libpappsomspp
Library for mass spectrometry
pappso::TimsFrameBase Class Reference

#include <timsframebase.h>

Inheritance diagram for pappso::TimsFrameBase:
pappso::TimsFrame

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...
 
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
 
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 64 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
timsIdtims frame identifier in the database
scanNumthe total number of scans contained in this frame

Definition at line 55 of file timsframebase.cpp.

55 {
56  m_accumulationTime = accumulation_time_ms;
57 }
58 
59 
60 void
61 TimsFrameBase::setMzCalibration(double temperature_correction,

References m_accumulationTime.

◆ TimsFrameBase() [2/2]

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

Copy constructor

Parameters
otherTODO

◆ ~TimsFrameBase()

pappso::TimsFrameBase::~TimsFrameBase ( )

Destructor

Definition at line 67 of file timsframebase.cpp.

68 {
69 

Member Function Documentation

◆ checkScanNum()

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

Definition at line 102 of file timsframebase.cpp.

107 {
108  throw PappsoException(
109  QObject::tr(
110  "ERROR unable to getMassSpectrumSPtr in TimsFrameBase for scan number %1")
111  .arg(scanNum));
112 }

◆ cumulateScanToTrace()

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

Reimplemented in pappso::TimsFrame.

Definition at line 132 of file timsframebase.cpp.

137 {
138  // http://www.alglib.net/equations/polynomial.php
139  // http://www.alglib.net/translator/man/manual.cpp.html#sub_polynomialsolve
140  // https://math.stackexchange.com/questions/1291208/number-of-roots-of-a-polynomial-of-non-integer-degree

◆ getDriftTime()

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

get drift time of a scan number in milliseconds

Parameters
scanNumthe scan number
Returns
time in milliseconds of mobility delay (drift time)

Definition at line 374 of file timsframebase.cpp.

◆ getId()

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

Definition at line 316 of file timsframebase.cpp.

316  {
317  throw pappso::PappsoException(QObject::tr(
318  "ERROR in TimsFrame::setTimsCalibration tims_model_type != 2"));
319  }

◆ getMassSpectrumSPtr()

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

Reimplemented in pappso::TimsFrame.

Definition at line 124 of file timsframebase.cpp.

125 {
126  // mz calibration
127  return (index * m_digitizerTimebase) + m_digitizerDelay;
128 }
129 double
130 TimsFrameBase::getTofFromIndex(quint32 index) const

References m_digitizerDelay, and m_digitizerTimebase.

◆ getMsLevel()

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

Definition at line 302 of file timsframebase.cpp.

314 {

◆ getMzFromTof()

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

get m/z from time of flight

Parameters
toftime of flight
Returns
m/z value

Definition at line 154 of file timsframebase.cpp.

