Package org.biojava.bio.seq.io
Class AlternateTokenization
java.lang.Object
org.biojava.utils.Unchangeable
org.biojava.bio.seq.io.AlternateTokenization
- All Implemented Interfaces:
Serializable,Annotatable,SymbolTokenization,Changeable
Implementation of SymbolTokenization which binds symbols to strings of characters. These tokenizations are intented to provide alternate way of writing sequences into Strings. Therefore they cannot be used for parsing files.
As this release, alternate tokenizations are available for the built-in DNA alphabet (write symbols as capital letter) and PROTEIN-TERM alphabet (write symbol as triplets of characters with the first one being a capital letter as in "Glu".
By convention, instances of AlternateTokenization should have an associated token starting by the word 'alternate'.
- Since:
- 1.5
- Author:
- George Waldon
- See Also:
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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 -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidbindSymbol(Symbol s, String str) Bind a Symbol to a string.The alphabet to which this tokenization applies.Should return the associated annotation object.Tokens have fixed size.intgetWidth()Get the width of the tokens.parseStream(SeqIOListener listener) Will throw an exception.parseToken(String token) Will throw an exception.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
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Constructor Details
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AlternateTokenization
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Method Details
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getAlphabet
Description copied from interface:SymbolTokenizationThe alphabet to which this tokenization applies.- Specified by:
getAlphabetin interfaceSymbolTokenization
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getTokenType
Tokens have fixed size.- Specified by:
getTokenTypein interfaceSymbolTokenization
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getAnnotation
Description copied from interface:AnnotatableShould return the associated annotation object.- Specified by:
getAnnotationin interfaceAnnotatable- Returns:
- an Annotation object, never null
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getWidth
Get the width of the tokens. -
bindSymbol
Bind a Symbol to a string.- Parameters:
s- the Symbol to bindstr- the string to bind it to
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parseToken
Will throw an exception.- 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
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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.
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tokenizeSymbolList
Description copied from interface:SymbolTokenizationReturn a string representation of a list of symbols.- Specified by:
tokenizeSymbolListin interfaceSymbolTokenization- Parameters:
sl- A SymbolList- Throws:
IllegalAlphabetException- if alphabets don't match
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parseStream
Will throw an exception.- Specified by:
parseStreamin interfaceSymbolTokenization- Parameters:
listener- The listener which gets notified of parsed symbols.
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