peptidefragment.cpp

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/**
 * \file pappsomspp/peptide/peptidefragment.h
 * \date 10/3/2015
 * \author Olivier Langella
 * \brief peptide fragment model
 */
 
/*******************************************************************************
 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
 *
 * This file is part of the PAPPSOms++ library.
 *
 *     PAPPSOms++ is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     PAPPSOms++ is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with PAPPSOms++.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
 *implementation
 ******************************************************************************/
 
#include "peptidefragment.h"
#include "pappsomspp/core/pappsoexception.h"
 
namespace pappso
{
 
 
PeptideFragment::PeptideFragment(const PeptideSp &sp_peptide,
                                 PeptideDirection direction,
                                 unsigned int size)
  : msp_peptide(sp_peptide), m_direction(direction), m_size(size)
{
  if(m_direction == PeptideDirection::Nter)
    {
      std::vector<Aa>::const_iterator it(msp_peptide.get()->begin());
      std::vector<Aa>::const_iterator end(msp_peptide.get()->end());
      unsigned int i = 0;
      while(i < m_size)
        {
          m_mass += it->getMass();
          it++;
          i++;
        }
 
      if(msp_peptide.get()->getNterModification() != nullptr)
        {
          m_mass += msp_peptide.get()->getNterModification()->getMass();
        }
    }
  else
    {
      std::vector<Aa>::const_reverse_iterator it(msp_peptide.get()->rbegin());
      std::vector<Aa>::const_reverse_iterator end(msp_peptide.get()->rend());
      unsigned int i = 0;
      while(i < m_size)
        {
          m_mass += it->getMass();
          it++;
          i++;
        }
      if(msp_peptide.get()->getCterModification() != nullptr)
        {
          m_mass += msp_peptide.get()->getCterModification()->getMass();
        }
    }
 
  m_mass += msp_peptide.get()->getCleavageNterModification()->getMass();
  m_mass += msp_peptide.get()->getCleavageCterModification()->getMass();
}
 
 
PeptideFragment::PeptideFragment(const PeptideFragment &other)
  : msp_peptide(other.msp_peptide), m_direction(other.m_direction), m_size(other.m_size)
{
  m_mass = other.m_mass;
}
 
 
PeptideFragment::PeptideFragment(PeptideFragment &&toCopy) // move constructor
  : msp_peptide(std::move(toCopy.msp_peptide)),
    m_direction(toCopy.m_direction),
    m_size(toCopy.m_size),
    m_mass(toCopy.m_mass)
{
}
 
 
PeptideFragment::~PeptideFragment()
{
}
 
const QString
PeptideFragment::getPeptideIonDirectionName(PeptideDirection direction)
{
  switch(direction)
    {
      case PeptideDirection::Cter:
        return "Cter";
        break;
      case PeptideDirection::Nter:
        return "Nter";
        break;
      default:
        throw PappsoException(QString("direction name not implemented"));
        break;
    }
}
 
const QString
PeptideFragment::getSequence() const
{
  QString sequence = msp_peptide.get()->getSequence();
  int diffSize     = msp_peptide.get()->size() - m_size;
  if(m_direction == PeptideDirection::Nter)
    {
      sequence = sequence.mid(0, m_size);
    }
  else
    {
      sequence = sequence.mid(diffSize, m_size);
    }
  return sequence;
}
 
 
int
PeptideFragment::getNumberOfAtom(Enums::AtomIsotopeSurvey atom) const
{
  int number = 0;
  if(m_direction == PeptideDirection::Nter)
    {
      std::vector<Aa>::const_iterator it(msp_peptide.get()->begin());
      std::vector<Aa>::const_iterator end(msp_peptide.get()->end());
      unsigned int i = 0;
      while(i < m_size)
        {
          number += it->getNumberOfAtom(atom);
          it++;
          i++;
        }
      if(msp_peptide.get()->getNterModification() != nullptr)
        {
          number += msp_peptide.get()->getNterModification()->getNumberOfAtom(atom);
        }
    }
  else
    {
      std::vector<Aa>::const_reverse_iterator it(msp_peptide.get()->rbegin());
      std::vector<Aa>::const_reverse_iterator end(msp_peptide.get()->rend());
      unsigned int i = 0;
      while(i < m_size)
        {
          number += it->getNumberOfAtom(atom);
          it++;
          i++;
        }
      if(msp_peptide.get()->getCterModification() != nullptr)
        {
          number += msp_peptide.get()->getCterModification()->getNumberOfAtom(atom);
        }
    }
  number += msp_peptide.get()->getCleavageNterModification()->getNumberOfAtom(atom);
  number += msp_peptide.get()->getCleavageCterModification()->getNumberOfAtom(atom);
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}
 
int
PeptideFragment::getNumberOfIsotope(Enums::Isotope isotope) const
{
  int number = 0;
  if(m_direction == PeptideDirection::Nter)
    {
      std::vector<Aa>::const_iterator it(msp_peptide.get()->begin());
      std::vector<Aa>::const_iterator end(msp_peptide.get()->end());
      unsigned int i = 0;
      while(i < m_size)
        {
          number += it->getNumberOfIsotope(isotope);
          it++;
          i++;
        }
      if(msp_peptide.get()->getNterModification() != nullptr)
        {
          number += msp_peptide.get()->getNterModification()->getNumberOfIsotope(isotope);
        }
    }
  else
    {
      std::vector<Aa>::const_reverse_iterator it(msp_peptide.get()->rbegin());
      std::vector<Aa>::const_reverse_iterator end(msp_peptide.get()->rend());
      unsigned int i = 0;
      while(i < m_size)
        {
          number += it->getNumberOfIsotope(isotope);
          it++;
          i++;
        }
      if(msp_peptide.get()->getCterModification() != nullptr)
        {
          number += msp_peptide.get()->getCterModification()->getNumberOfIsotope(isotope);
        }
    }
  number += msp_peptide.get()->getCleavageNterModification()->getNumberOfIsotope(isotope);
  number += msp_peptide.get()->getCleavageCterModification()->getNumberOfIsotope(isotope);
  // number += m_nterCterCleavage->getNumberOfIsotope(atom);
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}
 
 
const PeptideSp &
PeptideFragment::getPeptideSp() const
{
  return msp_peptide;
};
unsigned int
PeptideFragment::size() const
{
  return m_size;
}
 
pappso_double
PeptideFragment::getMass() const
{
  return m_mass;
}
 
PeptideDirection
PeptideFragment::getPeptideIonDirection() const
{
  return m_direction;
}
 
bool
PeptideFragment::isPalindrome() const
{
  return msp_peptide.get()->isPalindrome();
}
 
 
} // namespace pappso