Ribonucleotide.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: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CONCEPT/HashUtils.h>
#include <functional>
#include <iosfwd>
 
namespace OpenMS
{
  class OPENMS_DLLAPI Ribonucleotide
  {
    friend class RibonucleotideDB;
  public:
 
    enum TermSpecificityNuc
    {
      ANYWHERE,
      FIVE_PRIME,
      THREE_PRIME,
      NUMBER_OF_TERM_SPECIFICITY
    };
 
    Ribonucleotide(const String& name = "unknown ribonucleotide",
                   const String& code = ".",
                   const String& new_code = "",
                   const String& html_code = ".",
                   const EmpiricalFormula& formula = EmpiricalFormula(),
                   char origin = '.',
                   double mono_mass = 0.0,
                   double avg_mass = 0.0,
                   enum TermSpecificityNuc term_spec = ANYWHERE,
                   const EmpiricalFormula& baseloss_formula =
                   default_baseloss_);
 
    Ribonucleotide(const Ribonucleotide& ribo) = default;
 
    virtual ~Ribonucleotide();
 
    Ribonucleotide& operator=(const Ribonucleotide& ribo) = default;
 
 
    bool operator==(const Ribonucleotide& ribonucleotide) const;
 
 
    const String getCode() const;
 
    void setCode(const String& code);
 
    const String getName() const;
 
    void setName(const String& name);
 
    const EmpiricalFormula getFormula() const;
 
    void setFormula(const EmpiricalFormula& formula);
 
    double getMonoMass() const;
 
    void setMonoMass(double mono_mass);
 
    double getAvgMass() const;
 
    void setAvgMass(double avg_mass);
 
    const String getNewCode() const;
 
    void setNewCode(const String &new_code);
 
    friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Ribonucleotide& ribo);
 
    char getOrigin() const;
 
    void setOrigin(char origin);
 
    String getHTMLCode() const;
 
    void setHTMLCode(const String& html_code);
 
    enum TermSpecificityNuc getTermSpecificity() const;
 
    void setTermSpecificity(enum TermSpecificityNuc term_spec);
 
    const EmpiricalFormula getBaselossFormula() const;
 
    void setBaselossFormula(const EmpiricalFormula& formula);
 
 
    bool isModified() const;
 
    bool isAmbiguous() const;
 
  protected:
    static const EmpiricalFormula default_baseloss_;
 
    String name_; 
    String code_; 
    String new_code_; 
    String html_code_; 
    EmpiricalFormula formula_; 
    char origin_; 
    double mono_mass_; 
    double avg_mass_; 
    enum TermSpecificityNuc term_spec_; 
    EmpiricalFormula baseloss_formula_; 
  };
 
  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Ribonucleotide& ribo);
 
  using RibonucleotideChainEnd = Ribonucleotide;
 
} // namespace OpenMS
 
// Hash function specialization for Ribonucleotide
// Placed in std namespace to allow use with std::unordered_map/set
namespace std
{
  template<>
  struct hash<OpenMS::Ribonucleotide>
  {
    std::size_t operator()(const OpenMS::Ribonucleotide& ribo) const noexcept
    {
      std::size_t seed = 0;
 
      // Hash all fields used in operator==
      // String fields: name_, code_, new_code_, html_code_
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(ribo.getName()));
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(ribo.getCode()));
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(ribo.getNewCode()));
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(ribo.getHTMLCode()));
 
      // EmpiricalFormula fields: formula_, baseloss_formula_
      OpenMS::hash_combine(seed, std::hash<OpenMS::EmpiricalFormula>{}(ribo.getFormula()));
      OpenMS::hash_combine(seed, std::hash<OpenMS::EmpiricalFormula>{}(ribo.getBaselossFormula()));
 
      // Primitive fields: origin_ (char), mono_mass_, avg_mass_ (double), term_spec_ (enum)
      OpenMS::hash_combine(seed, OpenMS::hash_char(ribo.getOrigin()));
      OpenMS::hash_combine(seed, OpenMS::hash_float(ribo.getMonoMass()));
      OpenMS::hash_combine(seed, OpenMS::hash_float(ribo.getAvgMass()));
      OpenMS::hash_combine(seed, OpenMS::hash_int(static_cast<int>(ribo.getTermSpecificity())));
 
      return seed;
    }
  };
} // namespace std