org.biojava.bio.seq.io

Class CrossProductTokenization

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.io.WordTokenization

org.biojava.bio.seq.io.CrossProductTokenization

All Implemented Interfaces:

Serializable, Annotatable, SymbolTokenization, Changeable

public class CrossProductTokenization
extends WordTokenization

Tokenization for cross-product alphabets. This class handles the general case of tokens of the form (foo bar baz), where each element is handled by a sub-tokenization. By default, these will be the "name" tokenizations of each of the sub-alphabets, but any tokenization can be used.

Since:

1.2

Author:

Thomas Down, Greg Cox

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
CrossProductTokenization(Alphabet alpha)
CrossProductTokenization(Alphabet alpha, List tokenizers)

Method Summary

Methods

Modifier and Type	Method and Description
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, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

CrossProductTokenization

public CrossProductTokenization(Alphabet alpha)
                         throws BioException

Throws:

BioException

CrossProductTokenization

public CrossProductTokenization(Alphabet alpha,
                        List tokenizers)

Method Detail

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.