#include <xtandemspectrumprocess.h>

Public Member Functions
	XtandemSpectrumProcess ()

	XtandemSpectrumProcess (const XtandemSpectrumProcess &copy)

	~XtandemSpectrumProcess ()

MassSpectrum	process (const MassSpectrum &spectrum, pappso_double parent_ion_mass, unsigned int parent_charge) const
	process raw spectrum to prepare hyperscore computation

void	setMinimumMz (pappso_double minimum_mz)

void	setNmostIntense (unsigned int nmost_intense)

void	setDynamicRange (pappso::pappso_double dynamic_range)

void	setRemoveIsotope (bool remove_isotope)

void	setExcludeParent (bool exclude_parent)

void	setExcludeParentNeutralLoss (bool neutral_loss)

void	setNeutralLossMass (pappso::pappso_double neutral_loss_mass)

void	setNeutralLossWindowDalton (pappso::pappso_double neutral_loss_precision)

void	setRefineSpectrumModel (bool refine)

void	setIonScore (Enums::PeptideIon ion_type, bool compute_score)

pappso_double	getMinimumMz () const

unsigned int	getNmostIntense () const

pappso::pappso_double	getDynamicRange () const

bool	getRemoveIsotope () const

bool	getExcludeParent () const

bool	getExcludeParentNeutralLoss () const

pappso::pappso_double	getNeutralLossMass () const

pappso::pappso_double	getNeutralLossWindowDalton () const

bool	getRefineSpectrumModel () const

bool	getIonScore (Enums::PeptideIon ion_type) const

Private Attributes
FilterResampleKeepGreater	m_filter_keep_greater

FilterGreatestY	m_n_most_intense

FilterRescaleY	m_filter_rescale

FilterTandemDeisotope	m_filter_remove_c13 = FilterTandemDeisotope(1.5, 200)

FilterFloorY	m_filter_floor

FilterHighPass	m_filter_highpass

bool	m_isRemoveIsotope = true

bool	m_isExcludeParent = false

pappso::pappso_double	m_isExcludeParent_lower_dalton = 2

pappso::pappso_double	m_isExcludeParent_upper_dalton = 2

bool	m_isExcludeParent_neutral_loss = false

pappso::pappso_double	m_neutralLossMass = MASSH2O

pappso::pappso_double	m_neutralLossWindowDalton = 0.5

bool	m_isRefineSpectrumModel = true

bool	_y_ions = true

bool	_ystar_ions = false

bool	_b_ions = true

bool	_bstar_ions = false

bool	_c_ions = false

bool	_z_ions = false

bool	_a_ions = false

bool	_x_ions = false

bool	_astar_ions = false

bool	_ao_ions = false

bool	_bo_ions = false

bool	_yo_ions = false

Detailed Description

Definition at line 41 of file xtandemspectrumprocess.h.

Constructor & Destructor Documentation

◆ XtandemSpectrumProcess() [1/2]

pappso::XtandemSpectrumProcess::XtandemSpectrumProcess ( )

Definition at line 37 of file xtandemspectrumprocess.cpp.

  : m_filter_keep_greater(150), m_n_most_intense(100), m_filter_rescale(100), m_filter_highpass(0.9)
{
}

References m_filter_highpass, m_filter_keep_greater, m_filter_rescale, and m_n_most_intense.

Referenced by XtandemSpectrumProcess().

◆ XtandemSpectrumProcess() [2/2]

pappso::XtandemSpectrumProcess::XtandemSpectrumProcess ( const XtandemSpectrumProcess & copy )

Definition at line 42 of file xtandemspectrumprocess.cpp.

