libpappsomspp
Library for mass spectrometry
obopsimodterm.cpp
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1
2/*******************************************************************************
3 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
4 *
5 * This file is part of the PAPPSOms++ library.
6 *
7 * PAPPSOms++ is free software: you can redistribute it and/or modify
8 * it under the terms of the GNU General Public License as published by
9 * the Free Software Foundation, either version 3 of the License, or
10 * (at your option) any later version.
11 *
12 * PAPPSOms++ is distributed in the hope that it will be useful,
13 * but WITHOUT ANY WARRANTY; without even the implied warranty of
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 * GNU General Public License for more details.
16 *
17 * You should have received a copy of the GNU General Public License
18 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
19 *
20 * Contributors:
21 * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
22 *implementation
23 ******************************************************************************/
24
25#include <QDebug>
26#include "obopsimodterm.h"
27#include "../pappsoexception.h"
28
30 qRegisterMetaType<pappso::OboPsiModTerm>("pappso::OboPsiModTerm");
31
32inline void
34{
35 Q_INIT_RESOURCE(libpappsomsppresources);
36}
37
38
39namespace pappso
40{
41
42QRegularExpression OboPsiModTerm::m_firstParse("^([a-z,A-Z]+):\\s(.*)$");
44 "^(.*)\\sEXACT\\sPSI-MOD-label\\s\\[\\]$");
45
46// synonym: "Carbamidomethyl" RELATED PSI-MS-label []
48 "^(.*)\\sRELATED\\sPSI-MS-label\\s\\[\\]$");
49
50bool
52{
53 return (!m_accession.isEmpty());
54}
55
56void
57OboPsiModTerm::parseLine(const QString &line)
58{
59 // qDebug() << "OboPsiModTerm::parseLine begin " << line;
60 // id: MOD:00007
61 QRegularExpressionMatch match_line = m_firstParse.match(line);
62 if(match_line.hasMatch())
63 {
64 QStringList pline = match_line.capturedTexts();
65 // qDebug() << "OboPsiModTerm::parseLine match " << pline[0] << pline[1];
66 if(pline[1] == "id")
67 {
68 m_accession = pline[2].trimmed();
69 // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession;
70 }
71 else if(pline[1] == "name")
72 {
73 m_name = pline[2].trimmed();
74 // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession;
75 }
76 else if(pline[1] == "xref")
77 {
78 // xref: DiffMono: "1.007276"
79 QRegularExpressionMatch match_subline = m_firstParse.match(pline[2]);
80 if(match_subline.hasMatch())
81 {
82 QStringList psecond = match_subline.capturedTexts();
83 if(psecond[1] == "DiffMono")
84 {
85 m_diffMono = psecond[2].replace("\"", "").toDouble();
86 // qDebug() << "OboPsiModTerm::parseLine m_diffMono = " <<
87 // m_diffMono;
88 }
89 else if(psecond[1] == "DiffFormula")
90 {
91 m_diffFormula = psecond[2].trimmed().replace("\"", "");
92 // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
93 // m_diffFormula<<"|";
94 }
95 else if(psecond[1] == "Origin")
96 {
97 m_origin =
98 psecond[2].trimmed().replace("\"", "").replace(",", "");
99 // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
100 // m_diffFormula<<"|";
101 }
102 }
103 }
104 else if(pline[1] == "synonym")
105 {
106 // synonym: "Se(S)Res" EXACT PSI-MOD-label []
107 QRegularExpressionMatch match_exact_psimod =
108 m_findExactPsiModLabel.match(pline[2]);
109 if(match_exact_psimod.hasMatch())
110 {
112 match_exact_psimod.captured(1).trimmed().replace("\"", "");
113 // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" <<
114 // m_psiModLabel<<"|";
115 }
116 else
117 {
118 QRegularExpressionMatch match_related_psims =
119 m_findRelatedPsiMsLabel.match(pline[2]);
120 if(match_related_psims.hasMatch())
121 {
123 match_related_psims.captured(1).trimmed().replace("\"", "");
124 // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" <<
125 // m_psiModLabel<<"|";
126 }
127 }
128 }
129 else if(pline[1] == "def")
130 {
131 // def: "A protein modification that modifies an L-asparagine
132 // residue." [PubMed:18688235]
133 m_definition = pline[2];
134 }
135 }
136}
137void
139{
140 m_accession = "";
141 m_name = "";
142 m_definition = "";
143 m_psiModLabel = "";
144 m_diffFormula = "";
145 m_diffMono = 0;
146 m_origin = "";
147}
148
149} // namespace pappso
static QRegularExpression m_firstParse
Definition: obopsimodterm.h:58
void parseLine(const QString &line)
static QRegularExpression m_findRelatedPsiMsLabel
Definition: obopsimodterm.h:60
static QRegularExpression m_findExactPsiModLabel
Definition: obopsimodterm.h:59
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
void initMyResource()
int oboPsiModTermMetaTypeId