xtandemsaxhandler.h

/**
 * \file input/xtandemsaxhandler.h
 * \date 5/4/2017
 * \author Olivier Langella
 * \brief parse XML X!Tandem result file
 */


/*******************************************************************************
* 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 XTANDEMSAXHANDLER_H
#define XTANDEMSAXHANDLER_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"

class XtandemSaxHandler: public QXmlDefaultHandler
{
public:
    XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group, 
    IdentificationDataSource * p_identification_data_source);
    ~XtandemSaxHandler();

    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;


private:
    bool startElement_group(QXmlAttributes attrs);
    bool startElement_protein(QXmlAttributes attributes);
    bool startElement_note(QXmlAttributes attributes);
    bool startElement_file(QXmlAttributes attributes);
    bool startElement_aa(QXmlAttributes attributes);
    bool startElement_domain(QXmlAttributes attributes);
    bool endElement_domain();
    bool endElement_note();

    pappso::AaModificationP getAaModificationP(pappso::mz mass) const;

private:
    std::vector<QString> _tag_stack;
    QString _errorStr;
    QString _current_text;

    Project * _p_project;
    IdentificationGroup * _p_identification_group;
    IdentificationDataSource * _p_identification_data_source;
    MsRunSp _sp_msrun;

    ProteinMatch * _p_protein_match;
    PeptideMatch * _p_peptide_match;
    ProteinXtp _current_protein;
    PeptideXtpSp _current_peptide_sp;

    QMap<QString, pappso::AaModificationP> _map_massstr_aamod;

    QString _current_group_label;
    QString _current_group_type;
    QString _current_note_label;
    QString _current_note_type;
    unsigned int _scan;
    pappso::pappso_double _mhplus_obser;
    unsigned int _charge;
    pappso::pappso_double _retention_time;
    bool _is_protein_description = false;
};

#endif // XTANDEMSAXHANDLER_H