net.maizegenetics.dna.snp.byte2d.Byte2DBuilder Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of tassel6 Show documentation

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.

There is a newer version: 6.0.1

Show newest version

/*
 *  Byte2DBuilder
 */
package net.maizegenetics.dna.snp.byte2d;

import net.maizegenetics.dna.snp.score.SiteScore;
import net.maizegenetics.taxa.TaxaList;
import net.maizegenetics.util.SuperByteMatrix;
import net.maizegenetics.util.SuperByteMatrixBuilder;

/**
 * Builder to store 2 dimensional byte encoded values.
 *
 * @author Terry Casstevens
 */
public class Byte2DBuilder {

    private SuperByteMatrix myValues = null;
    private final int myNumSites;
    private int myNumTaxa = 0;
    private final SiteScore.SITE_SCORE_TYPE mySiteScoreType;
    private final TaxaList myTaxaList;

    private Byte2DBuilder(int numTaxa, int numSites, SiteScore.SITE_SCORE_TYPE siteScoreType, TaxaList taxaList) {
        myNumSites = numSites;
        myNumTaxa = numTaxa;
        mySiteScoreType = siteScoreType;
        myValues = SuperByteMatrixBuilder.getInstance(myNumTaxa, myNumSites);
        myTaxaList = taxaList;
    }

    public static Byte2DBuilder getInstance(int numTaxa, int numSites, SiteScore.SITE_SCORE_TYPE siteScoreType, TaxaList taxaList) {
        return new Byte2DBuilder(numTaxa, numSites, siteScoreType, taxaList);
    }

    /**
     * Add taxon and set values for all sites for that taxon.
     *
     * @param taxon taxon
     * @param values values
     *
     * @return builder
     */
    public Byte2DBuilder addTaxon(int taxon, byte[] values) {

        if (values.length != myNumSites) {
            throw new IllegalStateException("Byte2DBuilder: addTaxon: Number of sites: " + values.length + " should be: " + myNumSites);
        }

        for (int s = 0; s < myNumSites; s++) {
            myValues.set(taxon, s, values[s]);
        }

        return this;
    }

    /**
     * Set values for range of sites and alleles for a taxon simultaneously.
     *
     * @param taxon Index of taxon
     * @param siteOffset site offset
     * @param values array[sites] range of values
     *
     * @return builder
     */
    public Byte2DBuilder setDepthRangeForTaxon(int taxon, int siteOffset, byte[] values) {

        for (int s = 0; s < values.length; s++) {
            myValues.set(taxon, s + siteOffset, values[s]);
        }

        return this;

    }

    public void reorderPositions(int[] newIndices) {
        if (myValues == null) {
            throw new IllegalStateException("Byte2DBuilder: reorderPositions: this is not an in-memory builder.");
        }
        myValues.reorderColumns(newIndices);
    }

    public Byte2D build() {
        SuperByteMatrix temp = myValues;
        myValues = null;
        return new MemoryByte2D(mySiteScoreType, temp);
    }
}