libpappsomspp
Library for mass spectrometry
peptidestrparser.cpp
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1/*******************************************************************************
2 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
3 *
4 * This file is part of the PAPPSOms++ library.
5 *
6 * PAPPSOms++ is free software: you can redistribute it and/or modify
7 * it under the terms of the GNU General Public License as published by
8 * the Free Software Foundation, either version 3 of the License, or
9 * (at your option) any later version.
10 *
11 * PAPPSOms++ is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
18 *
19 * Contributors:
20 * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
21 *implementation
22 ******************************************************************************/
23
24#include <QStringList>
25#include "peptidestrparser.h"
26#include "../obo/filterobopsimodtermlabel.h"
27#include "../obo/filterobopsimodsink.h"
28
29namespace pappso
30{
31
32
33QRegularExpression PeptideStrParser::_mod_parser("\\([^)]*\\)");
34QRegularExpression PeptideStrParser::_rx_psimod("MOD:[0-9]+");
35QRegularExpression PeptideStrParser::_rx_modmass("[-+]?[0-9]+\\.?[0-9]*");
36
37void
38PeptideStrParser::parseStringToPeptide(const QString &pepstr, Peptide &peptide)
39{
40 // Peptide
41 // peptide2("C(MOD:00397+MOD:01160)C(MOD:00397)AADDKEAC(MOD:00397)FAVEGPK");
42 // CCAADDKEACFAVEGPK
43 /*
44 <psimod position="1" accession="MOD:00397"/>
45 <psimod position="2" accession="MOD:00397"/>
46 <psimod position="10" accession="MOD:00397"/>
47 <psimod position="1" accession="MOD:01160"/>
48 */
49 int matched_length_cumul = 0;
50 int pos = 0;
51
52 QRegularExpressionMatch match_mod = _mod_parser.match(pepstr, pos);
53
54 while(match_mod.hasMatch())
55 {
56 pos = match_mod.capturedStart(0);
57 QString captured = match_mod.captured(0);
58 qDebug() << " captured=" << captured << " pos=" << pos
59 << " match_mod.lastCapturedIndex()="
60 << match_mod.lastCapturedIndex();
61 QStringList mod_list = captured.mid(1, captured.size() - 2)
62 .split(QRegularExpression("[+,\\,]"));
63 for(QString &mod : mod_list)
64 {
65 qDebug() << "PeptideStrParser::parseString mod " << mod;
66 QRegularExpressionMatch match_psimod = _rx_psimod.match(mod);
67 if(match_psimod.hasMatch())
68 {
69 qDebug() << "PeptideStrParser::parseString pos-1 "
70 << (pos - 1 - matched_length_cumul);
72 pos - 1 - matched_length_cumul);
73 }
74 else if(mod.startsWith("internal:Nter_"))
75 {
78 }
79 else if(mod.startsWith("internal:Cter_"))
80 {
83 }
84 else
85 {
86 qDebug() << "mod=" << mod;
87 QRegularExpressionMatch match_modmass = _rx_modmass.match(mod);
88 if(match_modmass.hasMatch())
89 {
90 // number
91 qDebug() << "number mod=" << mod
92 << " cap=" << match_modmass.captured(0);
93 if(!mod.contains("."))
94 {
95 // integer
96 qDebug() << "integer mod=" << mod;
97 mod = "MOD:0000" + mod;
98 while(mod.size() > 9)
99 {
100 mod = mod.replace(4, 1, "");
101 }
102 peptide.addAaModification(
104 pos - 1 - matched_length_cumul);
105 }
106 else
107 {
108 qDebug() << "double mod=" << mod;
109 peptide.addAaModification(
111 mod.toDouble()),
112 pos - 1 - matched_length_cumul);
113 }
114 }
115 else
116 {
117 qDebug() << "not a number mod=" << mod;
118 FilterOboPsiModSink term_list;
119 FilterOboPsiModTermLabel filter_label(term_list, mod);
120
121 OboPsiMod psimod(filter_label);
122
123 peptide.addAaModification(
125 pos - 1 - matched_length_cumul);
126 }
127 }
128 }
129 matched_length_cumul += captured.size();
130 match_mod = _mod_parser.match(pepstr, pos + 1);
131 }
132}
133
135PeptideStrParser::parseString(const QString &pepstr)
136{
137
138 // QMutexLocker locker(&_mutex);
139 Peptide peptide(QString(pepstr).replace(_mod_parser, ""));
141
142 return (peptide.makePeptideSp());
143}
144
147{
148
149 // QMutexLocker locker(&_mutex);
150 Peptide peptide(QString(pepstr).replace(_mod_parser, ""));
152
153 return (peptide.makeNoConstPeptideSp());
154}
155} // namespace pappso
static AaModificationP getInstance(const QString &accession)
static AaModificationP getInstanceCustomizedMod(pappso_double modificationMass)
const OboPsiModTerm & getFirst()
static NoConstPeptideSp parseNoConstString(const QString &pepstr)
static QRegularExpression _rx_psimod
static PeptideSp parseString(const QString &pepstr)
static void parseStringToPeptide(const QString &pepstr, Peptide &peptide)
static QRegularExpression _rx_modmass
static QRegularExpression _mod_parser
PeptideSp makePeptideSp() const
Definition: peptide.cpp:125
NoConstPeptideSp makeNoConstPeptideSp() const
Definition: peptide.cpp:131
void setInternalCterModification(AaModificationP mod)
Definition: peptide.cpp:470
void setInternalNterModification(AaModificationP mod)
Definition: peptide.cpp:447
void addAaModification(AaModificationP aaModification, unsigned int position)
adds a modification to amino acid sequence
Definition: peptide.cpp:137
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const Peptide > PeptideSp
std::shared_ptr< Peptide > NoConstPeptideSp
Definition: peptide.h:97