Package org.biojava3.core.sequence.storage

Class TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound>

java.lang.Object

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

org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker<C>

Type Parameters:

C - Must extend NucleotideCompound

Enclosing class:

TwoBitSequenceReader<C extends NucleotideCompound>

public static class TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound>
extends BitSequenceReader.BitArrayWorker<C>

Extension of the BitArrayWorker which provides the 2bit implementation code. This is intended to work with the 4 basic nucelotide types. If you require a different version of the encoding used here then extend and override as required.

Field Summary

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

BYTES_PER_INT

Constructor Summary

Constructors

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

TwoBitArrayWorker

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

TwoBitArrayWorker

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

TwoBitArrayWorker

public TwoBitArrayWorker(Sequence<C> sequence)

TwoBitArrayWorker

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