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/**
* \file /input/mascot/mascotdatparser.h
* \date 17/2/2018
* \author Olivier Langella
* \brief MASCOT dat file parser
*/
/*******************************************************************************
* Copyright (c) 2018 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 MASCOTDATPARSER_H
#define MASCOTDATPARSER_H
#include "../../core/project.h"
class MascotDatParser
{
public:
MascotDatParser(Project * p_project, IdentificationGroup * p_identification_group,
IdentificationDataSource * p_identification_data_source);
virtual ~MascotDatParser();
void parse(QIODevice * in_stream);
private:
void parseProteinLine(const QString & protein_line);
void parseHeaderLine(const QString & protein_line);
void parsePeptidesLine(const QString & peptide_line);
void parseQueryLine(const QString & query_line);
void parseSummaryLine(const QString & summary_line);
void saveQuery();
void saveAndClearPeptide();
struct PeptideLine {
unsigned int query_index=0;
unsigned int peptide_index=0;
QString subst;
QStringList peptide_string_list;
QStringList protein_string_list;
std::vector<FastaFileSp> fasta_file_list;
};
struct QueryLine {
unsigned int query_index=0;
unsigned int charge=0;
pappso::pappso_double rt=0;
QString title;
};
struct SummaryLine {
unsigned int match=0;
pappso::pappso_double exp_mass=0;
pappso::pappso_double plug_hole=0;
};
private:
Project * _p_project;
IdentificationGroup * _p_identification_group;
IdentificationDataSource * _p_identification_data_source;
ProteinXtp _current_protein;
std::vector<FastaFileSp> _fasta_file_list;
QRegExp _regexp_header_line;
unsigned int _number_of_queries=0;
unsigned int _number_of_residues=0;
std::vector<std::vector<PeptideLine>> _query_peptide_results;