htsjdk.samtools.util.MergingIterator Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import java.util.Collection;
import java.util.Comparator;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.PriorityQueue;
/**
* An iterator over Iterators that return Ts. Calling next() returns the next T ordered according
* to Comparator provided at construction time. Importantly, the elements in the input Iterators
* must already be sorted according to the provided Comparator.
*/
public class MergingIterator implements CloseableIterator {
/*
* An Iterator whose natural ordering is by the T that will be returned by the next call to
* next().
*/
private class ComparableIterator extends PeekableIterator implements Comparable {
public ComparableIterator(final Iterator iterator) {
super(iterator);
}
@Override
public int compareTo(final ComparableIterator that) {
if (comparator.getClass() != comparator.getClass()) {
throw new IllegalStateException("Can't compare two ComparableIterators that have different orderings.");
}
return comparator.compare(this.peek(), that.peek());
}
}
/*
* The general flow is to pull the "top" (according to the ComparableIterator's compareTo())
* iterator off on calls to this.next(), get iterator.next() and then re-add the iterator to
* the queue. Readding reorders the queue so the next "top" iterator is ready.
*/
private final PriorityQueue queue;
private final Comparator comparator;
// This is the last T returned by the call to next(). It's used to make sure that the comparators
// always return correctly ordered Ts.
private T lastReturned;
/**
* Creates a MergingIterator over the given Collection of iterators whose elements will be
* returned in the order defined by the given Comparator.
*/
public MergingIterator(final Comparator comparator, final Collection> iterators) {
if (iterators.isEmpty()) throw new IllegalArgumentException("One or more CloseableIterators must be provided.");
this.comparator = comparator;
this.queue = new PriorityQueue();
for (final CloseableIterator iterator : iterators) {
this.addIfNotEmpty(new ComparableIterator(iterator));
}
// If there are no iterators to read from after adding them all to the prioqueue,
// should we throw? it's prob'ly an error.
}
@Override
public boolean hasNext() {
return ! this.queue.isEmpty();
}
@Override
public T next() {
if ( ! this.hasNext()) throw new NoSuchElementException();
final ComparableIterator recordIterator = this.queue.poll();
// Assumes the iterator is closed & removed from the queue before recordIterator.hasNext() == false
final T next = recordIterator.next();
// I don't like having to test for null here -- it's really only null before the first call
// to next() -- but I don't see any other way
if (this.lastReturned != null && this.comparator.compare(lastReturned, next) > 0) {
throw new IllegalStateException(
"The elements of the input Iterators are not sorted according to the comparator " +
this.comparator.getClass().getName());
}
addIfNotEmpty(recordIterator);
this.lastReturned = next;
return next;
}
/**
* Unsupported.
*/
@Override
public void remove() {
throw new UnsupportedOperationException();
}
/**
* Closes every CloseableIterator in this MergingIterator. After calling, calls to
* hasNext() will always return false.
*/
@Override
public void close() {
final Iterator iterator = this.queue.iterator();
while (iterator.hasNext()) {
final ComparableIterator subIterator = iterator.next();
subIterator.close();
iterator.remove();
}
}
private void addIfNotEmpty(final ComparableIterator iterator) {
if (iterator.hasNext()) queue.offer(iterator);
else iterator.close();
}
}