net.maizegenetics.dna.snp.bit

Interface BitStorage

All Known Implementing Classes:

DynamicBitStorage

public 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.

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:

org.jetbrains.dokka.NodeRenderContent@785ac439: 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:

org.jetbrains.dokka.NodeRenderContent@2522ccce: sequence of true/false values.

allelePresenceForSitesBlock

kotlin.Array[] 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:

org.jetbrains.dokka.NodeRenderContent@132609e6: 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:

org.jetbrains.dokka.NodeRenderContent@76ea5114: 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:

org.jetbrains.dokka.NodeRenderContent@58bf28fc: sequence of true/false values.

haplotypeAllelePresenceForSitesBlock

kotlin.Array[] 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:

org.jetbrains.dokka.NodeRenderContent@6b48db99: sequence of true/false values.