154  { 1 + sqrt((10^12)/670) * m2 + 207.775676931964 * (m2^2)
155 + 59.2526676368822 * (m2^3) }
156 > plot(eq2(1:sqrt(1000)), type='l')
157 */
158  // How to Factor a Trinomial with Fractions as Coefficients
159 
160  // formula
161  // a = c0 = 1
162  // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
163  // c = c2, c2 = 207.775676931964 * m
164  // d = c3, c3 = 59.2526676368822 * m^1.5 (3/2)
165  // double mz = 0;
166  std::vector<double> X;
167  X.push_back((m_mzCalibrationArr[0] - (double)tof));
168  X.push_back(m_mzCalibrationArr[1]);
169  if(m_mzCalibrationArr[2] != 0)
170  {
171  X.push_back(m_mzCalibrationArr[2]);
172  }
173  if(m_mzCalibrationArr[3] != 0)
174  {
175  X.push_back(m_mzCalibrationArr[3]);
176  }
177  else
178  {
179  qDebug() << m_mzCalibrationArr[3];
180  }
181 
182  alglib::real_1d_array polynom_array;
183  try
184  {
185  polynom_array.setcontent(X.size(), &(X[0]));
186  }
187  catch(alglib::ap_error &error)
188  {
189  // PolynomialSolve: A[N]=0
191  QObject::tr("ERROR in alglib::polynom_array.setcontent :\n%1")
192  .arg(error.msg.c_str()));
193  }
194 
195 
196  /*
197  alglib::polynomialsolve(
198 real_1d_array a,
199 ae_int_t n,
200 complex_1d_array& x,
201 polynomialsolverreport& rep,
202 const xparams _params = alglib::xdefault);
203 */
204  alglib::complex_1d_array m;
205  alglib::polynomialsolverreport rep;
206  // qDebug();
207  try
208  {
209  alglib::polynomialsolve(polynom_array, X.size() - 1, m, rep);
210  }
211  catch(alglib::ap_error &error)
212  {
213  qDebug() << " X.size() - 1 = " << X.size() - 1;
214  qDebug() << m_mzCalibrationArr[0];
215  qDebug() << m_mzCalibrationArr[1];
216  qDebug() << m_mzCalibrationArr[2];
217  qDebug() << m_mzCalibrationArr[3];
218 
219  // PolynomialSolve: A[N]=0
221  QObject::tr("ERROR in alglib::polynomialsolve :\n%1")
222  .arg(error.msg.c_str()));
223  }
224 
225 
226  // qDebug();
227 
228  if(m.length() == 0)
229  {
231  QObject::tr("ERROR in TimsFrame::getMzFromTof m.size() == 0"));
232  }
233  // qDebug();
234  if(m[0].y != 0)
235  {
237  QObject::tr("ERROR in TimsFrame::getMzFromTof m[0].y!= 0"));
238  }
239 
240  return pow(m[0].x, 2);
241 }
242 
243 quint32
244 TimsFrameBase::getRawIndexFromMz(double mz) const
245 {
246  // formula
247  // a = c0 = 1
248  // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
249  // c = c2, c2 = 207.775676931964 * m
250  // d = c3, c3 = 59.2526676368822 * m^1.5 (3/2)
251  qDebug() << "mz=" << mz;
252 
253  double tof = m_mzCalibrationArr[0];
254  qDebug() << "tof ( m_mzCalibrationArr[0])=" << tof;
255  // TODO cache value of std::sqrt((std::pow(10, 12) / m_mzCalibrationArr[1]))
256  tof += m_mzCalibrationArr[1] * std::sqrt(mz);
257  qDebug() << "tof=" << tof;
258  tof += m_mzCalibrationArr[2] * mz;
259  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 115 of file timsframebase.cpp.

116 {
117  throw PappsoException(
118  QObject::tr("ERROR unable to cumulateScanToTrace in TimsFrameBase for scan "
119  "number begin %1 end %2")
120  .arg(scanNumBegin)
121  .arg(scanNumEnd));

◆ getOneOverK0Transformation()

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

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

Parameters
scanNumthe scan number

Definition at line 380 of file timsframebase.cpp.

◆ getRawIndexFromMz()

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

get raw index of a given m/z

Parameters
mzthe mass to transform
Returns
integer x raw value

Definition at line 262 of file timsframebase.cpp.

271 {
272  m_time = time;
273 }
274 
275 void
276 TimsFrameBase::setMsMsType(quint8 type)
277 {
278 
279  qDebug() << " m_msMsType=" << type;
280  m_msMsType = type;
281 }
282 
283 unsigned int
285 {

◆ getScanNumFromOneOverK0()

std::size_t pappso::TimsFrameBase::getScanNumFromOneOverK0 ( double  one_over_k0) const

get the scan number from a given 1/Ko mobility value

Parameters
one_over_k0the mobility value to tranform
Returns
integer the scan number

Definition at line 387 of file timsframebase.cpp.

◆ getTime()

double pappso::TimsFrameBase::getTime ( ) const

Definition at line 310 of file timsframebase.cpp.

314 {

◆ getTofFromIndex() [1/2]

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

get time of flight from double index

Definition at line 142 of file timsframebase.cpp.

