ConsensusXMLFile.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// 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.
//  * Neither the name of any author or any participating institution
//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $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>
#include <OpenMS/METADATA/PeptideEvidence.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.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_;
    double it_;

    MetaInfoInterface* last_meta_;
    ProteinIdentification prot_id_;
    PeptideIdentification pep_id_;
    ProteinHit prot_hit_;
    PeptideHit pep_hit_;
    std::vector<PeptideEvidence> peptide_evidences_;
    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_FORMAT_CONSENSUSXMLFILE_H