Package org.biojava.bio.symbol
Class SoftMaskedAlphabet.CaseSensitiveTokenization
java.lang.Object
org.biojava.utils.Unchangeable
org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
- All Implemented Interfaces:
Annotatable,SymbolTokenization,Changeable
- Enclosing class:
- SoftMaskedAlphabet
public class SoftMaskedAlphabet.CaseSensitiveTokenization
extends Unchangeable
implements SymbolTokenization
This
SymbolTokenizer works with a delegate to softmask
symbol tokenization as appropriate. It should only be used in combination
with a SoftMaskedAlphabet.
You will never instantiate one of these yourself.
Copyright (c) 2004 Novartis Institute for Tropical Diseases
- Version:
- 1.0
- Author:
- Mark Schreiber
-
Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarderNested classes/interfaces inherited from interface org.biojava.bio.seq.io.SymbolTokenization
SymbolTokenization.TokenType -
Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATIONFields inherited from interface org.biojava.bio.seq.io.SymbolTokenization
CHARACTER, FIXEDWIDTH, SEPARATED, UNKNOWN -
Method Summary
Modifier and TypeMethodDescriptionThe alphabet to which this tokenization applies.Should return the associated annotation object.Determine the style of tokenization represented by this object.The current implementation only supports character parsing.parseToken(String token) Returns the symbol for a single token.Return a token representing a single symbol.Return a string representation of a list of symbols.Methods inherited from class org.biojava.utils.Unchangeable
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarderMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
-
Method Details
-
getAnnotation
Description copied from interface:AnnotatableShould return the associated annotation object.- Specified by:
getAnnotationin interfaceAnnotatable- Returns:
- an Annotation object, never null
-
getAlphabet
Description copied from interface:SymbolTokenizationThe alphabet to which this tokenization applies.- Specified by:
getAlphabetin interfaceSymbolTokenization
-
getTokenType
Description copied from interface:SymbolTokenizationDetermine the style of tokenization represented by this object.- Specified by:
getTokenTypein interfaceSymbolTokenization
-
parseToken
Description copied from interface:SymbolTokenizationReturns the symbol for a single token.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.
- Specified by:
parseTokenin interfaceSymbolTokenization- Parameters:
token- the token to retrieve a Symbol for- Returns:
- the Symbol for that token
- Throws:
IllegalSymbolException- if there is no Symbol for the token
-
tokenizeSymbolList
Description copied from interface:SymbolTokenizationReturn a string representation of a list of symbols.- Specified by:
tokenizeSymbolListin interfaceSymbolTokenization- Parameters:
sl- A SymbolList- Throws:
IllegalSymbolException
-
parseStream
The current implementation only supports character parsing. Word or fixed width parsing is not yet supported.- Specified by:
parseStreamin interfaceSymbolTokenization- Parameters:
l- theSeqIOListenerto callback to.- Returns:
- a
StreamParserthat theSeqIOListenertalks to.
-
tokenizeSymbol
Description copied from interface:SymbolTokenizationReturn a token representing a single symbol.- Specified by:
tokenizeSymbolin interfaceSymbolTokenization- Parameters:
s- The symbol- Throws:
IllegalSymbolException- if the symbol isn't recognized.
-