libpappsomspp
Library for mass spectrometry
pappso::MassSpectrum Class Reference

Class to represent a mass spectrum. More...

#include <massspectrum.h>

Inheritance diagram for pappso::MassSpectrum:
pappso::Trace

Public Member Functions

 MassSpectrum ()
 
 MassSpectrum (std::vector< std::pair< pappso_double, pappso_double >> &data_point_vector)
 
 MassSpectrum (std::vector< DataPoint > &data_point_vector)
 
 MassSpectrum (const MapTrace &other)
 
 MassSpectrum (const Trace &other)
 
 MassSpectrum (Trace &&other)
 
 MassSpectrum (const MassSpectrum &other)
 
 MassSpectrum (MassSpectrum &&other)
 
virtual ~MassSpectrum ()
 
virtual MassSpectrumoperator= (const MassSpectrum &other)
 
virtual MassSpectrumoperator= (MassSpectrum &&other)
 
MassSpectrumSPtr makeMassSpectrumSPtr () const
 
MassSpectrumCstSPtr makeMassSpectrumCstSPtr () const
 
virtual MassSpectrummassSpectrumFilter (const MassSpectrumFilterInterface &filter) final
 apply a filter on this MassSpectrum More...
 
pappso_double totalIonCurrent () const
 Compute the total ion current of this mass spectrum. More...
 
pappso_double tic () const
 Compute the total ion current of this mass spectrum. More...
 
pappso_double tic (double mzStart, double mzEnd)
 
const DataPointmaxIntensityDataPoint () const
 Find the DataPoint instance having the greatest intensity (y) value. More...
 
const DataPointminIntensityDataPoint () const
 Find the DataPoint instance having the smallest intensity (y) value. More...
 
void sortMz ()
 Sort the DataPoint instances of this spectrum. More...
 
bool equals (const MassSpectrum &other, PrecisionPtr precision) const
 Tells if this MassSpectrum is equal to massSpectrum. More...
 
MassSpectrum filterSum (const MzRange &mass_range) const
 
void debugPrintValues () const
 
- Public Member Functions inherited from pappso::Trace
 Trace ()
 
 Trace (const std::vector< pappso_double > &xVector, const std::vector< pappso_double > &yVector)
 
 Trace (const std::vector< std::pair< pappso_double, pappso_double >> &dataPoints)
 
 Trace (const std::vector< DataPoint > &dataPoints)
 
 Trace (const std::vector< DataPoint > &&dataPoints)
 
 Trace (const MapTrace &map_trace)
 
 Trace (const Trace &other)
 
 Trace (const Trace &&other)
 
virtual ~Trace ()
 
size_t initialize (const std::vector< pappso_double > &xVector, const std::vector< pappso_double > &yVector)
 
size_t initialize (const Trace &other)
 
size_t initialize (const std::map< pappso_double, pappso_double > &map)
 
virtual Traceoperator= (const Trace &x)
 
virtual Traceoperator= (Trace &&x)
 
TraceSPtr makeTraceSPtr () const
 
TraceCstSPtr makeTraceCstSPtr () const
 
std::vector< pappso_doublexValues () const
 
std::vector< pappso_doubleyValues () const
 
std::map< pappso_double, pappso_doubletoMap () const
 
DataPoint containsX (pappso_double value, PrecisionPtr precision_p=nullptr) const
 
const DataPointminYDataPoint () const
 
const DataPointmaxYDataPoint () const
 
pappso_double minY () const
 
pappso_double maxY () const
 
pappso_double maxY (double mzStart, double mzEnd) const
 
pappso_double sumY () const
 
pappso_double sumY (double mzStart, double mzEnd) const
 
void sortX ()
 
void sortY ()
 
void unique ()
 
virtual Tracefilter (const FilterInterface &filter) final
 apply a filter on this trace More...
 
QString toString () const
 

Additional Inherited Members

- Protected Member Functions inherited from pappso::Trace
std::size_t dataPointIndexWithX (pappso_double value) const
 
std::vector< DataPoint >::iterator dataPointIteratorWithX (pappso_double value)
 
std::vector< DataPoint >::const_iterator dataPointCstIteratorWithX (pappso_double value) const
 

Detailed Description

Class to represent a mass spectrum.

A mass spectrum is a collection of DataPoint instances. Moreover, it has internal data that represent the context of the acquisition of the data: retention time and drift time (if the experiment was an ion mobility mass spectrometry experiment).

A MassSpectrum cannot perform combinations. For combination of mass spectra, the class to use is MassSpectrumCombinator.

Definition at line 91 of file massspectrum.h.

Constructor & Destructor Documentation

◆ MassSpectrum() [1/8]

pappso::MassSpectrum::MassSpectrum ( )

Definition at line 76 of file massspectrum.cpp.

76 {
77 }
78 

◆ MassSpectrum() [2/8]

pappso::MassSpectrum::MassSpectrum ( std::vector< std::pair< pappso_double, pappso_double >> &  data_point_vector)

Definition at line 81 of file massspectrum.cpp.

