/*
* #%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 org.apache.commons.math3.util.FastMath;
import org.gitools.api.matrix.AbstractMatrixFunction;
import org.gitools.api.matrix.IMatrixIterable;
import org.gitools.api.matrix.IMatrixPosition;
import org.gitools.matrix.filter.NotNullPredicate;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
public class BenjaminiHochbergFdrMtcFunction extends AbstractMatrixFunction<Double, Double> {
private int n = 0;
private Map<String, Integer> ranks;
public BenjaminiHochbergFdrMtcFunction() {
}
@Override
public void onBeforeIterate(IMatrixIterable<Double> parentIterable) {
ranks = new HashMap<>((int) parentIterable.size());
n = 0;
int rank = 0;
Double lastValue = -1.0;
IMatrixIterable<Double> sortedIterable = parentIterable.filter(new NotNullPredicate<Double>()).sort();
for (Double value : sortedIterable) {
n++;
if (!lastValue.equals(value)) {
rank++;
}
String hash = hashKey(sortedIterable.getPosition());
ranks.put(hash, rank);
lastValue = value;
}
}
@Override
public Double apply(Double value, IMatrixPosition position) {
if (value == null) {
return null;
}
int rank = ranks.get(hashKey(position));
double result = FastMath.min(1.0, value * n / rank);
return result;
}
private String hashKey(IMatrixPosition position) {
//TODO improve performance
return Arrays.toString(position.toVector());
}
}