Package org.biojava.bio.seq.io

Class DoubleTokenization

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.io.WordTokenization

org.biojava.bio.seq.io.DoubleTokenization

All Implemented Interfaces:

Serializable, Annotatable, SymbolTokenization, Changeable

public class DoubleTokenization
extends WordTokenization

Author:

Thomas Down

See Also:

Serialized Form

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

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

Constructor Summary

Constructors

Constructor	Description
DoubleTokenization()

Method Summary

Modifier and Type	Method	Description
Symbol	parseToken(String seq)	Returns the symbol for a single token.
String	tokenizeSymbol(Symbol sym)	Return a token representing a single symbol.

Methods inherited from class org.biojava.bio.seq.io.WordTokenization

getAlphabet, getAnnotation, getTokenType, parseStream, parseString, splitString, tokenizeSymbolList

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

Constructor Detail

DoubleTokenization

public DoubleTokenization()

Method Detail

parseToken

public Symbol parseToken(String seq)
                  throws IllegalSymbolException

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.

Parameters:

seq - the token to retrieve a Symbol for

Returns:

the Symbol for that token

Throws:

IllegalSymbolException - if there is no Symbol for the token

tokenizeSymbol

public String tokenizeSymbol(Symbol sym)
                      throws IllegalSymbolException

Description copied from interface: SymbolTokenization

Return a token representing a single symbol.

Parameters:

sym - The symbol

Throws:

IllegalSymbolException - if the symbol isn't recognized.