libpappsomspp
Library for mass spectrometry
peptidevariablemodificationbuilder.h
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1 /*******************************************************************************
2  * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
3  *
4  * This file is part of the PAPPSOms++ library.
5  *
6  * PAPPSOms++ is free software: you can redistribute it and/or modify
7  * it under the terms of the GNU General Public License as published by
8  * the Free Software Foundation, either version 3 of the License, or
9  * (at your option) any later version.
10  *
11  * PAPPSOms++ is distributed in the hope that it will be useful,
12  * but WITHOUT ANY WARRANTY; without even the implied warranty of
13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14  * GNU General Public License for more details.
15  *
16  * You should have received a copy of the GNU General Public License
17  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
18  *
19  * Contributors:
20  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
21  *implementation
22  ******************************************************************************/
23 
24 #pragma once
25 
26 
27 #include "peptidemodificatorbase.h"
28 
29 namespace pappso
30 {
31 
32 
33 /** \brief Modify a peptide shared pointer with a variable modification on one
34  * AA
35  * */
36 class PMSPP_LIB_DECL PeptideVariableModificationBuilder
37  : public PeptideModificatorBase
38 {
39  public:
40  PeptideVariableModificationBuilder(AaModificationP mod);
41  virtual ~PeptideVariableModificationBuilder();
42  void setPeptideSp(std::int8_t sequence_database_id,
43  const ProteinSp &protein_sp,
44  bool is_decoy,
45  const PeptideSp &peptide_sp_original,
46  unsigned int start,
47  bool is_nter,
48  unsigned int missed_cleavage_number,
49  bool semi_enzyme) override;
50 
51  void addAa(char aa);
52 
53  void
54  setMaxNumberMod(unsigned int max_num)
55  {
56  m_maxNumberMod = max_num;
57  };
58  void
59  setMinNumberMod(unsigned int min_num)
60  {
61  m_minNumberMod = min_num;
62  };
63  void
64  setModificationCounter(unsigned int counter)
65  {
66  m_modificationCount = counter;
67  };
68 
69  void
70  setSink(PeptideModificatorInterface *sink) override
71  {
72  m_sink = sink;
73  };
74 
75 
76  /** \brief this modification concerns the Nter peptide
77  * */
78  void
79  setProtNter(bool arg1)
80  {
81  m_isProtNterMod = arg1;
82  };
83  /** \brief this modification concerns the Cter peptide
84  * */
85  void
86  setProtCter(bool arg1)
87  {
88  m_isProtCterMod = arg1;
89  };
90  /** \brief this modification concerns all peptides between Nter and Cter
91  * */
92  void
93  setProtElse(bool arg1)
94  {
95  m_isProtElseMod = arg1;
96  };
97 
98  protected:
99  static bool next_combination(const std::vector<unsigned int>::iterator first,
100  std::vector<unsigned int>::iterator k,
101  const std::vector<unsigned int>::iterator last);
102 
103  PeptideModificatorInterface *m_sink = nullptr;
104  AaModificationP mp_mod;
105  // minimum number of positions to modify
106  unsigned int m_minNumberMod = 0;
107  // maximum number of positions to modify
108  unsigned int m_maxNumberMod = 30000;
109  // modification counter per site
110  unsigned int m_modificationCount = 0;
111 
112  // protein Nter modification
113  bool m_isProtNterMod = true;
114  // protein Cter modification
115  bool m_isProtCterMod = true;
116 
117  bool m_isProtElseMod = true;
118 
119 
120  private:
121  QString m_aaModificationList;
122 };
123 
124 
125 } // namespace pappso
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
peptidemodificatorbase.h
base class for all peptide modification builders
pappso::AaModificationP
const AaModification * AaModificationP
Definition: aamodification.h:73
pappso::PeptideModificatorInterface
Definition: enzymeproductinterface.h:86
pappso::ProteinSp
std::shared_ptr< const Protein > ProteinSp
shared pointer on a Protein object
Definition: protein.h:64
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition: aamodification.h:68
pappso::AaModification
Definition: aamodification.h:78