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/**
* \file core/qvalue/computeqvalues.cpp
* \date 04/09/2019
* \author Olivier Langella
* \brief compute q-value for each peptide evidence (PSM) of a project
*/
/*******************************************************************************
* Copyright (c) 2019 Olivier Langella <olivier.langella@u-psud.fr>.
*
* This file is part of XTPcpp.
*
* XTPcpp 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.
*
* XTPcpp 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 XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#include "computeqvalues.h"
#include <pappsomspp/exception/exceptionnotimplemented.h>
ComputeQvalues::ComputeQvalues(ProjectSp project_sp)
{
std::vector<IdentificationDataSourceSp> identification_source_list =
project_sp.get()
->getIdentificationDataSourceStore()
.getIdentificationDataSourceList();
std::vector<PeptideEvidence *> tandem_peptide_evidence_list;
for(auto &identification_source_sp : identification_source_list)
{
if(identification_source_sp.get()->getIdentificationEngine() !=
IdentificationEngine::XTandem)
{
throw pappso::ExceptionNotImplemented(
QObject::tr("q-value computation for %1 identification engine is "
"not yet implemented")
.arg(
identification_source_sp.get()->getIdentificationEngineName()));
}
else
{
tandem_peptide_evidence_list.reserve(
tandem_peptide_evidence_list.size() +
identification_source_sp.get()->getPeptideEvidenceStore().size());
for(auto &pe_sp : identification_source_sp.get()
->getPeptideEvidenceStore()
.getPeptideEvidenceList())
{
tandem_peptide_evidence_list.push_back(pe_sp.get());
}
}
}
computeTandemPeptideEvidenceQvalues(tandem_peptide_evidence_list);
}
ComputeQvalues::~ComputeQvalues()
{
}
void
ComputeQvalues::computeTandemPeptideEvidenceQvalues(
std::vector<PeptideEvidence *> &tandem_peptide_evidence_list) const
{
// std::
}