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peptidefixedmodificationbuilder.h
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/*******************************************************************************
* Copyright (c) 2016 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 "peptidemodificatorbase.h"
namespace pappso
{
class PMSPP_LIB_DECL PeptideFixedModificationBuilder
: public PeptideModificatorBase
{
public:
PeptideFixedModificationBuilder(AaModificationP p_mod);
virtual ~PeptideFixedModificationBuilder();
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;
void addAa(char aa);
void
setSink(PeptideModificatorInterface *sink) override
{
m_sink = sink;
};
/** \brief this modification concerns the Nter peptide
* */
void
setProtNter(bool arg1)
{
m_isProtNterMod = arg1;
};
/** \brief this modification concerns the Cter peptide
* */
void
setProtCter(bool arg1)
{
m_isProtCterMod = arg1;
};
/** \brief this modification concerns all peptides between Nter and Cter
* */
void
setProtElse(bool arg1)
{
m_isProtElseMod = arg1;
};
private:
PeptideModificatorInterface *m_sink = nullptr;
const AaModificationP mp_mod;
// protein Nter modification
bool m_isProtNterMod = true;
// protein Cter modification
bool m_isProtCterMod = true;
// all peptide between Nter and Cter
bool m_isProtElseMod = true;
QString m_aaModificationList;
};
} // namespace pappso
pappso::AaModification
Definition aamodification.h:57
pappso::PeptideFixedModificationBuilder
Definition peptidefixedmodificationbuilder.h:35
pappso::PeptideFixedModificationBuilder::mp_mod
const AaModificationP mp_mod
Definition peptidefixedmodificationbuilder.h:80
pappso::PeptideFixedModificationBuilder::setProtElse
void setProtElse(bool arg1)
this modification concerns all peptides between Nter and Cter
Definition peptidefixedmodificationbuilder.h:72
pappso::PeptideFixedModificationBuilder::setProtCter
void setProtCter(bool arg1)
this modification concerns the Cter peptide
Definition peptidefixedmodificationbuilder.h:65
pappso::PeptideFixedModificationBuilder::setSink
void setSink(PeptideModificatorInterface *sink) override
Definition peptidefixedmodificationbuilder.h:51
pappso::PeptideFixedModificationBuilder::setProtNter
void setProtNter(bool arg1)
this modification concerns the Nter peptide
Definition peptidefixedmodificationbuilder.h:58
pappso::PeptideFixedModificationBuilder::m_aaModificationList
QString m_aaModificationList
Definition peptidefixedmodificationbuilder.h:89
pappso::PeptideModificatorBase
Definition peptidemodificatorbase.h:43
pappso::PeptideModificatorInterface
Definition enzymeproductinterface.h:65
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition exportinmportconfig.h:14
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition aamodification.h:48
pappso::ProteinSp
std::shared_ptr< const Protein > ProteinSp
shared pointer on a Protein object
Definition protein.h:47
peptidemodificatorbase.h
base class for all peptide modification builders