// --------------------------------------------------------------------------
//                   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:
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//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Juliane Schmachtenberg, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/QC/QCBase.h>

namespace OpenMS
{
  class FeatureMap;
  class PeptideIdentification;
  class TransformationDescription;

  /**
    @brief Take the original retention time before map alignment and use the alignment's trafoXML
           for calculation of the new alignment retention times.

    Sets meta values "rt_raw" and "rt_align" in PeptideIdentifications of the featureMap's PepIDs.
    It does <b>not</b> change the RT of the features.

    **/
  class OPENMS_DLLAPI RTAlignment : public QCBase
  {
  public:
    /// Constructor
    RTAlignment() = default;

    /// Destructor
    virtual ~RTAlignment() = default;

    /**
     @brief Calculates retention time after map alignment
            and sets meta values "rt_raw" and "rt_align" in all PepIDs (on features and all unassigned PepIDs)

     @param fm: FeatureMap to receive the new metavalues
     @param trafo: Transformation information to get needed data from
    **/
    void compute(FeatureMap& fm, const TransformationDescription& trafo) const;

    /**
    @brief Calculates retention time after map alignment
    and sets meta values "rt_raw" and "rt_align" in all PepIDs

    @param ids: PepIDs to receive the new metavalues
    @param trafo: Transformation information to get needed data from
    **/
    void compute(std::vector<PeptideIdentification>& ids, const TransformationDescription& trafo) const;

    /// returns the name of the metric
    const String& getName() const override;

    /// define the required input file: featureXML before map alignment (=POSTFDRFEAT), trafoXML after map alignment (=TRAFOALIGN)
    Status requirements() const override;

  private:
    /// name of the metric
    const String name_ = "RTAlignment";
  };
} // namespace OpenMS
