## org.biojava.bio.seq.io
Class AlternateTokenization

    java.lang.Object
      org.biojava.utils.Unchangeable
          org.biojava.bio.seq.io.AlternateTokenization

All Implemented Interfaces:
  Serializable, Annotatable, SymbolTokenization, Changeable

    public class AlternateTokenization

extends Unchangeable
implements SymbolTokenization, Serializable

Implementation of SymbolTokenization which binds symbols to strings of characters. These tokenizations are intented to provide alternate way of writing sequences into Strings. Therefore they cannot be used for parsing files.

As this release, alternate tokenizations are available for the built-in DNA alphabet (write symbols as capital letter) and PROTEIN-TERM alphabet (write symbol as triplets of characters with the first one being a capital letter as in "Glu".

By convention, instances of AlternateTokenization should have an associated token starting by the word 'alternate'.

Since:
  1.5
Author:
  George Waldon
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
`AlternateTokenization(Alphabet alpha, boolean caseSensitive)`

Method Summary
`void` `bindSymbol(Symbol s, String str)` Bind a Symbol to a string.
`Alphabet` `getAlphabet()` The alphabet to which this tokenization applies.
`Annotation` `getAnnotation()` Should return the associated annotation object.
`SymbolTokenization.TokenType` `getTokenType()` Tokens have fixed size.
`int` `getWidth()` Get the width of the tokens.
`StreamParser` `parseStream(SeqIOListener listener)` Will throw an exception.
`Symbol` `parseToken(String token)` Will throw an exception.
`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`

Constructor Detail

### AlternateTokenization

    public AlternateTokenization(Alphabet alpha,
                                 boolean caseSensitive)

Method Detail

### 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()

  Tokens have fixed size.

  Specified by:
    `getTokenType` in interface `SymbolTokenization`

### 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

### getWidth

    public int getWidth()

  Get the width of the tokens.

### bindSymbol

    public void bindSymbol(Symbol s,
                           String str)

  Bind a Symbol to a string.

  Parameters:
    `s` - the Symbol to bind
    `str` - the string to bind it to

### parseToken

    public Symbol parseToken(String token)
                      throws IllegalSymbolException

  Will throw an exception.

  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

### 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.

### tokenizeSymbolList

    public String tokenizeSymbolList(SymbolList sl)
                              throws IllegalAlphabetException

  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:
    `IllegalAlphabetException` - if alphabets don't match

### parseStream

    public StreamParser parseStream(SeqIOListener listener)

  Will throw an exception.

  Specified by:
    `parseStream` in interface `SymbolTokenization`
  Parameters:
    `listener` - The listener which gets notified of parsed symbols.