/**
 * \file input/xtpxpipsaxhandler.h
 * \date 17/11/2017
 * \author Olivier Langella
 * \brief parse new xpip files from xtpcpp
 */


/*******************************************************************************
* 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 XTPXPIPSAXHANDLER_H
#define XTPXPIPSAXHANDLER_H

#include <QXmlDefaultHandler>
#include <pappsomspp/pappsoexception.h>
#include "../core/proteinxtp.h"
#include "../core/peptidextp.h"
#include <pappsomspp/amino_acid/aamodification.h>
#include "../core/project.h"
#include "../core/proteinmatch.h"
#include "../utils/workmonitor.h"

class XtpXpipSaxHandler: public QXmlDefaultHandler
{
public:
    XtpXpipSaxHandler(WorkMonitorInterface * p_monitor, Project * p_project);
    ~XtpXpipSaxHandler();

    bool startElement(const QString & namespaceURI, const QString & localName,
                      const QString & qName, const QXmlAttributes & attributes);

    bool endElement(const QString & namespaceURI, const QString & localName,
                    const QString & qName);

    bool startDocument();

    bool endDocument();

    bool characters(const QString &str);

    bool fatalError(const QXmlParseException &exception);
    bool error(const QXmlParseException &exception);

    QString errorString() const;
    bool isXtpXpip() const;


private:
    bool startElement_filter_params(QXmlAttributes attributes);
    bool startElement_description(QXmlAttributes attributes);
    bool startElement_fasta_file(QXmlAttributes attributes);
    bool startElement_protein_match(QXmlAttributes attributes);
    bool startElement_peptide_match(QXmlAttributes attributes);
    bool startElement_peptide(QXmlAttributes attributes);
    bool startElement_peptide_evidence(QXmlAttributes attributes);
    bool startElement_protein(QXmlAttributes attributes);
    bool startElement_msrun(QXmlAttributes attributes);
    bool startElement_identification_source(QXmlAttributes attributes);
    bool startElement_modification(QXmlAttributes attributes);
    bool startElement_mod(QXmlAttributes attributes);
    //bool endElement_identification();
    bool endElement_sequence();
    bool endElement_protein();
    bool endElement_peptide();
    bool endElement_protein_match();

private:
    WorkMonitorInterface * _p_monitor;
    std::vector<QString> _tag_stack;
    QString _errorStr;
    QString _current_text;
    AutomaticFilterParameters _automatic_filter_parameters;

    Project * _p_project;
    ProteinMatch * _p_protein_match;
    PeptideMatch _current_peptide_match;
    PeptideEvidence * _p_peptide_evidence;
    IdentificationGroup * _current_identification_group_p;
    
    std::map<QString, pappso::AaModificationP> _map_modifs;
    std::map<QString, FastaFileSp> _map_fasta_files;
    std::map<QString, ProteinXtpSp> _map_proteins;
    std::map<QString, MsRunSp> _map_msruns;
    std::map<QString, IdentificationDataSourceSp> _map_ident_sources;
    std::map<QString, PeptideEvidenceSp> _map_peptide_evidences;
    ProteinXtp _current_protein;
    PeptideXtpSp _current_peptide_sp;
    std::map<QString, PeptideXtpSp> _map_peptides;
    uint _count_protein_match=0;
    uint _total_protein_match;
    bool _is_xtpcpp_xpip = false;
};

#endif // XTPXPIPSAXHANDLER_H