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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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package net.maizegenetics.stats.linearmodels;

import net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix;

/**
 * @author pbradbury
 *
 */
public interface ModelEffect {
	/**
	 * @return	an identifier for this factor
	 */
	Object getID();
	
	/**
	 * @param id	an identifier for this factor
	 */
	void setID(Object id);
	
	/**
	 * @return	the number of observations in the data set
	 */
	int getSize();
	
	/**
	 * @return	the design matrix for this factor
	 */
	DoubleMatrix getX();
	
	/**
	 * @return the crossproduct of the design matrix for this factor and itself
	 */
	DoubleMatrix getXtX();
	
	/**
	 * @param y	the dependent variable
	 * @return	the product of the transpose of the design matrix for this factor and the data, y
	 */
	DoubleMatrix getXty(double[] y);
	
	/**
	 * @param beta	 the effect estimate for each level of this factor
	 * @return	 the predicted value of this factor for each observation
	 */
	DoubleMatrix getyhat(DoubleMatrix beta);
	
	/**
	 * @param beta	 the effect estimate for each level of this factor
	 * @return the predicted value of this factor for each observation
	 */
	DoubleMatrix getyhat(double[] beta);
	
	/**
	 * @return	the number of observations for each level of this factor
	 */
	int[] getLevelCounts();
	
	/**
	 * @return	the number of levels in this factor
	 */
	int getNumberOfLevels();
	
	/**
	 * @return the number of columns in the design matrix.
	 * This will be the number of levels in this factor, if unrestricted. 1 - the number of levels, if restricted.
	 */
	int getEffectSize();
	
	/**
	 * @return	a copy of this model effect
	 */
	ModelEffect getCopy();
	
	/**
	 * @param sample       the index of samples to be returned
	 * @return             a new ModelEffect containing the samples in the index. Individual observations may be repeated in the subsample.
	 */
	ModelEffect getSubSample(int[] sample);
}