pappso::MassSpectrum Class Reference

Class to represent a mass spectrum. More...

#include <massspectrum.h>

Inheritance diagram for pappso::MassSpectrum:

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 MassSpectrum &	operator= (const MassSpectrum &other)
virtual MassSpectrum &	operator= (MassSpectrum &&other)
MassSpectrumSPtr	makeMassSpectrumSPtr () const
MassSpectrumCstSPtr	makeMassSpectrumCstSPtr () const
virtual MassSpectrum &	massSpectrumFilter (const MassSpectrumFilterInterface &filter) final
	apply a filter on this MassSpectrum
pappso_double	totalIonCurrent () const
	Compute the total ion current of this mass spectrum.
pappso_double	tic () const
	Compute the total ion current of this mass spectrum.
pappso_double	tic (double mzStart, double mzEnd)
const DataPoint &	maxIntensityDataPoint () const
	Find the DataPoint instance having the greatest intensity (y) value.
const DataPoint &	minIntensityDataPoint () const
	Find the DataPoint instance having the smallest intensity (y) value.
void	sortMz ()
	Sort the DataPoint instances of this spectrum.
bool	equals (const MassSpectrum &other, PrecisionPtr precision) const
	Tells if this MassSpectrum is equal to massSpectrum.
MassSpectrum	filterSum (const MzRange &mass_range) const
void	debugPrintValues () const
virtual Trace &	operator= (const Trace &x)
virtual Trace &	operator= (Trace &&x)
Public Member Functions inherited from pappso::Trace
	Trace ()
	Trace (const QString &text)
	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 QString &x_text, const QString &y_text)
size_t	initialize (const QString &space_sep_text)
size_t	initialize (const Trace &other)
size_t	initialize (const std::map< pappso_double, pappso_double > &map)
TraceSPtr	makeTraceSPtr () const
TraceCstSPtr	makeTraceCstSPtr () const
size_t	append (const DataPoint &data_point)
	appends a datapoint and return new size
std::vector< pappso_double >	xValues () const
std::vector< pappso_double >	yValues () const
std::map< pappso_double, pappso_double >	toMap () const
DataPoint	containsX (pappso_double value, PrecisionPtr precision_p=nullptr) const
const DataPoint &	minXDataPoint () const
const DataPoint &	maxXDataPoint () const
const DataPoint &	minYDataPoint () const
const DataPoint &	maxYDataPoint () const
pappso_double	minX () const
pappso_double	maxX () 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	sort (Enums::SortType sort_type, Enums::SortOrder sort_order=Enums::SortOrder::ascending)
void	sortX (Enums::SortOrder sort_order=Enums::SortOrder::ascending)
void	sortY (Enums::SortOrder sort_order=Enums::SortOrder::ascending)
void	unique ()
std::size_t	removeZeroYDataPoints ()
virtual Trace &	filter (const FilterInterface &filter) final
	apply a filter on this trace
QString	toString () const
QJsonObject	toJsonObject (const QString &x_label="x", const QString &y_label="y") const
	serialize a PAPPSO trace object to JSON
QByteArray	xAsBase64Encoded () const
QByteArray	yAsBase64Encoded () const
std::vector< DataPoint >::const_iterator	dataPointCstIteratorWithX (pappso_double value) const
	find datapoint with exactly x value

Additional Inherited Members
Protected Member Functions inherited from pappso::Trace
std::size_t	dataPointIndexWithX (pappso_double value) const
	Return a reference to the DataPoint instance that has its x member equal to value.
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 69 of file massspectrum.h.

Constructor & Destructor Documentation

MassSpectrum() [1/8]

pappso::MassSpectrum::MassSpectrum

(

)

Definition at line 59 of file massspectrum.cpp.

{
}

Referenced by MassSpectrum(), MassSpectrum(), equals(), filterSum(), operator=(), and operator=().

MassSpectrum() [2/8]

pappso::MassSpectrum::MassSpectrum

(

std::vector< std::pair< pappso_double, pappso_double > > &

data_point_vector

)

Definition at line 64 of file massspectrum.cpp.

