org.biojava.bio.symbol

Class PackedSymbolList

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.symbol.PackedSymbolList

All Implemented Interfaces:

Serializable, SymbolList, Changeable

public class PackedSymbolList
extends AbstractSymbolList
implements Serializable

A SymbolList that stores symbols as bit-patterns in an array of longs.

Bit-packed symbol lists are space efficient compared to the usual pointer storage model employed by implementations like SimpleSymbolList. This comes at the cost of encoding/decoding symbols from the storage. In practice, the decrease in memory when storing large sequences makes applications go quicker because of issues like page swapping.

Symbols can be mapped to and from bit-patterns. The Pattern interface encapsulates this. A SymbolList can then be stored by writing these bit-patterns into memory. This implementation stores the bits in the long elements of an array. The first symbol will be packed into bits 0 through packing.wordLength()-1 of the long at index 0.

Example Usage

 SymbolList symL = ...;
 SymbolList packed = new PackedSymbolList(
   PackingFactory.getPacking(symL.getAlphabet(), true),
   symL
 );
 

Author:

Matthew Pocock, David Huen (new constructor for Symbol arrays and some speedups)

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

Field Summary

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
PackedSymbolList(Packing packing, long[] syms, int length) Create a new PackedSymbolList directly from a bit pattern.
PackedSymbolList(Packing packing, Symbol[] symbols, int length, Alphabet alfa) Create a new PackedSymbolList from an array of Symbols.
PackedSymbolList(Packing packing, SymbolList symList) Create a new PackedSymbolList as a packed copy of another symbol list.

Method Summary

Methods

Modifier and Type	Method and Description
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
long[]	getSyms() Return the long array within which the symbols are bit-packed.
int	length() The number of symbols in this SymbolList.
Symbol	symbolAt(int indx) Return the symbol at index, counting from 1.

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList

edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

PackedSymbolList

public PackedSymbolList(Packing packing,
                long[] syms,
                int length)

Create a new PackedSymbolList directly from a bit pattern.

Warning: This is a risky developer method. You must be sure that the syms array is packed in a way that is consistent with the packing. Also, it is your responsibility to ensure that the length is sensible.

Parameters:

packing - the Packing used

syms - a long array containing already packed symbols

length - the length of the sequence packed in symbols

PackedSymbolList

public PackedSymbolList(Packing packing,
                SymbolList symList)
                 throws IllegalAlphabetException

Create a new PackedSymbolList as a packed copy of another symbol list.

This will create a new and independent symbol list that is a copy of the symbols in symList. Both lists can be modified independently.

Parameters:

packing - the way to bit-pack symbols

symList - the SymbolList to copy

Throws:

IllegalAlphabetException

PackedSymbolList

public PackedSymbolList(Packing packing,
                Symbol[] symbols,
                int length,
                Alphabet alfa)
                 throws IllegalAlphabetException,
                        IllegalArgumentException

Create a new PackedSymbolList from an array of Symbols.

This will create a new and independent SymbolList formed from the the symbol array.

Parameters:

packing - the way to bit-pack symbols

symbols - an array of Symbols

length - the number of Symbols to process from symbols

alfa - the alphabet from which the Symbols are drawn

Throws:

IllegalAlphabetException

IllegalArgumentException

Method Detail

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: SymbolList

The alphabet that this SymbolList is over.

Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

symbolAt

public Symbol symbolAt(int indx)

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

indx - the offset into this SymbolList

Returns:

the Symbol at that index

getSyms

public long[] getSyms()

Return the long array within which the symbols are bit-packed.

Warning: This is a risky developer method. This is the actual array that this object uses to store the bits representing symbols. You should not modify this in any way. If you do, you will modify the symbols returned by symbolAt(). This methd is provided primarily as an easy way for developers to extract the bit pattern for storage in such a way as it could be fetched later and fed into the appropriate constructor.

Returns:

the actual long array used to store bit-packed symbols