EDIT

/**

* Copyright (C) 2009 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.model.molecular;

import static org.junit.Assert.assertNotNull;

import static org.junit.Assert.assertNotSame;

import static org.junit.Assert.assertTrue;

import java.net.URISyntaxException;

import org.apache.log4j.Logger;

import org.junit.Before;

import org.junit.BeforeClass;

import org.junit.Test;

import eu.etaxonomy.cdm.model.common.Language;

import eu.etaxonomy.cdm.model.common.LanguageString;

import eu.etaxonomy.cdm.model.media.Media;

import eu.etaxonomy.cdm.model.term.DefaultTermInitializer;

import eu.etaxonomy.cdm.model.term.DefinedTerm;

public class MolecularTest {

	@SuppressWarnings("unused")

	private static Logger logger = Logger.getLogger(MolecularTest.class);

	private DnaSample dnaSample;

	private DefinedTerm marker;

	private PhylogeneticTree phyloTree;

	private Sequence seq;

	@BeforeClass

	public static void setUpBeforeClass() {

		DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();

		vocabularyStore.initialize();

	}

	@Before

	public void setUp() throws Exception {

		dnaSample = DnaSample.NewInstance();

		seq = new Sequence();

//		seq.setBarcode(true);

		seq.getConsensusSequence().setString("ATTGCCATC");

		seq.setGeneticAccessionNumber("HM347273");

//		seq.setGenBankUri(URI.create("http://www.abc.de"));

		Media chromatogram = Media.NewInstance();

		chromatogram.putTitle(LanguageString.NewInstance("chromatogram", Language.ENGLISH()));

//		seq.addChromatogram(chromatogram);

		Sequence otherSeq = Sequence.NewInstance("CATCGAGTTGC");

		otherSeq.getBarcodeSequencePart().setString("ATTGCC");

		dnaSample.addSequence(seq);

		dnaSample.addSequence(otherSeq);

		marker = DefinedTerm.NewDnaMarkerInstance("Test", "test marker", null);

		phyloTree = PhylogeneticTree.NewInstance();

		phyloTree.addUsedSequences(seq);

		phyloTree.addUsedSequences(otherSeq);

	}

/* ************************** TESTS **********************************************************/

	@Test

	public void testClone() throws URISyntaxException{

		PhylogeneticTree phyloTreeClone = phyloTree.clone();

		assertTrue(phyloTreeClone.getUsedSequences().size() == 2);

		assertNotSame(phyloTreeClone.getUsedSequences().iterator().next(), phyloTree.getUsedSequences().iterator().next());

		Sequence sequenceClone = seq.clone();

//		assertEquals(sequenceClone.getChromatograms().iterator().next().getAllTitles().get(0),seq.getChromatograms().iterator().next().getAllTitles().get(0));

//

//		Iterator<Media> mediaIteratorClone = sequenceClone.getChromatograms().iterator();

//		Iterator<Media> mediaIterator = seq.getChromatograms().iterator();

//		Media test = (Media)mediaIterator.next();

//		LanguageString title = test.getTitle(Language.ENGLISH());

//		test = (Media)mediaIteratorClone.next();

//		LanguageString titleClone = test.getTitle(Language.ENGLISH());

//		assertEquals(title, titleClone);

		assertTrue (sequenceClone.getGeneticAccessionNumber().equals(seq.getGeneticAccessionNumber()));

		assertNotNull(sequenceClone.getGenBankUri());

		assertTrue (sequenceClone.getGenBankUri().equals(seq.getGenBankUri()));

		DnaSample dnaSampleClone = dnaSample.clone();

		Sequence[] seqArray = new Sequence[dnaSample.getSequences().size()];

		seqArray = dnaSample.getSequences().toArray(seqArray);

		Sequence[] seqArrayClone = dnaSampleClone.getSequences().toArray(seqArray);

		boolean testBool = true;

		for (Sequence seqTest: seqArray){

			if (testBool == false) {

                break;

            }

			testBool = false;

			for (Sequence seq: seqArrayClone){

				if (seq.equals(seqTest)) {

					testBool = true;

					break;

				} else {

                    testBool = false;

                }

			}

		}

		assertTrue(testBool);

	}

}