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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.

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/*
 *  DistanceMatrixBuilder
 * 
 *  Created on Nov 20, 2015
 */
package net.maizegenetics.taxa.distance;

import net.maizegenetics.taxa.TaxaList;
import net.maizegenetics.taxa.TaxaListBuilder;
import net.maizegenetics.taxa.Taxon;
import net.maizegenetics.util.GeneralAnnotation;

/**
 *
 * @author Terry Casstevens
 */
public class DistanceMatrixBuilder {

    public static final String MATRIX_TYPE = "Matrix_Type";
    public static final String MATRIX_ALGORITHM_VARIATION = "Matrix_Variation";

    public static final String CENTERED_IBS_SUMPK = "Centered_IBS.SumPk";

    public static final String IBS_DISTANCE_MATRIX_TYPE = "IBS_Distance_Matrix";
    public static final String IBS_DISTANCE_MATRIX_NUM_ALLELES = "IBS_Distance_Matrix.NumAlleles";
    public static final String IBS_DISTANCE_MATRIX_AVE_TOTAL_SITES = "IBS_Distance_Matrix.AverageTotalSites";
    public static final String IBS_DISTANCE_MATRIX_TRUE_IBS = "IBS_Distance_Matrix.TrueIBS";

    private final int myNumTaxa;
    private final TaxaList myTaxa;
    private final float[][] myMatrix;
    private GeneralAnnotation myAnnotation = null;
    private final TaxaListBuilder myTaxaBuilder;
    private int[][] myCounts = null;

    private DistanceMatrixBuilder(int numTaxa, TaxaList taxa) {
        myTaxa = taxa;
        myNumTaxa = numTaxa;
        myMatrix = new float[myNumTaxa][];
        for (int i = 0; i < myNumTaxa; i++) {
            myMatrix[i] = new float[i + 1];
        }
        if (myTaxa == null) {
            myTaxaBuilder = new TaxaListBuilder();
        } else {
            myTaxaBuilder = null;
        }
    }

    public static DistanceMatrixBuilder getInstance(TaxaList taxa) {
        return new DistanceMatrixBuilder(taxa.numberOfTaxa(), taxa);
    }

    public static DistanceMatrixBuilder getInstance(int numTaxa) {
        return new DistanceMatrixBuilder(numTaxa, null);
    }

    public void set(int x, int y, float value) {
        if (x > y) {
            myMatrix[x][y] = value;
        } else {
            myMatrix[y][x] = value;
        }
    }

    public void set(int x, int y, double value) {
        if (x > y) {
            myMatrix[x][y] = (float) value;
        } else {
            myMatrix[y][x] = (float) value;
        }
    }

    public void addTaxon(Taxon taxon) {
        if (myTaxaBuilder == null) {
            throw new IllegalStateException("DistanceMatrixBuilder: addTaxon: this builder was given Taxa List at creation.");
        }
        myTaxaBuilder.add(taxon);
    }

    public DistanceMatrixBuilder annotation(GeneralAnnotation annotation) {
        myAnnotation = annotation;
        return this;
    }

    public void setCount(int x, int y, int value) {
        if (myCounts == null) {
            myCounts = new int[myNumTaxa][];
            for (int i = 0; i < myNumTaxa; i++) {
                myCounts[i] = new int[i + 1];
            }
        }
        if (x > y) {
            myCounts[x][y] = value;
        } else {
            myCounts[y][x] = value;
        }
    }

    public DistanceMatrix build() {

        TaxaList taxa = null;
        if (myTaxaBuilder == null) {
            taxa = myTaxa;
        } else {
            taxa = myTaxaBuilder.build();
        }

        if (myCounts == null) {
            return new DistanceMatrix(myMatrix, taxa, myAnnotation);
        } else {
            return new DistanceMatrixWithCounts(myMatrix, taxa, myAnnotation, myCounts);
        }

    }

}