pappso::XtandemSpectrumProcess Class Reference

#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 More...
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 (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 (PeptideIon ion_type) const

Private Attributes
FilterResampleKeepGreater	m_filter_keep_greater
FilterGreatestY	m_n_most_intense
FilterRescaleY	m_filter_rescale
FilterTandemRemoveC13	m_filter_remove_c13
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 60 of file xtandemspectrumprocess.h.

Constructor & Destructor Documentation

XtandemSpectrumProcess() [1/2]

pappso::XtandemSpectrumProcess::XtandemSpectrumProcess

(

)

Definition at line 57 of file xtandemspectrumprocess.cpp.

XtandemSpectrumProcess() [2/2]

pappso::XtandemSpectrumProcess::XtandemSpectrumProcess

(

const XtandemSpectrumProcess &

copy

)

Definition at line 65 of file xtandemspectrumprocess.cpp.

{
}
 
void
XtandemSpectrumProcess::setMinimumMz(pappso_double minimum_mz)
{
  m_filter_keep_greater = FilterResampleKeepGreater(minimum_mz);
}
void
XtandemSpectrumProcess::setNmostIntense(unsigned int nmost_intense)
{
  m_n_most_intense = FilterGreatestY(nmost_intense);
}
void
XtandemSpectrumProcess::setDynamicRange(pappso::pappso_double dynamic_range)
{
  m_filter_rescale = FilterRescaleY(dynamic_range);
}
 

~XtandemSpectrumProcess()

pappso::XtandemSpectrumProcess::~XtandemSpectrumProcess

(

)

Definition at line 95 of file xtandemspectrumprocess.cpp.

{

References m_isRemoveIsotope.

Member Function Documentation

getDynamicRange()

pappso::pappso_double pappso::XtandemSpectrumProcess::getDynamicRange

(

)

const

Definition at line 219 of file xtandemspectrumprocess.cpp.

{
  return m_neutralLossMass;
}

References m_neutralLossMass.

getExcludeParent()

bool pappso::XtandemSpectrumProcess::getExcludeParent

(

)

const

Definition at line 229 of file xtandemspectrumprocess.cpp.

{
  return m_isRefineSpectrumModel;

References m_isRefineSpectrumModel.

getExcludeParentNeutralLoss()

bool pappso::XtandemSpectrumProcess::getExcludeParentNeutralLoss

(

)

const

Definition at line 234 of file xtandemspectrumprocess.cpp.

{

getIonScore()

bool pappso::XtandemSpectrumProcess::getIonScore

(

PeptideIon

ion_type

)

const

Definition at line 257 of file xtandemspectrumprocess.cpp.

                      :
        return _z_ions;
 
      case PeptideIon::a:
        return _a_ions;
 
      case PeptideIon::astar:
        return _astar_ions;
      case PeptideIon::ao:
        return _ao_ions;
 
      case PeptideIon::c:
        return _c_ions;
      case PeptideIon::x:
        return _x_ions;
      default:
        break;
    }
  return false;
}
 
MassSpectrum
XtandemSpectrumProcess::process(const MassSpectrum &spectrum,
                                pappso_double parent_ion_mz,
                                unsigned int parent_charge) const
{
  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(

getMinimumMz()

pappso_double pappso::XtandemSpectrumProcess::getMinimumMz

(

)

const

Definition at line 209 of file xtandemspectrumprocess.cpp.

{
  return m_isExcludeParent;
}

References m_isExcludeParent.

getNeutralLossMass()

pappso::pappso_double pappso::XtandemSpectrumProcess::getNeutralLossMass

(

)

const

Definition at line 239 of file xtandemspectrumprocess.cpp.

    {
      case PeptideIon::y:
        return _y_ions;

References _y_ions, and pappso::y.

getNeutralLossWindowDalton()

pappso_double pappso::XtandemSpectrumProcess::getNeutralLossWindowDalton

(

)

const

Definition at line 244 of file xtandemspectrumprocess.cpp.

                      :
        return _b_ions;
 
      case PeptideIon::ystar:

getNmostIntense()

unsigned int pappso::XtandemSpectrumProcess::getNmostIntense

(

)

const

Definition at line 214 of file xtandemspectrumprocess.cpp.

{
  return m_isExcludeParent_neutral_loss;
}

References m_isExcludeParent_neutral_loss.

getRefineSpectrumModel()

bool pappso::XtandemSpectrumProcess::getRefineSpectrumModel

(

)

const

Definition at line 250 of file xtandemspectrumprocess.cpp.