  : Trace::Trace(data_point_vector)
{
}

References pappso::Trace::Trace().

MassSpectrum() [3/8]

pappso::MassSpectrum::MassSpectrum

(

std::vector< DataPoint > &

data_point_vector

)

Definition at line 69 of file massspectrum.cpp.

  : Trace::Trace(data_point_vector)
{
}

References pappso::Trace::Trace().

MassSpectrum() [4/8]

pappso::MassSpectrum::MassSpectrum

(

const MapTrace &

other

)

Definition at line 78 of file massspectrum.cpp.

                                                : Trace(other)
{
}

References pappso::Trace::Trace().

MassSpectrum() [5/8]

pappso::MassSpectrum::MassSpectrum

(

const Trace &

other

)

Definition at line 74 of file massspectrum.cpp.

                                             : Trace(other)
{
}

References pappso::Trace::Trace().

MassSpectrum() [6/8]

pappso::MassSpectrum::MassSpectrum

(

Trace &&

other

)

Definition at line 83 of file massspectrum.cpp.

                                        : Trace(std::move(other))
{
}

References pappso::Trace::Trace().

MassSpectrum() [7/8]

pappso::MassSpectrum::MassSpectrum

(

const MassSpectrum &

other

)

Definition at line 88 of file massspectrum.cpp.

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

References MassSpectrum(), and pappso::Trace::Trace().

MassSpectrum() [8/8]

pappso::MassSpectrum::MassSpectrum

(

MassSpectrum &&

other

)

Definition at line 94 of file massspectrum.cpp.

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

References MassSpectrum(), and pappso::Trace::Trace().

~MassSpectrum()

pappso::MassSpectrum::~MassSpectrum ( )

virtual

Definition at line 104 of file massspectrum.cpp.

{
}

Member Function Documentation

debugPrintValues()

void pappso::MassSpectrum::debugPrintValues

(

)

const

Definition at line 327 of file massspectrum.cpp.

{
 
  qDebug() << size();
  for(std::size_t i = 0; i < size(); i++)
    {
      qDebug() << "(" << this->operator[](i).x << "," << this->operator[](i).y << ")";
    }
}

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

massSpectrum	Mass spectrum to compare to this.
precision	Precision 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 221 of file massspectrum.cpp.

{
  if(size() != other.size())
    {
      qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
               << "The other mass spectrum size is not equal to *this size"
               << "*this size:" << size() << "trace size:" << other.size();
 
      return false;
    }
 
  PrecisionPtr precint = PrecisionFactory::getPpmInstance(10);
 
  auto trace_it = other.begin();
 
  for(auto &&data_point : *this)
    {
      qDebug() << "first:" << data_point.x << "," << data_point.y << " second:" << trace_it->x
               << "," << trace_it->y;
 
      if(!MzRange(data_point.x, precision).contains(trace_it->x))
        {
          qDebug() << "x:" << data_point.x << " != " << trace_it->x;
          return false;
        }
 
      if(!MzRange(data_point.y, precint).contains(trace_it->y))
        {
          qDebug() << "y:" << data_point.y << " != " << trace_it->y;
          return false;
        }
 
      trace_it++;
    }
 
  return true;
}

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

filterSum()

MassSpectrum pappso::MassSpectrum::filterSum

(

const MzRange &

mass_range

)

const

Definition at line 261 of file massspectrum.cpp.

