Package org.biojava.bio.seq.io

Class CharacterTokenization

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.io.CharacterTokenization

All Implemented Interfaces:

Serializable, Annotatable, SymbolTokenization, Changeable

public class CharacterTokenization
extends Unchangeable
implements SymbolTokenization, Serializable

Implementation of SymbolTokenization which binds symbols to single unicode characters.

Many alphabets (and all simple built-in alphabets like DNA, RNA and Protein) will have an instance of CharacterTokenization registered under the name 'token', so that you could say CharacterTokenization ct = (CharacterTokenization) alpha.getTokenization('token'); and expect it to work. When you construct a new instance of this class for an alphabet, there will be no initial associations of Symbols with characters. It is your responsibility to populate the new tokenization appropriately.

Since:

1.2

Author:

Thomas Down, Matthew Pocock, 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
CharacterTokenization(Alphabet alpha, boolean caseSensitive)

Method Summary

Modifier and Type	Method	Description
void	bindSymbol(Symbol s, char c)	Bind a Symbol to a character.
Alphabet	getAlphabet()	The alphabet to which this tokenization applies.
Annotation	getAnnotation()	Should return the associated annotation object.
protected Symbol[]	getTokenTable()
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.
protected Symbol	parseTokenChar(char c)
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

CharacterTokenization

public CharacterTokenization(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()

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

bindSymbol

public void bindSymbol(Symbol s,
                       char c)

Bind a Symbol to a character.

This method will ensure that when this char is observed, it resolves to this symbol. If it was previously associated with another symbol, the old binding is removed. If this is the first time the symbol has been bound to any character, then this character is taken to be the default tokenization of the Symbol. This means that when converting symbols into characters, this char will be used. If the symbol has previously been bound to another character, then this char will not be produced for the symbol when stringifying the symbol, but this symbol will be produced when tokenizing this character.

Parameters:

s - the Symbol to bind

c - the char to bind it to

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

getTokenTable

protected Symbol[] getTokenTable()

parseTokenChar

protected Symbol parseTokenChar(char c)
                         throws IllegalSymbolException

Throws:

IllegalSymbolException

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)

Description copied from interface: SymbolTokenization

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

Specified by:

parseStream in interface SymbolTokenization

Parameters:

listener - The listener which gets notified of parsed symbols.