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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.util.Iterator;
import junit.framework.TestCase;
import org.biojava.bio.SimpleAnnotation;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.FeatureFilter;
import org.biojava.bio.seq.FeatureHolder;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.symbol.LocationTools;
/**
* Abstract test class for <code>SequenceDB</code> implementations. To
* use this class, you should only have to create a subclass that
* implements the <code>getSequenceDB</code> method.
*
* @author Len Trigg
*/
public abstract class AbstractSequenceDBTest extends TestCase {
protected SequenceDB mSequenceDB = null;
public AbstractSequenceDBTest(String name) {
super(name);
}
/**
* Subclasses override this to supply the particular SequenceDB
* implementation to test.
*/
protected abstract SequenceDB getSequenceDB() throws Exception;
public void setUp() throws Exception {
mSequenceDB = getSequenceDB();
}
public void tearDown() throws Exception {
mSequenceDB = null;
}
// This is a simple test that BioSQLSequenceDB failed.
public void testAddFeature() throws Exception {
String name = "dna_1";
assertTrue(!mSequenceDB.ids().contains(name));
mSequenceDB.addSequence(DNATools.createDNASequence("atgctgatgatgatg", name));
assertTrue(mSequenceDB.ids().contains(name));
Sequence seq = mSequenceDB.getSequence(name);
// Uncommenting this line makes BioSQLSequenceDB pass the test
// assertTrue(seq.countFeatures() == 0);
Feature.Template template = new Feature.Template();
template.annotation = new SimpleAnnotation();
template.location = LocationTools.makeLocation(10, 15);
template.type = "noTS";
template.source = "asource";
seq.createFeature(template);
assertTrue(seq.countFeatures() == 1);
}
// This is a simple test that BioSQLSequenceDB failed.
public void testAddRemoveSequence() throws Exception {
String name = "dna_1";
assertTrue(!mSequenceDB.ids().contains(name));
mSequenceDB.addSequence(DNATools.createDNASequence("atgctgatgatgatg", name));
assertTrue(mSequenceDB.ids().contains(name));
Sequence seq = mSequenceDB.getSequence(name);
seq = seq==null?null:seq;//trick
mSequenceDB.removeSequence(name);
assertTrue(!mSequenceDB.ids().contains(name));
}
// A test that does a bit of feature editing
public void testEditFeatures() throws Exception {
String name = "dna_1";
Sequence seq = DNATools.createDNASequence("atgctgatgatgatg", name);
assertTrue(!mSequenceDB.ids().contains(name));
mSequenceDB.addSequence(seq);
assertTrue(mSequenceDB.ids().contains(name));
seq = mSequenceDB.getSequence(name);
String sourceType = "asource";
String annoTag = "anno";
String annoVal = "123456";
String anno2Tag = "blah";
String anno2Val = "blahblah";
// Create some features
Feature.Template template = new Feature.Template();
template.annotation = new SimpleAnnotation();
template.location = LocationTools.makeLocation(10, 15);
template.type = "noANNO";
template.source = sourceType;
Feature noANNO = seq.createFeature(template);
assertTrue(!noANNO.getAnnotation().containsProperty(annoTag));
assertTrue(seq.countFeatures() == 1);
// Re-use the template object
template.type = "yesANNO";
template.annotation.setProperty(annoTag, annoVal);
Feature yesANNO = seq.createFeature(template);
assertTrue(yesANNO.getAnnotation().containsProperty(annoTag));
assertTrue("createFeature should copy rather than referencing annotation.",
!noANNO.getAnnotation().containsProperty(annoTag));
assertTrue(seq.countFeatures() == 2);
// Check the features are both there
Iterator i = seq.features();
assertTrue(i.hasNext());
Feature feature = (Feature) i.next();
boolean yesFound = feature.getAnnotation().containsProperty(annoTag);
if (yesFound) {
assertTrue(feature.getType().equals("yesANNO"));
} else {
assertTrue(feature.getType().equals("noANNO"));
}
assertTrue(i.hasNext());
feature = (Feature) i.next();
if (yesFound) {
assertTrue(feature.getType().equals("noANNO"));
assertTrue(!feature.getAnnotation().containsProperty(annoTag));
} else {
assertTrue(feature.getType().equals("yesANNO"));
assertTrue(feature.getAnnotation().containsProperty(annoTag));
}
assertTrue(!i.hasNext());
//new org.biojava.bio.seq.io.GenbankFormat().writeSequence(seq, System.err);
// Delete the noANNO feature
FeatureHolder fh = seq.filter(new FeatureFilter.And(new FeatureFilter.BySource(sourceType),
new FeatureFilter.Not(new FeatureFilter.ByAnnotation(annoTag, annoVal))));
i = fh.features();
assertTrue(i.hasNext());
feature = (Feature) i.next();
assertTrue(!feature.getAnnotation().containsProperty(annoTag));
seq.removeFeature(feature);
//new org.biojava.bio.seq.io.GenbankFormat().writeSequence(seq, System.err);
// Check the yesANNO feature is still there.
i = seq.features();
assertTrue(i.hasNext());
feature = (Feature) i.next();
assertTrue(feature.getAnnotation().containsProperty(annoTag));
// Remove the annoTag annotation.
// First add another annotation. This triggered a bug in biosql binding.
feature.getAnnotation().setProperty(anno2Tag, anno2Val);
feature.getAnnotation().removeProperty(annoTag);
assertTrue(!feature.getAnnotation().containsProperty(annoTag));
//new org.biojava.bio.seq.io.GenbankFormat().writeSequence(seq, System.err);
}
}
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