FeatureXMLHandler.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Marc Sturm, Chris Bielow, Clemens Groepl $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/OPTIONS/FeatureFileOptions.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/ConvexHull2D.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
 
#include <iosfwd>
#include <map>
 
namespace OpenMS
{
  class Feature;
  class FeatureMap;
 
  namespace Internal
  {
 
  class OPENMS_DLLAPI FeatureXMLHandler :
    public Internal::XMLHandler,
    public ProgressLogger
  {
 
public:
 
    FeatureXMLHandler(FeatureMap& map, const std::string& filename);
    FeatureXMLHandler(const FeatureMap& map, const std::string& filename);
    ~FeatureXMLHandler() override;
 
 
    void writeTo(std::ostream& os) override;
 
    FeatureFileOptions& getOptions();
 
    const FeatureFileOptions& getOptions() const;
 
    void setOptions(const FeatureFileOptions&);
 
    void setSizeOnly(const bool size_only)
    {
      size_only_ = size_only;
    }
 
    Size getSize() const
    {
      return expected_size_;
    }
 
protected:
 
    // restore default state for next load/store operation
    void resetMembers_();
 
    // 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;
 
    void writeFeature_(const std::string& filename, std::ostream& os, const Feature& feat, const std::string& identifier_prefix, UInt64 identifier, UInt indentation_level);
 
    void writePeptideIdentification_(const std::string& filename, std::ostream& os, const PeptideIdentification& id, const std::string& tag_name, UInt indentation_level);
 
    void updateCurrentFeature_(bool create);
 
    Int disable_parsing_;
 
    Feature* current_feature_;
    FeatureMap* map_;
    const FeatureMap* cmap_;
    FeatureFileOptions options_;
    bool size_only_;
    Size expected_size_;
 
    Param param_;
    ConvexHull2D::PointArrayType current_chull_;
    DPosition<2> hull_position_;
 
    UInt dim_;
 
    bool in_description_;
 
    Int subordinate_feature_level_;
 
    MetaInfoInterface* last_meta_;
 
    ProteinIdentification prot_id_;
    PeptideIdentification pep_id_;
    ProteinHit prot_hit_;
    PeptideHit pep_hit_;
    std::map<std::string, std::string> proteinid_to_accession_;
    std::map<std::string, Size> accession_to_id_;
    std::map<std::string, std::string> identifier_id_;
    std::map<std::string, std::string> id_identifier_;
    ProteinIdentification::SearchParameters search_param_;
 
  };
 
} // namespace Internal
} // namespace OpenMS