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/*
* RawSequenceParserTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 27, 2002, 6:48 PM
*/
package edu.msu.cme.rdp.classifier.train;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;
/**
* A test class for RawSequenceParser.
* @author wangqion
*/
public class RawSequenceParserTest extends TestCase {
public RawSequenceParserTest(java.lang.String testName) {
super(testName);
}
public static void main(java.lang.String[] args) {
junit.textui.TestRunner.run(suite());
}
/**
* Tests RawSequenceParser next() method.
*/
public void testNext() throws FileNotFoundException, IOException{
System.out.println("testNext()");
InputStream aStream = System.class.getResourceAsStream("/test/classifier/testSeqParser.fasta");
LineageSequenceParser parser = new LineageSequenceParser(aStream);
boolean next = parser.hasNext();
assertTrue(next);
// test the first sequence
LineageSequence pSeq = parser.next();
String name = "X53199";
assertEquals(name, pSeq.getSeqName());
assertEquals("AZOSPIRILLUM_GROUP", (String) pSeq.getAncestors().get(4));
assertEquals("PROTEOBACTERIA", (String) pSeq.getAncestors().get(2));
assertEquals("GAEA", (String) pSeq.getAncestors().get(0) );
//test the last sequence
parser.next();
pSeq = parser.next();
name = "AB002485";
assertEquals(name, pSeq.getSeqName());
assertEquals("M.RRR_SUBGROUP", (String) pSeq.getAncestors().get(5) );
assertEquals("TTTT_GROUP", (String) pSeq.getAncestors().get(4) );
assertEquals("BELTA_SUBDIVISION", (String) pSeq.getAncestors().get(3) );
assertEquals("GAEA", (String) pSeq.getAncestors().get(0) );
String sequence = "AAAAUAtttAGUCCCCCCCCUG";
assertEquals(sequence, pSeq.getSeqString());
assertTrue(!parser.hasNext());
}
public static Test suite() {
TestSuite suite = new TestSuite(RawSequenceParserTest.class);
return suite;
}
}
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