try to detect complementary ions and assign maximum intensity of both elements More...

#include <filtercomplementionenhancer.h>

Inheritance diagram for pappso::FilterComplementIonEnhancer:

Public Member Functions
	FilterComplementIonEnhancer (double target_mz, PrecisionPtr precision_ptr)

	FilterComplementIonEnhancer (const QualifiedMassSpectrum &qmass_spectrum, PrecisionPtr precision_ptr)

	FilterComplementIonEnhancer (const QString &strBuildParams)

	FilterComplementIonEnhancer (const FilterComplementIonEnhancer &other)

virtual	~FilterComplementIonEnhancer ()

Trace &	filter (Trace &data_points) const override

void	buildFilterFromString (const QString &strBuildParams) override
	build this filter using a string

QString	name () const override

QString	toString () const override

Public Member Functions inherited from pappso::FilterNameInterface
virtual	~FilterNameInterface ()

Public Member Functions inherited from pappso::FilterInterface
virtual	~FilterInterface ()

Private Member Functions
void	enhanceComplementMassInRange (double new_intensity, double mz_lower_bound, double mz_upper_bound, std::vector< DataPoint >::iterator it_begin, std::vector< DataPoint >::iterator it_end) const

Private Attributes
double	m_targetMzSum

PrecisionPtr	m_precisionPtr

Detailed Description

try to detect complementary ions and assign maximum intensity of both elements

experimental filter

Definition at line 46 of file filtercomplementionenhancer.h.

Constructor & Destructor Documentation

◆ FilterComplementIonEnhancer() [1/4]

FilterComplementIonEnhancer::FilterComplementIonEnhancer	(	double	target_mz,
		PrecisionPtr	precision_ptr )

Parameters

target_mz	the targeted mass of the peak pair
precision_ptr	matching precision

Definition at line 33 of file filtercomplementionenhancer.cpp.

  : m_targetMzSum(target_mz), m_precisionPtr(precision_ptr)
{
}

References m_precisionPtr, and m_targetMzSum.

Referenced by FilterComplementIonEnhancer().

◆ FilterComplementIonEnhancer() [2/4]

pappso::FilterComplementIonEnhancer::FilterComplementIonEnhancer	(	const QualifiedMassSpectrum &	qmass_spectrum,
		pappso::PrecisionPtr	precision_ptr )

Parameters

qmass_spectrum	qualified mass spectrum to compute the targeted mass of the peak pair
precision_ptr	matching precision

Definition at line 45 of file filtercomplementionenhancer.cpp.

  : m_targetMzSum(((qmass_spectrum.getPrecursorMz() -
                    (qmass_spectrum.getPrecursorCharge() * MHPLUS /
                     qmass_spectrum.getPrecursorCharge())) *
                     qmass_spectrum.getPrecursorCharge() +
                   (MHPLUS + MHPLUS))),
    m_precisionPtr(precision_ptr)
{
}

References m_precisionPtr, m_targetMzSum, and pappso::MHPLUS().

◆ FilterComplementIonEnhancer() [3/4]

pappso::FilterComplementIonEnhancer::FilterComplementIonEnhancer ( const QString & strBuildParams )

Parameters

strBuildParams string to build the filter "complementIonEnhancer|456.567;0.02dalton"

Definition at line 57 of file filtercomplementionenhancer.cpp.

{
  buildFilterFromString(strBuildParams);
}

References buildFilterFromString().

◆ FilterComplementIonEnhancer() [4/4]

FilterComplementIonEnhancer::FilterComplementIonEnhancer ( const FilterComplementIonEnhancer & other )

Copy constructor

Parameters

other TODO

Definition at line 39 of file filtercomplementionenhancer.cpp.

  : m_targetMzSum(other.m_targetMzSum), m_precisionPtr(other.m_precisionPtr)
{
}

References FilterComplementIonEnhancer(), m_precisionPtr, and m_targetMzSum.

