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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.project;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.FeatureFilter;
import org.biojava.bio.seq.FilterUtils;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.StrandedFeature;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.seq.projection.ProjectedFeatureHolder;
import org.biojava.bio.seq.projection.ReparentContext;
import org.biojava.bio.seq.projection.TranslateFlipContext;
import org.biojava.bio.symbol.RangeLocation;
import org.biojava.utils.ChangeListener;
import org.biojava.utils.ChangeType;
import org.biojava.utils.ChangeVetoException;
/**
* Tests for ProjectedFeatureHolder
*
* @author Thomas Down
* @author Matthew Pocock
* @since 1.3
*/
public class ProjectedFeatureHolderTest extends TestCase
{
public ProjectedFeatureHolderTest(String name) {
super(name);
}
public void testReparentContext()
throws Exception
{
Sequence seq = new SimpleSequence(
DNATools.createDNA("gattaca"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
Sequence seq2 = new SimpleSequence(
DNATools.createDNA("-------"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
Feature.Template template = new Feature.Template();
template.type = "test";
template.source = "foo";
template.location = new RangeLocation(2, 4);
template.annotation = Annotation.EMPTY_ANNOTATION;
Feature origFeat = seq.createFeature(template);
ProjectedFeatureHolder pfh = new ProjectedFeatureHolder(
new ReparentContext(seq2, seq));
assertEquals("Same size", pfh.countFeatures(), seq.countFeatures());
Feature projFeat = (Feature) pfh.features().next();
assertEquals("getSource()", origFeat.getSource(), projFeat.getSource());
assertEquals("getType()", origFeat.getType(), projFeat.getType());
assertEquals("getLocation()", origFeat.getLocation(), projFeat.getLocation());
assertEquals("origFeat.getParent()", origFeat.getParent(), seq);
assertEquals("projFeat.getParent()", projFeat.getParent(), seq2);
}
public void testReparentContext_create()
throws Exception
{
Sequence seq = new SimpleSequence(
DNATools.createDNA("gattaca"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
Sequence seq2 = new SimpleSequence(
DNATools.createDNA("-------"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
Feature.Template template = new Feature.Template();
template.type = "test";
template.source = "foo";
template.location = new RangeLocation(2, 4);
template.annotation = Annotation.EMPTY_ANNOTATION;
ProjectedFeatureHolder pfh = new ProjectedFeatureHolder(
new ReparentContext(seq2, seq));
Feature projFeat = pfh.createFeature(template);
Feature origFeat = (Feature) seq.features().next();
assertEquals("Same size", pfh.countFeatures(), seq.countFeatures());
assertEquals("getSource()", origFeat.getSource(), projFeat.getSource());
assertEquals("getType()", origFeat.getType(), projFeat.getType());
assertEquals("getLocation()", origFeat.getLocation(), projFeat.getLocation());
assertEquals("origFeat.getParent()", origFeat.getParent(), seq);
assertEquals("projFeat.getParent()", projFeat.getParent(), seq2);
}
public void testTranslateFlipContext_translateOnly()
throws Exception {
Sequence seq = new SimpleSequence(
DNATools.createDNA("gattaca"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
Sequence seq2 = new SimpleSequence(
DNATools.createDNA("-------"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
StrandedFeature.Template template = new StrandedFeature.Template();
template.type = "test";
template.source = "foo";
template.location = new RangeLocation(2, 4);
template.annotation = Annotation.EMPTY_ANNOTATION;
template.strand = StrandedFeature.NEGATIVE;
StrandedFeature origFeat = (StrandedFeature) seq.createFeature(template);
ProjectedFeatureHolder pfh = new ProjectedFeatureHolder(
new TranslateFlipContext(seq2, seq, 3, false));
assertEquals("Same size", pfh.countFeatures(), seq.countFeatures());
StrandedFeature projFeat = (StrandedFeature) pfh.features().next();
assertEquals("getSource()", origFeat.getSource(), projFeat.getSource());
assertEquals("getType()", origFeat.getType(), projFeat.getType());
assertEquals("getLocation()", origFeat.getLocation().translate(3), projFeat.getLocation());
assertEquals("getStrand()", origFeat.getStrand(), projFeat.getStrand());
assertEquals("projFeat.getParent()", projFeat.getParent(), seq2);
assertEquals("pfh.filter(5,7).size() == 1",
1,
pfh.filter(FilterUtils.containedByLocation(projFeat.getLocation())).countFeatures());
assertTrue("pfh.filter(5,7).contains(projFeat)",
pfh.filter(FilterUtils.containedByLocation(projFeat.getLocation())).containsFeature(projFeat));
assertEquals("projFeat.filter(POSITIVE).size() == 1",
1,
