ProteinHit.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <iosfwd>
#include <vector>
#include <functional>
#include <set>
#include <map>
 
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CONCEPT/HashUtils.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ProteinHit :
    public MetaInfoInterface
  {
public:
    enum class TargetDecoyType
    {
      TARGET,       
      DECOY,        
      UNKNOWN       
    };
 
    static const double COVERAGE_UNKNOWN; // == -1
 
 
 
    class OPENMS_DLLAPI ProteinHitAccessionHash
    {
    public:
      size_t operator()(const ProteinHit & p)
      {
        return std::hash<std::string>{}(p.getAccession());
      }
 
    };
    class OPENMS_DLLAPI ProteinHitPtrAccessionHash
    {
    public:
      size_t operator()(const ProteinHit * p)
      {
        return std::hash<std::string>{}(p->getAccession());
      }
 
    };
 
 
 
    class OPENMS_DLLAPI ScoreMore
    {
    public:
      template<typename Arg>
      bool operator()(const Arg& a, const Arg& b) const
      {
        return std::make_tuple(a.getScore(), a.getAccession()) > std::make_tuple(b.getScore(), b.getAccession());
      }
    };
 
    class OPENMS_DLLAPI ScoreLess
    {
public:
      template <typename Arg>
      bool operator()(const Arg & a, const Arg & b) const
      {
        return std::make_tuple(a.getScore(), a.getAccession()) < std::make_tuple(b.getScore(), b.getAccession());
      }
 
    };
 
 
    ProteinHit();
 
    ProteinHit(double score, UInt rank, std::string accession, std::string sequence);
 
    ProteinHit(const ProteinHit &) = default;
 
    ProteinHit(ProteinHit&&) = default;
 
 
    ProteinHit & operator=(const ProteinHit &) = default;
 
    ProteinHit& operator=(ProteinHit&&) = default; // TODO: add noexcept (gcc 4.8 bug)
 
    ProteinHit & operator=(const MetaInfoInterface & source);
 
    bool operator==(const ProteinHit & rhs) const;
 
    bool operator!=(const ProteinHit & rhs) const;
 
 
 
    double getScore() const;
 
    UInt getRank() const;
 
    const std::string & getSequence() const;
 
    const std::string & getAccession() const;
    
    std::string getDescription() const;
 
    double getCoverage() const;
 
    void setScore(const double score);
 
    void setRank(UInt newrank);
 
    void setSequence(const std::string & sequence);
    void setSequence(std::string && sequence);
 
    void setAccession(const std::string & accession);
 
    void setDescription(const std::string & description);
 
    void setCoverage(const double coverage);
 
    const std::set<std::pair<Size, ResidueModification> >& getModifications() const;
 
    void setModifications(std::set<std::pair<Size, ResidueModification> >& mods);
 
    bool isDecoy() const;
 
    void setTargetDecoyType(TargetDecoyType type);
 
    TargetDecoyType getTargetDecoyType() const;
 
 
protected:
    double score_;       
    UInt rank_;          
    std::string accession_;   
    std::string sequence_;    
    double coverage_;    
    std::set<std::pair<Size, ResidueModification> > modifications_; 
  };
 
  OPENMS_DLLAPI std::ostream& operator<< (std::ostream& stream, const ProteinHit& hit);
 
} // namespace OpenMS
 
// Hash function specialization for ProteinHit
namespace std
{
  template<>
  struct hash<OpenMS::ProteinHit>
  {
    std::size_t operator()(const OpenMS::ProteinHit& hit) const noexcept
    {
      std::size_t seed = OpenMS::hash_float(hit.getScore());
      OpenMS::hash_combine(seed, OpenMS::hash_int(hit.getRank()));
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(hit.getAccession()));
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(hit.getSequence()));
      OpenMS::hash_combine(seed, OpenMS::hash_float(hit.getCoverage()));
 
      // Hash modifications (set of pairs: position + ResidueModification)
      for (const auto& mod_pair : hit.getModifications())
      {
        OpenMS::hash_combine(seed, OpenMS::hash_int(mod_pair.first)); // position (Size)
        // Use getFullId() for the modification, consistent with AASequence hashing
        OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(mod_pair.second.getFullId()));
      }
 
      return seed;
    }
  };
} // namespace std