XQuestResultXMLHandler.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 2002-2017.
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// $Maintainer: Lukas Zimmermann $
// $Authors: Lukas Zimmermann $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_HANDLERS_XQUESTRESULTXMLHANDLER_H
#define OPENMS_FORMAT_HANDLERS_XQUESTRESULTXMLHANDLER_H

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/CHEMISTRY/EnzymesDB.h>

namespace OpenMS
{
  namespace Internal
  {
    class OPENMS_DLLAPI XQuestResultXMLHandler :
      public XMLHandler
    {
    public:

      // Maps enzyme_num in xQuest result file to the enzyme name used by OpenMS
      static std::map< Size, String > enzymes;

      // Maps String encoding month to the numeric value
      static std::map<String, UInt> months;

      // Decoy string used by xQuest
      static const String decoy_string;

      XQuestResultXMLHandler(const String & filename,
                             std::vector< std::vector< PeptideIdentification > > & csms,
                             std::vector< ProteinIdentification > & prot_ids,
                             Size min_n_ions_per_spectrum,
                             bool load_to_peptideHit_);
      virtual ~XQuestResultXMLHandler();

      // Docu in base class
      void endElement(const XMLCh * const uri, const XMLCh * const local_name, const XMLCh * const qname);

      // Docu in base class
      void startElement(const XMLCh * const uri, const XMLCh * const local_name, const XMLCh * const qname, const xercesc::Attributes & attributes);

      double getMinScore() const;

      double getMaxScore() const;

      UInt getNumberOfHits() const;

    private:

      // Main data structures that are populated during loading the file
      std::vector< std::vector< PeptideIdentification > > & csms_;
      std::vector< ProteinIdentification > & prot_ids_;

      UInt n_hits_; // Total no. of hits found in the result XML file

      // Keeps track of the minscore and maxscore encountered
      double min_score_;
      double max_score_;

      Size min_n_ions_per_spectrum_;
      bool load_to_peptideHit_;  // Whether Meta data of peptide identification should also be loaded to peptide hit

      // Whether or not current xquest result tag comes from OpenProXL (xQuest otherwise)
      bool is_openproxl_;

      // Set of all protein accessions that are within the ProteinHits.
      std::set< String > accessions_;

      // The enzyme database for enzyme lookup
      EnzymesDB * enzymes_db_;

      // Keeps track of the charges of the hits
      std::set< UInt > charges_;
      UInt min_precursor_charge_;
      UInt max_precursor_charge_;

      // Current Retention time of light spectrum
      double rt_light_;

      // The masses of the Monolinks
      std::set< double > monolinks_masses_;

      // The current spectrum search
      std::vector< PeptideIdentification > current_spectrum_search_;

      // Stores the attributes of a record (peptide identification)
      std::map<String, DataValue> peptide_id_meta_values_;

      inline void extractDateTime_(const String & xquest_datetime_string, DateTime & date_time);

      void addMetaValues_(MetaInfoInterface & meta_info_interface);

      void getLinkPosition_(const xercesc::Attributes & attributes, std::pair<SignedSize, SignedSize> & pair);

      void setPeptideEvidence_(const String & prot_string, PeptideHit & pep_hit);

      void setMetaValue_(const String & key, const DataValue & datavalue, PeptideIdentification & pep_id, PeptideHit & alpha);

      void setMetaValue_(const String & key, const DataValue & datavalue, PeptideIdentification & pep_id, PeptideHit & alpha, PeptideHit & beta);
    };
  } // namespace Internal
} // namespace OpenMS
#endif // OPENMS_FORMAT_HANDLERS_XQUESTRESULTXMLHANDLER_H