UnimodXMLHandler.h

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// Copyright (c) 2002-present, OpenMS Inc. -- 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
  {
    class OPENMS_DLLAPI UnimodXMLHandler :
      public XMLHandler
    {
public:
      UnimodXMLHandler(std::vector<ResidueModification*>& mods, const std::string& filename);
 
      ~UnimodXMLHandler() override;
 
      // Docu in base class
      void onEndElement(const char16_t* qname) override;
 
      // Docu in base class
      void onStartElement(const char16_t* qname, const XMLAttributes& attributes) override;
 
      // Docu in base class
      void onCharacters(const char16_t* chars, Size /*length*/) override;
 
private:
 
      std::string tag_;
 
      double avge_mass_;
 
      double mono_mass_;
 
      EmpiricalFormula diff_formula_;
 
      bool collect_elements_{false};
 
      std::vector<EmpiricalFormula> neutral_loss_diff_formula_;
 
      double neutral_loss_mono_mass_{0.0};
      double neutral_loss_avge_mass_{0.0};
 
      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_;
      std::vector<std::vector<double>> neutral_loss_mono_masses_all_;
      std::vector<std::vector<double>> neutral_loss_avg_masses_all_;
 
      ResidueModification* modification_;
 
      std::vector<ResidueModification*>& modifications_;
 
      std::vector<char> sites_;
 
      std::vector<ResidueModification::TermSpecificity> term_specs_;
    };
 
  }   // namespace Internal
} // namespace OpenMS