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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.impl;
import java.util.Iterator;
import java.util.SortedSet;
import java.util.TreeSet;
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.FeatureHolder;
import org.biojava.bio.seq.GappedSequence;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.symbol.Location;
import org.biojava.bio.symbol.RangeLocation;
/**
* Test for GappedSequence. By dependancy, this also tests
* some functionality from GappedSymbolList.
*
* @author Thomas Down
* @since 1.3
*/
public class GappedSequenceTest extends TestCase
{
protected Sequence seq;
protected GappedSequence gappedSeq;
public GappedSequenceTest(String name) {
super(name);
}
protected void setUp() throws Exception {
seq = new SimpleSequence(DNATools.createDNA("aacgtaggttccatgc"),
"fragment1",
"fragment1",
Annotation.EMPTY_ANNOTATION);
Feature.Template sft = new Feature.Template();
sft.type = "normal";
sft.source = "test";
sft.annotation = Annotation.EMPTY_ANNOTATION;
sft.location = new RangeLocation(8, 10);
seq.createFeature(sft);
sft.type = "split";
sft.location = new RangeLocation(2, 10);
seq.createFeature(sft);
gappedSeq = new SimpleGappedSequence(seq);
gappedSeq.addGapsInSource(5, 2);
}
/**
* Ensure that a location wholly contained by a contiguous
* block in the gapped view is simply translated to the
* appropriate position
*/
public void testNonSplit()
throws Exception
{
FeatureHolder fh = gappedSeq.filter(new FeatureFilter.ByType("normal"), false);
Feature f = (Feature) fh.features().next();
Location fl = f.getLocation();
assertTrue(fl.isContiguous());
assertEquals(fl.getMin(), 10);
assertEquals(fl.getMax(), 12);
}
/**
* Ensure that a location straddling a gap is projected
* to a non-contiguous location, with appropriate
* boundaries.
*/
public void testSplit()
throws Exception
{
FeatureHolder fh = gappedSeq.filter(new FeatureFilter.ByType("split"), false);
Feature f = (Feature) fh.features().next();
Location fl = f.getLocation();
assertTrue(!fl.isContiguous());
assertEquals(fl.getMin(), 2);
assertEquals(fl.getMax(), 12);
Iterator bi = fl.blockIterator();
SortedSet sb = new TreeSet(Location.naturalOrder);
while (bi.hasNext()) {
sb.add(bi.next());
}
assertEquals(sb.size(), 2);
bi = sb.iterator();
Location block = (Location) bi.next();
assertEquals(block.getMin(), 2);
assertEquals(block.getMax(), 4);
block = (Location) bi.next();
assertEquals(block.getMin(), 7);
assertEquals(block.getMax(), 12);
}
public void testRemoveRemoteFeature()
throws Exception
{
seq = new SimpleSequence(DNATools.createDNA("aacgtaggttccatgc"),
"fragment1",
"fragment1",
Annotation.EMPTY_ANNOTATION);
Feature.Template sft = new Feature.Template();
sft.type = "normal";
sft.source = "test";
sft.annotation = Annotation.EMPTY_ANNOTATION;
sft.location = new RangeLocation(8, 10);
seq.createFeature(sft);
sft.type = "split";
sft.location = new RangeLocation(2, 10);
seq.createFeature(sft);
gappedSeq = new SimpleGappedSequence(seq);
gappedSeq.addGapsInSource(5, 2);
Feature split = (Feature) gappedSeq.filter(new FeatureFilter.ByType("split")).features().next();
assertEquals(seq.countFeatures(), 2);
gappedSeq.removeFeature(split);
assertEquals(seq.countFeatures(), 1);
}
public void testRemoveLocalFeature()
throws Exception
{
gappedSeq = new SimpleGappedSequence(seq);
gappedSeq.addGapsInSource(5, 2);
Feature.Template sft = new Feature.Template();
sft.type = "local";
sft.source = "test";
sft.annotation = Annotation.EMPTY_ANNOTATION;
sft.location = new RangeLocation(8, 10);
seq.createFeature(sft);
Feature local = (Feature) gappedSeq.filter(new FeatureFilter.ByType("local")).features().next();
assertEquals(gappedSeq.countFeatures(), 3);
gappedSeq.removeFeature(local);
assertEquals(gappedSeq.countFeatures(), 2);
}
}
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