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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/
*/
package org.biojava.bio.symbol;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.HashSet;
import java.util.Set;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.program.phred.PhredTools;
import org.biojava.bio.seq.DNATools;
/**
* <p>Title: AlphabetSerializationTest</p>
* <p>Description: Tests Alphabets after Serialization</p>
* <p>Copyright: Copyright (c) 2002</p>
* <p>Company: AgResearch</p>
* @author Mark Schreiber
* @version 1.0
*/
public class AlphabetSerializationTest extends TestCase {
IntegerAlphabet integer;
IntegerAlphabet.SubIntegerAlphabet subint;
DoubleAlphabet.SubDoubleAlphabet subdoub;
DoubleAlphabet doub;
FiniteAlphabet phred;
FiniteAlphabet dna;
SimpleAlphabet custom;
public AlphabetSerializationTest(String name){
super(name);
}
protected void setUp() throws java.lang.Exception {
super.setUp();
integer = IntegerAlphabet.getInstance();
subint = IntegerAlphabet.getSubAlphabet(20,99);
doub = DoubleAlphabet.getInstance();
subdoub = DoubleAlphabet.getSubAlphabet(20.0,99.0);
phred = PhredTools.getPhredAlphabet();
dna = DNATools.getDNA();
//make a custom alphabet
AtomicSymbol s0 = AlphabetManager.createSymbol("foo",Annotation.EMPTY_ANNOTATION);
AtomicSymbol s1 = AlphabetManager.createSymbol("goo",Annotation.EMPTY_ANNOTATION);
AtomicSymbol s2 = AlphabetManager.createSymbol("hoo",Annotation.EMPTY_ANNOTATION);
Set set = new HashSet(3);
set.add(s0); set.add(s1); set.add(s2);
custom = new SimpleAlphabet(set,"custom_test");
}
protected void tearDown() throws java.lang.Exception {
super.tearDown();
}
public void testIntegerSerialization()throws Exception{
IntegerAlphabet integer2 = (IntegerAlphabet)serialize(integer);
assertTrue(integer == integer2);
// static ref
//assertTrue(integer.getInstance() == integer2.getInstance());
assertTrue(integer.equals(integer2));
assertTrue(integer.getSymbol(12) == integer2.getSymbol(12));
assertTrue(integer.getSymbol(12).equals(integer2.getSymbol(12)));
assertTrue(!(integer.getSymbol(12).equals(integer2.getSymbol(13))));
//test tokenization
/*
int[] ints = {25,26,27,28,29};
SymbolList sl = integer.fromArray(ints);
SymbolList sl2 = integer2.fromArray(ints);
sl=sl==null?null:sl;//trick
sl2=sl2==null?null:sl2;//trick
// assertEquals(sl.seqString(),sl2.seqString());
* tests all wonky as mixing static and non static stuff
*/
}
public void testDoubleSerialization()throws Exception{
DoubleAlphabet doub2 = (DoubleAlphabet)serialize(doub);
assertTrue(doub == doub2);
// static methods are invalid from non static context
//assertTrue(doub.getInstance() == doub2.getInstance());
assertTrue(doub.equals(doub2));
assertTrue(doub.getSymbol(12.0) == doub2.getSymbol(12.0));
assertTrue(doub.getSymbol(12.0).equals(doub2.getSymbol(12.0)));
assertTrue(!(doub.getSymbol(12.0).equals(doub2.getSymbol(13.0))));
}
public void testSubInt()throws Exception{
IntegerAlphabet.SubIntegerAlphabet subint2 =
(IntegerAlphabet.SubIntegerAlphabet)serialize(subint);
assertTrue(subint == subint2);
assertTrue(subint.equals(subint2));
assertTrue(integer.getSymbol(80)== subint2.getSymbol(80));
assertTrue(subint.getSymbol(80)== subint2.getSymbol(80));
assertTrue(subint.getSymbol(80).equals(subint2.getSymbol(80)));
assertTrue(subint.getSymbol(81)!= subint2.getSymbol(80));
assertTrue(subint.size() == subint2.size());
}
public void testSubDouble()throws Exception{
DoubleAlphabet.SubDoubleAlphabet subdoub2 =
(DoubleAlphabet.SubDoubleAlphabet)serialize(subdoub);
assertTrue(subdoub == subdoub2);
assertTrue(subdoub.equals(subdoub2));
assertTrue(doub.getSymbol(80.0)== subdoub2.getSymbol(80.0));
assertTrue(subdoub.getSymbol(80.3)== subdoub2.getSymbol(80.3));
assertTrue(subdoub.getSymbol(80.3).equals(subdoub2.getSymbol(80.3)));
assertTrue(subdoub.getSymbol(81.9)!= subdoub2.getSymbol(80.0));
}
public void testDNASerialization()throws Exception{
FiniteAlphabet dna2 = (FiniteAlphabet)serialize(dna);
assertTrue(dna == dna2);
assertTrue(dna.size() == dna2.size());
assertTrue(equalSymbols(dna, dna2));
//test tokenization
assertTrue(dna.getTokenization("token").equals(dna2.getTokenization("token")));
}
public void testPhredSerialization()throws Exception{
//this tests a specific instance of a compound alphabet
FiniteAlphabet phred2 = (FiniteAlphabet)serialize(phred);
assertTrue(phred == phred2);
assertTrue(phred.size() == phred2.size());
assertTrue(equalSymbols(phred, phred2));
}
public void testCustom() throws Exception{
SimpleAlphabet custom2 = (SimpleAlphabet)custom;
assertTrue(custom == custom2);
assertTrue(custom.size() == custom.size());
assertTrue(equalSymbols(custom, custom2));
}
private Object serialize(Object alpha) throws Exception{
ByteArrayOutputStream os = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(os);
oos.writeObject(alpha);
oos.flush();
oos.close();
ObjectInputStream ois = new ObjectInputStream(
new ByteArrayInputStream(os.toByteArray()));
Object o = ois.readObject();
ois.close();
return o;
}
private boolean equalSymbols(FiniteAlphabet alpha, FiniteAlphabet alpha2)
{
AlphabetIndex index1 = AlphabetManager.getAlphabetIndex(alpha);
AlphabetIndex index2 = AlphabetManager.getAlphabetIndex(alpha2);
int aSize = alpha.size();
for (int i = 0; i < aSize; i++)
{
if (index1.symbolForIndex(i) != index2.symbolForIndex(i))
return false;
}
return true;
}
}
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