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/*
* 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<HierarchyTree, RankAssignment> determinedMap = new HashMap <HierarchyTree, RankAssignment>();
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());
}
}
}
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