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peptidefixedmodificationbuilder.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 "peptidefixedmodificationbuilder.h"
using namespace pappso;
PeptideFixedModificationBuilder::PeptideFixedModificationBuilder(
AaModificationP p_mod)
: mp_mod(p_mod)
{
}
PeptideFixedModificationBuilder::~PeptideFixedModificationBuilder()
{
}
void
PeptideFixedModificationBuilder::addAa(char aa)
{
m_aaModificationList.append(aa);
m_pattern.setPattern(QString("[%1]").arg(m_aaModificationList));
}
void
PeptideFixedModificationBuilder::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)
{
qDebug() << "PeptideFixedModificationBuilder::setPeptide begin";
std::vector<unsigned int> position_list;
getModificationPositionList(position_list,
peptide_sp_original.get()->getSequence());
Peptide peptide(*peptide_sp_original.get());
unsigned int size = peptide.size();
for(unsigned int pos : position_list)
{
if((m_isProtNterMod) && (is_nter))
{
peptide.addAaModification(mp_mod, pos);
}
else if((m_isProtCterMod) && (protein_sp.get()->size() == (start + size)))
{
peptide.addAaModification(mp_mod, pos);
}
else if(m_isProtElseMod)
{
peptide.addAaModification(mp_mod, pos);
}
}
PeptideSp peptide_sp = peptide.makePeptideSp();
// set fixed modifications
m_sink->setPeptideSp(sequence_database_id,
protein_sp,
is_decoy,
peptide_sp,
start,
is_nter,
missed_cleavage_number,
semi_enzyme);
qDebug() << "PeptideFixedModificationBuilder::setPeptide end";
}
pappso::AaModification
Definition aamodification.h:57
pappso::PeptideFixedModificationBuilder::PeptideFixedModificationBuilder
PeptideFixedModificationBuilder(AaModificationP p_mod)
Definition peptidefixedmodificationbuilder.cpp:29
pappso::PeptideFixedModificationBuilder::mp_mod
const AaModificationP mp_mod
Definition peptidefixedmodificationbuilder.h:80
pappso::PeptideFixedModificationBuilder::~PeptideFixedModificationBuilder
virtual ~PeptideFixedModificationBuilder()
Definition peptidefixedmodificationbuilder.cpp:35
pappso::PeptideFixedModificationBuilder::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 peptidefixedmodificationbuilder.cpp:51
pappso::PeptideFixedModificationBuilder::m_sink
PeptideModificatorInterface * m_sink
Definition peptidefixedmodificationbuilder.h:78
pappso::PeptideFixedModificationBuilder::m_isProtElseMod
bool m_isProtElseMod
Definition peptidefixedmodificationbuilder.h:87
pappso::PeptideFixedModificationBuilder::m_isProtNterMod
bool m_isProtNterMod
Definition peptidefixedmodificationbuilder.h:83
pappso::PeptideFixedModificationBuilder::m_isProtCterMod
bool m_isProtCterMod
Definition peptidefixedmodificationbuilder.h:85
pappso::PeptideFixedModificationBuilder::addAa
void addAa(char aa)
Definition peptidefixedmodificationbuilder.cpp:40
pappso::PeptideFixedModificationBuilder::m_aaModificationList
QString m_aaModificationList
Definition peptidefixedmodificationbuilder.h:89
pappso::PeptideModificatorBase::m_pattern
QRegularExpression m_pattern
Definition peptidemodificatorbase.h:66
pappso::PeptideModificatorBase::getModificationPositionList
virtual void getModificationPositionList(std::vector< unsigned int > &position_list, const QString &peptide_str) final
Definition peptidemodificatorbase.cpp:50
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:100
pappso::Peptide::makePeptideSp
PeptideSp makePeptideSp() const
Definition peptide.cpp:126
pappso::Peptide::size
unsigned int size() const override
Definition peptide.cpp:183
pappso::Peptide::addAaModification
void addAaModification(AaModificationP aaModification, unsigned int position)
adds a modification to amino acid sequence
Definition peptide.cpp:188
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
peptidefixedmodificationbuilder.h