libpappsomspp
Library for mass spectrometry
pappso::Trace Class Reference

A simple container of DataPoint instances. More...

#include <trace.h>

Inheritance diagram for pappso::Trace:
pappso::MassSpectrum pappso::Xic

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 Traceoperator= (const Trace &x)
 
virtual Traceoperator= (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_doublexValues () const
 
std::vector< pappso_doubleyValues () const
 
std::map< pappso_double, pappso_doubletoMap () const
 
DataPoint containsX (pappso_double value, PrecisionPtr precision_p=nullptr) const
 
const DataPointminYDataPoint () const
 
const DataPointmaxYDataPoint () 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 Tracefilter (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() [1/8]

pappso::Trace::Trace ( )

Definition at line 444 of file trace.cpp.

445 {
446 }

◆ Trace() [2/8]

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

Definition at line 449 of file trace.cpp.

451 {
452  initialize(xVector, yVector);
453 }
size_t initialize(const std::vector< pappso_double > &xVector, const std::vector< pappso_double > &yVector)
Definition: trace.cpp:523

References initialize().

◆ Trace() [3/8]

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

Definition at line 456 of file trace.cpp.

458 {
459  reserve(dataPoints.size());
460 
461  for(auto &dataPoint : dataPoints)
462  {
463  push_back(DataPoint(dataPoint));
464  }
465 
466  sortX();
467  // std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
468  // return (a.x < b.x);
469  //});
470 }
void sortX()
Definition: trace.cpp:956

References sortX().

◆ Trace() [4/8]

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

Definition at line 473 of file trace.cpp.

474  : std::vector<DataPoint>(dataPoints)
475 {
476  sortX();
477  // std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
478  // return (a.x < b.x);
479  //});
480 }

References sortX().

◆ Trace() [5/8]

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

Definition at line 483 of file trace.cpp.

484  : std::vector<DataPoint>(std::move(dataPoints))
485 {
486  // This constructor used by the MassSpectrum && constructor.
487 
488  sortX();
489  // std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
490  // return (a.x < b.x);
491  //});
492 }

References sortX().

◆ Trace() [6/8]

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

Definition at line 495 of file trace.cpp.

496 {
497  for(auto &&item : map_trace)
498  push_back(DataPoint(item.first, item.second));
499 
500  // No need to sort, maps are sorted by key (that is, x).
501 }

◆ Trace() [7/8]

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

Definition at line 503 of file trace.cpp.

503  : std::vector<DataPoint>(other)
504 {
505 }

◆ Trace() [8/8]

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

Definition at line 508 of file trace.cpp.

509  : std::vector<DataPoint>(std::move(other))
510 {
511  // This constructor used by the MassSpectrum && constructor.
512 }

◆ ~Trace()

pappso::Trace::~Trace ( )
virtual

Definition at line 515 of file trace.cpp.

516 {
517  // Calls the destructor for each DataPoint object in the vector.
518  clear();
519 }

Member Function Documentation

◆ append()

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

appends a datapoint and return new size

Definition at line 583 of file trace.cpp.

584 {
585  push_back(data_point);
586 
587  return size();
588 }

Referenced by pappso::TimsFramesMsRunReader::computeTicChromatogram().

◆ containsX()

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

Definition at line 735 of file trace.cpp.