  : m_filter_keep_greater(copy.m_filter_keep_greater),
    m_n_most_intense(copy.m_n_most_intense),
    m_filter_rescale(copy.m_filter_rescale),
    m_filter_highpass(copy.m_filter_highpass)
{
  m_isRemoveIsotope              = copy.m_isRemoveIsotope;
  m_isExcludeParent_neutral_loss = copy.m_isExcludeParent_neutral_loss;
  m_neutralLossMass              = copy.m_neutralLossMass;
  m_neutralLossWindowDalton      = copy.m_neutralLossWindowDalton;
 
  m_isExcludeParent              = copy.m_isExcludeParent;
  m_isExcludeParent_lower_dalton = copy.m_isExcludeParent_lower_dalton;
  m_isExcludeParent_upper_dalton = copy.m_isExcludeParent_upper_dalton;
  m_isRefineSpectrumModel        = copy.m_isRefineSpectrumModel;
  _y_ions                        = copy._y_ions;     // Enums::PeptideIon::y
  _b_ions                        = copy._b_ions;     // Enums::PeptideIon::b
  _ystar_ions                    = copy._ystar_ions; // Enums::PeptideIon::ystar
  _bstar_ions                    = copy._bstar_ions; // Enums::PeptideIon::bstar
  _c_ions                        = copy._c_ions;     // Enums::PeptideIon::c
  _z_ions                        = copy._z_ions;     // Enums::PeptideIon::z
  _a_ions                        = copy._a_ions;     // Enums::PeptideIon::a
  _x_ions                        = copy._x_ions;     // CO2
 
  _astar_ions = copy._astar_ions; // Enums::PeptideIon::a
  _ao_ions    = copy._ao_ions;
  _bo_ions    = copy._bo_ions;
  _yo_ions    = copy._yo_ions;
}

References XtandemSpectrumProcess(), _a_ions, _ao_ions, _astar_ions, _b_ions, _bo_ions, _bstar_ions, _c_ions, _x_ions, _y_ions, _yo_ions, _ystar_ions, _z_ions, m_filter_highpass, m_filter_keep_greater, m_filter_rescale, m_isExcludeParent, m_isExcludeParent_lower_dalton, m_isExcludeParent_neutral_loss, m_isExcludeParent_upper_dalton, m_isRefineSpectrumModel, m_isRemoveIsotope, m_n_most_intense, m_neutralLossMass, and m_neutralLossWindowDalton.

◆ ~XtandemSpectrumProcess()

pappso::XtandemSpectrumProcess::~XtandemSpectrumProcess ( )

Definition at line 71 of file xtandemspectrumprocess.cpp.

72{

73}

Member Function Documentation

◆ getDynamicRange()

pappso::pappso_double pappso::XtandemSpectrumProcess::getDynamicRange ( ) const

Definition at line 193 of file xtandemspectrumprocess.cpp.

{
  return m_filter_rescale.getDynamicRange();
}

References m_filter_rescale.

◆ getExcludeParent()

bool pappso::XtandemSpectrumProcess::getExcludeParent ( ) const

Definition at line 203 of file xtandemspectrumprocess.cpp.

{
  return m_isExcludeParent;
}

References m_isExcludeParent.

◆ getExcludeParentNeutralLoss()

bool pappso::XtandemSpectrumProcess::getExcludeParentNeutralLoss ( ) const

Definition at line 208 of file xtandemspectrumprocess.cpp.

{
  return m_isExcludeParent_neutral_loss;
}

References m_isExcludeParent_neutral_loss.

◆ getIonScore()

bool pappso::XtandemSpectrumProcess::getIonScore ( Enums::PeptideIon ion_type ) const

Definition at line 231 of file xtandemspectrumprocess.cpp.

{
  switch(ion_type)
    {
      case Enums::PeptideIon::y:
        return _y_ions;
 
      case Enums::PeptideIon::b:
        return _b_ions;
 
      case Enums::PeptideIon::ystar:
        return _ystar_ions;
 
      case Enums::PeptideIon::bstar:
        return _bstar_ions;
 
      case Enums::PeptideIon::yo:
        return _yo_ions;
 
      case Enums::PeptideIon::bo:
        return _bo_ions;
 
      case Enums::PeptideIon::z:
        return _z_ions;
 
      case Enums::PeptideIon::a:
        return _a_ions;
 
      case Enums::PeptideIon::astar:
        return _astar_ions;
      case Enums::PeptideIon::ao:
        return _ao_ions;
 
      case Enums::PeptideIon::c:
        return _c_ions;
      case Enums::PeptideIon::x:
        return _x_ions;
      default:
        break;
    }
  return false;
}

References _a_ions, _ao_ions, _astar_ions, _b_ions, _bo_ions, _bstar_ions, _c_ions, _x_ions, _y_ions, _yo_ions, _ystar_ions, _z_ions, pappso::Enums::a, pappso::Enums::ao, pappso::Enums::astar, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bstar, pappso::Enums::c, pappso::Enums::x, pappso::Enums::y, pappso::Enums::yo, pappso::Enums::ystar, and pappso::Enums::z.

