IdXMLFile.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: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>
 
#include <vector>
 
namespace OpenMS
{
  namespace Internal
  {
    class FeatureXMLHandler;
    class ConsensusXMLHandler;
  }
  class OPENMS_DLLAPI IdXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    // both ConsensusXMLFile and FeatureXMLFile use some protected IdXML helper functions to parse identifications without code duplication
    friend class Internal::ConsensusXMLHandler;
    friend class Internal::FeatureXMLHandler;
 
    IdXMLFile();
 
    void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, PeptideIdentificationList& peptide_ids);
 
    void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, PeptideIdentificationList& peptide_ids, String& document_id);
 
    void store(const String& filename, const std::vector<ProteinIdentification>& protein_ids, const PeptideIdentificationList& peptide_ids, const String& document_id = "");
 
 
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;
 
    void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
                           const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id, XMLHandler::ActionMode mode);
 
    void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
 
    static std::ostream& createFlankingAAXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
 
    static std::ostream& createPositionXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
 
 
    static void writeFragmentAnnotations_(const String & tag_name, std::ostream & os, 
                                          const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent);
 
    static void parseFragmentAnnotation_(const String& s, std::vector<PeptideHit::PeakAnnotation> & annotations);
    
 
 
    std::vector<ProteinIdentification>* prot_ids_;
    PeptideIdentificationList* pep_ids_;
    MetaInfoInterface* last_meta_;
    std::map<String, ProteinIdentification::SearchParameters> parameters_;
    ProteinIdentification::SearchParameters param_;
    String id_;
    ProteinIdentification prot_id_;
    PeptideIdentification pep_id_;
    ProteinHit prot_hit_;
    PeptideHit pep_hit_;
    PeptideHit::PepXMLAnalysisResult current_analysis_result_;
    std::vector<PeptideEvidence> peptide_evidences_;
    std::unordered_map<std::string, String> proteinid_to_accession_;
    String* document_id_;
    bool prot_id_in_run_;
  };
 
} // namespace OpenMS