libpappsomspp
Library for mass spectrometry
peptidemodificatorbase.cpp
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1 /**
2  * \file protein/peptidemodificatorbase.h
3  * \date 6/12/2016
4  * \author Olivier Langella
5  * \brief base class for all peptide modification builders
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms++ is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  * Contributors:
27  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
28  *implementation
29  ******************************************************************************/
30 
31 #include "peptidemodificatorbase.h"
32 
33 namespace pappso
34 {
36 {
37 }
38 
40 {
41 }
42 
43 void
45 {
46  m_pattern.setPattern(pattern);
47 }
48 
49 void
51  std::vector<unsigned int> &position_list, const QString &peptide_str)
52 {
53 
54  int pos = 0;
55  QRegularExpressionMatch match_pattern = m_pattern.match(peptide_str, pos);
56 
57  while(match_pattern.hasMatch())
58  {
59  pos = match_pattern.capturedStart(0);
60  if(match_pattern.lastCapturedIndex() == 0)
61  {
62  // no motif, just push position
63  position_list.push_back(pos);
64  pos++;
65  }
66  else
67  {
68  // there is a motif : target this position
69  pos = match_pattern.capturedStart(1);
70  if((position_list.size() > 0) &&
71  (position_list.back() == (unsigned int)pos))
72  {
73  pos = match_pattern.capturedStart(0) + 1;
74  }
75  else
76  {
77  position_list.push_back(pos);
78  pos = match_pattern.capturedStart(0) + 1;
79  }
80  }
81  match_pattern = m_pattern.match(peptide_str, pos);
82  }
83 }
84 
85 void
87  std::vector<unsigned int> &position_list,
88  const Peptide *p_peptide,
89  AaModificationP mod,
90  unsigned int modification_counter)
91 {
92 
93  int pos = 0;
94  const QString peptide_str = p_peptide->getSequence();
95  QRegularExpressionMatch match_pattern = m_pattern.match(peptide_str, pos);
96 
97  while(match_pattern.hasMatch())
98  {
99  pos = match_pattern.capturedStart(0);
100  if(match_pattern.lastCapturedIndex() == 0)
101  {
102  // no motif, just push position
103  if(p_peptide->getConstAa(pos).getNumberOfModification(mod) ==
104  modification_counter)
105  {
106  position_list.push_back(pos);
107  }
108  pos++;
109  }
110  else
111  {
112  // there is a motif : target this position
113  pos = match_pattern.capturedStart(1);
114  if((position_list.size() > 0) &&
115  (position_list.back() == (unsigned int)pos))
116  {
117  pos = match_pattern.capturedStart(0) + 1;
118  }
119  else
120  {
121  if(p_peptide->getConstAa(pos).getNumberOfModification(mod) ==
122  modification_counter)
123  {
124  position_list.push_back(pos);
125  }
126  pos = match_pattern.capturedStart(0) + 1;
127  }
128  }
129  match_pattern = m_pattern.match(peptide_str, pos);
130  }
131 }
132 } // namespace pappso
unsigned int getNumberOfModification(AaModificationP mod) const
Definition: aa.cpp:193
virtual void setModificationPattern(QString &pattern) final
set the pattern on which the modification will be applied (usually the list of concerned AA)
virtual void getModificationPositionList(std::vector< unsigned int > &position_list, const QString &peptide_str) final
const QString getSequence() const override
print amino acid sequence without modifications
Definition: peptide.cpp:155
const Aa & getConstAa(unsigned int position) const
Definition: peptide.cpp:545
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
base class for all peptide modification builders