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.api.service;

import java.util.Collection;

import java.util.List;

import java.util.Map;

import java.util.UUID;

//import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;

import eu.etaxonomy.cdm.api.service.pager.Pager;

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.taxon.Synonym;

import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;

import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;

import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;

import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;

public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{

	/**

	 * FIXME candidate for harmonization? 

	 */

	public abstract TaxonBase getTaxonByUuid(UUID uuid);

	/**

	 * FIXME candidate for harmonization? 

	 * save a taxon and return its UUID

	 */

	public abstract UUID saveTaxon(TaxonBase taxon);

	/**

	 * FIXME candidate for harmonization?

	 *  save a taxon and return its UUID

	 */

	//public abstract UUID saveTaxon(TaxonBase taxon, TransactionStatus txStatus);

	/**

	 * FIXME candidate for harmonization?

	 * save a collection of taxa and return its UUID

	 */

	public abstract Map<UUID, ? extends TaxonBase> saveTaxonAll(Collection<? extends TaxonBase> taxonCollection);

	/**

	 * FIXME candidate for harmonization?

	 * delete a taxon and return its UUID

	 */

	public abstract UUID removeTaxon(TaxonBase taxon);

	/**

	 * Computes all taxon bases.

	 * FIXME could substitute with list(Synonym.class, limit, start)

	 * @param limit

	 * @param start

	 * @return

	 */

	public abstract List<Synonym> getAllSynonyms(int limit, int start);

	/**

	 * Computes all taxon bases.

	 * FIXME could substitute with list(Taxon.class, limit,start)

	 * @param limit

	 * @param start

	 * @return

	 */

	public abstract List<Taxon> getAllTaxa(int limit, int start);

	/**

	 * Computes all taxon bases.

	 * FIXME could substitute with list(limit,start) from superclass

	 * @param limit

	 * @param start

	 * @return

	 */

	public abstract List<TaxonBase> getAllTaxonBases(int limit, int start);

	/**

	 * Computes all Taxon instances that do not have a taxonomic parent and has at least one child.

	 * @param sec The concept reference that the taxon belongs to

	 * @return The List<Taxon> of root taxa.

	 */

	public abstract List<Taxon> getRootTaxa(ReferenceBase sec);

	/**

	 * Computes all Taxon instances that do not have a taxonomic parent.

	 * @param sec The concept reference that the taxon belongs to

	 * 

	 * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.

	 * @return The List<Taxon> of root taxa.

	 */

	public abstract List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, boolean onlyWithChildren);

	/**

	 * Computes all Taxon instances that do not have a taxonomic parent.

	 * @param sec The concept reference that the taxon belongs to

	 * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.

	 * @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are

	 * the misapplied name are not returned.<Br>Default: true.

	 * @return The List<Taxon> of root taxa.

	 */

	public abstract List<Taxon> getRootTaxa(ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications);

	/**

	 * Computes all relationships.

	 * @param limit

	 * @param start

	 * @return

	 */

    public abstract List<RelationshipBase> getAllRelationships(int limit, int start);

	/**

	 * Returns TaxonRelationshipType vocabulary

	 * @return

	 */

	public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary();

	/** */

	public abstract List<TaxonBase> searchTaxaByName(String name, ReferenceBase sec);

	public Synonym makeTaxonSynonym (Taxon oldTaxon, Taxon newAcceptedTaxon, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference);

	/**

	 * Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied) 

	 * where the supplied taxon is relatedTo.

	 * 

	 * @param taxon The taxon that is relatedTo

	 * @param type The type of TaxonRelationship (can be null)

	 * @param pageSize The maximum number of relationships returned (can be null for all relationships)

	 * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

	 * @return a Pager of TaxonRelationship instances

	 */

	public Pager<TaxonRelationship> getRelatedTaxa(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber);

	/**

	 * Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) 

	 * where the supplied taxon is relatedTo.

	 * 

	 * @param taxon The taxon that is relatedTo

	 * @param type The type of SynonymRelationship (can be null)

	 * @param pageSize The maximum number of relationships returned (can be null for all relationships)

	 * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

	 * @return a Pager of SynonymRelationship instances

	 */

	public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber);

	/**

	 * Returns a List of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false) where the 

	 * taxonBase.name.nameCache property matches the String queryString (as interpreted by the Lucene QueryParser)

	 * 

	 * @param queryString

	 * @param accepted

	 * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)

	 * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

	 * @return a Pager Taxon instances

	 * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>

	 */

	public Pager<TaxonBase> searchTaxa(String queryString, Boolean accepted, Integer pageSize, Integer pageNumber);

	/**

	 * Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false) where the

	 * taxon.name properties match the parameters passed.

	 * 

	 * @param accepted Whether the taxon is accepted (true) a synonym (false), or either (null)

	 * @param uninomial 

	 * @param infragenericEpithet

	 * @param specificEpithet

	 * @param infraspecificEpithet

	 * @param rank

	 * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)

	 * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)

	 * @return a Pager of TaxonBase instances

	 */

	public Pager<TaxonBase> findTaxaByName(Boolean accepted, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);

	/**

	 * Returns a list of IdentifiableEntity instances (in particular, TaxonNameBase and TaxonBase instances)

	 * that match the properties specified in the configurator.

	 * @param configurator

	 * @return

	 */

	public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator);

}