net.maizegenetics.dna.snp

Class MaskMatrixBuilder

java.lang.Object

net.maizegenetics.dna.snp.MaskMatrixBuilder

public class MaskMatrixBuilder
extends Object

Author:

Terry Casstevens

Method Summary

Modifier and Type	Method and Description
MaskMatrix	build()
boolean	get(int taxon, int site)
static MaskMatrix	getInstance(GenotypeCallTable genotype, BiPredicate<Byte,Stats> predicate)
static MaskMatrix	getInstance(GenotypeCallTable genotype, Predicate<Byte> predicate)
static MaskMatrixBuilder	getInstance(int numTaxa, int numSites, boolean isSiteOptimized)
static MaskMatrixBuilder	getInstance(MaskMatrix orig)
static MaskMatrix	getInstanceRemoveHeterozygous(GenotypeCallTable genotype)
static MaskMatrix	getInstanceRemoveHomozygous(GenotypeCallTable genotype)
static MaskMatrix	getInstanceRemoveIndels(GenotypeCallTable genotype)
static MaskMatrix	getInstanceRemoveMinorSNPs(GenotypeCallTable genotype)
long	reduceMaskTo(double percent)
void	set(int taxon, int site)
void	setNext(boolean value)

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static MaskMatrixBuilder getInstance(int numTaxa,
                                            int numSites,
                                            boolean isSiteOptimized)

getInstance

public static MaskMatrixBuilder getInstance(MaskMatrix orig)

getInstanceRemoveMinorSNPs

public static MaskMatrix getInstanceRemoveMinorSNPs(GenotypeCallTable genotype)

getInstanceRemoveHeterozygous

public static MaskMatrix getInstanceRemoveHeterozygous(GenotypeCallTable genotype)

getInstanceRemoveHomozygous

public static MaskMatrix getInstanceRemoveHomozygous(GenotypeCallTable genotype)

getInstanceRemoveIndels

public static MaskMatrix getInstanceRemoveIndels(GenotypeCallTable genotype)

getInstance

public static MaskMatrix getInstance(GenotypeCallTable genotype,
                                     Predicate<Byte> predicate)

getInstance

public static MaskMatrix getInstance(GenotypeCallTable genotype,
                                     BiPredicate<Byte,Stats> predicate)

get

public boolean get(int taxon,
                   int site)

set

public void set(int taxon,
                int site)

setNext

public void setNext(boolean value)

reduceMaskTo

public long reduceMaskTo(double percent)

build

public MaskMatrix build()