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

There is a newer version: 5.2.94

package net.maizegenetics.matrixalgebra.decomposition;

import net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix;
import net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix;

import org.ejml.factory.DecompositionFactory;
import org.ejml.factory.EigenDecomposition;
import org.ejml.data.DenseMatrix64F;
import org.ejml.ops.EigenOps;

public class EJMLEigenvalueDecomposition implements EigenvalueDecomposition {
	final EigenDecomposition myDecomposition;
	boolean successful;
	
	public EJMLEigenvalueDecomposition(DoubleMatrix dm) {
		EJMLDoubleMatrix ejmldm = (EJMLDoubleMatrix) dm;
		myDecomposition = DecompositionFactory.eig(dm.numberOfRows(), true);
		successful = myDecomposition.decompose(ejmldm.myMatrix);
	}
	
	public EJMLEigenvalueDecomposition(DenseMatrix64F matrix) {
		myDecomposition = DecompositionFactory.eig(matrix.numRows, true);
		successful = myDecomposition.decompose(matrix);
		
	}
	
	public EJMLEigenvalueDecomposition(EigenDecomposition decomp) {
		myDecomposition = decomp;
	}
	
	@Override
	public double getEigenvalue(int i) {
		return myDecomposition.getEigenvalue(i).getReal();
	}

	@Override
	public DoubleMatrix getEigenvalueMatrix() {
		return new EJMLDoubleMatrix(EigenOps.createMatrixD(myDecomposition));
	}

	@Override
	public double[] getEigenvalues() {
		int n = myDecomposition.getNumberOfEigenvalues();
		double[] values = new double[n];
		for (int i = 0; i < n; i++) {
			values[i] = myDecomposition.getEigenvalue(i).getReal();
		}
		return values;
	}

	@Override
	public DoubleMatrix getEigenvectors() {
		return new EJMLDoubleMatrix(EigenOps.createMatrixV(myDecomposition));
	}

	public boolean wasSuccessful() { return successful; }
}