MapAlignmentTransformer.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche $
// --------------------------------------------------------------------------
 
 
#pragma once
 
#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>
#include <OpenMS/METADATA/ID/IdentificationData.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);
 
    static void transformRetentionTimes(IdentificationData& id_data,
                                        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