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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.association;
    
import net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix;
import net.maizegenetics.matrixalgebra.Matrix.*;
import net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.FactoryType;



public class RegRidgeEmmaDoubleMatrix {
		
	 
	private double[] GEBVs;
	private double[] mrkEsts;
	private DoubleMatrix GEBVsDM;
	private DoubleMatrix mrkEstsDM;
	
	private DoubleMatrix pheno;
	private boolean[] phenoMissing;
	private DoubleMatrix fixed;
	private DoubleMatrix geno;
	private int nLines;
	private int nObs;
	
	private DoubleMatrix kin = null;
	
	
	/** Constructor using native double arrays. Need to specify DoubleMatrix FactoryType
	 * @param phenotype; column matrix of phenotype values. Missing phenotype are coded as NaN. GEBVs are calculate for all lines including missing. 
	 * @param fixedEffects; 2D matrix of fixed effects; must not be singular
	 * @param genotypes; matrix of genotypes coded -1, 0, 1.  Missing Genotypes as NaN
	 * @param type; Tassel DoubleMatrix Type to use
	 */
	public RegRidgeEmmaDoubleMatrix(double[] phenotype, double[][] fixedEffects, double[][] genotypes, FactoryType type){
		DoubleMatrixFactory MF = new DoubleMatrixFactory(type);
		pheno = MF.make(phenotype.length, 1, phenotype);
		fixed = MF.make(fixedEffects);
		geno = MF.make(genotypes);
		phenoMissing = this.determineMissingPhenotypes();
	}
	
	
	/** Constructor using Tassel DoubleMatrix.
	 * @param phenotype; column matrix of phenotype values. Missing phenotype are coded as NaN. GEBVs are calculate for all lines including missing.
	 * @param fixedEffects; 2D matrix of fixed effects; must not be singular
	 * @param genotypes; matrix of genotypes coded -1, 0, 1.  Missing Genotypes as NaN
	 */
	public RegRidgeEmmaDoubleMatrix(DoubleMatrix phenotype, DoubleMatrix fixedEffects, DoubleMatrix genotypes){
		pheno = phenotype;
		fixed = fixedEffects;
		geno = genotypes;
		phenoMissing = this.determineMissingPhenotypes();
	}
	
	
	/** Constructor using Tassel DoubleMatrix. Use when kinship matrix from markers has already been calculated (XXt). 
	 * @param phenotype; column matrix of phenotype values. Missing phenotype are coded as NaN. GEBVs are calculate for all lines including missing.
	 * @param fixedEffects; 2D matrix of fixed effects; must not be singular
	 * @param genotypes; matrix of genotypes coded -1, 0, 1.  Missing Genotypes as NaN
	 * @param kinship; kinship matrix (XXt) calculated from marker matrix (X) 
	 */
	public RegRidgeEmmaDoubleMatrix(DoubleMatrix phenotype, DoubleMatrix fixedEffects, DoubleMatrix genotypes, DoubleMatrix kinship){
		pheno = phenotype;
		fixed = fixedEffects;
		geno = genotypes;
		kin = kinship;
		phenoMissing = this.determineMissingPhenotypes();
	}
	

	
	
	/**
	 * Solve the mixed model for line GEBVs and marker estimates
	 */
	public void solve() {
		
		double start = System.currentTimeMillis()/1000;
		
		int notMissing = 0;
		for (boolean b : phenoMissing) if (!b) notMissing++;
		int[] nmIndex = new int[notMissing];
		int count = 0;
		for (int i = 0; i < phenoMissing.length; i++) {
			if (!phenoMissing[i]) {nmIndex[count] = i; count++;}
		}
	
		DoubleMatrix nmPheno = pheno.getSelection(nmIndex, null);
		DoubleMatrix nmFixed = fixed.getSelection(nmIndex, null);

		nLines = pheno.numberOfRows();
		nObs = nmPheno.numberOfRows();
		
		this.replaceNaNwithMean();
		
		DoubleMatrix nmGeno = geno.getSelection(nmIndex, null);
		
		//calculate marker based kinship
		if (kin == null){kin = geno.mult(geno, false, true);}
		DoubleMatrix nmKin = kin.getSelection(nmIndex, nmIndex);
		
		// use EMMA to solve mixed model
		
		EMMAforDoubleMatrix lm = new EMMAforDoubleMatrix(nmPheno, nmFixed, nmKin, 0);
		lm.solve();
		double delta = lm.getDelta();
		System.out.println("Delta: " + delta);

	
		// solve mixed model for marker BLUPs
		DoubleMatrix aXZ = nmFixed.concatenate(nmGeno, false);
		 
		int nFixed = nmFixed.numberOfColumns();
		int nRandom = nmGeno.numberOfColumns();
		
		DoubleMatrix aCoefMat = aXZ.crossproduct();
		
		for (int i=nFixed; i