MzIdentMLHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: Mathias Walzer, Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
 
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/ControlledVocabulary.h>
#include <OpenMS/METADATA/IdentificationHit.h>
#include <OpenMS/METADATA/Identification.h>
#include <OpenMS/METADATA/ProteinHit.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/DigestionEnzymeProtein.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
 
#include <OpenMS/CONCEPT/LogStream.h>
 
#include <vector>
 
namespace OpenMS
{
  class ProgressLogger;
 
  namespace Internal
  {
 
    class OPENMS_DLLAPI MzIdentMLHandler :
      public XMLHandler
    {
public:
      MzIdentMLHandler(const Identification& id, const String& filename, const String& version, const ProgressLogger& logger);
      MzIdentMLHandler(const std::vector<ProteinIdentification>& pro_id, const std::vector<PeptideIdentification>& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
 
      MzIdentMLHandler(Identification& id, const String& filename, const String& version, const ProgressLogger& logger);
      MzIdentMLHandler(std::vector<ProteinIdentification>& pro_id, std::vector<PeptideIdentification>& pep_id, const String& filename, const String& version, const ProgressLogger& logger);
 
      ~MzIdentMLHandler() 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;
 
      // Docu in base class
      void characters(const XMLCh* const chars, const XMLSize_t length) override;
 
      //Docu in base class
      void writeTo(std::ostream& os) override;
 
protected:
      const ProgressLogger& logger_;
 
      ControlledVocabulary cv_;
      ControlledVocabulary unimod_;
 
      //~ PeakMap* ms_exp_;
 
      String tag_;
 
      Identification* id_;
      std::vector<ProteinIdentification>* pro_id_;
      std::vector<PeptideIdentification>* pep_id_;
 
      const Identification* cid_;
      const std::vector<ProteinIdentification>* cpro_id_;
      const std::vector<PeptideIdentification>* cpep_id_;
 
      SpectrumIdentification current_spectrum_id_;
 
      IdentificationHit current_id_hit_;
 
      void handleCVParam_(const String& parent_parent_tag, const String& parent_tag, const String& accession, /* const String& name, */ /* const String& value, */ const xercesc::Attributes& attributes, const String& cv_ref /* ,  const String& unit_accession="" */);
 
      void handleUserParam_(const String& parent_parent_tag, const String& parent_tag, const String& name, const String& type, const String& value);
 
      void writeMetaInfos_(String& s, const MetaInfoInterface& meta, UInt indent) const;
 
      ControlledVocabulary::CVTerm getChildWithName_(const String& parent_accession, const String& name) const;
 
      //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
 
      void writeEnzyme_(String& s, DigestionEnzymeProtein enzy, UInt miss, UInt indent) const;
 
      void writeModParam_(String& s, const std::vector<String>& mod_names, bool fixed, UInt indent) const;
 
      void writeFragmentAnnotations_(String& s, const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent, bool is_ppxl) const;
 
      String trimOpenMSfileURI(const String file) const;
 
      void writePeptideHit(const PeptideHit& hit,
                                std::vector<PeptideIdentification>::const_iterator& it,
                                std::map<String, String>& pep_ids,
                                String cv_ns, std::set<String>& sen_set,
                                std::map<String, String>& sen_ids,
                                std::map<String, std::vector<String> >& pep_evis,
                                std::map<String, double>& pp_identifier_2_thresh,
                                String& sidres);
 
      void writeXLMSPeptideHit(const PeptideHit& hit,
                                std::vector<PeptideIdentification>::const_iterator& it,
                                String ppxl_linkid, std::map<String, String>& pep_ids,
                                String cv_ns, std::set<String>& sen_set,
                                std::map<String, String>& sen_ids,
                                std::map<String, std::vector<String> >& pep_evis,
                                std::map<String, double>& pp_identifier_2_thresh,
                                double ppxl_crosslink_mass,
                                std::map<String, String>& ppxl_specref_2_element,
                                String& sid, bool alpha_peptide);
 
private:
      MzIdentMLHandler();
      MzIdentMLHandler(const MzIdentMLHandler& rhs);
      MzIdentMLHandler& operator=(const MzIdentMLHandler& rhs);
      Map<String, AASequence> pep_sequences_;
      std::map<String, String> pp_identifier_2_sil_; 
      std::map<String, String> sil_2_sdb_; 
      std::map<String, String> sil_2_sdat_; 
      std::map<String, String> ph_2_sdat_; 
      std::map<String, String> sil_2_sip_; 
      AASequence actual_peptide_;
      Int current_mod_location_;
      ProteinHit actual_protein_;
 
    };
  } // namespace Internal
} // namespace OpenMS