FeatureXMLFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Chris Bielow $
// $Authors: Marc Sturm, Chris Bielow, Clemens Groepl $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_FEATUREXMLFILE_H
#define OPENMS_FORMAT_FEATUREXMLFILE_H

#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 <OpenMS/DATASTRUCTURES/Map.h>

#include <iosfwd>

namespace OpenMS
{
  class Feature;
  class FeatureMap;

  class OPENMS_DLLAPI FeatureXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile,
    public ProgressLogger
  {

public:

    FeatureXMLFile();
    ~FeatureXMLFile();

    void load(const String& filename, FeatureMap& feature_map);

    Size loadSize(const String& filename);

    void store(const String& filename, const FeatureMap& feature_map);

    FeatureFileOptions& getOptions();

    const FeatureFileOptions& getOptions() const;

    void setOptions(const FeatureFileOptions&);

protected:

    // restore default state for next load/store operation
    void resetMembers_();

    // 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);

    void writeFeature_(const String& filename, std::ostream& os, const Feature& feat, const String& identifier_prefix, UInt64 identifier, UInt indentation_level);

    void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);


    void updateCurrentFeature_(bool create);

    Int disable_parsing_;

    Feature* current_feature_;
    FeatureMap* map_;
    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_;
    Map<String, String> proteinid_to_accession_;
    Map<String, Size> accession_to_id_;
    Map<String, String> identifier_id_;
    Map<String, String> id_identifier_;
    ProteinIdentification::SearchParameters search_param_;

  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_FeatureXMLFile_H