org.biojava.bio.symbol

Interface Packing

All Known Implementing Classes:

DNAAmbPack, DNANoAmbPack

public interface Packing

An encapsulation of the way symbols map to bit-patterns.

A packing will encapsulate the process of converting between symbols and bit-patterns. For example, in DNA you could use 00, 01, 10 and 11 to represent the four bases (a, g, c, t). Many applications may require a specific packing. You may need to store full ambiguity information, or perhaps you can discard this capability to reduce stoorage space. You may care about the bit-pattern produced because you need interoperability or an algorithm needs to be fed correctly, or you may not care about the packing at all. This interface is here to allow you to chose the most appropreate packing for your task.

Author:

Matthew Pocock

Method Summary

Methods

Modifier and Type	Method and Description
FiniteAlphabet	getAlphabet() The FiniteAlphabet this packing is for.
boolean	handlesAmbiguity() Flag to state if ambiguities are stored.
byte	pack(Symbol sym) Return a byte representing the packing of a symbol.
Symbol	unpack(byte packed) Return the symbol for a packing.
byte	wordSize() The number of bits required to pack a symbol.

Method Detail

getAlphabet

FiniteAlphabet getAlphabet()

The FiniteAlphabet this packing is for.

Returns:

the FiniteAlphabet that we can pack

pack

byte pack(Symbol sym)
          throws IllegalSymbolException

Return a byte representing the packing of a symbol. The bits will be from 1 >> 0 through to 1 >> (wordSize - 1).

Parameters:

sym - the Symbol to pack

Returns:

a byte containing the packed symbol

Throws:

IllegalSymbolException - if sym is not in getAlphabet().

unpack

Symbol unpack(byte packed)
              throws IllegalSymbolException

Return the symbol for a packing.

Parameters:

packed - the byte pattern for a Symbol

Returns:

the Symbol that was packed

Throws:

IllegalSymbolException - if the packing doesn't represent a valid Symbol

wordSize

byte wordSize()

The number of bits required to pack a symbol.

Returns:

the word size as a byte

handlesAmbiguity

boolean handlesAmbiguity()

Flag to state if ambiguities are stored.

Packings are free to either store ambiguity information or to discard it (presumably converting all ambiguities to a standard AtomicSymbol and then packing that). You can check wether ambiguities are handled by calling this method.

Returns:

true if ambiguities are stored, false otherwise