org.biojava3.core.sequence.storage
Class TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound>
java.lang.Object
org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>
org.biojava3.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.
Method Summary |
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 |
protected Map<C,Integer> |
generateCompoundsToIndex()
Returns a Map which encodes TCAG into positions 0,1,2,3. |
protected List<C> |
generateIndexToCompounds()
Returns a List which encodes TCAG into positions 0,1,2,3. |
Methods inherited from class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker |
bitsPerCompound, equals, getCompoundAt, getCompoundSet, getCompoundsToIndexLookup, getIndexToCompoundsLookup, getLength, hashCode, populate, populate, processUnknownCompound, seqArraySize, setCompoundAt, setCompoundAt |
TwoBitSequenceReader.TwoBitArrayWorker
public TwoBitSequenceReader.TwoBitArrayWorker(CompoundSet<C> compoundSet,
int length)
TwoBitSequenceReader.TwoBitArrayWorker
public TwoBitSequenceReader.TwoBitArrayWorker(CompoundSet<C> compoundSet,
int[] sequence)
TwoBitSequenceReader.TwoBitArrayWorker
public TwoBitSequenceReader.TwoBitArrayWorker(Sequence<C> sequence)
TwoBitSequenceReader.TwoBitArrayWorker
public TwoBitSequenceReader.TwoBitArrayWorker(String sequence,
CompoundSet<C> compoundSet)
bitMask
protected byte bitMask()
- Description copied from class:
BitSequenceReader.BitArrayWorker
- This 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:
bitMask
in class BitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
compoundsPerDatatype
protected int compoundsPerDatatype()
- Description copied from class:
BitSequenceReader.BitArrayWorker
- Should return the maximum amount of compounds we can encode per int
- Specified by:
compoundsPerDatatype
in class BitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
generateCompoundsToIndex
protected Map<C,Integer> generateCompoundsToIndex()
- Returns a Map which encodes TCAG into positions 0,1,2,3.
- Specified by:
generateCompoundsToIndex
in class BitSequenceReader.BitArrayWorker<C extends NucleotideCompound>
generateIndexToCompounds
protected List<C> generateIndexToCompounds()
- Returns a List which encodes TCAG into positions 0,1,2,3.
- Specified by:
generateIndexToCompounds
in class BitSequenceReader.BitArrayWorker<C extends NucleotideCompound>