net.maizegenetics.dna.snp.bit

Class DynamicBitStorage

java.lang.Object

net.maizegenetics.dna.snp.bit.DynamicBitStorage

All Implemented Interfaces:

BitStorage

public class DynamicBitStorage
extends Object
implements BitStorage

Provides rapid conversion routines and caching from byte encoding of nucleotides to bit encoding. Only two alleles are supported for each scope (e.g. Major and minor, or Reference and Alternate).

The cache is designed to support multiple scopes, but currently scope must be passed in at construction.

It is not clear that site or taxa optimization is needed. The code should be highly parallelizable as long as the gets are not for adjacent sites.

Author:

Ed Buckler

Constructor Summary

Constructors

Constructor and Description
DynamicBitStorage(GenotypeCallTable genotype, WHICH_ALLELE allele, byte[] prefAllele)

Method Summary

Modifier and Type	Method and Description
BitSet	allelePresenceForAllSites(int taxon) Returns sequence of true/false values indicating whether taxon at each site matches a specific allele.
BitSet	allelePresenceForAllTaxa(int site) Returns sequence of true/false values indicating whether site at each taxon matches a specific allele.
long[]	allelePresenceForSitesBlock(int taxon, int startBlock, int endBlock) Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) matches a specific allele.
static DynamicBitStorage	getUnknownInstance(GenotypeCallTable genotype)
BitSet	haplotypeAllelePresenceForAllSites(int taxon, boolean firstParent) Returns sequence of true/false values indicating whether taxon at each site for given parent matches a specific allele (based on frequency).
BitSet	haplotypeAllelePresenceForAllTaxa(int site, boolean firstParent) Returns sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency).
long[]	haplotypeAllelePresenceForSitesBlock(int taxon, boolean firstParent, int startBlock, int endBlock) Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency).

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DynamicBitStorage

public DynamicBitStorage(GenotypeCallTable genotype,
                         WHICH_ALLELE allele,
                         byte[] prefAllele)

Method Detail

allelePresenceForAllSites

public BitSet allelePresenceForAllSites(int taxon)

Description copied from interface: BitStorage

Returns sequence of true/false values indicating whether taxon at each site matches a specific allele.

Specified by:

allelePresenceForAllSites in interface BitStorage

Parameters:

taxon - taxon

Returns:

sequence of true/false values.

allelePresenceForAllTaxa

public BitSet allelePresenceForAllTaxa(int site)

Description copied from interface: BitStorage

Returns sequence of true/false values indicating whether site at each taxon matches a specific allele.

Specified by:

allelePresenceForAllTaxa in interface BitStorage

Parameters:

site - site

Returns:

sequence of true/false values.

allelePresenceForSitesBlock

public long[] allelePresenceForSitesBlock(int taxon,
                                          int startBlock,
                                          int endBlock)

Description copied from interface: BitStorage

Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) matches a specific allele.

Specified by:

allelePresenceForSitesBlock in interface BitStorage

Parameters:

taxon - taxon

startBlock - starting block

endBlock - end block

Returns:

sequence of true/false values.

haplotypeAllelePresenceForAllSites

public BitSet haplotypeAllelePresenceForAllSites(int taxon,
                                                 boolean firstParent)

Description copied from interface: BitStorage

Returns sequence of true/false values indicating whether taxon at each site for given parent matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.

Specified by:

haplotypeAllelePresenceForAllSites in interface BitStorage

Parameters:

taxon - taxon

firstParent - true for first parent (false for second parent)

Returns:

sequence of true/false values.

haplotypeAllelePresenceForAllTaxa

public BitSet haplotypeAllelePresenceForAllTaxa(int site,
                                                boolean firstParent)

Description copied from interface: BitStorage

Returns sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.

Specified by:

haplotypeAllelePresenceForAllTaxa in interface BitStorage

Parameters:

site - site

firstParent - true for first parent (false for second parent)

Returns:

sequence of true/false values.

haplotypeAllelePresenceForSitesBlock

public long[] haplotypeAllelePresenceForSitesBlock(int taxon,
                                                   boolean firstParent,
                                                   int startBlock,
                                                   int endBlock)

Description copied from interface: BitStorage

Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.

Specified by:

haplotypeAllelePresenceForSitesBlock in interface BitStorage

Parameters:

taxon - taxon

firstParent - true for first parent (false for second parent)

startBlock - starting block

endBlock - end block

Returns:

sequence of true/false values.

getUnknownInstance

public static DynamicBitStorage getUnknownInstance(GenotypeCallTable genotype)