◆ getMinimumMz()

pappso_double pappso::XtandemSpectrumProcess::getMinimumMz ( ) const

Definition at line 183 of file xtandemspectrumprocess.cpp.

{
  return m_filter_keep_greater.getThresholdX();
}

References m_filter_keep_greater.

◆ getNeutralLossMass()

pappso::pappso_double pappso::XtandemSpectrumProcess::getNeutralLossMass ( ) const

Definition at line 213 of file xtandemspectrumprocess.cpp.

{
  return m_neutralLossMass;
}

References m_neutralLossMass.

◆ getNeutralLossWindowDalton()

pappso_double pappso::XtandemSpectrumProcess::getNeutralLossWindowDalton ( ) const

Definition at line 218 of file xtandemspectrumprocess.cpp.

{
  return m_neutralLossWindowDalton;
}

References m_neutralLossWindowDalton.

◆ getNmostIntense()

unsigned int pappso::XtandemSpectrumProcess::getNmostIntense ( ) const

Definition at line 188 of file xtandemspectrumprocess.cpp.

{
  return m_n_most_intense.getNumberOfPoints();
}

References m_n_most_intense.

◆ getRefineSpectrumModel()

bool pappso::XtandemSpectrumProcess::getRefineSpectrumModel ( ) const

Definition at line 224 of file xtandemspectrumprocess.cpp.

{
  return m_isRefineSpectrumModel;
}

References m_isRefineSpectrumModel.

◆ getRemoveIsotope()

bool pappso::XtandemSpectrumProcess::getRemoveIsotope ( ) const

Definition at line 198 of file xtandemspectrumprocess.cpp.

{
  return m_isRemoveIsotope;
}

References m_isRemoveIsotope.

◆ process()

MassSpectrum pappso::XtandemSpectrumProcess::process	(	const MassSpectrum &	spectrum,
		pappso_double	parent_ion_mass,
		unsigned int	parent_charge ) const

process raw spectrum to prepare hyperscore computation

Definition at line 275 of file xtandemspectrumprocess.cpp.

{
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
           << " parent_charge==" << parent_charge;
 
  // 1) clean isotopes
  MassSpectrum spectrum_process(spectrum);
  if(m_isRemoveIsotope)
    {
      spectrum_process.massSpectrumFilter(FilterTandemDeisotope());
    }
  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
  // 2) remove parent ion mass
  if(m_isExcludeParent)
    {
      spectrum_process.massSpectrumFilter(MassSpectrumFilterResampleRemoveMzRange(MzRange(
        parent_ion_mz,
        PrecisionFactory::getDaltonInstance(m_isExcludeParent_lower_dalton / parent_charge),
        PrecisionFactory::getDaltonInstance(m_isExcludeParent_upper_dalton / parent_charge))));
    }
  qDebug() << spectrum_process.size();
  // 3) remove low masses
  // 4) normalization
  m_filter_keep_greater.filter(spectrum_process);
  qDebug() << spectrum_process.size();
  m_filter_rescale.filter(spectrum_process);
  qDebug() << spectrum_process.size();
  // m_filter_floor.filter(spectrum_process);
  m_filter_highpass.filter(spectrum_process);
 
  qDebug() << spectrum_process.size();
  // 5) remove neutral loss
  if(m_isExcludeParent_neutral_loss)
    {
      pappso_double parent_ion_mhplus =
        ((parent_ion_mz - (MHPLUS * parent_charge)) * parent_charge) + MHPLUS;
 
