pappso::Trace Class Reference

A simple container of DataPoint instances. More...

#include <trace.h>

Inheritance diagram for pappso::Trace:

Public Member Functions
	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 Trace &	operator= (const Trace &x)
virtual Trace &	operator= (Trace &&x)
TraceSPtr	makeTraceSPtr () const
TraceCstSPtr	makeTraceCstSPtr () const
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 &	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	sortY ()
void	unique ()
virtual Trace &	filter (const FilterInterface &filter) final
	apply a filter on this trace More...
QString	toString () const

Protected Member Functions
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

Friends
class	TraceCombiner
class	TraceMinusCombiner
class	TracePlusCombiner
class	MassSpectrumCombinerInterface

Detailed Description

A simple container of DataPoint instances.

Definition at line 131 of file trace.h.

Constructor & Destructor Documentation

Trace() [1/8]

pappso::Trace::Trace

(

)

Definition at line 375 of file trace.cpp.

{
}

Trace() [2/8]

pappso::Trace::Trace	(	const std::vector< pappso_double > &	xVector,
		const std::vector< pappso_double > &	yVector
	)

Definition at line 380 of file trace.cpp.

{
  initialize(xVector, yVector);
}

References initialize().

Trace() [3/8]

pappso::Trace::Trace

(

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

dataPoints

)

Definition at line 387 of file trace.cpp.

{
  reserve(dataPoints.size());
 
  for(auto &dataPoint : dataPoints)
    {
      push_back(DataPoint(dataPoint));
    }
 
  sortX();
  // std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
  // return (a.x < b.x);
  //});
}

References sortX().

Trace() [4/8]

pappso::Trace::Trace

(

const std::vector< DataPoint > &

dataPoints

)

Definition at line 404 of file trace.cpp.

  : std::vector<DataPoint>(dataPoints)
{
  sortX();
  // std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
  // return (a.x < b.x);
  //});
}

References sortX().

Trace() [5/8]

pappso::Trace::Trace

(

const std::vector< DataPoint > &&

dataPoints

)

Definition at line 414 of file trace.cpp.

  : std::vector<DataPoint>(std::move(dataPoints))
{
  // This constructor used by the MassSpectrum && constructor.
 
  sortX();
  // std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
  // return (a.x < b.x);
  //});
}

References sortX().

Trace() [6/8]

pappso::Trace::Trace ( const MapTrace &  map_trace )

explicit

Definition at line 426 of file trace.cpp.

{
  for(auto &&item : map_trace)
    push_back(DataPoint(item.first, item.second));
 
  // No need to sort, maps are sorted by key (that is, x).
}

Trace() [7/8]

pappso::Trace::Trace

(

const Trace &

other

)

Definition at line 434 of file trace.cpp.

                               : std::vector<DataPoint>(other)
{
}

Trace() [8/8]

pappso::Trace::Trace

(

const Trace &&

other

)

Definition at line 439 of file trace.cpp.

                                : std::vector<DataPoint>(std::move(other))
{
  // This constructor used by the MassSpectrum && constructor.
}

~Trace()

pappso::Trace::~Trace ( )

virtual

Definition at line 445 of file trace.cpp.

{
  // Calls the destructor for each DataPoint object in the vector.
  clear();
}

Member Function Documentation

containsX()

DataPoint pappso::Trace::containsX	(	pappso_double	value,
		PrecisionPtr	precision_p = nullptr
	)		const

Definition at line 656 of file trace.cpp.

{
  //qDebug() << qSetRealNumberPrecision(10) << "getting value:" << value
           //<< "and precision:" << precision_p->getNominal();
 
  pappso_double delta = precision_p->delta(value);
 
  double left_most  = value - delta;
  double right_most = value + delta;
 
  //qDebug() << qSetRealNumberPrecision(10) << "delta:" << delta
           //<< "left_most:" << left_most << "right_most:" << right_most;
 
  auto iterator = std::find_if(
    begin(),
    end(),
    [value, precision_p, delta, left_most, right_most](
      const DataPoint &data_point) {
      if(precision_p)
        {
          //qDebug() << qSetRealNumberPrecision(10)
                   //<< "Testing data_point.x:" << data_point.x;
 
          double diff_to_left_most = data_point.x - left_most;
 
          double diff_to_right_most = data_point.x - right_most;
 
          //qDebug() << qSetRealNumberPrecision(10)
                   //<< "diff_to_left_most:" << diff_to_left_most
                   //<< "diff_to_right_most:" << diff_to_right_most;
 
          //if(diff_to_left_most > 0)
            //{
              //qDebug() << qSetRealNumberPrecision(10)
                       //<< "point is right of left_most:" << diff_to_left_most;
            //}
          //if(diff_to_left_most < 0)
            //{
              //qDebug() << qSetRealNumberPrecision(10)
                       //<< "point is left of left_most:" << diff_to_left_most;
            //}
          //if(!diff_to_left_most)
            //{
              //qDebug() << qSetRealNumberPrecision(10)
                       //<< "point is spot on left_most:" << diff_to_left_most;
            //}
 
          //if(diff_to_right_most > 0)
            //{
              //qDebug() << qSetRealNumberPrecision(10)
                       //<< "point is right of right_most:" << diff_to_right_most;
            //}
          //if(diff_to_right_most < 0)
            //{
              //qDebug() << qSetRealNumberPrecision(10)
                       //<< "point is left or of right_most:"
                       //<< diff_to_right_most;
            //}
          //if(!diff_to_right_most)
            //{
              //qDebug() << qSetRealNumberPrecision(10)
                       //<< "point is spot on right_most:" << diff_to_right_most;
            //}
 
          if(diff_to_left_most >= 0 && diff_to_right_most <= 0)
            {
              //qDebug() << "The point is inside the range, should return true.";
              return true;
            }
          else
            {
              //qDebug()
                //<< "The point is outside the range, should return false.";
              return false;
            }
        }
      else
        {
          return (data_point.x == value);
        }
    });
 
  if(iterator != end())
    {
      // The returned data point is valid.
      return *iterator;
    }
  else
    {
      // The returned data point is invalid because it is not initialized.
      return DataPoint();
    }
}

References pappso::PrecisionBase::delta(), and pappso::DataPoint::x.

dataPointCstIteratorWithX()

std::vector< DataPoint >::const_iterator pappso::Trace::dataPointCstIteratorWithX ( pappso_double  value ) const

protected

Definition at line 631 of file trace.cpp.

{
  auto iterator =
    std::find_if(begin(), end(), [value](const DataPoint &dataPoint) {
      return (dataPoint.x == value);
    });
 
  return iterator;
}

References pappso::DataPoint::x.

Referenced by dataPointIndexWithX().

dataPointIndexWithX()

std::size_t pappso::Trace::dataPointIndexWithX ( pappso_double  value ) const

protected

Return a reference to the DataPoint instance that has its y member equal to value.

Definition at line 643 of file trace.cpp.

{
  std::vector<DataPoint>::const_iterator iterator =
    dataPointCstIteratorWithX(value);
 
  if(iterator != end())
    return std::distance(begin(), iterator);
 
  return std::numeric_limits<std::size_t>::max();
}

References dataPointCstIteratorWithX().

dataPointIteratorWithX()

std::vector< DataPoint >::iterator pappso::Trace::dataPointIteratorWithX ( pappso_double  value )

protected

Definition at line 619 of file trace.cpp.

{
  auto iterator =
    std::find_if(begin(), end(), [value](const DataPoint &dataPoint) {
      return (dataPoint.x == value);
    });
 
  return iterator;
}

References pappso::DataPoint::x.

filter()

Trace & pappso::Trace::filter ( const FilterInterface &  filter )

finalvirtual

apply a filter on this trace

Parameters

filter

to process the signal

Returns

reference on the modified Trace

Definition at line 899 of file trace.cpp.

{
  return filter.filter(*this);
}

References filter().

Referenced by pappso::MsRunRetentionTime< T >::align(), filter(), pappso::FilterSuiteString::filter(), pappso::FilterSuite::filter(), and pappso::MassSpectrum::massSpectrumFilter().

initialize() [1/3]

size_t pappso::Trace::initialize

(

const std::map< pappso_double, pappso_double > &

map

)

Definition at line 486 of file trace.cpp.

{
 
  // We are initializing, not appending.
  erase(begin(), end());
 
  for(auto &&item : map)
    {
      push_back(DataPoint(item.first, item.second));
    }
 
  // No need to sort, maps are sorted by key (that is, x).
 
  return size();
}

initialize() [2/3]

size_t pappso::Trace::initialize	(	const std::vector< pappso_double > &	xVector,
		const std::vector< pappso_double > &	yVector
	)

Definition at line 453 of file trace.cpp.

