libopenms-dev 1.11.1-3 / usr / include / OpenMS / METADATA / PeptideEvidence.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_METADATA_PEPTIDEEVIDENCE_H
#define OPENMS_METADATA_PEPTIDEEVIDENCE_H

#include <vector>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>

namespace OpenMS
{
  class AASequence;

  /**
    @brief Representation of a MzIdentML PeptideEvidence

        It contains information about the protein the peptide comes from
        and additional information were it is located in the protein.

        @todo implement CVParam

        @ingroup Metadata
  */
  class OPENMS_DLLAPI PeptideEvidence :
    public MetaInfoInterface
  {
public:

    /** @name Constructors and Destructor */
    //@{
    /// default constructor
    PeptideEvidence();

    /// values constructor
    PeptideEvidence(DoubleReal score,
                    UInt rank,
                    Int charge,
                    const AASequence & sequence);

    /// copy constructor
    PeptideEvidence(const PeptideEvidence & source);

    /// destructor
    virtual ~PeptideEvidence();
    //@}

    /// assignment operator
    PeptideEvidence & operator=(const PeptideEvidence & source);

    /// Equality operator
    bool operator==(const PeptideEvidence & rhs) const;

    /// Inequality operator
    bool operator!=(const PeptideEvidence & rhs) const;

    /**	@name Accessors
    */
    //@{
    /// returns the corresponding protein db sequence ref
    const String & getDBSequenceRef() const;

    /// sets the corresponding protein db sequence ref
    void setDBSequenceRef(const String & rhs);

    /// returns the translation table reference
    const String & getTranslationTableRef() const;

    /// sets the translation table reference
    void setTranslationTableRef(const String & rhs);

    /// start position in the sequence (xsd:int)
    void setStart(Int start);

    /// returns the start position in the sequence (xsd:int)
    Int getStart() const;

    /// sets the end position in the sequence
    void setEnd(Int end);

    /// returns the end position in the sequence
    Int getEnd() const;

    /// sets the amino acid before the sequence, "-" if N-terminal, "?" if not applicable (e.g. de novo)
    void setPre(char rhs);

    /// returns the amino acid before the sequence
    char getPre() const;

    /// sets the amino acid after the sequence, "-" if C-terminal, "?" if not applicable (e.g. de novo)
    void setPost(char rhs);

    /// returns the amino acid after the sequence
    char getPost() const;

    /// unique id of the file, set of files or repository
    void setId(const String & id);

    /// returns the unqiue id of the instance
    const String & getId() const;

    /// sets the potentially ambigous but human readable name
    void setName(const String & name);

    /// returns the human readable name
    const String & getName() const;

    /// sets the number of missed cleavages
    void setMissedCleavages(Int rhs);

    /// returns the number of missed cleavages
    Int getMissedCleavages() const;

    /// sets whether the hit is a decoy hit
    void setIsDecoy(bool is_decoy);

    /// returns the whether the hit is decoy
    bool getIsDecoy() const;

    /// Frame of the DB, e.g. from nucleic acids
    void setFrame(Int frame);

    /// returns the frame of the peptide evidence
    Int getFrame() const;
    //@}


protected:

    String db_sequence_ref_;
    String translation_table_ref_;
    Int start_;
    Int end_;
    char pre_;
    char post_;
    String id_;
    String name_;
    Int missed_cleavages_;
    bool is_decoy_;
    Int frame_;

  };

} // namespace OpenMS

#endif // OPENMS_METADATA_PEPTIDEEVIDENCE_H