/* * TrainingInfoTest.java * * Copyright 2006 Michigan State University Board of Trustees * * Created on September 19, 2003, 10:23 AM */ package edu.msu.cme.rdp.classifier.rrnaclassifier; import edu.msu.cme.rdp.classifier.ClassificationResult; import edu.msu.cme.rdp.classifier.Classifier; import edu.msu.cme.rdp.classifier.GenusWordConditionalProb; import edu.msu.cme.rdp.classifier.HierarchyTree; import edu.msu.cme.rdp.classifier.RankAssignment; import edu.msu.cme.rdp.classifier.TrainingInfo; import edu.msu.cme.rdp.classifier.utils.ClassifierSequence; import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.Reader; import java.util.HashMap; import java.util.Iterator; import java.util.List; import junit.framework.Test; import junit.framework.TestCase; import junit.framework.TestSuite; /** * A test class for TrainingInfo. * @author wangqion */ public class TrainingInfoTest extends TestCase { public TrainingInfoTest(java.lang.String testName) { super(testName); } public static void main(java.lang.String[] args) { junit.textui.TestRunner.run(suite()); } public static Test suite() { TestSuite suite = new TestSuite(TrainingInfoTest.class); return suite; } /** Test of createTree method, of class classification.TrainingInfo. */ public void testCreateTree() { System.out.println("testCreateTree"); } /** Test of createLogWordPriorArr method, of class classification.TrainingInfo. */ public void testCreateLogWordPriorArr() throws Exception{ System.out.println("testCreateLogWordPriorArr"); InputStream dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt"); Reader in = new InputStreamReader( dstream ); TrainingInfo train = new TrainingInfo(); train.createLogWordPriorArr(in); float wordPrior = train.getLogWordPrior(10); assertEquals(wordPrior, -2.77, 0.1); wordPrior = train.getLogWordPrior(55); assertEquals(wordPrior, -1.67, 0.1); // test getWordPairPriorDiff() wordPrior = train.getLogWordPrior(24573); assertEquals(wordPrior, -2.77, 0.01); float revWordPrior = train.getLogWordPrior(10912); assertEquals(revWordPrior, -1.67, 0.01); float wordPriorDiff = train.getWordPairPriorDiff(24573); assertEquals(wordPriorDiff, (wordPrior - revWordPrior), 0.01); float revWordPriorDiff = train.getWordPairPriorDiff(10912); assertEquals(revWordPriorDiff, (revWordPrior - wordPrior), 0.01); assertEquals( (wordPriorDiff + revWordPriorDiff), 0, 0.01); } /** Test of createGenusWordProbLis method, of class classification.TrainingInfo. */ public void testCreateGenusWordProbList() throws Exception{ System.out.println("testCreateGenusWordConditionalProbList"); InputStream dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testGenus_probList.txt"); Reader in = new InputStreamReader( dstream ); TrainingInfo train = new TrainingInfo(); train.createGenusWordProbList(in); GenusWordConditionalProb gProb = train.getWordConditionalProbObject(8); int genusIndex = gProb.getGenusIndex(); float prob = gProb.getProbability(); assertEquals(genusIndex, 4); assertEquals(prob, -0.15, 0.1); gProb = train.getWordConditionalProbObject(1865); genusIndex = gProb.getGenusIndex(); prob = gProb.getProbability(); assertEquals(genusIndex, 0); assertEquals(prob, -0.5, 0.1); } /** Test of makeProbIndexArr method, of class classification.TrainingInfo. */ public void testCreateProbIndexArr() throws Exception { System.out.println("testCreateProbIndexArr"); InputStream dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testProbIndex.txt"); Reader in = new InputStreamReader( dstream ); TrainingInfo train = new TrainingInfo(); train.createProbIndexArr(in); int start = train.getStartIndex(100); int stop = train.getStopIndex(65535); assertEquals(start, 1); assertEquals(stop, 1866); } /** Test of getRootTree method, of class classification.TrainingInfo. */ public void testCreateClassifier() throws Exception{ System.out.println("testCreateClassifier"); TrainingInfo train = new TrainingInfo(); InputStream dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testGenus_probList.txt"); Reader in = new InputStreamReader( dstream ); train.createGenusWordProbList(in); dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/test_bergeyTrainingTree.xml"); in = new InputStreamReader( dstream ); train.createTree(in); dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testProbIndex.txt"); in = new InputStreamReader( dstream ); train.createProbIndexArr(in); dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt"); in = new InputStreamReader( dstream ); train.createLogWordPriorArr(in); int genusNodeListSize = train.getGenusNodeListSize(); assertEquals(genusNodeListSize, 