libpappsomspp
Library for mass spectrometry
peptidevariablemodificationreplacement.h
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1 /**
2  * \file protein/peptidevariablemodificationreplacement.h
3  * \date 1/12/2016
4  * \author Olivier Langella
5  * \brief potential replacement of a modification by an other
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2016 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 
34 
35 namespace pappso
36 {
37 
38 
41 {
42  public:
44  AaModificationP mod_after);
46 
47  void setPeptideSp(std::int8_t sequence_database_id,
48  const ProteinSp &protein_sp,
49  bool is_decoy,
50  const PeptideSp &peptide_sp_original,
51  unsigned int start,
52  bool is_nter,
53  unsigned int missed_cleavage_number,
54  bool semi_enzyme) override;
55 
56 
57  private:
58  void replaceModificationsAtPosition(Peptide &new_peptide,
59  unsigned int position);
60 
62 };
63 
64 
65 } // namespace pappso
Modify a peptide shared pointer with a variable modification on one AA.
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const Peptide > PeptideSp
std::shared_ptr< const Protein > ProteinSp
shared pointer on a Protein object
Definition: protein.h:43