Java tutorial
/* * Copyright (C) 2009-2010 Institute for Computational Biomedicine, * Weill Medical College of Cornell University * * This file is part of the Goby IO API. * * The Goby IO API is free software: you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * The Goby IO API 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 Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with the Goby IO API. If not, see <http://www.gnu.org/licenses/>. */ package edu.cornell.med.icb.goby.alignments; import it.unimi.dsi.fastutil.objects.ObjectList; import junit.framework.Assert; import org.apache.commons.io.FileUtils; import org.apache.commons.io.FilenameUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.junit.AfterClass; import static org.junit.Assert.*; import org.junit.BeforeClass; import org.junit.Test; import java.io.File; import java.io.IOException; /** * @author Fabien Campagne * Date: Dec 10, 2010 * Time: 2:08:43 PM */ public class TestPositionSlices { /** * Used to log debug and informational messages. */ private static final Log LOG = LogFactory.getLog(TestSkipTo.class); private static final String BASE_TEST_DIR = "test-results/alignments-position-slices"; @BeforeClass public static void initializeTestDirectory() throws IOException { if (LOG.isDebugEnabled()) { LOG.debug("Creating base test directory: " + BASE_TEST_DIR); } FileUtils.forceMkdir(new File(BASE_TEST_DIR)); } @AfterClass public static void cleanupTestDirectory() throws IOException { if (LOG.isDebugEnabled()) { LOG.debug("Deleting base test directory: " + BASE_TEST_DIR); } FileUtils.forceDeleteOnExit(new File(BASE_TEST_DIR)); } @Test public void testAllEntries() throws IOException { final String basename = "align-position-slices-0"; buildAlignment(basename); { // check that we can read everything when the boundaries include everything: final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename), 0, 400, 4, 500); check(reader, 1, 12); check(reader, 1, 13); check(reader, 1, 13); check(reader, 1, 13); check(reader, 2, 123); check(reader, 2, 300); check(reader, 2, 300); reader.close(); } } @Test public void testOneSlice() throws IOException { final String basename = "align-position-slices-1"; buildAlignment(basename); {// check that we can read everything only 1 12-13: final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename), 0, 0, 1, 13); check(reader, 1, 12); check(reader, 1, 13); check(reader, 1, 13); check(reader, 1, 13); assertFalse(reader.hasNext()); reader.close(); } } @Test public void testTwoSlice() throws IOException { final String basename = "align-position-slices-2"; buildAlignment(basename); {// check that we can read everything only 1 12-13: final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename), 0, 0, 1, 12); check(reader, 1, 12); assertFalse(reader.hasNext()); reader.close(); } } @Test public void testThreeSlice() throws IOException { final String basename = "align-position-slices-3"; buildAlignment(basename); {// check that we can read everything only between 1 13 and 2 123: final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename), 1, 13, 2, 123); check(reader, 1, 13); check(reader, 1, 13); check(reader, 1, 13); check(reader, 2, 123); assertFalse(reader.hasNext()); reader.close(); } } @Test public void testFourSlice() throws IOException { final String basename = "align-position-slices-4"; buildAlignment(basename); {// check that we can read everything only between 1 13 and 1 13: final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename), 1, 13, 1, 13); check(reader, 1, 13); check(reader, 1, 13); check(reader, 1, 13); assertFalse(reader.hasNext()); reader.close(); } } @Test public void testBeforeSlice() throws IOException { final String basename = "align-position-slices-5"; buildAlignment(basename); {// check that we can read skipTo before the start of the slice and only get entries that are within the slice // boundaries. final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename), 2, 300, 2, 300); final Alignments.AlignmentEntry alignmentEntry = reader.skipTo(2, 0); assertNotNull(alignmentEntry); assertEquals(2, alignmentEntry.getTargetIndex()); assertEquals(300, alignmentEntry.getPosition()); check(reader, 2, 300); assertFalse(reader.hasNext()); reader.close(); } } @Test public void testIndexLocations() throws IOException { final String basename = "align-position-slices-index-locations1"; buildAlignment(basename); {// check that we can read skipTo before the start of the slice and only get entries that are within the slice // boundaries. final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename)); reader.readHeader(); ObjectList<ReferenceLocation> locations = reader.getLocations(1); reader.close(); Assert.assertEquals(1, locations.get(0).targetIndex); Assert.assertEquals(12, locations.get(0).position); Assert.assertEquals(1, locations.get(1).targetIndex); Assert.assertEquals(13, locations.get(1).position); Assert.assertEquals(2, locations.get(2).targetIndex); Assert.assertEquals(123, locations.get(2).position); Assert.assertEquals(2, locations.get(3).targetIndex); Assert.assertEquals(300, locations.get(3).position); Assert.assertEquals(4, locations.size()); } } private void buildAlignment(String basename) throws IOException { final AlignmentWriterImpl writer = new AlignmentWriterImpl(FilenameUtils.concat(BASE_TEST_DIR, basename)); writer.setNumAlignmentEntriesPerChunk(2); final int numTargets = 3; final int[] targetLengths = new int[numTargets]; for (int referenceIndex = 0; referenceIndex < numTargets; referenceIndex++) { targetLengths[referenceIndex] = 1000; } writer.setTargetLengths(targetLengths); // we write this alignment sorted: writer.setSorted(true); int constantQueryLength = 50; // chunk 1: writer.setAlignmentEntry(0, 1, 12, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(0, 1, 13, 1, false, constantQueryLength); writer.appendEntry(); // chunk 2: writer.setAlignmentEntry(0, 1, 13, 2, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(0, 1, 13, 3, false, constantQueryLength); writer.appendEntry(); // chunk 3: writer.setAlignmentEntry(0, 2, 123, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(0, 2, 300, 1, false, constantQueryLength); writer.appendEntry(); // chunk 4: writer.setAlignmentEntry(0, 2, 300, 2, false, constantQueryLength); writer.appendEntry(); writer.close(); writer.printStats(System.out); } private void check(AlignmentReader reader, int referenceIndex, int referencePosition) { assertTrue("Reader must have another entry", reader.hasNext()); final Alignments.AlignmentEntry a = reader.next(); assertNotNull(a); assertEquals(referenceIndex, a.getTargetIndex()); assertEquals(referencePosition, a.getPosition()); } }