Java tutorial
/************************************************************************* * * * This file is part of the 20n/act project. * * 20n/act enables DNA prediction for synthetic biology/bioengineering. * * Copyright (C) 2017 20n Labs, Inc. * * * * Please direct all queries to act@20n.com. * * * * 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 com.act.lcms.v2.fullindex; import com.act.lcms.LCMSSpectrum; import com.act.utils.MockRocksDBAndHandles; import org.apache.commons.lang3.tuple.Pair; import org.junit.Before; import org.junit.Test; import java.nio.ByteBuffer; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; public class BuilderTest { public static final double FP_TOLERANCE = 0.000001; public static final double[] TIMES = { 1.0, 2.0, 3.0 }; public static final double[][] MZS = { { 100.000, 100.005, 100.010 }, { 100.005, 100.010, 100.015 }, { 100.010, 100.015, 100.020 }, }; public static final double[][] INTENSITIES = { { 1.0, 2.0, 3.0 }, { 10.0, 20.0, 30.0 }, { 100.0, 200.0, 300.0 }, }; public static final List<MZWindow> MZ_WINDOWS = new ArrayList<MZWindow>() { { add(new MZWindow(0, 100.000)); add(new MZWindow(1, 100.010)); add(new MZWindow(2, 100.020)); } }; public Map<Integer, MZWindow> windowIdsToWindows = new HashMap<Integer, MZWindow>() { { for (MZWindow window : MZ_WINDOWS) { put(window.getIndex(), window); } } }; public static MockRocksDBAndHandles<ColumnFamilies> populateTestDB() throws Exception { List<LCMSSpectrum> spectra = new ArrayList<>(TIMES.length); for (int i = 0; i < TIMES.length; i++) { List<Pair<Double, Double>> mzIntensities = new ArrayList<>(); double totalIntensity = 0.0; for (int j = 0; j < MZS[i].length; j++) { mzIntensities.add(Pair.of(MZS[i][j], INTENSITIES[i][j])); totalIntensity += INTENSITIES[i][j]; } spectra.add(new LCMSSpectrum(i, TIMES[i], "s", mzIntensities, null, null, null, i, totalIntensity)); } MockRocksDBAndHandles<ColumnFamilies> testDB = new MockRocksDBAndHandles<>(ColumnFamilies.values()); Builder builder = new Builder(testDB); builder.extractTriples(spectra.iterator(), MZ_WINDOWS); builder.writeWindowsToDB(MZ_WINDOWS); return testDB; } public MockRocksDBAndHandles<ColumnFamilies> fakeDB; @Before public void setup() throws Exception { fakeDB = populateTestDB(); } @Test public void testExtractTriples() throws Exception { // Verify all TMzI triples are stored correctly. Map<Long, TMzI> deserializedTriples = new HashMap<>(); assertEquals("All triples should have entries in the DB", 9, fakeDB.getFakeDB().get(ColumnFamilies.ID_TO_TRIPLE).size()); for (Map.Entry<List<Byte>, byte[]> entry : fakeDB.getFakeDB().get(ColumnFamilies.ID_TO_TRIPLE).entrySet()) { Long id = ByteBuffer.wrap(fakeDB.byteListToArray(entry.getKey())).getLong(); TMzI triple = TMzI.readNextFromByteBuffer(ByteBuffer.wrap(entry.getValue())); Float expectedTime = Double.valueOf(TIMES[id.intValue() / 3]).floatValue(); Double expectedMZ = MZS[id.intValue() / 3][id.intValue() % 3]; Float expectedIntensity = Double.valueOf(INTENSITIES[id.intValue() / 3][id.intValue() % 3]) .floatValue(); assertEquals("Time matches expected", expectedTime, triple.getTime(), FP_TOLERANCE); // No error expected assertEquals("M/z matches expected", expectedMZ, triple.getMz(), FP_TOLERANCE); assertEquals("Intensity matches expected", expectedIntensity, triple.getIntensity(), FP_TOLERANCE); deserializedTriples.put(id, triple); } for (Map.Entry<List<Byte>, byte[]> entry : fakeDB.getFakeDB().get(ColumnFamilies.WINDOW_ID_TO_TRIPLES) .entrySet()) { int windowId = ByteBuffer.wrap(fakeDB.byteListToArray(entry.getKey())).getInt(); MZWindow window = windowIdsToWindows.get(windowId); List<Long> tmziIds = new ArrayList<>(entry.getValue().length / Long.BYTES); ByteBuffer valBuffer = ByteBuffer.wrap(entry.getValue()); while (valBuffer.hasRemaining()) { tmziIds.add(valBuffer.getLong()); } for (Long tripleId : tmziIds) { TMzI triple = deserializedTriples.get(tripleId); assertTrue("Triple m/z falls within range of containing window", triple.getMz() >= window.getMin() && triple.getMz() <= window.getMax()); } } for (Map.Entry<List<Byte>, byte[]> entry : fakeDB.getFakeDB().get(ColumnFamilies.TIMEPOINT_TO_TRIPLES) .entrySet()) { float time = ByteBuffer.wrap(fakeDB.byteListToArray(entry.getKey())).getFloat(); List<Long> tmziIds = new ArrayList<>(entry.getValue().length / Long.BYTES); ByteBuffer valBuffer = ByteBuffer.wrap(entry.getValue()); while (valBuffer.hasRemaining()) { tmziIds.add(valBuffer.getLong()); } for (Long tripleId : tmziIds) { TMzI triple = deserializedTriples.get(tripleId); assertEquals("Triple time matches key time", time, triple.getTime(), FP_TOLERANCE); } } } @Test public void testAppendOrRealloc() throws Exception { ByteBuffer dest = ByteBuffer.allocate(4); assertEquals("Initial buffer capacity matches expected", 4, dest.capacity()); dest = Utils.appendOrRealloc(dest, ByteBuffer.wrap(new byte[] { 'a', 'b', 'c', 'd' })); // No need to flip w/ wrap(). assertEquals("Post-append (fits) buffer capacity matches expected", 4, dest.capacity()); assertEquals("Post-append (fits) buffer position matches expected", 4, dest.position()); dest = Utils.appendOrRealloc(dest, ByteBuffer.wrap(new byte[] { 'e' })); assertEquals("Post-append (too large) buffer capacity has doubled", 8, dest.capacity()); assertEquals("Post-append (too large) buffer position matches expected", 5, dest.position()); dest = Utils.appendOrRealloc(dest, ByteBuffer.wrap(new byte[] { 'f', 'g', 'h' })); assertEquals("Post-append (fits) buffer capacity matches expected", 8, dest.capacity()); assertEquals("Post-append (fits) buffer position matches expected", 8, dest.position()); dest = Utils.appendOrRealloc(dest, ByteBuffer.wrap(new byte[] { 'i' })); assertEquals("Post-append (too large) buffer capacity has doubled", 16, dest.capacity()); assertEquals("Post-append (too large) buffer position matches expected", 9, dest.position()); } }