net.maizegenetics.dna.snp

Interface MaskMatrix

All Known Implementing Classes:

AbstractMaskMatrix, MaskGenotypeMatrix, MaskGenotypeStatsMatrix, MaskSiteMatrix, MaskTaxaMatrix

public MaskMatrix

Method Detail

get

boolean get(int taxon,
            int site)

isTaxonMaskedHint

boolean isTaxonMaskedHint(int taxon)

Returns false if specified taxon is definitely not masked. Otherwise returns true. A true returned doesn't necessarily mean this taxon is masked. This can be used to optimize performance of masked genotype table components. If false returned, checking for masking can be skipped.

Parameters:

taxon - taxon

Returns:

org.jetbrains.dokka.NodeRenderContent@2612eac9: false if taxon definitely not masked, true otherwise

maskForTaxon

BitSet maskForTaxon(int taxon)

Mask for specified taxon

Parameters:

taxon - taxon

Returns:

org.jetbrains.dokka.NodeRenderContent@69241b55: mask

isSiteMaskedHint

boolean isSiteMaskedHint(int site)

Returns false if specified site is definitely not masked. Otherwise returns true. A true returned doesn't necessarily mean this site is masked. This can be used to optimize performance of masked genotype table components. If false returned, checking for masking can be skipped.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@12940835: false if site definitely not masked, true otherwise

maskForSite

BitSet maskForSite(int site)

Mask for specified site

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@35031c74: mask

numTaxa

int numTaxa()

numSites

int numSites()

isSiteOptimized

boolean isSiteOptimized()