EDIT

/**

* Copyright (C) 2007 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 java.util.HashSet;

import java.util.Set;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.JoinColumn;

import javax.persistence.JoinTable;

import javax.persistence.ManyToMany;

import javax.validation.constraints.NotNull;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlElement;

import javax.xml.bind.annotation.XmlElementWrapper;

import javax.xml.bind.annotation.XmlIDREF;

import javax.xml.bind.annotation.XmlRootElement;

import javax.xml.bind.annotation.XmlSchemaType;

import javax.xml.bind.annotation.XmlType;

import org.apache.log4j.Logger;

import org.hibernate.envers.Audited;

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

/**

 * "A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the

 * inferred evolutionary relationships among various biological species or other entities

 * based upon similarities and differences in their physical and/or genetic characteristics.

 * The taxa joined together in the tree are implied to have descended from a common ancestor."

 * (Wikipedia).

 * <BR> In the CDM we currently store phylogenetic trees only as media. This may change in future.

 *

 * @author m.doering

 * @created 08-Nov-2007

 */

@XmlAccessorType(XmlAccessType.FIELD)

@XmlType(name = "PhylogeneticTree", propOrder = {

	"usedSequences"

})

@XmlRootElement(name = "PhylogeneticTree")

@Entity

//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search

//@Indexed(index = "eu.etaxonomy.cdm.model.media.Media")

@Audited

public class PhylogeneticTree extends Media implements Cloneable{

	private static final long serialVersionUID = -7020182117362324067L;

	private static final  Logger logger = Logger.getLogger(PhylogeneticTree.class);

	@XmlElementWrapper(name = "UsedSequences")

	@XmlElement(name = "UsedSequence")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToMany(fetch = FetchType.LAZY)

	//preliminary  #5369

    @JoinTable(

            joinColumns = @JoinColumn( name="Media_id")

    )

    @NotNull

	private Set<Sequence> usedSequences = new HashSet<Sequence>();

//********************** Factory Method **********************************/

    /**

     * Factory method

     * @return

     */

    public static PhylogeneticTree NewInstance(){

        return new PhylogeneticTree();

    }

//***************** Constructor ****************************/

    private PhylogeneticTree(){

    	super();

    }

// ********************** GETTER / SETTER **************************/

	public Set<Sequence> getUsedSequences() {

		if(usedSequences == null) {

			this.usedSequences = new HashSet<Sequence>();

		}

		return usedSequences;

	}

	public void addUsedSequences(Sequence usedSequence) {

		this.usedSequences.add(usedSequence);

	}

	public void removeUsedSequences(Sequence usedSequence) {

		this.usedSequences.remove(usedSequence);

	}

//*********** CLONE **********************************/

	/**

	 * Clones <i>this</i> phylogenetic tree. This is a shortcut that enables to

	 * create a new instance that differs only slightly from <i>this</i> phylogenetic tree

	 * by modifying only some of the attributes.<BR>

	 * This method overrides the clone method from {@link Media Media}.

	 *

	 * @see eu.etaxonomy.cdm.model.media.Media#clone()

	 * @see java.lang.Object#clone()

	 */

	@Override

	public Object clone(){

		PhylogeneticTree result;

		try{

			result= (PhylogeneticTree) super.clone();

			result.usedSequences = new HashSet<Sequence>();

			for (Sequence seq: this.usedSequences){

				result.addUsedSequences((Sequence)seq.clone());

			}

			return result;

		}catch (CloneNotSupportedException e) {

			logger.warn("Object does not implement cloneable");

			e.printStackTrace();

			return null;

		}

	}

}