Class TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound>
java.lang.Object
org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>
org.biojava.nbio.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.
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Field Summary
Fields inherited from class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
BYTES_PER_INT -
Constructor Summary
ConstructorsConstructorDescriptionTwoBitArrayWorker(String sequence, CompoundSet<C> compoundSet) TwoBitArrayWorker(CompoundSet<C> compoundSet, int length) TwoBitArrayWorker(CompoundSet<C> compoundSet, int[] sequence) TwoBitArrayWorker(Sequence<C> sequence) -
Method Summary
Modifier and TypeMethodDescriptionprotected bytebitMask()This method should return the bit mask to be used to extract the bytes you are interested in working with.protected intShould return the maximum amount of compounds we can encode per intReturns a Map which encodes TCAG into positions 0,1,2,3.Returns a List which encodes TCAG into positions 0,1,2,3.Methods inherited from class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
bitsPerCompound, equals, getCompoundAt, getCompoundSet, getCompoundsToIndexLookup, getIndexToCompoundsLookup, getLength, hashCode, populate, populate, processUnknownCompound, seqArraySize, setCompoundAt, setCompoundAt
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Constructor Details
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TwoBitArrayWorker
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TwoBitArrayWorker
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TwoBitArrayWorker
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TwoBitArrayWorker
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Method Details
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bitMask
protected byte bitMask()Description copied from class:BitSequenceReader.BitArrayWorkerThis method should return the bit mask to be used to extract the bytes you are interested in working with. See solid implementations on how to create these- Specified by:
bitMaskin classBitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
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compoundsPerDatatype
protected int compoundsPerDatatype()Description copied from class:BitSequenceReader.BitArrayWorkerShould return the maximum amount of compounds we can encode per int- Specified by:
compoundsPerDatatypein classBitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
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generateCompoundsToIndex
Returns a Map which encodes TCAG into positions 0,1,2,3.- Specified by:
generateCompoundsToIndexin classBitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
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generateIndexToCompounds
Returns a List which encodes TCAG into positions 0,1,2,3.- Specified by:
generateIndexToCompoundsin classBitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
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