Java tutorial
/** * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. */ /* -------------------------------- Package --------------------------------- */ package com.github.jessemull.microflexinteger.stat; /* ------------------------------ Dependencies ------------------------------ */ import static org.junit.Assert.*; import java.io.OutputStream; import java.io.PrintStream; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.TreeMap; import java.util.Map; import java.util.Random; import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import org.apache.commons.math3.util.Precision; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.FixMethodOrder; import org.junit.Test; import org.junit.runners.MethodSorters; import com.github.jessemull.microflexinteger.plate.Plate; import com.github.jessemull.microflexinteger.plate.Well; import com.github.jessemull.microflexinteger.plate.WellSet; import com.github.jessemull.microflexinteger.stat.GeometricMean; import com.github.jessemull.microflexinteger.util.RandomUtil; /** * This class tests the methods in the mean integer class. * @author Jesse L. Mull * @update Updated Oct 18, 2016 * @address http://www.jessemull.com * @email hello@jessemull.com */ @FixMethodOrder(MethodSorters.NAME_ASCENDING) public class GeometricMeanTest { /* ---------------------------- Local Fields -----------------------------*/ /* Minimum and maximum values for random well and lists */ private static int minValue = 0; // Minimum integer value for wells private static int maxValue = 100; // Maximum integer value for wells private static Random random = new Random(); // Generates random integers private static int precision = 10; // Precision for double results /* The addition operation */ private static GeometricMean mean = new GeometricMean(); /* Random objects and numbers for testing */ private static int rows = 5; private static int columns = 4; private static int length = 5; private static int lengthIndices = 10; private static int plateNumber = 10; private static int plateNumberIndices = 5; private static Plate[] array = new Plate[plateNumber]; private static Plate[] arrayIndices = new Plate[plateNumberIndices]; /* Value of false redirects System.err */ private static boolean error = true; private static PrintStream originalOut = System.out; /** * Generates random objects and numbers for testing. */ @BeforeClass public static void setUp() { if (error) { System.setErr(new PrintStream(new OutputStream() { public void write(int x) { } })); } for (int j = 0; j < array.length; j++) { Plate plate = RandomUtil.randomPlateInteger(rows, columns, minValue, maxValue, length, "Plate1-" + j); array[j] = plate; } for (int j = 0; j < arrayIndices.length; j++) { Plate plateIndices = RandomUtil.randomPlateInteger(rows, columns, minValue, maxValue, lengthIndices, "Plate1-" + j); arrayIndices[j] = plateIndices; } } /** * Toggles system error. */ @AfterClass public static void restoreErrorOut() { System.setErr(originalOut); } /* ---------------------------- Constructors -----------------------------*/ /** * Tests the default constructor. */ @Test public void testConstructor() { GeometricMean test = new GeometricMean(); assertNotNull(test); } /* ---------------- Well statistics for all plate wells ----------------- */ /** * Tests the plate statistics method. */ @Test public void testPlate() { for (Plate plate : array) { Map<Well, Double> resultMap = new TreeMap<Well, Double>(); Map<Well, Double> returnedMap = mean.plate(plate); for (Well well : plate) { double[] input = new double[well.size()]; int index = 0; for (double bd : well) { input[index++] = bd; ; } DescriptiveStatistics stat = new DescriptiveStatistics(input); double result = stat.getGeometricMean(); resultMap.put(well, result); } for (Well well : plate) { double result = Precision.round(resultMap.get(well), precision); double returned = Precision.round(returnedMap.get(well), precision); assertTrue(result == returned); } } } /** * Tests the plate statistics method using the values between the indices. */ @Test public void testPlateIndices() { for (Plate plate : arrayIndices) { int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); Map<Well, Double> resultMap = new TreeMap<Well, Double>(); Map<Well, Double> returnedMap = mean.plate(plate, begin, end - begin); for (Well well : plate) { double[] input = new double[well.size()]; int index = 0; for (double bd : well) { input[index++] = bd; ; } DescriptiveStatistics stat = new