ConsensusXMLHandler.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 2002-2022.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Clemens Groepl, Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/METADATA/PeptideEvidence.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <unordered_map>
#include <map>

namespace OpenMS
{
namespace Internal
{
  class OPENMS_DLLAPI ConsensusXMLHandler :
    public Internal::XMLHandler,
    public ProgressLogger
  {
public:
    ConsensusXMLHandler(ConsensusMap& map, const String& filename);
    ConsensusXMLHandler(const ConsensusMap& map, const String& filename);
    ~ConsensusXMLHandler() override;

    PeakFileOptions& getOptions();

    void setOptions(const PeakFileOptions&);

    const PeakFileOptions& getOptions() const;

    void writeTo(std::ostream& os) override;

protected:

    // 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;

    void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);

    void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
                           const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id,
                           const String& runid, XMLHandler::ActionMode mode);

    void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);

    PeakFileOptions options_;


    ConsensusMap* consensus_map_;
    const ConsensusMap* cconsensus_map_;
    ConsensusFeature act_cons_element_;
    DPosition<2> pos_;
    double it_;

    MetaInfoInterface* last_meta_;
    ProteinIdentification prot_id_;
    PeptideIdentification pep_id_;
    ProteinHit prot_hit_;
    PeptideHit pep_hit_;
    std::vector<PeptideEvidence> peptide_evidences_;
    std::map<String, String> proteinid_to_accession_;
    std::unordered_map<std::string, UInt> accession_to_id_;
    std::map<String, String> identifier_id_;
    std::map<String, String> id_identifier_;
    ProteinIdentification::SearchParameters search_param_;

    UInt progress_;
  };
} // namespace Internal
} // namespace OpenMS