      MassSpectrumFilterResampleRemoveMzRange filter_parent(
        MzRange(parent_ion_mhplus - m_neutralLossMass,
                PrecisionFactory::getDaltonInstance(m_neutralLossWindowDalton)));
 
      filter_parent.filter(spectrum_process);
    }
  // 6) clean isotopes
  // 7) keep n most intense peaks
  qDebug() << spectrum_process.size() << " parent_charge==" << parent_charge;
  // return spectrum_process.massSpectrumFilter(m_filter_remove_c13)
  // .filter(m_nMostIntense);
 
  m_filter_remove_c13.filter(spectrum_process);
  m_n_most_intense.filter(spectrum_process);
  qDebug() << spectrum_process.size();
  return spectrum_process;
}

References pappso::MassSpectrumFilterResampleRemoveMzRange::filter(), pappso::PrecisionFactory::getDaltonInstance(), m_filter_highpass, m_filter_keep_greater, m_filter_remove_c13, m_filter_rescale, m_isExcludeParent, m_isExcludeParent_lower_dalton, m_isExcludeParent_neutral_loss, m_isExcludeParent_upper_dalton, m_isRemoveIsotope, m_n_most_intense, m_neutralLossMass, m_neutralLossWindowDalton, pappso::MassSpectrum::massSpectrumFilter(), and pappso::MHPLUS().

◆ setDynamicRange()

void pappso::XtandemSpectrumProcess::setDynamicRange ( pappso::pappso_double dynamic_range )

Definition at line 86 of file xtandemspectrumprocess.cpp.

{
  m_filter_rescale = FilterRescaleY(dynamic_range);
}

References m_filter_rescale.

◆ setExcludeParent()

void pappso::XtandemSpectrumProcess::setExcludeParent ( bool exclude_parent )

Definition at line 98 of file xtandemspectrumprocess.cpp.

{
  m_isExcludeParent = exclude_parent;
}

References m_isExcludeParent.

◆ setExcludeParentNeutralLoss()

void pappso::XtandemSpectrumProcess::setExcludeParentNeutralLoss ( bool neutral_loss )

Definition at line 103 of file xtandemspectrumprocess.cpp.

{
  m_isExcludeParent_neutral_loss = neutral_loss;
}

References m_isExcludeParent_neutral_loss.

◆ setIonScore()

void pappso::XtandemSpectrumProcess::setIonScore	(	Enums::PeptideIon	ion_type,
		bool	compute_score )

Definition at line 127 of file xtandemspectrumprocess.cpp.

{
  switch(ion_type)
    {
      case Enums::PeptideIon::y:
        _y_ions = compute_score;
        break;
 
      case Enums::PeptideIon::b:
        _b_ions = compute_score;
        break;
 
      case Enums::PeptideIon::ystar:
        _ystar_ions = compute_score;
        break;
 
      case Enums::PeptideIon::bstar:
        _bstar_ions = compute_score;
        break;
 
      case Enums::PeptideIon::yo:
        _yo_ions = compute_score;
        break;
 
      case Enums::PeptideIon::bo:
        _bo_ions = compute_score;
        break;
 
      case Enums::PeptideIon::z:
        _z_ions = compute_score;
        break;
 
      case Enums::PeptideIon::a:
        _a_ions = compute_score;
        break;
 
      case Enums::PeptideIon::astar:
        _astar_ions = compute_score;
        break;
      case Enums::PeptideIon::ao:
        _ao_ions = compute_score;
        break;
      case Enums::PeptideIon::c:
        _c_ions = compute_score;
        break;
      case Enums::PeptideIon::x:
        _x_ions = compute_score;
        break;
 
      case Enums::PeptideIon::bp:
      case Enums::PeptideIon::yp:
        break;
    }
}

References _a_ions, _ao_ions, _astar_ions, _b_ions, _bo_ions, _bstar_ions, _c_ions, _x_ions, _y_ions, _yo_ions, _ystar_ions, _z_ions, pappso::Enums::a, pappso::Enums::ao, pappso::Enums::astar, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bp, pappso::Enums::bstar, pappso::Enums::c, pappso::Enums::x, pappso::Enums::y, pappso::Enums::yo, pappso::Enums::yp, pappso::Enums::ystar, and pappso::Enums::z.

◆ setMinimumMz()

void pappso::XtandemSpectrumProcess::setMinimumMz ( pappso_double minimum_mz )

Definition at line 76 of file xtandemspectrumprocess.cpp.

