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

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

    • getAlphabet

      The FiniteAlphabet this packing is for.
      Returns:
      the FiniteAlphabet that we can pack
    • pack

      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