Package org.biojava.bio.symbol

Class DNAAmbPack

java.lang.Object
org.biojava.bio.symbol.DNAAmbPack
All Implemented Interfaces:
Serializable, Packing
public class DNAAmbPack extends Object implements Packing, Serializable
Packing utility class for DNA. Also represents ambiguity.
Author:
Matthew Pocock, David Huen (bugfix)
See Also:

  • Constructor Details

  • Method Details

    • getAlphabet

      public FiniteAlphabet getAlphabet()
      Description copied from interface: Packing
      The FiniteAlphabet this packing is for.
      Specified by:
      getAlphabet in interface Packing
      Returns:
      the FiniteAlphabet that we can pack

    • pack

      public byte pack(Symbol sym)
      Description copied from interface: Packing

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

      Specified by:
      pack in interface Packing
      Parameters:
      sym - the Symbol to pack
      Returns:
      a byte containing the packed symbol

    • unpack

      public Symbol unpack(byte b)
      Description copied from interface: Packing

      Return the symbol for a packing.

      Specified by:
      unpack in interface Packing
      Parameters:
      b - the byte pattern for a Symbol
      Returns:
      the Symbol that was packed

    • wordSize

      public byte wordSize()
      Description copied from interface: Packing

      The number of bits required to pack a symbol.

      Specified by:
      wordSize in interface Packing
      Returns:
      the word size as a byte

    • handlesAmbiguity

      public boolean handlesAmbiguity()
      Description copied from interface: Packing

      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.

      Specified by:
      handlesAmbiguity in interface Packing
      Returns:
      true if ambiguities are stored, false otherwise