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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 "pappsomspp/export-import-config.h"
namespace pappso
{
class PeptideFragmentIonListBase;
typedef std::shared_ptr<const PeptideFragmentIonListBase> PeptideFragmentIonListBaseSp;
class PMSPP_LIB_DECL PeptideFragmentIonListBase
{
using IonList = std::list<Enums::PeptideIon>;
public:
PeptideFragmentIonListBase(const PeptideSp &peptide, const IonList &ions);
PeptideFragmentIonListBase(const PeptideFragmentIonListBase &other);
virtual ~PeptideFragmentIonListBase();
PeptideFragmentIonListBaseSp makePeptideFragmentIonListBaseSp() const;
const std::list<Enums::PeptideIon> &getIonList() const;
unsigned int getPhosphorylationNumber() const;
virtual const PeptideSp &getPeptideSp() const;
const std::list<PeptideFragmentIonSp> getPeptideFragmentIonSp(Enums::PeptideIon ion_type) const;
const PeptideFragmentIonSp &getPeptideFragmentIonSp(Enums::PeptideIon ion_type, unsigned int size) const;
const PeptideFragmentIonSp &getPeptideFragmentIonSp(
Enums::PeptideIon ion_type, unsigned int size, unsigned int number_of_neutral_phospho_loss) const;
std::list<PeptideFragmentIonSp>::const_iterator begin() const;
std::list<PeptideFragmentIonSp>::const_iterator end() const;
const std::list<PeptideFragmentIonSp> &getPeptideFragmentIonList() const;
static std::list<Enums::PeptideIon> getCIDionList();
static std::list<Enums::PeptideIon> getETDionList();
std::size_t size() const;
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);
};
} // namespace pappso
pappso::PeptideFragmentIonListBase
Definition peptidefragmentionlistbase.h:45
pappso::PeptideFragmentIonListBase::msp_peptide_fragment_ion_list
std::list< PeptideFragmentIonSp > msp_peptide_fragment_ion_list
Definition peptidefragmentionlistbase.h:82
pappso::PeptideFragmentIonListBase::IonList
std::list< Enums::PeptideIon > IonList
Definition peptidefragmentionlistbase.h:46
pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp
const std::list< PeptideFragmentIonSp > getPeptideFragmentIonSp(Enums::PeptideIon ion_type) const
Definition peptidefragmentionlistbase.cpp:226
pappso::PeptideFragmentIonListBase::getPhosphorylationNumber
unsigned int getPhosphorylationNumber() const
Definition peptidefragmentionlistbase.cpp:292
pappso::PeptideFragmentIonListBase::makePeptideFragmentIonListBaseSp
PeptideFragmentIonListBaseSp makePeptideFragmentIonListBaseSp() const
Definition peptidefragmentionlistbase.cpp:189
pappso::PeptideFragmentIonListBase::getETDionList
static std::list< Enums::PeptideIon > getETDionList()
Definition peptidefragmentionlistbase.cpp:59
pappso::PeptideFragmentIonListBase::getIonList
const std::list< Enums::PeptideIon > & getIonList() const
Definition peptidefragmentionlistbase.cpp:73
pappso::PeptideFragmentIonListBase::getPeptideSp
virtual const PeptideSp & getPeptideSp() const
Definition peptidefragmentionlistbase.cpp:286
pappso::PeptideFragmentIonListBase::PeptideFragmentIonListBase
PeptideFragmentIonListBase(const PeptideSp &peptide, const IonList &ions)
Definition peptidefragmentionlistbase.cpp:78
pappso::PeptideFragmentIonListBase::end
std::list< PeptideFragmentIonSp >::const_iterator end() const
Definition peptidefragmentionlistbase.cpp:304
pappso::PeptideFragmentIonListBase::m_ionList
IonList m_ionList
Definition peptidefragmentionlistbase.h:83
pappso::PeptideFragmentIonListBase::getPeptideFragmentList
static const std::list< PeptideFragmentSp > getPeptideFragmentList(const PeptideSp &peptide)
Definition peptidefragmentionlistbase.cpp:200
pappso::PeptideFragmentIonListBase::size
std::size_t size() const
Definition peptidefragmentionlistbase.cpp:274
pappso::PeptideFragmentIonListBase::getCIDionList
static std::list< Enums::PeptideIon > getCIDionList()
Definition peptidefragmentionlistbase.cpp:41
pappso::PeptideFragmentIonListBase::m_phosphorylationNumber
unsigned int m_phosphorylationNumber
Definition peptidefragmentionlistbase.h:84
pappso::PeptideFragmentIonListBase::begin
std::list< PeptideFragmentIonSp >::const_iterator begin() const
Definition peptidefragmentionlistbase.cpp:298
pappso::PeptideFragmentIonListBase::msp_peptide
const PeptideSp msp_peptide
Definition peptidefragmentionlistbase.h:81
pappso::PeptideFragmentIonListBase::getPeptideFragmentIonList
const std::list< PeptideFragmentIonSp > & getPeptideFragmentIonList() const
Definition peptidefragmentionlistbase.cpp:280
export-import-config.h
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
pappso::Enums::PeptideIon
PeptideIon
Enums::PeptideIon enum defines all types of ions (Nter or Cter).
Definition types.h:286
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::PeptideFragmentIonSp
std::shared_ptr< const PeptideFragmentIon > PeptideFragmentIonSp
Definition peptidefragmention.h:46
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition aamodification.h:48
pappso::PeptideFragmentIonListBaseSp
std::shared_ptr< const PeptideFragmentIonListBase > PeptideFragmentIonListBaseSp
Definition peptidefragmentionlistbase.h:42
peptidefragmention.h