peptideevidencestore.cpp

/**
 * \file utils/peptideevidencestore.cpp
 * \date 18/11/2017
 * \author Olivier Langella
 * \brief store unique instances of peptide evidences
 */



/*******************************************************************************
* Copyright (c) 2017 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/>.
*
* Contributors:
*     Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
******************************************************************************/

#include "peptideevidencestore.h"
#include <QDebug>
#include <pappsomspp/pappsoexception.h>

#include "../core/peptideevidence.h"
std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::recordInstance(const PeptideEvidence * p_peptide_evidence) {
    _peptide_evidence_list.push_back(p_peptide_evidence->makePeptideEvidenceSp());

    //qDebug() << "PeptideEvidenceStore::getInstance end " << find_it->second.get()->getScan() << " size=" << _multimap_scan_evidence.size();
    return _peptide_evidence_list.back();
}

std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::getInstance(const PeptideEvidence * p_peptide_evidence) {
    //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " scan=" << p_peptide_evidence->getScan();
    //qDebug() << "PeptideEvidenceStore::getInstance begin" ;
    std::multimap<unsigned int ,PeptideEvidenceSp>::iterator it = _multimap_scan_evidence.find(p_peptide_evidence->getScan());
    std::multimap<unsigned int ,PeptideEvidenceSp>::iterator find_it = _multimap_scan_evidence.end();


    while ((find_it == _multimap_scan_evidence.end()) && (it->first == p_peptide_evidence->getScan()) && (it != find_it)) {
        if (it->second.get()->getPeptideXtpSp().get() == p_peptide_evidence->getPeptideXtpSp().get()) {
            //it is the same peptide
            find_it = it;
        }
        else {
            //throw pappso::PappsoException(QObject::tr("PeptideEvidenceStore::getInstance multiple peptide for scan %1").arg(p_peptide_evidence->getScan()));
        }
        it++;
    }

    if (find_it == _multimap_scan_evidence.end()) {
        // insert it
        find_it = _multimap_scan_evidence.insert(std::pair<unsigned int , PeptideEvidenceSp>(p_peptide_evidence->getScan(), p_peptide_evidence->makePeptideEvidenceSp()));
        _peptide_evidence_list.push_back(find_it->second);
    }
    //qDebug() << "PeptideEvidenceStore::getInstance end " << find_it->second.get()->getScan() << " size=" << _multimap_scan_evidence.size();
    //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
    return find_it->second;

}


std::size_t PeptideEvidenceStore::size() const {
    return _peptide_evidence_list.size();
}

void PeptideEvidenceStore::clearMap() {
    qDebug() << "PeptideEvidenceStore::clearMap begin" ;
    _multimap_scan_evidence.clear();
    qDebug() << "PeptideEvidenceStore::clearMap end" ;

}

void PeptideEvidenceStore::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
    qDebug() << "PeptideEvidenceStore::updateAutomaticFilters begin" ;
    for (PeptideEvidenceSp & peptide_evidence_sp:_peptide_evidence_list) {
        peptide_evidence_sp.get()->updateAutomaticFilters(automatic_filter_parameters);
    }
    qDebug() << "PeptideEvidenceStore::updateAutomaticFilters end" ;

}

const std::vector<std::shared_ptr<PeptideEvidence>> & PeptideEvidenceStore::getPeptideEvidenceList() const {
    return _peptide_evidence_list;
}


void PeptideEvidenceStore::getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const {
    for (const PeptideEvidenceSp & peptide_evidence_sp:_peptide_evidence_list) {
        if (p_msrun != peptide_evidence_sp.get()->getMsRunP()) continue;
        else if (p_peptide != peptide_evidence_sp.get()->getPeptideXtpSp().get()) continue;
        else if (charge != peptide_evidence_sp.get()->getCharge()) continue;
        peptide_evidence_list.push_back(peptide_evidence_sp.get());
    }
}