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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.ChromInterval;
import blbutil.Const;
import blbutil.SampleFileIt;
import java.io.File;
import java.util.NoSuchElementException;
/**
* <p>Class {@code IntervalVcfIterator} is a sample file iterator whose
* {@code next()} method returns a marker container.</p>
*
* @param <E> the type parameter
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class IntervalVcfIt<E extends MarkerContainer>
implements SampleFileIt<E> {
private final SampleFileIt<E> it;
private final ChromInterval interval;
private E next;
/**
* Constructs a new {@code IntervalVcfIterator} instance.
* @param it an iterator whose {@code next()} method returns a marker
* container
* @param chromInt a chromosome interval
* @throws NullPointerException if {@code it == null || interval == null}
*/
public IntervalVcfIt(SampleFileIt<E> it, ChromInterval chromInt) {
E firstRecord = readFirstRecord(it, chromInt);
if (firstRecord==null) {
String s = "No VCF records found in the specified interval."
+ Const.nl + "Check chromosome identifier and interval: "
+ chromInt.toString();
throw new IllegalArgumentException(s);
}
this.it = it;
this.interval = chromInt;
this.next = firstRecord;
}
@Override
public File file() {
return it.file();
}
@Override
public Samples samples() {
return it.samples();
}
/**
* Returns {@code true} if the iteration has more elements.
* @return {@code true} if the iteration has more elements.
*/
@Override
public boolean hasNext() {
return (next != null);
}
/**
* Returns the next element in the iteration.
* @return the next element in the iteration.
* @throws NoSuchElementException if the iteration has no more elements.
*/
@Override
public E next() {
if (!hasNext()) {
throw new NoSuchElementException();
}
E current = next;
this.next = readNextRecord(it, interval);
return current;
}
private E readFirstRecord(SampleFileIt<E> it, ChromInterval interval) {
E nextRecord = null;
while (nextRecord==null && it.hasNext()) {
E candidate = it.next();
if (inInterval(interval, candidate.marker())) {
nextRecord = candidate;
}
}
return nextRecord;
}
private E readNextRecord(SampleFileIt<E> it, ChromInterval interval) {
E nextRecord = null;
if (it.hasNext()) {
E candidate = it.next();
if (inInterval(interval, candidate.marker())) {
nextRecord = candidate;
}
}
return nextRecord;
}
private static boolean inInterval(ChromInterval interval, Marker marker) {
return (marker.chromIndex() == interval.chromIndex()
&& interval.start() <= marker.pos()
&& marker.pos() <= interval.inclEnd());
}
/**
* The {@code remove} method is not supported by this iterator.
* @throws UnsupportedOperationException if this method is invoked
*/
@Override
public void remove() {
throw new UnsupportedOperationException(this.getClass().toString());
}
@Override
public void close() {
it.close();
next = null;
}
}
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