pappso::PeptideFragmentIonListBase Class Reference

#include <peptidefragmentionlistbase.h>

Public Member Functions
	PeptideFragmentIonListBase (const PeptideSp &peptide, const IonList &ions)
	PeptideFragmentIonListBase (const PeptideFragmentIonListBase &other)
virtual	~PeptideFragmentIonListBase ()
PeptideFragmentIonListBaseSp	makePeptideFragmentIonListBaseSp () const
const std::list< Enums::PeptideIon > &	getIonList () const
unsigned int	getPhosphorylationNumber () const
virtual const PeptideSp &	getPeptideSp () const
const std::list< PeptideFragmentIonSp >	getPeptideFragmentIonSp (Enums::PeptideIon ion_type) const
const PeptideFragmentIonSp &	getPeptideFragmentIonSp (Enums::PeptideIon ion_type, unsigned int size) const
const PeptideFragmentIonSp &	getPeptideFragmentIonSp (Enums::PeptideIon ion_type, unsigned int size, unsigned int number_of_neutral_phospho_loss) const
std::list< PeptideFragmentIonSp >::const_iterator	begin () const
std::list< PeptideFragmentIonSp >::const_iterator	end () const
const std::list< PeptideFragmentIonSp > &	getPeptideFragmentIonList () const
std::size_t	size () const

Static Public Member Functions
static std::list< Enums::PeptideIon >	getCIDionList ()
static std::list< Enums::PeptideIon >	getETDionList ()

Static Protected Member Functions
static const std::list< PeptideFragmentSp >	getPeptideFragmentList (const PeptideSp &peptide)

Protected Attributes
const PeptideSp	msp_peptide
std::list< PeptideFragmentIonSp >	msp_peptide_fragment_ion_list
IonList	m_ionList
unsigned int	m_phosphorylationNumber

Private Types
using	IonList = std::list<Enums::PeptideIon>

Detailed Description

Definition at line 44 of file peptidefragmentionlistbase.h.

Member Typedef Documentation

IonList

using pappso::PeptideFragmentIonListBase::IonList = std::list<Enums::PeptideIon>

private

Definition at line 46 of file peptidefragmentionlistbase.h.

Constructor & Destructor Documentation

PeptideFragmentIonListBase() [1/2]

pappso::PeptideFragmentIonListBase::PeptideFragmentIonListBase	(	const PeptideSp &	peptide,
		const IonList &	ions )

Definition at line 78 of file peptidefragmentionlistbase.cpp.

  : msp_peptide(peptide), m_ionList(ions)
{
  try
    {
      qDebug() << "PeptideFragmentIonListBase::PeptideFragmentIonListBase begin " << ions.size();
      std::list<PeptideFragmentSp> fragment_list =
        PeptideFragmentIonListBase::getPeptideFragmentList(msp_peptide);
 
      m_phosphorylationNumber             = 0;
      AaModificationP phosphorylation_mod = nullptr;
 
