Package org.biojava3.core.sequence.storage

Class FourBitSequenceReader.FourBitArrayWorker<C extends Compound>

java.lang.Object

org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>

org.biojava3.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.biojava3.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

Methods inherited from class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker

equals, getCompoundAt, getCompoundSet, getLength, hashCode, populate, populate, seqArraySize, setCompoundAt, setCompoundAt

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Details

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)