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 &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)
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
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

Protected Member Functions
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)

Friends
class	TraceCombiner
class	TraceMinusCombiner
class	TracePlusCombiner
class	MassSpectrumCombinerInterface

Detailed Description

A simple container of DataPoint instances.

Definition at line 151 of file trace.h.

Constructor & Destructor Documentation

◆ Trace() [1/9]

pappso::Trace::Trace ( )

Definition at line 455 of file trace.cpp.

456{

457}

Referenced by pappso::MassSpectrum::MassSpectrum(), pappso::MassSpectrum::MassSpectrum(), pappso::MassSpectrum::MassSpectrum(), pappso::MassSpectrum::MassSpectrum(), pappso::MassSpectrum::MassSpectrum(), pappso::MassSpectrum::MassSpectrum(), pappso::MassSpectrum::MassSpectrum(), Trace(), Trace(), pappso::Xic::Xic(), initialize(), MassSpectrumCombinerInterface, operator=(), and operator=().

◆ Trace() [2/9]

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

Definition at line 460 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 466 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 533 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 549 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 558 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 570 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 578 of file trace.cpp.

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

References Trace().

◆ Trace() [9/9]

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

Definition at line 583 of file trace.cpp.

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

References Trace().

◆ ~Trace()

pappso::Trace::~Trace ( )

virtual

Definition at line 589 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 657 of file trace.cpp.

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

Referenced by pappso::TimsFramesMsRunReader::computeTicChromatogram(), pappso::incrementByValueX(), pappso::incrementByValueY(), initialize(), initialize(), MassSpectrumCombinerInterface, and pappso::HighResPeakPicker::pick().

◆ containsX()

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

Definition at line 802 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, 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%S 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.

Referenced by MassSpectrumCombinerInterface.

◆ dataPointCstIteratorWithX()

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

find datapoint with exactly x value

Definition at line 780 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(), and MassSpectrumCombinerInterface.

◆ dataPointIndexWithX()

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

protected

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

Definition at line 790 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().

Referenced by MassSpectrumCombinerInterface.

◆ dataPointIteratorWithX()

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

protected

Definition at line 770 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 MassSpectrumCombinerInterface.

◆ 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 1185 of file trace.cpp.

{
  return filter.filter(*this);
}

References filter().

Referenced by filter(), MassSpectrumCombinerInterface, and pappso::MassSpectrum::massSpectrumFilter().

◆ initialize() [1/5]

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

Definition at line 473 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();
 
      // Remove any parentheses and replace comma and semicolumn with space.
      // line.remove(QChar('('));
      // line.remove(QChar(')'));
 
      // line.replace(QChar(','), QChar(' '));
      // line.replace(QChar(';'), QChar(' '));
 
      qDebug() << "Now appending DataPoint as this line:" << line;
      append(DataPoint(line));
    }
 
  return size();
}

References append(), and line.

◆ initialize() [2/5]

size_t pappso::Trace::initialize	(	const QString &	x_text,
		const QString &	y_text )

Definition at line 506 of file trace.cpp.

{
  QStringList x_string_list = x_text.split("\n", Qt::SkipEmptyParts);
  QStringList y_string_list = y_text.split("\n", Qt::SkipEmptyParts);
 
  if(x_string_list.size() != y_string_list.size())
    throw ExceptionNotPossible(
      "trace.cpp -- ERROR x_text and y_text must have the same number of "
      "lines.");
 
  for(int iter = 0; iter < x_string_list.size(); ++iter)
    {
      QString x_line = x_string_list.at(iter);
      QString y_line = y_string_list.at(iter);
 
      // 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.
      x_line = x_line.simplified();
      y_line = y_line.simplified();
 
      append(DataPoint(x_line + " " + y_line));
    }
  return size();
}

References append().

◆ initialize() [3/5]

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

Definition at line 629 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() [4/5]

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

Definition at line 597 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(), Trace(), pappso::cbor::mzcbor::Spectrum::decodeTrace(), and MassSpectrumCombinerInterface.