 
      qDebug();
      for(auto &&fragment_sp : fragment_list)
        {
          // qDebug()<< "PeptideFragmentIonListBase::PeptideFragmentIonListBase
          // ition";
          if(fragment_sp.get()->getPeptideIonDirection() == PeptideDirection::Cter)
            {
              for(auto &&ion_type : m_ionList)
                {
                  // qDebug()<<
                  // "PeptideFragmentIonListBase::PeptideFragmentIonListBase
                  // ition";
                  if((ion_type == Enums::PeptideIon::y) || (ion_type == Enums::PeptideIon::ystar) ||
                     (ion_type == Enums::PeptideIon::yo) || (ion_type == Enums::PeptideIon::z))
                    {
                      msp_peptide_fragment_ion_list.push_back(
                        std::make_shared<PeptideFragmentIon>(fragment_sp, ion_type));
                    }
                  else if(ion_type == Enums::PeptideIon::yp)
                    {
                      if(phosphorylation_mod == nullptr)
                        {
                          phosphorylation_mod = AaModification::getInstance("MOD:00696");
                          m_phosphorylationNumber =
                            peptide.get()->getNumberOfModification(phosphorylation_mod);
                        }
                      for(unsigned int i = 0; i < m_phosphorylationNumber; i++)
                        {
                          msp_peptide_fragment_ion_list.push_back(
                            std::make_shared<PeptideFragmentIon>(fragment_sp, ion_type, i + 1));
                        }
                    }
                }
            }
          else
            {
              for(auto &&ion_type : m_ionList)
                {
                  // b, bstar, bo, a
                  if((ion_type == Enums::PeptideIon::b) || (ion_type == Enums::PeptideIon::bstar) ||
                     (ion_type == Enums::PeptideIon::bo) || (ion_type == Enums::PeptideIon::a) ||
                     (ion_type == Enums::PeptideIon::c))
                    {
                      msp_peptide_fragment_ion_list.push_back(
                        std::make_shared<PeptideFragmentIon>(fragment_sp, ion_type));
                    }
                  else if(ion_type == Enums::PeptideIon::bp)
                    {
                      if(phosphorylation_mod == nullptr)
                        {
                          phosphorylation_mod = AaModification::getInstance("MOD:00696");
                          m_phosphorylationNumber =
                            peptide.get()->getNumberOfModification(phosphorylation_mod);
                        }
                      for(unsigned int i = 0; i < m_phosphorylationNumber; i++)
                        {
                          msp_peptide_fragment_ion_list.push_back(
                            std::make_shared<PeptideFragmentIon>(fragment_sp, ion_type, i + 1));
                        }
                    }
                }
            }
        }
      qDebug() << "PeptideFragmentIonListBase::PeptideFragmentIonListBase end " << ions.size();
    }
  catch(PappsoException &exception_pappso)
    {
      QString errorStr =
        QObject::tr("ERROR building PeptideFragmentIonListBase, PAPPSO exception:\n%1")
          .arg(exception_pappso.qwhat());
      qDebug() << "PeptideFragmentIonListBase::PeptideFragmentIonListBase "
                  "PappsoException :\n"
               << errorStr;
      throw PappsoException(errorStr);
    }
  catch(std::exception &exception_std)
    {
      QString errorStr =
        QObject::tr("ERROR building PeptideFragmentIonListBase, std exception:\n%1")
          .arg(exception_std.what());
      qDebug() << "PeptideFragmentIonListBase::PeptideFragmentIonListBase "
                  "std::exception :\n"
               << errorStr;
      throw PappsoException(errorStr);
    }
}

References pappso::Enums::a, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bp, pappso::Enums::bstar, pappso::Enums::c, pappso::Cter, pappso::AaModification::getInstance(), getPeptideFragmentList(), m_ionList, m_phosphorylationNumber, msp_peptide, msp_peptide_fragment_ion_list, pappso::PappsoException::qwhat(), pappso::Enums::y, pappso::Enums::yo, pappso::Enums::yp, pappso::Enums::ystar, and pappso::Enums::z.

Referenced by PeptideFragmentIonListBase().

PeptideFragmentIonListBase() [2/2]

pappso::PeptideFragmentIonListBase::PeptideFragmentIonListBase

(

const PeptideFragmentIonListBase &

other

)

Definition at line 179 of file peptidefragmentionlistbase.cpp.

  : msp_peptide(other.msp_peptide),
    msp_peptide_fragment_ion_list(other.msp_peptide_fragment_ion_list),
    m_ionList(other.m_ionList),
    m_phosphorylationNumber(other.m_phosphorylationNumber)
{
}

References PeptideFragmentIonListBase(), m_ionList, m_phosphorylationNumber, msp_peptide, and msp_peptide_fragment_ion_list.

~PeptideFragmentIonListBase()

pappso::PeptideFragmentIonListBase::~PeptideFragmentIonListBase ( )

virtual

Definition at line 195 of file peptidefragmentionlistbase.cpp.

{
}

Member Function Documentation

begin()

std::list< pappso::PeptideFragmentIonSp >::const_iterator pappso::PeptideFragmentIonListBase::begin

(

)

const

Definition at line 298 of file peptidefragmentionlistbase.cpp.

{
  return msp_peptide_fragment_ion_list.begin();
}

References msp_peptide_fragment_ion_list.

end()

std::list< pappso::PeptideFragmentIonSp >::const_iterator pappso::PeptideFragmentIonListBase::end

(

)

const

Definition at line 304 of file peptidefragmentionlistbase.cpp.

