org.biojava.bio.symbol

Class DNANoAmbPack

java.lang.Object

org.biojava.bio.symbol.DNANoAmbPack

All Implemented Interfaces:

Serializable, Packing

public class DNANoAmbPack
extends Object
implements Packing, Serializable

A Packing implementation which handles the DNA alphabet, without any support for ambiguity symbols. In normal use, the only returns values between 0 and 3, and so requires only two bits of storage per symbol.

Since:

1.3

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
DNANoAmbPack(byte placeHolder) Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols).
DNANoAmbPack(Symbol placeHolderSymbol) Construct a new packing which translates unknown symbols into the specified symbol.

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 b) Return the symbol for a packing.
byte	wordSize() The number of bits required to pack a symbol.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DNANoAmbPack

public DNANoAmbPack(byte placeHolder)

Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols). This might be outside the normal range of return values (0-3), allowing callers to detect ambiguity symbols and ignore them.

DNANoAmbPack

public DNANoAmbPack(Symbol placeHolderSymbol)

Construct a new packing which translates unknown symbols into the specified symbol.

Method Detail

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)
              throws IllegalSymbolException

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

Throws:

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

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