public class AlternateTokenization extends Unchangeable implements SymbolTokenization, Serializable
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'.
SymbolTokenization.TokenTypeAnnotatable.AnnotationForwarderCHARACTER, FIXEDWIDTH, SEPARATED, UNKNOWNANNOTATION| Constructor and Description |
|---|
AlternateTokenization(Alphabet alpha,
boolean caseSensitive) |
| Modifier and Type | Method and Description |
|---|---|
void |
bindSymbol(Symbol s,
String str)
Bind a Symbol to a string.
|
Alphabet |
getAlphabet()
The alphabet to which this tokenization applies.
|
Annotation |
getAnnotation()
Should return the associated annotation object.
|
SymbolTokenization.TokenType |
getTokenType()
Tokens have fixed size.
|
int |
getWidth()
Get the width of the tokens.
|
StreamParser |
parseStream(SeqIOListener listener)
Will throw an exception.
|
Symbol |
parseToken(String token)
Will throw an exception.
|
String |
tokenizeSymbol(Symbol s)
Return a token representing a single symbol.
|
String |
tokenizeSymbolList(SymbolList sl)
Return a string representation of a list of symbols.
|
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarderclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerpublic AlternateTokenization(Alphabet alpha, boolean caseSensitive)
public Alphabet getAlphabet()
SymbolTokenizationgetAlphabet in interface SymbolTokenizationpublic SymbolTokenization.TokenType getTokenType()
getTokenType in interface SymbolTokenizationpublic Annotation getAnnotation()
AnnotatablegetAnnotation in interface Annotatablepublic int getWidth()
public void bindSymbol(Symbol s, String str)
s - the Symbol to bindstr - the string to bind it topublic Symbol parseToken(String token) throws IllegalSymbolException
parseToken in interface SymbolTokenizationtoken - the token to retrieve a Symbol forIllegalSymbolException - if there is no Symbol for the tokenpublic String tokenizeSymbol(Symbol s) throws IllegalSymbolException
SymbolTokenizationtokenizeSymbol in interface SymbolTokenizations - The symbolIllegalSymbolException - if the symbol isn't recognized.public String tokenizeSymbolList(SymbolList sl) throws IllegalAlphabetException
SymbolTokenizationtokenizeSymbolList in interface SymbolTokenizationsl - A SymbolListIllegalAlphabetException - if alphabets don't matchpublic StreamParser parseStream(SeqIOListener listener)
parseStream in interface SymbolTokenizationlistener - The listener which gets notified of parsed symbols.Copyright © 2014 BioJava. All rights reserved.