net.maizegenetics.analysis.modelfitter.AdditiveSite Maven / Gradle / Ivy

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TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.

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package net.maizegenetics.analysis.modelfitter;

import java.io.Serializable;
import java.util.List;

public interface AdditiveSite extends Comparable, Serializable {

    public static enum CRITERION {
        pval,
        aic,
        bic,
        mbic;
    }

    /**
     * @return		the covariate for this site
     */
    double[] getCovariate();

    /**
     * @param subset	an int array indexing a subset of taxa
     * @return			the covariate for the subset of taxa for this sites
     */
    double[] getCovariate(int[] subset);

    /**
     * @return	the site index corresponding to the site number in the source GenotypeTable
     */
    int siteNumber();

    /**
     * @return  the name of the chromosome of this site
     */
    String chromosomeName();

    /**
     * @return  the chromosomal position of this site
     */
    int position();

    /**
     * @return  the name (SNPID) of this site
     */
    String siteName();

    /**
     * @return     the value of the selection criterion for this site
     */
    double criterionValue();

    /**
     * @param value        the value of the selection criterion for this site
     */
    void criterionValue(double value);

    /**
     * @return     the selection criterion used for this site
     */
    CRITERION selectionCriterion();

    /**
     * This method re-indexes the taxa in the additive site so that the returned covariate will match the taxon order in the target phenotype
     * @param taxaIndex         an index of taxa that matches the order in the target phenotype
     * @param uniqueTaxa        a unique list of index values used to recalculate major allele frequency for the taxa indexed
     */
    void reindexTaxa(int[] taxaIndex, List uniqueTaxa);

    /**
     *
     * @return a copy of this AdditiveSite
     */
    AdditiveSite copy();
}