identificationpwizfile.cpp

/**
 * \filed core/identification_sources/identificationpwizfile.cpp
 * \date 17/6/2017
 * \author Olivier Langella
 * \brief read identification files with proteowizard library
 */


/*******************************************************************************
* 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 "identificationpwizfile.h"
#include <pappsomspp/pappsoexception.h>
#include "../project.h"
#include "../../input/identificationpwizreader.h"

IdentificationPwizFile::IdentificationPwizFile(const QFileInfo & ident_file) : IdentificationDataSource(ident_file.absoluteFilePath()), _ident_file(ident_file)
{
    //_engine = IdentificationEngine::XTandem;
  _engine = IdentificationEngine::peptider;
}

IdentificationPwizFile::IdentificationPwizFile(const IdentificationPwizFile& other) : IdentificationDataSource(other),_ident_file (other._ident_file)
{
    _engine = other._engine;
}

IdentificationPwizFile::~IdentificationPwizFile()
{

}

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

}

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


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

    IdentificationPwizReader pwiz_reader(_ident_file);

    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunName());
    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->addIdentificationDataSourceP(this);
    pwiz_reader.read(this, p_project, identification_group_p);


    qDebug() << "IdentificationPwizFile::parseTo end";
      //  throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
    

}