◆ initialize() [5/5]

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

Definition at line 647 of file trace.cpp.

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

References Trace().

◆ makeTraceCstSPtr()

TraceCstSPtr pappso::Trace::makeTraceCstSPtr ( ) const

Definition at line 690 of file trace.cpp.

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

Referenced by MassSpectrumCombinerInterface.

◆ makeTraceSPtr()

TraceSPtr pappso::Trace::makeTraceSPtr ( ) const

Definition at line 683 of file trace.cpp.

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

Referenced by pappso::TimsFrameMobilityTraces::extractMobilityTraces(), and MassSpectrumCombinerInterface.

◆ maxX()

pappso_double pappso::Trace::maxX ( ) const

Definition at line 989 of file trace.cpp.

{
  return maxXDataPoint().x;
}

References maxXDataPoint(), and pappso::DataPoint::x.

Referenced by MassSpectrumCombinerInterface.

◆ maxXDataPoint()

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

Definition at line 934 of file trace.cpp.

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

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

Referenced by MassSpectrumCombinerInterface, and maxX().

◆ maxY() [1/2]

pappso_double pappso::Trace::maxY ( ) const

Definition at line 1003 of file trace.cpp.

{
  return maxYDataPoint().y;
}

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

Referenced by MassSpectrumCombinerInterface.

◆ maxY() [2/2]

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

Definition at line 1040 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 966 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(), MassSpectrumCombinerInterface, pappso::MassSpectrum::maxIntensityDataPoint(), and maxY().

◆ minX()

pappso_double pappso::Trace::minX ( ) const

Definition at line 982 of file trace.cpp.

{
  return minXDataPoint().x;
}

References minXDataPoint(), and pappso::DataPoint::x.

Referenced by MassSpectrumCombinerInterface.

◆ minXDataPoint()

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

Definition at line 918 of file trace.cpp.

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

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

Referenced by MassSpectrumCombinerInterface, and minX().

◆ minY()

pappso_double pappso::Trace::minY ( ) const

Definition at line 996 of file trace.cpp.

{
  return minYDataPoint().y;
}

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

Referenced by MassSpectrumCombinerInterface.

◆ minYDataPoint()

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

Definition at line 950 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 MassSpectrumCombinerInterface, pappso::MassSpectrum::minIntensityDataPoint(), and minY().

◆ operator=() [1/2]

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

virtual

Reimplemented in pappso::MassSpectrum, and pappso::Xic.

Definition at line 666 of file trace.cpp.

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

References Trace().

Referenced by MassSpectrumCombinerInterface.

◆ operator=() [2/2]

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

virtual

Reimplemented in pappso::MassSpectrum, and pappso::Xic.

Definition at line 675 of file trace.cpp.

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

References Trace().

◆ removeZeroYDataPoints()

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

Definition at line 1101 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().

Referenced by MassSpectrumCombinerInterface.

◆ sort()

void pappso::Trace::sort	(	Enums::SortType	sort_type,
		Enums::SortOrder	sort_order = Enums::SortOrder::ascending )

Definition at line 1058 of file trace.cpp.

{
  if(sort_type == Enums::SortType::none)
    return;
 
  if(sort_type == Enums::SortType::x)
    return sortX(sort_order);
  else
    return sortY(sort_order);
}

References pappso::Enums::none, sortX(), sortY(), and pappso::Enums::x.

Referenced by MassSpectrumCombinerInterface.

◆ sortX()

void pappso::Trace::sortX ( Enums::SortOrder sort_order = Enums::SortOrder::ascending )

Definition at line 1071 of file trace.cpp.

