// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    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"
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------

#ifndef OPENMS_METADATA_PROTEINHIT_H
#define OPENMS_METADATA_PROTEINHIT_H

#include <vector>

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

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

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

        @ingroup Metadata
  */
  class OPENMS_DLLAPI ProteinHit :
    public MetaInfoInterface
  {
public:
    static const double COVERAGE_UNKNOWN; // == -1

    /// @name Comparators ProteinHit
    //@{
    /// Greater predicate for scores of hits
    class OPENMS_DLLAPI ScoreMore
    {
public:
      template <typename Arg>
      bool operator()(const Arg & a, const Arg & b)
      {
#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Wfloat-equal"
        if (a.getScore() != b.getScore())
#pragma clang diagnostic pop
        {
          return a.getScore() > b.getScore();
        }
        return a.getAccession() > b.getAccession();
      }

    };

    /// Lesser predicate for scores of hits
    class OPENMS_DLLAPI ScoreLess
    {
public:
      template <typename Arg>
      bool operator()(const Arg & a, const Arg & b)
      {
#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Wfloat-equal"
        if (a.getScore() != b.getScore())
#pragma clang diagnostic pop
        {
          return a.getScore() < b.getScore();
        }
        return a.getAccession() < b.getAccession();
      }

    };
    //@}

    /** @name Constructors and Destructor */
    //@{

    /// default constructor
    ProteinHit();

    /// values constructor
    ProteinHit(double score, UInt rank, String accession, String sequence);

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

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

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

    /// assignment for MetaInfo
    ProteinHit & operator=(const MetaInfoInterface & source);

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

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


    /** @name Accessors */
    //@{

    /// returns the score of the protein hit
    float getScore() const;

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

    /// returns the protein sequence
    const String & getSequence() const;

    /// returns the accession of the protein
    const String & getAccession() const;
    
    /// returns the description of the protein
    String getDescription() const;

    /// returns the coverage (in percent) of the protein hit based upon matched peptides
    double getCoverage() const;

    /// sets the score of the protein hit
    void setScore(const double score);

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

    /// sets the protein sequence
    void setSequence(const String & sequence);

    /// sets the accession of the protein
    void setAccession(const String & accession);

    /// sets the description of the protein
    void setDescription(const String & description);

    /// sets the coverage (in percent) of the protein hit based upon matched peptides
    void setCoverage(const double coverage);

    //@}

protected:
    float score_;                        ///< the score of the protein hit
    UInt rank_;                         ///< the position(rank) where the hit appeared in the hit list
    String accession_;          ///< the protein identifier
    String sequence_;               ///< the amino acid sequence of the protein hit
    double coverage_;         ///< coverage of the protein based upon the matched peptide sequences

  };

} // namespace OpenMS

#endif // OPENMS_METADATA_PROTEINHIT_H