{
  MassSpectrum massSpectrum;
 
  std::vector<DataPoint>::const_iterator it    = begin();
  std::vector<DataPoint>::const_iterator itEnd = end();
 
  std::vector<DataPoint>::const_reverse_iterator itRev    = rbegin();
  std::vector<DataPoint>::const_reverse_iterator itRevEnd = rend();
 
  pappso_double lower = range.lower();
  pappso_double upper = range.upper();
 
  while((it != itEnd) && (it->x <= itRev->x) && (itRev != itRevEnd))
    {
      pappso_double sumX = it->x + itRev->x;
 
      if(sumX < lower)
        {
          ++it;
        }
      else if(sumX > upper)
        {
            ++itRev;
        }
      else
        {
          massSpectrum.push_back(*it);
          massSpectrum.push_back(*itRev);
 
          std::vector<DataPoint>::const_reverse_iterator itRevIn = itRev;
          ++itRevIn;
 
          // FIXME Attention buggy code FR 20180626.
          sumX = it->x + itRevIn->x;
          while((sumX > lower) && (it->x <= itRevIn->x) && (itRevIn != itRevEnd))
            {
              sumX = it->x + itRevIn->x;
              // trace.push_back(*it);
              massSpectrum.push_back(*itRevIn);
              ++itRevIn;
            }
            ++it;
        }
    }
 
  // Sort all the data points in increasing order by x
  std::sort(massSpectrum.begin(), massSpectrum.end(), [](const DataPoint &a, const DataPoint &b) {
    return (a.x < b.x);
  });
 
  // Remove all the but the first element of a series of elements that are
  // considered equal. Sort of deduplication.
  std::vector<DataPoint>::iterator itEndFix = std::unique(
    massSpectrum.begin(), massSpectrum.end(), [](const DataPoint &a, const DataPoint &b) {
      // Return true if both elements should be considered equal.
      return (a.x == b.x) && (a.y == b.y);
    });
 
  massSpectrum.resize(std::distance(massSpectrum.begin(), itEndFix));
 
  return massSpectrum;
}

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

makeMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::MassSpectrum::makeMassSpectrumCstSPtr

(

)

const

Definition at line 135 of file massspectrum.cpp.

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

makeMassSpectrumSPtr()

MassSpectrumSPtr pappso::MassSpectrum::makeMassSpectrumSPtr

(

)

const

Definition at line 128 of file massspectrum.cpp.

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

Referenced by pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::cbor::psm::PsmFileReaderBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), and pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel().

massSpectrumFilter()

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

finalvirtual

apply a filter on this MassSpectrum

Parameters

filter

to process the MassSpectrum

Returns

reference on the modified MassSpectrum

Definition at line 394 of file massspectrum.cpp.

{
  return filter.filter(*this);
}

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 180 of file massspectrum.cpp.

{
  return Trace::maxYDataPoint();
}

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 192 of file massspectrum.cpp.

{
  return Trace::minYDataPoint();
}

References pappso::Trace::minYDataPoint().

operator=() [1/4]

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

virtual

Definition at line 110 of file massspectrum.cpp.

{
  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
 
  assign(other.begin(), other.end());
  return *this;
}

References MassSpectrum().

operator=() [2/4]

Trace & pappso::Trace::operator= ( const Trace & x )

virtual

Reimplemented from pappso::Trace.

Definition at line 182 of file trace.cpp.

{
  assign(other.begin(), other.end());
 
  return *this;
}

operator=() [3/4]

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

virtual

Definition at line 120 of file massspectrum.cpp.

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

References MassSpectrum().

operator=() [4/4]

Trace & pappso::Trace::operator= ( Trace && x )

virtual

Reimplemented from pappso::Trace.

Definition at line 183 of file trace.cpp.

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

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 204 of file massspectrum.cpp.

{
  Trace::sortX();
}

References pappso::Trace::sortX().

Referenced by pappso::MzIntegrationParams::createDataBasedBins(), pappso::MzIntegrationParams::createDataBasedBinsOld(), 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 161 of file massspectrum.cpp.

{
  return totalIonCurrent();
}

References totalIonCurrent().

tic() [2/2]

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

Definition at line 168 of file massspectrum.cpp.

{
  return Trace::sumY(mzStart, mzEnd);
}

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 150 of file massspectrum.cpp.

{
  return Trace::sumY();
}

References pappso::Trace::sumY().

Referenced by tic().

---

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

• pappsomspp/core/massspectrum/massspectrum.h
• pappsomspp/core/massspectrum/massspectrum.cpp