Loading...
Searching...
No Matches
peptidevariablemodificationreplacement.h
Go to the documentation of this file.
/**
* \file protein/peptidevariablemodificationreplacement.h
* \date 1/12/2016
* \author Olivier Langella
* \brief potential replacement of a modification by an other
*/
/*******************************************************************************
* 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 "peptidevariablemodificationbuilder.h"
namespace pappso
{
class PMSPP_LIB_DECL PeptideVariableModificationReplacement
: public PeptideVariableModificationBuilder
{
public:
PeptideVariableModificationReplacement(AaModificationP mod_before,
AaModificationP mod_after);
virtual ~PeptideVariableModificationReplacement();
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;
private:
void replaceModificationsAtPosition(Peptide &new_peptide,
unsigned int position);
AaModificationP mp_modAfter;
};
} // namespace pappso
pappso::PeptideVariableModificationBuilder::PeptideVariableModificationBuilder
PeptideVariableModificationBuilder(AaModificationP mod)
Definition peptidevariablemodificationbuilder.cpp:72
pappso::PeptideVariableModificationReplacement::PeptideVariableModificationReplacement
PeptideVariableModificationReplacement(AaModificationP mod_before, AaModificationP mod_after)
Definition peptidevariablemodificationreplacement.cpp:35
pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition
void replaceModificationsAtPosition(Peptide &new_peptide, unsigned int position)
Definition peptidevariablemodificationreplacement.cpp:51
pappso::PeptideVariableModificationReplacement::mp_modAfter
AaModificationP mp_modAfter
Definition peptidevariablemodificationreplacement.h:61
pappso::PeptideVariableModificationReplacement::setPeptideSp
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
function to give the products of modifications for a digested peptide
Definition peptidevariablemodificationreplacement.cpp:67
pappso::Peptide
Definition peptide.h:102
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.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::AaModificationP
const AaModification * AaModificationP
Definition aamodification.h:52
pappso::ProteinSp
std::shared_ptr< const Protein > ProteinSp
shared pointer on a Protein object
Definition protein.h:47
peptidevariablemodificationbuilder.h