{
  return msp_peptide_fragment_ion_list.end();
}

References msp_peptide_fragment_ion_list.

getCIDionList()

std::list< Enums::PeptideIon > pappso::PeptideFragmentIonListBase::getCIDionList ( )

static

Definition at line 41 of file peptidefragmentionlistbase.cpp.

{
  IonList ret;
  // populate ret
 
  ret.push_back(Enums::PeptideIon::y);
  ret.push_back(Enums::PeptideIon::yp);
  ret.push_back(Enums::PeptideIon::ystar);
  ret.push_back(Enums::PeptideIon::yo);
  ret.push_back(Enums::PeptideIon::b);
  ret.push_back(Enums::PeptideIon::bp);
  ret.push_back(Enums::PeptideIon::a);
  ret.push_back(Enums::PeptideIon::bstar);
  ret.push_back(Enums::PeptideIon::bo);
  return ret;
}

References pappso::Enums::a, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bp, pappso::Enums::bstar, pappso::Enums::y, pappso::Enums::yo, pappso::Enums::yp, and pappso::Enums::ystar.

Referenced by pappso::MassSpectrumWidget::MassSpectrumWidget(), and pappso::cbor::psm::PsmIonSeriesScan::process().

getETDionList()

std::list< Enums::PeptideIon > pappso::PeptideFragmentIonListBase::getETDionList ( )

static

Definition at line 59 of file peptidefragmentionlistbase.cpp.

{
  IonList ret;
  // populate ret
 
  ret.push_back(Enums::PeptideIon::y);
  ret.push_back(Enums::PeptideIon::c);
  ret.push_back(Enums::PeptideIon::z);
  ret.push_back(Enums::PeptideIon::ystar);
  ret.push_back(Enums::PeptideIon::yo);
  return ret;
}

References pappso::Enums::c, pappso::Enums::y, pappso::Enums::yo, pappso::Enums::ystar, and pappso::Enums::z.

getIonList()

const std::list< Enums::PeptideIon > & pappso::PeptideFragmentIonListBase::getIonList

(

)

const

Definition at line 73 of file peptidefragmentionlistbase.cpp.

{
  return m_ionList;
}

References m_ionList.

getPeptideFragmentIonList()

const std::list< pappso::PeptideFragmentIonSp > & pappso::PeptideFragmentIonListBase::getPeptideFragmentIonList

(

)

const

Definition at line 280 of file peptidefragmentionlistbase.cpp.

{
  return msp_peptide_fragment_ion_list;
}

References msp_peptide_fragment_ion_list.

getPeptideFragmentIonSp() [1/3]

const std::list< PeptideFragmentIonSp > pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp

(

Enums::PeptideIon

ion_type

)

const

Definition at line 226 of file peptidefragmentionlistbase.cpp.

{
  std::list<PeptideFragmentIonSp> ion_list;
  for(auto &&peptide_fragment_ion_sp : msp_peptide_fragment_ion_list)
    {
      if(peptide_fragment_ion_sp.get()->getPeptideIonType() == ion_type)
        {
          ion_list.push_back(peptide_fragment_ion_sp);
        }
    }
  return (ion_list);
}

References msp_peptide_fragment_ion_list.

Referenced by pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(), pappso::specglob::PeptideSpectrum::PeptideSpectrum(), getPeptideFragmentIonSp(), and pappso::PeptideSpectrumMatch::privMatchIonList().

getPeptideFragmentIonSp() [2/3]

const PeptideFragmentIonSp & pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp	(	Enums::PeptideIon	ion_type,
		unsigned int	size ) const

Definition at line 240 of file peptidefragmentionlistbase.cpp.

{
 
  return getPeptideFragmentIonSp(ion_type, size, 0);
}

References getPeptideFragmentIonSp(), and size().

getPeptideFragmentIonSp() [3/3]

const PeptideFragmentIonSp & pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp	(	Enums::PeptideIon	ion_type,
		unsigned int	size,
		unsigned int	number_of_neutral_phospho_loss ) const

Definition at line 248 of file peptidefragmentionlistbase.cpp.

