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>
Implementation of the 2bit encoding. This will default to the following
encodings:
- 0 - T
- 1 - C
- 2 - A
- 3 - G
- Author:
- ayates
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic classExtension 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
ConstructorsConstructorDescriptionTwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet) TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession) 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, setContentsMethods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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TwoBitSequenceReader
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TwoBitSequenceReader
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TwoBitSequenceReader
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TwoBitSequenceReader
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TwoBitSequenceReader
public TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker, AccessionID accession)
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