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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 blbutil.DoubleArray;
import ints.IntList;
/**
* <p>Class {@code Steps} represents a partition of a list of markers into
* a sequence of sets of consecutive markers (the steps).</p>
*
* <p>Instances of class {@code Steps} are immutable.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class Steps {
private final MarkerMap map;
private final int[] stepEnds;
/**
* Constructs a new {@code Steps} instance from the specified data.
* @param map the marker map
* @param minStep the minimum distance between the first markers in
* consecutive steps
*
* @throws IllegalArgumentException if
* {@code minStep <= 0f || Float.isFinite(minStep) == false}
* @throws NullPointerException if {@code map == null}
*/
public Steps(MarkerMap map, float minStep) {
if (minStep <= 0f || Float.isFinite(minStep)==false) {
throw new IllegalArgumentException(String.valueOf(minStep));
}
this.map = map;
this.stepEnds = stepEnds(map, minStep);
}
private static int[] stepEnds(MarkerMap map, double minStep) {
DoubleArray genPos = map.genPos();
int nMarkers = genPos.size();
IntList indices = new IntList(nMarkers>>1);
int end = 0;
while (end<nMarkers) {
double minGenPos = genPos.get(end) + minStep;
++end;
while (end<genPos.size() && genPos.get(end)<minGenPos) {
++end;
}
indices.add(end);
}
return indices.toArray();
}
/**
* Returns the number of steps.
* @return the number of steps
*/
public int size() {
return stepEnds.length;
}
/**
* Returns the index of the first marker in the specified step.
* @param step a step index
* @return the index of the first marker in the specified step
* @throws IllegalArgumentException if
* {@code step < 0 || step >= this.nSteps()}
*/
public int start(int step) {
return step==0 ? 0 : stepEnds[step-1];
}
/**
* Returns the index of the last marker (exclusive) in the specified step.
* @param step a step index
* @return the index of the last marker (exclusive) in the specified step
* @throws IllegalArgumentException if
* {@code step < 0 || step >= this.nSteps()}
*/
public int end(int step) {
return stepEnds[step];
}
/**
* Return the marker map.
* @return the marker map
*/
public MarkerMap map() {
return map;
}
}
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