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 java.lang.reflect.Method;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.ManyToOne;

import javax.persistence.Transient;

import javax.validation.constraints.NotNull;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlAttribute;

import javax.xml.bind.annotation.XmlElement;

import javax.xml.bind.annotation.XmlIDREF;

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.annotations.Index;

import org.hibernate.annotations.Table;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.IndexedEmbedded;

import org.springframework.security.access.prepost.PreFilter;

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

import eu.etaxonomy.cdm.model.description.TaxonNameDescription;

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

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

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

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

import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;

import eu.etaxonomy.cdm.validation.Level2;

import eu.etaxonomy.cdm.validation.Level3;

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

/**

 * The upmost (abstract) class for the use of a {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} in a {@link eu.etaxonomy.cdm.model.reference.Reference reference}

 * or within a taxonomic view/treatment either as a {@link Taxon taxon}

 * ("accepted" respectively "correct" name) or as a (junior) {@link Synonym synonym}.

 * Within a taxonomic view/treatment or a reference a taxon name can be used

 * only in one of both described meanings. The reference using the taxon name

 * is generally cited with "sec." (secundum, sensu). For instance:

 * "<i>Juncus longirostris</i> Kuvaev sec. Kirschner, J. et al. 2002".

 * <P>

 * This class corresponds to: <ul>

 * <li> TaxonConcept according to the TDWG ontology

 * <li> TaxonConcept according to the TCS

 * </ul>

 * 

 * @author m.doering

 * @version 1.0

 * @created 08-Nov-2007 13:06:56

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

    "name",

    "sec",

    "doubtful",

    "appendedPhrase",

    "useNameCache"

})

@Entity

@Audited

//@PreFilter("hasPermission(filterObject, 'edit')")

@Table(appliesTo="TaxonBase", indexes = { @Index(name = "taxonBaseTitleCacheIndex", columnNames = { "titleCache" }) })

@TaxonNameCannotBeAcceptedAndSynonym(groups = Level3.class)

public abstract class TaxonBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableEntity<S> implements Cloneable {

	private static final long serialVersionUID = -3589185949928938529L;

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

	private static Method methodTaxonNameAddTaxonBase;

	static {

		try {

			methodTaxonNameAddTaxonBase = TaxonNameBase.class.getDeclaredMethod("addTaxonBase", TaxonBase.class);

			methodTaxonNameAddTaxonBase.setAccessible(true);

		} catch (Exception e) {

			logger.error(e);

			for(StackTraceElement ste : e.getStackTrace()) {

				logger.error(ste);

			}

		}

	}

	//The assignment to the Taxon or to the Synonym class is not definitive

    @XmlAttribute(name = "isDoubtful")

	private boolean doubtful;

    @XmlElement(name = "Name", required = true)

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

//	@JoinColumn(name="name_id")

	@IndexedEmbedded

	@Cascade(CascadeType.SAVE_UPDATE)

	@NotNull(groups = Level2.class)

	private TaxonNameBase name;

	// The concept reference

    @XmlElement(name = "Sec")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

    @IndexedEmbedded

    @Cascade(CascadeType.SAVE_UPDATE)

    @NotNull(groups = Level2.class)

	private Reference sec;

	@XmlElement(name = "AppendedPhrase")

	private String appendedPhrase;

	@XmlAttribute(name= "UseNameCache")

	private boolean useNameCache = false;

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

	/** 

	 * Class constructor: creates a new empty (abstract) taxon.

	 * 

	 * @see 	#TaxonBase(TaxonNameBase, Reference)

	 */

	protected TaxonBase(){

		super();

	}

	/** 

	 * Class constructor: creates a new (abstract) taxon with the

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

	 * using it.

	 * 

	 * @param  taxonNameBase	the taxon name used

	 * @param  sec				the reference using the taxon name

	 * @see    #TaxonBase()

	 */

	protected TaxonBase(TaxonNameBase taxonNameBase, Reference sec){

		super();

		if (taxonNameBase != null){

			this.invokeSetMethod(methodTaxonNameAddTaxonBase, taxonNameBase);  

		}

		this.setSec(sec);

	}

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

	/**

	 * Generates and returns the string with the full scientific name (including

	 * authorship) of the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used in <i>this</i>

	 * (abstract) taxon as well as the title of the {@link eu.etaxonomy.cdm.model.reference.Reference reference} using

	 * this taxon name. This string may be stored in the inherited

	 * {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache() titleCache} attribute.