{
  if(sort_order == Enums::SortOrder::ascending)
    std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) { return (a.x < b.x); });
  else
    std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) { return (a.x > b.x); });
}

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

Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), Trace(), Trace(), Trace(), pappso::MsRunRetentionTime< T >::align(), pappso::TimsFrame::cumulateScansToTrace(), pappso::FilterChargeDeconvolution::filter(), pappso::FilterComplementIonEnhancer::filter(), pappso::FilterGreatestYperWindow::filter(), pappso::FilterMzExclusion::filter(), pappso::FilterPeakDelta::filter(), pappso::FilterRemoveC13::filter(), pappso::FilterTriangle::filter(), pappso::MsRunRetentionTime< T >::getCommonDeltaRt(), pappso::PsmFeatures::getIonIsotopeLinearRegression(), pappso::TimsFrameBase::getTraceFromTofIndexIntensityMap(), initialize(), MassSpectrumCombinerInterface, sort(), pappso::Xic::sortByRetentionTime(), and pappso::MassSpectrum::sortMz().

◆ sortY()

void pappso::Trace::sortY ( Enums::SortOrder sort_order = Enums::SortOrder::ascending )

Definition at line 1081 of file trace.cpp.

{
  if(sort_order == Enums::SortOrder::ascending)
    std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) { return (a.y < b.y); });
  else
    std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) { return (a.y > b.y); });
}

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

Referenced by pappso::TimsFrameMobilityTraces::extractMobilityTraces(), pappso::FilterChargeDeconvolution::filter(), pappso::FilterMzExclusion::filter(), MassSpectrumCombinerInterface, and sort().

◆ sumY() [1/2]

pappso_double pappso::Trace::sumY ( ) const

Definition at line 1010 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::DataPoint::y.

Referenced by MassSpectrumCombinerInterface, 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 1030 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().

◆ toJsonObject()

QJsonObject pappso::Trace::toJsonObject	(	const QString &	x_label = "x",
		const QString &	y_label = "y" ) const

serialize a PAPPSO trace object to JSON

Parameters

x_label	label for first dimension (x by default)
y_label	label for second dimension (y by default)

Returns: a JSON object

Definition at line 1191 of file trace.cpp.

{
  QJsonObject json_trace;
  QJsonArray x_arr;
  QJsonArray y_arr;
 
  for(auto &&data_point : *this)
    {
      x_arr.push_back(data_point.x);
      y_arr.push_back(data_point.y);
    }
  json_trace.insert(x_label, x_arr);
  json_trace.insert(y_label, y_arr);
 
  return json_trace;
}

Referenced by MassSpectrumCombinerInterface, and pappso::cbor::mzcbor::Spectrum::toJsonObject().

◆ toMap()

std::map< pappso_double, pappso_double > pappso::Trace::toMap ( ) const

Definition at line 725 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() << "It is odd that the Trace contains multiple same keys.";
 
          // No insertion, then increment the y value.
          ret.first->second += dataPoint.y;
        }
    }
 
  return map;
}

Referenced by MassSpectrumCombinerInterface.

◆ toString()

QString pappso::Trace::toString ( ) const

Definition at line 1128 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\n").arg(dataPoint.toString()));
    }
 
  return text;
}

Referenced by MassSpectrumCombinerInterface.

◆ unique()

void pappso::Trace::unique ( )

Definition at line 1091 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(), and MassSpectrumCombinerInterface.

◆ xAsBase64Encoded()

QByteArray pappso::Trace::xAsBase64Encoded ( ) const

Definition at line 1143 of file trace.cpp.

{
  QByteArray unencoded_array;
 
  for(auto &&data_point : *this)
    {
      QByteArray local_array;
      local_array.setNum(data_point.x, 'f', 12);
      local_array.append("\n");
 
      unencoded_array.append(local_array);
    }
 
  QByteArray base64_encoded_array =
    unencoded_array.toBase64(QByteArray::Base64Encoding | QByteArray::OmitTrailingEquals);
 
  return base64_encoded_array;
}

Referenced by MassSpectrumCombinerInterface.

◆ xValues()

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

Definition at line 697 of file trace.cpp.

