libpappsomspp
Library for mass spectrometry
Loading...
Searching...
No Matches
peptidemodificatorbase.h
Go to the documentation of this file.
1/**
2 * \file protein/peptidemodificatorbase.h
3 * \date 6/12/2016
4 * \author Olivier Langella
5 * \brief base class for all peptide modification builders
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
33
35
36namespace pappso
37{
38
39
43{
44
45 public:
48
49
50 /** \brief set the pattern on which the modification will be applied (usually
51 * the list of concerned AA) \details the pattern is a standard regular
52 * expression : it describes the target site to modify. This standard regular
53 * expression is used to make a replacement of all motifs describes by an
54 * underscore ("_") The underscore is taken as a landmark to apply the
55 * modification. \param pattern the regular expression pattern ( [YST] to
56 * replace Y, S and T with _ and modify it ). The pattern can also contain the
57 * / separator to eventually specify the replacement motif. This can be used
58 * to described very complex modification patterns
59 *
60 */
61 // :
62 virtual void setModificationPattern(QString &pattern) final;
63
64
65 protected:
66 QRegularExpression m_pattern;
67
68 virtual void
69 getModificationPositionList(std::vector<unsigned int> &position_list,
70 const QString &peptide_str) final;
71 virtual void
72 getModificationPositionList(std::vector<unsigned int> &position_list,
73 const Peptide *p_peptide,
75 unsigned int modification_counter);
76};
77
78
79} // namespace pappso
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39