XTandemXMLFile.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 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
#include <stack>
 
namespace OpenMS
{
  class String;
  class ProteinIdentification;
 
  class OPENMS_DLLAPI XTandemXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:
 
    XTandemXMLFile();
 
    ~XTandemXMLFile() override;
    void load(const String& filename, ProteinIdentification& protein_identification, std::vector<PeptideIdentification>& id_data, ModificationDefinitionsSet& mod_def_set);
 
 
protected:
 
    // 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 endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
 
    // Docu in base class
    void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
 
    XTandemXMLFile(const XTandemXMLFile& rhs);
 
    XTandemXMLFile& operator=(const XTandemXMLFile& rhs);
 
private:
 
    ProteinIdentification* protein_identification_;
 
    // true during "note" element containing protein accession
    bool is_protein_note_;
 
    // true during "note" element containing spectrum ID
    bool is_spectrum_note_;
 
    // true after non-new protein entries, so that with the next "protein note" the
    // accession will not be updated again
    bool skip_protein_acc_update_;
 
    // peptide hits per spectrum
    std::map<UInt, std::vector<PeptideHit> > peptide_hits_;
 
    // protein hits
    std::vector<ProteinHit> protein_hits_;
 
    // protein unique IDs (assigned by X! Tandem), to keep track of which proteins were already seen
    std::set<UInt> protein_uids_;
 
    // accession of the current protein
    String current_protein_;
 
    // charge of current peptide
    Int current_charge_;
 
    // X! Tandem ID of current peptide
    UInt current_id_;
 
    // tag
    String tag_;
 
    // start position of current peptide in protein sequence
    UInt current_start_;
 
    // stop position of current peptide in protein sequence
    UInt current_stop_;
 
    // previous peptide sequence
    String previous_seq_;
 
    // mapping from X! Tandem ID to spectrum ID
    std::map<UInt, String> spectrum_ids_;
 
    // modification definitions
    ModificationDefinitionsSet mod_def_set_;
 
    // modifications used by X! Tandem by default
    ModificationDefinitionsSet default_nterm_mods_;
 
    // the possible type attributes of the group tag elements
    enum class GroupType
    {
      MODEL,
      PARAMETERS,
      SUPPORT
    };
 
    // stack of types of the group elements
    // they can be nested (e.g. a support group in a model group)
    // parsing of child elements sometimes depends on the group type
    std::stack<GroupType> group_type_stack_;
    
  };
 
} // namespace OpenMS