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/*
* RawHierarchyTreeTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 25, 2002, 3:59 PM
*/
package edu.msu.cme.rdp.classifier.train;
import junit.framework.*;
import java.io.*;
/**
* A test class for RawHierarchyTree.
* @author wangqion
*/
public class RawHierarchyTreeTest extends TestCase {
public RawHierarchyTreeTest(java.lang.String testName) {
super(testName);
}
public static void main(java.lang.String[] args) {
junit.textui.TestRunner.run(suite());
}
/**
* Tests the RawHierarchyTree initWordOccurrence() methods.
*/
public void testInitWordOccurrence() throws FileNotFoundException, IOException {
System.out.println("testInitWordOccurrence()");
float[] wordPriorArr = new float[65536];
Taxonomy rootTaxon = new Taxonomy(1, "Fam1", 0, 0, "FAMILY");
RawHierarchyTree root = new RawHierarchyTree("ROOT", null, rootTaxon);
Taxonomy c1Taxon = new Taxonomy(2, "G1", 1, 1, "GENUS");
RawHierarchyTree c1 = new RawHierarchyTree("child1", root, c1Taxon);
Taxonomy c2Taxon = new Taxonomy(3, "G2", 1, 1, "GENUS");
RawHierarchyTree c2 = new RawHierarchyTree("child2", root, c2Taxon);
LineageSequenceParser parser = new LineageSequenceParser(System.class.getResourceAsStream("/test/classifier/testTrainingSet.fasta"));
// test the first sequence
LineageSequence pSeq = parser.next();
c1.initWordOccurrence(pSeq, wordPriorArr);
pSeq = parser.next();
c1.initWordOccurrence(pSeq, wordPriorArr);
pSeq = parser.next();
c2.initWordOccurrence(pSeq, wordPriorArr);
assertEquals(2, c1.getLeaveCount());
assertEquals(1, c2.getLeaveCount());
assertEquals(3, root.getLeaveCount());
assertEquals(2, root.getSizeofSubclasses());
assertEquals(1, c1.getWordOccurrence(0)); //AAAAAAAA
assertEquals(2, c1.getWordOccurrence(2)); //AAAAAAAG
assertEquals(1, c1.getWordOccurrence(65535)); //CCCCCCCC
assertEquals(1, c2.getWordOccurrence(64)); //AAAAUAAA
assertEquals(0, c2.getWordOccurrence(0));
assertEquals(c1.getParent().getName(), root.getName());
for (int i = 0; i < wordPriorArr.length; i++) {
if (wordPriorArr[i] != 0) {
// System.err.println("word: " + i + " Ccc : " + wordPriorArr[i] );
}
wordPriorArr[i] = (float) ((wordPriorArr[i] + 0.5) / (3 + 1));
if (i == 0) {
assertEquals(wordPriorArr[i], 0.375, 0.5);
}
}
}
public static Test suite() {
TestSuite suite = new TestSuite(RawHierarchyTreeTest.class);
return suite;
}
}
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