libopenms-dev 1.11.1-3 / usr / include / OpenMS / METADATA / PeptideHit.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: Nico Pfeifer $
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#ifndef OPENMS_METADATA_PEPTIDEHIT_H
#define OPENMS_METADATA_PEPTIDEHIT_H

#include <vector>

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

namespace OpenMS
{
  /**
    @brief Representation of a peptide hit

    It contains the fields score, score_type, rank, and sequence.

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

    /// @name Comparators for PeptideHit and ProteinHit
    //@{
    /// Greater predicate for scores of hits
    class OPENMS_DLLAPI ScoreMore
    {
public:
      template <typename Arg>
      bool operator()(const Arg & a, const Arg & b)
      {
        return a.getScore() > b.getScore();
      }

    };

    /// Lesser predicate for scores of hits
    class OPENMS_DLLAPI ScoreLess
    {
public:
      template <typename Arg>
      bool operator()(const Arg & a, const Arg & b)
      {
        return a.getScore() < b.getScore();
      }

    };
    //@}

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

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

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

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

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

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

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

    /**	@name Accessors
    */
    //@{
    /// returns the score of the peptide hit
    DoubleReal getScore() const;

    /// returns the rank of the peptide hit
    UInt getRank() const;

    /// returns the peptide sequence without trailing or following spaces
    const AASequence & getSequence() const;

    /// returns the carge of the peptide
    Int getCharge() const;

    /// returns the corresponding protein accessions
    const std::vector<String> & getProteinAccessions() const;

    /// sets the corresponding protein accessions
    void setProteinAccessions(const std::vector<String> & accessions);

    /// sets the score of the peptide hit
    void setScore(DoubleReal score);

    /// sets the rank
    void setRank(UInt newrank);

    /// sets the peptide sequence
    void setSequence(const AASequence & sequence);

    /// sets the charge of the peptide
    void setCharge(Int charge);

    /// adds an accession of a protein which contains this peptide hit
    void addProteinAccession(const String & accession);

    /// sets the amino acid before the sequence
    void setAABefore(char acid);
    /// returns the amino acid before the sequence
    char getAABefore() const;

    /// sets the amino acid after the sequence
    void setAAAfter(char acid);
    /// returns the amino acid after the sequence
    char getAAAfter() const;


    //@}


protected:
    DoubleReal score_;          ///< the score of the peptide hit
    UInt rank_;                         ///< the position(rank) where the hit appeared in the hit list
    Int charge_;         ///< the charge of the peptide
    AASequence sequence_;                               ///< the amino acid sequence of the peptide hit
    char aa_before_;     ///< Amino acid before the sequence
    char aa_after_;     ///< Amino acid after the sequence
    std::vector<String> corresponding_protein_accessions_;     ///< the accessions of the corresponding proteins

  };

} // namespace OpenMS

#endif // OPENMS_METADATA_PEPTIDEHIT_H