{
  // Sanity check
  if(xVector.size() != yVector.size())
    throw ExceptionNotPossible(
      "trace.cpp -- ERROR xVector and yVector must have the same size.");
 
  // We are initializing, not appending.
  erase(begin(), end());
 
  for(std::size_t iter = 0; iter < xVector.size(); ++iter)
    {
      push_back(DataPoint(xVector.at(iter), yVector.at(iter)));
    }
 
  sortX();
  // std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
  // return (a.x < b.x);
  //});
 
#if 0
  for(auto &item : *this)
  {
    std::cout << item.x << "-" << item.y;
  }
#endif
 
  return size();
}

References sortX().

Referenced by Trace().

initialize() [3/3]

size_t pappso::Trace::initialize

(

const Trace &

other

)

Definition at line 504 of file trace.cpp.

{
  *this = other;
 
  return size();
}

makeTraceCstSPtr()

TraceCstSPtr pappso::Trace::makeTraceCstSPtr

(

)

const

Definition at line 537 of file trace.cpp.

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

makeTraceSPtr()

TraceSPtr pappso::Trace::makeTraceSPtr

(

)

const

Definition at line 530 of file trace.cpp.

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

maxY() [1/2]

pappso_double pappso::Trace::maxY

(

)

const

Definition at line 797 of file trace.cpp.

{
  return maxYDataPoint().y;
}

References maxYDataPoint(), and pappso::DataPoint::y.

maxY() [2/2]

pappso_double pappso::Trace::maxY	(	double	mzStart,
		double	mzEnd
	)		const

Definition at line 836 of file trace.cpp.

{
  std::vector<DataPoint>::const_iterator begin_it =
    findFirstEqualOrGreaterX(this->begin(), this->end(), mzStart);
 
  double max_y = 0;
 
  while(begin_it != findFirstGreaterX(begin_it, this->end(), mzEnd))
    {
      if(begin_it->y > max_y)
        max_y = begin_it->y;
      begin_it++;
    }
  return max_y;
}

References pappso::findFirstEqualOrGreaterX(), and pappso::findFirstGreaterX().

maxYDataPoint()

const DataPoint & pappso::Trace::maxYDataPoint

(

)

const

Definition at line 771 of file trace.cpp.

{
  auto dataPoint = std::max_element(
    begin(), end(), [](const DataPoint &a, const DataPoint &b) {
      return (a.y < b.y);
    });
 
  if(dataPoint == end())
    {
      throw ExceptionOutOfRange(
        QObject::tr("unable to get max peak intensity on spectrum size %1")
          .arg(size()));
    }
 
  return (*dataPoint);
}

References pappso::a, and pappso::b.

Referenced by pappso::flooredLocalMaxima(), pappso::MassSpectrum::maxIntensityDataPoint(), and maxY().

minY()

pappso_double pappso::Trace::minY

(

)

const

Definition at line 790 of file trace.cpp.

{
  return minYDataPoint().y;
}

References minYDataPoint(), and pappso::DataPoint::y.

minYDataPoint()

const DataPoint & pappso::Trace::minYDataPoint

(

)

const

Definition at line 752 of file trace.cpp.

{
  auto dataPoint = std::min_element(
    begin(), end(), [](const DataPoint &a, const DataPoint &b) {
      return (a.y < b.y);
    });
 
  if(dataPoint == end())
    {
      throw ExceptionOutOfRange(
        QObject::tr("unable to get min peak intensity on spectrum size %1")
          .arg(size()));
    }
 
  return (*dataPoint);
}

References pappso::a, and pappso::b.

Referenced by pappso::MassSpectrum::minIntensityDataPoint(), and minY().

operator=() [1/2]

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

virtual

Definition at line 513 of file trace.cpp.

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

operator=() [2/2]

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

virtual

Definition at line 522 of file trace.cpp.

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

sortX()

void pappso::Trace::sortX

(

)

Definition at line 854 of file trace.cpp.

{
  std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
    return (a.x < b.x);
  });
}

References pappso::a, and pappso::b.

Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), Trace(), pappso::MsRunRetentionTime< T >::align(), pappso::TimsFrame::cumulateScanToTrace(), pappso::FilterChargeDeconvolution::filter(), pappso::FilterComplementIonEnhancer::filter(), pappso::FilterMzExclusion::filter(), pappso::FilterGreatestYperWindow::filter(), pappso::FilterRemoveC13::filter(), pappso::FilterTriangle::filter(), pappso::MsRunRetentionTime< T >::getCommonDeltaRt(), pappso::TimsFrameBase::getTraceFromCumulatedScans(), pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid(), initialize(), pappso::Xic::sortByRetentionTime(), and pappso::MassSpectrum::sortMz().

sortY()

void pappso::Trace::sortY

(

)

Definition at line 862 of file trace.cpp.

