Ribonucleotide.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
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#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <iostream>
 
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;
 
}