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 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $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 <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() override;

    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
    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 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