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; import org.apache.commons.lang3.tuple.Pair; import org.junit.Test; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.stream.Collectors; import java.util.stream.StreamSupport; import static org.junit.Assert.assertEquals; import static org.junit.Assert.fail; public class MassChargeCalculatorTest { private static final double MASS_ERROR_TOLERANCE = 0.0000001; // Use the fuzzy FP assertEquals over lists of values private static void assertEqualsWithFPErr(String msg, List<Double> expected, List<Double> actual) { if (expected.size() != actual.size()) { fail(msg + ": unequal list sizes"); } for (int i = 0; i < expected.size(); i++) { assertEquals(msg, expected.get(i), actual.get(i), MASS_ERROR_TOLERANCE); } } private static void assertEqualsWithFPErr(String msg, Set<Double> expected, Set<Double> actual) { List<Double> expectedList = new ArrayList<>(expected); Collections.sort(expectedList); List<Double> actualList = new ArrayList<>(actual); Collections.sort(actualList); assertEqualsWithFPErr(msg, expectedList, actualList); } private static <T> void assertEqualsPairWithFPErr(String msg, List<Pair<T, Double>> expected, List<Pair<T, Double>> actual) { if (expected.size() != actual.size()) { fail(msg + ": unequal list sizes"); } for (int i = 0; i < expected.size(); i++) { assertEquals(msg, expected.get(i).getLeft(), actual.get(i).getLeft()); assertEquals(msg, expected.get(i).getRight(), actual.get(i).getRight(), MASS_ERROR_TOLERANCE); } } @Test public void testMakeMassChargeMap() throws Exception { List<MassChargeCalculator.MZSource> sources = Arrays.asList( new MassChargeCalculator.MZSource("InChI=1S/C7H7NO2/c8-6-3-1-5(2-4-6)7(9)10/h1-4H,8H2,(H,9,10)"), // PABA new MassChargeCalculator.MZSource("InChI=1S/C7H7NO2/c1-10-7(9)6-3-2-4-8-5-6/h2-5H,1H3")); // Something crazy. MassChargeCalculator.MassChargeMap massChargeMap = MassChargeCalculator.makeMassChargeMap(sources, new HashSet<>(Arrays.asList("M+H", "M+Na"))); Double expectedMonoMass = 137.047679; List<Double> expectedIonMZs = Arrays.asList(138.054979, 160.036879); // M+H and M+Na of PABA // This is package private, but we'll use its ordering to speed testing. List<Double> actualIonMasses = massChargeMap.ionMZsSorted(); assertEqualsWithFPErr("Unique ionic masses match expected list", expectedIonMZs, actualIonMasses); assertEqualsPairWithFPErr("M+H ion mz maps to source mass and ion name", Arrays.asList(Pair.of("M+H", expectedMonoMass)), massChargeMap.ionMZtoMonoMassAndIonName(actualIonMasses.get(0))); assertEqualsPairWithFPErr("M+Na ion mz maps to source mass and ion name", Arrays.asList(Pair.of("M+Na", expectedMonoMass)), massChargeMap.ionMZtoMonoMassAndIonName(actualIonMasses.get(1))); // Test reverse mapping. for (Double ionMZ : actualIonMasses) { assertEquals(String.format("Ionic masses for %f map to two MZSources", ionMZ), new HashSet<>(sources), massChargeMap.ionMZToMZSources(ionMZ)); } // Test iterators cover all values. assertEqualsWithFPErr("Iterable ionMZs match expected", new HashSet<>(expectedIonMZs), StreamSupport.stream(massChargeMap.ionMZIter().spliterator(), false).collect(Collectors.toSet())); assertEqualsWithFPErr("Iterable monoisotopic masses match expected", Collections.singleton(expectedMonoMass), StreamSupport.stream(massChargeMap.monoisotopicMassIter().spliterator(), false) .collect(Collectors.toSet())); assertEquals("Iterable mzSources match expected", new HashSet<>(sources), StreamSupport .stream(massChargeMap.mzSourceIter().spliterator(), false).collect(Collectors.toSet())); } @Test public void testComputeMass() throws Exception { List<Pair<MassChargeCalculator.MZSource, Double>> testCases = Arrays.asList( Pair.of(new MassChargeCalculator.MZSource( "InChI=1S/C8H9NO2/c1-6(10)9-7-2-4-8(11)5-3-7/h2-5,11H,1H3,(H,9,10)"), 151.063329), Pair.of(new MassChargeCalculator.MZSource(151.063329), 151.063329), Pair.of(new MassChargeCalculator.MZSource(Pair.of("APAP", 151.063329)), 151.063329)); for (Pair<MassChargeCalculator.MZSource, Double> testCase : testCases) { Double actualMass = MassChargeCalculator.computeMass(testCase.getLeft()); assertEquals( String.format("(Case %d) Actual mass is within bounds: %.6f ~ %.6f", testCase.getLeft().getId(), testCase.getRight(), actualMass), testCase.getRight(), actualMass, MASS_ERROR_TOLERANCE); } } }