peptidesemienzyme.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 "peptidesemienzyme.h"
#include "../exception/exceptionnotpossible.h"
namespace pappso
{
PeptideSemiEnzyme::PeptideSemiEnzyme()
{
}
PeptideSemiEnzyme::~PeptideSemiEnzyme()
{
}
void
PeptideSemiEnzyme::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 (start == 1) {
// m_sink->setPeptide(protein_sp, peptide, start);
// 2 begin
// size = 6
// i=5
//}
if(semi_enzyme)
{
throw ExceptionNotPossible(
QObject::tr("ERROR : semi_ensyme flag is true.\n This is not possible, "
"because only PeptideSemiEnzyme is autorized to set it "
"true, and this can not be used several times."));
}
m_sink->setPeptide(sequence_database_id,
protein_sp,
is_decoy,
peptide,
start,
is_nter,
missed_cleavage_number,
false); // transmits orignal peptide
unsigned int max = peptide.size();
// unsigned int maxi = max-1;
for(unsigned int i = 1; i < max; i++)
{
m_sink->setPeptide(sequence_database_id,
protein_sp,
is_decoy,
peptide.left(i),
start,
is_nter,
missed_cleavage_number,
true);
m_sink->setPeptide(sequence_database_id,
protein_sp,
is_decoy,
peptide.right(i),
start + (max - i),
false,
missed_cleavage_number,
true);
}
}
} // namespace pappso
pappso::EnzymeProductInterface::setPeptide
virtual void setPeptide(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideStr &peptide, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
function to give the products of a protein digestion by an enzyme
pappso::ExceptionNotPossible
Definition: exceptionnotpossible.h:29
pappso::PeptideSemiEnzyme::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: peptidesemienzyme.cpp:39
pappso::PeptideSemiEnzyme::PeptideSemiEnzyme
PeptideSemiEnzyme()
Definition: peptidesemienzyme.cpp:30
pappso::PeptideSemiEnzyme::~PeptideSemiEnzyme
virtual ~PeptideSemiEnzyme()
Definition: peptidesemienzyme.cpp:34
pappso::PeptideSemiEnzyme::m_sink
EnzymeProductInterface * m_sink
Definition: peptidesemienzyme.h:65
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:43
pappso::XicExtractMethod::max
@ max
maximum of intensities
peptidesemienzyme.h