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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;
import java.util.Iterator;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.seq.impl.SimpleSequence;
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
* @since 1.2
*/
public class NewSimpleAssemblyTest extends TestCase
{
protected Sequence fragment1;
protected Sequence fragment2;
protected Sequence fragment3;
protected Sequence fragment4;
protected Sequence fragment5;
protected Sequence fragment6;
protected Sequence assembly;
public NewSimpleAssemblyTest(String name) {
super(name);
}
protected void setUp() throws Exception {
fragment1 = new SimpleSequence(DNATools.createDNA("aacgta"),
"fragment1",
"fragment1",
Annotation.EMPTY_ANNOTATION);
fragment2 = new SimpleSequence(DNATools.createDNA("ttgatgc"),
"fragment2",
"fragment2",
Annotation.EMPTY_ANNOTATION);
fragment3 = new SimpleSequence(DNATools.createDNA("aagctt"),
"fragment3",
"fragment3",
Annotation.EMPTY_ANNOTATION);
fragment4 = new SimpleSequence(DNATools.createDNA("ttagat"),
"fragment4",
"fragment4",
Annotation.EMPTY_ANNOTATION);
fragment5 = new SimpleSequence(DNATools.createDNA("ggatcc"),
"fragment5",
"fragment5",
Annotation.EMPTY_ANNOTATION);
fragment6 = new SimpleSequence(DNATools.createDNA("atctgg"),
"fragment6",
"fragment6",
Annotation.EMPTY_ANNOTATION);
StrandedFeature.Template sft = new StrandedFeature.Template();
sft.type = "project_test";
sft.source = "test";
sft.annotation = Annotation.EMPTY_ANNOTATION;
sft.strand = StrandedFeature.NEGATIVE;
sft.location = new RangeLocation(1, 3);
fragment2.createFeature(sft);
assembly = new NewSimpleAssembly(31, "test", "test");
ComponentFeature.Template templ = new ComponentFeature.Template();
templ.type = "component";
templ.source = "test";
templ.annotation = Annotation.EMPTY_ANNOTATION;
templ.strand = StrandedFeature.POSITIVE;
templ.location = new RangeLocation(1, 4);
templ.componentSequence = fragment1;
templ.componentLocation = new RangeLocation(2, 5);
assembly.createFeature(templ);
templ.strand = StrandedFeature.NEGATIVE;
templ.location = new RangeLocation(6, 12);
templ.componentSequence = fragment2;
templ.componentLocation = new RangeLocation(1, fragment2.length());
assembly.createFeature(templ);
templ.strand = StrandedFeature.POSITIVE;
templ.location = new RangeLocation(14, 19);
templ.componentSequence = fragment3;
templ.componentLocation = new RangeLocation(1, fragment3.length());
assembly.createFeature(templ);
templ.strand = StrandedFeature.POSITIVE;
templ.location = new RangeLocation(18, 23);
templ.componentSequence = fragment4;
templ.componentLocation = new RangeLocation(1, fragment4.length());
assembly.createFeature(templ);
templ.strand = StrandedFeature.POSITIVE;
templ.location = new RangeLocation(26, 31);
templ.componentSequence = fragment5;
templ.componentLocation = new RangeLocation(1, fragment5.length());
assembly.createFeature(templ);
templ.strand = StrandedFeature.POSITIVE;
templ.location = new RangeLocation(22, 27);
templ.componentSequence = fragment6;
templ.componentLocation = new RangeLocation(1, fragment6.length());
assembly.createFeature(templ);
}
public void testAssembledSymbols()
throws Exception
{
assertTrue(compareSymbolList(assembly,
DNATools.createDNA("acgtngcatcaanaagcttagatctggatcc")));
assertTrue(compareSymbolList(assembly.subList(1,4),
DNATools.createDNA("acgt")));
assertTrue(compareSymbolList(assembly.subList(1,5),
DNATools.createDNA("acgtn")));
assertTrue(compareSymbolList(assembly.subList(5,5),
DNATools.createDNA("n")));
assertTrue(compareSymbolList(assembly.subList(11, 12),
DNATools.createDNA("aa")));
}
public void testProjectedFeatures()
throws Exception
{
FeatureHolder f = assembly.filter(new FeatureFilter.ByType("project_test"), true);
assertEquals(f.countFeatures(), 1);
Feature pf = (Feature) f.features().next();
Location pfl = pf.getLocation();
assertEquals(pfl.getMin(), 10);
assertEquals(pfl.getMax(), 12);
}
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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