org.biojava.nbio.core.sequence.storage

Class TwoBitSequenceReader<C extends NucleotideCompound>

java.lang.Object

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

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

All Implemented Interfaces:

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

public class TwoBitSequenceReader<C extends NucleotideCompound>
extends BitSequenceReader<C>

Implementation of the 2bit encoding. This will default to the following encodings:

• 0 - T
• 1 - C
• 2 - A
• 3 - G

We also do not support case sensitive encodings therefore if you pass a lowercased a this will be treated as if it is an uppercase A and we will erase that information.

Author:

ayates

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound> Extension of the BitArrayWorker which provides the 2bit implementation 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
TwoBitSequenceReader(Sequence<C> sequence)
TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet)
TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker)
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker, 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

TwoBitSequenceReader

public TwoBitSequenceReader(Sequence<C> sequence)

TwoBitSequenceReader

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

TwoBitSequenceReader

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

TwoBitSequenceReader

public TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker)

TwoBitSequenceReader

public TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker,
                            AccessionID accession)