TwoBitSequenceReader

java.lang.Object
- org.biojava.nbio.core.sequence.storage.BitSequenceReader<C>
- - org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader<C>

All Implemented Interfaces:

java.lang.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	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	Description
`TwoBitSequenceReader(java.lang.String sequence, CompoundSet<C> compoundSet)`
`TwoBitSequenceReader(java.lang.String sequence, CompoundSet<C> compoundSet, AccessionID accession)`
`TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker)`
`TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker, AccessionID accession)`
`TwoBitSequenceReader(Sequence<C> sequence)`

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 interface java.lang.Iterable
  forEach, spliterator
- Methods inherited from class java.lang.Object
  clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TwoBitSequenceReader

public TwoBitSequenceReader(Sequence<C> sequence)

TwoBitSequenceReader

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

TwoBitSequenceReader

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

TwoBitSequenceReader

public TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker)

TwoBitSequenceReader

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

Class TwoBitSequenceReader<C extends NucleotideCompound>

Nested Class Summary

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

Constructor Summary

Method Summary

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

Methods inherited from interface java.lang.Iterable

Methods inherited from class java.lang.Object

Constructor Detail

TwoBitSequenceReader

TwoBitSequenceReader

TwoBitSequenceReader

TwoBitSequenceReader

TwoBitSequenceReader