org.biojava.bio.symbol

Class IntegerAlphabet

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.symbol.IntegerAlphabet

All Implemented Interfaces:

Serializable, Annotatable, Alphabet, Changeable

public final class IntegerAlphabet
extends Unchangeable
implements Alphabet, Serializable

An efficient implementation of an Alphabet over the infinite set of integer values.

This class can be used to represent lists of integer numbers as a SymbolList with the alphabet IntegerAlphabet. These lists can then be annotated with features, or fed into dynamic-programming algorithms, or processed as per any other SymbolList object.

Object identity should be used to decide if two IntegerSymbol objects are the same. IntegerAlphabet ensures that all IntegerSymbol instances are canonicalized.

Author:

Matthew Pocock, Mark Schreiber, Thomas Down

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IntegerAlphabet.IntegerSymbol A single int value.
static class	IntegerAlphabet.SubIntegerAlphabet A class to represent a finite contiguous subset of the infinite IntegerAlphabet

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

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
static IntegerAlphabet	INSTANCE The singleton instance of the IntegerAlphabet class.

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 and Description
boolean	contains(Symbol s) Returns whether or not this Alphabet contains the symbol.
static SymbolList	fromArray(int[] iArray) Retrieve a SymbolList view of an array of integers.
List	getAlphabets() Return an ordered List of the alphabets which make up a compound alphabet.
Symbol	getAmbiguity(Set symSet) Get a symbol that represents the set of symbols in syms.
Annotation	getAnnotation() Should return the associated annotation object.
Symbol	getGapSymbol() Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
static IntegerAlphabet	getInstance() Retrieve the single IntegerAlphabet instance.
String	getName() Get the name of the alphabet.
static IntegerAlphabet.SubIntegerAlphabet	getSubAlphabet(int min, int max) Construct a finite contiguous subset of the IntegerAlphabet.
IntegerAlphabet.IntegerSymbol	getSymbol(int val) Retrieve the Symbol for an int.
Symbol	getSymbol(List symList) Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
SymbolTokenization	getTokenization(String name) Creates a new parser (Mark Schreiber 3 May 2001).
void	validate(Symbol s) Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.

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

Field Detail

INSTANCE

public static IntegerAlphabet INSTANCE

The singleton instance of the IntegerAlphabet class.

Method Detail

getSubAlphabet

public static IntegerAlphabet.SubIntegerAlphabet getSubAlphabet(int min,
                                                                int max)
                                                         throws IllegalArgumentException

Construct a finite contiguous subset of the IntegerAlphabet. Useful for making CrossProductAlphabets with other FiniteAlphabets.

Parameters:

min - the lower bound of the Alphabet

max - the upper bound of the Alphabet

Returns:

A FiniteAlphabet from min to max inclusive.

Throws:

IllegalArgumentException - if max < min

fromArray

public static SymbolList fromArray(int[] iArray)

Retrieve a SymbolList view of an array of integers.

The returned object is a view onto the underlying array, and does not copy it. Changes made to the original array will alter the symulting SymbolList.

Parameters:

iArray - the array of integers to view

Returns:

a SymbolList over the IntegerAlphabet that represent the values in iArray

getInstance

public static IntegerAlphabet getInstance()

Retrieve the single IntegerAlphabet instance.

Returns:

the singleton IntegerAlphabet instance

getSymbol

public IntegerAlphabet.IntegerSymbol getSymbol(int val)

Retrieve the Symbol for an int.

Parameters:

val - the int to view

Returns:

a IntegerSymbol embodying val

getGapSymbol

public 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

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

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.

Specified by:

getAlphabets in interface Alphabet

Returns:

a List of alphabets

getSymbol

public Symbol getSymbol(List symList)
                 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:

symList - A list of Symbol instances

Throws:

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

getAmbiguity

public Symbol getAmbiguity(Set symSet)
                    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:

symSet - 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

contains

public boolean contains(Symbol s)

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:

s - the Symbol to check

Returns:

boolean true if the Alphabet contains the symbol and false otherwise

validate

public void validate(Symbol s)
              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:

s - the Symbol to validate

Throws:

IllegalSymbolException - if r is not contained in this alphabet

getName

public String getName()

Description copied from interface: Alphabet

Get the name of the alphabet.

Specified by:

getName in interface Alphabet

Returns:

the name as a string.

getTokenization

public SymbolTokenization getTokenization(String name)

Creates a new parser (Mark Schreiber 3 May 2001).

Specified by:

getTokenization in interface Alphabet

Parameters:

name - Currently only "token" is supported. You may also use "default" as a synonym of "token"

Returns:

an IntegerParser.