identificationxtandemfile.cpp

/*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
******************************************************************************/
#include "identificationxtandemfile.h"
#include <pappsomspp/pappsoexception.h>
#include "../project.h"
#include "../../input/xtandemsaxhandler.h"

IdentificationXtandemFile::IdentificationXtandemFile(const QFileInfo & xtandem_file) : IdentificationDataSource(xtandem_file.absoluteFilePath()), _xtandem_file(xtandem_file)
{
}

IdentificationXtandemFile::IdentificationXtandemFile(const IdentificationXtandemFile& other) : IdentificationDataSource(other),_xtandem_file (other._xtandem_file)
{
}

IdentificationXtandemFile::~IdentificationXtandemFile()
{

}

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

}

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


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

    qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";

    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_xtandem_file).baseName());
    setMsRunSp(msrun_sp);
    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
    IdentificationGroup * identification_group_p = nullptr;
    if (p_project->isCombineMode()) {
        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->contains(msrun_sp.get())) {
                identification_group_p = identification_p_flist;
                break;
            }
        }
        if (identification_group_p == nullptr) {
            identification_group_p = p_project->newIdentificationGroup();
        }
    }
    
    identification_group_p->addMsRunSp(msrun_sp);
    XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p, this);

    QXmlSimpleReader simplereader;
    simplereader.setContentHandler(parser);
    simplereader.setErrorHandler(parser);

    QFile qfile(_xtandem_file.absoluteFilePath());
    QXmlInputSource xmlInputSource(&qfile);

    if (simplereader.parse(xmlInputSource)) {

        qfile.close();
    } else {
        qDebug() << parser->errorString();
        // throw PappsoException(
        //    QObject::tr("error reading tandem XML result file :\n").append(
        //         parser->errorString()));

        qfile.close();

        throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
    }

}