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.ManyToOne;

import javax.persistence.OneToMany;

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.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.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.IndexedEmbedded;

import eu.etaxonomy.cdm.model.occurrence.Collection;

import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;

import eu.etaxonomy.cdm.strategy.cache.occurrence.DnaSampleDefaultCacheStrategy;

/**

 * A DNA Sample is the extracted DNA of a given tissue sample. It may be stored in

 * a DNA Bank and should then be handled as a collection unit.

 * DNA Sample are used to determine their {@link Sequence DNA sequences}

 * starting with a process called {@link Amplification amplification}.

 *

 * @author m.doering

 * @since 08-Nov-2007

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

    "sequences",

    "amplificationResults",

    "dnaQuality"

})

@XmlRootElement(name = "DnaSample")

@Entity

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

//@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")

@Audited

public class DnaSample extends DerivedUnit {

	private static final long serialVersionUID = -2978411330023671805L;

	@SuppressWarnings("unused")

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

// ****************** FACTORY METHOD *****************/

	/**

	 * Factory method

	 * @return a new and empty DnaSample

	 */

	public static DnaSample NewInstance(){

		return new DnaSample(SpecimenOrObservationType.DnaSample);

	}

    public static DnaSample NewTissueSampleAsDnaSampleInstance(){

        return new DnaSample(SpecimenOrObservationType.TissueSample);

    }

// ************** ATTRIBUTES ****************************/

//	@XmlElement(name = "BankNumber")

//	private String bankNumber;

	@XmlElementWrapper(name = "Sequences")

	@XmlElement(name = "sequence")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)

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

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

	@XmlElementWrapper(name = "AmplificationResults")

	@XmlElement(name = "AmplificationResult")

	@OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)

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

    @NotNull

	private final Set<AmplificationResult> amplificationResults = new HashSet<>();

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

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

    @IndexedEmbedded

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

    private DnaQuality dnaQuality;

// ******************* CONSTRUCTOR *************************/

    /**

     * @deprecated for hibernate use only

     */

    @Deprecated

	protected DnaSample() {  //protected for Javassist, otherwise private

		super();

	}

	private  DnaSample(SpecimenOrObservationType type) {  //protected for Javassist, otherwise private

        super(type);

    }

    @Override

    protected void initDefaultCacheStrategy() {

        if (this.getRecordBasis() == null || SpecimenOrObservationType.DnaSample.equals(this.getRecordBasis())){

            this.cacheStrategy = new DnaSampleDefaultCacheStrategy();

        }else{

            super.initDefaultCacheStrategy();

        }

    }

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

    //sequencings

	public Set<Sequence> getSequences() {

		return sequences;

	}

	public void addSequence(Sequence sequence) {

		if (sequence.getDnaSample() != null){

			sequence.getDnaSample().removeSequence(sequence);

		}

		this.sequences.add(sequence);

		sequence.setDnaSample(this);

	}

	public void removeSequence(Sequence sequence) {

		sequence.setDnaSample(null);

		this.sequences.remove(sequence);

	}

	//amplifications

	public Set<AmplificationResult> getAmplificationResults() {

		return amplificationResults;

	}

	public void addAmplificationResult(AmplificationResult amplificationResult) {

		this.amplificationResults.add(amplificationResult);

		amplificationResult.setDnaSample(this);

	}

	public void removeAmplificationResult(AmplificationResult amplificationResult) {

		this.amplificationResults.remove(amplificationResult);

		amplificationResult.setDnaSample(null);

	}

	public DnaQuality getDnaQuality() {

		return dnaQuality;

	}

	public void setDnaQuality(DnaQuality dnaQuality) {

		this.dnaQuality = dnaQuality;

	}

// ************* Convenience Getter / Setter ************/

	@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}.

	 * @throws CloneNotSupportedException

	 *

	 * @see Specimen#clone()

	 * @see DerivedUnit#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<>();

		for(Sequence sequence : this.sequences) {

			result.addSequence(sequence.clone());

		}

		//no changes to: bankNumber

		return result;

	}

}