SearchEngineBase.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/APPLICATIONS/OpenMS_CLIConfig.h>
 
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/APPLICATIONS/TOPPExternalToolBase.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
 
namespace OpenMS
{
  
  class OPENMS_CLI_DLLAPI SearchEngineBase : public TOPPExternalToolBase
  {
  public:
    SearchEngineBase() = delete;
 
    SearchEngineBase(const SearchEngineBase&) = delete;
 
    SearchEngineBase(const std::string& name, const std::string& description, const std::vector<Citation>& citations = {}, bool toolhandler_test = true);
 
    ~SearchEngineBase() override;
 
    std::string getRawfileName(int ms_level = 2) const;
 
 
    std::string getDBFilename(const std::string& db = "") const;
 
 
    virtual void registerPeptideIndexingParameter_(Param peptide_indexing_parameter);
 
    virtual SearchEngineBase::ExitCodes reindex_(
      std::vector<ProteinIdentification>& protein_identifications,
      PeptideIdentificationList& peptide_identifications) const;
  }; // end SearchEngineBase
 
}   // end NS OpenMS