IdXMLFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
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#pragma once

#include <OpenMS/CONCEPT/ProgressLogger.h>
#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
{
  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, std::vector<PeptideIdentification>& peptide_ids);

    void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, String& document_id);

    void store(const String& filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& 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_;
    std::vector<PeptideIdentification>* 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