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.AnnotationForwarder
Nested classes/interfaces inherited from interface org.biojava.bio.seq.io.SymbolTokenization
SymbolTokenization.TokenType
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Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.seq.io.SymbolTokenization
CHARACTER, FIXEDWIDTH, SEPARATED, UNKNOWN
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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, removeForwarder
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Method Details
-
getAnnotation
Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
-
getAlphabet
Description copied from interface:SymbolTokenization
The alphabet to which this tokenization applies.- Specified by:
getAlphabet
in interfaceSymbolTokenization
-
getTokenType
Description copied from interface:SymbolTokenization
Determine the style of tokenization represented by this object.- Specified by:
getTokenType
in interfaceSymbolTokenization
-
parseToken
Description copied from interface:SymbolTokenization
Returns 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:
parseToken
in 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:SymbolTokenization
Return a string representation of a list of symbols.- Specified by:
tokenizeSymbolList
in 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:
parseStream
in interfaceSymbolTokenization
- Parameters:
l
- theSeqIOListener
to callback to.- Returns:
- a
StreamParser
that theSeqIOListener
talks to.
-
tokenizeSymbol
Description copied from interface:SymbolTokenization
Return a token representing a single symbol.- Specified by:
tokenizeSymbol
in interfaceSymbolTokenization
- Parameters:
s
- The symbol- Throws:
IllegalSymbolException
- if the symbol isn't recognized.
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