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/**
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* Copyright (C) 2009 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.molecular;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertNotSame;
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import static org.junit.Assert.assertTrue;
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import java.net.URISyntaxException;
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import org.apache.log4j.Logger;
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import org.junit.Before;
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import org.junit.Test;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.test.unit.EntityTestBase;
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public class MolecularTest extends EntityTestBase {
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@SuppressWarnings("unused")
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private static Logger logger = Logger.getLogger(MolecularTest.class);
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private DnaSample dnaSample;
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private DefinedTerm marker;
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private PhylogeneticTree phyloTree;
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private Sequence seq;
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@Before
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public void setUp() throws Exception {
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dnaSample = DnaSample.NewInstance();
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seq = new Sequence();
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// seq.setBarcode(true);
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seq.getConsensusSequence().setString("ATTGCCATC");
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seq.setGeneticAccessionNumber("HM347273");
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// seq.setGenBankUri(URI.create("http://www.abc.de"));
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Media chromatogram = Media.NewInstance();
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chromatogram.putTitle(LanguageString.NewInstance("chromatogram", Language.ENGLISH()));
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// seq.addChromatogram(chromatogram);
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Sequence otherSeq = Sequence.NewInstance("CATCGAGTTGC");
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otherSeq.getBarcodeSequencePart().setString("ATTGCC");
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dnaSample.addSequence(seq);
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dnaSample.addSequence(otherSeq);
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marker = DefinedTerm.NewDnaMarkerInstance("Test", "test marker", null);
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phyloTree = PhylogeneticTree.NewInstance();
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phyloTree.addUsedSequences(seq);
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phyloTree.addUsedSequences(otherSeq);
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}
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/* ************************** TESTS **********************************************************/
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@Test
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public void testClone() throws URISyntaxException{
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PhylogeneticTree phyloTreeClone = phyloTree.clone();
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assertTrue(phyloTreeClone.getUsedSequences().size() == 2);
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assertNotSame(phyloTreeClone.getUsedSequences().iterator().next(), phyloTree.getUsedSequences().iterator().next());
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Sequence sequenceClone = seq.clone();
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// assertEquals(sequenceClone.getChromatograms().iterator().next().getAllTitles().get(0),seq.getChromatograms().iterator().next().getAllTitles().get(0));
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//
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// Iterator<Media> mediaIteratorClone = sequenceClone.getChromatograms().iterator();
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// Iterator<Media> mediaIterator = seq.getChromatograms().iterator();
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// Media test = (Media)mediaIterator.next();
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// LanguageString title = test.getTitle(Language.ENGLISH());
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// test = (Media)mediaIteratorClone.next();
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// LanguageString titleClone = test.getTitle(Language.ENGLISH());
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// assertEquals(title, titleClone);
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assertTrue (sequenceClone.getGeneticAccessionNumber().equals(seq.getGeneticAccessionNumber()));
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assertNotNull(sequenceClone.getGenBankUri());
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assertTrue (sequenceClone.getGenBankUri().equals(seq.getGenBankUri()));
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DnaSample dnaSampleClone = dnaSample.clone();
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Sequence[] seqArray = new Sequence[dnaSample.getSequences().size()];
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seqArray = dnaSample.getSequences().toArray(seqArray);
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Sequence[] seqArrayClone = dnaSampleClone.getSequences().toArray(seqArray);
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boolean testBool = true;
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for (Sequence seqTest: seqArray){
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if (testBool == false) {
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break;
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}
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testBool = false;
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for (Sequence seq: seqArrayClone){
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if (seq.equals(seqTest)) {
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testBool = true;
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break;
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} else {
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testBool = false;
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}
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}
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}
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assertTrue(testBool);
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}
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}
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