pfh.filter(FilterUtils.byStrand(origFeat.getStrand())).countFeatures());
}
public void testTranslateFlipContext_translateAndFlip()
throws Exception {
Sequence seq = new SimpleSequence(
DNATools.createDNA("gattaca"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
Sequence seq2 = new SimpleSequence(
DNATools.createDNA("-------"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
StrandedFeature.Template template = new StrandedFeature.Template();
template.type = "test";
template.source = "foo";
template.location = new RangeLocation(2, 3);
template.annotation = Annotation.EMPTY_ANNOTATION;
template.strand = StrandedFeature.NEGATIVE;
StrandedFeature origFeat = (StrandedFeature) seq.createFeature(template);
ProjectedFeatureHolder pfh = new ProjectedFeatureHolder(
new TranslateFlipContext(seq2, seq, seq.length() + 1, true));
assertEquals("Same size", pfh.countFeatures(), seq.countFeatures());
StrandedFeature projFeat = (StrandedFeature) pfh.features().next();
assertEquals("getSource()", origFeat.getSource(), projFeat.getSource());
assertEquals("getType()", origFeat.getType(), projFeat.getType());
assertEquals("getLocation()",
new RangeLocation(5,6),
projFeat.getLocation());
assertEquals("getStrand()", StrandedFeature.POSITIVE, projFeat.getStrand());
assertEquals("projFeat.getParent()", projFeat.getParent(), seq2);
assertEquals("pfh.filter(5,6).size() == 1",
1,
pfh.filter(FilterUtils.containedByLocation(projFeat.getLocation())).countFeatures());
assertTrue("pfh.filter(5,6).contains(projFeat)",
pfh.filter(FilterUtils.containedByLocation(projFeat.getLocation())).containsFeature(projFeat));
assertEquals("projFeat.filter(NEGATIVE).size() == 0",
0,
pfh.filter(FilterUtils.byStrand(StrandedFeature.NEGATIVE)).countFeatures());
assertEquals("projFeat.filter(POSITIVE).size() == 1",
1,
pfh.filter(FilterUtils.byStrand(StrandedFeature.POSITIVE)).countFeatures());
}
public void testTranslateFlipContext_translateAndFlip_create()
throws Exception {
Sequence seq = new SimpleSequence(
DNATools.createDNA("gattaca"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
Sequence seq2 = new SimpleSequence(
DNATools.createDNA("-------"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
StrandedFeature.Template template = new StrandedFeature.Template();
template.type = "test";
template.source = "foo";
template.location = new RangeLocation(5, 6);
template.annotation = Annotation.EMPTY_ANNOTATION;
template.strand = StrandedFeature.POSITIVE;
ProjectedFeatureHolder pfh = new ProjectedFeatureHolder(
new TranslateFlipContext(seq2, seq, seq.length() + 1, true));
StrandedFeature projFeat = (StrandedFeature) pfh.createFeature(template);
Feature origFeat = (StrandedFeature) seq.features().next();
assertEquals("Same size", pfh.countFeatures(), seq.countFeatures());
assertEquals("getSource()", origFeat.getSource(), projFeat.getSource());
assertEquals("getType()", origFeat.getType(), projFeat.getType());
assertEquals("getLocation()",
new RangeLocation(5,6),
projFeat.getLocation());
assertEquals("getStrand()", StrandedFeature.POSITIVE, projFeat.getStrand());
assertEquals("projFeat.getParent()", projFeat.getParent(), seq2);
assertEquals("pfh.filter(5,6).size() == 1",
1,
pfh.filter(FilterUtils.containedByLocation(projFeat.getLocation())).countFeatures());
assertTrue("pfh.filter(5,6).contains(projFeat)",
pfh.filter(FilterUtils.containedByLocation(projFeat.getLocation())).containsFeature(projFeat));
assertEquals("projFeat.filter(NEGATIVE).size() == 0",
0,
pfh.filter(FilterUtils.byStrand(StrandedFeature.NEGATIVE)).countFeatures());
assertEquals("projFeat.filter(POSITIVE).size() == 1",
1,
pfh.filter(FilterUtils.byStrand(StrandedFeature.POSITIVE)).countFeatures());
}
public void testFeatureChangeEvent()
throws Exception
{
Sequence seq = new SimpleSequence(
DNATools.createDNA("gattaca"),
"test",
"test",
Annotation.EMPTY_ANNOTATION
);
Feature.Template template = new Feature.Template();
template.type = "test";
template.source = "foo";
template.location = new RangeLocation(2, 4);
template.annotation = Annotation.EMPTY_ANNOTATION;
Feature seqFeature = seq.createFeature(template);
ProjectedFeatureHolder pfh = new ProjectedFeatureHolder(
new TranslateFlipContext(seq, seq, 7, true));
Feature pfhFeature = (Feature) pfh.filter(new FeatureFilter.ByType("test")).features().next();
pfhFeature.addChangeListener(ChangeListener.ALWAYS_VETO, ChangeType.UNKNOWN);
boolean vetoed = false;
try {
seqFeature.setLocation(new RangeLocation(1, 3));
} catch (ChangeVetoException cve) {
vetoed = true;
}
assertTrue(vetoed);
pfhFeature.removeChangeListener(ChangeListener.ALWAYS_VETO, ChangeType.UNKNOWN);
seqFeature.setLocation(new RangeLocation(1, 3));
}
}
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