/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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
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* THE SOFTWARE.
*/
package org.broad.igv.feature;
import junit.framework.AssertionFailedError;
import org.broad.igv.AbstractHeadlessTest;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static junit.framework.Assert.*;
/**
* User: jacob
* Date: 2011/12/15
*/
public class FeatureDBTest extends AbstractHeadlessTest {
public static final int LARGE = 500;
private static final String CHECK_STR = "ABC";
private static boolean reload = false;
public static void main(String[] args) {
}
@BeforeClass
public static void setUpClass() throws Exception {
AbstractHeadlessTest.setUpClass();
reload = false;
}
@Before
public void setUpTest() throws Exception {
try {
if (FeatureDB.size() == 0) {
reload = true;
}
} catch (NullPointerException e) {
reload = true;
}
if (reload) {
setUpClass();
}
}
@Test
public void testFeaturesMap() throws Exception {
Map<String, List<NamedFeature>> fMap = FeatureDB.getFeaturesMap(CHECK_STR);
for (String k : fMap.keySet()) {
assertTrue(k.startsWith(CHECK_STR));
}
}
@Test
public void testFeatureListSize() throws Exception {
List<NamedFeature> features = FeatureDB.getFeaturesList(CHECK_STR, 3);
assertEquals(3, features.size());
features = FeatureDB.getFeaturesList(CHECK_STR, LARGE);
assertTrue(features.size() < LARGE);
int expected = 50;
assertEquals(expected, features.size());
}
@Test
public void testFeatureList() throws Exception {
List<NamedFeature> features = FeatureDB.getFeaturesList(CHECK_STR, LARGE);
for (NamedFeature f : features) {
assertTrue(f.getName().startsWith(CHECK_STR));
assertNotNull(FeatureDB.getFeature(f.getName()));
}
}
/**
* Test thread safety by trying to read the map and clear it at the same time.
*
* @throws Exception
*/
@Test
public void testThreadSafety() throws Exception {
final Map<Integer, AssertionFailedError> map = new HashMap<Integer, AssertionFailedError>();
List<NamedFeature> features = FeatureDB.getFeaturesList(CHECK_STR, LARGE);
final int expected = features.size();
Thread read = new Thread(new Runnable() {
public void run() {
try {
List<NamedFeature> features = FeatureDB.getFeaturesList(CHECK_STR, LARGE);
for (NamedFeature f : features) {
//Check for data corruption
assertTrue(f.getName().startsWith(CHECK_STR));
}
assertEquals(expected, features.size());
} catch (AssertionFailedError e) {
map.put(0, e);
}
}
});
Thread write = new Thread(new Runnable() {
public void run() {
FeatureDB.clearFeatures();
}
});
read.start();
write.start();
read.join();
write.join();
features = FeatureDB.getFeaturesList(CHECK_STR, LARGE);
assertEquals(0, features.size());
if (map.containsKey(0)) {
AssertionFailedError e = map.get(0);
throw e;
}
}
@Test
public void testMultiRetrieve() throws Exception {
String checkstr = "EGFLAM";
Map<String, List<NamedFeature>> fMap = FeatureDB.getFeaturesMap(checkstr);
List<NamedFeature> data = fMap.get(checkstr);
assertEquals(4, data.size());
}
@Test
public void testMultipleEntries() throws Exception {
String checkstr = "EG";
Map<String, List<NamedFeature>> fMap = FeatureDB.getFeaturesMap(checkstr);
for (String k : fMap.keySet()) {
List<NamedFeature> data = fMap.get(k);
//System.out.println("key " + k + " has " + data.size());
for (int ii = 0; ii < data.size() - 1; ii++) {
NamedFeature feat1 = data.get(ii);
NamedFeature feat2 = data.get(ii + 1);
int len1 = feat1.getEnd() - feat1.getStart();
int len2 = feat2.getEnd() - feat2.getStart();
assertTrue("Data for key " + k + " not sorted", len1 >= len2);
}
}
}
@Test
public void testMutationSearch() throws Exception {
String name = "EGFR";
// EGFR starts with proteins MRPSG
String[] symbols = new String[]{"M", "R", "P", "S", "G"};
//All of these should be possible with a SNP from the EGFR sequence
String[] muts = new String[]{"I", "R", "P", "P", "R"};
Map<Integer, BasicFeature> matches;
for (int ii = 0; ii < symbols.length; ii++) {
matches = FeatureDB.getMutationAA(name, ii + 1, symbols[ii], muts[ii], genome);
assertEquals(1, matches.size());
for (int pos : matches.keySet()) {
assertEquals(name, matches.get(pos).getName());
}
}
name = "EGFLAM";
int exp_start = 38439399;
matches = FeatureDB.getMutationAA(name, 2, "H", "H", genome);
assertEquals(1, matches.size());
for (int geneloc : matches.keySet()) {
assertEquals(exp_start, matches.get(geneloc).getStart());
}
String[] others = new String[]{"I", "M", "T"};
for (String c : others) {
matches = FeatureDB.getMutationAA(name, 2, "H", c, genome);
assertEquals(0, matches.size());
}
}
@Test
public void testMutationSearchNegStrand() throws Exception {
String name = "KRAS";
int exp_start = 25249446;
Map<Integer, BasicFeature> matches = FeatureDB.getMutationAA(name, 1, "M", "I", genome);
assertEquals(1, matches.size());
for (int geneloc : matches.keySet()) {
assertEquals(exp_start, matches.get(geneloc).getStart());
}
}
@Test
public void testMutationSearchFail() throws Exception {
String name = "EGFR";
String[] symbols = "R,P,S,G,M".split(",");
Map<Integer, BasicFeature> matches;
for (int ii = 0; ii < symbols.length; ii++) {
matches = FeatureDB.getMutationAA(name, ii + 1, symbols[ii], "M", genome);
assertEquals(0, matches.size());
}
}
@Test
public void testMutationSearchNT() throws Exception {
String name = "EGFR";
String[] bps = new String[]{"A", "T", "G"};
Map<Integer, BasicFeature> matches;
for (int ii = 0; ii < bps.length; ii++) {
matches = FeatureDB.getMutationNT(name, ii + 1, bps[ii], genome);
assertEquals(1, matches.size());
}
}
@Test
public void testMutationSearchNTNegStrand() throws Exception {
String name = "KRAS";
String[] bps = new String[]{"A", "T", "G"};
Map<Integer, BasicFeature> matches;
for (int ii = 0; ii < bps.length; ii++) {
matches = FeatureDB.getMutationNT(name, ii + 1, bps[ii], genome);
assertEquals(1, matches.size());
}
//Exon 3 of KRAS, starting at amino acid 56
int startNT = (56 - 1) * 3;
char[] bps2 = "CTCGACACAGCAGGT".toCharArray();
for (int ii = 0; ii < bps2.length; ii++) {
matches = FeatureDB.getMutationNT(name, ii + startNT + 1, String.valueOf(bps2[ii]), genome);
assertEquals(1, matches.size());
}
}
}