736 {
737  // std::cout << std::setprecision(10) << "getting value: " << value
738  //<< " and precision: " << precision_p->getNominal() << std::endl;
739 
740  pappso_double delta = precision_p->delta(value);
741 
742  double left_most = value - delta;
743  double right_most = value + delta;
744 
745  // std::cout << std::setprecision(10) << "delta: " << delta
746  //<< " left_most: " << left_most << " right_most: " << right_most
747  //<< std::endl;
748 
749  auto iterator =
750  std::find_if(begin(),
751  end(),
752  [value, precision_p, delta, left_most, right_most](
753  const DataPoint &data_point) {
754  if(precision_p)
755  {
756 
757  // FIXME: unbelievable behaviour: when building in
758  // release mode this code, under i386 (but not x86_64),
759  // this code fails if the following cout statement is
760  // missing.
761 
762  // std::cout << std::setprecision(10)
763  //<< "Testing data_point.x: " << data_point.x
764  //<< std::endl;
765 
766  // For this reason I had to deactivate the related tests
767  // for i386 in tests/test_trace.cpp
768 
769  double diff_to_left_most = data_point.x - left_most;
770  double diff_to_right_most = data_point.x - right_most;
771 
772  // std::cout << std::setprecision(10)
773  //<< "diff_to_left_most: " << diff_to_left_most
774  //<< " diff_to_right_most: " << diff_to_right_most <<
775  // std::endl;
776 
777  // if(diff_to_left_most > 0)
778  //{
779  // std::cout << std::setprecision(10)
780  //<< " point is right of left_most: " <<
781  // diff_to_left_most
782  //<< std::endl;
783  //}
784  // if(diff_to_left_most < 0)
785  //{
786  // std::cout << std::setprecision(10)
787  //<< "point is left of left_most: " << diff_to_left_most
788  //<< std::endl;
789  //}
790  // if(!diff_to_left_most)
791  //{
792  // std::cout << std::setprecision(10)
793  //<< "point is spot on left_most: " << diff_to_left_most
794  //<< std::endl;
795  //}
796 
797  // if(diff_to_right_most > 0)
798  //{
799  // std::cout << std::setprecision(10)
800  //<< "point is right of right_most: " <<
801  // diff_to_right_most
802  //<< std::endl;
803  //}
804  // if(diff_to_right_most < 0)
805  //{
806  // std::cout << std::setprecision(10)
807  //<< "point is left or of right_most: "
808  //<< diff_to_right_most << std::endl;
809  //}
810  // if(!diff_to_right_most)
811  //{
812  // std::cout << std::setprecision(10)
813  //<< "point is spot on right_most: " <<
814  // diff_to_right_most
815  //<< std::endl;
816  //}
817 
818  if(diff_to_left_most >= 0 && diff_to_right_most <= 0)
819  {
820  // std::cout << "The point is inside the range,
821  // should return true."
822  //<< std::endl;
823  return true;
824  }
825  else
826  {
827  // std::cout
828  //<< "The point is outside the range, should return
829  // false."
830  //<< std::endl;
831  return false;
832  }
833  }
834  else
835  {
836  return (data_point.x == value);
837  }
838  });
839 
840  if(iterator != end())
841  {
842  // The returned data point is valid.
843  return *iterator;
844  }
845  else
846  {
847  // The returned data point is invalid because it is not initialized.
848  return DataPoint();
849  }
850 }
double pappso_double
A type definition for doubles.
Definition: types.h:49

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 710 of file trace.cpp.

711 {
712  auto iterator =
713  std::find_if(begin(), end(), [value](const DataPoint &dataPoint) {
714  return (dataPoint.x == value);
715  });
716 
717  return iterator;
718 }

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 722 of file trace.cpp.

723 {
724  std::vector<DataPoint>::const_iterator iterator =
726 
727  if(iterator != end())
728  return std::distance(begin(), iterator);
729 
730  return std::numeric_limits<std::size_t>::max();
731 }
std::vector< DataPoint >::const_iterator dataPointCstIteratorWithX(pappso_double value) const
find datapoint with exactly x value
Definition: trace.cpp:710

References dataPointCstIteratorWithX().

◆ dataPointIteratorWithX()

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

Definition at line 698 of file trace.cpp.

699 {
700  auto iterator =
701  std::find_if(begin(), end(), [value](const DataPoint &dataPoint) {
702  return (dataPoint.x == value);
703  });
704 
705  return iterator;
706 }

References pappso::DataPoint::x.

◆ filter()

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

apply a filter on this trace

Parameters
filterto process the signal
Returns
reference on the modified Trace

Definition at line 1001 of file trace.cpp.

1002 {
1003  return filter.filter(*this);
1004 }
virtual Trace & filter(const FilterInterface &filter) final
apply a filter on this trace
Definition: trace.cpp:1001

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 556 of file trace.cpp.

557 {
558 
559  // We are initializing, not appending.
560  erase(begin(), end());
561 
562  for(auto &&item : map)
563  {
564  push_back(DataPoint(item.first, item.second));
565  }
566 
567  // No need to sort, maps are sorted by key (that is, x).
568 
569  return size();
570 }

◆ initialize() [2/3]

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

Definition at line 523 of file trace.cpp.

525 {
526  // Sanity check
527  if(xVector.size() != yVector.size())
528  throw ExceptionNotPossible(
529  "trace.cpp -- ERROR xVector and yVector must have the same size.");
530 
531  // We are initializing, not appending.
532  erase(begin(), end());
533 
534  for(std::size_t iter = 0; iter < xVector.size(); ++iter)
535  {
536  push_back(DataPoint(xVector.at(iter), yVector.at(iter)));
537  }
538 
539  sortX();
540  // std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
541  // return (a.x < b.x);
542  //});
543 
544 #if 0
545  for(auto &item : *this)
546  {
547  std::cout << item.x << "-" << item.y;
548  }
549 #endif
550 
551  return size();
552 }

References sortX().

Referenced by Trace().

◆ initialize() [3/3]

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

Definition at line 574 of file trace.cpp.

575 {
576  *this = other;
577 
578  return size();
579 }

◆ makeTraceCstSPtr()

TraceCstSPtr pappso::Trace::makeTraceCstSPtr ( ) const

Definition at line 616 of file trace.cpp.

617 {
618  return std::make_shared<const Trace>(*this);
619 }

◆ makeTraceSPtr()

TraceSPtr pappso::Trace::makeTraceSPtr ( ) const

Definition at line 609 of file trace.cpp.

610 {
611  return std::make_shared<Trace>(*this);
612 }

◆ maxY() [1/2]

pappso_double pappso::Trace::maxY ( ) const

Definition at line 899 of file trace.cpp.

900 {
901  return maxYDataPoint().y;
902 }
const DataPoint & maxYDataPoint() const
Definition: trace.cpp:873
pappso_double y
Definition: datapoint.h:24

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

◆ maxY() [2/2]

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

Definition at line 938 of file trace.cpp.

939 {
940  std::vector<DataPoint>::const_iterator begin_it =
941  findFirstEqualOrGreaterX(this->begin(), this->end(), mzStart);
942 
943  double max_y = 0;
944 
945  while(begin_it != findFirstGreaterX(begin_it, this->end(), mzEnd))
946  {
947  if(begin_it->y > max_y)
948  max_y = begin_it->y;
949  begin_it++;
950  }
951  return max_y;
952 }
std::vector< DataPoint >::iterator findFirstEqualOrGreaterX(std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value)
find the first element in which X is equal or greater than the value searched important : it implies ...
Definition: trace.cpp:69
std::vector< DataPoint >::iterator findFirstGreaterX(std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value)
find the first element in which X is greater than the value searched important : it implies that Trac...
Definition: trace.cpp:97

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

◆ maxYDataPoint()

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

Definition at line 873 of file trace.cpp.

874 {
875  auto dataPoint = std::max_element(
876  begin(), end(), [](const DataPoint &a, const DataPoint &b) {
877  return (a.y < b.y);
878  });
879 
880  if(dataPoint == end())
881  {
882  throw ExceptionOutOfRange(
883  QObject::tr("unable to get max peak intensity on spectrum size %1")
884  .arg(size()));
885  }
886 
887  return (*dataPoint);
888 }

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 892 of file trace.cpp.

