Package org.biojava.bio.symbol

Class SoftMaskedAlphabet.CaseSensitiveTokenization

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization

All Implemented Interfaces:

Annotatable, SymbolTokenization, Changeable

Enclosing class:

SoftMaskedAlphabet

public class SoftMaskedAlphabet.CaseSensitiveTokenization
extends Unchangeable
implements SymbolTokenization

This SymbolTokenizer works with a delegate to softmask symbol tokenization as appropriate. It should only be used in combination with a SoftMaskedAlphabet. You will never instantiate one of these yourself.

Copyright (c) 2004 Novartis Institute for Tropical Diseases

Version:

1.0

Author:

Mark Schreiber

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

Method Summary

Modifier and Type	Method	Description
Alphabet	getAlphabet()	The alphabet to which this tokenization applies.
Annotation	getAnnotation()	Should return the associated annotation object.
SymbolTokenization.TokenType	getTokenType()	Determine the style of tokenization represented by this object.
StreamParser	parseStream(SeqIOListener l)	The current implementation only supports character parsing.
Symbol	parseToken(String token)	Returns the symbol for a single token.
String	tokenizeSymbol(Symbol s)	Return a token representing a single symbol.
String	tokenizeSymbolList(SymbolList sl)	Return a string representation of a list of symbols.

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

Method Detail

getAnnotation

public Annotation getAnnotation()

Description copied from interface: Annotatable

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: SymbolTokenization

The alphabet to which this tokenization applies.

Specified by:

getAlphabet in interface SymbolTokenization

getTokenType

public SymbolTokenization.TokenType getTokenType()

Description copied from interface: SymbolTokenization

Determine the style of tokenization represented by this object.

Specified by:

getTokenType in interface SymbolTokenization

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.

Specified by:

parseToken in interface SymbolTokenization

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

tokenizeSymbolList

public String tokenizeSymbolList(SymbolList sl)
                          throws IllegalSymbolException

Description copied from interface: SymbolTokenization

Return a string representation of a list of symbols.

Specified by:

tokenizeSymbolList in interface SymbolTokenization

Parameters:

sl - A SymbolList

Throws:

IllegalSymbolException

parseStream

public StreamParser parseStream(SeqIOListener l)

The current implementation only supports character parsing. Word or fixed width parsing is not yet supported.

Specified by:

parseStream in interface SymbolTokenization

Parameters:

l - the SeqIOListener to callback to.

Returns:

a StreamParser that the SeqIOListener talks to.

tokenizeSymbol

public String tokenizeSymbol(Symbol s)
                      throws IllegalSymbolException

Description copied from interface: SymbolTokenization

Return a token representing a single symbol.

Specified by:

tokenizeSymbol in interface SymbolTokenization

Parameters:

s - The symbol

Throws:

IllegalSymbolException - if the symbol isn't recognized.