Package org.biojava.bio.symbol

Class IntegerAlphabet.SubIntegerAlphabet

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractAlphabet

org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet

All Implemented Interfaces:

Serializable, Annotatable, Alphabet, FiniteAlphabet, Changeable

Enclosing class:

IntegerAlphabet

public static class IntegerAlphabet.SubIntegerAlphabet
extends AbstractAlphabet

A class to represent a finite contiguous subset of the infinite IntegerAlphabet

Since:

1.3

Author:

Mark Schreiber, Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

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

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from class org.biojava.bio.symbol.AbstractAlphabet

serialVersionUID

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

EMPTY_ALPHABET, PARSERS, SYMBOLS

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Modifier and Type	Method	Description
protected void	addSymbolImpl(AtomicSymbol sym)
protected boolean	containsImpl(AtomicSymbol sym)
List	getAlphabets()	Return an ordered List of the alphabets which make up a compound alphabet.
Annotation	getAnnotation()	Should return the associated annotation object.
String	getName()	Get the name of the alphabet.
IntegerAlphabet.IntegerSymbol	getSymbol(int val)
protected AtomicSymbol	getSymbolImpl(List symL)
SymbolTokenization	getTokenization(String name)	Get a SymbolTokenization by name.
Iterator	iterator()	Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
void	removeSymbol(Symbol sym)	Remove a symbol from this alphabet.
int	size()	The number of symbols in the alphabet.

Methods inherited from class org.biojava.bio.symbol.AbstractAlphabet

addSymbol, contains, getAmbiguity, getAmbiguityImpl, getGapSymbol, getSymbol, putTokenization, readResolve, toString, validate

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.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

getName

public String getName()

Description copied from interface: Alphabet

Get the name of the alphabet.

Returns:

the name as a string.

containsImpl

protected boolean containsImpl(AtomicSymbol sym)

Specified by:

containsImpl in class AbstractAlphabet

getTokenization

public SymbolTokenization getTokenization(String name)

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

Overrides:

getTokenization in class AbstractAlphabet

Parameters:

name - Currently only "token" is supported.

Returns:

an IntegerParser.

getSymbol

public IntegerAlphabet.IntegerSymbol getSymbol(int val)
                                        throws IllegalSymbolException

Throws:

IllegalSymbolException

size

public int size()

Description copied from interface: FiniteAlphabet

The number of symbols in the alphabet.

Returns:

the size of the alphabet

getAlphabets

public List getAlphabets()

Description copied from interface: Alphabet

Return an ordered List of the alphabets which make up a compound alphabet. For simple alphabets, this will return a singleton list of itself. The returned list should be immutable.

Returns:

a List of alphabets

getSymbolImpl

protected AtomicSymbol getSymbolImpl(List symL)
                              throws IllegalSymbolException

Specified by:

getSymbolImpl in class AbstractAlphabet

Throws:

IllegalSymbolException

addSymbolImpl

protected void addSymbolImpl(AtomicSymbol sym)
                      throws ChangeVetoException

Specified by:

addSymbolImpl in class AbstractAlphabet

Throws:

ChangeVetoException

removeSymbol

public void removeSymbol(Symbol sym)
                  throws ChangeVetoException

Description copied from interface: FiniteAlphabet

Remove a symbol from this alphabet.

If the symbol matches multiple AtomicSymbols, then each matching symbol it will be removed.

Parameters:

sym - the Symbol to removeintGot

Throws:

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

iterator

public Iterator iterator()

Description copied from interface: FiniteAlphabet

Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.

Each AtomicSymbol as for which this.contains(as) is true will be returned exactly once by this iterator in no specified order.

Returns:

an Iterator over the contained AtomicSymbol objects

getAnnotation

public Annotation getAnnotation()

Description copied from interface: Annotatable

Should return the associated annotation object.

Returns:

an Annotation object, never null