MzIdentMLHandler.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: Mathias Walzer $
// $Authors: Mathias Walzer, Andreas Bertsch $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H
#define OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H

#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/CONCEPT/UniqueIdGenerator.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.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);

      virtual ~MzIdentMLHandler();


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

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

      // Docu in base class
      virtual void characters(const XMLCh * const chars, const XMLSize_t length);

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

protected:

      const ProgressLogger & logger_;

      ControlledVocabulary cv_;
      ControlledVocabulary unimod_;

      //~ MSExperiment<>* 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 writeUserParam_(std::ostream & os, 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);


private:
      MzIdentMLHandler();
      MzIdentMLHandler(const MzIdentMLHandler & rhs);
      MzIdentMLHandler & operator=(const MzIdentMLHandler & rhs);
      Map<String, AASequence> pep_sequences_;
      AASequence actual_peptide_;
      Int current_mod_location_;
      ProteinHit actual_protein_;

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

#endif