BasisSymbol (biojava-legacy 1.9.5 API)

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
  
  All Methods Instance Methods Abstract Methods
  Modifier and Type Method Description
  
  List getSymbols()
  The list of symbols that this symbol is composed from.
  - Methods inherited from interface org.biojava.bio.Annotatable
    getAnnotation
  - Methods inherited from interface org.biojava.utils.Changeable
    addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
  - Methods inherited from interface org.biojava.bio.symbol.Symbol
    getMatches, getName

- 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