Packing (biojava-legacy 1.9.5 API)

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

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	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