81 {
82 }
83 
84 
85 MassSpectrum::MassSpectrum(const MassSpectrum &other) : Trace(other)

◆ MassSpectrum() [3/8]

pappso::MassSpectrum::MassSpectrum ( std::vector< DataPoint > &  data_point_vector)

Definition at line 87 of file massspectrum.cpp.

◆ MassSpectrum() [4/8]

pappso::MassSpectrum::MassSpectrum ( const MapTrace other)

Definition at line 96 of file massspectrum.cpp.

◆ MassSpectrum() [5/8]

pappso::MassSpectrum::MassSpectrum ( const Trace other)

Definition at line 92 of file massspectrum.cpp.

92 {
93  // Specify std::move so that && reference is passed to the Trace constructor
94  // that takes std::vector<DataPoint> && as rvalue reference.

◆ MassSpectrum() [6/8]

pappso::MassSpectrum::MassSpectrum ( Trace &&  other)

Definition at line 101 of file massspectrum.cpp.

102 {
103 }

◆ MassSpectrum() [7/8]

pappso::MassSpectrum::MassSpectrum ( const MassSpectrum other)

Definition at line 106 of file massspectrum.cpp.

108 {
109  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";

◆ MassSpectrum() [8/8]

pappso::MassSpectrum::MassSpectrum ( MassSpectrum &&  other)

Definition at line 112 of file massspectrum.cpp.

118 {
119  vector<DataPoint>::operator=(std::move(other));

◆ ~MassSpectrum()

pappso::MassSpectrum::~MassSpectrum ( )
virtual

Definition at line 122 of file massspectrum.cpp.

Member Function Documentation

◆ debugPrintValues()

void pappso::MassSpectrum::debugPrintValues ( ) const

Definition at line 348 of file massspectrum.cpp.

348  {
349  outstream << peak;
350  }
351 
352  return outstream;
353 }
354 
355 
356 QDataStream &
357 operator>>(QDataStream &instream, MassSpectrum &massSpectrum)
358 {
359 
360  quint32 vector_size;

◆ equals()

bool pappso::MassSpectrum::equals ( const MassSpectrum other,
PrecisionPtr  precision 
) const

Tells if this MassSpectrum is equal to massSpectrum.

To compare this to massSpectrum, a tolerance is applied to both the x and y values, that is defined using precision.

Parameters
massSpectrumMass spectrum to compare to this.
precisionPrecision to be used to perform the comparison of the x and y values of the data points in this and \massSpectrum mass spectra.

Definition at line 239 of file massspectrum.cpp.

239  {
240  qDebug() << "x:" << data_point.x << " != " << trace_it->x;
241  return false;
242  }
243 
244  if(!MzRange(data_point.y, precint).contains(trace_it->y))
245  {
246  qDebug() << "y:" << data_point.y << " != " << trace_it->y;
247  return false;
248  }
249 
250  trace_it++;
251  }
252 
253  return true;
254 }
255 
256 
258 MassSpectrum::filterSum(const MzRange &range) const
259 {
260  MassSpectrum massSpectrum;
261 
262  std::vector<DataPoint>::const_iterator it = begin();
263  std::vector<DataPoint>::const_iterator itEnd = end();
264 
265  std::vector<DataPoint>::const_reverse_iterator itRev = rbegin();
266  std::vector<DataPoint>::const_reverse_iterator itRevEnd = rend();
267 
268  pappso_double lower = range.lower();
269  pappso_double upper = range.upper();
270 
271  while((it != itEnd) && (it->x <= itRev->x) && (itRev != itRevEnd))
272  {
273  pappso_double sumX = it->x + itRev->x;
274 
275  if(sumX < lower)

◆ filterSum()

MassSpectrum pappso::MassSpectrum::filterSum ( const MzRange mass_range) const

Definition at line 279 of file massspectrum.cpp.

280  {
281  itRev++;
282  }
283  else
284  {
285  massSpectrum.push_back(*it);
286  massSpectrum.push_back(*itRev);
287 
288  std::vector<DataPoint>::const_reverse_iterator itRevIn = itRev;
289  itRevIn++;
290 
291  // FIXME Attention buggy code FR 20180626.
292  sumX = it->x + itRevIn->x;
293  while((sumX > lower) && (it->x <= itRevIn->x) &&
294  (itRevIn != itRevEnd))
295  {
296  sumX = it->x + itRevIn->x;
297  // trace.push_back(*it);
298  massSpectrum.push_back(*itRevIn);
299  itRevIn++;
300  }
301  it++;
302  }
303  }
304 
305  // Sort all the data points in increasing order by x
306  std::sort(massSpectrum.begin(),
307  massSpectrum.end(),
308  [](const DataPoint &a, const DataPoint &b) { return (a.x < b.x); });
309 
310  // Remove all the but the first element of a series of elements that are
311  // considered equal. Sort of deduplication.
312  std::vector<DataPoint>::iterator itEndFix =
313  std::unique(massSpectrum.begin(),
314  massSpectrum.end(),
315  [](const DataPoint &a, const DataPoint &b) {
316  // Return true if both elements should be considered equal.
317  return (a.x == b.x) && (a.y == b.y);
318  });
319 
320  massSpectrum.resize(std::distance(massSpectrum.begin(), itEndFix));
321 
322  return massSpectrum;
323 }
324 
325 
326 void
328 {
329 
330  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << size();
331  for(std::size_t i = 0; i < size(); i++)
332  {
333  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
334  qDebug() << "mz = " << this->operator[](i).x
335  << ", int = " << this->operator[](i).y;
336  }
337 
338  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
339 }
340 
341 
342 QDataStream &
343 operator<<(QDataStream &outstream, const MassSpectrum &massSpectrum)
344 {

