// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>

#include <vector>

namespace OpenMS
{
  namespace Internal
  {
    /**
    @brief Handler that is used for parsing XTandemXML data

  */
    class OPENMS_DLLAPI UnimodXMLHandler :
      public XMLHandler
    {
public:
      /// Default constructor
      UnimodXMLHandler(std::vector<ResidueModification*>& mods, const String& filename);

      /// Destructor
      ~UnimodXMLHandler() override;

      // Docu in base class
      void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;

      // Docu in base class
      void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;

      // Docu in base class
      void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;

private:

      String tag_;

      double avge_mass_;

      double mono_mass_;

      EmpiricalFormula diff_formula_;

      std::vector<EmpiricalFormula> neutral_loss_diff_formula_;

      bool was_valid_peptide_modification_;
      std::vector<std::vector<EmpiricalFormula>> neutral_loss_diff_formulas_;
      std::vector<double> neutral_loss_mono_masses_;
      std::vector<double> neutral_loss_avg_masses_;

      ResidueModification* modification_;

      std::vector<ResidueModification*>& modifications_;

      std::vector<char> sites_;

      std::vector<ResidueModification::TermSpecificity> term_specs_;
    };

  }   // namespace Internal
} // namespace OpenMS
