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 2002-2018.
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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;

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

    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;

    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);

    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_;
  };
}