org.biojava.bio.seq.io

Class SubIntegerTokenization

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.io.WordTokenization

org.biojava.bio.seq.io.SubIntegerTokenization

All Implemented Interfaces:

Serializable, Annotatable, SymbolTokenization, Changeable

public class SubIntegerTokenization
extends WordTokenization

Author:

Mark Schreiber

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
SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet alpha)

Method Summary

Methods

Modifier and Type	Method and 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

SubIntegerTokenization

public SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet alpha)

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.