Package org.biojava.nbio.core.sequence.storage

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.

Field Summary

Fields inherited from class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

BYTES_PER_INT

Constructor Summary

Constructors

Constructor	Description
TwoBitArrayWorker(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 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
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.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

bitsPerCompound, equals, getCompoundAt, getCompoundSet, getCompoundsToIndexLookup, getIndexToCompoundsLookup, getLength, hashCode, populate, populate, processUnknownCompound, seqArraySize, setCompoundAt, setCompoundAt

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TwoBitArrayWorker

public TwoBitArrayWorker(CompoundSet<C> compoundSet,
                         int length)

TwoBitArrayWorker

public TwoBitArrayWorker(CompoundSet<C> compoundSet,
                         int[] sequence)

TwoBitArrayWorker

public TwoBitArrayWorker(Sequence<C> sequence)

TwoBitArrayWorker

public TwoBitArrayWorker(String sequence,
                         CompoundSet<C> compoundSet)

Method Detail

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>