FeatureXMLFile.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 2002-2012.
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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/KERNEL/FeatureMap.h>
#include <OpenMS/FORMAT/OPTIONS/FeatureFileOptions.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

#include <iostream>

namespace OpenMS
{
  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;

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<Feature> * map_;
    FeatureFileOptions options_;
    bool size_only_;
    Size expected_size_;

    ModelDescription<2> model_desc_;
    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