net.maizegenetics.analysis.distance

Class EndelmanDistanceMatrix

net.maizegenetics.analysis.distance.EndelmanDistanceMatrix

public class EndelmanDistanceMatrix

Method Detail

getInstance

public static DistanceMatrix getInstance(GenotypeTable genotype)

Compute Endelman Kinship Matrix. Maximum alleles per site to evaluate defaults to 2.

Parameters:

genotype - Genotype Table used to compute kinship

Returns:

org.jetbrains.dokka.NodeRenderContent@7dd55e1d: Endelman Kinship Matrix

getInstance

public static DistanceMatrix getInstance(GenotypeTable genotype,
                                         int maxAlleles)

Compute Endelman Kinship Matrix

Parameters:

genotype - Genotype Table used to compute kinship

maxAlleles - maximum alleles per site to evaluate. i.e. Set to 3 to evaluate the three most frequent allele states.

Returns:

org.jetbrains.dokka.NodeRenderContent@7dc57ddb: Endelman Kinship Matrix

getInstance

public static DistanceMatrix getInstance(GenotypeTable genotype,
                                         ProgressListener listener)

Compute Endelman Kinship Matrix. Maximum alleles per site to evaluate defaults to 2.

Parameters:

genotype - Genotype Table used to compute kinship

listener - Progress listener

Returns:

org.jetbrains.dokka.NodeRenderContent@7544e9b4: Endelman Kinship Matrix

getInstance

public static DistanceMatrix getInstance(GenotypeTable genotype,
                                         int maxAlleles,
                                         ProgressListener listener)

Compute Endelman Kinship Matrix

Parameters:

genotype - Genotype Table used to compute kinship

maxAlleles - maximum alleles per site to evaluate. i.e. Set to 3 to evaluate the three most frequent allele states.

listener - Progress listener

Returns:

org.jetbrains.dokka.NodeRenderContent@8535f59: Endelman Kinship Matrix

subtractEndelmanDistance

public static DistanceMatrix subtractEndelmanDistance(DistanceMatrix[] matrices,
                                                      DistanceMatrix superMatrix,
                                                      ProgressListener listener)

addEndelmanDistance

public static DistanceMatrix addEndelmanDistance(DistanceMatrix[] matrices,
                                                 ProgressListener listener)

fireProgress

protected static void fireProgress(int percent,
                                   ProgressListener listener)