                          :
        return _bstar_ions;
 
      case PeptideIon::yo:

getRemoveIsotope()

bool pappso::XtandemSpectrumProcess::getRemoveIsotope

(

)

const

Definition at line 224 of file xtandemspectrumprocess.cpp.

{
  return m_neutralLossWindowDalton;
}

References m_neutralLossWindowDalton.

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 301 of file xtandemspectrumprocess.cpp.

    {
      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() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
           << " 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() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "
           << spectrum_process.size();
  return spectrum_process;
}
 
 
} // namespace pappso

setDynamicRange()

void pappso::XtandemSpectrumProcess::setDynamicRange

(

pappso::pappso_double

dynamic_range

)

Definition at line 110 of file xtandemspectrumprocess.cpp.

{

setExcludeParent()

void pappso::XtandemSpectrumProcess::setExcludeParent

(

bool

exclude_parent

)

Definition at line 122 of file xtandemspectrumprocess.cpp.

setExcludeParentNeutralLoss()

void pappso::XtandemSpectrumProcess::setExcludeParentNeutralLoss

(

bool

neutral_loss

)

Definition at line 127 of file xtandemspectrumprocess.cpp.

{
  m_isRefineSpectrumModel = refine;
}
 

References m_isRefineSpectrumModel.

setIonScore()

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

Definition at line 153 of file xtandemspectrumprocess.cpp.

                       :
        _yo_ions = compute_score;
        break;
 
      case PeptideIon::bo:
        _bo_ions = compute_score;
        break;
 
      case PeptideIon::z:
        _z_ions = compute_score;
        break;
 
      case PeptideIon::a:
        _a_ions = compute_score;
        break;
 
      case PeptideIon::astar:
        _astar_ions = compute_score;
        break;
      case PeptideIon::ao:
        _ao_ions = compute_score;
        break;
      case PeptideIon::c:
        _c_ions = compute_score;
        break;
      case PeptideIon::x:
        _x_ions = compute_score;
        break;
 
      case PeptideIon::bp:
      case PeptideIon::yp:
        break;
    }
}
 
pappso_double
XtandemSpectrumProcess::getMinimumMz() const
{
  return m_filter_keep_greater.getThresholdX();
}
unsigned int
XtandemSpectrumProcess::getNmostIntense() const
{
  return m_n_most_intense.getNumberOfPoints();
}
pappso::pappso_double
XtandemSpectrumProcess::getDynamicRange() const
{
  return m_filter_rescale.getDynamicRange();
}
bool
XtandemSpectrumProcess::getRemoveIsotope() const
{
  return m_isRemoveIsotope;

setMinimumMz()

void pappso::XtandemSpectrumProcess::setMinimumMz

(

pappso_double

minimum_mz

)

Definition at line 100 of file xtandemspectrumprocess.cpp.

{

References m_isExcludeParent.

setNeutralLossMass()

void pappso::XtandemSpectrumProcess::setNeutralLossMass

(

pappso::pappso_double

neutral_loss_mass

)

Definition at line 132 of file xtandemspectrumprocess.cpp.

{
  switch(ion_type)
    {

References pappso::y.

setNeutralLossWindowDalton()

void pappso::XtandemSpectrumProcess::setNeutralLossWindowDalton

(

pappso::pappso_double

neutral_loss_precision

)

Definition at line 138 of file xtandemspectrumprocess.cpp.

                      :
        _b_ions = compute_score;

setNmostIntense()

void pappso::XtandemSpectrumProcess::setNmostIntense

(

unsigned int

nmost_intense

)

Definition at line 105 of file xtandemspectrumprocess.cpp.

{

setRefineSpectrumModel()

void pappso::XtandemSpectrumProcess::setRefineSpectrumModel

(

bool

refine

)

Definition at line 146 of file xtandemspectrumprocess.cpp.

                          :
        _bstar_ions = compute_score;

setRemoveIsotope()

void pappso::XtandemSpectrumProcess::setRemoveIsotope

(

bool

remove_isotope

)

Definition at line 116 of file xtandemspectrumprocess.cpp.

{

Member Data Documentation

_a_ions

bool pappso::XtandemSpectrumProcess::_a_ions = false

private

Definition at line 106 of file xtandemspectrumprocess.h.