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

Referenced by pappso::BaseTracePlotWidget::addBars(), pappso::BaseTracePlotWidget::addTrace(), MassSpectrumCombinerInterface, pappso::cbor::CborStreamWriter::writeTrace(), and pappso::masschroq::CborOutputStream::writeTrace().

◆ yAsBase64Encoded()

QByteArray pappso::Trace::yAsBase64Encoded ( ) const

Definition at line 1164 of file trace.cpp.

{
  QByteArray unencoded_array;
 
  for(auto &&data_point : *this)
    {
      QByteArray local_array;
      local_array.setNum(data_point.y, 'f', 12);
      local_array.append("\n");
 
      unencoded_array.append(local_array);
    }
 
  QByteArray base64_encoded_array =
    unencoded_array.toBase64(QByteArray::Base64Encoding | QByteArray::OmitTrailingEquals);
 
  return base64_encoded_array;
}

Referenced by MassSpectrumCombinerInterface.

◆ yValues()

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

Definition at line 711 of file trace.cpp.

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

Referenced by pappso::BaseTracePlotWidget::addBars(), pappso::BaseTracePlotWidget::addTrace(), pappso::MsRunRetentionTime< T >::align(), MassSpectrumCombinerInterface, pappso::masschroq::CborOutputStream::writeMsRunRetentionTime(), pappso::cbor::CborStreamWriter::writeTrace(), and pappso::masschroq::CborOutputStream::writeTrace().

◆ MassSpectrumCombinerInterface

friend class MassSpectrumCombinerInterface

friend

Definition at line 158 of file trace.h.

References Trace(), append(), pappso::Enums::ascending, containsX(), dataPointCstIteratorWithX(), dataPointIndexWithX(), dataPointIteratorWithX(), filter(), initialize(), makeTraceCstSPtr(), makeTraceSPtr(), MassSpectrumCombinerInterface, maxX(), maxXDataPoint(), maxY(), maxYDataPoint(), minX(), minXDataPoint(), minY(), minYDataPoint(), operator=(), removeZeroYDataPoints(), sort(), sortX(), sortY(), sumY(), toJsonObject(), toMap(), toString(), unique(), xAsBase64Encoded(), xValues(), yAsBase64Encoded(), and yValues().

Referenced by MassSpectrumCombinerInterface.

◆ TraceCombiner

friend class TraceCombiner

friend

Definition at line 154 of file trace.h.

References TraceCombiner.

Referenced by TraceCombiner.

◆ TraceMinusCombiner

friend class TraceMinusCombiner

friend

Definition at line 155 of file trace.h.

References TraceMinusCombiner.

Referenced by TraceMinusCombiner.

◆ TracePlusCombiner

friend class TracePlusCombiner

friend

Definition at line 156 of file trace.h.

References TracePlusCombiner.

Referenced by TracePlusCombiner.

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

pappsomspp/core/trace/trace.h
pappsomspp/core/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() [1/5]

◆ initialize() [2/5]

◆ initialize() [3/5]

◆ initialize() [4/5]

◆ initialize() [5/5]

◆ makeTraceCstSPtr()

◆ makeTraceSPtr()

◆ maxX()

◆ maxXDataPoint()

◆ maxY() [1/2]

◆ maxY() [2/2]

◆ maxYDataPoint()

◆ minX()

◆ minXDataPoint()

◆ minY()

◆ minYDataPoint()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ removeZeroYDataPoints()

◆ sort()

◆ sortX()

◆ sortY()

◆ sumY() [1/2]

◆ sumY() [2/2]

◆ toJsonObject()

◆ toMap()

◆ toString()

◆ unique()

◆ xAsBase64Encoded()

◆ xValues()

◆ yAsBase64Encoded()

◆ yValues()

Friends And Related Symbol Documentation

◆ MassSpectrumCombinerInterface

◆ TraceCombiner

◆ TraceMinusCombiner

◆ TracePlusCombiner