Java tutorial
/* * Copyright (C) 2009-2011 Institute for Computational Biomedicine, * Weill Medical College of Cornell University * * This program 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. * * This program 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 edu.cornell.med.icb.goby.alignments; import it.unimi.dsi.fastutil.objects.ObjectList; import static junit.framework.Assert.assertEquals; 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.assertFalse; import static org.junit.Assert.assertNotNull; import org.junit.BeforeClass; import org.junit.Test; import java.io.File; import java.io.IOException; /** * @author Fabien Campagne * Date: May 6, 2011 * Time: 4:48:24 PM */ public class TestAlignmentIndex { /** * This test triggers an issue with Goby 1.9.5 indices. Using pre 1.9.6 indices, the skipTo method could fail * to return alignments if they occured at a position after the length of the next sequence. This test will fail * with any version of Goby prior to 1.9.6, and will success with Goby 1.9.6. Old alignments can be upgraded to * the index structures used by Goby 1.9.6 with the goby upgrade mode. * * @throws IOException */ @Test public void test_1_9_5_IndexIssue() throws IOException { int[] targetLengths = new int[] { 100, 50, 20, 10, 5 }; final String basename1 = FilenameUtils.concat(BASE_TEST_DIR, "align-index-error-1"); final AlignmentWriterImpl writer = new AlignmentWriterImpl(basename1); writer.setTargetLengths(targetLengths); writer.setNumAlignmentEntriesPerChunk(1); writer.setSorted(true); int queryIndex = 0; writer.setAlignmentEntry(queryIndex++, 0, 99, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(queryIndex++, 1, 0, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(queryIndex++, 1, 1, 30, false, constantQueryLength); writer.appendEntry(); writer.close(); AlignmentReaderImpl reader = new AlignmentReaderImpl(basename1); reader.reposition(0, 99); Alignments.AlignmentEntry entry = reader.next(); assertEquals(0, entry.getTargetIndex()); assertEquals(99, entry.getPosition()); entry = reader.next(); assertEquals(1, entry.getTargetIndex()); assertEquals(0, entry.getPosition()); entry = reader.next(); assertEquals(1, entry.getTargetIndex()); assertEquals(1, entry.getPosition()); assertFalse(reader.hasNext()); // Now check that the locations were stored in the index and can be decoded correctly: ObjectList<ReferenceLocation> locations = reader.getLocations(1); assertEquals(0, locations.get(0).targetIndex); assertEquals(99, locations.get(0).position); assertEquals(1, locations.get(1).targetIndex); assertEquals(0, locations.get(1).position); assertEquals(1, locations.get(2).targetIndex); assertEquals(1, locations.get(2).position); assertEquals("with modulo=1, must recover three locations.", 3, locations.size()); } @Test public void test_1_9_5_IndexIssueExtraTests() throws IOException { int[] targetLengths = new int[] { 100, 50, 20, 10, 5 }; final String basename1 = FilenameUtils.concat(BASE_TEST_DIR, "align-index-error-2"); final AlignmentWriterImpl writer = new AlignmentWriterImpl(basename1); writer.setTargetLengths(targetLengths); writer.setNumAlignmentEntriesPerChunk(1); writer.setSorted(true); int queryIndex = 0; writer.setAlignmentEntry(queryIndex++, 0, 99, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(queryIndex++, 1, 0, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(queryIndex++, 1, 1, 30, false, constantQueryLength); writer.appendEntry(); writer.close(); AlignmentReaderImpl reader = new AlignmentReaderImpl(basename1); reader.reposition(1, 0); // will be (0,99) because reposition goes one chunk before. The previous chunk // will have the indexed entry as first entry, plus some other entry, possibly including an entry with // position equal to the reposition argument. Repositioning to the chunk before garantees that skipTo will // not miss these entries, and appropriately filter the beginning of the chunk with position before (1,0). Alignments.AlignmentEntry entry = reader.next(); assertEquals(0, entry.getTargetIndex()); assertEquals(99, entry.getPosition()); entry = reader.next(); assertEquals(1, entry.getTargetIndex()); assertEquals(0, entry.getPosition()); entry = reader.next(); assertEquals(1, entry.getTargetIndex()); assertEquals(1, entry.getPosition()); assertFalse(reader.hasNext()); // Now check that the locations were stored in the index and can be decoded correctly: ObjectList<ReferenceLocation> locations = reader.getLocations(1); assertEquals(0, locations.get(0).targetIndex); assertEquals(99, locations.get(0).position); assertEquals(1, locations.get(1).targetIndex); assertEquals(0, locations.get(1).position); assertEquals(1, locations.get(2).targetIndex); assertEquals(1, locations.get(2).position); assertEquals("with modulo=1, must recover three locations.", 3, locations.size()); reader = new AlignmentReaderImpl(basename1); entry = reader.skipTo(1, 1); assertEquals(1, entry.getTargetIndex()); assertEquals(1, entry.getPosition()); assertFalse(reader.hasNext()); } @Test public void test_1_9_5_IndexIssueWithSkipTo() throws IOException { int[] targetLengths = new int[] { 100, 50, 20, 10, 5 }; final String basename1 = FilenameUtils.concat(BASE_TEST_DIR, "align-index-error-2"); final AlignmentWriterImpl writer = new AlignmentWriterImpl(basename1); writer.setTargetLengths(targetLengths); writer.setNumAlignmentEntriesPerChunk(1); writer.setSorted(true); int queryIndex = 0; writer.setAlignmentEntry(queryIndex++, 0, 99, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(queryIndex++, 1, 0, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(queryIndex++, 1, 1, 30, false, constantQueryLength); writer.appendEntry(); writer.close(); AlignmentReaderImpl reader = new AlignmentReaderImpl(basename1); reader.readHeader(); Alignments.AlignmentEntry entry = reader.skipTo(1, 0); assertEquals(1, entry.getTargetIndex()); assertEquals(0, entry.getPosition()); entry = reader.next(); assertEquals(1, entry.getTargetIndex()); assertEquals(1, entry.getPosition()); assertFalse(reader.hasNext()); // Now check that the locations were stored in the index and can be decoded correctly: ObjectList<ReferenceLocation> locations = reader.getLocations(1); assertEquals(0, locations.get(0).targetIndex); assertEquals(99, locations.get(0).position); assertEquals(1, locations.get(1).targetIndex); assertEquals(0, locations.get(1).position); assertEquals(1, locations.get(2).targetIndex); assertEquals(1, locations.get(2).position); assertEquals("with modulo=1, must recover three locations.", 3, locations.size()); } @Test public void testReposition() throws IOException { int[] targetLengths = new int[] { 100, 50, 20, 10, 5 }; final String basename1 = FilenameUtils.concat(BASE_TEST_DIR, "align-index-error-2"); final AlignmentWriterImpl writer = new AlignmentWriterImpl(basename1); writer.setTargetLengths(targetLengths); writer.setNumAlignmentEntriesPerChunk(1); writer.setSorted(true); int queryIndex = 0; writer.setAlignmentEntry(queryIndex++, 0, 99, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(queryIndex++, 1, 0, 30, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(queryIndex++, 1, 1, 30, false, constantQueryLength); writer.appendEntry(); writer.close(); AlignmentReaderImpl reader = new AlignmentReaderImpl(basename1); reader.readHeader(); assertNotNull(reader.skipTo(1, 0)); // now reposition to an earlier position (since 1.9.6): reader.reposition(0, 99); assertNotNull(reader.skipTo(1, 0)); assertNotNull(reader.skipTo(1, 1)); reader.reposition(0, 99); assertNotNull(reader.skipTo(1, 0)); assertNotNull(reader.skipTo(1, 1)); } /** * Used to log debug and informational messages. */ private static final Log LOG = LogFactory.getLog(TestReadWriteAlignments.class); private static final String BASE_TEST_DIR = "test-results/alignment-index"; private int constantQueryLength = 40; @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)); } }