◆ makeMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::MassSpectrum::makeMassSpectrumCstSPtr ( ) const

Definition at line 153 of file massspectrum.cpp.

References totalIonCurrent().

◆ makeMassSpectrumSPtr()

MassSpectrumSPtr pappso::MassSpectrum::makeMassSpectrumSPtr ( ) const

Definition at line 146 of file massspectrum.cpp.

148 {
149  return Trace::sumY();

References pappso::Trace::sumY().

Referenced by pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().

◆ massSpectrumFilter()

MassSpectrum & pappso::MassSpectrum::massSpectrumFilter ( const MassSpectrumFilterInterface filter)
finalvirtual

apply a filter on this MassSpectrum

Parameters
filterto process the MassSpectrum
Returns
reference on the modified MassSpectrum

Definition at line 422 of file massspectrum.cpp.

◆ maxIntensityDataPoint()

const DataPoint & pappso::MassSpectrum::maxIntensityDataPoint ( ) const

Find the DataPoint instance having the greatest intensity (y) value.

Returns
<const DataPoint &> The data point having the maximum intensity (y) value of the whole mass spectrum.

Definition at line 198 of file massspectrum.cpp.

202 {

References pappso::Trace::sortX().

◆ minIntensityDataPoint()

const DataPoint & pappso::MassSpectrum::minIntensityDataPoint ( ) const

Find the DataPoint instance having the smallest intensity (y) value.

Returns
<const DataPoint &> The data point having the minimum intensity (y) value of the whole mass spectrum.

Definition at line 210 of file massspectrum.cpp.

◆ operator=() [1/2]

MassSpectrum & pappso::MassSpectrum::operator= ( const MassSpectrum other)
virtual

Definition at line 128 of file massspectrum.cpp.

133 {
134  return std::make_shared<const MassSpectrum>(*this);

◆ operator=() [2/2]

MassSpectrum & pappso::MassSpectrum::operator= ( MassSpectrum &&  other)
virtual

Definition at line 138 of file massspectrum.cpp.

◆ sortMz()

void pappso::MassSpectrum::sortMz ( )

Sort the DataPoint instances of this spectrum.

The DataPoint instances are sorted according to the x value (the m/z value) and in increasing order.

Definition at line 222 of file massspectrum.cpp.

224  :" << size() << "trace size:" << other.size();
225 

◆ tic() [1/2]

pappso_double pappso::MassSpectrum::tic ( ) const

Compute the total ion current of this mass spectrum.

Convenience function that returns totalIonCurrent();

Definition at line 179 of file massspectrum.cpp.

◆ tic() [2/2]

pappso_double pappso::MassSpectrum::tic ( double  mzStart,
double  mzEnd 
)

Definition at line 186 of file massspectrum.cpp.

190 {

References pappso::Trace::minYDataPoint().

◆ totalIonCurrent()

pappso_double pappso::MassSpectrum::totalIonCurrent ( ) const

Compute the total ion current of this mass spectrum.

The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass massSpectrum or in a specified m/z range of a mass massSpectrum. MS:1000285

Returns
<pappso_double> The total ion current.

Definition at line 168 of file massspectrum.cpp.

Referenced by makeMassSpectrumCstSPtr().


The documentation for this class was generated from the following files:
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:69
pappso::Trace::Trace
Trace()
Definition: trace.cpp:375
pappso::MassSpectrum::debugPrintValues
void debugPrintValues() const
Definition: massspectrum.cpp:348
pappso::MassSpectrum::MassSpectrum
MassSpectrum()
Definition: massspectrum.cpp:76
pappso::MassSpectrum::filterSum
MassSpectrum filterSum(const MzRange &mass_range) const
Definition: massspectrum.cpp:279
pappso::Trace::sumY
pappso_double sumY() const
Definition: trace.cpp:741
pappso::operator>>
QDataStream & operator>>(QDataStream &instream, MassSpectrum &massSpectrum)
Definition: massspectrum.cpp:378
pappso::operator<<
QDataStream & operator<<(QDataStream &outstream, const MassSpectrum &massSpectrum)
Definition: massspectrum.cpp:364