A simple container of DataPoint instances. More...

#include <trace.h>

Inheritance diagram for pappso::Trace:

Public Member Functions
	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 space_sep_text)

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

size_t	append (const DataPoint &data_point)
	appends a datapoint and return new size More...

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 ()

std::size_t	removeZeroYDataPoints ()

virtual Trace &	filter (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...

Protected Member Functions
std::size_t	dataPointIndexWithX (pappso_double value) const

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

Friends
class	TraceCombiner

class	TraceMinusCombiner

class	TracePlusCombiner

class	MassSpectrumCombinerInterface

Detailed Description

A simple container of DataPoint instances.

Definition at line 147 of file trace.h.

Constructor & Destructor Documentation

◆ Trace() [1/9]

pappso::Trace::Trace ( )

Definition at line 444 of file trace.cpp.

445{

446}

◆ Trace() [2/9]

pappso::Trace::Trace ( const QString & text )

Definition at line 449 of file trace.cpp.

{
  initialize(text);
}

References initialize().

◆ Trace() [3/9]

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

Definition at line 455 of file trace.cpp.

{
  initialize(xVector, yVector);
}

References initialize().

◆ Trace() [4/9]

pappso::Trace::Trace ( const std::vector< std::pair< pappso_double, pappso_double > > & dataPoints )

Definition at line 488 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() [5/9]

pappso::Trace::Trace ( const std::vector< DataPoint > & dataPoints )

Definition at line 505 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() [6/9]

pappso::Trace::Trace ( const std::vector< DataPoint > && dataPoints )

Definition at line 515 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() [7/9]

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

explicit

Definition at line 527 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() [8/9]

pappso::Trace::Trace ( const Trace & other )

Definition at line 535 of file trace.cpp.

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

◆ Trace() [9/9]

pappso::Trace::Trace ( const Trace && other )

Definition at line 540 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 546 of file trace.cpp.

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

Member Function Documentation

◆ append()

size_t pappso::Trace::append ( const DataPoint & data_point )

appends a datapoint and return new size

Definition at line 614 of file trace.cpp.

{
  push_back(data_point);
 
  return size();
}

Referenced by pappso::TimsFramesMsRunReader::computeTicChromatogram(), and initialize().

◆ containsX()

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

Definition at line 766 of file trace.cpp.

{
  // std::cout << std::setprecision(10) << "getting value: " << value
  //<< " and precision: " << precision_p->getNominal() << std::endl;
 
  pappso_double delta = precision_p->delta(value);
 
  double left_most  = value - delta;
  double right_most = value + delta;
 
  // std::cout << std::setprecision(10) << "delta: " << delta
  //<< " left_most: " << left_most << " right_most: " << right_most
  //<< std::endl;
 
  auto iterator =
    std::find_if(begin(),
                 end(),
                 [value, precision_p, delta, left_most, right_most](
                   const DataPoint &data_point) {
                   if(precision_p)
                     {
 
                       // FIXME: unbelievable behaviour: when building in
                       // release mode this code, under i386 (but not x86_64),
                       // this code fails if the following cout statement is
                       // missing.
 
                       // std::cout << std::setprecision(10)
                       //<< "Testing data_point.x: " << data_point.x
                       //<< std::endl;
 
                       // For this reason I had to deactivate the related tests
                       // for i386 in tests/test_trace.cpp
 
                       double diff_to_left_most  = data_point.x - left_most;
                       double diff_to_right_most = data_point.x - right_most;
 
                       // std::cout << std::setprecision(10)
                       //<< "diff_to_left_most: " << diff_to_left_most
                       //<< " diff_to_right_most: " << diff_to_right_most <<
                       // std::endl;
 
                       // if(diff_to_left_most > 0)
                       //{
                       // std::cout << std::setprecision(10)
                       //<< " point is right of left_most: " <<
                       // diff_to_left_most
                       //<< std::endl;
                       //}
                       // if(diff_to_left_most < 0)
                       //{
                       // std::cout << std::setprecision(10)
                       //<< "point is left of left_most: " << diff_to_left_most
                       //<< std::endl;
                       //}
                       // if(!diff_to_left_most)
                       //{
                       // std::cout << std::setprecision(10)
                       //<< "point is spot on left_most: " << diff_to_left_most
                       //<< std::endl;
                       //}
 
                       // if(diff_to_right_most > 0)
                       //{
                       // std::cout << std::setprecision(10)
                       //<< "point is right of right_most: " <<
                       // diff_to_right_most
                       //<< std::endl;
                       //}
                       // if(diff_to_right_most < 0)
                       //{
                       // std::cout << std::setprecision(10)
                       //<< "point is left or of right_most: "
                       //<< diff_to_right_most << std::endl;
                       //}
                       // if(!diff_to_right_most)
                       //{
                       // std::cout << std::setprecision(10)
                       //<< "point is spot on right_most: " <<
                       // diff_to_right_most
                       //<< std::endl;
                       //}
 
                       if(diff_to_left_most >= 0 && diff_to_right_most <= 0)
                         {
                           // std::cout << "The point is inside the range,
                           // should return true."
                           //<< std::endl;
                           return true;
                         }
                       else
                         {
                           // std::cout
                           //<< "The point is outside the range, should return
                           // false."
                           //<< std::endl;
                           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

find datapoint with exactly x value

Definition at line 741 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 753 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 729 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 1059 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() [1/4]

size_t pappso::Trace::initialize ( const QString space_sep_text )

Definition at line 463 of file trace.cpp.

