C
- Must extend NucleotideCompoundpublic static class FourBitSequenceReader.FourBitArrayWorker<C extends Compound> extends BitSequenceReader.BitArrayWorker<C>
BYTES_PER_INT
Constructor | Description |
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FourBitArrayWorker(java.lang.String sequence,
CompoundSet<C> compoundSet) |
|
FourBitArrayWorker(CompoundSet<C> compoundSet,
int length) |
|
FourBitArrayWorker(CompoundSet<C> compoundSet,
int[] sequence) |
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FourBitArrayWorker(Sequence<C> sequence) |
Modifier and Type | Method | Description |
---|---|---|
protected byte |
bitMask() |
This method should return the bit mask to be used to extract the
bytes you are interested in working with.
|
protected int |
compoundsPerDatatype() |
Should return the maximum amount of compounds we can encode per int
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protected java.util.Map<C,java.lang.Integer> |
generateCompoundsToIndex() |
Returns a Map which encodes the contents of CompoundSet.
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protected java.util.List<C> |
generateIndexToCompounds() |
Returns a List which reverse encodes the Compound, Integer map
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bitsPerCompound, equals, getCompoundAt, getCompoundSet, getCompoundsToIndexLookup, getIndexToCompoundsLookup, getLength, hashCode, populate, populate, processUnknownCompound, seqArraySize, setCompoundAt, setCompoundAt
public FourBitArrayWorker(CompoundSet<C> compoundSet, int length)
public FourBitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)
public FourBitArrayWorker(java.lang.String sequence, CompoundSet<C> compoundSet)
protected byte bitMask()
BitSequenceReader.BitArrayWorker
bitMask
in class BitSequenceReader.BitArrayWorker<C extends Compound>
protected int compoundsPerDatatype()
BitSequenceReader.BitArrayWorker
compoundsPerDatatype
in class BitSequenceReader.BitArrayWorker<C extends Compound>
protected java.util.Map<C,java.lang.Integer> generateCompoundsToIndex()
generateCompoundsToIndex
in class BitSequenceReader.BitArrayWorker<C extends Compound>
protected java.util.List<C> generateIndexToCompounds()
generateIndexToCompounds
in class BitSequenceReader.BitArrayWorker<C extends Compound>