ProtXMLFile.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>
 
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ProtXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:
 
    typedef ProteinIdentification::ProteinGroup ProteinGroup;
 
    ProtXMLFile();
 
    void load(const String & filename, ProteinIdentification & protein_ids, PeptideIdentification & peptide_ids);
 
    void store(const String & filename, const ProteinIdentification & protein_ids, const PeptideIdentification & peptide_ids, const String & document_id = "");
 
protected:
 
    void resetMembers_();
 
    void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
 
    void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
 
    void registerProtein_(const String & protein_name);
 
    void matchModification_(const double mass, const String & origin, String & modification_description);
 
 
    ProteinIdentification * prot_id_;
    PeptideIdentification * pep_id_;
    PeptideHit * pep_hit_;
    ProteinGroup protein_group_;
 
 
  };
 
} // namespace OpenMS