libpappsomspp
Library for mass spectrometry
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scorevalues.h
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1/**
2 * \file pappsomspp/processing/specglob/scorevalues.h
3 * \date 06/11/2023
4 * \author Olivier Langella
5 * \brief scores to apply in comparisons
6 *
7 * C++ implementation of the SpecGlob algorithm described in :
8 * 1. Prunier, G. et al. Fast alignment of mass spectra in large proteomics
9 * datasets, capturing dissimilarities arising from multiple complex
10 * modifications of peptides. BMC Bioinformatics 24, 421 (2023).
11 *
12 * HAL Id : hal-04296170 , version 1
13 * Mot de passe : hxo20cl
14 * DOI : 10.1186/s12859-023-05555-y
15 */
16
17
18/*
19 * SpecGlobTool, Spectra to peptide alignment tool
20 * Copyright (C) 2023 Olivier Langella
21 * <olivier.langella@universite-paris-saclay.fr>
22 *
23 * This program is free software: you can redistribute it and/or modify
24 * it under the terms of the GNU General Public License as published by
25 * the Free Software Foundation, either version 3 of the License, or
26 * (at your option) any later version.
27 *
28 * This program is distributed in the hope that it will be useful,
29 * but WITHOUT ANY WARRANTY; without even the implied warranty of
30 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
31 * GNU General Public License for more details.
32 *
33 * You should have received a copy of the GNU General Public License
34 * along with this program. If not, see <http://www.gnu.org/licenses/>.
35 *
36 */
37
38#pragma once
39
40#include <cstdint>
42#include "types.h"
43
44
45namespace pappso
46{
47namespace specglob
48{
49
50/**
51 * @todo write docs
52 */
54{
55 public:
56 /**
57 * Default constructor
58 */
60
61
62 ScoreValues(const ScoreValues &other);
63
64 /**
65 * Destructor
66 */
67 virtual ~ScoreValues();
68
69 const ScoreValues &operator=(const ScoreValues &other);
70
71 int get(ScoreValueType type);
72
73 void set(ScoreValueType type, int value);
74
75 private:
76 int m_scoreTable[10];
77};
78} // namespace specglob
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
SpecGlobTool types definition.