ConsensusXMLFile.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: Clemens Groepl $
// $Authors: Clemens Groepl, Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_CONSENSUSXMLFILE_H
#define OPENMS_FORMAT_CONSENSUSXMLFILE_H

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/KERNEL/ConsensusMap.h>

namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusXMLFile :
    public Internal::XMLHandler,
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    ConsensusXMLFile();
    ~ConsensusXMLFile();


    void load(const String & filename, ConsensusMap & map);

    void store(const String & filename, const ConsensusMap & consensus_map);

    PeakFileOptions & getOptions();

    const PeakFileOptions & getOptions() const;

protected:

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


    PeakFileOptions options_;


    ConsensusMap * consensus_map_;
    ConsensusFeature act_cons_element_;
    DPosition<2> pos_;
    DoubleReal it_;
    UInt last_map_;

    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_;

    UInt progress_;

  };
} // namespace OpenMS

#endif // OPENMS_FOMAT_CONSENSUSXMLFILE_H