IdXMLFile.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 2002-2012.
//
// 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: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_IDXMLFILE_H
#define OPENMS_FORMAT_IDXMLFILE_H

#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>

#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI IdXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:

    IdXMLFile();

    void load(const String & filename, std::vector<ProteinIdentification> & protein_ids, std::vector<PeptideIdentification> & peptide_ids);

    void load(const String & filename, std::vector<ProteinIdentification> & protein_ids, std::vector<PeptideIdentification> & peptide_ids, String & document_id);

    void store(String filename, const std::vector<ProteinIdentification> & protein_ids, const std::vector<PeptideIdentification> & peptide_ids, const String & document_id = "");

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);

    void addProteinGroups_(MetaInfoInterface & meta, const std::vector<ProteinIdentification::ProteinGroup> & groups, const String & group_name, const std::map<String, UInt> & accession_to_id);

    void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup> & groups, const String & group_name);



    std::vector<ProteinIdentification> * prot_ids_;
    std::vector<PeptideIdentification> * pep_ids_;
    MetaInfoInterface * last_meta_;
    std::map<String, ProteinIdentification::SearchParameters> parameters_;
    ProteinIdentification::SearchParameters param_;
    String id_;
    ProteinIdentification prot_id_;
    PeptideIdentification pep_id_;
    ProteinHit prot_hit_;
    PeptideHit pep_hit_;
    std::map<String, String> proteinid_to_accession_;
    String * document_id_;
    bool prot_id_in_run_;
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_IDXMLFILE_H