pappso::specpeptidoms::PeptideModel Class Reference

modelize peptide sequence to facilitate rendering in bracket or proforma More...

#include <peptidemodel.h>

Inheritance diagram for pappso::specpeptidoms::PeptideModel:

Public Member Functions
	PeptideModel ()
virtual	~PeptideModel ()
void	reset ()
void	setCterShift (double mass_shift)
void	setNterShift (double mass_shift)
QString	toProForma () const
QString	toInterpretation () const
void	setPrecursorMass (double mass)
double	getPrecursorMass () const
double	getMass () const
double	getNonAlignedMass () const
	Return the difference between the precursor's mass and the mass modelized by the PeptideModel.

Static Public Member Functions
static QString	toProFormaMass (double mass)

Private Attributes
double	m_cterShift = 0
double	m_nterShift = 0
double	m_precursorMass = 0

Detailed Description

modelize peptide sequence to facilitate rendering in bracket or proforma

Definition at line 55 of file peptidemodel.h.

Constructor & Destructor Documentation

PeptideModel()

pappso::specpeptidoms::PeptideModel::PeptideModel

(

)

Default constructor

Definition at line 80 of file peptidemodel.cpp.

{
}

~PeptideModel()

pappso::specpeptidoms::PeptideModel::~PeptideModel ( )

virtual

Destructor

Definition at line 84 of file peptidemodel.cpp.

{
}

Member Function Documentation

getMass()

double pappso::specpeptidoms::PeptideModel::getMass

(

)

const

Definition at line 133 of file peptidemodel.cpp.

{
  double mass = m_cterShift + m_nterShift + MASSH2O;
  // qWarning() << mass;
  for(auto &aa : *this)
    {
      // qWarning() << aa.m_aminoAcid.toProForma();
      mass += aa.m_aminoAcid.getMass() + aa.m_massDifference;
    }
  return mass;
}

References m_cterShift, m_nterShift, and pappso::MASSH2O().

Referenced by getNonAlignedMass(), and toProForma().

getNonAlignedMass()

double pappso::specpeptidoms::PeptideModel::getNonAlignedMass

(

)

const

Return the difference between the precursor's mass and the mass modelized by the PeptideModel.

Definition at line 204 of file peptidemodel.cpp.

{
  return getPrecursorMass() - getMass();
}

References getMass(), and getPrecursorMass().

getPrecursorMass()

double pappso::specpeptidoms::PeptideModel::getPrecursorMass

(

)

const

Definition at line 115 of file peptidemodel.cpp.

{
  return m_precursorMass;
}

References m_precursorMass.

Referenced by getNonAlignedMass().

reset()

void pappso::specpeptidoms::PeptideModel::reset

(

)

Definition at line 89 of file peptidemodel.cpp.

{
  this->clear();
  m_cterShift     = 0;
  m_nterShift     = 0;
  m_precursorMass = 0;
}

References m_cterShift, m_nterShift, and m_precursorMass.

setCterShift()

void pappso::specpeptidoms::PeptideModel::setCterShift

(

double

mass_shift

)

Definition at line 97 of file peptidemodel.cpp.

{
  m_cterShift = mass_shift;
}

References m_cterShift.

setNterShift()

void pappso::specpeptidoms::PeptideModel::setNterShift

(

double

mass_shift

)

Definition at line 103 of file peptidemodel.cpp.

{
  m_nterShift = mass_shift;
}

References m_nterShift.

setPrecursorMass()

void pappso::specpeptidoms::PeptideModel::setPrecursorMass

(

double

mass

)

Definition at line 109 of file peptidemodel.cpp.

{
  m_precursorMass = mass;
}

References m_precursorMass.

toInterpretation()

QString pappso::specpeptidoms::PeptideModel::toInterpretation

(

)

const

Definition at line 181 of file peptidemodel.cpp.

{
  QString proforma;
 
  if(size() > 0)
    {
      if(m_nterShift > 0)
        {
          proforma = '[' + QString::number(m_nterShift) + "]";
        }
      for(auto &aa : *this)
        {
          proforma.append(aa.toInterpretation());
        }
      if(m_cterShift > 0)
        {
          proforma = "[" + QString::number(m_cterShift) + ']';
        }
    }
  return proforma;
}

References m_cterShift, and m_nterShift.

Referenced by pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::storeAlignment().

toProForma()

QString pappso::specpeptidoms::PeptideModel::toProForma

(

)

const

Definition at line 146 of file peptidemodel.cpp.

{
 
  double mass_delta = m_precursorMass - getMass();
 
  QString proforma("[");
  if(mass_delta > 0)
    {
      proforma.append("+");
    }
  proforma.append(QString("%1]?").arg(QString::number(mass_delta, 'f', 4)));
  proforma.replace("[+0.0000]?", "");
  proforma.replace("[-0.0000]?", "");
 
 
  // QString proforma;
 
  if(size() > 0)
    {
      if(m_nterShift != 0)
        {
          proforma = '[' + toProFormaMass(m_nterShift) + "]-";
        }
      for(auto &aa : *this)
        {
          proforma.append(aa.toProForma());
        }
      if(m_cterShift != 0)
        {
          proforma = "-[" + toProFormaMass(m_cterShift) + ']';
        }
    }
  return proforma;
}

References getMass(), m_cterShift, m_nterShift, m_precursorMass, and toProFormaMass().

Referenced by pappso::cbor::psm::PsmSpecPeptidOmsScan::storeAlignment().

toProFormaMass()

QString pappso::specpeptidoms::PeptideModel::toProFormaMass ( double mass )

static

Definition at line 120 of file peptidemodel.cpp.

{
  if(mass > 0)
    {
      return QString("+%1").arg(QString::number(mass, 'f', 4));
    }
  else
    {
      return QString("%1").arg(QString::number(mass, 'f', 4));
    }
}

Referenced by pappso::specpeptidoms::AminoAcidModel::toProForma(), and toProForma().

Member Data Documentation

m_cterShift

double pappso::specpeptidoms::PeptideModel::m_cterShift = 0

private

Definition at line 92 of file peptidemodel.h.

Referenced by getMass(), reset(), setCterShift(), toInterpretation(), and toProForma().

m_nterShift

double pappso::specpeptidoms::PeptideModel::m_nterShift = 0

private

Definition at line 93 of file peptidemodel.h.

Referenced by getMass(), reset(), setNterShift(), toInterpretation(), and toProForma().

m_precursorMass

double pappso::specpeptidoms::PeptideModel::m_precursorMass = 0

private

Definition at line 94 of file peptidemodel.h.

Referenced by getPrecursorMass(), reset(), setPrecursorMass(), and toProForma().

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

• pappsomspp/core/processing/specpeptidoms/peptidemodel.h
• pappsomspp/core/processing/specpeptidoms/peptidemodel.cpp