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peptidenaturalisotope.h
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/**
* \file pappsomspp/peptide/peptidenaturalisotope.h
* \date 8/3/2015
* \author Olivier Langella
* \brief peptide natural isotope 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 "../exportinmportconfig.h"
namespace pappso
{
class PeptideNaturalIsotope;
typedef std::shared_ptr<const PeptideNaturalIsotope> PeptideNaturalIsotopeSp;
class PMSPP_LIB_DECL PeptideNaturalIsotope : public PeptideInterface
{
public:
PeptideNaturalIsotope(const PeptideInterfaceSp &peptide,
const std::map<Isotope, int> &map_isotope);
PeptideNaturalIsotope(const PeptideNaturalIsotope &other);
virtual ~PeptideNaturalIsotope();
virtual unsigned int size() const override;
virtual const QString getSequence() const override;
pappso_double getMass() const override;
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override;
virtual int getNumberOfIsotope(Isotope isotope) const override;
pappso_double getIntensityRatio(unsigned int charge) const;
const std::map<Isotope, int> &getIsotopeMap() const;
virtual unsigned int getIsotopeNumber() const;
virtual bool isPalindrome() const override;
private:
const PeptideInterfaceSp m_peptide;
const std::map<Isotope, int> m_mapIsotope;
pappso_double m_ratio;
pappso_double m_mass;
};
} // namespace pappso
pappso::PeptideInterface
Definition peptideinterface.h:43
pappso::PeptideNaturalIsotope
Definition peptidenaturalisotope.h:46
pappso::PeptideNaturalIsotope::m_mass
pappso_double m_mass
Definition peptidenaturalisotope.h:73
pappso::PeptideNaturalIsotope::m_peptide
const PeptideInterfaceSp m_peptide
Definition peptidenaturalisotope.h:69
pappso::PeptideNaturalIsotope::m_ratio
pappso_double m_ratio
Definition peptidenaturalisotope.h:72
pappso::PeptideNaturalIsotope::m_mapIsotope
const std::map< Isotope, int > m_mapIsotope
Definition peptidenaturalisotope.h:71
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::PeptideNaturalIsotopeSp
std::shared_ptr< const PeptideNaturalIsotope > PeptideNaturalIsotopeSp
Definition peptidenaturalisotope.h:43
pappso::PeptideInterfaceSp
std::shared_ptr< const PeptideInterface > PeptideInterfaceSp
Definition peptideinterface.h:39
pappso::AtomIsotopeSurvey
AtomIsotopeSurvey
Definition types.h:89
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition types.h:50
pappso::Isotope
Isotope
Definition types.h:104
peptide.h
peptide model