BonferroniMtcFunction.java example

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/*
 * #%L
 * gitools-core
 * %%
 * Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
 * %%
 * 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/gpl-3.0.html>.
 * #L%
 */
package org.gitools.analysis.stats.mtc;

import com.google.common.collect.Iterators;
import org.gitools.api.matrix.AbstractMatrixFunction;
import org.gitools.api.matrix.IMatrixIterable;
import org.gitools.api.matrix.IMatrixPosition;
import org.gitools.matrix.filter.InvalidDoubleFilter;

public class BonferroniMtcFunction extends AbstractMatrixFunction<Double, Double> {

    private int n = 0;

    public BonferroniMtcFunction() {
    }

    @Override
    public void onBeforeIterate(IMatrixIterable<Double> parentIterable) {
        n = Iterators.size(parentIterable.filter(new InvalidDoubleFilter()).iterator());
    }

    @Override
    public Double apply(Double value, IMatrixPosition position) {
        return value == null ? value : Math.min(1.0, value * n);
    }

}