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java.lang.Objectorg.biojava.utils.Unchangeable
org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
public class SoftMaskedAlphabet.CaseSensitiveTokenization
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
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.io.SymbolTokenization |
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SymbolTokenization.TokenType |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary |
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Fields inherited from interface org.biojava.bio.seq.io.SymbolTokenization |
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CHARACTER, FIXEDWIDTH, SEPARATED, UNKNOWN |
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. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
SymbolTokenization.TokenType |
getTokenType()
Determine the style of tokenization represented by this object. |
StreamParser |
parseStream(SeqIOListener l)
The current implementation only supports character parsing. |
Symbol |
parseToken(String token)
Returns the symbol for a single token. |
String |
tokenizeSymbol(Symbol s)
Return a token representing a single symbol. |
String |
tokenizeSymbolList(SymbolList sl)
Return a string representation of a list of symbols. |
Methods inherited from class org.biojava.utils.Unchangeable |
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addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Method Detail |
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public Annotation getAnnotation()
Annotatable
getAnnotation
in interface Annotatable
public Alphabet getAlphabet()
SymbolTokenization
getAlphabet
in interface SymbolTokenization
public SymbolTokenization.TokenType getTokenType()
SymbolTokenization
getTokenType
in interface SymbolTokenization
public Symbol parseToken(String token) throws IllegalSymbolException
SymbolTokenization
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.
parseToken
in interface SymbolTokenization
token
- the token to retrieve a Symbol for
IllegalSymbolException
- if there is no Symbol for the tokenpublic String tokenizeSymbolList(SymbolList sl) throws IllegalSymbolException
SymbolTokenization
tokenizeSymbolList
in interface SymbolTokenization
sl
- A SymbolList
IllegalSymbolException
public StreamParser parseStream(SeqIOListener l)
parseStream
in interface SymbolTokenization
l
- the SeqIOListener
to callback to.
StreamParser
that the SeqIOListener
talks to.public String tokenizeSymbol(Symbol s) throws IllegalSymbolException
SymbolTokenization
tokenizeSymbol
in interface SymbolTokenization
s
- The symbol
IllegalSymbolException
- if the symbol isn't recognized.
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