Package 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.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

Constructor Summary

Constructors

Constructor	Description
AlternateTokenization(Alphabet alpha, boolean caseSensitive)

Method Summary

Modifier and Type	Method	Description
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.