{
  m_filter_keep_greater = FilterResampleKeepGreater(minimum_mz);
}

References m_filter_keep_greater.

◆ setNeutralLossMass()

void pappso::XtandemSpectrumProcess::setNeutralLossMass ( pappso::pappso_double neutral_loss_mass )

Definition at line 108 of file xtandemspectrumprocess.cpp.

{
  m_neutralLossMass = neutral_loss_mass;
}

References m_neutralLossMass.

◆ setNeutralLossWindowDalton()

void pappso::XtandemSpectrumProcess::setNeutralLossWindowDalton ( pappso::pappso_double neutral_loss_precision )

Definition at line 113 of file xtandemspectrumprocess.cpp.

{
  m_neutralLossWindowDalton = neutral_loss_precision;
}

References m_neutralLossWindowDalton.

◆ setNmostIntense()

void pappso::XtandemSpectrumProcess::setNmostIntense ( unsigned int nmost_intense )

Definition at line 81 of file xtandemspectrumprocess.cpp.

{
  m_n_most_intense = FilterGreatestY(nmost_intense);
}

References m_n_most_intense.

◆ setRefineSpectrumModel()

void pappso::XtandemSpectrumProcess::setRefineSpectrumModel ( bool refine )

Definition at line 120 of file xtandemspectrumprocess.cpp.

{
  m_isRefineSpectrumModel = refine;
}

References m_isRefineSpectrumModel.

◆ setRemoveIsotope()

void pappso::XtandemSpectrumProcess::setRemoveIsotope ( bool remove_isotope )

Definition at line 92 of file xtandemspectrumprocess.cpp.

{
  m_isRemoveIsotope = remove_isotope;
}

References m_isRemoveIsotope.

Member Data Documentation

◆ _a_ions

bool pappso::XtandemSpectrumProcess::_a_ions = false

private

Definition at line 100 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _ao_ions

bool pappso::XtandemSpectrumProcess::_ao_ions = false

private

Definition at line 103 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _astar_ions

bool pappso::XtandemSpectrumProcess::_astar_ions = false

private

Definition at line 102 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _b_ions

bool pappso::XtandemSpectrumProcess::_b_ions = true

private

Definition at line 96 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _bo_ions

bool pappso::XtandemSpectrumProcess::_bo_ions = false

private

Definition at line 104 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _bstar_ions

bool pappso::XtandemSpectrumProcess::_bstar_ions = false

private

Definition at line 97 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _c_ions

bool pappso::XtandemSpectrumProcess::_c_ions = false

private

Definition at line 98 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _x_ions

bool pappso::XtandemSpectrumProcess::_x_ions = false

private

Definition at line 101 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _y_ions

bool pappso::XtandemSpectrumProcess::_y_ions = true

private

Definition at line 94 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _yo_ions

bool pappso::XtandemSpectrumProcess::_yo_ions = false

private

Definition at line 105 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _ystar_ions

bool pappso::XtandemSpectrumProcess::_ystar_ions = false

private

Definition at line 95 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ _z_ions

bool pappso::XtandemSpectrumProcess::_z_ions = false

private

Definition at line 99 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().

◆ m_filter_floor

FilterFloorY pappso::XtandemSpectrumProcess::m_filter_floor

private

Definition at line 84 of file xtandemspectrumprocess.h.

◆ m_filter_highpass

FilterHighPass pappso::XtandemSpectrumProcess::m_filter_highpass

private

Definition at line 85 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), XtandemSpectrumProcess(), and process().

◆ m_filter_keep_greater

FilterResampleKeepGreater pappso::XtandemSpectrumProcess::m_filter_keep_greater

private

Definition at line 80 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), XtandemSpectrumProcess(), getMinimumMz(), process(), and setMinimumMz().

◆ m_filter_remove_c13

FilterTandemDeisotope pappso::XtandemSpectrumProcess::m_filter_remove_c13 = FilterTandemDeisotope(1.5, 200)

private

Definition at line 83 of file xtandemspectrumprocess.h.

Referenced by process().

