peptidefragment.h
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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
******************************************************************************/
#pragma once
#include "peptide.h"
#include "../pappsoexception.h"
#include "../exportinmportconfig.h"
namespace pappso
{
class PeptideFragment;
typedef std::shared_ptr<const PeptideFragment> PeptideFragmentSp;
class PMSPP_LIB_DECL PeptideFragment : public PeptideInterface
{
public:
PeptideFragment(const PeptideSp &sp_peptide,
PeptideDirection direction,
unsigned int size);
PeptideFragment(const PeptideFragment &other);
PeptideFragment(PeptideFragment &&toCopy); // move constructor
virtual ~PeptideFragment();
virtual const PeptideSp &getPeptideSp() const;
virtual unsigned int size() const override;
virtual const QString getSequence() const override;
virtual pappso_double getMass() const override;
static const QString getPeptideIonDirectionName(PeptideDirection direction);
PeptideDirection getPeptideIonDirection() const;
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override;
virtual int getNumberOfIsotope(Isotope isotope) const override;
virtual bool isPalindrome() const override;
private:
const PeptideSp msp_peptide;
const PeptideDirection m_direction;
const unsigned int m_size = 0;
// the aa modification to add on Nter or Cter aa (depending on peptide
// direction)
AaModificationP m_nterCterCleavage;
pappso_double m_mass = 0;
};
} // namespace pappso
pappso::AaModification
Definition: aamodification.h:57
pappso::PeptideFragment
Definition: peptidefragment.h:48
pappso::PeptideFragment::msp_peptide
const PeptideSp msp_peptide
Definition: peptidefragment.h:74
pappso::PeptideFragment::m_nterCterCleavage
AaModificationP m_nterCterCleavage
Definition: peptidefragment.h:79
pappso::PeptideFragment::m_direction
const PeptideDirection m_direction
Definition: peptidefragment.h:75
pappso::PeptideInterface
Definition: peptideinterface.h:43
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition: exportinmportconfig.h:14
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition: aamodification.h:47
pappso::PeptideDirection
PeptideDirection
Definition: peptide.h:46
pappso::AtomIsotopeSurvey
AtomIsotopeSurvey
Definition: types.h:76
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:48
pappso::Isotope
Isotope
Definition: types.h:91
pappso::getPeptideIonDirection
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
Definition: peptide.cpp:54
pappso::PeptideFragmentSp
std::shared_ptr< const PeptideFragment > PeptideFragmentSp
Definition: peptidefragment.h:43
peptide.h
peptide model