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grpsubgroup.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 <memory>
#include <vector>
#include "grpprotein.h"
#include "grppeptideset.h"
namespace pappso
{
class GrpSubGroup;
typedef std::shared_ptr<const GrpSubGroup> GrpSubGroupSpConst;
typedef std::shared_ptr<GrpSubGroup> GrpSubGroupSp;
class GrpSubGroup
{
private:
std::vector<GrpProtein *> m_grpProteinPtrList;
GrpPeptideSet m_peptidePtrList;
unsigned int m_subGroupNumber = 0;
unsigned int m_groupNumber = 0;
public:
GrpSubGroup(GrpProtein *p_protein);
GrpSubGroup(const GrpSubGroup &other);
/** \brief sort subgroups between each other
* a subgroup containing less peptides is weaker (less) than the other
*/
bool operator<(const GrpSubGroup &other) const;
~GrpSubGroup();
GrpSubGroupSp makeGrpSubGroupSp();
const GrpPeptideSet &getPeptideSet() const;
bool merge(GrpSubGroup *p_subgroup);
bool includes(const GrpSubGroup *p_subgroup) const;
void numbering();
void setSubGroupNumber(unsigned int i);
void setGroupNumber(unsigned int i);
const QString &getFirstAccession() const;
std::size_t peptideListSize() const;
unsigned int maxCount() const;
const QString getGroupingId() const;
unsigned int getGroupNumber() const;
unsigned int getSubGroupNumber() const;
const std::vector<GrpProtein *> &getGrpProteinList() const;
};
} // namespace pappso
pappso::GrpPeptideSet
Definition grppeptideset.h:36
pappso::GrpProtein
Definition grpprotein.h:40
pappso::GrpSubGroup
Definition grpsubgroup.h:43
pappso::GrpSubGroup::operator<
bool operator<(const GrpSubGroup &other) const
sort subgroups between each other a subgroup containing less peptides is weaker (less) than the other
Definition grpsubgroup.cpp:86
pappso::GrpSubGroup::m_grpProteinPtrList
std::vector< GrpProtein * > m_grpProteinPtrList
Definition grpsubgroup.h:45
pappso::GrpSubGroup::getSubGroupNumber
unsigned int getSubGroupNumber() const
Definition grpsubgroup.cpp:52
pappso::GrpSubGroup::getGroupNumber
unsigned int getGroupNumber() const
Definition grpsubgroup.cpp:47
pappso::GrpSubGroup::~GrpSubGroup
~GrpSubGroup()
Definition grpsubgroup.cpp:122
pappso::GrpSubGroup::setSubGroupNumber
void setSubGroupNumber(unsigned int i)
Definition grpsubgroup.cpp:186
pappso::GrpSubGroup::getPeptideSet
const GrpPeptideSet & getPeptideSet() const
Definition grpsubgroup.cpp:132
pappso::GrpSubGroup::GrpSubGroup
GrpSubGroup(GrpProtein *p_protein)
Definition grpsubgroup.cpp:36
pappso::GrpSubGroup::getGroupingId
const QString getGroupingId() const
Definition grpsubgroup.cpp:62
pappso::GrpSubGroup::numbering
void numbering()
Definition grpsubgroup.cpp:196
pappso::GrpSubGroup::setGroupNumber
void setGroupNumber(unsigned int i)
Definition grpsubgroup.cpp:176
pappso::GrpSubGroup::includes
bool includes(const GrpSubGroup *p_subgroup) const
Definition grpsubgroup.cpp:163
pappso::GrpSubGroup::peptideListSize
std::size_t peptideListSize() const
Definition grpsubgroup.cpp:237
pappso::GrpSubGroup::maxCount
unsigned int maxCount() const
Definition grpsubgroup.cpp:73
pappso::GrpSubGroup::m_groupNumber
unsigned int m_groupNumber
Definition grpsubgroup.h:48
pappso::GrpSubGroup::getFirstAccession
const QString & getFirstAccession() const
Definition grpsubgroup.cpp:223
pappso::GrpSubGroup::merge
bool merge(GrpSubGroup *p_subgroup)
Definition grpsubgroup.cpp:138
pappso::GrpSubGroup::m_subGroupNumber
unsigned int m_subGroupNumber
Definition grpsubgroup.h:47
pappso::GrpSubGroup::getGrpProteinList
const std::vector< GrpProtein * > & getGrpProteinList() const
Definition grpsubgroup.cpp:57
pappso::GrpSubGroup::m_peptidePtrList
GrpPeptideSet m_peptidePtrList
Definition grpsubgroup.h:46
pappso::GrpSubGroup::makeGrpSubGroupSp
GrpSubGroupSp makeGrpSubGroupSp()
Definition grpsubgroup.cpp:126
grppeptideset.h
grpprotein.h
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::GrpSubGroupSpConst
std::shared_ptr< const GrpSubGroup > GrpSubGroupSpConst
Definition grpsubgroup.h:38
pappso::GrpSubGroupSp
std::shared_ptr< GrpSubGroup > GrpSubGroupSp
Definition grpsubgroup.h:39