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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 vcf;
import beagleutil.ChromIds;
/**
* <p>Class {@code PositionMap} represents a genetic map obtained by
* multiplying chromosome position by a scale factor.
* </p>
* <p>Instances of class {@code PositionMap} are immutable.
* </p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class PositionMap implements GeneticMap {
private final double scaleFactor;
private final double invScaleFactor;
/**
* Returns the scale factor that is multiplied by the chromosome position
* to obtain the corresponding genetic map position
* @return the scale factor.
*/
public double scaleFactor() {
return scaleFactor;
}
/**
* Constructs a new {@code PositionMap} instance.
* @param scaleFactor the factor that is multiplied by
* a base position to obtain the corresponding genetic map position
* @throws IllegalArgumentException if
* {@code scaleFactor <= 0d || Double.isFinite(scaleFactor) == false}
*/
public PositionMap(double scaleFactor) {
if (Double.isFinite(scaleFactor) == false || scaleFactor <= 0d) {
throw new IllegalArgumentException(String.valueOf(scaleFactor));
}
this.scaleFactor = scaleFactor;
this.invScaleFactor = 1.0/scaleFactor;
}
@Override
public int basePos(int chrom, double geneticPosition) {
if (chrom < 0 || chrom >= ChromIds.instance().size()) {
throw new IndexOutOfBoundsException(String.valueOf(chrom));
}
long pos = Math.round(geneticPosition*invScaleFactor);
if (pos>Integer.MAX_VALUE) {
String s = "An estimated base position exceeds the maximum integer value"
+ blbutil.Const.nl
+ "Is the window parameter in cM units?";
throw new IllegalArgumentException(s);
}
return (int) pos;
}
@Override
public double genPos(Marker marker) {
return scaleFactor*marker.pos();
}
@Override
public double genPos(int chrom, int basePosition) {
if (chrom < 0 || chrom >= ChromIds.instance().size()) {
throw new IndexOutOfBoundsException(String.valueOf(chrom));
}
return scaleFactor*basePosition;
}
}
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