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peptidemodificatorpipeline.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 "enzymeproductinterface.h"
#include "peptidemodificatortee.h"
namespace pappso
{
class PMSPP_LIB_DECL PeptideModificatorPipeline
: public PeptideModificatorInterface,
public PeptideSpSinkInterface,
public EnzymeProductInterface
{
public:
PeptideModificatorPipeline();
PeptideModificatorPipeline(const PeptideModificatorPipeline &other);
virtual ~PeptideModificatorPipeline();
void addFixedModificationString(const QString &mod_str);
// protein Nter modification
void addFixedNterModificationString(const QString &mod_str);
// protein Cter modification
void addFixedCterModificationString(const QString &mod_str);
void addPotentialModificationString(const QString &mod_str);
// protein Nter modification
void addPotentialNterModificationString(const QString &mod_str);
// protein Cter modification
void addPotentialCterModificationString(const QString &mod_str);
void setSink(PeptideModificatorInterface *sink) override;
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 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 addLabeledModificationString(const QString &mod_str);
private:
PeptideModificatorTee *mp_peptideModificatorTee = nullptr;
PeptideModificatorInterface *m_sink = nullptr;
PeptideSpSinkInterface *mp_lastPeptideSinkInterface;
PeptideModificatorInterface *mp_firstModificator = nullptr;
std::vector<PeptideModificatorInterface *> m_pepModificatorPtrList;
void parseFixedModification(const QString &mod_str,
bool Nter,
bool Cter,
bool else_prot);
void privAddFixedModificationString(const QString &mod_str,
bool Nter,
bool Cter,
bool else_prot);
void parsePotentialModification(const QString &mod_str,
bool Nter,
bool Cter,
bool else_prot);
void privAddPotentialModificationString(const QString &mod_str,
bool Nter,
bool Cter,
bool else_prot);
void parseLabeledModification(const QString &mod_str,
bool Nter,
bool Cter,
bool else_prot);
};
} // namespace pappso
pappso::EnzymeProductInterface
Definition enzymeproductinterface.h:34
pappso::PeptideModificatorInterface
Definition enzymeproductinterface.h:65
pappso::PeptideModificatorPipeline
Definition peptidemodificatorpipeline.h:37
pappso::PeptideModificatorPipeline::m_pepModificatorPtrList
std::vector< PeptideModificatorInterface * > m_pepModificatorPtrList
Definition peptidemodificatorpipeline.h:86
pappso::PeptideModificatorPipeline::mp_lastPeptideSinkInterface
PeptideSpSinkInterface * mp_lastPeptideSinkInterface
Definition peptidemodificatorpipeline.h:82
pappso::PeptideModificatorTee
Definition peptidemodificatortee.h:35
pappso::PeptideSpSinkInterface
Definition enzymeproductinterface.h:108
enzymeproductinterface.h
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
peptidemodificatortee.h