libpappsomspp
Library for mass spectrometry
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types.h
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1/**
2 * \file pappsomspp/processing/specglob/types.h
3 * \date 14/11/2023
4 * \author Olivier Langella
5 * \brief SpecGlobTool types definition
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 * ANR founded project :
17 * https://anr.fr/Project-ANR-18-CE45-0004
18 */
19
20
21/*
22 * SpecGlobTool, Spectra to peptide alignment tool
23 * Copyright (C) 2023 Olivier Langella
24 * <olivier.langella@universite-paris-saclay.fr>
25 *
26 * This program is free software: you can redistribute ipetide to spectrum
27 * alignmentt and/or modify it under the terms of the GNU General Public License
28 * as published by the Free Software Foundation, either version 3 of the
29 * License, or (at your option) any later version.
30 *
31 * This program is distributed in the hope that it will be useful,
32 * but WITHOUT ANY WARRANTY; without even the implied warranty of
33 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
34 * GNU General Public License for more details.
35 *
36 * You should have received a copy of the GNU General Public License
37 * along with this program. If not, see <http://www.gnu.org/licenses/>.
38 *
39 */
40
41#pragma once
42
43namespace pappso
44{
45namespace specglob
46{
47enum class SpectralAlignmentType : std::uint8_t
48{
49 nonAlign =
50 0, ///< the type of alignment to put in origin matrix NON Alignment (0 - NA)
51 reAlign = 1, ///< Re Alignment (1 - RE)
52 align = 2, ///< Alignment (2 - AL)
53};
54
55
56enum class ScoreValueType : std::uint8_t
57{
58 scoreNonAlign = 0, ///< Score for non alignment (int)
59
60 scoreReAlignNative = 1, ////algorithm< Score for re-alignment native (int)
61 scoreReAlignSym = 2, ///< Score for re-alignment symetric (int)
62 scoreReAlignBoth = 3, ///< Score for re-alignment both (int)
63
64
65 scoreAlignNative = 4, ///< Score for good alignment native (int)
66 scoreAlignSym = 5, ///< Score for good alignment symetric (int)
67 scoreAlignBoth = 6, ///< Score for good alignment both (int)
68
70 7, ///< Score for re-alignment without offset native (int)
72 8, ///< Score for re-alignment without offset symetric (int)
73 scoreReAlignBothNO = 9, ///< Score for re-alignment without offset both (int)
74};
75
76
77enum class ExperimentalSpectrumDataPointType : std::uint8_t
78{
79 native = 0, ///< native peak, but has no mz counterpart (the complement ion),
80 ///< we had to compute the symetric mass
81 symetric =
82 1, ///< new peak : computed symetric mass from a corresponding native peak
83 both =
84 2, ///< both, the ion and the complement exists in the original spectrum
85 synthetic =
86 3, ///< does not correspond to existing peak, for computational purpose
87};
88} // namespace specglob
89} // namespace pappso
@ scoreAlignNative
Score for good alignment native (int)
@ scoreReAlignSymNO
Score for re-alignment without offset symetric (int)
@ scoreNonAlign
Score for non alignment (int)
@ scoreAlignBoth
Score for good alignment both (int)
@ scoreReAlignBoth
Score for re-alignment both (int)
@ scoreReAlignBothNO
Score for re-alignment without offset both (int)
@ scoreReAlignSym
Score for re-alignment symetric (int)
@ scoreAlignSym
Score for good alignment symetric (int)
@ scoreReAlignNativeNO
Score for re-alignment without offset native (int)
@ nonAlign
the type of alignment to put in origin matrix NON Alignment (0 - NA)
ExperimentalSpectrumDataPointType
Definition types.h:78
@ symetric
new peak : computed symetric mass from a corresponding native peak
@ synthetic
does not correspond to existing peak, for computational purpose
@ both
both, the ion and the complement exists in the original spectrum
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39