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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
/*
* LinearAlphabetIndexTest.java
* JUnit based test
*
* Created on July 10, 2007, 3:19 PM
*/
package org.biojava.bio.symbol;
import junit.framework.*;
import java.lang.ref.Reference;
import java.lang.ref.WeakReference;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import org.biojava.bio.Annotation;
import org.biojava.bio.BioError;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.DNATools;
import org.biojava.utils.AbstractChangeable;
import org.biojava.utils.ChangeEvent;
import org.biojava.utils.ChangeForwarder;
import org.biojava.utils.ChangeListener;
import org.biojava.utils.ChangeSupport;
import org.biojava.utils.ChangeType;
import org.biojava.utils.ChangeVetoException;
/**
*
* @author Mark Schreiber
*/
public class LinearAlphabetIndexTest extends TestCase {
FiniteAlphabet DNA = DNATools.getDNA();
public LinearAlphabetIndexTest(String testName) {
super(testName);
}
public static Test suite() {
TestSuite suite = new TestSuite(LinearAlphabetIndexTest.class);
return suite;
}
/**
* Test of getAlphabet method, of class org.biojava.bio.symbol.LinearAlphabetIndex.
*/
public void testGetAlphabet() {
System.out.println("getAlphabet");
LinearAlphabetIndex instance = new LinearAlphabetIndex(DNA);
FiniteAlphabet expResult = DNA;
FiniteAlphabet result = instance.getAlphabet();
assertEquals(expResult, result);
}
/**
* Test of symbolForIndex method, of class org.biojava.bio.symbol.LinearAlphabetIndex.
*/
public void testSymbolForIndex() {
System.out.println("symbolForIndex");
LinearAlphabetIndex instance = new LinearAlphabetIndex(DNA);
for(int i = 0; i < DNA.size(); i++){
Symbol result = instance.symbolForIndex(i);
assertNotNull(result);
assertTrue(DNA.contains(result));
}
//unfortunately we can't test the order of the index as it is not guarenteed
//to be the same on all JVMs
}
/**
* Test of indexForSymbol method, of class org.biojava.bio.symbol.LinearAlphabetIndex.
*/
public void testIndexForSymbol() throws Exception {
System.out.println("indexForSymbol");
for(Iterator<Symbol> i = DNA.iterator(); i.hasNext();){
Symbol s = i.next();
LinearAlphabetIndex instance = new LinearAlphabetIndex(DNA);
int result = instance.indexForSymbol(s);
assertTrue(result >= 0);
}
}
/**
* Tests that the index rebuilds when it's size changes
*/
public void testBugFix2330() throws Exception{
SimpleAlphabet alpha = new SimpleAlphabet();
LinearAlphabetIndex index = new LinearAlphabetIndex(alpha);
Symbol s0 = AlphabetManager.createSymbol("s0");
alpha.addSymbol(s0);
assertNotNull(index.symbolForIndex(0));
assertTrue(index.symbolForIndex(0) == s0);
assertTrue(index.indexForSymbol(s0) == 0);
alpha.removeSymbol(s0);
try{
index.symbolForIndex(0);
fail("Expected exception, there should be no Symbol at index 0");
}catch (Exception ex){}
}
}
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