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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 beagleutil;
/**
* <p>Class {@code CompHapSegment} represents a copied haplotype segment
* in a composite reference haplotype.</p>
*
* <p>Instances of class {@code CompHapSegment} are not thread-safe.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class CompHapSegment implements Comparable<CompHapSegment> {
private int hap;
private int startMarker;
private int ibsStep;
private final int compHapIndex;
/**
* Constructs a new {@code CompHapSegment} from the specified data.
* @param hap the haplotype
* @param start the index of the first marker in the haplotype segment
* @param ibsStep the last recorded IBS ibsStep
* @param compHapIndex the composite haplotype index
*/
public CompHapSegment(int hap, int start, int ibsStep, int compHapIndex) {
this.hap = hap;
this.startMarker = start;
this.ibsStep = ibsStep;
this.compHapIndex = compHapIndex;
}
/**
* Update the haplotype, the first marker in the haplotype segment,
* and the last recorded IBS ibsStep.
* @param hap the haplotype
* @param start the index of the first marker in the haplotype segment
* @param ibsStep the last recorded IBS ibsStep
*/
public void updateSegment(int hap, int start, int ibsStep) {
this.hap = hap;
this.startMarker = start;
this.ibsStep = ibsStep;
}
/**
* Updates the last recorded IBS ibsStep to the specified value
* @param ibsStep the last recorded IBS ibsStep
*/
public void updateStep(int ibsStep) {
this.ibsStep = ibsStep;
}
/**
* Returns the haplotype.
* @return the haplotype
*/
public int hap() {
return hap;
}
/**
* Returns the first marker in the haplotype segment
* @return the first marker in the haplotype segment
*/
public int startMarker() {
return startMarker;
}
/**
* Returns the last recorded IBS ibsStep for {@code this.hap()}.
* @return the last recorded IBS ibsStep for {@code this.hap()}
*/
public int ibsStep() {
return ibsStep;
}
/**
* Returns the composite haplotype index.
* @return the composite haplotype index
*/
public int compHapIndex() {
return compHapIndex;
}
/**
* Compares the specified segment to {@code this} for order. Returns
* -1, 0, or 1 according to whether {@code this.end()} is less than,
* equal, or greater than {@code seg.end()}.
* @param seg the object to be compared
* @return -1, 0, or 1 according to whether {@code this.end()} is less
* than, equal, or greater than {@code seg.end()}
*/
@Override
public int compareTo(CompHapSegment seg) {
if (this.ibsStep!=seg.ibsStep) {
return this.ibsStep<seg.ibsStep ? -1 : 1;
} else {
return 0;
}
}
}
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