CNNClassificationModelPredict.java

/*  $RCSfile$
 *  $Author$
 *  $Date$
 *  $Revision$
 *
 *  Copyright (C) 2004-2008  Rajarshi Guha <rajarshi.guha@gmail.com>
 *
 *  Contact: cdk-devel@lists.sourceforge.net
 *
 *  This program is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public License
 *  as published by the Free Software Foundation; either version 2.1
 *  of the License, or (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */

package org.openscience.cdk.qsar.model.R;

/**
 * A class that wraps the return value from the R function, predict.nnet for classification models.
 *
 * This is an internal class used by R to return the result of
 * the call to <a href="http://stat.ethz.ch/R-manual/R-patched/library/nnet/html/predict.nnet.html">predict.nnet</a>.
 * As a result it should not be instantiated by the user. The actual modeling
 * class, <code>CNNClassificationModel</code>, provides acess to the various
 * fields of this object.
 * 
 *
 * @author Rajarshi Guha
 * @cdk.require r-project
 * @cdk.module qsar
 * @cdk.githash
 * @deprecated
 */
public class CNNClassificationModelPredict {
    private int noutput;
    private double[][] predvalraw;
    private String[] predvalclass;

    private double[][] vectorToMatrix(double[] v, int nrow, int ncol) {
        double[][] m = new double[nrow][ncol];
        for (int i = 0; i < ncol; i++) {
            for (int j = 0; j < nrow; j++) {
                m[j][i] = v[j + i*nrow];
            }
        }
        return(m);
    }
    /**
     * Create an object to hold predictions from a previously built CNN model.
     *
     * This class should not be accessed directly
     *
     * @param noutput The number of predicted variables
     * @param values The predicted probabilities
     */
    public CNNClassificationModelPredict(int noutput, double[] values) { 
        this.noutput = noutput;
        int nrow = values.length / noutput;
        setPredictedRaw(vectorToMatrix(values,nrow,noutput));
    }
    /**
     * Create an object to hold predictions from a previously built CNN model.
     *
     * This class should not be accessed directly. Required for the case of a single
     * predicted value.
     *
     * @param noutput The number of predicted variables
     * @param values The predicted probabilities
     */
    public CNNClassificationModelPredict(int noutput, double values) { 
        this.noutput = noutput;
        setPredictedRaw(new double[][] { {values} });
    }
    
    /**
     * Create an object to hold predictions from a previously built CNN model.
     *
     * This class should not be accessed directly
     *
     * @param values An array of String containing the predicted class
     */
    public CNNClassificationModelPredict(String[] values) {
        this.predvalclass = new String[values.length];
        for (int i = 0; i < values.length; i++) {
            this.predvalclass[i] = values[i];
        }
    }
    /**
     * Create an object to hold predictions from a previously built CNN model.
     *
     * This class should not be accessed directly. Required for the 
     * case of a single predicted value
     *
     * @param values An array of String containing the predicted class
     */
    public CNNClassificationModelPredict(String values) {
        this.predvalclass = new String[1];
        this.predvalclass[1] = values;
    }

    /**
     * Get the raw probabilities of the classification result.
     * 
     * This class should not be accessed directly
     * 
     * @return A 2-dimensional array containing the predicted probabilities. The rows
     * contain the observations and the columns contain the predicted variables
     * @see #setPredictedRaw
     */
    public double[][] getPredictedRaw() { return(this.predvalraw); }
    /**
     * Get the raw probabilities of the classification result.
     * 
     * This class should not be accessed directly
     * 
     * @param predicted A 2-dimensional array containing the predicted probabilities. The rows
     * contain the observations and the columns contain the predicted variables
     * @see #getPredictedRaw
     */
    public void setPredictedRaw(double[][] predicted) { 
        this.predvalraw = new double[predicted.length][this.noutput];
        for (int i = 0; i < predicted.length; i++) {
            for (int j = 0; j < this.noutput; j++) {
                this.predvalraw[i][j] = predicted[i][j];
            }
        }
    }

    /**
     * Get the predicted classes.
     * 
     * This class should not be accessed directly
     *
     * @return An array of String containing the predicted classes
     */
    public String[] getPredictedClass() { return(this.predvalclass); };
}