Uses of Interface
net.maizegenetics.dna.snp.MaskMatrix

Packages that use MaskMatrix

Package	Description
net.maizegenetics.dna.snp	Data structures for holding SNP and indel variation across taxa (samples) and genomic positions.
net.maizegenetics.dna.snp.genotypecall	Genotype calls for all the taxa and genomic positions scored.
net.maizegenetics.dna.snp.score	Support for site scores (for example quality scores or imputation accuracy).

Uses of MaskMatrix in net.maizegenetics.dna.snp

Classes in net.maizegenetics.dna.snp that implement MaskMatrix

Modifier and Type	Class and Description
class	AbstractMaskMatrix
class	MaskGenotypeMatrix
class	MaskGenotypeStatsMatrix
class	MaskSiteMatrix
class	MaskTaxaMatrix

Methods in net.maizegenetics.dna.snp that return MaskMatrix

Modifier and Type	Method and Description
MaskMatrix	MaskMatrixBuilder.build()
static MaskMatrix	MaskMatrixBuilder.getInstance(GenotypeCallTable genotype, BiPredicate<Byte,Stats> predicate)
static MaskMatrix	MaskMatrixBuilder.getInstance(GenotypeCallTable genotype, Predicate<Byte> predicate)
static MaskMatrix	MaskMatrixBuilder.getInstanceRemoveHeterozygous(GenotypeCallTable genotype)
static MaskMatrix	MaskMatrixBuilder.getInstanceRemoveHomozygous(GenotypeCallTable genotype)
static MaskMatrix	MaskMatrixBuilder.getInstanceRemoveIndels(GenotypeCallTable genotype)
static MaskMatrix	MaskMatrixBuilder.getInstanceRemoveMinorSNPs(GenotypeCallTable genotype)

Methods in net.maizegenetics.dna.snp with parameters of type MaskMatrix

Modifier and Type	Method and Description
static GenotypeTable	GenotypeTableBuilder.getInstance(GenotypeTable base, MaskMatrix mask)
static MaskMatrixBuilder	MaskMatrixBuilder.getInstance(MaskMatrix orig)

Uses of MaskMatrix in net.maizegenetics.dna.snp.genotypecall

Constructors in net.maizegenetics.dna.snp.genotypecall with parameters of type MaskMatrix

Constructor and Description
MaskGenotypeCallTable(GenotypeCallTable base, MaskMatrix mask)

Uses of MaskMatrix in net.maizegenetics.dna.snp.score

Methods in net.maizegenetics.dna.snp.score that return MaskMatrix

Modifier and Type	Method and Description
MaskMatrix	MaskAlleleDepth.mask()
MaskMatrix	MaskAlleleProbability.mask()

Methods in net.maizegenetics.dna.snp.score with parameters of type MaskMatrix

Modifier and Type	Method and Description
static AlleleDepth	AlleleDepthBuilder.getMaskInstance(AlleleDepth base, MaskMatrix mask)
static AlleleProbability	AlleleProbabilityBuilder.getMaskInstance(AlleleProbability base, MaskMatrix mask)
static Dosage	DosageBuilder.getMaskInstance(Dosage base, MaskMatrix mask)
static ReferenceProbability	ReferenceProbabilityBuilder.getMaskInstance(ReferenceProbability base, MaskMatrix mask)

Constructors in net.maizegenetics.dna.snp.score with parameters of type MaskMatrix

Constructor and Description
MaskAlleleDepth(AlleleDepth depth, MaskMatrix mask)
MaskAlleleProbability(AlleleProbability probability, MaskMatrix mask)