Package org.biojava.bio.symbol

Class FundamentalAtomicSymbol

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbol
org.biojava.bio.symbol.FundamentalAtomicSymbol
All Implemented Interfaces:
Serializable, Annotatable, AtomicSymbol, BasisSymbol, Symbol, Changeable
Direct Known Subclasses:
SimpleDotState, SimpleModelInState
public class FundamentalAtomicSymbol extends AbstractSymbol implements AtomicSymbol, Serializable
An atomic symbol consisting only of itself. This is the fundamental type of symbol, and needs a special implementation. If you wish to construct new Symbols, you should normally do so via utility methods on AlphabetManager. This may be useful as a base-class for other Symbol implementations.
Since:
1.1
Author:
Thomas Down
See Also:

  • Constructor Details

  • Method Details

    • 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

    • 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

    • getSymbols

      public 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

    • 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