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.taxon;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.ManyToOne;

import javax.persistence.Transient;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlElement;

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.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.ContainedIn;

import org.hibernate.search.annotations.Indexed;

import org.springframework.beans.factory.annotation.Configurable;

import eu.etaxonomy.cdm.model.name.HomotypicalGroup;

import eu.etaxonomy.cdm.model.name.TaxonNameBase;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.strategy.cache.taxon.ITaxonCacheStrategy;

import eu.etaxonomy.cdm.strategy.cache.taxon.TaxonBaseDefaultCacheStrategy;

import eu.etaxonomy.cdm.validation.Level3;

import eu.etaxonomy.cdm.validation.annotation.HomotypicSynonymsShouldBelongToGroup;

/**

 * The class for synonyms: these are {@link TaxonBase taxa} the {@link name.TaxonNameBase taxon names}

 * of which are not used by the {@link TaxonBase#getSec() reference} to designate a real

 * taxon but are mentioned as taxon names that were oder are used by some other

 * unspecified references to designate (at least to some extent) the same

 * particular real taxon. Synonyms that are involved in no

 * {@link SynonymRelationship synonym relationship} are actually meaningless.<BR>

 * Splitting taxa in "accepted/correct" and "synonyms"

 * makes it easier to handle particular relationships between

 * ("accepted/correct") {@link Taxon taxa} on the one hand and between ("synonym") taxa

 * and ("accepted/correct") taxa on the other.

 *

 * @author m.doering

 * @version 1.0

 * @created 08-Nov-2007 13:06:55

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

    "acceptedTaxon",

    "type",

    "proParte",

    "partial"

})

@XmlRootElement(name = "Synonym")

@Entity

@Indexed(index = "eu.etaxonomy.cdm.model.taxon.TaxonBase")

@Audited

@Configurable

@HomotypicSynonymsShouldBelongToGroup(groups = Level3.class)

public class Synonym extends TaxonBase<ITaxonCacheStrategy<Synonym>> {

	private static final long serialVersionUID = -454067515022159757L;

	@SuppressWarnings("unused")

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

    @XmlElement(name = "acceptedTaxon")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

    @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})

    @ContainedIn

//  @NotEmpty(groups = Level2.class,message="{eu.etaxonomy.cdm.model.taxon.Synonym.noOrphanedSynonyms.message}")

//    @NotNull(groups = Level2.class)

    private Taxon acceptedTaxon;

    @XmlElement(name = "IsProParte")

    private boolean proParte = false;

    @XmlElement(name = "IsPartial")

    private boolean partial = false;

    @XmlElement(name = "Type")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch=FetchType.EAGER)

    private SynonymRelationshipType type;

//************************************* FACTORY ****************************/

    /**

     * Creates a new synonym instance with

     * the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used and the {@link eu.etaxonomy.cdm.model.reference.Reference reference}

     * using it as a synonym and not as an ("accepted/correct") {@link Taxon taxon}.

     *

     * @param  taxonNameBase    the taxon name used

     * @param  sec              the reference using the taxon name

     * @see                     #Synonym(TaxonNameBase, Reference)

     */

    public static Synonym NewInstance(TaxonNameBase taxonName, Reference sec){

        Synonym result = new Synonym(taxonName, sec, null);

        return result;

    }

    public static Synonym NewInstance(TaxonNameBase taxonName, Reference sec, String secDetail){

        Synonym result = new Synonym(taxonName, sec, secDetail);

        return result;

    }

// ************* CONSTRUCTORS *************/

	/**

	 * Class constructor: creates a new empty synonym instance.

	 *

	 * @see 	#Synonym(TaxonNameBase, Reference)

	 */

	//TODO should be private, but still produces Spring init errors

	public Synonym(){

		this.cacheStrategy = new TaxonBaseDefaultCacheStrategy<Synonym>();

	}

	private Synonym(TaxonNameBase taxonNameBase, Reference sec, String secDetail){

		super(taxonNameBase, sec, secDetail);

		this.cacheStrategy = new TaxonBaseDefaultCacheStrategy<Synonym>();

	}

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

	/**

	 * Returns the "accepted/valid" {@link Taxon taxon}

	 *

	 */

	public Taxon getAcceptedTaxon() {

		return this.acceptedTaxon;

	}

    /**

     * @param acceptedTaxon the acceptedTaxon to set

     */

    protected void setAcceptedTaxon(Taxon acceptedTaxon) {

        if (acceptedTaxon == null){

            Taxon oldTaxon = this.acceptedTaxon;

            this.acceptedTaxon = null;

            oldTaxon.removeSynonym(this);

        }else{

            if (this.acceptedTaxon != null){

                this.acceptedTaxon.removeSynonym(this, false);

            }

            this.acceptedTaxon = acceptedTaxon;

            this.acceptedTaxon.addSynonym(this);

            checkHomotypic();

        }

    }

    /**

     * Returns "true" if the proParte flag is set.