{
  for(auto &&peptide_fragment_ion_sp : msp_peptide_fragment_ion_list)
    {
      if(peptide_fragment_ion_sp.get()->getPeptideIonType() == ion_type)
        {
          if(peptide_fragment_ion_sp.get()->size() == size)
            {
              if(peptide_fragment_ion_sp.get()->getNumberOfNeutralPhosphoLoss() ==
                 number_of_neutral_phospho_loss)
                {
                  return (peptide_fragment_ion_sp);
                }
            }
        }
    }
 
  throw PappsoException(QString("PeptideFragmentIon %1 of size %2 not found")
                          .arg(PeptideFragmentIon::getPeptideIonName(ion_type))
                          .arg(size));
}

References pappso::PeptideFragmentIon::getPeptideIonName(), msp_peptide_fragment_ion_list, and size().

getPeptideFragmentList()

const std::list< PeptideFragmentSp > pappso::PeptideFragmentIonListBase::getPeptideFragmentList ( const PeptideSp & peptide )

staticprotected

Definition at line 200 of file peptidefragmentionlistbase.cpp.

{
 
  qDebug();
  std::list<PeptideFragmentSp> peptide_fragment_list;
 
  if(peptide.get()->size() < 1)
    {
      return peptide_fragment_list;
    }
 
  unsigned int max = peptide.get()->size() - 1;
 
  for(unsigned int i = 0; i < max; i++)
    {
 
      peptide_fragment_list.push_back(
        std::make_shared<PeptideFragment>(peptide, PeptideDirection::Nter, i + 1));
      peptide_fragment_list.push_back(
        std::make_shared<PeptideFragment>(peptide, PeptideDirection::Cter, i + 1));
    }
  qDebug();
  return peptide_fragment_list;
}

References pappso::Cter, and pappso::Nter.

Referenced by PeptideFragmentIonListBase().

getPeptideSp()

const pappso::PeptideSp & pappso::PeptideFragmentIonListBase::getPeptideSp ( ) const

virtual

Definition at line 286 of file peptidefragmentionlistbase.cpp.

{
  return msp_peptide;
}

References msp_peptide.

getPhosphorylationNumber()

unsigned int pappso::PeptideFragmentIonListBase::getPhosphorylationNumber

(

)

const

Definition at line 292 of file peptidefragmentionlistbase.cpp.

{
  return m_phosphorylationNumber;
}

References m_phosphorylationNumber.

makePeptideFragmentIonListBaseSp()

PeptideFragmentIonListBaseSp pappso::PeptideFragmentIonListBase::makePeptideFragmentIonListBaseSp

(

)

const

Definition at line 189 of file peptidefragmentionlistbase.cpp.

{
  return std::make_shared<const PeptideFragmentIonListBase>(*this);
}

size()

std::size_t pappso::PeptideFragmentIonListBase::size

(

)

const

Definition at line 274 of file peptidefragmentionlistbase.cpp.

{
  return msp_peptide_fragment_ion_list.size();
}

References msp_peptide_fragment_ion_list.

Referenced by pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(), getPeptideFragmentIonSp(), and getPeptideFragmentIonSp().

Member Data Documentation

m_ionList

IonList pappso::PeptideFragmentIonListBase::m_ionList

protected

Definition at line 83 of file peptidefragmentionlistbase.h.

Referenced by PeptideFragmentIonListBase(), PeptideFragmentIonListBase(), and getIonList().

m_phosphorylationNumber

unsigned int pappso::PeptideFragmentIonListBase::m_phosphorylationNumber

protected

Definition at line 84 of file peptidefragmentionlistbase.h.

Referenced by PeptideFragmentIonListBase(), PeptideFragmentIonListBase(), and getPhosphorylationNumber().

msp_peptide

const PeptideSp pappso::PeptideFragmentIonListBase::msp_peptide

protected

Definition at line 81 of file peptidefragmentionlistbase.h.

Referenced by PeptideFragmentIonListBase(), PeptideFragmentIonListBase(), and getPeptideSp().

msp_peptide_fragment_ion_list

std::list<PeptideFragmentIonSp> pappso::PeptideFragmentIonListBase::msp_peptide_fragment_ion_list

protected

Definition at line 82 of file peptidefragmentionlistbase.h.

Referenced by PeptideFragmentIonListBase(), PeptideFragmentIonListBase(), begin(), end(), getPeptideFragmentIonList(), getPeptideFragmentIonSp(), getPeptideFragmentIonSp(), and size().

---

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

• pappsomspp/core/peptide/peptidefragmentionlistbase.h
• pappsomspp/core/peptide/peptidefragmentionlistbase.cpp