libpappsomspp
Library for mass spectrometry
peptidefixedmodificationbuilder.cpp
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1
2/*******************************************************************************
3 * Copyright (c) 2016 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
26
27using namespace pappso;
28
29PeptideFixedModificationBuilder::PeptideFixedModificationBuilder(
30 AaModificationP p_mod)
31 : mp_mod(p_mod)
32{
33}
34
36{
37}
38
39void
41{
42
43
44 m_aaModificationList.append(aa);
45
46 m_pattern.setPattern(QString("[%1]").arg(m_aaModificationList));
47}
48
49
50void
52 std::int8_t sequence_database_id,
53 const ProteinSp &protein_sp,
54 bool is_decoy,
55 const PeptideSp &peptide_sp_original,
56 unsigned int start,
57 bool is_nter,
58 unsigned int missed_cleavage_number,
59 bool semi_enzyme)
60{
61
62 qDebug() << "PeptideFixedModificationBuilder::setPeptide begin";
63
64 std::vector<unsigned int> position_list;
65 getModificationPositionList(position_list,
66 peptide_sp_original.get()->getSequence());
67
68 Peptide peptide(*peptide_sp_original.get());
69 unsigned int size = peptide.size();
70
71 for(unsigned int pos : position_list)
72 {
73 if((m_isProtNterMod) && (is_nter))
74 {
75 peptide.addAaModification(mp_mod, pos);
76 }
77 else if((m_isProtCterMod) && (protein_sp.get()->size() == (start + size)))
78 {
79 peptide.addAaModification(mp_mod, pos);
80 }
81 else if(m_isProtElseMod)
82 {
83 peptide.addAaModification(mp_mod, pos);
84 }
85 }
86
87 PeptideSp peptide_sp = peptide.makePeptideSp();
88 // set fixed modifications
89 m_sink->setPeptideSp(sequence_database_id,
90 protein_sp,
91 is_decoy,
92 peptide_sp,
93 start,
94 is_nter,
95 missed_cleavage_number,
96 semi_enzyme);
97 qDebug() << "PeptideFixedModificationBuilder::setPeptide end";
98}
void setPeptideSp(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp_original, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override
function to give the products of modifications for a digested peptide
virtual void getModificationPositionList(std::vector< unsigned int > &position_list, const QString &peptide_str) final
virtual void setPeptideSp(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
function to give the products of modifications for a digested peptide
PeptideSp makePeptideSp() const
Definition: peptide.cpp:125
unsigned int size() const override
Definition: peptide.h:185
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< const Protein > ProteinSp
shared pointer on a Protein object
Definition: protein.h:47