root/trunk/cdmlib/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java

/**
* 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.OneToMany;
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.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 org.hibernate.search.annotations.Indexed;

import eu.etaxonomy.cdm.model.occurrence.Collection;
import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
import eu.etaxonomy.cdm.model.occurrence.Specimen;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;

/**
 * @author m.doering
 * @version 1.0
 * @created 08-Nov-2007 13:06:22
 */
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "DnaSample", propOrder = {
    "sequences"
})
@XmlRootElement(name = "DnaSample")
@Entity
@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
@Audited
public class DnaSample extends Specimen implements Cloneable {
        private static final long serialVersionUID = -2978411330023671805L;
        private static final Logger logger = Logger.getLogger(DnaSample.class);
        
        /**
         * Factory method
         * @return
         */
        public static DnaSample NewInstance(){
                return new DnaSample();
        }

        
//      @XmlElement(name = "BankNumber")
//      private String bankNumber;
        
        @XmlElementWrapper(name = "Sequences")
        @XmlElement(name = "sequence")
    @XmlIDREF
    @XmlSchemaType(name = "IDREF")
    @OneToMany(fetch = FetchType.LAZY)
        private Set<Sequence> sequences = new HashSet<Sequence>();

        
        
        /**
         * Constructor
         */
        private DnaSample() {
                super();
                this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Specimen>();
        }
        
        public Set<Sequence> getSequences() {
                return sequences;
        }

        // FIXME shouldn't this be the singular? i.e. addSequence( . . . )
        public void addSequences(Sequence sequence) {
                this.sequences.add(sequence);
        }

        // FIXME shouldn't this be the singular? i.e. removeSequence( . . . )
        public void removeSequences(Sequence sequence) {
                this.sequences.remove(sequence);
        }

        @Transient
        public Collection getStoredAt(){
                return this.getCollection();
        }
        
        public void setStoredAt(Collection storedAt){
                this.setCollection(storedAt);
        }

        @Transient
        public Set<SpecimenOrObservationBase> getExtractedFrom(){
                return getOriginals();
        }

        @Transient
        public String getBankNumber(){
                return this.getCatalogNumber();
        }
        
        public void setBankNumber(String bankNumber){
                this.setCatalogNumber(bankNumber);
        }
        

//*********** CLONE **********************************/ 
        
        /** 
         * Clones <i>this</i> dna sample. This is a shortcut that enables to
         * create a new instance that differs only slightly from <i>this</i> dna sample
         * by modifying only some of the attributes.<BR>
         * This method overrides the clone method from {@link Specimen Specimen}.
         * 
         * @see Specimen#clone()
         * @see DerivedUnitBase#clone()
         * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
         * @see java.lang.Object#clone()
         */
        @Override
        public DnaSample clone(){
                DnaSample result = (DnaSample)super.clone();
                //sequenceSet
                result.sequences = new HashSet<Sequence>();
                for(Sequence sequence : this.sequences) {
                        result.addSequences(sequence);
                }
                //no changes to: bankNumber
                return result;
        }
}