{
  QStringList string_list = space_sep_text.split("\n", Qt::SkipEmptyParts);
 
  //qDebug() << "Split text into" << string_list.size()
           //<< "substrings:" << string_list;
  ;
 
  for(int iter = 0; iter < string_list.size(); ++iter)
    {
      QString line = string_list.at(iter);
      //qDebug() << "Now processing line:" << line;
 
      // Returns a string that has whitespace removed from the start and the
      // end, and that has each sequence of internal whitespace replaced with a
      // single space.
      line = line.simplified();
 
      append(DataPoint(line));
    }
 
  return size();
}

References append(), and line.

◆ initialize() [2/4]

size_t pappso::Trace::initialize ( const std::map< pappso_double, pappso_double > & map )

Definition at line 587 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() [3/4]

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

Definition at line 554 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() [4/4]

size_t pappso::Trace::initialize ( const Trace & other )

Definition at line 605 of file trace.cpp.

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

◆ makeTraceCstSPtr()

TraceCstSPtr pappso::Trace::makeTraceCstSPtr ( ) const

Definition at line 647 of file trace.cpp.

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

◆ makeTraceSPtr()

TraceSPtr pappso::Trace::makeTraceSPtr ( ) const

Definition at line 640 of file trace.cpp.

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

◆ maxY() [1/2]

pappso_double pappso::Trace::maxY ( ) const

Definition at line 930 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 969 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 904 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 923 of file trace.cpp.

{
  return minYDataPoint().y;
}

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

◆ minYDataPoint()

const DataPoint & pappso::Trace::minYDataPoint ( ) const

Definition at line 885 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 623 of file trace.cpp.

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

◆ operator=() [2/2]

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

virtual

Definition at line 632 of file trace.cpp.

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

◆ removeZeroYDataPoints()

std::size_t pappso::Trace::removeZeroYDataPoints ( )

Definition at line 1015 of file trace.cpp.

{
  qDebug();
 
  auto it     = begin();
  auto end_it = end();
 
  std::size_t count = 0;
 
  while(it != end_it)
    {
      if(Utils::almostEqual(it->y, 0))
        {
          // erase returns an iterator to the next item in the vector.
          it = erase(it);
          ++count;
        }
      else
        // We need to increment (no call to erase here).
        ++it;
    }
 
  return count;
}

References pappso::Utils::almostEqual().

◆ sortX()

void pappso::Trace::sortX ( )

Definition at line 987 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 995 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 937 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::PsmFeatures::setPeptideSpectrumCharge(), pappso::MassSpectrum::tic(), and pappso::MassSpectrum::totalIonCurrent().

◆ sumY() [2/2]

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

Definition at line 959 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 682 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 1042 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 1003 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 654 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().

◆ yValues()

std::vector< pappso_double > pappso::Trace::yValues ( ) const

Definition at line 668 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(), and pappso::MsRunRetentionTime< T >::align().

Friends And Related Function Documentation

◆ MassSpectrumCombinerInterface

friend class MassSpectrumCombinerInterface

friend

Definition at line 154 of file trace.h.

◆ TraceCombiner

friend class TraceCombiner

friend

Definition at line 150 of file trace.h.

◆ TraceMinusCombiner

friend class TraceMinusCombiner

friend

Definition at line 151 of file trace.h.

◆ TracePlusCombiner

friend class TracePlusCombiner

friend

Definition at line 152 of file trace.h.

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

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

Public Member Functions

Protected Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Trace() [1/9]

◆ Trace() [2/9]

◆ Trace() [3/9]

◆ Trace() [4/9]

◆ Trace() [5/9]

◆ Trace() [6/9]

◆ Trace() [7/9]

◆ Trace() [8/9]

◆ Trace() [9/9]

◆ ~Trace()

Member Function Documentation

◆ append()

◆ containsX()

◆ dataPointCstIteratorWithX()

◆ dataPointIndexWithX()

◆ dataPointIteratorWithX()

◆ filter()

◆ initialize() [1/4]

◆ initialize() [2/4]

◆ initialize() [3/4]

◆ initialize() [4/4]

◆ makeTraceCstSPtr()

◆ makeTraceSPtr()

◆ maxY() [1/2]

◆ maxY() [2/2]

◆ maxYDataPoint()

◆ minY()

◆ minYDataPoint()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ removeZeroYDataPoints()

◆ sortX()

◆ sortY()

◆ sumY() [1/2]

◆ sumY() [2/2]

◆ toMap()

◆ toString()

◆ unique()

◆ xValues()

◆ yValues()

Friends And Related Function Documentation

◆ MassSpectrumCombinerInterface

◆ TraceCombiner

◆ TraceMinusCombiner

◆ TracePlusCombiner