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grpexperiment.h
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/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
#pragma once
#include <map>
#include <QString>
#include <QDebug>
#include "../types.h"
#include "grpgroupingmonitor.h"
#include "grppeptideset.h"
#include "grpmappeptidetogroup.h"
#include "grpgroup.h"
#include "grpsubgroup.h"
namespace pappso
{
class PMSPP_LIB_DECL GrpExperiment
{
private:
GrpGroupingMonitorInterface *mp_monitor = nullptr;
bool m_isRemoveNonInformativeSubgroups = true;
std::map<QString, GrpProteinSp> m_mapProteins;
std::map<QString, std::map<unsigned long, GrpPeptideSp>> m_mapPeptides;
std::list<GrpPeptideSp> m_grpPeptideList;
std::list<GrpProteinSp> m_grpProteinList;
bool m_isGroupingStarted = false;
std::list<GrpProtein *> m_remainingGrpProteinList;
GrpPeptideSet m_grpPostGroupingProteinListRemoval;
GrpPeptideSet m_grpPreGroupingProteinListRemoval;
std::list<GrpGroupSp> m_grpGroupSpList;
void addSubGroupSp(GrpMapPeptideToGroup &grp_map_peptide_to_group,
GrpSubGroupSp &grpSubGroupSp) const;
void numbering();
void removeNonInformativeSubGroups();
public:
GrpProteinSp &getGrpProteinSp(const QString &acc, const QString &description);
GrpPeptideSp &setGrpPeptide(const GrpProteinSp &proteinSp,
const QString &sequence,
pappso_double mass);
GrpExperiment(GrpGroupingMonitorInterface *p_monitor);
virtual ~GrpExperiment();
void startGrouping();
std::vector<GrpProteinSpConst> getGrpProteinSpList() const;
void setRemoveNonInformativeSubgroups(bool ok);
/** @brief protein to remove with its entire group after grouping is completed
* typically : to use with protein contaminants if you want to ignore any
* group containing one contaminant protein
*/
void addPostGroupingGrpProteinSpRemoval(GrpProteinSp sp_protein);
/** @brief protein peptides to remove before grouping
* typically : remove protein contaminants in special metaproteomics cases
*/
void addPreGroupingGrpProteinSpRemoval(GrpProteinSp sp_protein);
std::vector<GrpGroupSpConst> getGrpGroupSpList() const;
};
} // namespace pappso
pappso::GrpExperiment
Definition grpexperiment.h:42
pappso::GrpExperiment::m_grpGroupSpList
std::list< GrpGroupSp > m_grpGroupSpList
Definition grpexperiment.h:58
pappso::GrpExperiment::m_grpPeptideList
std::list< GrpPeptideSp > m_grpPeptideList
Definition grpexperiment.h:49
pappso::GrpExperiment::m_grpPreGroupingProteinListRemoval
GrpPeptideSet m_grpPreGroupingProteinListRemoval
Definition grpexperiment.h:56
pappso::GrpExperiment::m_mapPeptides
std::map< QString, std::map< unsigned long, GrpPeptideSp > > m_mapPeptides
Definition grpexperiment.h:47
pappso::GrpExperiment::m_grpProteinList
std::list< GrpProteinSp > m_grpProteinList
Definition grpexperiment.h:50
pappso::GrpExperiment::m_grpPostGroupingProteinListRemoval
GrpPeptideSet m_grpPostGroupingProteinListRemoval
Definition grpexperiment.h:54
pappso::GrpExperiment::m_remainingGrpProteinList
std::list< GrpProtein * > m_remainingGrpProteinList
Definition grpexperiment.h:52
pappso::GrpExperiment::m_mapProteins
std::map< QString, GrpProteinSp > m_mapProteins
Definition grpexperiment.h:46
pappso::GrpGroupingMonitorInterface
Definition grpgroupingmonitor.h:33
pappso::GrpMapPeptideToGroup
Definition grpmappeptidetogroup.h:43
pappso::GrpPeptideSet
Definition grppeptideset.h:36
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition exportinmportconfig.h:14
grpgroup.h
grpgroupingmonitor.h
grpmappeptidetogroup.h
grppeptideset.h
grpsubgroup.h
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::GrpProteinSp
std::shared_ptr< GrpProtein > GrpProteinSp
Definition grpprotein.h:37
pappso::GrpSubGroupSp
std::shared_ptr< GrpSubGroup > GrpSubGroupSp
Definition grpsubgroup.h:39
pappso::GrpPeptideSp
std::shared_ptr< GrpPeptide > GrpPeptideSp
Definition grppeptide.h:40
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition types.h:50