SearchEngineBase.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
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#pragma once

#include "OpenMS/METADATA/ProteinIdentification.h"
#include <OpenMS/APPLICATIONS/TOPPBase.h>


namespace OpenMS
{
  
  class OPENMS_DLLAPI SearchEngineBase : public TOPPBase
  {
  public:
    SearchEngineBase() = delete;

    SearchEngineBase(const SearchEngineBase&) = delete;

    SearchEngineBase(const String& name, const String& description, bool official = true, const std::vector<Citation>& citations = {}, bool toolhandler_test = true);

    ~SearchEngineBase() override;

    String getRawfileName(int ms_level = 2) const;


    String getDBFilename(const String& db = "") const;


    virtual void registerPeptideIndexingParameter_(Param peptide_indexing_parameter);

    virtual SearchEngineBase::ExitCodes reindex_(
      std::vector<ProteinIdentification>& protein_identifications, 
      std::vector<PeptideIdentification>& peptide_identifications) const;
  }; // end SearchEngineBase

}   // end NS OpenMS