Package org.biojava.bio.symbol

Class SimpleAtomicSymbol

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbol
org.biojava.bio.symbol.SimpleAtomicSymbol
All Implemented Interfaces:
Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable
public class SimpleAtomicSymbol extends AbstractSymbol implements AtomicSymbol, Serializable
A basic implementation of AtomicSymbol. If you wish to construct new Symbols, you should normally do so via utility methods on AlphabetManager. This may be a useful base class for custom implementations.
Author:
Matthew Pocock
See Also:

  • Field Details

    • symbols

      protected List symbols

    • matches

      protected Alphabet matches

  • Constructor Details

  • Method Details

    • createMatches

      protected Alphabet createMatches()

    • getSymbols

      public final List getSymbols()
      Description copied from interface: BasisSymbol

      The list of symbols that this symbol is composed from.

      In the usual case, this list will contain just this single symbol. In the case where a symbol represents an ordered combination of other symbols, the list will contain each of these BasisSymbols.

      Specified by:
      getSymbols in interface BasisSymbol
      Returns:
      the List of Symbols that this Symbol is built from

    • createSymbols

      protected List createSymbols()

    • getAnnotation

      public Annotation getAnnotation()
      Description copied from interface: Annotatable
      Should return the associated annotation object.
      Specified by:
      getAnnotation in interface Annotatable
      Returns:
      an Annotation object, never null

    • getMatches

      public Alphabet getMatches()
      Description copied from interface: Symbol
      The alphabet containing the symbols matched by this ambiguity symbol.

      This alphabet contains all of, and only, the symbols matched by this symbol. For example, the symbol representing the DNA ambiguity code for W would contain the symbol for A and T from the DNA alphabet.

      Specified by:
      getMatches in interface Symbol
      Returns:
      the Alphabet of symbols matched by this symbol

    • getName

      public String getName()
      Description copied from interface: Symbol
      The long name for the symbol.
      Specified by:
      getName in interface Symbol
      Returns:
      the long name