MapAlignmentTransformer.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 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche $
// --------------------------------------------------------------------------


#ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTTRANSFORMER_H
#define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTTRANSFORMER_H

#include <vector>
#include <OpenMS/config.h>

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>

namespace OpenMS
{
  class TransformationDescription;
  class ConsensusMap;
  class PeptideIdentification;
  class ConsensusFeature;

  class OPENMS_DLLAPI MapAlignmentTransformer
  {

  public:
    static void transformRetentionTimes(PeakMap& msexp,
                                        const TransformationDescription& trafo,
                                        bool store_original_rt = false);

    static void transformRetentionTimes(
      FeatureMap& fmap, const TransformationDescription& trafo,
      bool store_original_rt = false);

    static void transformRetentionTimes(
      ConsensusMap& cmap, const TransformationDescription& trafo,
      bool store_original_rt = false);

    static void transformRetentionTimes(
      std::vector<PeptideIdentification>& pep_ids,
      const TransformationDescription& trafo, bool store_original_rt = false);

  private:
    static void applyToFeature_(Feature& feature,
                                const TransformationDescription& trafo,
                                bool store_original_rt = false);

    static void applyToBaseFeature_(BaseFeature& feature,
                                    const TransformationDescription& trafo,
                                    bool store_original_rt = false);

    static void applyToConsensusFeature_(
      ConsensusFeature& feature, const TransformationDescription& trafo,
      bool store_original_rt = false);

    static bool storeOriginalRT_(MetaInfoInterface& meta_info,
                                 double original_rt);

  };
} // namespace OpenMS

#endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTTRANSFORMER_H