proticdbml.h

/**
 * \file output/proticdbml.h
 * \date 11/5/2017
 * \author Olivier Langella
 * \brief PROTICdbML writer
 */

/*******************************************************************************
* 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
******************************************************************************/

#ifndef PROTICDBML_H
#define PROTICDBML_H

#include <QXmlStreamWriter>
#include <QFile>
#include <QString>
#include <QTime>
#include <pappsomspp/amino_acid/aamodification.h>
#include "../core/project.h"
#include "../grouping/groupinggroup.h"

struct ProticPeptideHit;

class ProticdbMl
{
    public:
    ProticdbMl(const QString & out_filename);
    ~ProticdbMl();

    void write(ProjectSp sp_project);
    void close();
    
private :
    void writeOboModif(pappso::AaModificationP mod);
    void writeCvParam(QString acc, QString value, QString description);
    void writeSequence(ProteinMatch * p_protein_match);
    void writeProject();
    void writeIdentMethod();
    void writeSamples();
    void writeMsRuns();
    void writeIdentificationRun(IdentificationGroup * p_identification);
    void writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source);
    void writepeptideHits(IdentificationGroup * p_identification);
    void writepeptideHitsbyGroup(GroupingGroup * p_group);
    void writePeptideHit(QString xml_id, ProticPeptideHit & protic_peptide_hit);
    void writePtms(PeptideXtp * p_peptide);
    void writeMatchs(IdentificationGroup * p_identification);
    
private :
    QFile * _output_file;
    QXmlStreamWriter * _output_stream;
    ProjectSp _sp_project;
    IdentificationGroup * _p_identification_group;
    QTime _duracel;
    std::map<QString, QString> _map_accession2xmlid;
    std::map<QString, QString> _sample_to_id;
    std::map<QString, QString> _peptidekey_to_id;
};

#endif // PROTICDBML_H