net.maizegenetics.analysis.clustering

Class Haplotype

net.maizegenetics.analysis.clustering.Haplotype

public class Haplotype

A Haplotype is a sequence which can be either a true haplotype or a genotype. The natural ordering is by number of non-missing values, descending.

Field Detail

seq

public kotlin.Array[] seq

The haplotype (or genotype) sequence

notMissingCount

public int notMissingCount

The number of non missing values in the sequence

seqlen

public int seqlen

The length of the sequence

N

public static byte N

The byte value for missing

taxonIndex

public int taxonIndex

The index of the taxon from the originating alignment from which this sequence was taken

Constructor Detail

Haplotype

public Haplotype(kotlin.Array[] hap,
                 int taxon)

Parameters:

hap - the haplotype or genotype sequence

taxon - the taxon index

Haplotype

public Haplotype(kotlin.Array[] hap)

Parameters:

hap - the haplotype or genotype sequence

Method Detail

makeHetsConsistent

public kotlin.Array[] makeHetsConsistent(kotlin.Array[] seqIn)

countNotMissing

public void countNotMissing()

compareTo

public int compareTo(Haplotype arg0)

numberOfHets

public int numberOfHets()

distanceFrom

public int distanceFrom(Haplotype h0)

Distance is defined as the sum of the distances between each pair of sites. If one or both of the sites are missing then the distance is zero. If the sites are equal the distance is zero. If both sites are homozygous but different, the distance is 2. If one site is heterozygous, the distance is 1.

Parameters:

h0 - another Haplotype. Both haplotypes must have the same sequence length.

Returns:

org.jetbrains.dokka.NodeRenderContent@259f2cdb: the distance between the haplotypes

subHaplotype

public Haplotype subHaplotype(int size,
                              boolean fromStart)

getDistance

public static int getDistance(Haplotype hap0,
                              Haplotype hap1)

Parameters:

hap0 - the first Haplotype

hap1 - the second Haplotype

Returns:

org.jetbrains.dokka.NodeRenderContent@675b4e2d: distance as defined by distanceFrom(Haplotype h0)

getDistance

public static int getDistance(kotlin.Array[] hap0,
                              kotlin.Array[] hap1)

Parameters:

hap0 - the first Haplotype

hap1 - the second Haplotype

Returns:

org.jetbrains.dokka.NodeRenderContent@2ffe2e1c: distance as defined by distanceFrom(Haplotype h0)

See Also:

#distanceFrom(Haplotype h0)

toString

public java.lang.String toString()