libpappsomspp
Library for mass spectrometry
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grpmappeptidetogroup.cpp
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1/**
2 * \file pappsomspp/grouping/grpmappeptidegroup.cpp
3 * \date 15/12/2017
4 * \author Olivier Langella
5 * \brief keep trace of peptide to group assignment
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.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@u-psud.fr> - initial API and
28 *implementation
29 ******************************************************************************/
30
32
33namespace pappso
34{
35
39
41 : m_mapPeptideToGroup(other.m_mapPeptideToGroup)
42{
43}
44
48
49void
51 const GrpPeptideSet &peptide_set_in,
52 std::list<GrpGroupSp> &impacted_group_list) const
53{
54 auto it_peptide_end = peptide_set_in.m_peptidePtrList.end();
55 std::map<GrpPeptide *, GrpGroupSp>::const_iterator it_map_end =
57
58 for(auto it_peptide = peptide_set_in.m_peptidePtrList.begin();
59 it_peptide != it_peptide_end;
60 it_peptide++)
61 {
62 std::map<GrpPeptide *, GrpGroupSp>::const_iterator it_map =
63 m_mapPeptideToGroup.find(*it_peptide);
64 if(it_map != it_map_end)
65 {
66 impacted_group_list.push_back(it_map->second);
67 }
68 }
69 impacted_group_list.sort();
70 impacted_group_list.unique();
71}
72
73void
75 GrpGroupSp grp_group)
76{
77
78 auto it_peptide_end = peptide_set_in.m_peptidePtrList.end();
79
80 for(auto it_peptide = peptide_set_in.m_peptidePtrList.begin();
81 it_peptide != it_peptide_end;
82 it_peptide++)
83 {
84 std::pair<std::map<GrpPeptide *, GrpGroupSp>::iterator, bool> ret =
86 std::pair<GrpPeptide *, GrpGroupSp>(*it_peptide, grp_group));
87 if(ret.second == false)
88 { //=> key already exists : replace by grp_group
89 ret.first->second = grp_group;
90 }
91 }
92}
93void
94GrpMapPeptideToGroup::clear(std::list<GrpGroupSp> &grp_group_list)
95{
96
97 std::list<GrpGroupSp> new_list;
98 for(auto &pair_map : m_mapPeptideToGroup)
99 {
100 new_list.push_back(pair_map.second);
101 }
102 new_list.sort();
103 new_list.unique();
104
105 grp_group_list.splice(grp_group_list.end(), new_list);
106 m_mapPeptideToGroup.clear();
107}
108} // namespace pappso
void clear(std::list< GrpGroupSp > &grp_group_list)
std::map< GrpPeptide *, GrpGroupSp > m_mapPeptideToGroup
void getGroupList(const GrpPeptideSet &peptide_set_in, std::list< GrpGroupSp > &impacted_group_list) const
get all groups concerned by a list of peptides
void set(const GrpPeptideSet &peptide_set_in, GrpGroupSp grp_group)
set peptide keys pointing on the group
std::list< GrpPeptide * > m_peptidePtrList
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
std::shared_ptr< GrpGroup > GrpGroupSp
Definition grpgroup.h:39