libpappsomspp
Library for mass spectrometry
peptidefixedmodificationbuilder.h
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1 
2 /*******************************************************************************
3  * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
4  *
5  * This file is part of the PAPPSOms++ library.
6  *
7  * PAPPSOms++ is free software: you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation, either version 3 of the License, or
10  * (at your option) any later version.
11  *
12  * PAPPSOms++ is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
19  *
20  * Contributors:
21  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
22  *implementation
23  ******************************************************************************/
24 
25 #pragma once
26 
27 
28 #include "peptidemodificatorbase.h"
29 
30 namespace pappso
31 {
32 
34  : public PeptideModificatorBase
35 {
36  public:
39  void setPeptideSp(std::int8_t sequence_database_id,
40  const ProteinSp &protein_sp,
41  bool is_decoy,
42  const PeptideSp &peptide_sp_original,
43  unsigned int start,
44  bool is_nter,
45  unsigned int missed_cleavage_number,
46  bool semi_enzyme) override;
47 
48  void addAa(char aa);
49 
50  void
52  {
53  m_sink = sink;
54  };
55  /** \brief this modification concerns the Nter peptide
56  * */
57  void
58  setProtNter(bool arg1)
59  {
60  m_isProtNterMod = arg1;
61  };
62  /** \brief this modification concerns the Cter peptide
63  * */
64  void
65  setProtCter(bool arg1)
66  {
67  m_isProtCterMod = arg1;
68  };
69  /** \brief this modification concerns all peptides between Nter and Cter
70  * */
71  void
72  setProtElse(bool arg1)
73  {
74  m_isProtElseMod = arg1;
75  };
76 
77  private:
78  PeptideModificatorInterface *m_sink = nullptr;
79 
81 
82  // protein Nter modification
83  bool m_isProtNterMod = true;
84  // protein Cter modification
85  bool m_isProtCterMod = true;
86  // all peptide between Nter and Cter
87  bool m_isProtElseMod = true;
88 
90 };
91 
92 } // namespace pappso
void setProtElse(bool arg1)
this modification concerns all peptides between Nter and Cter
void setProtCter(bool arg1)
this modification concerns the Cter peptide
void setSink(PeptideModificatorInterface *sink) override
void setProtNter(bool arg1)
this modification concerns the Nter peptide
#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
base class for all peptide modification builders