Package org.biojava.bio.symbol

Class AbstractAlphabet

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractAlphabet

All Implemented Interfaces:

Serializable, Annotatable, Alphabet, FiniteAlphabet, Changeable

Direct Known Subclasses:

IntegerAlphabet.SubIntegerAlphabet, SimpleAlphabet, SingletonAlphabet

public abstract class AbstractAlphabet
extends AbstractChangeable
implements FiniteAlphabet, Serializable

An abstract implementation of Alphabet.

This provides the frame-work for maintaining the SymbolParser <-> name mappings and also for the ChangeListeners.

This class is for developers to derive from, not for use directly.

Since:

1.1

Author:

Matthew Pocock, Greg Cox, Francois Pepin, Mark Schreiber

See Also:

Serialized Form

Nested Class Summary

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

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field	Description
static long	serialVersionUID

Fields inherited from interface org.biojava.bio.symbol.Alphabet

EMPTY_ALPHABET, PARSERS, SYMBOLS

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractAlphabet()

Method Summary

Modifier and Type	Method	Description
void	addSymbol(Symbol s)	Adds a symbol to this alphabet.
protected abstract void	addSymbolImpl(AtomicSymbol s)
boolean	contains(Symbol sym)	Returns whether or not this Alphabet contains the symbol.
protected abstract boolean	containsImpl(AtomicSymbol s)
Symbol	getAmbiguity(Set syms)	Get a symbol that represents the set of symbols in syms.
protected Symbol	getAmbiguityImpl(Set syms)	Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
Symbol	getGapSymbol()	Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
Symbol	getSymbol(List syms)	Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
protected abstract AtomicSymbol	getSymbolImpl(List symList)
SymbolTokenization	getTokenization(String name)	Get a SymbolTokenization by name.
void	putTokenization(String name, SymbolTokenization parser)	Assigns a symbol parser to a String object.
protected Object	readResolve()	To prevent duplication of a what should be a single instance of an existing alphabet.
String	toString()
void	validate(Symbol sym)	Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.bio.symbol.Alphabet

getAlphabets, getName

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.symbol.FiniteAlphabet

iterator, removeSymbol, size

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

AbstractAlphabet

protected AbstractAlphabet()

Method Detail

readResolve

protected Object readResolve()
                      throws ObjectStreamException

To prevent duplication of a what should be a single instance of an existing alphabet. This method was written as protected so that subclasses even from other packages will inherit it. It should only be overridden with care.

Throws:

ObjectStreamException

putTokenization

public void putTokenization(String name,
                            SymbolTokenization parser)

Assigns a symbol parser to a String object.

Afterwards, the parser can be retrieved using the getTokenization(Sting name) method.

getTokenization

public SymbolTokenization getTokenization(String name)
                                   throws NoSuchElementException,
                                          BioException

Description copied from interface: Alphabet

Get a SymbolTokenization by name.

The parser returned is guaranteed to return Symbols and SymbolLists that conform to this alphabet.

Every alphabet should have a SymbolTokenzation under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolTokenization under the name 'name' that uses symbol names to identify symbols. Any other names may also be defined, but the behavior of the returned SymbolTokenization is not defined here.

A SymbolTokenization under the name 'default' should be defined for all sequences, that determines the behavior when printing out a sequence. Standard behavior is to define the 'token' SymbolTokenization as default if it exists, else to define the 'name' SymbolTokenization as the default, but others are possible.

Specified by:

getTokenization in interface Alphabet

Parameters:

name - the name of the parser

Returns:

a parser for that name

Throws:

NoSuchElementException - if the name is unknown

BioException - if for any reason the tokenization could not be built

getAmbiguity

public final Symbol getAmbiguity(Set syms)
                          throws IllegalSymbolException

Description copied from interface: Alphabet

Get a symbol that represents the set of symbols in syms.

Syms must be a set of Symbol instances each of which is contained within this alphabet. This method is used to retrieve ambiguity symbols.

Specified by:

getAmbiguity in interface Alphabet

Parameters:

syms - the Set of Symbols that will be found in getMatches of the returned symbol

Returns:

a Symbol (possibly fly-weighted) for the Set of symbols in syms

Throws:

IllegalSymbolException

getAmbiguityImpl

protected Symbol getAmbiguityImpl(Set syms)
                           throws IllegalSymbolException

Backend for getAmbiguity, called when it is actually necessarly to create a new symbol. By default, calls AlphabetManager.createSymbol.

Throws:

IllegalSymbolException

Since:

1.3

getSymbol

public final Symbol getSymbol(List syms)
                       throws IllegalSymbolException

Description copied from interface: Alphabet

Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.

The symbol at i in the list must be a member of the i'th alphabet in getAlphabets. If all of the symbols in rl are atomic, then the resulting symbol will also be atomic. If any one of them is an ambiguity symbol then the resulting symbol will be the appropriate ambiguity symbol.

Specified by:

getSymbol in interface Alphabet

Parameters:

syms - A list of Symbol instances

Throws:

IllegalSymbolException - if the members of rl are not Symbols over the alphabets returned from getAlphabets

getSymbolImpl

protected abstract AtomicSymbol getSymbolImpl(List symList)
                                       throws IllegalSymbolException

Throws:

IllegalSymbolException

addSymbolImpl

protected abstract void addSymbolImpl(AtomicSymbol s)
                               throws IllegalSymbolException,
                                      ChangeVetoException

Throws:

IllegalSymbolException

ChangeVetoException

addSymbol

public final void addSymbol(Symbol s)
                     throws IllegalSymbolException,
                            ChangeVetoException

Description copied from interface: FiniteAlphabet

Adds a symbol to this alphabet.

If the symbol matches more than one AtomicSymbol, then each symbol matching it will be added.

Specified by:

addSymbol in interface FiniteAlphabet

Parameters:

s - the Symbol to add

Throws:

IllegalSymbolException - if the symbol is null, or if for any reason it can't be added

ChangeVetoException - if either the alphabet doesn't allow symbols to be added, or the change was vetoed

contains

public final boolean contains(Symbol sym)

Description copied from interface: Alphabet

Returns whether or not this Alphabet contains the symbol.

An alphabet contains an ambiguity symbol iff the ambiguity symbol's getMatches() returns an alphabet that is a proper sub-set of this alphabet. That means that every one of the symbols that could match the ambiguity symbol is also a member of this alphabet.

Specified by:

contains in interface Alphabet

Parameters:

sym - the Symbol to check

Returns:

boolean true if the Alphabet contains the symbol and false otherwise

getGapSymbol

public final Symbol getGapSymbol()

Description copied from interface: Alphabet

Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.

In general, this will be a BasisSymbol that represents a list of AlphabetManager.getGapSymbol() the same length as the getAlphabets list.

Specified by:

getGapSymbol in interface Alphabet

Returns:

the appropriate gap Symbol instance

validate

public final void validate(Symbol sym)
                    throws IllegalSymbolException

Description copied from interface: Alphabet

Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.

This function is used all over the code to validate symbols as they enter a method. Also, the code is littered with catches for IllegalSymbolException. There is a preferred style of handling this, which should be covererd in the package documentation.

Specified by:

validate in interface Alphabet

Parameters:

sym - the Symbol to validate

Throws:

IllegalSymbolException - if r is not contained in this alphabet

containsImpl

protected abstract boolean containsImpl(AtomicSymbol s)

toString

public String toString()

Overrides:

toString in class Object