libpappsomspp
Library for mass spectrometry
deepprotenum.h
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1/**
2 * \file pappsomspp/psm/deepprot/deepprotenum.h
3 * \date 22/1/2021
4 * \author Olivier Langella <olivier.langella@universite-paris-saclay.fr>
5 * \brief base type definition to use in DeepProt
6 *
7 * DeepProt is the C++ implementation of the SpecOMS algorithm
8 *
9 */
10
11/*******************************************************************************
12 * Copyright (c) 2021 Olivier Langella
13 *<olivier.langella@universite-paris-saclay.fr>.
14 *
15 * This file is part of the PAPPSOms++ library.
16 *
17 * PAPPSOms++ is free software: you can redistribute it and/or modify
18 * it under the terms of the GNU General Public License as published by
19 * the Free Software Foundation, either version 3 of the License, or
20 * (at your option) any later version.
21 *
22 * PAPPSOms++ is distributed in the hope that it will be useful,
23 * but WITHOUT ANY WARRANTY; without even the implied warranty of
24 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 * GNU General Public License for more details.
26 *
27 * You should have received a copy of the GNU General Public License
28 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
29 *
30 ******************************************************************************/
31
32#pragma once
33#include "../../exportinmportconfig.h"
34#include <QString>
35
36namespace pappso
37{
38
39/** @brief definition of different class of PSMs used by DeepProt
40 */
41enum class DeepProtMatchType : std::uint8_t
42{
43 uncategorized = 0, ///< precursor mass was not compared
44 ZeroMassDelta = 1, ///< peptide candidate is in precursor mz range
46 2, ///< peptide candidate with missed cleavage is in precursor mz range
48 3, ///< semi tryptic peptide candidate is in precursor mz range
49 DeltaPosition = 4, ///< spectrum shifter on peptide candidate has detected a
50 ///< position for the mass delta
51 NoDeltaPosition = 5, ///< spectrum shifter on peptide candidate has not
52 ///< detected a position for the mass delta
53 last = 6
54};
55
56
57/** @brief definition of different status for potential peptide candidates on
58 * the same spectrum
59 */
60enum class DeepProtPeptideCandidateStatus : std::uint8_t
61{
62 unmodified = 0, ///< precursor mass was not compared
63 ZeroMassDelta = 1,
64 CterRemoval = 2,
65 NterRemoval = 3,
67 DeltaPosition = 5,
69 last = 7
70};
71
73{
74 public:
75 static const QString toString(DeepProtMatchType match_type);
76 static const QString toString(DeepProtPeptideCandidateStatus status);
77
79 DeepProtPeptideCandidateStatusFromString(const QString &name);
80 static DeepProtMatchType DeepProtMatchTypeFromString(const QString &name);
81};
82
83} // namespace pappso
84
85
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
DeepProtMatchType
definition of different class of PSMs used by DeepProt
Definition: deepprotenum.h:42
@ ZeroMassDeltaMissedCleavage
peptide candidate with missed cleavage is in precursor mz range
@ uncategorized
precursor mass was not compared
@ ZeroMassDelta
peptide candidate is in precursor mz range
@ ZeroMassDeltaSemiTryptic
semi tryptic peptide candidate is in precursor mz range
DeepProtPeptideCandidateStatus
definition of different status for potential peptide candidates on the same spectrum
Definition: deepprotenum.h:61
@ unmodified
precursor mass was not compared