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 70 of file massspectrum.h.

Constructor & Destructor Documentation

◆ MassSpectrum() [1/8]

pappso::MassSpectrum::MassSpectrum ( )

Definition at line 55 of file massspectrum.cpp.

56 {
57 }

◆ MassSpectrum() [2/8]

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

Definition at line 60 of file massspectrum.cpp.

62  : Trace::Trace(data_point_vector)
63 {
64 }

◆ MassSpectrum() [3/8]

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

Definition at line 66 of file massspectrum.cpp.

67  : Trace::Trace(data_point_vector)
68 {
69 }

◆ MassSpectrum() [4/8]

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

Definition at line 75 of file massspectrum.cpp.

75  : Trace(other)
76 {
77 }

◆ MassSpectrum() [5/8]

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

Definition at line 71 of file massspectrum.cpp.

71  : Trace(other)
72 {
73 }

◆ MassSpectrum() [6/8]

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

Definition at line 80 of file massspectrum.cpp.

80  : Trace(std::move(other))
81 {
82 }

◆ MassSpectrum() [7/8]

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

Definition at line 85 of file massspectrum.cpp.

85  : Trace(other)
86 {
87  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
88 }

◆ MassSpectrum() [8/8]

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

Definition at line 91 of file massspectrum.cpp.

91  : Trace(std::move(other))
92 {
93  // Specify std::move so that && reference is passed to the Trace constructor
94  // that takes std::vector<DataPoint> && as rvalue reference.
95 
96  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
97  //<< "Moving MassSpectrum::MassSpectrum(MassSpectrum &&)";
98 }

◆ ~MassSpectrum()

pappso::MassSpectrum::~MassSpectrum ( )
virtual

Definition at line 101 of file massspectrum.cpp.

102 {
103 }

Member Function Documentation

◆ debugPrintValues()

void pappso::MassSpectrum::debugPrintValues ( ) const

Definition at line 327 of file massspectrum.cpp.

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 }

◆ 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 218 of file massspectrum.cpp.

219 {
220  if(size() != other.size())
221  {
222  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
223  << "The other mass spectrum size is not equal to *this size"
224  << "*this size:" << size() << "trace size:" << other.size();
225 
226  return false;
227  }
228 
230 
231  auto trace_it = other.begin();
232 
233  for(auto &&data_point : *this)
234  {
235  qDebug() << "first:" << data_point.x << "," << data_point.y
236  << " second:" << trace_it->x << "," << trace_it->y;
237 
238  if(!MzRange(data_point.x, precision).contains(trace_it->x))
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 }
static PrecisionPtr getPpmInstance(pappso_double value)
get a ppm precision pointer
Definition: precision.cpp:149
const PrecisionBase * PrecisionPtr
Definition: precision.h:122

References pappso::MzRange::contains(), and pappso::PrecisionFactory::getPpmInstance().

◆ filterSum()

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

Definition at line 258 of file massspectrum.cpp.

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)
276  {
277  it++;
278  }
279  else if(sumX > upper)
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 }
double pappso_double
A type definition for doubles.
Definition: types.h:48

References pappso::a, pappso::b, pappso::MzRange::lower(), and pappso::MzRange::upper().

◆ makeMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::MassSpectrum::makeMassSpectrumCstSPtr ( ) const

Definition at line 132 of file massspectrum.cpp.

133 {
134  return std::make_shared<const MassSpectrum>(*this);
135 }

◆ makeMassSpectrumSPtr()

MassSpectrumSPtr pappso::MassSpectrum::makeMassSpectrumSPtr ( ) const

Definition at line 125 of file massspectrum.cpp.

126 {
127  return std::make_shared<MassSpectrum>(*this);
128 }

Referenced by pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and 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 401 of file massspectrum.cpp.

402 {
403  return filter.filter(*this);
404 }
virtual Trace & filter(const FilterInterface &filter) final
apply a filter on this trace
Definition: trace.cpp:923

References pappso::Trace::filter().

Referenced by pappso::XtandemSpectrumProcess::process().

◆ 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 177 of file massspectrum.cpp.

178 {
179  return Trace::maxYDataPoint();
180 }
const DataPoint & maxYDataPoint() const
Definition: trace.cpp:795

References pappso::Trace::maxYDataPoint().

◆ 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 189 of file massspectrum.cpp.

190 {
191  return Trace::minYDataPoint();
192 }
const DataPoint & minYDataPoint() const
Definition: trace.cpp:776

References pappso::Trace::minYDataPoint().

◆ operator=() [1/2]

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

Definition at line 107 of file massspectrum.cpp.

108 {
109  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
110 
111  assign(other.begin(), other.end());
112  return *this;
113 }

◆ operator=() [2/2]

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

Definition at line 117 of file massspectrum.cpp.

118 {
119  vector<DataPoint>::operator=(std::move(other));
120  return *this;
121 }

◆ 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 201 of file massspectrum.cpp.

202 {
203  Trace::sortX();
204 }
void sortX()
Definition: trace.cpp:878

References pappso::Trace::sortX().

Referenced by pappso::MzIntegrationParams::createDataBasedBins(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().

◆ 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 158 of file massspectrum.cpp.

159 {
160  return totalIonCurrent();
161 }
pappso_double totalIonCurrent() const
Compute the total ion current of this mass spectrum.

References totalIonCurrent().

◆ tic() [2/2]

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

Definition at line 165 of file massspectrum.cpp.

166 {
167  return Trace::sumY(mzStart, mzEnd);
168 }
pappso_double sumY() const
Definition: trace.cpp:828

References pappso::Trace::sumY().

◆ 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 147 of file massspectrum.cpp.

148 {
149  return Trace::sumY();
150 }

References pappso::Trace::sumY().

Referenced by tic().


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