{
  std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
    return (a.y > b.y);
  });
}

References pappso::a, and pappso::b.

Referenced by pappso::FilterChargeDeconvolution::filter(), and pappso::FilterMzExclusion::filter().

sumY() [1/2]

pappso_double pappso::Trace::sumY

(

)

const

Definition at line 804 of file trace.cpp.

{
  // double sum = 0;
 
  // for(auto &&dp : m_dataPoints)
  // sum += dp.y;
 
  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()"
  //<< "Returning sum/tic:" << sum;
 
  // return sum;
 
  return std::accumulate(begin(),
                         end(),
                         (double)0,
                         [](pappso_double sum, const DataPoint &dataPoint) {
                           return (sum + dataPoint.y);
                         });
}

References pappso::sum, and pappso::DataPoint::y.

Referenced by pappso::MassSpectrum::tic(), and pappso::MassSpectrum::totalIonCurrent().

sumY() [2/2]

pappso_double pappso::Trace::sumY	(	double	mzStart,
		double	mzEnd
	)		const

Definition at line 826 of file trace.cpp.

{
  auto begin_it = findFirstEqualOrGreaterX(this->begin(), this->end(), mzStart);
  auto end_it   = findFirstGreaterX(begin_it, this->end(), mzEnd);
 
  return sumYTrace(begin_it, end_it, 0);
}

References pappso::findFirstEqualOrGreaterX(), pappso::findFirstGreaterX(), and pappso::sumYTrace().

toMap()

std::map< pappso_double, pappso_double > pappso::Trace::toMap

(

)

const

Definition at line 572 of file trace.cpp.

{
  std::map<pappso_double, pappso_double> map;
 
  std::pair<std::map<pappso_double, pappso_double>::iterator, bool> ret;
 
  for(auto &&dataPoint : *this)
    {
      ret = map.insert(
        std::pair<pappso_double, pappso_double>(dataPoint.x, dataPoint.y));
 
      if(ret.second == false)
        {
          qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
                   << "It is odd that the Trace contains multiple same keys.";
 
          // No insertion, then increment the y value.
          ret.first->second += dataPoint.y;
        }
    }
 
  return map;
}

toString()

QString pappso::Trace::toString

(

)

const

Definition at line 882 of file trace.cpp.

{
  // Even if the spectrum is empty, we should return an empty string.
  QString text;
 
  for(auto &&dataPoint : *this)
    {
      text.append(QString("%1 %2\n")
                    .arg(dataPoint.x, 0, 'f', 10)
                    .arg(dataPoint.y, 0, 'f', 10));
    }
 
  return text;
}

Referenced by pappso::FilterSuiteString::filter(), and pappso::FilterSuiteString::toString().

unique()

void pappso::Trace::unique

(

)

Definition at line 870 of file trace.cpp.

{
  auto last =
    std::unique(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
      return (a.x == b.x);
    });
 
  erase(last, end());
}

References pappso::a, pappso::b, and pappso::last.

Referenced by pappso::MsRunRetentionTime< T >::getCommonDeltaRt().

xValues()

std::vector< pappso_double > pappso::Trace::xValues

(

)

const

Definition at line 544 of file trace.cpp.

{
  std::vector<pappso_double> values;
 
  for(auto &&dataPoint : *this)
    {
      values.push_back(dataPoint.x);
    }
 
  return values;
}

Referenced by pappso::BaseTracePlotWidget::addTrace(), and pappso::FilterPseudoCentroid::filter().

yValues()

std::vector< pappso_double > pappso::Trace::yValues

(

)

const

Definition at line 558 of file trace.cpp.

{
  std::vector<pappso_double> values;
 
  for(auto &&dataPoint : *this)
    {
      values.push_back(dataPoint.y);
    }
 
  return values;
}

Referenced by pappso::BaseTracePlotWidget::addTrace(), pappso::MsRunRetentionTime< T >::align(), and pappso::FilterPseudoCentroid::filter().

Friends And Related Function Documentation

MassSpectrumCombinerInterface

friend class MassSpectrumCombinerInterface

friend

Definition at line 138 of file trace.h.

TraceCombiner

friend class TraceCombiner

friend

Definition at line 134 of file trace.h.

TraceMinusCombiner

friend class TraceMinusCombiner

friend

Definition at line 135 of file trace.h.

TracePlusCombiner

friend class TracePlusCombiner

friend

Definition at line 136 of file trace.h.

---

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

• pappsomspp/trace/trace.h
• pappsomspp/trace/trace.cpp