DescriptiveStatistics(ArrayUtils.subarray(input, begin, end)); double result = stat.getGeometricMean(); resultMap.put(well, result); } for (Well well : plate) { double result = Precision.round(resultMap.get(well), precision); double returned = Precision.round(returnedMap.get(well), precision); assertTrue(result == returned); } } } /* --------------------- Aggregated plate statistics ------------------- */ /** * Tests the aggregated plate statistics method. */ @Test public void testAggregatedPlate() { for (Plate plate : array) { List<Double> resultList = new ArrayList<Double>(); double aggregatedReturned = Precision.round(mean.platesAggregated(plate), precision); for (Well well : plate) { resultList.addAll(well.toDouble()); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double resultAggregated = Precision.round(statAggregated.getGeometricMean(), precision); assertTrue(resultAggregated == aggregatedReturned); } } /** * Tests the aggregated plate statistics method using a collection. */ @Test public void testAggregatedPlateCollection() { List<Plate> collection = Arrays.asList(array); Map<Plate, Double> aggregatedReturnedMap = mean.platesAggregated(collection); Map<Plate, Double> aggregatedResultMap = new TreeMap<Plate, Double>(); for (Plate plate : collection) { List<Double> resultList = new ArrayList<Double>(); for (Well well : plate) { resultList.addAll(well.toDouble()); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double aggregatedResult = statAggregated.getGeometricMean(); aggregatedResultMap.put(plate, aggregatedResult); } for (Plate plate : collection) { double result = Precision.round(aggregatedResultMap.get(plate), precision); double returned = Precision.round(aggregatedReturnedMap.get(plate), precision); assertTrue(result == returned); } } /** * Tests the aggregated plate statistics method using an array. */ @Test public void testAggregatedPlateArray() { Map<Plate, Double> aggregatedReturnedMap = mean.platesAggregated(array); Map<Plate, Double> aggregatedResultMap = new TreeMap<Plate, Double>(); for (Plate plate : array) { List<Double> resultList = new ArrayList<Double>(); for (Well well : plate) { resultList.addAll(well.toDouble()); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double aggregatedResult = statAggregated.getGeometricMean(); aggregatedResultMap.put(plate, aggregatedResult); } for (Plate plate : array) { double result = Precision.round(aggregatedResultMap.get(plate), precision); double returned = Precision.round(aggregatedReturnedMap.get(plate), precision); assertTrue(result == returned); } } /** * Tests the aggregated plate statistics method using the values between the indices. */ @Test public void testAggregatedPlateIndices() { for (Plate plate : arrayIndices) { int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); List<Double> resultList = new ArrayList<Double>(); double aggregatedReturned = Precision.round(mean.platesAggregated(plate, begin, end - begin), precision); for (Well well : plate) { resultList.addAll(well.toDouble().subList(begin, end)); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double aggregatedResult = Precision.round(statAggregated.getGeometricMean(), precision); assertTrue(aggregatedResult == aggregatedReturned); } } /** * Tests the aggregated plate statistics method using the values between the indices of * the collection. */ @Test public void testAggregatedPlateCollectionIndices() { int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); List<Plate> collection = Arrays.asList(arrayIndices); Map<Plate, Double> aggregatedReturnedMap = mean.platesAggregated(collection, begin, end - begin); Map<Plate, Double> aggregatedResultMap = new TreeMap<Plate, Double>(); for (Plate plate : collection) { List<Double> resultList = new ArrayList<Double>(); for (Well well : plate) { resultList.addAll(well.toDouble().subList(begin, end)); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double resultAggregated = statAggregated.getGeometricMean(); aggregatedResultMap.put(plate, resultAggregated); } for (Plate plate : collection) { double result = Precision.round(aggregatedResultMap.get(plate), precision); double returned = Precision.round(aggregatedReturnedMap.get(plate), precision); assertTrue(result == returned); } } /** * Tests the aggregated plate statistics method using the values between the indices of * the array. */ @Test public void testAggregatedPlateArrayIndices() { int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); Map<Plate, Double> aggregatedReturnedMap = mean.platesAggregated(arrayIndices, begin, end - begin); Map<Plate, Double> aggregatedResultMap = new TreeMap<Plate, Double>(); for (Plate plate : arrayIndices) { List<Double> resultList = new ArrayList<Double>(); for (Well well : plate) { resultList.addAll(well.toDouble().subList(begin, end)); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double aggregatedResult = statAggregated.getGeometricMean(); aggregatedResultMap.put(plate, aggregatedResult); } for (Plate plate : arrayIndices) { double result = Precision.round(aggregatedResultMap.get(plate), precision); double returned = Precision.round(aggregatedReturnedMap.get(plate), precision); assertTrue(result == returned); } } /* --------------- Well statistics for all wells in a set -------------- */ /** * Tests set calculation. */ @Test public void testSet() { for (Plate plate : array) { Map<Well, Double> resultMap = new TreeMap<Well, Double>(); Map<Well, Double> returnedMap = mean.set(plate.dataSet()); for (Well well : plate) { double[] input = new double[well.size()]; int index = 0; for (double bd : well) { input[index++] = bd; ; } DescriptiveStatistics stat = new DescriptiveStatistics(input); double result = stat.getGeometricMean(); resultMap.put(well, result); } for (Well well : plate) { double result = Precision.round(resultMap.get(well), precision); double returned = Precision.round(returnedMap.get(well), precision); assertTrue(result == returned); } } } /** * Tests set calculation using indices. */ @Test public void testSetIndices() { for (Plate plate : arrayIndices) { int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); Map<Well, Double> resultMap = new TreeMap<Well, Double>(); Map<Well, Double> returnedMap = mean.set(plate.dataSet(), begin, end - begin); for (Well well : plate) { double[] input = new double[well.size()]; int index = 0; for (double bd : well) { input[index++] = bd; ; } DescriptiveStatistics stat = new DescriptiveStatistics(ArrayUtils.subarray(input, begin, end)); double result = stat.getGeometricMean(); resultMap.put(well, result); } for (Well well : plate) { double result = Precision.round(resultMap.get(well), precision); double returned = Precision.round(returnedMap.get(well), precision); assertTrue(result == returned); } } } /* ---------------------- Aggregated set statistics -------------------- */ /** * Tests the aggregated plate statistics method. */ @Test public void testAggregatedSet() { for (Plate plate : array) { List<Double> resultList = new ArrayList<Double>(); double aggregatedReturned = Precision.round(mean.setsAggregated(plate.dataSet()), precision); for (Well well : plate) { resultList.addAll(well.toDouble()); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double resultAggregated = Precision.round(statAggregated.getGeometricMean(), precision); assertTrue(resultAggregated == aggregatedReturned); } } /** * Tests the aggregated plate statistics method using a collection. */ @Test public void testAggregatedSetCollection() { List<WellSet> collection = new ArrayList<WellSet>(); for (Plate plate : array) { collection.add(plate.dataSet()); } Map<WellSet, Double> aggregatedReturnedMap = mean.setsAggregated(collection); Map<WellSet, Double> aggregatedResultMap = new TreeMap<WellSet, Double>(); for (WellSet set : collection) { List<Double> resultList = new ArrayList<Double>(); for (Well well : set) { resultList.addAll(well.toDouble()); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double aggregatedResult = statAggregated.getGeometricMean(); aggregatedResultMap.put(set, aggregatedResult); } for (WellSet set : collection) { double result = Precision.round(aggregatedResultMap.get(set), precision); double returned = Precision.round(aggregatedReturnedMap.get(set), precision); assertTrue(result == returned); } } /** * Tests the aggregated plate statistics method using an array. */ @Test public void testAggregatedSetArray() { WellSet[] setArray = new WellSet[array.length]; for (int i = 0; i < setArray.length; i++) { setArray[i] = array[i].dataSet(); } Map<WellSet, Double> aggregatedReturnedMap = mean.setsAggregated(setArray); Map<WellSet, Double> aggregatedResultMap = new TreeMap<WellSet, Double>(); for (WellSet set : setArray) { List<Double> resultList = new ArrayList<Double>(); for (Well well : set) { resultList.addAll(well.toDouble()); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double aggregatedResult = statAggregated.getGeometricMean(); aggregatedResultMap.put(set, aggregatedResult); } for (WellSet set : setArray) { double result = Precision.round(aggregatedResultMap.get(set), precision); double returned = Precision.round(aggregatedReturnedMap.get(set), precision); assertTrue(result == returned); } } /** * Tests the aggregated plate statistics method using the values between the indices. */ @Test public void testAggregatedSetIndices() { for (Plate plate : arrayIndices) { int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); List<Double> resultList = new ArrayList<Double>(); double aggregatedReturned = Precision.round(mean.setsAggregated(plate.dataSet(), begin, end - begin), precision); for (Well well : plate) { resultList.addAll(well.toDouble().subList(begin, end)); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double resultAggregated = Precision.round(statAggregated.getGeometricMean(), precision); assertTrue(resultAggregated == aggregatedReturned); } } /** * Tests the aggregated plate statistics method using the values between the indices of * the collection. */ @Test public void testAggregatedSetCollectionIndices() { int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); List<WellSet> collection = new ArrayList<WellSet>(); for (Plate plate : arrayIndices) { collection.add(plate.dataSet()); } Map<WellSet, Double> aggregatedReturnedMap = mean.setsAggregated(collection, begin, end - begin); Map<WellSet, Double> aggregatedResultMap = new TreeMap<WellSet, Double>(); for (WellSet set : collection) { List<Double> resultList = new ArrayList<Double>(); for (Well well : set) { resultList.addAll(well.toDouble().subList(begin, end)); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double aggregatedResult = statAggregated.getGeometricMean(); aggregatedResultMap.put(set, aggregatedResult); } for (WellSet set : collection) { double result = Precision.round(aggregatedResultMap.get(set), precision); double returned = Precision.round(aggregatedReturnedMap.get(set), precision); assertTrue(result == returned); } } /** * Tests the aggregated plate statistics method using the values between the indices of * the array. */ @Test public void testAggregatedSetArrayIndices() { int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); WellSet[] setArrayIndices = new WellSet[arrayIndices.length]; for (int i = 0; i < setArrayIndices.length; i++) { setArrayIndices[i] = arrayIndices[i].dataSet(); } Map<WellSet, Double> aggregatedReturnedMap = mean.setsAggregated(setArrayIndices, begin, end - begin); Map<WellSet, Double> aggregatedResultMap = new TreeMap<WellSet, Double>(); for (WellSet set : setArrayIndices) { List<Double> resultList = new ArrayList<Double>(); for (Well well : set) { resultList.addAll(well.toDouble().subList(begin, end)); } double[] inputAggregated = new double[resultList.size()]; for (int i = 0; i < resultList.size(); i++) { inputAggregated[i] = resultList.get(i); } DescriptiveStatistics statAggregated = new DescriptiveStatistics(inputAggregated); double aggregatedResult = statAggregated.getGeometricMean(); aggregatedResultMap.put(set, aggregatedResult); } for (WellSet plate : setArrayIndices) { double result = Precision.round(aggregatedResultMap.get(plate), precision); double returned = Precision.round(aggregatedReturnedMap.get(plate), precision); assertTrue(result == returned); } } /* -------------------------- Well statistics -------------------------- */ /** * Tests well calculation. */ @Test public void testWell() { for (Plate plate : array) { for (Well well : plate) { double[] input = new double[well.size()]; int index = 0; for (double bd : well) { input[index++] = bd; ; } DescriptiveStatistics stat = new DescriptiveStatistics(input); double result = Precision.round(stat.getGeometricMean(), precision); double returned = Precision.round(mean.well(well), precision); assertTrue(result == returned); } } } /** * Tests well calculation using indices. */ @Test public void testWellIndices() { for (Plate plate : arrayIndices) { for (Well well : plate) { double[] input = new double[well.size()]; int index = 0; for (double bd : well) { input[index++] = bd; ; } int size = arrayIndices[0].first().size(); int begin = random.nextInt(size - 5); int end = (begin + 4) + random.nextInt(size - (begin + 4) + 1); DescriptiveStatistics stat = new DescriptiveStatistics(ArrayUtils.subarray(input, begin, end)); double result = Precision.round(stat.getGeometricMean(), precision); double returned = Precision.round(mean.well(well, begin, end - begin), precision); assertTrue(result == returned); } } } }