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 2002-2021.
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
 
#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(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