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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle 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.
*
* Beagle 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 phase;
import java.util.concurrent.atomic.AtomicLong;
/**
* <p>Class {@code SwapRate} stores the proportion of unphased heterozygotes
* whose phase with respect to the previous heteroygote has been reversed.
* </p>
* <p>Instances of class {@code SwapRate} are thread-safe.
* </p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class SwapRate {
private static final AtomicLong nSwaps = new AtomicLong(0);
private static final AtomicLong nUnphHets = new AtomicLong(0);
private SwapRate() {
// private constructor to prevent instantiation
}
/**
* Returns the proportion of unphased heterozygotes whose phase
* relative to the previous heterozygote has been reversed.
* The counters for the number of heterozygotes whose phase has been
* reversed and for the total number of unphased heterozygotes are then
* set to 0.
* @return the proportion of unphased heterozygotes whose phase
* has been changed
*/
public static double getAndResetSwapRate() {
double rate = (double) nSwaps.get() / nUnphHets.get();
nSwaps.set(0);
nUnphHets.set(0);
return rate;
}
/**
* Increments the number of unphased heterozygotes and the number of
* unphased heterozygotes whose phase with respect to the preceding
* heterozygote has been reversed.
* @param nUnphHets the value that will be added to number of
* unphased heterozygotes
* @param nSwaps the value that will be added to number of unphased
* heterozygotes whose phase has been reversed
*/
public static void increment(int nUnphHets, int nSwaps) {
SwapRate.nSwaps.addAndGet(nSwaps);
SwapRate.nUnphHets.addAndGet(nUnphHets);
}
}
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