Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
/**
* \file /input/mascot/mascotdatparser.h
* \date 17/2/2018
* \author Olivier Langella
* \brief MASCOT dat file parser
*/
/*******************************************************************************
* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
*
* This file is part of XTPcpp.
*
* XTPcpp is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* XTPcpp is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
******************************************************************************/
#include "mascotdatparser.h"
#include "mimeparser.h"
#include <QDebug>
MascotDatParser::MascotDatParser(Project * p_project, IdentificationGroup * p_identification_group,
IdentificationDataSource * p_identification_data_source) {
_p_project = p_project;
_p_identification_group = p_identification_group;
_p_identification_data_source = p_identification_data_source;
}
MascotDatParser::~MascotDatParser() {
}
void MascotDatParser::parse(QIODevice * in_stream) {
qDebug() << "MascotDatParser::parse begin";
MimeParser mime_parser(in_stream);
mime_parser.open();
for(bool more=mime_parser.goToFirstFile(); more; more=mime_parser.goToNextFile()) {
qDebug() << "MascotDatParser::parse mimetype=" << mime_parser.getCurrentMimeType() << " filename=" << mime_parser.getCurrentFileName();
if (mime_parser.getCurrentFileName() == "proteins") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parseProteinLine( mime_parser.getCurrentTextStream().readLine());
}
}
}
mime_parser.close();
qDebug() << "MascotDatParser::parse end";
}
void MascotDatParser::parseProteinLine(const QString & protein_line) {
//02::"tr|A0A0D9SF80|A0A0D9SF80_HUMAN"=55120.88,"General transcription factor II-I repeat domain-containing protein 2A OS=Homo sapiens GN=GTF2IRD2B PE=4 SV=1"
QRegExp regexp_protein("^(.*)::\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
if (regexp_protein.exactMatch(protein_line)) {
QStringList protein_list = regexp_protein.capturedTexts();
}
else {
QRegExp regexp_proteinb("^\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
if (regexp_proteinb.exactMatch(protein_line)) {
QStringList protein_list = regexp_proteinb.capturedTexts();
}
else {
qDebug() << "MascotDatParser::parseProteinLine error " << protein_line;
}
}
}