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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 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.RemoteFeature;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.symbol.Location;
import org.biojava.bio.symbol.RangeLocation;
import org.biojava.bio.symbol.SymbolList;
/**
* Tests for SimpleAssembly. By dependancy, this also
* tests ProjectedFeatureHolder and SimpleAssembly.
*
* @author Thomas Down
* @author Matthew Pocock
* @since 1.3
*/
public class SubSequenceTest extends TestCase {
protected Sequence seq;
protected Sequence subseq;
public SubSequenceTest(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.source = "test1";
sft.annotation = Annotation.EMPTY_ANNOTATION;
sft.location = new RangeLocation(1, 3);
seq.createFeature(sft);
sft.type = "test2";
sft.location = new RangeLocation(10, 12);
seq.createFeature(sft);
sft.type = "test3";
sft.location = new RangeLocation(5, 13);
Feature choppedFeature = seq.createFeature(sft);
sft.type = "test4";
sft.location = new RangeLocation(5, 6);
choppedFeature.createFeature(sft);
sft.type = "test5";
sft.location = new RangeLocation(9, 10);
choppedFeature.createFeature(sft);
subseq = new SubSequence(seq, 8, 14);
}
public void testSymbols()
throws Exception {
assertTrue(compareSymbolList(subseq,
DNATools.createDNA("gttccat")));
}
public void testFeatureClipping()
throws Exception {
assertEquals("subseq.countFeatures()", 2, subseq.countFeatures());
}
public void testFeatureProjection()
throws Exception {
Feature f = (Feature) subseq.filter(new FeatureFilter.Not(new FeatureFilter.ByClass(RemoteFeature.class)), false).features().next();
Location fl = f.getLocation();
assertEquals("projection.getMin()", 3, fl.getMin());
assertEquals("projection.getMax()", 5, fl.getMax());
}
public void testRemoteFeature()
throws Exception {
FeatureHolder remotes = subseq.filter(new FeatureFilter.ByClass(RemoteFeature.class), false);
assertEquals("One remote feature: ", 1, remotes.countFeatures());
Feature f = (Feature) remotes.features().next();
assertTrue("Feature implements RemoteFeature", f instanceof RemoteFeature);
RemoteFeature rf = (RemoteFeature) f;
Location fl = rf.getLocation();
assertEquals("remote feature getMin()", 1, fl.getMin());
assertEquals("remote feature getMax()", 6, fl.getMax());
assertEquals("remote feature name", seq.getName(), rf.getRemoteFeature().getSequence().getName());
}
public void testRemoteChildFeature()
throws Exception {
FeatureHolder remotes = subseq.filter(new FeatureFilter.ByClass(RemoteFeature.class), false);
assertEquals("One remote feature: ", 1, remotes.countFeatures());
Feature f = (Feature) remotes.features().next();
assertTrue("Feature implements RemoteFeature", f instanceof RemoteFeature);
RemoteFeature rf = (RemoteFeature) f;
assertEquals("child remote features should be pruned - counting them", 1, rf.countFeatures());
Feature cf = (Feature) rf.features().next();
Location cfl = cf.getLocation();
assertEquals("cf.getMin()", 2, cfl.getMin());
assertEquals("cf.getMax()", 3, cfl.getMax());
}
public void testCreateOnSubsequence()
throws Exception {
Feature.Template templ = new Feature.Template();
templ.type = "create_on_subsequence";
templ.source = "test";
templ.location = new RangeLocation(2, 3);
templ.annotation = Annotation.EMPTY_ANNOTATION;
subseq.createFeature(templ);
Feature f = (Feature) seq.filter(new FeatureFilter.ByType("create_on_subsequence"), false).features().next();
Location fl = f.getLocation();
assertEquals("fl.getMin()", 9, fl.getMin());
assertEquals("fl.getMax()", 10, fl.getMax());
}
public void testCreateOnSubsequenceFeature()
throws Exception {
Feature.Template templ = new Feature.Template();
templ.type = "create_on_subsequence_feature";
templ.source = "test";
templ.location = new RangeLocation(3, 4);
templ.annotation = Annotation.EMPTY_ANNOTATION;
Feature subf = (Feature) subseq.filter(new FeatureFilter.Not(new FeatureFilter.ByClass(RemoteFeature.class)), false).features().next();
subf.createFeature(templ);
Feature f = (Feature) seq.filter(new FeatureFilter.ByType("create_on_subsequence_feature"), true).features().next();
Location fl = f.getLocation();
assertEquals(fl.getMin(), 10);
assertEquals(fl.getMax(), 11);
}
public void testRemoveFeatureFromSubsequence()
throws Exception {
FeatureHolder fh = subseq.filter(new FeatureFilter.Not(new FeatureFilter.ByClass(RemoteFeature.class)), false);
assertEquals(fh.countFeatures(), 1);
Feature f = (Feature) fh.features().next();
subseq.removeFeature(f);
fh = subseq.filter(new FeatureFilter.Not(new FeatureFilter.ByClass(RemoteFeature.class)), false);
assertEquals(fh.countFeatures(), 0);
}
private boolean compareSymbolList(SymbolList sl1, SymbolList sl2) {
if (sl1.length() != sl2.length()) {
return false;
}
Iterator si1 = sl1.iterator();
Iterator si2 = sl2.iterator();
while (si1.hasNext()) {
if (!(si1.next() == si2.next())) {
return false;
}
}
return true;
}
}
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