Package kmer.balance.core

Interface KMerBalancer

All Known Implementing Classes:

DefaultKMerBalancer

public interface KMerBalancer

Author:

Dennis Cosgrove

Method Summary

Modifier and Type	Method	Description
int	calculateReasonableThreshold(List<byte[]> sequences, int k)	Calculate a reasonable threshold to be used with createSlices(List, int, IntPredicate) where reasonable is defined to mean will create between 2X and 10X tasks per available processor.
default List<ByteArrayRange>	createReasonableSlices(List<byte[]> sequences, int k)
List<ByteArrayRange>	createSlices(List<byte[]> sequences, int k, IntPredicate slicePredicate)	Should create a list of slices from the given list of sequences.

Method Details

createSlices

List<ByteArrayRange> createSlices(List<byte[]> sequences,
 int k,
 IntPredicate slicePredicate)

Should create a list of slices from the given list of sequences. Each sequence may be divided many times or not divided at all, depending on its size relative to the sliceThreshold. Any sequence whose length is less than k should be omitted.

Parameters:

sequences - a list of sequences of nucleobases

k - the k in k-mer

slicePredicate - predicate which if returns true when tested with the range length from min to max indicates that continued slicing is appropriate

Returns:

the list of slices

calculateReasonableThreshold

int calculateReasonableThreshold(List<byte[]> sequences,
 int k)

Calculate a reasonable threshold to be used with createSlices(List, int, IntPredicate) where reasonable is defined to mean will create between 2X and 10X tasks per available processor.

Parameters:

sequences - a list of nucleobase sequences

k - the k in k-mer

Returns:

a reasonable threshold

See Also:

• Runtime.availableProcessors()

createReasonableSlices

default List<ByteArrayRange> createReasonableSlices(List<byte[]> sequences,
 int k)