org.biojava.bio.seq.io
Class CrossProductTokenization

java.lang.Object
  extended by org.biojava.utils.Unchangeable
      extended by org.biojava.bio.seq.io.WordTokenization
          extended by 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
CrossProductTokenization(Alphabet alpha)
           
CrossProductTokenization(Alphabet alpha, List tokenizers)
           
 
Method Summary
 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.