peptidefragmentionlistbase.h
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/**
* \file pappsomspp/peptide/peptidefragmentionlistbase.h
* \date 10/3/2015
* \author Olivier Langella
* \brief fragmentation base object
*/
/*******************************************************************************
* 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 <list>
#include "peptidefragmention.h"
#include "../exportinmportconfig.h"
namespace pappso
{
class PeptideFragmentIonListBase;
typedef std::shared_ptr<const PeptideFragmentIonListBase>
PeptideFragmentIonListBaseSp;
class PMSPP_LIB_DECL PeptideFragmentIonListBase
{
using IonList = std::list<PeptideIon>;
protected:
const PeptideSp msp_peptide;
std::list<PeptideFragmentIonSp> msp_peptide_fragment_ion_list;
IonList m_ionList;
unsigned int m_phosphorylationNumber;
static const std::list<PeptideFragmentSp>
getPeptideFragmentList(const PeptideSp &peptide);
public:
PeptideFragmentIonListBase(const PeptideSp &peptide, const IonList &ions);
PeptideFragmentIonListBase(const PeptideFragmentIonListBase &other);
virtual ~PeptideFragmentIonListBase();
PeptideFragmentIonListBaseSp makePeptideFragmentIonListBaseSp() const;
const std::list<PeptideIon> &getIonList() const;
unsigned int
getPhosphorylationNumber() const
{
return m_phosphorylationNumber;
};
virtual const PeptideSp &
getPeptideSp() const
{
return msp_peptide;
};
const std::list<PeptideFragmentIonSp>
getPeptideFragmentIonSp(PeptideIon ion_type) const;
const PeptideFragmentIonSp &getPeptideFragmentIonSp(PeptideIon ion_type,
unsigned int size) const;
const PeptideFragmentIonSp &
getPeptideFragmentIonSp(PeptideIon ion_type,
unsigned int size,
unsigned int number_of_neutral_phospho_loss) const;
std::list<PeptideFragmentIonSp>::const_iterator
begin() const
{
return msp_peptide_fragment_ion_list.begin();
}
std::list<PeptideFragmentIonSp>::const_iterator
end() const
{
return msp_peptide_fragment_ion_list.end();
}
const std::list<PeptideFragmentIonSp> &
getPeptideFragmentIonList() const
{
return msp_peptide_fragment_ion_list;
}
static std::list<PeptideIon> getCIDionList();
static std::list<PeptideIon> getETDionList();
unsigned int
size() const
{
return msp_peptide_fragment_ion_list.size();
};
};
} // namespace pappso
pappso::PeptideFragmentIonListBase
Definition: peptidefragmentionlistbase.h:46
pappso::PeptideFragmentIonListBase::msp_peptide_fragment_ion_list
std::list< PeptideFragmentIonSp > msp_peptide_fragment_ion_list
Definition: peptidefragmentionlistbase.h:51
pappso::PeptideFragmentIonListBase::getPhosphorylationNumber
unsigned int getPhosphorylationNumber() const
Definition: peptidefragmentionlistbase.h:66
pappso::PeptideFragmentIonListBase::begin
std::list< PeptideFragmentIonSp >::const_iterator begin() const
Definition: peptidefragmentionlistbase.h:88
pappso::PeptideFragmentIonListBase::IonList
std::list< PeptideIon > IonList
Definition: peptidefragmentionlistbase.h:47
pappso::PeptideFragmentIonListBase::getPeptideSp
virtual const PeptideSp & getPeptideSp() const
Definition: peptidefragmentionlistbase.h:72
pappso::PeptideFragmentIonListBase::size
unsigned int size() const
Definition: peptidefragmentionlistbase.h:111
pappso::PeptideFragmentIonListBase::m_ionList
IonList m_ionList
Definition: peptidefragmentionlistbase.h:52
pappso::PeptideFragmentIonListBase::end
std::list< PeptideFragmentIonSp >::const_iterator end() const
Definition: peptidefragmentionlistbase.h:94
pappso::PeptideFragmentIonListBase::getPeptideFragmentIonList
const std::list< PeptideFragmentIonSp > & getPeptideFragmentIonList() const
Definition: peptidefragmentionlistbase.h:101
pappso::PeptideFragmentIonListBase::m_phosphorylationNumber
unsigned int m_phosphorylationNumber
Definition: peptidefragmentionlistbase.h:53
pappso::PeptideFragmentIonListBase::msp_peptide
const PeptideSp msp_peptide
Definition: peptidefragmentionlistbase.h:50
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::PeptideIon
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:385
pappso::PeptideFragmentIonSp
std::shared_ptr< const PeptideFragmentIon > PeptideFragmentIonSp
Definition: peptidefragmention.h:44
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition: aamodification.h:47
pappso::PeptideFragmentIonListBaseSp
std::shared_ptr< const PeptideFragmentIonListBase > PeptideFragmentIonListBaseSp
Definition: peptidefragmentionlistbase.h:41
peptidefragmention.h
peptide ion model