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peptidebuilder.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 "enzymeproductinterface.h"
namespace pappso
{
/** \brief builds a peptide shared pointer from peptide string and adds fixed
* modifications
* */
class PMSPP_LIB_DECL PeptideBuilder : public EnzymeProductInterface,
PeptideSpSinkInterface
{
public:
PeptideBuilder();
virtual ~PeptideBuilder();
void setPeptide(std::int8_t sequence_database_id,
const ProteinSp &protein_sp,
bool is_decoy,
const QString &peptide_str,
unsigned int start,
bool is_nter,
unsigned int missed_cleavage_number,
bool semi_enzyme) override;
void addFixedAaModification(char aa, AaModificationP modification);
void
setSink(PeptideModificatorInterface *sink) override
{
m_sink = sink;
};
private:
PeptideModificatorInterface *m_sink = nullptr;
std::list<std::pair<char, AaModificationP>> m_fixedModificationList;
};
} // namespace pappso
pappso::EnzymeProductInterface
Definition enzymeproductinterface.h:34
pappso::PeptideBuilder::setSink
void setSink(PeptideModificatorInterface *sink) override
Definition peptidebuilder.h:54
pappso::PeptideBuilder::m_fixedModificationList
std::list< std::pair< char, AaModificationP > > m_fixedModificationList
Definition peptidebuilder.h:62
pappso::PeptideBuilder::setPeptide
void setPeptide(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const QString &peptide_str, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override
function to give the products of a protein digestion by an enzyme
Definition peptidebuilder.cpp:44
pappso::PeptideBuilder::PeptideBuilder
PeptideBuilder()
Definition peptidebuilder.cpp:29
pappso::PeptideBuilder::m_sink
PeptideModificatorInterface * m_sink
Definition peptidebuilder.h:60
pappso::PeptideBuilder::addFixedAaModification
void addFixedAaModification(char aa, AaModificationP modification)
Definition peptidebuilder.cpp:37
pappso::PeptideModificatorInterface
Definition enzymeproductinterface.h:65
pappso::PeptideSpSinkInterface
Definition enzymeproductinterface.h:108
enzymeproductinterface.h
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::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