edu.dfci.cccb.mev.hcl.domain.contract.Metric.java Source code

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Here is the source code for edu.dfci.cccb.mev.hcl.domain.contract.Metric.java

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/**
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package edu.dfci.cccb.mev.hcl.domain.contract;

import static ch.lambdaj.Lambda.sum;
import static org.apache.commons.math3.util.FastMath.abs;
import static org.apache.commons.math3.util.FastMath.pow;
import static org.apache.commons.math3.util.FastMath.sqrt;

import java.util.AbstractList;
import java.util.List;

/**
 * @author levk
 * 
 */
public enum Metric {
    EUCLIDEAN("euclidean", "euc", "e") {
        /* (non-Javadoc)
         * @see
         * edu.dfci.cccb.mev.hcl.domain.concrete.Metrics#aggregate(java.util.List) */
        @Override
        protected double aggregate(List<Double> correlations) {
            return sqrt(sum(correlations).doubleValue());
        }

        /* (non-Javadoc)
         * @see edu.dfci.cccb.mev.hcl.domain.concrete.Metrics#correlate(double,
         * double) */
        @Override
        protected double correlate(double from, double to) {
            return pow(from - to, 2);
        }
    },
    MANHATTAN("manhattan", "man", "m") {
        /* (non-Javadoc)
         * @see
         * edu.dfci.cccb.mev.hcl.domain.concrete.Metrics#aggregate(java.util.List) */
        @Override
        protected double aggregate(List<Double> correlations) {
            return sum(correlations).doubleValue();
        }

        /* (non-Javadoc)
         * @see edu.dfci.cccb.mev.hcl.domain.concrete.Metrics#correlate(double,
         * double) */
        @Override
        protected double correlate(double from, double to) {
            return abs(from - to);
        }
    },
    PEARSON("pearson", "pea", "p") {
        /* (non-Javadoc)
         * @see
         * edu.dfci.cccb.mev.hcl.domain.concrete.Metrics#aggregate(java.util.List) */
        @Override
        protected double aggregate(List<Double> correlations) {
            return -sum(correlations).doubleValue() / correlations.size();
        }

        /* (non-Javadoc)
         * @see edu.dfci.cccb.mev.hcl.domain.concrete.Metrics#correlate(double,
         * double) */
        @Override
        protected double correlate(double from, double to) {
            return from * to;
        }
    };

    private final String[] aliases;

    private Metric(String... aliases) {
        this.aliases = aliases;
    }

    public static Metric from(String string) throws InvalidMetricException {
        for (Metric metric : values())
            for (String alias : metric.aliases)
                if (alias.equalsIgnoreCase(string))
                    return metric;
        throw new InvalidMetricException().name(string);
    }

    public double distance(List<Double> from, List<Double> to) {
        return aggregate(correlate(from, to));
    }

    protected abstract double aggregate(List<Double> correlations);

    protected List<Double> correlate(final List<Double> from, final List<Double> to) {
        return new AbstractList<Double>() {

            @Override
            public Double get(int index) {
                return correlate(from.get(index), to.get(index));
            }

            @Override
            public int size() {
                return from.size();
            }
        };
    }

    protected abstract double correlate(double from, double to);
}