libpappsomspp
Library for mass spectrometry
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grpexperiment.h
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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#pragma once
26
27#include <map>
28#include <QString>
29#include <QDebug>
30#include "../types.h"
31#include "grpgroupingmonitor.h"
32#include "grppeptideset.h"
34#include "grpgroup.h"
35#include "grpsubgroup.h"
36
37namespace pappso
38{
39
40
42{
43 private:
44 GrpGroupingMonitorInterface *mp_monitor = nullptr;
45 bool m_isRemoveNonInformativeSubgroups = true;
46 std::map<QString, GrpProteinSp> m_mapProteins;
47 std::map<QString, std::map<unsigned long, GrpPeptideSp>> m_mapPeptides;
48
49 std::list<GrpPeptideSp> m_grpPeptideList;
50 std::list<GrpProteinSp> m_grpProteinList;
51 bool m_isGroupingStarted = false;
52 std::list<GrpProtein *> m_remainingGrpProteinList;
53
55
57
58 std::list<GrpGroupSp> m_grpGroupSpList;
59
60 void addSubGroupSp(GrpMapPeptideToGroup &grp_map_peptide_to_group,
61 GrpSubGroupSp &grpSubGroupSp) const;
62 void numbering();
63 void removeNonInformativeSubGroups();
64
65 public:
66 GrpProteinSp &getGrpProteinSp(const QString &acc, const QString &description);
67 GrpPeptideSp &setGrpPeptide(const GrpProteinSp &proteinSp,
68 const QString &sequence,
69 pappso_double mass);
70
72 virtual ~GrpExperiment();
73
74 void startGrouping();
75
76 std::vector<GrpProteinSpConst> getGrpProteinSpList() const;
77
78 void setRemoveNonInformativeSubgroups(bool ok);
79
80 /** @brief protein to remove with its entire group after grouping is completed
81 * typically : to use with protein contaminants if you want to ignore any
82 * group containing one contaminant protein
83 */
84 void addPostGroupingGrpProteinSpRemoval(GrpProteinSp sp_protein);
85
86 /** @brief protein peptides to remove before grouping
87 * typically : remove protein contaminants in special metaproteomics cases
88 */
89 void addPreGroupingGrpProteinSpRemoval(GrpProteinSp sp_protein);
90
91 std::vector<GrpGroupSpConst> getGrpGroupSpList() const;
92};
93
94
95} // namespace pappso
std::list< GrpGroupSp > m_grpGroupSpList
std::list< GrpPeptideSp > m_grpPeptideList
GrpPeptideSet m_grpPreGroupingProteinListRemoval
std::map< QString, std::map< unsigned long, GrpPeptideSp > > m_mapPeptides
std::list< GrpProteinSp > m_grpProteinList
GrpPeptideSet m_grpPostGroupingProteinListRemoval
std::list< GrpProtein * > m_remainingGrpProteinList
std::map< QString, GrpProteinSp > m_mapProteins
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
std::shared_ptr< GrpProtein > GrpProteinSp
Definition grpprotein.h:37
std::shared_ptr< GrpSubGroup > GrpSubGroupSp
Definition grpsubgroup.h:39
std::shared_ptr< GrpPeptide > GrpPeptideSp
Definition grppeptide.h:40
double pappso_double
A type definition for doubles.
Definition types.h:50