// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/config.h> // OPENMS_DLLAPI
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <boost/regex.hpp>
#include <fstream>

namespace OpenMS
{
  /**
    @brief Load Chromeleon HPLC text file and save it into a `MSExperiment`.

    An example of the expected format:
    > Raw Data:
    > Time (min)	Step (s)	Value (mAU)
    > 0.003333	0.200	-0.002496
    > 0.006667	0.200	-0.017589
    > ...
  */
  class OPENMS_DLLAPI ChromeleonFile
  {
public:
    /// Constructor
    ChromeleonFile() = default;
    /// Destructor
    virtual ~ChromeleonFile() = default;

    /**
      @brief Load the file's data and metadata, and save it into a `MSExperiment`.

      @param[in] filename Path to the Chromeleon input file
      @param[out] experiment The variable into which the extracted information will be saved
    */
    void load(const String& filename, MSExperiment& experiment) const;

    /**
      @brief Remove commas from the string (used as thousands separators) and
      parse its value

      @param[in] number A string representing a floating-point number
      @return The value converted to `double`
    */
    double removeCommasAndParseDouble(String& number) const;
  };
}

