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
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
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Method Summary
Modifier and TypeMethodDescriptionThe 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
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Method Details
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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
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