893 {
894  return minYDataPoint().y;
895 }
const DataPoint & minYDataPoint() const
Definition: trace.cpp:854

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

◆ minYDataPoint()

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

Definition at line 854 of file trace.cpp.

855 {
856  auto dataPoint = std::min_element(
857  begin(), end(), [](const DataPoint &a, const DataPoint &b) {
858  return (a.y < b.y);
859  });
860 
861  if(dataPoint == end())
862  {
863  throw ExceptionOutOfRange(
864  QObject::tr("unable to get min peak intensity on spectrum size %1")
865  .arg(size()));
866  }
867 
868  return (*dataPoint);
869 }

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 592 of file trace.cpp.

593 {
594  assign(other.begin(), other.end());
595 
596  return *this;
597 }

◆ operator=() [2/2]

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

Definition at line 601 of file trace.cpp.

602 {
603  vector<DataPoint>::operator=(std::move(other));
604  return *this;
605 }

◆ sortX()

◆ sortY()

void pappso::Trace::sortY ( )

Definition at line 964 of file trace.cpp.

965 {
966  std::sort(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
967  return (a.y > b.y);
968  });
969 }

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 906 of file trace.cpp.

907 {
908  // double sum = 0;
909 
910  // for(auto &&dp : m_dataPoints)
911  // sum += dp.y;
912 
913  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()"
914  //<< "Returning sum/tic:" << sum;
915 
916  // return sum;
917 
918  return std::accumulate(begin(),
919  end(),
920  (double)0,
921  [](pappso_double sum, const DataPoint &dataPoint) {
922  return (sum + dataPoint.y);
923  });
924 }

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 928 of file trace.cpp.

929 {
930  auto begin_it = findFirstEqualOrGreaterX(this->begin(), this->end(), mzStart);
931  auto end_it = findFirstGreaterX(begin_it, this->end(), mzEnd);
932 
933  return sumYTrace(begin_it, end_it, 0);
934 }
double sumYTrace(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init)
calculate the sum of y value of a trace
Definition: trace.cpp:244

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

◆ toMap()

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

Definition at line 651 of file trace.cpp.

652 {
653  std::map<pappso_double, pappso_double> map;
654 
655  std::pair<std::map<pappso_double, pappso_double>::iterator, bool> ret;
656 
657  for(auto &&dataPoint : *this)
658  {
659  ret = map.insert(
660  std::pair<pappso_double, pappso_double>(dataPoint.x, dataPoint.y));
661 
662  if(ret.second == false)
663  {
664  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
665  << "It is odd that the Trace contains multiple same keys.";
666 
667  // No insertion, then increment the y value.
668  ret.first->second += dataPoint.y;
669  }
670  }
671 
672  return map;
673 }

◆ toString()

QString pappso::Trace::toString ( ) const

Definition at line 984 of file trace.cpp.

985 {
986  // Even if the spectrum is empty, we should return an empty string.
987  QString text;
988 
989  for(auto &&dataPoint : *this)
990  {
991  text.append(QString("%1 %2\n")
992  .arg(dataPoint.x, 0, 'f', 10)
993  .arg(dataPoint.y, 0, 'f', 10));
994  }
995 
996  return text;
997 }

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

◆ unique()

void pappso::Trace::unique ( )

Definition at line 972 of file trace.cpp.

973 {
974  auto last =
975  std::unique(begin(), end(), [](const DataPoint &a, const DataPoint &b) {
976  return (a.x == b.x);
977  });
978 
979  erase(last, end());
980 }

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 623 of file trace.cpp.

624 {
625  std::vector<pappso_double> values;
626 
627  for(auto &&dataPoint : *this)
628  {
629  values.push_back(dataPoint.x);
630  }
631 
632  return values;
633 }

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

◆ yValues()

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

Definition at line 637 of file trace.cpp.

638 {
639  std::vector<pappso_double> values;
640 
641  for(auto &&dataPoint : *this)
642  {
643  values.push_back(dataPoint.y);
644  }
645 
646  return values;
647 }

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: