All Known Implementing Classes:

DNAAmbPack, DNANoAmbPack

public interface Packing 

Author:

Matthew Pocock

• Method Summary

  All 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