identificationmascotdatfile.cpp

/**
 * \file /core/identification_sources/identificationmascotdatfile.cpp
 * \date 17/2/2018
 * \author Olivier Langella
 * \brief mascot dat identification file handler
 */

/*******************************************************************************
* Copyright (c) 2018 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 "identificationmascotdatfile.h"

#include <pappsomspp/pappsoexception.h>
#include "../project.h"
#include "../../input/mascot/mascotdatparser.h"

IdentificationMascotDatFile::IdentificationMascotDatFile(const QFileInfo & mascot_dat_file) : IdentificationDataSource(mascot_dat_file.absoluteFilePath()), _mascot_dat_file(mascot_dat_file)
{
    _engine = IdentificationEngine::mascot;
}

IdentificationMascotDatFile::IdentificationMascotDatFile(const IdentificationMascotDatFile& other) : IdentificationDataSource(other),_mascot_dat_file (other._mascot_dat_file)
{
    _engine = IdentificationEngine::mascot;
}

IdentificationMascotDatFile::~IdentificationMascotDatFile()
{

}

bool IdentificationMascotDatFile::operator==(const IdentificationMascotDatFile& other) const
{

}

pappso::SpectrumSp IdentificationMascotDatFile::getSpectrumSp(unsigned int scan_number) const {
    pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
    return spectrum_sp;
}


void IdentificationMascotDatFile::parseTo(Project* p_project) {
    qDebug() << "IdentificationMascotDatFile::parseTo begin";

    qDebug() << "Read Mascot dat result file '" << _mascot_dat_file.absoluteFilePath() << "'";

    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_mascot_dat_file).baseName());
    setMsRunSp(msrun_sp);
    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
    IdentificationGroup * identification_group_p = nullptr;
    if (p_project->getProjectMode() == ProjectMode::combined) {
        if (identification_list.size() == 0) {
            identification_group_p = p_project->newIdentificationGroup();
        }
        else {
            identification_group_p = identification_list[0];
        }
    }
    else {
        for (IdentificationGroup * identification_p_flist : identification_list) {
            if (identification_p_flist->containSample(msrun_sp.get()->getSampleName())) {
                identification_group_p = identification_p_flist;
                break;
            }
        }
        if (identification_group_p == nullptr) {
            identification_group_p = p_project->newIdentificationGroup();
        }
    }

    identification_group_p->addIdentificationDataSourceP(this);
    MascotDatParser mascot_parser(p_project, identification_group_p, this);

    QFile qfile(_mascot_dat_file.absoluteFilePath());
    mascot_parser.parse(&qfile);
    
    qfile.close();

    qDebug() << "IdentificationMascotDatFile::parseTo end";
}


const bool IdentificationMascotDatFile::isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const {
  
       return true;
}