General purpose merging iterator implementation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1593 348d0f76-0448-11de-a6fe-93d51630548a
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package org.broadinstitute.sting.utils;
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import org.broadinstitute.sting.gatk.iterators.PeekingIterator;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import java.util.*;
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public class MergingIterator<E extends Comparable<E>> implements Iterator<E>, PeekingIterator<E>, Iterable<E> {
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PriorityQueue<Element> queue = new PriorityQueue<Element>();
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private class Element implements Comparable<Element> {
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public Iterator<E> it = null;
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public E value = null;
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public Element(Iterator<E> it) {
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this.it = it;
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update();
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}
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public Element update() {
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if ( ! it.hasNext() )
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throw new RuntimeException("it is empty");
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E prev = value;
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value = it.next();
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//System.out.printf("Updating %s to prev=%s, next=%s%n", this, prev, value);
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return this;
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}
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public int compareTo(Element other) {
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return value.compareTo(other.value);
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}
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}
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public Iterator<E> iterator() {
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return this;
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}
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public MergingIterator() {
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;
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}
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public MergingIterator(Iterator<E> it) {
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add(it);
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}
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public MergingIterator(Collection<Iterator<E>> its) {
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for ( Iterator<E> it : its ) {
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add(it);
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}
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}
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public void add(Iterator<E> it) {
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if ( it.hasNext() )
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queue.add(new Element(it));
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}
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public boolean hasNext() {
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return ! queue.isEmpty();
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}
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public E next() {
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Element e = queue.poll();
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E value = e.value;
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if ( e.it != null && e.it.hasNext() )
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queue.add(new Element(e.it));
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//System.out.printf("Element is %s%n", e.value);
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return value;
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}
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public E peek() {
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return queue.peek().value;
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}
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public Collection<E> allElementsLTE(E elt) {
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return allElementsLTE(elt, true);
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}
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public Collection<E> allElementsLTE(E elt, boolean includeElt) {
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LinkedList<E> all = new LinkedList<E>();
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if ( includeElt ) all.add(elt);
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while ( hasNext() ) {
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E x = peek();
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//System.out.printf("elt.compareTo(x) == %d%n", elt.compareTo(x));
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//System.out.printf("In allElementLTE%n");
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int cmp = elt.compareTo(x);
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//System.out.printf("x=%s%n elt=%s%n => elt.compareTo(x) == %d%n", x, elt, cmp);
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if ( cmp >= 0 ) {
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//System.out.printf(" Adding element x=%s, size = %d%n", x, all.size());
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all.add(next());
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//System.out.printf(" Added size = %d%n", all.size());
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}
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else {
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//System.out.printf("breaking...%n");
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break;
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}
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}
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return all;
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}
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public void remove() {
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throw new UnsupportedOperationException();
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}
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}
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@ -0,0 +1,119 @@
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// our package
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package org.broadinstitute.sting.utils;
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// the imports for unit testing.
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import org.junit.Assert;
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import org.junit.Test;
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import org.junit.Before;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.gatk.walkers.recalibration.RecalData;
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import org.broadinstitute.sting.utils.QualityUtils;
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import java.util.*;
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/**
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* Basic unit test for RecalData
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*/
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public class MergingIteratorTest extends BaseTest {
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List<Integer> one_to_ten = Arrays.asList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10);
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List<Integer> evens = Arrays.asList(2, 4, 6, 8, 10);
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List<Integer> three_four_five = Arrays.asList(3, 4, 5);
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List<Integer> bigs = Arrays.asList(100, 200, 500);
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MergingIterator<Integer> x = null;
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@Before
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public void before() {
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x = null;
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}
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@Test
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public void testOneToOne() {
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logger.warn("Executing testOneToOne");
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x = new MergingIterator<Integer>(one_to_ten.iterator());
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for ( int i = 1; i < 11; i++ ) {
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int elt = x.next();
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logger.warn(String.format("Testing %d == %d", i, elt));
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Assert.assertEquals(elt, i);
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}
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Assert.assertFalse(x.hasNext());
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}
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@Test
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public void testMerging10Evens() {
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logger.warn("Executing testMerging10Evens");
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x = new MergingIterator<Integer>(one_to_ten.iterator());
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x.add(evens.iterator());
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List<Integer> expected = Arrays.asList(1, 2, 2, 3, 4, 4, 5, 6, 6, 7, 8, 8, 9, 10, 10);
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testExpected( x, expected );
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Assert.assertFalse(x.hasNext());
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}
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@Test
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public void testMerging3() {
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logger.warn("Executing testMerging3");
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x = new MergingIterator<Integer>(Arrays.asList(bigs.iterator(), evens.iterator(), three_four_five.iterator()));
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List<Integer> expected = Arrays.asList(2, 3, 4, 4, 5, 6, 8, 10, 100, 200, 500);
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testExpected( x, expected );
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Assert.assertFalse(x.hasNext());
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}
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@Test
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public void testCollectLTE() {
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logger.warn("Executing testCollectLTE");
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x = new MergingIterator<Integer>(Arrays.asList(bigs.iterator(), evens.iterator(), three_four_five.iterator()));
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//for ( int i : x ) {
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// System.out.printf("i=%d%n", i);
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//}
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logger.warn("Testing next element...");
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Assert.assertEquals( 2, (int)x.next());
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logger.warn("Testing allElementsLTE(2) = 2 ...");
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assertListsEqual( x.allElementsLTE(2), Arrays.asList(2) );
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logger.warn("Testing allElementsLTE(3) = 3 ...");
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Assert.assertEquals(3, (int)x.next());
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assertListsEqual( x.allElementsLTE(3), Arrays.asList(3) );
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logger.warn("Testing allElementsLTE(4) = 4, 4 ...");
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Assert.assertEquals(4, (int)x.next());
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assertListsEqual( x.allElementsLTE(4), Arrays.asList(4, 4) );
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logger.warn("Testing allElementsLTE(8) = 5, 6, 8 ...");
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assertListsEqual( x.allElementsLTE(8, false), Arrays.asList(5, 6, 8) );
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logger.warn("Testing remaining...");
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testExpected( x, Arrays.asList(10, 100, 200, 500) );
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Assert.assertFalse(x.hasNext());
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}
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private void testExpected( MergingIterator<Integer> mi, List<Integer> expected ) {
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for ( int expect : expected ) {
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int elt = mi.next();
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logger.warn(String.format("Testing elt=%d == expected=%d", elt, expect));
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Assert.assertEquals(expect, elt);
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}
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}
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private void assertListsEqual( Collection<Integer> l, List<Integer> expected ) {
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logger.warn("Size is " + l.size());
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Iterator<Integer> lit = l.iterator();
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for ( int expect : expected ) {
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Assert.assertTrue(lit.hasNext());
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int elt = lit.next();
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logger.warn(String.format("Testing elt=%d == expected=%d", elt, expect));
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Assert.assertEquals(expect, elt);
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}
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}
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}
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