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Similarities for Feature Vectors and Time Series thereof, such as Cosine and Dynamic Time Warping.

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/*
 * Maltcms, modular application toolkit for chromatography-mass spectrometry.
 * Copyright (C) 2008-2014, The authors of Maltcms. All rights reserved.
 *
 * Project website: http://maltcms.sf.net
 *
 * Maltcms may be used under the terms of either the
 *
 * GNU Lesser General Public License (LGPL)
 * http://www.gnu.org/licenses/lgpl.html
 *
 * or the
 *
 * Eclipse Public License (EPL)
 * http://www.eclipse.org/org/documents/epl-v10.php
 *
 * As a user/recipient of Maltcms, you may choose which license to receive the code
 * under. Certain files or entire directories may not be covered by this
 * dual license, but are subject to licenses compatible to both LGPL and EPL.
 * License exceptions are explicitly declared in all relevant files or in a
 * LICENSE file in the relevant directories.
 *
 * Maltcms 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. Please consult the relevant license documentation
 * for details.
 */
package maltcms.math.functions.similarities;

import cross.cache.CacheFactory;
import cross.cache.ICacheDelegate;
import maltcms.math.functions.IArraySimilarity;
import ucar.ma2.Array;

/**
 * SimilarityTools class.
 *
 * @author Nils Hoffmann
 * 
 */
public class SimilarityTools {

    /**
     * toSimilarity.
     *
     * @param distance a double.
     * @return a double.
     */
    public static double toSimilarity(double distance) {
        return -distance;
    }

    /**
     * Converts the given similarity s(a,b) to d(a,b):=sqrt(s(a,a)+s(b,b)-
     * 2*s(a,b)).
     *
     * @param sim a {@link maltcms.math.functions.IArraySimilarity} object.
     * @param a a {@link ucar.ma2.Array} object.
     * @param b a {@link ucar.ma2.Array} object.
     * @return a double.
     */
    public static double toDistance(IArraySimilarity sim, Array a, Array b) {
        double dist = 0.0d;
        dist += sim.apply(a, a);
        dist += sim.apply(b, b);
        dist -= (2 * sim.apply(a, b));
        return Math.sqrt(dist);
    }

    /**
     * newValueCache.
     *
     * @param name a {@link java.lang.String} object.
     * @param  a K object.
     * @param  a V object.
     * @return a {@link cross.cache.ICacheDelegate} object.
     * @since 1.3.2
     */
    public static  ICacheDelegate newValueCache(String name) {
        return CacheFactory.createVolatileCache(name, 30, 60, 100000);
    }
}