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
 
size_t append (const DataPoint &data_point)
 appends a datapoint and return new size More...
 
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
 
std::vector< DataPoint >::const_iterator dataPointCstIteratorWithX (pappso_double value) const
 find datapoint with exactly x value More...
 

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)
 

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 61 of file massspectrum.cpp.

62 {
63 }

◆ MassSpectrum() [2/8]

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

Definition at line 66 of file massspectrum.cpp.

68  : Trace::Trace(data_point_vector)
69 {
70 }

◆ MassSpectrum() [3/8]

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

Definition at line 72 of file massspectrum.cpp.

73  : Trace::Trace(data_point_vector)
74 {
75 }

◆ MassSpectrum() [4/8]

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

Definition at line 81 of file massspectrum.cpp.

81  : Trace(other)
82 {
83 }

◆ MassSpectrum() [5/8]

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

Definition at line 77 of file massspectrum.cpp.

77  : Trace(other)
78 {
79 }

◆ MassSpectrum() [6/8]

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

Definition at line 86 of file massspectrum.cpp.

86  : Trace(std::move(other))
87 {
88 }

◆ MassSpectrum() [7/8]

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

Definition at line 91 of file massspectrum.cpp.

91  : Trace(other)
92 {
93  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
94 }

◆ MassSpectrum() [8/8]

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

Definition at line 97 of file massspectrum.cpp.

97  : Trace(std::move(other))
98 {
99  // Specify std::move so that && reference is passed to the Trace constructor
100  // that takes std::vector<DataPoint> && as rvalue reference.
101 
102  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
103  //<< "Moving MassSpectrum::MassSpectrum(MassSpectrum &&)";
104 }

◆ ~MassSpectrum()

pappso::MassSpectrum::~MassSpectrum ( )
virtual

Definition at line 107 of file massspectrum.cpp.

108 {
109 }

Member Function Documentation

◆ debugPrintValues()

void pappso::MassSpectrum::debugPrintValues ( ) const

Definition at line 333 of file massspectrum.cpp.

334 {
335 
336  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << size();
337  for(std::size_t i = 0; i < size(); i++)
338  {
339  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
340  qDebug() << "mz = " << this->operator[](i).x
341  << ", int = " << this->operator[](i).y;
342  }
343 
344  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
345 }

◆ 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 224 of file massspectrum.cpp.

225 {
226  if(size() != other.size())
227  {
228  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
229  << "The other mass spectrum size is not equal to *this size"
230  << "*this size:" << size() << "trace size:" << other.size();
231 
232  return false;
233  }
234 
236 
237  auto trace_it = other.begin();
238 
239  for(auto &&data_point : *this)
240  {
241  qDebug() << "first:" << data_point.x << "," << data_point.y
242  << " second:" << trace_it->x << "," << trace_it->y;
243 
244  if(!MzRange(data_point.x, precision).contains(trace_it->x))
245  {
246  qDebug() << "x:" << data_point.x << " != " << trace_it->x;
247  return false;
248  }
249 
250  if(!MzRange(data_point.y, precint).contains(trace_it->y))
251  {
252  qDebug() << "y:" << data_point.y << " != " << trace_it->y;
253  return false;
254  }
255 
256  trace_it++;
257  }
258 
259  return true;
260 }
static PrecisionPtr getPpmInstance(pappso_double value)
get a ppm precision pointer
Definition: precision.cpp:150
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 264 of file massspectrum.cpp.

