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< 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

Protected Member Functions
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

Friends
class	TraceCombiner
class	TraceMinusCombiner
class	TracePlusCombiner
class	MassSpectrumCombinerInterface

Detailed Description

A simple container of DataPoint instances.

Definition at line 125 of file trace.h.

Constructor & Destructor Documentation

Trace() [1/7]

pappso::Trace::Trace

(

)

Definition at line 354 of file trace.cpp.

{
}

Trace() [2/7]

pappso::Trace::Trace

(

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

dataPoints

)

Definition at line 359 of file trace.cpp.

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

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

Trace() [3/7]

pappso::Trace::Trace

(

const std::vector< DataPoint > &

dataPoints

)

Definition at line 375 of file trace.cpp.

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

Trace() [4/7]

pappso::Trace::Trace

(

const std::vector< DataPoint > &&

dataPoints

)

Definition at line 381 of file trace.cpp.

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

Trace() [5/7]

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

explicit

Definition at line 388 of file trace.cpp.

{
  for(auto &&item : map_trace)
    push_back(DataPoint(item.first, item.second));
}

Trace() [6/7]

pappso::Trace::Trace

(

const Trace &

other

)

Definition at line 394 of file trace.cpp.

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

Trace() [7/7]

pappso::Trace::Trace

(

const Trace &&

other

)

Definition at line 399 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 405 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 607 of file trace.cpp.

{
  auto iterator = std::find_if(
    begin(), end(), [value, precision_p](const DataPoint &data_point) {
      if(precision_p)
        {
          pappso_double delta = precision_p->delta(value);
 
          if(data_point.x >= (value - delta) && data_point.x <= (value + delta))
            return true;
          else
            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::DataPoint::x.

dataPointCstIteratorxWithX()

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

protected

Definition at line 582 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 594 of file trace.cpp.

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

References dataPointCstIteratorxWithX().

dataPointIteratorxWithX()

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

protected

Definition at line 570 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 807 of file trace.cpp.

{
  return filter.filter(*this);
}

References filter().

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

initialize() [1/3]

size_t pappso::Trace::initialize

(

const std::map< pappso_double, pappso_double > &

map

)

Definition at line 441 of file trace.cpp.

{
 
  // Do not force the release of the all the vector space, because we prefer
  // resizing.  clear(false);
 
  resize(map.size());
 
  for(auto &&item : map)
    {
      push_back(DataPoint(item.first, item.second));
    }
 
  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 413 of file trace.cpp.

{
  // Sanity check
  if(xVector.size() != yVector.size())
    qFatal(
      "Fatal error at %s@%d -- %s(). "
      "xVector and yVector must have the same size."
      "Program aborted.",
      __FILE__,
      __LINE__,
      __FUNCTION__);
 
  // Do not force the release of the all the vector space, because we prefer
  // resizing.  clear();
 
  resize(xVector.size());
 
  for(std::size_t iter = 0; iter < xVector.size(); ++iter)
    {
      push_back(DataPoint(xVector.at(iter), yVector.at(iter)));
    }
 
  return size();
}

initialize() [3/3]

size_t pappso::Trace::initialize

(

const Trace &

other

)

Definition at line 459 of file trace.cpp.

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

makeTraceCstSPtr()

TraceCstSPtr pappso::Trace::makeTraceCstSPtr

(

)

const

Definition at line 492 of file trace.cpp.

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

makeTraceSPtr()

TraceSPtr pappso::Trace::makeTraceSPtr

(

)

const

Definition at line 485 of file trace.cpp.

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

maxY() [1/2]

pappso_double pappso::Trace::maxY

(

)

const

Definition at line 685 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 723 of file trace.cpp.

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

References pappso::findFirstEqualOrGreaterX().

maxYDataPoint()

const DataPoint & pappso::Trace::maxYDataPoint

(

)

const

Definition at line 659 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(), maxY(), and pappso::MassSpectrum::tic().

minY()

pappso_double pappso::Trace::minY

(

)

const

Definition at line 678 of file trace.cpp.

{
  return minYDataPoint().y;
}

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

minYDataPoint()

const DataPoint & pappso::Trace::minYDataPoint

(

)

const

Definition at line 640 of file trace.cpp.

{
  auto dataPoint = std::min_element(
    begin(), end(), [](const DataPoint &a, const DataPoint &b) {
      return (b.y < a.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 minY(), and pappso::MassSpectrum::tic().

operator=() [1/2]

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

virtual

Definition at line 468 of file trace.cpp.

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

operator=() [2/2]

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

virtual

Definition at line 477 of file trace.cpp.

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

sortX()

void pappso::Trace::sortX

(

)

Definition at line 741 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::MsRunRetentionTime< T >::align(), pappso::FilterTriangle::filter(), pappso::MsRunRetentionTime< T >::getCommonDeltaRt(), pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), pappso::MassSpectrum::maxIntensityDataPoint(), and pappso::Xic::sortByRetentionTime().

sumY() [1/2]

pappso_double pappso::Trace::sumY

(

)

const

Definition at line 692 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::makeMassSpectrumSPtr().

sumY() [2/2]

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

Definition at line 714 of file trace.cpp.

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

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

toMap()

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

(

)

const

Definition at line 523 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 790 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;
}

unique()

void pappso::Trace::unique

(

)

Definition at line 750 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().

xToVector()

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

(

)

const

Definition at line 499 of file trace.cpp.

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

Referenced by pappso::BaseTracePlotWidget::addTrace().

xValues()

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

(

)

Definition at line 762 of file trace.cpp.

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

Referenced by pappso::FilterPseudoCentroid::filter().

yToVector()

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

(

)

const

Definition at line 511 of file trace.cpp.

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

Referenced by pappso::BaseTracePlotWidget::addTrace().

yValues()

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

(

)

Definition at line 776 of file trace.cpp.

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

Referenced by pappso::FilterPseudoCentroid::filter().

Friends And Related Function Documentation

MassSpectrumCombinerInterface

friend class MassSpectrumCombinerInterface

friend

Definition at line 132 of file trace.h.

TraceCombiner

friend class TraceCombiner

friend

Definition at line 128 of file trace.h.

TraceMinusCombiner

friend class TraceMinusCombiner

friend

Definition at line 129 of file trace.h.

TracePlusCombiner

friend class TracePlusCombiner

friend

Definition at line 130 of file trace.h.

---

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

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