pappso::FilterComplementIonEnhancer Class Reference

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 44 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 55 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 101 of file filtercomplementionenhancer.cpp.

{
}

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 61 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 130 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 106 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 83 of file filtercomplementionenhancer.cpp.

{
  return "complementIonEnhancer";
}

Referenced by toString().

toString()

QString pappso::FilterComplementIonEnhancer::toString ( ) const

overridevirtual

Implements pappso::FilterNameInterface.

Definition at line 90 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;
}

References m_precisionPtr, m_targetMzSum, and name().

Member Data Documentation

m_precisionPtr

PrecisionPtr pappso::FilterComplementIonEnhancer::m_precisionPtr

private

Definition at line 99 of file filtercomplementionenhancer.h.

Referenced by FilterComplementIonEnhancer(), FilterComplementIonEnhancer(), FilterComplementIonEnhancer(), buildFilterFromString(), filter(), and toString().

m_targetMzSum

double pappso::FilterComplementIonEnhancer::m_targetMzSum

private

Definition at line 98 of file filtercomplementionenhancer.h.

Referenced by FilterComplementIonEnhancer(), FilterComplementIonEnhancer(), FilterComplementIonEnhancer(), buildFilterFromString(), filter(), and toString().

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

• pappsomspp/core/processing/filters/filtercomplementionenhancer.h
• pappsomspp/core/processing/filters/filtercomplementionenhancer.cpp