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peptidemethioninremove.cpp
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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
******************************************************************************/
#include "peptidemethioninremove.h"
namespace pappso
{
PeptideMethioninRemove::PeptideMethioninRemove(bool ism_isPotential)
{
m_isPotential = ism_isPotential;
}
PeptideMethioninRemove::~PeptideMethioninRemove()
{
}
void
PeptideMethioninRemove::setPeptide(std::int8_t sequence_database_id,
const ProteinSp &protein_sp,
bool is_decoy,
const QString &peptide,
unsigned int start,
bool is_nter,
unsigned int missed_cleavage_number,
bool semi_enzyme)
{
if(is_nter)
{
// Nter is often acetylated : MOD:00394
if(peptide[0] == 'M')
{
if(m_isPotential)
{
m_sink->setPeptide(sequence_database_id,
protein_sp,
is_decoy,
peptide,
start,
is_nter,
missed_cleavage_number,
semi_enzyme);
}
// peptide = peptide.right(peptide.size()-1);
m_sink->setPeptide(sequence_database_id,
protein_sp,
is_decoy,
peptide.right(peptide.size() - 1),
start + 1,
is_nter,
missed_cleavage_number,
semi_enzyme);
}
else
{
m_sink->setPeptide(sequence_database_id,
protein_sp,
is_decoy,
peptide,
start,
is_nter,
missed_cleavage_number,
semi_enzyme);
}
}
else
{
m_sink->setPeptide(sequence_database_id,
protein_sp,
is_decoy,
peptide,
start,
is_nter,
missed_cleavage_number,
semi_enzyme);
}
}
} // namespace pappso
pappso::PeptideMethioninRemove::m_sink
EnzymeProductInterface * m_sink
Definition peptidemethioninremove.h:38
pappso::PeptideMethioninRemove::setPeptide
void setPeptide(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const QString &peptide, 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 peptidemethioninremove.cpp:37
pappso::PeptideMethioninRemove::m_isPotential
bool m_isPotential
Definition peptidemethioninremove.h:39
pappso::PeptideMethioninRemove::PeptideMethioninRemove
PeptideMethioninRemove(bool ism_isPotential)
Definition peptidemethioninremove.cpp:27
pappso::PeptideMethioninRemove::~PeptideMethioninRemove
virtual ~PeptideMethioninRemove()
Definition peptidemethioninremove.cpp:32
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::ProteinSp
std::shared_ptr< const Protein > ProteinSp
shared pointer on a Protein object
Definition protein.h:47
peptidemethioninremove.h