org.biojava.bio.symbol
Class PackingFactory
java.lang.Object
org.biojava.bio.symbol.PackingFactory
- public class PackingFactory
- extends java.lang.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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PackingFactory
public PackingFactory()
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-packedambiguity
- true if the packing should store ambiguity and false
if it can discard ambiguity information
- Throws:
IllegalAlphabetException
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)