libpappsomspp
Library for mass spectrometry
obopsimod.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 <QDir>
26 #include <QDebug>
27 #include "obopsimod.h"
28 #include "../pappsoexception.h"
29 #include <iostream>
30 
31 inline void
33 {
34  Q_INIT_RESOURCE(libpappsomsppresources);
35 }
36 
37 
38 namespace pappso
39 {
40 
41 OboPsiMod::OboPsiMod(OboPsiModHandlerInterface &handler) : m_handler(handler)
42 {
43  qDebug();
45  parse();
46 }
47 
49 {
50 }
51 
52 
53 void
55 {
56  // std::cout << "OboPsiMod::parse Begin parsing OBO file" << std::endl;
57  qDebug() << "OboPsiMod::parse Begin parsing OBO file";
58  QFile obofile(":/resources/PSI-MOD.obo");
59  if(!obofile.exists())
60  {
61  throw PappsoException(
62  QObject::tr("PSI-MOD OBO resource file : %1 not found")
63  .arg(obofile.fileName()));
64  }
65  obofile.open(QIODevice::ReadOnly);
66  QTextStream p_in(&obofile);
67 
68  // Search accession conta
69  // QTextStream in(p_in);
70  QString line = p_in.readLine();
71  bool in_term = false;
72  while(!p_in.atEnd())
73  {
74  // qDebug() << "OboPsiMod::parse line "<< line;
75  if(line.startsWith("[Term]"))
76  {
77  in_term = true;
78  m_term.clearTerm();
79  }
80  else if(line.isEmpty())
81  {
82  if(in_term)
83  {
85  in_term = false;
86  }
87  }
88  else
89  {
90  if(in_term)
91  m_term.parseLine(line);
92  // m_handler.setSequence(line);
93  }
94  line = p_in.readLine();
95  }
96  if(in_term)
97  {
99  }
100  // p_in->close();
101 
102  obofile.close();
103 }
104 
105 } // namespace pappso
virtual void setOboPsiModTerm(const OboPsiModTerm &term)=0
triggered function on each obo term when parsing obo file
void parseLine(const QString &line)
OboPsiMod(OboPsiModHandlerInterface &handler)
Definition: obopsimod.cpp:41
void parse()
starts reading obo file and reports each term with the callback function
Definition: obopsimod.cpp:54
OboPsiModTerm m_term
Definition: obopsimod.h:41
OboPsiModHandlerInterface & m_handler
Definition: obopsimod.h:42
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
void initMyResource()
Definition: obopsimod.cpp:32