◆ getTofFromIndex() [2/2]

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

get time of flight from raw index

Parameters
indexdigitizer x raw value
Returns
tof time of flight

Definition at line 148 of file timsframebase.cpp.

150  :1000), type='l')
151 
152 

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

◆ getVoltageTransformation()

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

Definition at line 352 of file timsframebase.cpp.

357 {
358  return (m_accumulationTime / (double)m_scanNumber) * ((double)scanNum);
359 }
360 
361 double
362 TimsFrameBase::getOneOverK0Transformation(std::size_t scanNum) const
363 {
364  return 1 / (m_timsC6 + (m_timsC7 / getVoltageTransformation(scanNum)));
365 }
366 
367 
368 std::size_t
369 TimsFrameBase::getScanNumFromOneOverK0(double one_over_k0) const
370 {
371  double temp = 1 / one_over_k0;
372  temp = temp - m_timsC6;

◆ setAccumulationTime()

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

Definition at line 72 of file timsframebase.cpp.

◆ setMsMsType()

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

Definition at line 294 of file timsframebase.cpp.

299 {

◆ setMzCalibration()

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

Definition at line 79 of file timsframebase.cpp.

85 {
86  if(scanNum >= m_scanNumber)
87  {
89  QObject::tr("Invalid scan number : scanNum%1 > m_scanNumber")
90  .arg(scanNum));
91  }
92 
93  return true;
94 }
95 
96 std::size_t
97 TimsFrameBase::getNbrPeaks(std::size_t scanNum) const
98 {
99  throw PappsoException(

◆ setTime()

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

Definition at line 288 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 321 of file timsframebase.cpp.

335 {
336  double v = m_timsDvStart +
337  m_timsSlope * ((double)scanNum - m_timsTtrans - m_timsNdelay);
338 
339  if(v < m_timsVmin)
340  {
342  QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
343  "calibration, v < m_timsVmin"));
344  }
345 
346 
347  if(v > m_timsVmax)
348  {
350  QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "

Member Data Documentation

◆ m_accumulationTime

double pappso::TimsFrameBase::m_accumulationTime = 0
protected

accumulation time in milliseconds

Definition at line 176 of file timsframebase.h.

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

◆ m_digitizerDelay

double pappso::TimsFrameBase::m_digitizerDelay = 0
protected

Definition at line 179 of file timsframebase.h.

Referenced by getMassSpectrumSPtr().

◆ m_digitizerTimebase

double pappso::TimsFrameBase::m_digitizerTimebase = 0
protected

Definition at line 178 of file timsframebase.h.

Referenced by getMassSpectrumSPtr().

◆ m_msMsType

quint8 pappso::TimsFrameBase::m_msMsType = 0
protected

Definition at line 185 of file timsframebase.h.

◆ m_mzCalibrationArr

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

MZ calibration parameters.

Definition at line 183 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 166 of file timsframebase.h.

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

◆ m_time

double pappso::TimsFrameBase::m_time = 0
protected

retention time

Definition at line 189 of file timsframebase.h.

◆ m_timsC6

double pappso::TimsFrameBase::m_timsC6 = 0
protected

Definition at line 199 of file timsframebase.h.

◆ m_timsC7

double pappso::TimsFrameBase::m_timsC7 = 0
protected

Definition at line 200 of file timsframebase.h.

◆ m_timsDvStart

double pappso::TimsFrameBase::m_timsDvStart = 0
protected

Definition at line 191 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 172 of file timsframebase.h.

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

◆ m_timsNdelay

double pappso::TimsFrameBase::m_timsNdelay = 0
protected

Definition at line 196 of file timsframebase.h.

◆ m_timsSlope

double pappso::TimsFrameBase::m_timsSlope
protected
Initial value:
=
0

Definition at line 192 of file timsframebase.h.

◆ m_timsTtrans

double pappso::TimsFrameBase::m_timsTtrans = 0
protected

Definition at line 195 of file timsframebase.h.

