net.maizegenetics.dna.snp.bit

Interface BitStorage

All Known Implementing Classes:

DynamicBitStorage

public interface BitStorage

Interface provides genotypes in a binary fashion to be used in rapid computation. See the package descriptions net.maizegenetics.dna.snp.bit for more information on how bits encoding is used throughout TASSEL.

Author:

Terry Casstevens, Ed Buckler

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.
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).

Method Detail

allelePresenceForAllSites

BitSet allelePresenceForAllSites(int taxon)

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

Parameters:

taxon - taxon

Returns:

sequence of true/false values.

allelePresenceForAllTaxa

BitSet allelePresenceForAllTaxa(int site)

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

Parameters:

site - site

Returns:

sequence of true/false values.

allelePresenceForSitesBlock

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.

Parameters:

taxon - taxon

startBlock - starting block

endBlock - end block

Returns:

sequence of true/false values.

haplotypeAllelePresenceForAllSites

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). 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.

Parameters:

taxon - taxon

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

Returns:

sequence of true/false values.

haplotypeAllelePresenceForAllTaxa

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). 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.

Parameters:

site - site

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

Returns:

sequence of true/false values.

haplotypeAllelePresenceForSitesBlock

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). 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.

Parameters:

taxon - taxon

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

startBlock - starting block

endBlock - end block

Returns:

sequence of true/false values.