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 2002-2023.
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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_;
 
      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