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public interface SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation.
Nested Class Summary | |
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static class |
SymbolTokenization.TokenType
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Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary | |
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static SymbolTokenization.TokenType |
CHARACTER
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static SymbolTokenization.TokenType |
FIXEDWIDTH
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static SymbolTokenization.TokenType |
SEPARATED
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static SymbolTokenization.TokenType |
UNKNOWN
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Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Method Summary | |
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Alphabet |
getAlphabet()
The alphabet to which this tokenization applies. |
SymbolTokenization.TokenType |
getTokenType()
Determine the style of tokenization represented by this object. |
StreamParser |
parseStream(SeqIOListener listener)
Return an object which can parse an arbitrary character stream into symbols. |
Symbol |
parseToken(java.lang.String token)
Returns the symbol for a single token. |
java.lang.String |
tokenizeSymbol(Symbol sym)
Return a token representing a single symbol. |
java.lang.String |
tokenizeSymbolList(SymbolList symList)
Return a string representation of a list of symbols. |
Methods inherited from interface org.biojava.bio.Annotatable |
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getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
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static final SymbolTokenization.TokenType CHARACTER
static final SymbolTokenization.TokenType FIXEDWIDTH
static final SymbolTokenization.TokenType SEPARATED
static final SymbolTokenization.TokenType UNKNOWN
Method Detail |
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Alphabet getAlphabet()
SymbolTokenization.TokenType getTokenType()
Symbol parseToken(java.lang.String token) throws IllegalSymbolException
The Symbol will be a member of the alphabet. If the token is not recognized as mapping to a symbol, an exception will be thrown.
token
- the token to retrieve a Symbol for
IllegalSymbolException
- if there is no Symbol for the tokenStreamParser parseStream(SeqIOListener listener)
listener
- The listener which gets notified of parsed symbols.java.lang.String tokenizeSymbol(Symbol sym) throws IllegalSymbolException
sym
- The symbol
IllegalSymbolException
- if the symbol isn't recognized.java.lang.String tokenizeSymbolList(SymbolList symList) throws IllegalAlphabetException, IllegalSymbolException
symList
- A SymbolList
IllegalAlphabetException
- if alphabets don't match
IllegalSymbolException
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