TraMLHandler.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: Hannes Roest $
// $Authors: Andreas Bertsch, Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/ControlledVocabulary.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/METADATA/SourceFile.h>
#include <OpenMS/METADATA/CVTermList.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

namespace OpenMS
{
  namespace Internal
  {

    class OPENMS_DLLAPI TraMLHandler :
      public XMLHandler
    {
public:

      typedef std::vector<ReactionMonitoringTransition::Product> ProductListType;
      typedef std::vector<ReactionMonitoringTransition::Configuration> ConfigurationListType;

      TraMLHandler(const TargetedExperiment & exp, const String & filename, const String & version, const ProgressLogger & logger);

      TraMLHandler(TargetedExperiment & exp, const String & filename, const String & version, const ProgressLogger & logger);

      ~TraMLHandler() 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_;

      TargetedExperiment * exp_;

      const TargetedExperiment * cexp_;

      TargetedExperiment::Publication actual_publication_;

      TargetedExperiment::Contact actual_contact_;

      TargetedExperiment::Instrument actual_instrument_;

      TargetedExperiment::Prediction actual_prediction_;

      Software actual_software_;

      TargetedExperiment::Protein actual_protein_;

      TargetedExperiment::RetentionTime actual_rt_;

      TargetedExperiment::Peptide actual_peptide_;

      TargetedExperiment::Compound actual_compound_;

      ReactionMonitoringTransition actual_transition_;

      IncludeExcludeTarget actual_target_;

      CVTermList actual_validation_;

      TargetedExperiment::Interpretation actual_interpretation_;

      std::vector<ReactionMonitoringTransition::Product> actual_intermediate_products_;

      ReactionMonitoringTransition::Product actual_product_;

      ReactionMonitoringTransition::Configuration actual_configuration_;

      SourceFile actual_sourcefile_;

      void handleCVParam_(const String & parent_parent_tag, const String & parent_tag, const CVTerm & cv_term);

      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;

      void writeUserParams_(std::ostream & os, const std::vector<MetaInfoInterface> & meta, UInt indent) const;

      template <typename CVTList>
      void writeCVParams_(std::ostream & os, const CVTList & cv_terms, UInt indent) const
      {
        for (Map<String, std::vector<CVTerm> >::const_iterator it = cv_terms.getCVTerms().begin(); 
            it != cv_terms.getCVTerms().end(); ++it)
        {
          for (std::vector<CVTerm>::const_iterator cit = it->second.begin(); cit != it->second.end(); ++cit)
          {
            os << String(2 * indent, ' ') << "<cvParam cvRef=\"" << cit->getCVIdentifierRef() << "\" accession=\"" << cit->getAccession() << "\" name=\"" << cit->getName() << "\"";
            if (cit->hasValue() && !cit->getValue().isEmpty() && !cit->getValue().toString().empty())
            {
              os << " value=\"" << cit->getValue().toString() << "\"";
            }

            if (cit->hasUnit())
            {
              os << " unitCvRef=\"" << cit->getUnit().cv_ref << "\" unitAccession=\"" << cit->getUnit().accession << "\" unitName=\"" << cit->getUnit().name << "\"";
            }
            os << "/>" << "\n";
          }
        }
      }

      // subfunctions of write
      void writeTarget_(std::ostream & os, const std::vector<IncludeExcludeTarget>::const_iterator & it) const;

      void writeRetentionTime_(std::ostream& os, const TargetedExperimentHelper::RetentionTime& rt) const;

      void writeProduct_(std::ostream & os, const std::vector<ReactionMonitoringTransition::Product>::const_iterator & prod_it) const;

      void writeConfiguration_(std::ostream & os, const std::vector<ReactionMonitoringTransition::Configuration>::const_iterator & cit) const;

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

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

private:

      TraMLHandler();
      TraMLHandler(const TraMLHandler & rhs);
      TraMLHandler & operator=(const TraMLHandler & rhs);
    };
  } // namespace Internal
} // namespace OpenMS