     * This indicates that the {@link name.TaxonNameBase taxon name} used as a

     * {@link Synonym synonym} designated originally a real taxon which later has

     * been split. In this case the synonym is therefore the synonym of at least

     * two different ("accepted/valid") {@link Taxon taxa}.

     */

    public boolean isProParte() {

        return proParte;

    }

    /**

     * @see #isProParte()

     */

    public void setProParte(boolean proParte) {

        this.proParte = proParte;

    }

    /**

     * Returns "true" if the ProParte flag is set.

     * This indicates that the {@link name.TaxonNameBase taxon name} used as <code>this</code>

     * {@link Synonym synonym} designated originally a real taxon which later has

     * been lumped together with another one. In this case the

     * ("accepted/valid") {@link Taxon taxon} has therefore at least

     * two different synonyms (for the two lumped real taxa).

     */

    public boolean isPartial() {

        return partial;

    }

    /**

     * @see #isPartial()

     */

    public void setPartial(boolean partial) {

        this.partial = partial;

    }

    public SynonymRelationshipType getType() {

        return type;

    }

    public void setType(SynonymRelationshipType type) {

        this.type = type;

        checkHomotypic();

    }

//***************** METHODS **************************/

	/**

	 * Returns true if <i>this</i> is a synonym of the given taxon.

	 *

	 * @param taxon	the taxon to check synonym for

	 * @return	true if <i>this</i> is a synonm of the given taxon

	 *

	 * @see #getAcceptedTaxon()

	 */

	@Transient

	public boolean isSynonymOf(Taxon taxon){

		return taxon != null && taxon.equals(this.acceptedTaxon);

	}

	@Override

    @Transient

	public boolean isOrphaned() {

	    return this.acceptedTaxon == null || this.acceptedTaxon.isOrphaned();

	}

	/**

	 * Replaces ALL accepted taxa of this synonym by the new accepted taxon.

	 * The citation information (citation /microcitation) of the synonym relationship

	 * is kept.

	 * @param newAcceptedTaxon

	 * 			the new accepted taxon

	 * @param relType

	 * 			if not <code>null</code> the relationship type is changed to relType

	 * @param copyCitationInfo

	 * 			if true the citation and the microcitation of relationship

	 * 			is not changed.

	 * @param citation

	 * 			if copyCitationInfo is <code>false</code> this citation is set

	 * 			to the synonym relationship.

	 * @param microCitation

	 * 			if copyCitationInfo is <code>false</code> this micro citation is set

	 * 			to the synonym relationship.

	 * @param acceptedTaxon

	 */

	public void replaceAcceptedTaxon(Taxon newAcceptedTaxon, SynonymRelationshipType relType) {

//		Taxon oldAcceptedTaxon = this.getAcceptedTaxon();

//

//		oldAcceptedTaxon.removeSynonym(this, false);

		this.setAcceptedTaxon(newAcceptedTaxon);

//		newAcceptedTaxon.getSynonyms().add(this);x;

		if (relType != null){

		    this.setType(relType);

		}

	}

	public void replaceAcceptedTaxonAndSecundum(Taxon newAcceptedTaxon, SynonymRelationshipType relType, Reference sec, String microSec) {

	    replaceAcceptedTaxon(newAcceptedTaxon, relType);

	    this.setSec(sec);

        this.setSecMicroReference(microSec);

	}

    /**

     * Checks if the synonym relationship type is homotypic. If it is

     * the name of <code>this</code> synonym is added to the {@link HomotypicalGroup

     * homotypic group} of the {@link Taxon accepted taxon}.

     */

    private void checkHomotypic() {

        if (type != null && type.equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())

                && acceptedTaxon != null && acceptedTaxon.getName() != null){

                acceptedTaxon.getName().getHomotypicalGroup().addTypifiedName(this.getName());

        }

    }

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

	@Override

	public Object clone() {

		Synonym result;

		result = (Synonym)super.clone();

		//no changes to accepted taxon, type, partial, proParte

		return result;

	}

}