libopenms-dev 1.11.1-5 / usr / include / OpenMS / CHEMISTRY / ResidueDB.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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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;

  /** @ingroup Chemistry

          @brief residue data base which holds residues

          The residues stored in this DB are defined in a
          XML file under data/CHEMISTRY/residues.xml

          By default no modified residues are stored in an instance. However, if one
          queries the instance with getModifiedResidue, a new modified residue is
          added.
  */
  class OPENMS_DLLAPI ResidueDB
  {
public:

    /** @name Typedefs
    */
    //@{
    typedef std::set<Residue *>::iterator ResidueIterator;
    typedef std::set<const Residue *>::const_iterator ResidueConstIterator;
    //@}

    /// this member function serves as a replacement of the constructor
    inline static ResidueDB * getInstance()
    {
      static ResidueDB * db_ = 0;
      if (db_ == 0)
      {
        db_ = new ResidueDB;
      }
      return db_;
    }

    /** @name Constructors and Destructors
    */
    //@{
    /// destructor
    virtual ~ResidueDB();
    //@}

    /** @name Accessors
    */
    //@{
    /// returns the number of residues stored
    Size getNumberOfResidues() const;

    Size getNumberOfModifiedResidues() const;

    /// returns a pointer to the residue with name, 3 letter code or 1 letter code name
    const Residue * getResidue(const String & name) const;

    ///
    const Residue * getModifiedResidue(const String & name);

    ///
    const Residue * getModifiedResidue(const Residue * residue, const String & name);

    /** @brief returns a set of all residues stored in this residue db

            The possible residues are defined in share/OpenMS/CHEMISTRY/Residues.xml. At
            the moment the following sets are available:
                All - all residues stored in the file
                Natural20 - default 20 naturally occuring residues
                Natural19WithoutI - default natural amino acids, excluding isoleucine (isobaric to leucine)
                Natural19WithoutL - default natural amino acids, excluding leucine (isobaric to isoleucine)
                Natural19J - default natural amino acids,  (isobaric leucine/isoleucine are marked by 'J')
                AmbiguousWithoutX -  all amino acids, including ambiguous ones
                                 B (asparagine or aspartate)
                                                         Z (glutamine or glutamate)
                                                         J (isoleucine or leucine)
                Ambiguous - all amino acids including all ambiguous ones (X can be every other amino acid)
                AllNatural - naturally occuring residues, including selenocysteine (U)
    */
    const std::set<const Residue *> getResidues(const String & residue_set = "All") const;

    /// returns all residue sets that are registered which this instance
    const std::set<String> & getResidueSets() const;

    /// sets the residues from given file
    void setResidues(const String & filename);

    /// adds a residue, i.e. a unkown residue, where only the weight is known
    void addResidue(const Residue & residue);
    //@}

    /** @name Predicates
    */
    //@{
    /// returns true if the db contains a residue with the given name
    bool hasResidue(const String & name) const;

    /// returns true if the db contains the residue of the given pointer
    bool hasResidue(const Residue * residue) const;
    //@}

    /** @name Iterators
    */
    //@{
    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:

    /** @name Private Constructors
    */
    //@{
    /// default constructor
    ResidueDB();

    ///copy constructor
    ResidueDB(const ResidueDB & residue_db);
    //@}

    /** @name Assignment
*/
    //@{
    /// assignment operator
    ResidueDB & operator=(const ResidueDB & aa);
    //@}

    /// reads residues from the given file
    void readResiduesFromFile_(const String & filename);

    /// parses a residue, given the key/value pairs from i.e. an XML file
    Residue * parseResidue_(Map<String, String> & values);

    /// deletes all sub-instances of the stored data like modifications and residues
    void clear_();

    /// clears the residues
    void clearResidues_();

    /// builds an index of residue names for fast access, synonyms are also considered
    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