MzQuantMLHandler.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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// $Maintainer: Mathias Walzer $
// $Authors: Mathias Walzer $
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#pragma once

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/ControlledVocabulary.h>
#include <OpenMS/METADATA/MSQuantifications.h>

namespace OpenMS
{
  class ProgressLogger;

  namespace Internal
  {

    class OPENMS_DLLAPI MzQuantMLHandler :
      public XMLHandler
    {
public:
      MzQuantMLHandler(const MSQuantifications & msq, const String & filename, const String & version, const ProgressLogger & logger);

      MzQuantMLHandler(MSQuantifications & msq, const String & filename, const String & version, const ProgressLogger & logger);

      ~MzQuantMLHandler() 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_;

      String tag_;

      MSQuantifications * msq_;

      const MSQuantifications * cmsq_;

      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);

      //~ TODO rewirte writeCVParams_ in baseclass to be more convenient
      //~ void MzQuantMLHandler::writeCVParams_(std::ostream& os, const Map< String, std::vector < CVTerm > > & , UInt indent);
      void writeCVParams_(String & s, const Map<String, std::vector<CVTerm> > &, UInt indent);

      void writeUserParams_(std::ostream & os, const MetaInfoInterface & meta, UInt indent);
      void writeUserParams_(String & s, const MetaInfoInterface & meta, UInt indent);

      ControlledVocabulary::CVTerm getChildWithName_(const String & parent_accession, const String & name) const;


      void writeFeature_(String & feature_xml, const std::vector<FeatureMap >& fm, UInt indentation_level);

      //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);


private:
      MzQuantMLHandler();
      MzQuantMLHandler(const MzQuantMLHandler & rhs);
      MzQuantMLHandler & operator=(const MzQuantMLHandler & rhs);

      std::map<String, std::vector<ExperimentalSettings> > current_files_;           // 1.rawfilesgroup_ref 2.inputfiles for each assay as ExperimentalSettings
      String current_id_;
      String current_cf_id_;
      Size current_count_;

      std::vector<MetaInfo> up_stack_;
      std::vector<CVTerm> cvp_stack_;
      MSQuantifications::Assay current_assay_;

      std::multimap<String, String> cm_cf_ids_;
      std::map<String, String> f_cf_ids_;
      std::map<String, ConsensusFeature> cf_cf_obj_;
      std::map<String, FeatureHandle> f_f_obj_;
      std::map<String, ConsensusFeature::Ratio> r_rtemp_;
      std::map<String, String> numden_r_ids_;
      std::map<String, ConsensusFeature::Ratio> r_r_obj_;

      //~ Software current_sw_;
      std::map<String, Software> current_sws_;
      std::map<int, DataProcessing> current_orderedps_;
      std::pair<int, DataProcessing> current_dp_;
      std::set<DataProcessing::ProcessingAction> current_pas_;

      std::vector<String> current_col_types_;
      std::vector<double> current_dm_values_;
      std::vector<double> current_row_;

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