ConsensusXMLFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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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/FORMAT/XMLFile.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/METADATA/PeptideEvidence.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <unordered_map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusXMLFile :
    public Internal::XMLHandler,
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    ConsensusXMLFile();
    ~ConsensusXMLFile() override;
 
    void load(const String& filename, ConsensusMap& map);
 
    void store(const String& filename, const ConsensusMap& consensus_map);
 
    PeakFileOptions& getOptions();
 
    const PeakFileOptions& getOptions() const;
 
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_;
    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_;
    Map<String, String> proteinid_to_accession_;
    std::unordered_map<std::string, UInt> accession_to_id_;
    Map<String, String> identifier_id_;
    Map<String, String> id_identifier_;
    ProteinIdentification::SearchParameters search_param_;
 
    UInt progress_;
  };
} // namespace OpenMS