Package org.biojava.bio.symbol

Class PackingFactory

java.lang.Object

org.biojava.bio.symbol.PackingFactory

public class PackingFactory
extends Object

A factory that is used to maintain associations between alphabets and preferred bit-packings for them.

There are many ways to pack the symbols for an alphabet as binary. Different applications will wish to have different representations for reasons such as integration with external formats, whether to store ambiguity or not and what algorithms may be used on the bit-packed representation. Also, it has utility methods to arrange the bit-strings for symbols within a Java int primitive.

Author:

Matthew Pocock, Thomas Down

Constructor Summary

Constructors

Constructor	Description
PackingFactory()

Method Summary

Modifier and Type	Method	Description
static void	binary(int val)
static void	binary(long val)
static Packing	getPacking(FiniteAlphabet alpha, boolean ambiguity)	Get the default packing for an alphabet.
static int	nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing)
static int	primeWord(SymbolList symList, int wordLength, Packing packing)

Methods inherited from class java.lang.Object

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

Constructor Detail

PackingFactory

public PackingFactory()

Method Detail

getPacking

public static Packing getPacking(FiniteAlphabet alpha,
                                 boolean ambiguity)
                          throws IllegalAlphabetException

Get the default packing for an alphabet.

Parameters:

alpha - the FiniteAlphabet that will be bit-packed

ambiguity - true if the packing should store ambiguity and false if it can discard ambiguity information

Throws:

IllegalAlphabetException - if this combination of alphabet and ambiguity can not be handled

primeWord

public static int primeWord(SymbolList symList,
                            int wordLength,
                            Packing packing)
                     throws IllegalSymbolException

Throws:

IllegalSymbolException

nextWord

public static int nextWord(SymbolList symList,
                           int word,
                           int offset,
                           int wordLength,
                           Packing packing)
                    throws IllegalSymbolException

Throws:

IllegalSymbolException

binary

public static void binary(long val)

binary

public static void binary(int val)