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 2002-2018.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Eugen Netz $
// $Authors: Lukas Zimmermann $
// --------------------------------------------------------------------------
#pragma once

#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/ProteaseDB.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;

      XQuestResultXMLHandler(const String & filename,
                             std::vector< PeptideIdentification > & pep_ids,
                             std::vector< ProteinIdentification > & prot_ids
                             );

      XQuestResultXMLHandler(const std::vector<ProteinIdentification>& pro_id,
                             const std::vector<PeptideIdentification>& pep_id,
                             const String& filename,
                             const String& version
                           );

      ~XQuestResultXMLHandler() 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 startElement(const XMLCh * const uri, const XMLCh * const local_name, const XMLCh * const qname, const xercesc::Attributes & attributes) override;

      double getMinScore() const;

      double getMaxScore() const;

      UInt getNumberOfHits() const;

      //Docu in base class
      virtual void writeTo(std::ostream& os) override;

      // TODO move these to StringUtils?
      static StringList splitByNth(const String& input, const char separator, const Size n);

      static StringList splitByMiddle(const String& input, const char separator);

    private:


      // Decoy string used by xQuest
      String decoy_string_;
      int spectrum_index_light_;
      int spectrum_index_heavy_;
      String cross_linker_name_;

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

      // internal ID items for writing files
      const std::vector<ProteinIdentification>* cpro_id_;
      const std::vector<PeptideIdentification>* cpep_id_;

      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_;

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

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

      // The enzyme database for enzyme lookup
      ProteaseDB* 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 spectrum pair
      double rt_light_;
      double rt_heavy_;

      // Current experimental m/z of spectrum pair
      double mz_light_;
      double mz_heavy_;

      // primary MS run path
      StringList ms_run_path_;
      String spectrum_input_file_;

      // 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);

    };
  } // namespace Internal
} // namespace OpenMS