// --------------------------------------------------------------------------
//                   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.
// --------------------------------------------------------------------------
// 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;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest$
// $Authors: Hannes Roest$
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/config.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>

#include <vector>

namespace OpenMS
{

  /**
   * @brief Class to read a file describing the Swath Windows
   *
   * The file must of be tab delimited and of the following format:
   *    window_lower window_upper
   *    400 425
   *    425 450
   *    ...
   *
   * Note that the first line is a header and will be skipped.
   *
   */
  class OPENMS_DLLAPI SwathWindowLoader
  {

  public:

    /**
       @brief Annotate a Swath map using a Swath window file specifying the individual windows
     
       @note It is assumed that the files in the swath_maps vector are in the
       same order as the windows in the provided file (usually from lowest to
       highest).

       @param filename The filename of the tab delimited file
       @param swath_maps The list of SWATH maps (assumed to be in the same order as in the file)
       @param do_sort Sort the windows after reading in ascending order
       @param force Force overriding the window boundaries, even if the new boundaries are wider than the data boundaries
       
       @throw Exception::IllegalArgument if the number of maps in the file and the provided input maps to not match, or if the new boundaries are outside of the data boundaries (unless force==true)
    */
    static void annotateSwathMapsFromFile(const std::string& filename,
                                          std::vector<OpenSwath::SwathMap>& swath_maps,
                                          bool do_sort,
                                          bool force);

    /**
      @brief Reading a tab delimited file specifying the SWATH windows
     
      The file must of be tab delimited and of the following format:
         window_lower window_upper
         400 425
         425 450
         ...
     
      Note that the first line is a header and will be skipped.
     
      @param filename The filename of the tab delimited file
      @param swath_prec_lower The output vector for the window start
      @param swath_prec_upper The output vector for the window end

      @throw Exception::InvalidValue if window's start >= end

     *
     */
    static void readSwathWindows(const std::string& filename,
                                 std::vector<double>& swath_prec_lower,
                                 std::vector<double>& swath_prec_upper);
  };
}

