Package org.biojava.bio.seq.io

Class WordTokenization

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.io.WordTokenization

All Implemented Interfaces:

Serializable, Annotatable, SymbolTokenization, Changeable

Direct Known Subclasses:

CrossProductTokenization, DoubleTokenization, IntegerTokenization, NameTokenization, SubIntegerTokenization

public abstract class WordTokenization
extends Unchangeable
implements SymbolTokenization, Serializable

Base class for tokenizations which accept whitespace-separated `words'. Splits at whitespace, except when it is quoted by either double-quotes ("), brackets (), or square brackets [].

Since:

1.2

Author:

Thomas Down, Greg Cox, Keith James

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
WordTokenization(Alphabet fab)

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 siol)	Return an object which can parse an arbitrary character stream into symbols.
protected Symbol[]	parseString(String s)
protected List	splitString(String str)
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

Methods inherited from interface org.biojava.bio.seq.io.SymbolTokenization

parseToken, tokenizeSymbol

Constructor Detail

WordTokenization

public WordTokenization(Alphabet fab)

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()

Description copied from interface: SymbolTokenization

Determine the style of tokenization represented by this object.

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

tokenizeSymbolList

public String tokenizeSymbolList(SymbolList sl)
                          throws IllegalSymbolException,
                                 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

IllegalSymbolException

parseStream

public StreamParser parseStream(SeqIOListener siol)

Description copied from interface: SymbolTokenization

Return an object which can parse an arbitrary character stream into symbols.

Specified by:

parseStream in interface SymbolTokenization

Parameters:

siol - The listener which gets notified of parsed symbols.

splitString

protected List splitString(String str)
                    throws IllegalSymbolException

Throws:

IllegalSymbolException

parseString

protected Symbol[] parseString(String s)
                        throws IllegalSymbolException

Throws:

IllegalSymbolException