org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree Maven / Gradle / Ivy

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package org.snpeff.snpEffect.testCases.unity;

import java.util.Random;

import org.junit.Before;
import org.junit.Test;
import org.snpeff.interval.Chromosome;
import org.snpeff.interval.Genome;
import org.snpeff.interval.Marker;
import org.snpeff.interval.Markers;
import org.snpeff.interval.tree.IntervalTree;
import org.snpeff.interval.tree.Itree;
import org.snpeff.util.Gpr;

import junit.framework.Assert;

/**
 * Test case for interval tree structure
 */
public class TestCasesIntervalTree {

	public static int MAX_SMALL_MARKER_SIZE = 5;
	public static int NUM_LARGE_INTERVALS = 100;
	public static int NUM_SMALL_INTERVALS = 10 * NUM_LARGE_INTERVALS;
	public static int CHR_SIZE = 10 * 1000;

	protected boolean debug = false;
	protected boolean verbose = false || debug;
	protected Random rand;
	protected Genome genome;
	protected Chromosome chromosome;
	protected Markers markers;

	public TestCasesIntervalTree() {
		super();
	}

	/**
	 * Perform a query using 'naive' lookup and interval forest.
	 * Compare results and throw an exception if any difference exists
	 */
	protected int compareQuery(Marker m, Itree intTree) {
		if (debug) Gpr.debug("Query: " + m);
		Markers resultsNaive = queryNaive(m);
		Markers resultsIntForest = intTree.query(m);

		if (debug) {
			Gpr.debug("Query: " + m + "\n\tResults: " + resultsIntForest.size());
			for (Marker res : resultsIntForest)
				System.err.println("\t" + res + (res.intersects(m) ? "" : "\tERROR!"));
		}

		// Compare all results
		String resultsNaiveStr = resultsNaive.sort().toString();
		String resultsIntForestStr = resultsIntForest.sort().toString();
		Assert.assertEquals("Results differ for query '" + m + "'.", resultsNaiveStr, resultsIntForestStr);

		return resultsNaive.size();
	}

	protected Markers createRandomLargeMarkers(Chromosome chr, int num) {
		Markers markers = new Markers();

		for (int i = 0; i < num; i++) {
			int start = rand.nextInt(chr.size());
			int end = rand.nextInt(chr.size());

			if (end < start) {
				int tmp = end;
				end = start;
				start = tmp;
			}

			Marker m = new Marker(chr, start, end, false, "ID_" + i);
			markers.add(m);
		}

		return markers;
	}

	protected Markers createRandomMarkers() {
		Markers markers = new Markers();
		markers.addAll(createRandomLargeMarkers(chromosome, NUM_LARGE_INTERVALS));
		markers.addAll(createRandomSmallMarkers(chromosome, NUM_SMALL_INTERVALS));
		return markers;
	}

	protected Markers createRandomSmallMarkers(Chromosome chr, int num) {
		Markers markers = new Markers();

		for (int i = 0; i < num; i++) {
			int start = rand.nextInt(chr.size());
			int end = start + rand.nextInt(MAX_SMALL_MARKER_SIZE) + 1;

			if (end < start) {
				int tmp = end;
				end = start;
				start = tmp;
			}

			Marker m = new Marker(chr, start, end, false, "ID_" + i);
			markers.add(m);
		}

		return markers;
	}

	@Before
	public void init() {
		int randSeed = 20151117;
		rand = new Random(randSeed);
		genome = new Genome();
		chromosome = new Chromosome(genome, 0, CHR_SIZE, "1");
		markers = createRandomMarkers();
	}

	/**
	 * Naively find all intervals intersecting 'marker'
	 */
	protected Markers queryNaive(Marker query) {
		Markers results = new Markers();

		// For each marker, fid if intersects query
		for (Marker m : markers)
			if (query.intersects(m)) results.add(m);

		return results;
	}

	protected Itree newItree(Markers markers) {
		return new IntervalTree(markers);
	}

	/**
	 * Test small intervals
	 */
	@Test
	public void test_01() {
		Gpr.debug("Test");

		Itree intTree = newItree(markers);
		intTree.build();

		Markers queries = createRandomSmallMarkers(chromosome, 100000);

		int i = 0;
		int totalResults = 0;
		for (Marker m : queries) {
			totalResults += compareQuery(m, intTree);
			Gpr.showMark(i++, 100);
		}

		Assert.assertTrue("Not a signle result found in all queries!", totalResults > 0);
		System.err.println("");
	}

	/**
	 * Test large intervals
	 */
	@Test
	public void test_02() {
		Gpr.debug("Test");

		Itree intForest = newItree(markers);
		intForest.build();

		Markers queries = createRandomLargeMarkers(chromosome, 10000);
		int i = 0;
		int totalResults = 0;
		for (Marker m : queries) {
			totalResults += compareQuery(m, intForest);
			Gpr.showMark(i++, 10);
		}

		Assert.assertTrue("Not a signle result found in all queries!", totalResults > 0);
		System.err.println("");

	}
}