◆ ~FilterComplementIonEnhancer()

FilterComplementIonEnhancer::~FilterComplementIonEnhancer ( )

virtual

Destructor

Definition at line 108 of file filtercomplementionenhancer.cpp.

109{

110}

Member Function Documentation

◆ buildFilterFromString()

void pappso::FilterComplementIonEnhancer::buildFilterFromString ( const QString & strBuildParams )

overridevirtual

build this filter using a string

Parameters

strBuildParams a string coding the filter and its parameters "filterName|param1;param2;param3"

Implements pappso::FilterNameInterface.

Definition at line 64 of file filtercomplementionenhancer.cpp.

{
  //"complementIonEnhancer|456.567;0.02dalton"
  if(strBuildParams.startsWith("complementIonEnhancer|"))
    {
      QStringList params = strBuildParams.split("|").back().split(";");
 
      m_targetMzSum     = params.at(0).toDouble();
      QString precision = params.at(1);
      m_precisionPtr =
        PrecisionFactory::fromString(precision.replace("dalton", " dalton")
                                       .replace("ppm", " ppm")
                                       .replace("res", " res"));
    }
  else
    {
      throw pappso::ExceptionNotRecognized(
        QString(
          "building FilterComplementIonEnhancer from string %1 is not possible")
          .arg(strBuildParams));
    }
}

References pappso::PrecisionFactory::fromString(), m_precisionPtr, and m_targetMzSum.

Referenced by FilterComplementIonEnhancer().

◆ enhanceComplementMassInRange()

void pappso::FilterComplementIonEnhancer::enhanceComplementMassInRange	(	double	new_intensity,
		double	mz_lower_bound,
		double	mz_upper_bound,
		std::vector< DataPoint >::iterator	it_begin,
		std::vector< DataPoint >::iterator	it_end ) const

private

Definition at line 138 of file filtercomplementionenhancer.cpp.

{
  for(std::vector<DataPoint>::iterator it = it_begin; it != it_end; it++)
    {
      if((it->x >= mz_lower_bound) && (it->x <= mz_upper_bound))
        {
          if(it->y < new_intensity)
            {
              it->y = new_intensity;
            }
        }
    }
}

Referenced by filter().

◆ filter()

pappso::Trace & pappso::FilterComplementIonEnhancer::filter ( pappso::Trace & data_points ) const

overridevirtual

Implements pappso::FilterInterface.

Definition at line 113 of file filtercomplementionenhancer.cpp.

{
 
  auto it_end = data_points.end();
  std::sort(data_points.begin(),
            it_end,
            [](const DataPoint &a, const DataPoint &b) { return (a.y > b.y); });
 
  for(auto it = data_points.begin(); it != it_end; it++)
    {
      double mz_complement = m_targetMzSum - it->x;
      if(mz_complement > 0)
        {
          MzRange mz_range(mz_complement, m_precisionPtr);
          enhanceComplementMassInRange(
            it->y, mz_range.lower(), mz_range.upper(), it, it_end);
        }
    }
 
  data_points.sortX();
  return data_points;
}

References pappso::a, pappso::b, enhanceComplementMassInRange(), pappso::MzRange::lower(), m_precisionPtr, m_targetMzSum, pappso::Trace::sortX(), and pappso::MzRange::upper().

◆ name()

QString pappso::FilterComplementIonEnhancer::name ( ) const

overridevirtual

Implements pappso::FilterNameInterface.

Definition at line 90 of file filtercomplementionenhancer.cpp.

{
  return "complementIonEnhancer";
}

Referenced by toString().

◆ toString()

QString pappso::FilterComplementIonEnhancer::toString ( ) const

overridevirtual

Implements pappso::FilterNameInterface.

Definition at line 97 of file filtercomplementionenhancer.cpp.

{
  QString strCode = QString("%1|%2;%3")
                      .arg(name())
                      .arg(QString::number(m_targetMzSum, 'g', 15))
                      .arg(m_precisionPtr->toString());
  strCode.replace(" ", "");
 
  return strCode;
}