libpappsomspp
Library for mass spectrometry
deepprotenum.cpp
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1/**
2 * \file pappsomspp/psm/deepprot/deepprotenum.cpp
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#include <QObject>
33
34#include "deepprotenum.h"
35#include "../../pappsoexception.h"
36
39{
41 if(name == "delta_position")
42 {
44 }
45 else if(name == "no_delta_position")
46 {
48 }
49 else if(name == "uncategorized")
50 {
52 }
53 else if(name == "zero_mass_delta")
54 {
56 }
57 else if(name == "zero_mass_delta_mc")
58 {
60 }
61 else if(name == "zero_mass_delta_st")
62 {
64 }
65 else
66 {
68 QObject::tr("DeepProtMatchType unknown :\n%1").arg(name));
69 }
70 return match_type;
71}
72
73
76 const QString &name)
77{
78
81 if(name == "cter_removal")
82 {
84 }
85 else if(name == "delta_position")
86 {
88 }
89 else if(name == "missed_cleavage")
90 {
92 }
93 else if(name == "no_delta_position")
94 {
96 }
97 else if(name == "nter_removal")
98 {
100 }
101 else if(name == "zero_mass_delta")
102 {
104 }
105
106 else
107 {
109 QObject::tr("DeepProtPeptideCandidateStatus unknown :\n%1").arg(name));
110 }
111 return status;
112}
113
114const QString
116{
117
118 QString match_type_str;
119 switch(match_type)
120 {
122 match_type_str = "delta_position";
123 break;
125 match_type_str = "no_delta_position";
126 break;
128 match_type_str = "uncategorized";
129 break;
131 match_type_str = "zero_mass_delta";
132 break;
134 match_type_str = "zero_mass_delta_mc";
135 break;
137 match_type_str = "zero_mass_delta_st";
138 break;
139
140 default:
142 QObject::tr("DeepProtMatchType unknown :\n%1")
143 .arg((std::uint8_t)match_type));
144 }
145 return match_type_str;
146}
147
148const QString
150{
151
152 QString status_str;
153 switch(status)
154 {
156 status_str = "cter_removal";
157 break;
159 status_str = "delta_position";
160 break;
162 status_str = "missed_cleavage";
163 break;
165 status_str = "no_delta_position";
166 break;
168 status_str = "nter_removal";
169 break;
171 status_str = "zero_mass_delta";
172 break;
173
174 default:
176 QObject::tr("DeepProtPeptideCandidateStatus unknown :\n%1")
177 .arg((std::uint8_t)status));
178 }
179
180 return status_str;
181}
static const QString toString(DeepProtMatchType match_type)
static DeepProtMatchType DeepProtMatchTypeFromString(const QString &name)
static DeepProtPeptideCandidateStatus DeepProtPeptideCandidateStatusFromString(const QString &name)
base type definition to use in DeepProt
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