org.biojava.bio.seq.io

Class NameTokenization

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.io.WordTokenization

org.biojava.bio.seq.io.NameTokenization

All Implemented Interfaces:

Serializable, Annotatable, SymbolTokenization, Changeable

public class NameTokenization
extends WordTokenization

Simple implementation of SymbolTokenization which uses the `name' field of the symbols. This class works with any non-cross-product FiniteAlphabet, and doesn't need any extra data to be provided.

Since:

1.2

Author:

Thomas Down

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.seq.io.SymbolTokenization

SymbolTokenization.TokenType

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojava.bio.seq.io.SymbolTokenization

CHARACTER, FIXEDWIDTH, SEPARATED, UNKNOWN

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Constructor and Description
NameTokenization(FiniteAlphabet fab) Construct a new NameTokenization, defaulting to case-insensitive.
NameTokenization(FiniteAlphabet fab, boolean caseSensitive)

Method Summary

Modifier and Type	Method and Description
protected void	finalize()
protected Map	getNameToSymbol()
Symbol	parseToken(String token) Returns the symbol for a single token.
String	tokenizeSymbol(Symbol s) 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, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

NameTokenization

public NameTokenization(FiniteAlphabet fab,
                        boolean caseSensitive)

NameTokenization

public NameTokenization(FiniteAlphabet fab)

Construct a new NameTokenization, defaulting to case-insensitive.

Method Detail

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

getNameToSymbol

protected Map getNameToSymbol()

parseToken

public Symbol parseToken(String token)
                  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:

token - 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 s)
                      throws IllegalSymbolException

Description copied from interface: SymbolTokenization

Return a token representing a single symbol.

Parameters:

s - The symbol

Throws:

IllegalSymbolException - if the symbol isn't recognized.