ResidueDB.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 $
// $Authors: Andreas Bertsch, Jang Jang Jin$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <unordered_map>
#include <OpenMS/DATASTRUCTURES/StringUtils.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 const ResidueDB* getInstance();
 
    virtual ~ResidueDB();
 
    Size getNumberOfResidues() const;
 
    Size getNumberOfModifiedResidues() const;
 
    const Residue* getResidue(const std::string& name) const;
 
    const Residue* getResidue(const unsigned char& one_letter_code) const;
 
    const Residue* getModifiedResidue(const std::string& name) const;
 
    const Residue* getModifiedResidue(const Residue* residue, const std::string& name) const;
 
    const Residue* getModifiedResidue(const Residue* residue, const ResidueModification* mod) const;
 
    const std::set<const Residue*> getResidues(const std::string& residue_set = "All") const;
 
    const std::set<std::string> getResidueSets() const;
 
 
    bool hasResidue(const std::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<std::string>& residue_sets);
 
    void addModifiedResidue_(Residue* residue) const;
 
    void addResidueNames_(const Residue*);
 
    void addModifiedResidueNames_(const Residue*) const;
 
    mutable std::map<std::string, std::map<std::string, const Residue*> > residue_mod_names_;
 
    std::set<const Residue*> const_residues_;
 
    mutable std::set<const Residue*> const_modified_residues_;
 
    std::set<std::string> residue_sets_;
 
    std::unordered_map<std::string, const Residue*> residue_names_;
 
    std::array<const Residue*, 256> residue_by_one_letter_code_ = {{nullptr}};
 
    std::map<std::string, std::set<const Residue*> > residues_by_set_;    
  };
}