aa.cpp

Go to the documentation of this file.

/**
 * \file pappsomspp/amino_acid/aaBase.cpp
 * \date 7/3/2015
 * \author Olivier Langella
 * \brief amino acid 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 "pappsomspp/core/amino_acid/aa.h"
#include <QDebug>
#include <vector>
#include <QStringList>
#include <algorithm>
 
 
namespace pappso
{
 
Aa::Aa(char aa_letter) : AaBase(aa_letter)
{
}
 
 
Aa::Aa(Enums::AminoAcidChar aa_char) : AaBase(aa_char)
{
}
 
Aa::Aa(const Aa &other) : AaBase(other), m_listMod(other.m_listMod)
{
}
 
 
Aa::Aa(Aa &&toCopy) // move constructor
  : AaBase(toCopy), m_listMod(std::move(toCopy.m_listMod))
{
}
 
Aa::~Aa()
{
}
 
Aa &
Aa::operator=(const Aa &toCopy)
{
  m_aaLetter = toCopy.m_aaLetter;
  m_listMod  = toCopy.m_listMod;
  return *this;
}
 
const std::vector<AaModificationP> &
Aa::getModificationList() const
{
  return m_listMod;
}
 
double
Aa::getTotalModificationMass() const
{
  double mass = 0;
  for(auto &&mod : m_listMod)
    {
      mass += mod->getMass();
    }
  return mass;
}
 
pappso_double
Aa::getMass() const
{
  // qDebug() << "Aa::getMass() begin";
  pappso_double mass = AaBase::getMass();
  for(auto &&mod : m_listMod)
    {
      mass += mod->getMass();
    }
 
  // qDebug() << "Aa::getMass() end " << mass;
  return mass;
}
 
const QString
Aa::toAbsoluteString() const
{
  QString seq = "";
  seq += this->getLetter();
  auto it(m_listMod.begin());
  if(it != m_listMod.end())
    {
      QStringList modification_str_list;
      while(it != m_listMod.end())
        {
          modification_str_list << (*it)->getAccession();
          it++;
        }
      if(modification_str_list.size() > 0)
        seq += QString("(%1)").arg(modification_str_list.join(","));
    }
  return seq;
}
 
const QString
Aa::toString() const
{
  QString seq = "";
  seq += this->getLetter();
  auto it(m_listMod.begin());
  if(it != m_listMod.end())
    {
      QStringList modification_str_list;
      while(it != m_listMod.end())
        {
          if(!(*it)->isInternal())
            {
              modification_str_list << (*it)->getAccession();
            }
          it++;
        }
      if(modification_str_list.size() > 0)
        seq += QString("(%1)").arg(modification_str_list.join(","));
    }
  return seq;
}
 
const QString
Aa::toProForma() const
{
  QString seq = "";
  seq += this->getLetter();
 
  std::vector<AaModificationP> copy_mod_list = m_listMod;
  std::sort(copy_mod_list.begin(),
            copy_mod_list.end(),
            [](const AaModificationP &a, const AaModificationP &b) {
              return a->getAccession() < b->getAccession();
            });
  auto it(copy_mod_list.begin());
  if(it != copy_mod_list.end())
    {
      QStringList modification_str_list;
      while(it != copy_mod_list.end())
        {
          if(!(*it)->isInternal())
            {
              modification_str_list << (*it)->toProForma();
            }
          it++;
        }
      if(modification_str_list.size() > 0)
        seq += QString("[%1]").arg(modification_str_list.join("]["));
    }
  return seq;
}
 
void
Aa::removeAaModification(AaModificationP mod)
{
  std::vector<AaModificationP>::iterator it = std::find(m_listMod.begin(), m_listMod.end(), mod);
  if(it != m_listMod.end())
    {
      m_listMod.erase(it);
    }
 
  qDebug() << m_listMod << Qt::endl;
}
 
void
Aa::addAaModification(AaModificationP aaModification)
{
  qDebug();
  qDebug() << aaModification->getAccession();
  m_listMod.push_back(aaModification);
  sort(m_listMod.begin(), m_listMod.end());
  qDebug();
}
 
void
Aa::replaceAaModification(AaModificationP oldmod, AaModificationP newmod)
{
  std::replace(m_listMod.begin(), m_listMod.end(), oldmod, newmod);
  sort(m_listMod.begin(), m_listMod.end());
}
 
int
Aa::getNumberOfAtom(Enums::AtomIsotopeSurvey atom) const
{
  int number_of_carbon = AaBase::getNumberOfAtom(atom);
  for(auto &&mod : m_listMod)
    {
      number_of_carbon += mod->getNumberOfAtom(atom);
    }
 
  // qDebug() << "Aa::getMass() end " << mass;
  return number_of_carbon;
}
 
 
int
Aa::getNumberOfIsotope(Enums::Isotope isotope) const
{
  int number = 0;
  for(auto &&mod : m_listMod)
    {
      number += mod->getNumberOfIsotope(isotope);
    }
 
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}
 
unsigned int
Aa::getNumberOfModification(AaModificationP mod) const
{
  unsigned int number_of_mod = 0;
  for(auto &&modb : m_listMod)
    {
      if(modb == mod)
        number_of_mod += 1;
    }
 
  // qDebug() << "Aa::getMass() end " << mass;
  return number_of_mod;
}
 
void
Aa::removeAllButInternalModification()
{
 
  m_listMod.clear();
}
 
bool
Aa::isLesser(Aa const &r) const
{
  qDebug() << m_listMod << "//" << r.m_listMod;
  // qDebug() << "operator<(const Aa& l, const Aa& r)";
  if(m_aaLetter == r.m_aaLetter)
    {
      std::size_t a = m_listMod.size();
      std::size_t b = r.m_listMod.size();
 
      if(a == b)
        {
          return (m_listMod < r.m_listMod);
        }
      else
        {
          return (a < b);
        }
    }
  else
    {
      return (m_aaLetter < r.m_aaLetter);
    }
}
 
bool
Aa::isAaEqual(Aa const &r) const
{
 
  return (std::tie(m_aaLetter, m_listMod) == std::tie(r.m_aaLetter, r.m_listMod));
}
 
bool
operator==(Aa const &l, Aa const &r)
{
  return l.isAaEqual(r);
}
 
bool
operator<(Aa const &l, Aa const &r)
{
  return l.isLesser(r);
}
} /* namespace pappso */