_ao_ions

bool pappso::XtandemSpectrumProcess::_ao_ions = false

private

Definition at line 109 of file xtandemspectrumprocess.h.

_astar_ions

bool pappso::XtandemSpectrumProcess::_astar_ions = false

private

Definition at line 108 of file xtandemspectrumprocess.h.

_b_ions

bool pappso::XtandemSpectrumProcess::_b_ions = true

private

Definition at line 102 of file xtandemspectrumprocess.h.

_bo_ions

bool pappso::XtandemSpectrumProcess::_bo_ions = false

private

Definition at line 110 of file xtandemspectrumprocess.h.

_bstar_ions

bool pappso::XtandemSpectrumProcess::_bstar_ions = false

private

Definition at line 103 of file xtandemspectrumprocess.h.

_c_ions

bool pappso::XtandemSpectrumProcess::_c_ions = false

private

Definition at line 104 of file xtandemspectrumprocess.h.

_x_ions

bool pappso::XtandemSpectrumProcess::_x_ions = false

private

Definition at line 107 of file xtandemspectrumprocess.h.

_y_ions

bool pappso::XtandemSpectrumProcess::_y_ions = true

private

Definition at line 100 of file xtandemspectrumprocess.h.

Referenced by getNeutralLossMass().

_yo_ions

bool pappso::XtandemSpectrumProcess::_yo_ions = false

private

Definition at line 111 of file xtandemspectrumprocess.h.

_ystar_ions

bool pappso::XtandemSpectrumProcess::_ystar_ions = false

private

Definition at line 101 of file xtandemspectrumprocess.h.

_z_ions

bool pappso::XtandemSpectrumProcess::_z_ions = false

private

Definition at line 105 of file xtandemspectrumprocess.h.

m_filter_floor

FilterFloorY pappso::XtandemSpectrumProcess::m_filter_floor

private

Definition at line 90 of file xtandemspectrumprocess.h.

m_filter_highpass

FilterHighPass pappso::XtandemSpectrumProcess::m_filter_highpass

private

Definition at line 91 of file xtandemspectrumprocess.h.

m_filter_keep_greater

FilterResampleKeepGreater pappso::XtandemSpectrumProcess::m_filter_keep_greater

private

Definition at line 86 of file xtandemspectrumprocess.h.

m_filter_remove_c13

FilterTandemRemoveC13 pappso::XtandemSpectrumProcess::m_filter_remove_c13

private

Definition at line 89 of file xtandemspectrumprocess.h.

m_filter_rescale

FilterRescaleY pappso::XtandemSpectrumProcess::m_filter_rescale

private

Definition at line 88 of file xtandemspectrumprocess.h.

m_isExcludeParent

bool pappso::XtandemSpectrumProcess::m_isExcludeParent = false

private

Definition at line 93 of file xtandemspectrumprocess.h.

Referenced by getMinimumMz(), and setMinimumMz().

m_isExcludeParent_lower_dalton

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

private

Definition at line 94 of file xtandemspectrumprocess.h.

m_isExcludeParent_neutral_loss

bool pappso::XtandemSpectrumProcess::m_isExcludeParent_neutral_loss = false

private

Definition at line 96 of file xtandemspectrumprocess.h.

Referenced by getNmostIntense().

m_isExcludeParent_upper_dalton

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

private

Definition at line 95 of file xtandemspectrumprocess.h.

m_isRefineSpectrumModel

bool pappso::XtandemSpectrumProcess::m_isRefineSpectrumModel = true

private

Definition at line 99 of file xtandemspectrumprocess.h.

Referenced by getExcludeParent(), and setExcludeParentNeutralLoss().

m_isRemoveIsotope

bool pappso::XtandemSpectrumProcess::m_isRemoveIsotope = true

private

Definition at line 92 of file xtandemspectrumprocess.h.

Referenced by ~XtandemSpectrumProcess().

m_n_most_intense

FilterGreatestY pappso::XtandemSpectrumProcess::m_n_most_intense

private

Definition at line 87 of file xtandemspectrumprocess.h.

m_neutralLossMass

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

private

Definition at line 97 of file xtandemspectrumprocess.h.

Referenced by getDynamicRange().

m_neutralLossWindowDalton

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

private

Definition at line 98 of file xtandemspectrumprocess.h.

Referenced by getRemoveIsotope().

---

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

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