Package org.biojava.bio.seq.io

Interface SymbolTokenization

All Superinterfaces:

Annotatable, Changeable

All Known Implementing Classes:

AlternateTokenization, CharacterTokenization, CrossProductTokenization, DoubleTokenization, IntegerTokenization, NameTokenization, SoftMaskedAlphabet.CaseSensitiveTokenization, SubIntegerTokenization, WordTokenization

public interface SymbolTokenization
extends Annotatable

Encapsulate a mapping between BioJava Symbol objects and some string representation.

Since:

1.2

Author:

Thomas Down

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	SymbolTokenization.TokenType

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field	Description
static SymbolTokenization.TokenType	CHARACTER
static SymbolTokenization.TokenType	FIXEDWIDTH
static SymbolTokenization.TokenType	SEPARATED
static SymbolTokenization.TokenType	UNKNOWN

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Modifier and Type	Method	Description
Alphabet	getAlphabet()	The alphabet to which this tokenization applies.
SymbolTokenization.TokenType	getTokenType()	Determine the style of tokenization represented by this object.
StreamParser	parseStream(SeqIOListener listener)	Return an object which can parse an arbitrary character stream into symbols.
Symbol	parseToken(String token)	Returns the symbol for a single token.
String	tokenizeSymbol(Symbol sym)	Return a token representing a single symbol.
String	tokenizeSymbolList(SymbolList symList)	Return a string representation of a list of symbols.

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

CHARACTER

static final SymbolTokenization.TokenType CHARACTER

FIXEDWIDTH

static final SymbolTokenization.TokenType FIXEDWIDTH

SEPARATED

static final SymbolTokenization.TokenType SEPARATED

UNKNOWN

static final SymbolTokenization.TokenType UNKNOWN

Method Detail

getAlphabet

Alphabet getAlphabet()

The alphabet to which this tokenization applies.

getTokenType

SymbolTokenization.TokenType getTokenType()

Determine the style of tokenization represented by this object.

parseToken

Symbol parseToken(String token)
           throws IllegalSymbolException

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.

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

parseStream

StreamParser parseStream(SeqIOListener listener)

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

Parameters:

listener - The listener which gets notified of parsed symbols.

tokenizeSymbol

String tokenizeSymbol(Symbol sym)
               throws IllegalSymbolException

Return a token representing a single symbol.

Parameters:

sym - The symbol

Throws:

IllegalSymbolException - if the symbol isn't recognized.

tokenizeSymbolList

String tokenizeSymbolList(SymbolList symList)
                   throws IllegalAlphabetException,
                          IllegalSymbolException

Return a string representation of a list of symbols.

Parameters:

symList - A SymbolList

Throws:

IllegalAlphabetException - if alphabets don't match

IllegalSymbolException