265 {
266  MassSpectrum massSpectrum;
267 
268  std::vector<DataPoint>::const_iterator it = begin();
269  std::vector<DataPoint>::const_iterator itEnd = end();
270 
271  std::vector<DataPoint>::const_reverse_iterator itRev = rbegin();
272  std::vector<DataPoint>::const_reverse_iterator itRevEnd = rend();
273 
274  pappso_double lower = range.lower();
275  pappso_double upper = range.upper();
276 
277  while((it != itEnd) && (it->x <= itRev->x) && (itRev != itRevEnd))
278  {
279  pappso_double sumX = it->x + itRev->x;
280 
281  if(sumX < lower)
282  {
283  it++;
284  }
285  else if(sumX > upper)
286  {
287  itRev++;
288  }
289  else
290  {
291  massSpectrum.push_back(*it);
292  massSpectrum.push_back(*itRev);
293 
294  std::vector<DataPoint>::const_reverse_iterator itRevIn = itRev;
295  itRevIn++;
296 
297  // FIXME Attention buggy code FR 20180626.
298  sumX = it->x + itRevIn->x;
299  while((sumX > lower) && (it->x <= itRevIn->x) &&
300  (itRevIn != itRevEnd))
301  {
302  sumX = it->x + itRevIn->x;
303  // trace.push_back(*it);
304  massSpectrum.push_back(*itRevIn);
305  itRevIn++;
306  }
307  it++;
308  }
309  }
310 
311  // Sort all the data points in increasing order by x
312  std::sort(massSpectrum.begin(),
313  massSpectrum.end(),
314  [](const DataPoint &a, const DataPoint &b) { return (a.x < b.x); });
315 
316  // Remove all the but the first element of a series of elements that are
317  // considered equal. Sort of deduplication.
318  std::vector<DataPoint>::iterator itEndFix =
319  std::unique(massSpectrum.begin(),
320  massSpectrum.end(),
321  [](const DataPoint &a, const DataPoint &b) {
322  // Return true if both elements should be considered equal.
323  return (a.x == b.x) && (a.y == b.y);
324  });
325 
326  massSpectrum.resize(std::distance(massSpectrum.begin(), itEndFix));
327 
328  return massSpectrum;
329 }
double pappso_double
A type definition for doubles.
Definition: types.h:49

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

◆ makeMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::MassSpectrum::makeMassSpectrumCstSPtr ( ) const

Definition at line 138 of file massspectrum.cpp.

139 {
140  return std::make_shared<const MassSpectrum>(*this);
141 }

◆ makeMassSpectrumSPtr()

MassSpectrumSPtr pappso::MassSpectrum::makeMassSpectrumSPtr ( ) const

Definition at line 131 of file massspectrum.cpp.

132 {
133  return std::make_shared<MassSpectrum>(*this);
134 }

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 407 of file massspectrum.cpp.

408 {
409  return filter.filter(*this);
410 }
virtual Trace & filter(const FilterInterface &filter) final
apply a filter on this trace
Definition: trace.cpp:1001

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 183 of file massspectrum.cpp.

184 {
185  return Trace::maxYDataPoint();
186 }
const DataPoint & maxYDataPoint() const
Definition: trace.cpp:873

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 195 of file massspectrum.cpp.

196 {
197  return Trace::minYDataPoint();
198 }
const DataPoint & minYDataPoint() const
Definition: trace.cpp:854

References pappso::Trace::minYDataPoint().

◆ operator=() [1/2]

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

Definition at line 113 of file massspectrum.cpp.

114 {
115  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
116 
117  assign(other.begin(), other.end());
118  return *this;
119 }

◆ operator=() [2/2]

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

Definition at line 123 of file massspectrum.cpp.

124 {
125  vector<DataPoint>::operator=(std::move(other));
126  return *this;
127 }

◆ 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 207 of file massspectrum.cpp.

208 {
209  Trace::sortX();
210 }
void sortX()
Definition: trace.cpp:956

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 164 of file massspectrum.cpp.

165 {
166  return totalIonCurrent();
167 }
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 171 of file massspectrum.cpp.

172 {
173  return Trace::sumY(mzStart, mzEnd);
174 }
pappso_double sumY() const
Definition: trace.cpp:906

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 153 of file massspectrum.cpp.

154 {
155  return Trace::sumY();
156 }

References pappso::Trace::sumY().

Referenced by tic().


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