net.maizegenetics.analysis.modelfitter

Class GenotypeAdditiveSite

java.lang.Object

net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite

net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite

All Implemented Interfaces:

Serializable, Comparable<AdditiveSite>, AdditiveSite

public class GenotypeAdditiveSite
extends AbstractAdditiveSite

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface net.maizegenetics.analysis.modelfitter.AdditiveSite

AdditiveSite.CRITERION

Constructor Summary

Constructors

Constructor and Description
GenotypeAdditiveSite(int site, String chr, int pos, String id, AdditiveSite.CRITERION selectionCriterion, byte[] genotype, byte majorAllele, double majorAlleleFrequency)

Method Summary

Modifier and Type	Method and Description
double[]	getCovariate()
double[]	getCovariate(int[] subset)
double[]	getCovariateNoReindex()
double[]	getCovariateNoReindex(int[] subset)
double[]	getCovariateWithReindex()
double[]	getCovariateWithReindex(int[] subset)
void	reindexTaxa(int[] taxaIndex, List<Integer> uniqueTaxa) This method re-indexes the taxa in the additive site so that the returned covariate will match the taxon order in the target phenotype
static void	serializeAdditiveSites(GenotypeTable geno, String outFile)

Methods inherited from class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite

chromosomeName, compareTo, criterionValue, criterionValue, position, selectionCriterion, siteName, siteNumber

Methods inherited from class java.lang.Object

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

Constructor Detail

GenotypeAdditiveSite

public GenotypeAdditiveSite(int site,
                            String chr,
                            int pos,
                            String id,
                            AdditiveSite.CRITERION selectionCriterion,
                            byte[] genotype,
                            byte majorAllele,
                            double majorAlleleFrequency)

Parameters:

site - the site index from the originating GenotypeTable

genotype - genotypeAllTaxa for this site

majorAllele - major allele

majorAlleleFrequency - major allele frequency

Method Detail

reindexTaxa

public void reindexTaxa(int[] taxaIndex,
                        List<Integer> uniqueTaxa)

Description copied from interface: AdditiveSite

This method re-indexes the taxa in the additive site so that the returned covariate will match the taxon order in the target phenotype

Parameters:

taxaIndex - an index of taxa that matches the order in the target phenotype

uniqueTaxa - a unique list of index values used to recalculate major allele frequency for the taxa indexed

getCovariate

public double[] getCovariate()

Returns:

the covariate for this site

getCovariate

public double[] getCovariate(int[] subset)

Parameters:

subset - an int array indexing a subset of taxa

Returns:

the covariate for the subset of taxa for this sites

getCovariateNoReindex

public double[] getCovariateNoReindex()

getCovariateNoReindex

public double[] getCovariateNoReindex(int[] subset)

getCovariateWithReindex

public double[] getCovariateWithReindex()

getCovariateWithReindex

public double[] getCovariateWithReindex(int[] subset)

serializeAdditiveSites

public static void serializeAdditiveSites(GenotypeTable geno,
                                          String outFile)