◆ m_filter_rescale

FilterRescaleY pappso::XtandemSpectrumProcess::m_filter_rescale

private

Definition at line 82 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), XtandemSpectrumProcess(), getDynamicRange(), process(), and setDynamicRange().

◆ m_isExcludeParent

bool pappso::XtandemSpectrumProcess::m_isExcludeParent = false

private

Definition at line 87 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getExcludeParent(), process(), and setExcludeParent().

◆ m_isExcludeParent_lower_dalton

pappso::pappso_double pappso::XtandemSpectrumProcess::m_isExcludeParent_lower_dalton = 2

private

Definition at line 88 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), and process().

◆ m_isExcludeParent_neutral_loss

bool pappso::XtandemSpectrumProcess::m_isExcludeParent_neutral_loss = false

private

Definition at line 90 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getExcludeParentNeutralLoss(), process(), and setExcludeParentNeutralLoss().

◆ m_isExcludeParent_upper_dalton

pappso::pappso_double pappso::XtandemSpectrumProcess::m_isExcludeParent_upper_dalton = 2

private

Definition at line 89 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), and process().

◆ m_isRefineSpectrumModel

bool pappso::XtandemSpectrumProcess::m_isRefineSpectrumModel = true

private

Definition at line 93 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getRefineSpectrumModel(), and setRefineSpectrumModel().

◆ m_isRemoveIsotope

bool pappso::XtandemSpectrumProcess::m_isRemoveIsotope = true

private

Definition at line 86 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getRemoveIsotope(), process(), and setRemoveIsotope().

◆ m_n_most_intense

FilterGreatestY pappso::XtandemSpectrumProcess::m_n_most_intense

private

Definition at line 81 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), XtandemSpectrumProcess(), getNmostIntense(), process(), and setNmostIntense().

◆ m_neutralLossMass

pappso::pappso_double pappso::XtandemSpectrumProcess::m_neutralLossMass = MASSH2O

private

Definition at line 91 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getNeutralLossMass(), process(), and setNeutralLossMass().

◆ m_neutralLossWindowDalton

pappso::pappso_double pappso::XtandemSpectrumProcess::m_neutralLossWindowDalton = 0.5

private

Definition at line 92 of file xtandemspectrumprocess.h.

Referenced by XtandemSpectrumProcess(), getNeutralLossWindowDalton(), process(), and setNeutralLossWindowDalton().

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

pappsomspp/core/psm/xtandem/xtandemspectrumprocess.h
pappsomspp/core/psm/xtandem/xtandemspectrumprocess.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ XtandemSpectrumProcess() [1/2]

◆ XtandemSpectrumProcess() [2/2]

◆ ~XtandemSpectrumProcess()

Member Function Documentation

◆ getDynamicRange()

◆ getExcludeParent()

◆ getExcludeParentNeutralLoss()

◆ getIonScore()

◆ getMinimumMz()

◆ getNeutralLossMass()

◆ getNeutralLossWindowDalton()

◆ getNmostIntense()

◆ getRefineSpectrumModel()

◆ getRemoveIsotope()

◆ process()

◆ setDynamicRange()

◆ setExcludeParent()

◆ setExcludeParentNeutralLoss()

◆ setIonScore()

◆ setMinimumMz()

◆ setNeutralLossMass()

◆ setNeutralLossWindowDalton()

◆ setNmostIntense()

◆ setRefineSpectrumModel()

◆ setRemoveIsotope()

Member Data Documentation

◆ _a_ions

◆ _ao_ions

◆ _astar_ions

◆ _b_ions

◆ _bo_ions

◆ _bstar_ions

◆ _c_ions

◆ _x_ions

◆ _y_ions

◆ _yo_ions

◆ _ystar_ions

◆ _z_ions

◆ m_filter_floor

◆ m_filter_highpass

◆ m_filter_keep_greater

◆ m_filter_remove_c13

◆ m_filter_rescale

◆ m_isExcludeParent

◆ m_isExcludeParent_lower_dalton

◆ m_isExcludeParent_neutral_loss

◆ m_isExcludeParent_upper_dalton

◆ m_isRefineSpectrumModel

◆ m_isRemoveIsotope

◆ m_n_most_intense

◆ m_neutralLossMass

◆ m_neutralLossWindowDalton