libpappsomspp
Library for mass spectrometry
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peptidefragmentionlistbase.h
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1/**
2 * \file pappsomspp/peptide/peptidefragmentionlistbase.h
3 * \date 10/3/2015
4 * \author Olivier Langella
5 * \brief fragmentation base object
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
10 *
11 * This file is part of the PAPPSOms++ library.
12 *
13 * PAPPSOms++ is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms++ is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25 *
26 * Contributors:
27 * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
28 *implementation
29 ******************************************************************************/
30
31#pragma once
32
33#include <list>
34
35#include "peptidefragmention.h"
37
38namespace pappso
39{
40
41class PeptideFragmentIonListBase;
42typedef std::shared_ptr<const PeptideFragmentIonListBase>
44
46{
47 using IonList = std::list<PeptideIon>;
48
49 protected:
51 std::list<PeptideFragmentIonSp> msp_peptide_fragment_ion_list;
54
55 static const std::list<PeptideFragmentSp>
56 getPeptideFragmentList(const PeptideSp &peptide);
57
58 public:
59 PeptideFragmentIonListBase(const PeptideSp &peptide, const IonList &ions);
62 PeptideFragmentIonListBaseSp makePeptideFragmentIonListBaseSp() const;
63
64 const std::list<PeptideIon> &getIonList() const;
65 unsigned int
67 {
68 return m_phosphorylationNumber;
69 };
70
71 virtual const PeptideSp &
73 {
74 return msp_peptide;
75 };
76
77 const std::list<PeptideFragmentIonSp>
78 getPeptideFragmentIonSp(PeptideIon ion_type) const;
79 const PeptideFragmentIonSp &getPeptideFragmentIonSp(PeptideIon ion_type,
80 unsigned int size) const;
82 getPeptideFragmentIonSp(PeptideIon ion_type,
83 unsigned int size,
84 unsigned int number_of_neutral_phospho_loss) const;
85
86
87 std::list<PeptideFragmentIonSp>::const_iterator
88 begin() const
89 {
90 return msp_peptide_fragment_ion_list.begin();
91 }
92
93 std::list<PeptideFragmentIonSp>::const_iterator
94 end() const
95 {
96 return msp_peptide_fragment_ion_list.end();
97 }
98
99
100 const std::list<PeptideFragmentIonSp> &
102 {
103 return msp_peptide_fragment_ion_list;
104 }
105
106 static std::list<PeptideIon> getCIDionList();
107 static std::list<PeptideIon> getETDionList();
108
109
110 unsigned int
111 size() const
112 {
113 return msp_peptide_fragment_ion_list.size();
114 };
115};
116
117
118} // namespace pappso
std::list< PeptideFragmentIonSp > msp_peptide_fragment_ion_list
std::list< PeptideFragmentIonSp >::const_iterator begin() const
virtual const PeptideSp & getPeptideSp() const
const std::list< PeptideFragmentIonSp > & getPeptideFragmentIonList() const
std::list< PeptideFragmentIonSp >::const_iterator end() const
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition types.h:432
std::shared_ptr< const PeptideFragmentIon > PeptideFragmentIonSp
std::shared_ptr< const Peptide > PeptideSp
std::shared_ptr< const PeptideFragmentIonListBase > PeptideFragmentIonListBaseSp
peptide ion model