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/*
* TreeFileParserTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 11, 2003, 12:07 PM
*/
package edu.msu.cme.rdp.classifier.rrnaclassifier;
import edu.msu.cme.rdp.classifier.HierarchyTree;
import edu.msu.cme.rdp.classifier.utils.HierarchyVersion;
import edu.msu.cme.rdp.classifier.io.TreeFileParser;
import java.io.*;
import junit.framework.*;
import java.util.Iterator;
/**
* A test class for TreeFileParser.
* @author wangqion
*/
public class TreeFileParserTest extends TestCase {
public TreeFileParserTest(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(TreeFileParserTest.class);
return suite;
}
/** Test of parseTreeFile method, of class classification.TrainingFileParser. */
public void testParseTreeFile() throws Exception{
System.out.println("testParseTreeFile");
TreeFileParser parser = new TreeFileParser();
InputStream dstream = TreeFileParserTest.class.getResourceAsStream("/test/classifier/testTreeFile.xml");
HierarchyVersion hVersion = null;
Reader in = new InputStreamReader( dstream );
HierarchyTree root = parser.createTree(in, null);
assertEquals(root.getName(), "BACTERIA");
assertEquals(root.getLeaveCount(), 4123);
assertEquals(root.getSizeofSubclasses(), 3);
//displayTrainingTree(root);
Iterator i = root.getSubclasses().iterator();
while (i.hasNext()){
HierarchyTree child = (HierarchyTree)i.next();
if (child.getTaxid() == 1247){ //PLANCTOMYCETES
assertEquals(child.getName(), "PLANCTOMYCETES");
assertEquals(child.getRank(), "PHYLUM");
assertEquals(child.getLeaveCount(), 11);
assertEquals(child.getSizeofSubclasses(), 1);
}
}
}
private void displayTrainingTree(HierarchyTree root) throws IOException{
System.err.print(" name=" + root.getName() + " leaveCount=" +
root.getLeaveCount() + " genusIndex=" + root.getGenusIndex() + " taxid=" + root.getTaxid() );
if (root.getParent() != null){
System.err.print(" parentTaxid=" + root.getParent().getTaxid() + " rank="+ root.getRank() +"\n");
}else {
System.err.print( " rank="+ root.getRank() +"\n");
}
Iterator i = root.getSubclasses().iterator();
while (i.hasNext()){
displayTrainingTree( (HierarchyTree)i.next() );
}
}
}
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