org.biojava.bio.symbol

Interface AtomicSymbol

All Superinterfaces:

Annotatable, BasisSymbol, Changeable, Symbol

All Known Subinterfaces:

DotState, EmissionState, ModelInState, State

All Known Implementing Classes:

DoubleAlphabet.DoubleSymbol, FundamentalAtomicSymbol, IntegerAlphabet.IntegerSymbol, MagicalState, ProfileEmissionState, SimpleAtomicSymbol, SimpleDotState, SimpleEmissionState, SimpleModelInState

public interface AtomicSymbol
extends BasisSymbol

A symbol that is not ambiguous.

Atomic symbols are the real underlying elements that a SymbolList is meant to be composed of. DNA nucleotides are atomic, as are amino-acids. The getMatches() method should return an alphabet containing just the one Symbol.

The Symbol instances for single codons would be instances of AtomicSymbol as they can only be represented as a Set of symbols from their alphabet that contains just that one symbol.

AtomicSymbol instances guarantee that getMatches returns an Alphabet containing just that Symbol and each element of the List returned by getSymbols is also atomic.

Since:

1.1

Author:

Matthew Pocock

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Methods inherited from interface org.biojava.bio.symbol.BasisSymbol

getSymbols

Methods inherited from interface org.biojava.bio.symbol.Symbol

getMatches, getName

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener