ResidueDB.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: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
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#pragma once
 
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <boost/unordered_map.hpp>
#include <OpenMS/DATASTRUCTURES/String.h>
 
#include <set>
 
namespace OpenMS
{
  // forward declarations
  class ResidueModification;
  class Residue;
 
  class OPENMS_DLLAPI ResidueDB
  {
public:
 
    typedef std::set<Residue*>::iterator ResidueIterator;
    typedef std::set<const Residue*>::const_iterator ResidueConstIterator;
 
    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 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;
 
    inline ResidueIterator beginResidue() { return residues_.begin(); }
 
    inline ResidueIterator endResidue() { return residues_.end(); }
 
    inline ResidueConstIterator beginResidue() const { return const_residues_.begin(); }
 
    inline ResidueConstIterator endResidue() const { return const_residues_.end(); }
 
protected:
    void setResidues_(const String& filename);
 
    ResidueDB();
 
    ResidueDB(const ResidueDB& residue_db);
 
    ResidueDB& operator=(const ResidueDB& aa);
 
    void readResiduesFromFile_(const String& filename);
 
    Residue* parseResidue_(Map<String, String>& values);
 
    void clear_();
 
    void clearResidues_();
 
    void clearResidueModifications_();
 
    void buildResidueNames_();
 
    void addResidue_(Residue* residue);
 
    boost::unordered_map<String, Residue*> residue_names_;
 
    // fast lookup table for residues
    Residue* residue_by_one_letter_code_[256];
 
    Map<String, Map<String, Residue*> > residue_mod_names_;
 
    std::set<Residue*> residues_;
 
    std::set<const Residue*> const_residues_;
 
    std::set<Residue*> modified_residues_;
 
    std::set<const Residue*> const_modified_residues_;
 
    Map<String, std::set<const Residue*> > residues_by_set_;
 
    std::set<String> residue_sets_;
  };
}