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
	)

Definition at line 324 of file timsframebase.cpp.

 {
   double v = m_timsDvStart +
              m_timsSlope * ((double)scanNum - m_timsTtrans - m_timsNdelay);
  
   if(v < m_timsVmin)
     {
       throw pappso::PappsoException(
         QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
                     "calibration, v < m_timsVmin"));
     }
  
  
   if(v > m_timsVmax)
     {

Member Data Documentation

◆ m_accumulationTime

double pappso::TimsFrameBase::m_accumulationTime = 0

protected

accumulation time in milliseconds

Definition at line 169 of file timsframebase.h.

Referenced by pappso::TimsFrame::getTraceFromCumulatedScans(), and TimsFrameBase().

◆ m_digitizerDelay

double pappso::TimsFrameBase::m_digitizerDelay = 0

protected

Definition at line 172 of file timsframebase.h.

Referenced by cumulateScanToTrace().

◆ m_digitizerTimebase

double pappso::TimsFrameBase::m_digitizerTimebase = 0

protected

Definition at line 171 of file timsframebase.h.

Referenced by cumulateScanToTrace().

◆ m_msMsType

quint8 pappso::TimsFrameBase::m_msMsType = 0

protected

Definition at line 178 of file timsframebase.h.

◆ m_mzCalibrationArr

std::vector<double> pappso::TimsFrameBase::m_mzCalibrationArr

protected

MZ calibration parameters.

Definition at line 176 of file timsframebase.h.

Referenced by getMzFromTof().

◆ m_scanNumber

quint32 pappso::TimsFrameBase::m_scanNumber

protected

total number of scans contained in this frame

Definition at line 159 of file timsframebase.h.

◆ m_time

double pappso::TimsFrameBase::m_time = 0

protected

retention time

Definition at line 182 of file timsframebase.h.

Referenced by setMsMsType().

◆ m_timsC6

double pappso::TimsFrameBase::m_timsC6 = 0

protected

Definition at line 192 of file timsframebase.h.

◆ m_timsC7

double pappso::TimsFrameBase::m_timsC7 = 0

protected

Definition at line 193 of file timsframebase.h.

◆ m_timsDvStart

double pappso::TimsFrameBase::m_timsDvStart = 0

protected

Definition at line 184 of file timsframebase.h.

◆ m_timsId

std::size_t pappso::TimsFrameBase::m_timsId

protected

Tims frame database id (the SQL identifier of this frame)

Warning: in sqlite, there is another field called TimsId : this is not that, because it is in fact an offset in bytes in the binary file.

Definition at line 165 of file timsframebase.h.

◆ m_timsNdelay

double pappso::TimsFrameBase::m_timsNdelay = 0

protected

Definition at line 189 of file timsframebase.h.

◆ m_timsSlope

double pappso::TimsFrameBase::m_timsSlope

protected

Initial value:

=

0

Definition at line 185 of file timsframebase.h.

◆ m_timsTtrans

double pappso::TimsFrameBase::m_timsTtrans = 0

protected

Definition at line 188 of file timsframebase.h.

◆ m_timsVmax

double pappso::TimsFrameBase::m_timsVmax = 0

protected

Definition at line 191 of file timsframebase.h.

◆ m_timsVmin

double pappso::TimsFrameBase::m_timsVmin = 0

protected

Definition at line 190 of file timsframebase.h.

The documentation for this class was generated from the following files:

pappsomspp/vendors/tims/timsframebase.h
pappsomspp/vendors/tims/timsframebase.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TimsFrameBase() [1/2]

◆ TimsFrameBase() [2/2]

◆ ~TimsFrameBase()

Member Function Documentation

◆ checkScanNum()

◆ cumulateScanToTrace()

◆ getDriftTime()

◆ getId()

◆ getMassSpectrumSPtr()

◆ getMsLevel()

◆ getMzFromTof()

◆ getNbrPeaks()

◆ getOneOverK0Transformation()

◆ getRawIndexFromMz()

◆ getTime()

◆ getTofFromIndex() [1/2]

◆ getTofFromIndex() [2/2]

◆ getVoltageTransformation()

◆ setAccumulationTime()

◆ setMsMsType()

◆ setMzCalibration()

◆ setTime()

◆ setTimsCalibration()

Member Data Documentation

◆ m_accumulationTime

◆ m_digitizerDelay

◆ m_digitizerTimebase

◆ m_msMsType

◆ m_mzCalibrationArr

◆ m_scanNumber

◆ m_time

◆ m_timsC6

◆ m_timsC7

◆ m_timsDvStart

◆ m_timsId

◆ m_timsNdelay

◆ m_timsSlope

◆ m_timsTtrans

◆ m_timsVmax

◆ m_timsVmin