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package org.biojava.bio.seq.impl;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.SmallAnnotation;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceTools;
import org.biojava.bio.symbol.DummySymbolList;
import org.biojava.bio.symbol.LocationTools;
import org.biojava.ontology.OntoTools;
/**
*
*
* @author Matthew Pocock
*/
public class ViewSequenceTest
extends TestCase
{
public void testEquivalentOriginals()
throws Throwable
{
Sequence original = SequenceTools.createSequence(new DummySymbolList(DNATools.getDNA(), 1000),
"dummy",
"dummy",
Annotation.EMPTY_ANNOTATION);
Feature.Template tplt = new Feature.Template();
tplt.annotation = new SmallAnnotation();
tplt.annotation.setProperty("geneID", "braca1");
tplt.location = LocationTools.makeLocation(1,2);
tplt.type = "synth";
tplt.typeTerm = OntoTools.ANY;
tplt.source = "my head";
tplt.sourceTerm = OntoTools.ANY;
Feature made = original.createFeature(tplt);
ViewSequence view = new ViewSequence(original);
Feature viewed = (Feature) view.features().next();
Feature.Template copy = viewed.makeTemplate();
System.out.println("template: " + tplt);
System.out.println("orignal: " + made.makeTemplate());
System.out.println("copy: " + copy);
assertEquals("templates are equal", tplt, copy);
assertEquals("made are equal", tplt, made.makeTemplate());
assertEquals("both are equal", made.makeTemplate(), copy);
}
public void testEquivalentViews()
throws Throwable
{
Sequence original = SequenceTools.createSequence(new DummySymbolList(DNATools.getDNA(), 1000),
"dummy",
"dummy",
Annotation.EMPTY_ANNOTATION);
Feature.Template tplt = new Feature.Template();
tplt.annotation = new SmallAnnotation();
tplt.annotation.setProperty("geneID", "braca1");
tplt.location = LocationTools.makeLocation(1, 2);
tplt.type = "synth";
tplt.typeTerm = OntoTools.ANY;
tplt.source = "my head";
tplt.sourceTerm = OntoTools.ANY;
ViewSequence view = new ViewSequence(original);
Feature made = view.createFeature(tplt);
Feature viewed = (Feature) view.features().next();
Feature.Template copy = viewed.makeTemplate();
System.out.println("template: " + tplt);
System.out.println("orignal: " + made.makeTemplate());
System.out.println("copy: " + copy);
assertEquals("templates are equal", tplt, copy);
assertEquals("made are equal", tplt, made.makeTemplate());
assertEquals("both are equal", made.makeTemplate(), copy);
}
}
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