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 >> &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 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 DataPoint &	maxIntensityDataPoint () const
	Find the DataPoint instance having the greatest intensity (y) value. More...
const DataPoint &	lowestIntensityDataPoint () 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< 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 Trace &	operator= (const Trace &x)
virtual Trace &	operator= (Trace &&x)
TraceSPtr	makeTraceSPtr () const
TraceCstSPtr	makeTraceCstSPtr () const
std::vector< pappso_double >	xToVector () const
std::vector< pappso_double >	yToVector () const
std::map< pappso_double, pappso_double >	toMap () const
DataPoint	containsX (pappso_double value, PrecisionPtr precision_p=nullptr) const
const DataPoint &	minYDataPoint () const
const DataPoint &	maxYDataPoint () 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	unique ()
std::vector< pappso_double >	xValues ()
std::vector< pappso_double >	yValues ()
virtual Trace &	filter (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	dataPointIteratorxWithX (pappso_double value)
std::vector< DataPoint >::const_iterator	dataPointCstIteratorxWithX (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() [1/7]

pappso::MassSpectrum::MassSpectrum

(

)

Definition at line 76 of file massspectrum.cpp.

{
}
 

MassSpectrum() [2/7]

pappso::MassSpectrum::MassSpectrum

(

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

vector

)

Definition at line 81 of file massspectrum.cpp.

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

MassSpectrum() [3/7]

pappso::MassSpectrum::MassSpectrum

(

const MapTrace &

other

)

Definition at line 91 of file massspectrum.cpp.

MassSpectrum() [4/7]

pappso::MassSpectrum::MassSpectrum

(

const Trace &

other

)

Definition at line 87 of file massspectrum.cpp.

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

MassSpectrum() [5/7]

pappso::MassSpectrum::MassSpectrum

(

Trace &&

other

)

Definition at line 96 of file massspectrum.cpp.

{
}

MassSpectrum() [6/7]

pappso::MassSpectrum::MassSpectrum

(

const MassSpectrum &

other

)

Definition at line 101 of file massspectrum.cpp.

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

MassSpectrum() [7/7]

pappso::MassSpectrum::MassSpectrum

(

MassSpectrum &&

other

)

Definition at line 107 of file massspectrum.cpp.

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

~MassSpectrum()

pappso::MassSpectrum::~MassSpectrum ( )

virtual

Definition at line 117 of file massspectrum.cpp.

Member Function Documentation

debugPrintValues()

void pappso::MassSpectrum::debugPrintValues

(

)

const

Definition at line 343 of file massspectrum.cpp.

    {
      outstream << peak;
    }
 
  return outstream;
}
 
 
QDataStream &
operator>>(QDataStream &instream, MassSpectrum &massSpectrum)
{
 
  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

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 234 of file massspectrum.cpp.

        {
          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;
}
 
 
MassSpectrum
MassSpectrum::filterSum(const MzRange &range) const
{
  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)

filterSum()

MassSpectrum pappso::MassSpectrum::filterSum

(

const MzRange &

mass_range

)

const

Definition at line 274 of file massspectrum.cpp.

        {
          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;
}
 
 
void
MassSpectrum::debugPrintValues() const
{
 
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << size();
  for(std::size_t i = 0; i < size(); i++)
    {
      qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
      qDebug() << "mz = " << this->operator[](i).x
               << ", int = " << this->operator[](i).y;
    }
 
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
 
 
QDataStream &
operator<<(QDataStream &outstream, const MassSpectrum &massSpectrum)
{

lowestIntensityDataPoint()

const DataPoint & pappso::MassSpectrum::lowestIntensityDataPoint

(

)

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 205 of file massspectrum.cpp.

makeMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::MassSpectrum::makeMassSpectrumCstSPtr

(

)

const

Definition at line 148 of file massspectrum.cpp.

References totalIonCurrent().

makeMassSpectrumSPtr()

MassSpectrumSPtr pappso::MassSpectrum::makeMassSpectrumSPtr

(

)

const

Definition at line 141 of file massspectrum.cpp.

{
  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

filter

to process the MassSpectrum

Returns

reference on the modified MassSpectrum

Definition at line 417 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 193 of file massspectrum.cpp.

{

References pappso::Trace::sortX().

operator=() [1/2]

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

virtual

Definition at line 123 of file massspectrum.cpp.

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

operator=() [2/2]

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

virtual

Definition at line 133 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 217 of file massspectrum.cpp.

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

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 174 of file massspectrum.cpp.

tic() [2/2]

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

Definition at line 181 of file massspectrum.cpp.

{

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 163 of file massspectrum.cpp.

Referenced by makeMassSpectrumCstSPtr().

---

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

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