◆ m_timsVmax

double pappso::TimsFrameBase::m_timsVmax = 0
protected

Definition at line 198 of file timsframebase.h.

◆ m_timsVmin

double pappso::TimsFrameBase::m_timsVmin = 0
protected

Definition at line 197 of file timsframebase.h.


The documentation for this class was generated from the following files:
pappso::TimsFrameBase::m_digitizerTimebase
double m_digitizerTimebase
Definition: timsframebase.h:178
pappso::TimsFrameBase::getMsLevel
unsigned int getMsLevel() const
Definition: timsframebase.cpp:302
pappso::TimsFrameBase::m_timsSlope
double m_timsSlope
Definition: timsframebase.h:192
pappso::TimsFrameBase::m_timsC7
double m_timsC7
Definition: timsframebase.h:200
pappso::TimsFrameBase::setMzCalibration
void setMzCalibration(double temperature_correction, double digitizerTimebase, double digitizerDelay, double C0, double C1, double C2, double C3)
Definition: timsframebase.cpp:79
pappso::TimsFrameBase::getNbrPeaks
virtual std::size_t getNbrPeaks(std::size_t scanNum) const
Definition: timsframebase.cpp:115
pappso::TimsFrameBase::getRawIndexFromMz
quint32 getRawIndexFromMz(double mz) const
get raw index of a given m/z
Definition: timsframebase.cpp:262
pappso::TimsFrameBase::m_accumulationTime
double m_accumulationTime
accumulation time in milliseconds
Definition: timsframebase.h:176
pappso::TimsFrameBase::m_time
double m_time
retention time
Definition: timsframebase.h:189
pappso::ExceptionOutOfRange
Definition: exceptionoutofrange.h:52
pappso::TimsFrameBase::getVoltageTransformation
double getVoltageTransformation(std::size_t scanNum) const
Definition: timsframebase.cpp:352
pappso::TimsFrameBase::m_timsDvStart
double m_timsDvStart
Definition: timsframebase.h:191
pappso::TimsFrameBase::getScanNumFromOneOverK0
std::size_t getScanNumFromOneOverK0(double one_over_k0) const
get the scan number from a given 1/Ko mobility value
Definition: timsframebase.cpp:387
pappso::TimsFrameBase::setMsMsType
void setMsMsType(quint8 type)
Definition: timsframebase.cpp:294
pappso::TimsFrameBase::m_timsNdelay
double m_timsNdelay
Definition: timsframebase.h:196
pappso::TimsFrameBase::m_timsVmin
double m_timsVmin
Definition: timsframebase.h:197
pappso::TimsFrameBase::getOneOverK0Transformation
double getOneOverK0Transformation(std::size_t scanNum) const
get 1/K0 value of a given scan (mobility value)
Definition: timsframebase.cpp:380
pappso::PrecisionUnit::mz
@ mz
pappso::TimsFrameBase::m_scanNumber
quint32 m_scanNumber
total number of scans contained in this frame
Definition: timsframebase.h:166
pappso::TimsFrameBase::m_timsC6
double m_timsC6
Definition: timsframebase.h:199
pappso::TimsFrameBase::getTofFromIndex
double getTofFromIndex(quint32 index) const
get time of flight from raw index
Definition: timsframebase.cpp:148
pappso::TimsFrameBase::m_digitizerDelay
double m_digitizerDelay
Definition: timsframebase.h:179
pappso::TimsFrameBase::m_mzCalibrationArr
std::vector< double > m_mzCalibrationArr
MZ calibration parameters.
Definition: timsframebase.h:183
pappso::TimsFrameBase::m_msMsType
quint8 m_msMsType
Definition: timsframebase.h:185
pappso::TimsFrameBase::m_timsVmax
double m_timsVmax
Definition: timsframebase.h:198
pappso::TimsFrameBase::m_timsTtrans
double m_timsTtrans
Definition: timsframebase.h:195
pappso::PappsoException
Definition: pappsoexception.h:62