identificationdatasource.h

/*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
******************************************************************************/
#ifndef IDENTIFICATIONDATASOURCE_H
#define IDENTIFICATIONDATASOURCE_H


#include <pappsomspp/spectrum/spectrum.h>
#include <memory>
#include "../msrun.h"
#include "../../utils/fastafilestore.h"

class Project;

class IdentificationDataSource;
typedef std::shared_ptr<IdentificationDataSource> IdentificationDataSourceSp;

class IdentificationDataSource
{
public:

    IdentificationDataSource(const QString resource_name);
    IdentificationDataSource(const IdentificationDataSource& other);
    ~IdentificationDataSource();
    bool operator==(const IdentificationDataSource& other) const;

    const QString & getResourceName () const;
    const QString getSampleName () const;
    void setMsRunSp (MsRunSp ms_run_sp);
    MsRunSp getMsRunSp () const;
    /** @brief get the spectrum with scan number
     * */
    virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const;
    
    
    /** \brief read source content to store it in project
     */
    virtual void parseTo(Project* p_project)=0;
    
    /** \brief identification engine
     */
    virtual IdentificationEngine getIdentificationEngine() const;
    
    /** \brief identification engine version
     */
    virtual const QString& getIdentificationEngineVersion() const;
    /** \brief set identification engine version
     */
    virtual void setIdentificationEngineVersion(const QString& version);
    
    /** \brief set identification engine parameter value
     */
    virtual void setIdentificationEngineParam(IdentificationEngineParam param, const QString& value);
    
    /** \brief add Fastafile used by the identification engine
     */
    void addFastaFile (FastaFile file);
    
    const std::vector<FastaFileSp> & getFastaFileList() const;

protected :
    QString _resource_name;
    IdentificationEngine _engine = IdentificationEngine::unknown;
private :
    //static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
    static FastaFileStore _fasta_file_store;
    QString _version;
    MsRunSp _ms_run_sp = nullptr;
    std::map<IdentificationEngineParam, QString> _params;
    std::vector<FastaFileSp> _fastafile_list;
};

#endif // IDENTIFICATIONDATASOURCE_H