MapAlignerBase.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: Hendrik Weisser $
// $Authors: Marc Sturm, Clemens Groepl, Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/FileTypes.h>
 
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/KERNEL/StandardTypes.h>
 
#include <vector>
 
//-------------------------------------------------------------
// Doxygen docu
//-------------------------------------------------------------
 
// We do not want this class to show up in the docu:
 
namespace OpenMS
{
  // @brief stores model defaults for map aligner algorithms
  struct OPENMS_DLLAPI MapAlignerBase
  {
    static Param getModelDefaults(const std::string& default_model);
  };
 
 
class OPENMS_DLLAPI TOPPMapAlignerBase :
  public TOPPBase, public MapAlignerBase
{
 
public:
  TOPPMapAlignerBase(std::string name, std::string description, bool official = true) :
    TOPPBase(name, description, official), ref_params_(REF_NONE)
  {
  }
 
protected:
 
  // Kind of reference parameters that the tool offers:
  // - REF_NONE: no reference
  // - REF_RESTRICTED: reference file must have same type as input files
  // - REF_FLEXIBLE: reference file can have any supported file type
  enum ReferenceParameterKind { REF_NONE, REF_RESTRICTED, REF_FLEXIBLE }
    ref_params_;
 
  void registerOptionsAndFlagsMapAligners_(const std::string& file_formats,
                                           enum ReferenceParameterKind ref_params);
 
  ExitCodes checkParameters_();
 
  void transformSpectraFiles_(const StringList& in_spectra_files, 
                              const StringList& out_spectra_files,
                              const std::vector<TransformationDescription>& transformations,
                              bool store_original_rt);
 
};
 
}