org.biojava.nbio.core.sequence.storage

Class FourBitSequenceReader<C extends Compound>

java.lang.Object

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

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

All Implemented Interfaces:

Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

public class FourBitSequenceReader<C extends Compound>
extends BitSequenceReader<C>

Four bit encoding of the bit formats. This can support up to 16 compounds from a compound set. To allow us to support the redundant set of Nucleotide compounds this class will use case-insensitive encoding. The values assigned to these compounds is also done at runtime; if you want a predictable ordering then override and use your own encodings. However all encodings are calculated using lexographical ordering of the compounds so if a CompoundSet does not change then this encoding should not cauuse a problem.

Author:

ayates

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FourBitSequenceReader.FourBitArrayWorker<C extends Compound> A four bit per compound implementation of the bit array worker code.

Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.storage.BitSequenceReader

BitSequenceReader.BitArrayWorker<C extends Compound>

Constructor Summary

Constructors

Constructor and Description
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C> worker)
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C> worker, AccessionID accession)
FourBitSequenceReader(Sequence<C> sequence)
FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet)
FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)

Method Summary

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

countCompounds, equals, getAccession, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence, getSubSequence, hashCode, iterator, setCompoundSet, setContents

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

FourBitSequenceReader

public FourBitSequenceReader(Sequence<C> sequence)

FourBitSequenceReader

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

FourBitSequenceReader

public FourBitSequenceReader(String sequence,
                             CompoundSet<C> compoundSet,
                             AccessionID accession)

FourBitSequenceReader

public FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C> worker)

FourBitSequenceReader

public FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C> worker,
                             AccessionID accession)