ResidueDB.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch, Jang Jang Jin$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <unordered_map>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Macros.h> // for OPENMS_PRECONDITION
 
#include <map>
#include <set>
#include <array>
 
namespace OpenMS
{
  // forward declarations
  class ResidueModification;
  class Residue;
 
  class OPENMS_DLLAPI ResidueDB
  {
public:
    static ResidueDB* getInstance();
 
    virtual ~ResidueDB();
 
    Size getNumberOfResidues() const;
 
    Size getNumberOfModifiedResidues() const;
 
    const Residue* getResidue(const String& name) const;
 
    const Residue* getResidue(const unsigned char& one_letter_code) const;
 
    const Residue* getModifiedResidue(const String& name);
 
    const Residue* getModifiedResidue(const Residue* residue, const String& name);
 
    const Residue* getModifiedResidue(const Residue* residue, const ResidueModification* mod);
 
    const std::set<const Residue*> getResidues(const String& residue_set = "All") const;
 
    const std::set<String> getResidueSets() const;
 
 
    bool hasResidue(const String& name) const;
 
    bool hasResidue(const Residue* residue) const;
 
protected:
    void initResidues_();
 
    ResidueDB();
 
    ResidueDB(const ResidueDB& residue_db);
 
    ResidueDB& operator=(const ResidueDB& aa) = delete;
 
   // construct all residues 
    void buildResidues_();
    
    void insertResidueAndAssociateWithResidueSet_(Residue* residue, const std::vector<String>& residue_sets);
 
    void addResidue_(Residue* residue);
 
    void addResidueNames_(const Residue*);
 
    void addModifiedResidueNames_(const Residue*);
    
    std::map<String, std::map<String, const Residue*> > residue_mod_names_;
 
    std::set<const Residue*> const_residues_;
 
    std::set<const Residue*> const_modified_residues_;
 
    std::set<String> residue_sets_;
 
    std::unordered_map<String, const Residue*> residue_names_;
 
    std::array<const Residue*, 256> residue_by_one_letter_code_ = {{nullptr}};
 
    std::map<String, std::set<const Residue*> > residues_by_set_;    
  };
}