libopenms-dev 1.11.1-3 / usr / include / OpenMS / FORMAT / OMSSAXMLFile.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 2002-2013.
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_OMSSAXMLFILE_H
#define OPENMS_FORMAT_OMSSAXMLFILE_H

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>

#include <vector>

namespace OpenMS
{
  class String;
  class ModificationsDB;

  /**
    @brief Used to load OMSSAXML files

    This class is used to load documents that implement
    the schema of OMSSAXML files.

    @ingroup FileIO
  */
  class OPENMS_DLLAPI OMSSAXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:

    /// Default constructor
    OMSSAXMLFile();

    /// Destructor
    virtual ~OMSSAXMLFile();
    /**
      @brief loads data from a OMSSAXML file

      @param filename the file to be loaded
      @param protein_identification protein identifications belonging to the whole experiment
      @param id_data the identifications with m/z and RT
          @param load_proteins if this flag is set to false, the protein identifications are not loaded

      This class serves to read in a OMSSAXML file. The information can be
      retrieved via the load function.

          @exception FileNotFound
          @exception ParseError

      @ingroup FileIO
    */
    void load(const String & filename, ProteinIdentification & protein_identification, std::vector<PeptideIdentification> & id_data, bool load_proteins = true);

    /// sets the valid modifications
    void setModificationDefinitionsSet(const ModificationDefinitionsSet & rhs);

protected:
    // Docu in base class
    void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);

    // Docu in base class
    void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);

    // Docu in base class
    void characters(const XMLCh * const chars, const XMLSize_t /*length*/);

private:

    OMSSAXMLFile(const OMSSAXMLFile & rhs);

    OMSSAXMLFile & operator=(const OMSSAXMLFile & rhs);

    /// reads the mapping file needed for modifications
    void readMappingFile_();

    /// the identifications (storing the peptide hits)
    std::vector<PeptideIdentification> * peptide_identifications_;

    ProteinHit actual_protein_hit_;

    PeptideHit actual_peptide_hit_;

    PeptideIdentification actual_peptide_id_;

    ProteinIdentification actual_protein_id_;

    String tag_;

    /// site of the actual modification (simple position in the peptide)
    UInt actual_mod_site_;

    /// type of the modification
    String actual_mod_type_;

    /// modifications of the peptide defined by site and type
    std::vector<std::pair<UInt, String> > modifications_;

    /// should protein hits be read from the file?
    bool load_proteins_;

    /// modifications mapping file from OMSSA mod num to UniMod accession
    Map<UInt, std::vector<ResidueModification> > mods_map_;

    /// modification mapping reverse, from the modification to the mod_num
    Map<String, UInt> mods_to_num_;

    /// modification definitions set of the search, needed to annotate fixed modifications
    ModificationDefinitionsSet mod_def_set_;
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_OMSSAXMLFILE_H