Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD

## 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
`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

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD