org.biojava.bio.symbol
Class SoftMaskedAlphabet.CaseSensitiveTokenization

java.lang.Object
  extended by org.biojava.utils.Unchangeable
      extended by 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.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
 
Method Summary
 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.