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
29
30namespace pappso
31{
32
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:47
base class for all peptide modification builders