org.biojava.bio.symbol

Interface BasisSymbol

All Superinterfaces:

Annotatable, Changeable, Symbol

All Known Subinterfaces:

AtomicSymbol, DotState, EmissionState, ModelInState, State

All Known Implementing Classes:

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

public interface BasisSymbol
extends Symbol

A symbol that can be represented as a string of Symbols.

BasisSymbol instances can always be represented uniquely as a single List of BasisSymbol instances. The symbol N is a BasisSymbol - it can be uniquely represented by N. It matches {a, g, c, t}. Similarly, the symbol atn is a BasisSymbol, as it can be uniquely represented with a single list of symbols [a, t, n]. Its getMatches will return the set {ata, att, atg, atc}.

The getSymbols method returns the unique list of BasisSymbol instances that this is composed from. For example, the codon ambiguity symbol atn will have a getSymbols method that returns the list [a, t, n]. The getMatches method will return an Alphabet containing each AtomicSymbol that can be made by expanding the list of BasisSymbol instances.

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

Modifier and Type	Method and Description
List	getSymbols() The list of symbols that this symbol is composed from.

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

Method Detail

getSymbols

List getSymbols()

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.

Returns:

the List of Symbols that this Symbol is built from