ResidueModification.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
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//

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>

#include <set>

namespace OpenMS
{
  // forward declaration
  class Residue;

  class OPENMS_DLLAPI ResidueModification
  {
public:

    enum TermSpecificity
    {
      ANYWHERE = 0,        
      C_TERM = 1,          
      N_TERM = 2,          
      PROTEIN_C_TERM = 3,  
      PROTEIN_N_TERM = 4,  
      NUMBER_OF_TERM_SPECIFICITY
    };

    enum SourceClassification
    {
      ARTIFACT = 0,           
      HYPOTHETICAL,           
      NATURAL,                
      POSTTRANSLATIONAL,      
      MULTIPLE,               
      CHEMICAL_DERIVATIVE,    
      ISOTOPIC_LABEL,         
      PRETRANSLATIONAL,       
      OTHER_GLYCOSYLATION,    
      NLINKED_GLYCOSYLATION,  
      AA_SUBSTITUTION,        
      OTHER,                  
      NONSTANDARD_RESIDUE,    
      COTRANSLATIONAL,        
      OLINKED_GLYCOSYLATION,  
      UNKNOWN,                
      NUMBER_OF_SOURCE_CLASSIFICATIONS
    };


    ResidueModification();

    ResidueModification(const ResidueModification&) = default;

    ResidueModification(ResidueModification&&) = default;

    virtual ~ResidueModification();


    ResidueModification& operator=(const ResidueModification&) = default;

    ResidueModification& operator=(ResidueModification&&) & = default;

    void setId(const String& id);

    const String& getId() const;

    void setFullId(const String& full_id = "");


    const String& getFullId() const;

    void setUniModRecordId(const Int& id);

    const Int& getUniModRecordId() const;

    const String getUniModAccession() const;

    void setPSIMODAccession(const String& id);

    const String& getPSIMODAccession() const;

    void setFullName(const String& full_name);

    const String& getFullName() const;

    void setName(const String& name);

    const String& getName() const;

    void setTermSpecificity(TermSpecificity term_spec);

    void setTermSpecificity(const String& name);

    TermSpecificity getTermSpecificity() const;

    String getTermSpecificityName(TermSpecificity term_spec = NUMBER_OF_TERM_SPECIFICITY) const;

    void setOrigin(char origin);

    char getOrigin() const;

    void setSourceClassification(const String& classification);

    void setSourceClassification(SourceClassification classification);

    SourceClassification getSourceClassification() const;

    String getSourceClassificationName(SourceClassification classification = NUMBER_OF_SOURCE_CLASSIFICATIONS) const;

    void setAverageMass(double mass);

    double getAverageMass() const;

    void setMonoMass(double mass);

    double getMonoMass() const;

    void setDiffAverageMass(double mass);

    double getDiffAverageMass() const;

    void setDiffMonoMass(double mass);

    double getDiffMonoMass() const;

    void setFormula(const String& composition);

    const String& getFormula() const;

    void setDiffFormula(const EmpiricalFormula& diff_formula);

    const EmpiricalFormula& getDiffFormula() const;

    void setSynonyms(const std::set<String>& synonyms);

    void addSynonym(const String& synonym);

    const std::set<String>& getSynonyms() const;

    void setNeutralLossDiffFormulas(const std::vector<EmpiricalFormula>& diff_formulas);

    const std::vector<EmpiricalFormula>& getNeutralLossDiffFormulas() const;

    void setNeutralLossMonoMasses(std::vector<double> mono_masses);

    std::vector<double> getNeutralLossMonoMasses() const;

    void setNeutralLossAverageMasses(std::vector<double> average_masses);

    std::vector<double> getNeutralLossAverageMasses() const;

    bool hasNeutralLoss() const;

    bool isUserDefined() const;

    bool operator==(const ResidueModification& modification) const;

    bool operator!=(const ResidueModification& modification) const;

    bool operator<(const ResidueModification& modification) const;



    static const ResidueModification* createUnknownFromMassString(const String& mod,
                                                                  const double mass,
                                                                  const bool delta_mass,
                                                                  const TermSpecificity specificity,
                                                                  const Residue* residue = nullptr);

    static const ResidueModification* combineMods(const ResidueModification* base,
                                                  const std::set<const ResidueModification*>& addons,
                                                  bool allow_unknown_masses = false,
                                                  const Residue* residue = nullptr);

    String toString() const;

    static String getDiffMonoMassString(const double diff_mono_mass);

    static String getDiffMonoMassWithBracket(const double diff_mono_mass);

    static String getMonoMassWithBracket(const double mono_mass);

protected:
    String id_;

    String full_id_;

    String psi_mod_accession_;

    // The UniMod record id (an integer)
    Int unimod_record_id_;

    String full_name_;

    String name_;

    TermSpecificity term_spec_;

    char origin_;

    SourceClassification classification_;

    double average_mass_;

    double mono_mass_;

    double diff_average_mass_;

    double diff_mono_mass_;

    String formula_;

    EmpiricalFormula diff_formula_;

    std::set<String> synonyms_;

    std::vector<EmpiricalFormula> neutral_loss_diff_formulas_;

    std::vector<double> neutral_loss_mono_masses_;

    std::vector<double> neutral_loss_average_masses_;
  };
}