	 * This method overrides the generic and inherited generateTitle() method

	 * from {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity IdentifiableEntity}.

	 *

	 * @return  the string with the full scientific name of the taxon name

	 *			and with the title of the reference involved in <i>this</i> (abstract) taxon

	 * @see  	eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()

	 * @see  	eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()

	 */

//	@Override

//	public String generateTitle() {

//		String title;

//		if (name != null && name.getTitleCache() != null){

//			title = name.getTitleCache() + " sec. ";

//			if (sec != null){

//				title += sec.getTitleCache();

//			}else{

//				title += "???";

//			}

//		}else{

//			title = this.toString();

//		}

//		return title;

//	}

	/** 

	 * Returns the {@link TaxonNameBase taxon name} used in <i>this</i> (abstract) taxon.

	 */

	public TaxonNameBase getName(){

		return this.name;

	}

	/* 

	 * @see #getName

	 */

	public void setName(TaxonNameBase name) {

		if(name != null) {

			name.getTaxonBases().add(this);

		}

		this.name = name;

	}

	/** 

	 * Returns the {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical group} of the

	 * {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used in <i>this</i> (abstract) taxon.

	 */

	@Transient

	public HomotypicalGroup getHomotypicGroup(){

		if (this.getName() == null){

			return null;

		}else{

			return this.getName().getHomotypicalGroup();

		}

	}

	/**

	 * Returns the boolean value indicating whether the assignment of <i>this</i>

	 * (abstract) taxon to the {@link Taxon Taxon} or to the {@link Synonym Synonym} class is definitive

	 * (false) or not (true). If this flag is set the use of <i>this</i> (abstract)

	 * taxon as an "accepted/correct" name or as a (junior) "synonym" might

	 * still change in the course of taxonomical working process. 

	 */

	public boolean isDoubtful(){

		return this.doubtful;

	}

	/**

	 * @see  #isDoubtful()

	 */

	public void setDoubtful(boolean doubtful){

		this.doubtful = doubtful;

	}

	/** 

	 * Returns the {@link eu.etaxonomy.cdm.model.reference.Reference reference} of <i>this</i> (abstract) taxon.

	 * This is the reference or the treatment using the {@link TaxonNameBase taxon name}

	 * in <i>this</i> (abstract) taxon.

	 */

	public Reference getSec() {

		return sec;

	}

	/**

	 * @see  #getSec()

	 */

	public void setSec(Reference sec) {

		this.sec = sec;

	}

	/**

	 * An appended phrase is a phrase that is added to the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name}

	 * 's title cache to be used just in this taxon. E.g. the phrase "sensu latu" may be added

	 * to the name to describe this taxon more precisely.

	 * If {@link #isUseNameCache()} 

	 * @return the appendedPhrase

	 */

	public String getAppendedPhrase() {

		return appendedPhrase;

	}

	/**

	 * @param appendedPhrase the appendedPhrase to set

	 */

	public void setAppendedPhrase(String appendedPhrase) {

		this.appendedPhrase = appendedPhrase;

	}

	/**

	 * @return the useNameCache

	 */

	public boolean isUseNameCache() {

		return useNameCache;

	}

	/**

	 * @param useNameCache the useNameCache to set

	 */

	public void setUseNameCache(boolean useNameCache) {

		this.useNameCache = useNameCache;

	}

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

	/** 

	 * Clones <i>this</i> taxon. This is a shortcut that enables to create

	 * a new instance with empty taxon name and sec reference.

	 *  

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

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

	 */

	@Override

	public Object clone() {

		TaxonBase result;

		try {

			result = (TaxonBase)super.clone();

			result.setSec(null);

			return result;

		} catch (CloneNotSupportedException e) {

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

			e.printStackTrace();

			return null;

		}

	}

}