C
- Must extend NucleotideCompoundpublic static class TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound> extends BitSequenceReader.BitArrayWorker<C>
BYTES_PER_INT
Constructor | Description |
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TwoBitArrayWorker(java.lang.String sequence,
CompoundSet<C> compoundSet) |
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TwoBitArrayWorker(CompoundSet<C> compoundSet,
int length) |
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TwoBitArrayWorker(CompoundSet<C> compoundSet,
int[] sequence) |
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TwoBitArrayWorker(Sequence<C> sequence) |
Modifier and Type | Method | Description |
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protected byte |
bitMask() |
This method should return the bit mask to be used to extract the
bytes you are interested in working with.
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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 TCAG into positions 0,1,2,3.
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protected java.util.List<C> |
generateIndexToCompounds() |
Returns a List which encodes TCAG into positions 0,1,2,3.
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bitsPerCompound, equals, getCompoundAt, getCompoundSet, getCompoundsToIndexLookup, getIndexToCompoundsLookup, getLength, hashCode, populate, populate, processUnknownCompound, seqArraySize, setCompoundAt, setCompoundAt
public TwoBitArrayWorker(CompoundSet<C> compoundSet, int length)
public TwoBitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)
public TwoBitArrayWorker(java.lang.String sequence, CompoundSet<C> compoundSet)
protected byte bitMask()
BitSequenceReader.BitArrayWorker
bitMask
in class BitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
protected int compoundsPerDatatype()
BitSequenceReader.BitArrayWorker
compoundsPerDatatype
in class BitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
protected java.util.Map<C,java.lang.Integer> generateCompoundsToIndex()
generateCompoundsToIndex
in class BitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
protected java.util.List<C> generateIndexToCompounds()
generateIndexToCompounds
in class BitSequenceReader.BitArrayWorker<C extends NucleotideCompound>