6); HierarchyTree genusNode = train.getGenusNodebyIndex(3); assertEquals(genusNode.getGenusIndex(), 3); assertEquals(genusNode.getName(), "Pseudomonas"); int leaveCount = genusNode.getLeaveCount(); float logLeaveCount = train.getLogLeaveCount(1); assertEquals((double)leaveCount, Math.exp(logLeaveCount) -1, 0.1); HierarchyTree rootTree = train.getRootTree(); assertEquals(rootTree.getName(), "Bacteria"); assertNotNull( rootTree.getSubclasses()); Classifier aClassifier = train.createClassifier(); //test addConfidence() HashMap determinedMap = new HashMap (); HierarchyTree determinedGenusNode = train.getGenusNodebyIndex(4); HierarchyTree Enterobacteriales = determinedGenusNode.getParent().getParent(); HierarchyTree Gammaproteobacteria = Enterobacteriales.getParent(); HierarchyTree aNode = determinedGenusNode; while (aNode != null){ determinedMap.put(aNode, new RankAssignment(aNode, 0)); aNode = aNode.getParent(); } HierarchyTree bestNode = train.getGenusNodebyIndex(1); // Vibrio aClassifier.addConfidence(bestNode, determinedMap); assertEquals( determinedMap.get(determinedGenusNode).getConfidence(), 0.0f, 0.0001); //Enterobacter assertEquals( determinedMap.get(Enterobacteriales).getConfidence(), 0.0f, 0.0001); //Enterobacteriales assertEquals( determinedMap.get(Gammaproteobacteria).getConfidence(), 1.0f, 0.0001); //Gammaproteobacteria bestNode = train.getGenusNodebyIndex(4); //Enterobacter aClassifier.addConfidence(bestNode, determinedMap); assertEquals( determinedMap.get(determinedGenusNode).getConfidence(), 1.0f, 0.0001); //Enterobacter assertEquals( determinedMap.get(Enterobacteriales).getConfidence(), 1.0f, 0.0001); //Enterobacteriales assertEquals( determinedMap.get(Gammaproteobacteria).getConfidence(), 2.0f, 0.0001); //Gammaproteobacteria aClassifier.addConfidence(train.getGenusNodebyIndex(4), determinedMap); //Enterobacter aClassifier.addConfidence(train.getGenusNodebyIndex(0), determinedMap); //Clostridium assertEquals( determinedMap.get(determinedGenusNode).getConfidence(), 2.0f, 0.0001); //Enterobacter assertEquals( determinedMap.get(Enterobacteriales).getConfidence(), 2.0f, 0.0001); //Enterobacteriales assertEquals( determinedMap.get(Gammaproteobacteria).getConfidence(), 3.0f, 0.0001); //Gammaproteobacteria assertEquals( determinedMap.get(rootTree).getConfidence(), 4.0f, 0.0001); //Bacteria // end test addConfidence() // end of dstream = TrainingInfoTest.class.getResourceAsStream("/test/classifier/testQuerySeq.fasta"); in = new InputStreamReader( dstream ); BufferedReader infile = new BufferedReader(in); // test the first sequence String sequence = ""; infile.readLine(); sequence = infile.readLine(); sequence = sequence.toUpperCase(); ClassifierSequence pSeq = new ClassifierSequence("name", "title", sequence); ClassificationResult result = aClassifier.classify(pSeq); Iterator it = result.getAssignments().iterator(); RankAssignment classResult = (RankAssignment) it.next(); assertEquals(classResult.getBestClass().getName() , rootTree.getName()); assertEquals(classResult.getConfidence(), 1.0, 0.1); classResult = (RankAssignment) it.next(); assertEquals(classResult.getBestClass().getName() , "Proteobacteria"); it.next(); classResult = (RankAssignment) it.next(); assertEquals(classResult.getBestClass().getName() , "Rhizobiales"); it.next(); classResult = (RankAssignment) it.next(); assertEquals(classResult.getBestClass().getName() , "Rhizobium"); //displayResult(result); // end of test first sequence // test the second sequence infile.readLine(); sequence = infile.readLine(); sequence = sequence.toUpperCase(); pSeq = new ClassifierSequence("name", "title", sequence); result = aClassifier.classify(pSeq); it = result.getAssignments().iterator(); classResult = (RankAssignment) it.next(); assertEquals(classResult.getBestClass().getName() , rootTree.getName()); assertEquals(classResult.getConfidence(), 1.0, 0.1); classResult = (RankAssignment) it.next(); assertEquals(classResult.getBestClass().getName() , "Firmicutes"); it.next(); classResult = (RankAssignment) it.next(); assertEquals(classResult.getBestClass().getName() , "Clostridiales"); it.next(); classResult = (RankAssignment) it.next(); assertEquals(classResult.getBestClass().getName() , "Clostridium"); // end of test second sequence } private void displayResult(ClassificationResult result){ List assignments = result.getAssignments(); Iterator it = assignments.iterator(); while (it.hasNext()){ RankAssignment classResult = (RankAssignment) it.next(); System.err.print("\n" + classResult.getBestClass().getName() + " " + classResult.getConfidence()); } } }