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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.seq.db;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.NoSuchElementException;
import java.util.Set;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.SequenceTools;
import org.biojava.bio.symbol.SymbolList;
import org.biojava.utils.ChangeVetoException;
/**
* Tests for HashSequenceDB
* @author Mark Schreiber
*/
public class TestHashSequenceDB extends TestCase {
private HashSequenceDB hashSequenceDB = null;
private HashSequenceDB hashSequenceDB2 = null;
private Sequence seq = null;
public TestHashSequenceDB(String name) {
super(name);
}
protected void setUp() throws Exception {
super.setUp();
hashSequenceDB = new HashSequenceDB();
hashSequenceDB2 = new HashSequenceDB(new IDMaker.ByURN(), "seqDB");
SymbolList syms = ProteinTools.createProtein("hgfds");
Sequence seq = SequenceTools.createSequence(syms, "urn:biojava:bar", "bar",
Annotation.EMPTY_ANNOTATION);
hashSequenceDB.addSequence(seq);
hashSequenceDB2.addSequence(seq);
}
protected void tearDown() throws Exception {
hashSequenceDB = null;
super.tearDown();
}
public void testAddSequence1() throws ChangeVetoException {
String id = "myseq";
hashSequenceDB.addSequence(id, seq);
hashSequenceDB2.addSequence(id, seq);
}
public void testGetName() {
String expectedReturn = "seqDB";
String actualReturn = hashSequenceDB2.getName();
assertEquals("return value", expectedReturn, actualReturn);
}
public void testGetSequence() throws IllegalIDException {
String id = "bar";
String urn = "urn:biojava:bar";
Sequence s = hashSequenceDB.getSequence(id);
if(s == null)
fail("no sequence returned for :"+id);
assertTrue(s.getName().equals (id));
s = hashSequenceDB2.getSequence(urn);
if(s == null)
fail("no sequence returned for :"+urn);
assertTrue(s.getURN().equals(urn));
}
public void testIds() {
Set ids = hashSequenceDB.ids();
assertNotNull(ids);
assertTrue(ids.contains("bar"));
assertTrue(ids.size() == 1);
ids = hashSequenceDB2.ids();
assertNotNull(ids);
assertTrue(ids.contains("urn:biojava:bar"));
assertTrue(ids.size() == 1);
}
public void testRemoveSequence() throws BioException, ChangeVetoException {
String id = "bar";
String urn = "urn:biojava:bar";
hashSequenceDB.removeSequence(id);
hashSequenceDB2.removeSequence(urn);
assertFalse(hashSequenceDB.ids().contains(id));
assertFalse(hashSequenceDB.ids().contains(urn));
assertTrue(hashSequenceDB.ids().size() == 0);
assertTrue(hashSequenceDB2.ids().size() == 0);
}
public void testSequenceIterator() {
SequenceIterator iter = hashSequenceDB.sequenceIterator();
assertNotNull(iter);
Sequence s = null;
try {
s = iter.nextSequence();
} catch (BioException ex) {
fail(ex.getMessage());
} catch (NoSuchElementException ex) {
ex.getMessage();
}
assertNotNull(s);
//should be no more
assertFalse(iter.hasNext());
}
public void testSerialization() throws IOException, ClassNotFoundException{
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(baos);
oos.writeObject(hashSequenceDB);
oos.writeObject(hashSequenceDB2);
oos.flush();
ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
ObjectInputStream ois = new ObjectInputStream(bais);
HashSequenceDB seqdb = (HashSequenceDB)ois.readObject();
HashSequenceDB seqdb2 = (HashSequenceDB)ois.readObject();
bais.close();
ois.close();
oos.close();
baos.close();
Sequence s = null;
try {
assertNotNull(seqdb);
s = seqdb.getSequence("bar");
assertNotNull(s);
} catch (IllegalIDException ex) {
fail(ex.getMessage());
}
try {
assertNotNull(seqdb2);
s = seqdb2.getSequence("urn:biojava:bar");
assertNotNull(s);
} catch (IllegalIDException ex1) {
fail(ex1.getMessage());
}
}
}
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