libopenms-dev 1.11.1-3 / usr / include / OpenMS / FORMAT / ConsensusXMLFile.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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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
{
  /**
    @brief This class provides Input functionality for ConsensusMaps and Output functionality for
    alignments and quantitation.

    This class can be used to load the content of a consensusXML file into a ConsensusMap
    or to save the content of an ConsensusMap object into an XML file.

    A documented schema for this format can be found at http://open-ms.sourceforge.net/schemas/.

  @todo Take care that unique ids are assigned properly by TOPP tools before calling ConsensusXMLFile::store().  There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class.  (all developers)

    @ingroup FileIO
  */
  class OPENMS_DLLAPI ConsensusXMLFile :
    public Internal::XMLHandler,
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    ///Default constructor
    ConsensusXMLFile();
    ///Destructor
    ~ConsensusXMLFile();


    /**
    @brief Loads a consensus map from file and calls updateRanges

    @exception Exception::FileNotFound is thrown if the file could not be opened
    @exception Exception::ParseError is thrown if an error occurs during parsing
    @exception Exception::MissingInformation is thrown if source files are missing/duplicated or map-IDs are referencing non-existing maps
    */
    void load(const String & filename, ConsensusMap & map);

    /**
    @brief Stores a consensus map to file

    @exception Exception::UnableToCreateFile is thrown if the file name is not writable
    @exception Exception::IllegalArgument is thrown if the consensus map is not valid
    @exception Exception::MissingInformation is thrown if source files are missing/duplicated or map-IDs are referencing non-existing maps
    */
    void store(const String & filename, const ConsensusMap & consensus_map);

    /// Mutable access to the options for loading/storing
    PeakFileOptions & getOptions();

    /// Non-mutable access to the options for loading/storing
    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);


    /// Writes a peptide identification to a stream (for assigned/unassigned peptide identifications)
    void writePeptideIdentification_(const String & filename, std::ostream & os, const PeptideIdentification & id, const String & tag_name, UInt indentation_level);


    /// Options that can be set
    PeakFileOptions options_;

    ///@name Temporary variables for parsing
    //@{
    ConsensusMap * consensus_map_;
    ConsensusFeature act_cons_element_;
    DPosition<2> pos_;
    DoubleReal it_;
    //@}

    /// Pointer to last read object as a MetaInfoInterface, or null.
    MetaInfoInterface * last_meta_;
    /// Temporary protein ProteinIdentification
    ProteinIdentification prot_id_;
    /// Temporary peptide ProteinIdentification
    PeptideIdentification pep_id_;
    /// Temporary protein hit
    ProteinHit prot_hit_;
    /// Temporary peptide hit
    PeptideHit pep_hit_;
    /// Map from protein id to accession
    Map<String, String> proteinid_to_accession_;
    /// Map from search identifier concatenated with protein accession to id
    Map<String, Size> accession_to_id_;
    /// Map from identification run identifier to file xs:id (for linking peptide identifications to the corresponding run)
    Map<String, String> identifier_id_;
    /// Map from file xs:id to identification run identifier (for linking peptide identifications to the corresponding run)
    Map<String, String> id_identifier_;
    /// Temporary search parameters file
    ProteinIdentification::SearchParameters search_param_;

    UInt progress_;

  };
} // namespace OpenMS

#endif // OPENMS_FOMAT_CONSENSUSXMLFILE_H