Package org.biojava.nbio.core.sequence.storage

Class FourBitSequenceReader.FourBitArrayWorker<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>

org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker<C>

Type Parameters:

C - Must extend NucleotideCompound

Enclosing class:

FourBitSequenceReader<C extends Compound>

public static class FourBitSequenceReader.FourBitArrayWorker<C extends Compound>
extends BitSequenceReader.BitArrayWorker<C>

A four bit per compound implementation of the bit array worker code. This version can handle upto 16 compounds but this does mean that its ability to compress a normal sequence is halved (compared to the 1/4 performance seen with the 2bit workers).

Field Summary

Fields inherited from class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

BYTES_PER_INT

Constructor Summary

Constructors

Constructor	Description
FourBitArrayWorker(String sequence, CompoundSet<C> compoundSet)
FourBitArrayWorker(CompoundSet<C> compoundSet, int length)
FourBitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)
FourBitArrayWorker(Sequence<C> sequence)

Method Summary

Modifier and Type	Method	Description
protected byte	bitMask()	This method should return the bit mask to be used to extract the bytes you are interested in working with.
protected int	compoundsPerDatatype()	Should return the maximum amount of compounds we can encode per int
protected Map<C,Integer>	generateCompoundsToIndex()	Returns a Map which encodes the contents of CompoundSet.
protected List<C>	generateIndexToCompounds()	Returns a List which reverse encodes the Compound, Integer map

Methods inherited from class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

bitsPerCompound, equals, getCompoundAt, getCompoundSet, getCompoundsToIndexLookup, getIndexToCompoundsLookup, getLength, hashCode, populate, populate, processUnknownCompound, seqArraySize, setCompoundAt, setCompoundAt

Methods inherited from class java.lang.Object

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

Constructor Detail

FourBitArrayWorker

public FourBitArrayWorker(CompoundSet<C> compoundSet,
                          int length)

FourBitArrayWorker

public FourBitArrayWorker(CompoundSet<C> compoundSet,
                          int[] sequence)

FourBitArrayWorker

public FourBitArrayWorker(Sequence<C> sequence)

FourBitArrayWorker

public FourBitArrayWorker(String sequence,
                          CompoundSet<C> compoundSet)

Method Detail

bitMask

protected byte bitMask()

Description copied from class: BitSequenceReader.BitArrayWorker

This method should return the bit mask to be used to extract the bytes you are interested in working with. See solid implementations on how to create these

Specified by:

bitMask in class BitSequenceReader.BitArrayWorker<C extends Compound>

compoundsPerDatatype

protected int compoundsPerDatatype()

Description copied from class: BitSequenceReader.BitArrayWorker

Should return the maximum amount of compounds we can encode per int

Specified by:

compoundsPerDatatype in class BitSequenceReader.BitArrayWorker<C extends Compound>

generateCompoundsToIndex

protected Map<C,Integer> generateCompoundsToIndex()

Returns a Map which encodes the contents of CompoundSet. This version is case-insensitive i.e. C and c both encode for the same position. We sort lexigraphically so if the compound set has not changed then neither will this.

Specified by:

generateCompoundsToIndex in class BitSequenceReader.BitArrayWorker<C extends Compound>

generateIndexToCompounds

protected List<C> generateIndexToCompounds()

Returns a List which reverse encodes the Compound, Integer map

Specified by:

generateIndexToCompounds in class BitSequenceReader.BitArrayWorker<C extends Compound>