ResidueDB.h

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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_CHEMISTRY_RESIDUEDB_H
#define OPENMS_CHEMISTRY_RESIDUEDB_H

#include <OpenMS/DATASTRUCTURES/Map.h>
#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;

    inline static ResidueDB * getInstance()
    {
      static ResidueDB * db_ = 0;
      if (db_ == 0)
      {
        db_ = new ResidueDB;
      }
      return db_;
    }


    virtual ~ResidueDB();


    Size getNumberOfResidues() const;

    Size getNumberOfModifiedResidues() const;

    const Residue * getResidue(const String & name) 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;

    void setResidues(const String & filename);

    void addResidue(const Residue & residue);


    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:


    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 buildResidueNames_();

    void addResidue_(Residue * residue);

    Map<String, Residue *> residue_names_;

    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_;
  };
}
#endif