peptidebuilder.cpp
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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
******************************************************************************/
#include "peptidebuilder.h"
#include <QDebug>
namespace pappso
{
PeptideBuilder::PeptideBuilder()
{
}
PeptideBuilder::~PeptideBuilder()
{
}
void
PeptideBuilder::addFixedAaModification(char aa, AaModificationP modification)
{
m_fixedModificationList.push_back(
std::pair<char, AaModificationP>(aa, modification));
}
void
PeptideBuilder::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)
{
qDebug() << "PeptideBuilder::setPeptide begin";
Peptide peptide(peptide_str);
for(auto &&aamod_pair : m_fixedModificationList)
{
std::vector<unsigned int> position_list =
peptide.getAaPositionList(aamod_pair.first);
for(auto &&position : position_list)
{
peptide.addAaModification(aamod_pair.second, position);
}
}
PeptideSp peptide_sp = peptide.makePeptideSp();
// set fixed modifications
qDebug() << "PeptideBuilder::setPeptide m_sink->setPeptideSp";
m_sink->setPeptideSp(sequence_database_id,
protein_sp,
is_decoy,
peptide_sp,
start,
is_nter,
missed_cleavage_number,
semi_enzyme);
qDebug() << "PeptideBuilder::setPeptide end";
}
} // namespace pappso
pappso::AaModification
Definition: aamodification.h:57
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:45
pappso::PeptideBuilder::PeptideBuilder
PeptideBuilder()
Definition: peptidebuilder.cpp:29
pappso::PeptideBuilder::m_sink
PeptideModificatorInterface * m_sink
Definition: peptidebuilder.h:60
pappso::PeptideBuilder::~PeptideBuilder
virtual ~PeptideBuilder()
Definition: peptidebuilder.cpp:33
pappso::PeptideBuilder::addFixedAaModification
void addFixedAaModification(char aa, AaModificationP modification)
Definition: peptidebuilder.cpp:37
pappso::PeptideModificatorInterface::setPeptideSp
virtual void setPeptideSp(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
function to give the products of modifications for a digested peptide
pappso::Peptide
Definition: peptide.h:93
pappso::Peptide::makePeptideSp
PeptideSp makePeptideSp() const
Definition: peptide.cpp:109
pappso::Peptide::getAaPositionList
std::vector< unsigned int > getAaPositionList(char aa) const
get positions of one amino acid in peptide
Definition: peptide.cpp:344
pappso::Peptide::addAaModification
void addAaModification(AaModificationP aaModification, unsigned int position)
adds a modification to amino acid sequence
Definition: peptide.cpp:121
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:47
pappso::ProteinSp
std::shared_ptr< const Protein > ProteinSp
shared pointer on a Protein object
Definition: protein.h:43
peptidebuilder.h