UnimodXMLHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
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#pragma once

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

#include <vector>

namespace OpenMS
{
  namespace Internal
  {
    class OPENMS_DLLAPI UnimodXMLHandler :
      public XMLHandler
    {
public:
      UnimodXMLHandler(std::vector<ResidueModification*>& mods, const String& filename);

      ~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_;

      EmpiricalFormula neutral_loss_diff_formula_;

      bool was_valid_peptide_modification_;
      std::vector<EmpiricalFormula> neutral_loss_diff_formulas_;

      ResidueModification* modification_;

      std::vector<ResidueModification*>& modifications_;

      std::vector<char> sites_;

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

  }   // namespace Internal
} // namespace OpenMS